This page is a gathering point for links from our phage sequence
database system into the literature. We accumulate various notes
here about the contents of papers that we have had reason to refer
to from inside the database system. This page is not intended to be
a comprehensive review of phage literature, although if it is
helpful to anyone, they are welcome to use it. -- Stephen C. Hardies
A large genome phage with similarity to coliphage PBECO4 and
Klebsiella phage vB_KleM-ReK2
Abrescla NGA Cockburn JJB Grimes JM Sutton GC Dipros JM Butcher SJ
Fuller SD San Martin C Burnett RM Stuart DI Bamford DH Bamford JKH.
Insights into assembly from structural analysis of bacteriophage
PRD1. Nature 432:68-74.
Complete 3D structure. 1W8X
Hard to orient.
Abrescia NG, Bamford DH, Grimes JM, and Stuart DI. 2012. Structure
unifies the viral universe Annu. Rev. Biochem 81: 796-822. PMID 22482909.
Mainly devoted to similarities extending across eucaryotic
Has a capsid structure tree where Caudoviruses are one branch
on a larger tree.
This does raise the question of if you were to root this tree,
wouldn't the root be on the procaryotic side, not within the
Abuladze NK, Gingery M, Tsai J,
Eiserling FA. 1994. Tail Length Determination in Bacteriophage
States that gp29, formally a baseplate hub protein required in
6 copies and acts to initiate the hub, is the tape measure
protein for T4.
Demonstrated by changing length of protein and noting change
in the morphological length of the resulting tails.
Bkg: tail tube then assembled as 24 hexameric rings of gp19.
Adriaenssens EM Ackermann H-W Anany H Blasdel B Connerton IF
Goulding D Griffiths MW Hooton SP Kutter EM Kropinski AM Lee J-H
Maes M Pickard D Ryu S Sepehrizadeh Z Shahrbabak SS Toribio AL
Lavigne R. (2012) A suggested new bacteriophage genus:
"Viunalikevirus". Arch Virol 157:2035-2046. PMID 22707403.
A group within T4 related myoviruses.
Type phage is Salmonella phage ViI.
Agirrezabala X, Martin-Benito
J, Caston JR, Miranda R, Valpuesta M, and Carrascosa JL. 2005.
Maturation of phage T7 involves structural modification of both
shell and inner core components. EMBO J.
Cryo EM of T7 prohead and mature head
Commentary on the scaffold
The portal and the core move upon maturation, in addition to
the expansion of the shell
Contact of the terminase is discussed.
Draws a comparison between dsRNA phage ATPase P4 and terminase
Agirrezabala, X., Martin-Benito, J., Valle, M., Gonzalez, J.M.,
Valencia, A., Valpuesta, J.M., and Carrascosa, J.L. (2005) Structure
of the connector of bacteriophage T7 at 8A resolution:
structural homologies of a basic component of a DNA
translocating machinery. J Mol Biol 347: 895–902.
Aksyuk AA, Leiman PG, Shneider MM, Mesyanzhinov VV, Rossmann
MG. 2009. The structure of gene product 6 of
bacteriphage T4, the hinge-pin of the baseplate. Structure 17:
Akita F, Chong KT, Tanaka H, Yamashita E, Miyazaki N, Nakaishi Y,
Suzuld M, Namba K, Ono Y, Tsukihara T, and Nakagawa A. 2007.
the crstal structure of a virus-like particle from the
hyperthermophilic archaeon Pyrococcus furiosius provides insight
into the evolution of viruses. J. Mol. Biol. 268: 1469-1483.
A spherical (non-tailed) bacterial virus with fold in common
with HK97 and some eucaryotic viruses.
Aksyuk AA, Leiman PG, Kurochkina LP, Shneider MM, Kostyuchenko VA,
Mesyanzhinov VV, Rossman MG. 2009. The tail sheath structure of
bacteriphage T4: a molecular machine for infecting bacteria. EMBO J. 28:821-9.
Aksyuk AA, Bowman VD, Kaufmann , Fields C, Klose T, Holdawayt
HA,.Fischetti VA, Rossmann MG. 2012. Structural investigation
sof a Podoviridae streptococcus phage C1, implications for the
mechanism of viral entry. PNAS 109:14001-14006. PMID 22891295.
There is no internal body.
Notes the belief that adhesins are often catalytic.
Albert A, Munoz-Espin D, Jimenez M,
Asensio JL, Hermoso JA, Salas M, and Meljer WJJ. 2005. Structural
basis for membrane anchorage of viral phi29 DNA during
replication. J. Biol. Chem. 280: 42486-42488.
Structure of p16.7
Has a transmembrane domain, a coiled coil domain, and a ds DNA
Allison GE. Angeles D. Tran-Dinh N. Verma NK. 2002. Complete
Genomic Sequence of SfV, a Serotype-Converting Temperate
Bacteriophage of Shigella flexneri. J.Bact.184:1974-87.
lambda-like gene organization.
Mu like structural and tail genes.
similarity to14 and KpLE1 K-12 prophages.
Subsequently characterized orfs 1,2,3 as small ter, large ter,
and portal: Vir 308 (1):114-127 (2003).
Altermann, E., Klein, J. R. & Henrich, B. (1999). Primary
structure and features of the genome of the Lactobacillus gasseri temperate bacteriophage phi adh. Gene 236; 333-346.
Has a ClpP protease and discussion of that function.
Andrews D, Butler JS, Al-Bassam J, Joss L, Winn-Stapley DA, Casjens
S, and Cin golani G. 2004. Bacteriophage P22 tail accessory factor
GP26 is a long triple-stranded coiled-coil. J. Biol. Chem.
Dec. 27 in press.
P22 has a short tail causing it to be classified as a
podovirus, but mostly lambdoid genes.
? Are there any homologies of the tail genes known to other
Says tail includes gp1:portal ring (12 mer), tail accessory
factors gp4, gp10, gp26, and 6 trimeric copies of tail spike:
gp9. [Is it true that what would be called tape measure in
long tailed phages is an internal virion protein in P22; as
Order of addition is gp4, 10, 26, 9. Only gp4 and 10
are required for gp 9 addition. gp26 is required to stabilize
against loss of the DNA.
Tail accessory proteins also called "head completion
They postulate that gp 4 and gp 10 form the visible 180 A tail
that the tail spikes mount upon, and that gp26 forms a 250 A
thin tail tip fiber.
Conclude that gp26 is a triple stranded coiled-coil resembling
membrane fusions proteins.
By sedimentation they conclude it assembles in vitro into an
Coiled coil pattern looks like several genes in phageD and
There is some confusion in their proposed structure, in that
sometimes they describe it as a three stranded coiled coil with
each polypeptide extended, and sometimes they talk of it as a
trimeric bundle of hairpins?? The elongated form was
predicted to be 210 A, which seems too short. Could there
be a spectrin like structure that concatenates?
For review of the refered viral membrane fusion proteins, they
cite: Eckert, D. M., and Kim, P. S. (2001) Annu Rev Biochem 70,
See also: Del Angel, V. D., Dupuis, F., Mornon, J. P., and
Callebaut, I. (2002) Biochem Biophys Res
Commun 293, 1153-1160
Aravind, L., Makarova, K. S. & Koonin, E. V. (2000). Survey and
summary. Holliday junction
resolvases and related nucleases: identification of new families,
phyletic distribution and evolutionary
trajectories. Nucleic Acids Res 28, 3417-3432.
Arisaka F, Takeda S, Funane K, Nishijima N, and Ishii S. 1990.
Structural studies of the contractile tail sheath protein of
bacteriophage T4. 2. Structural analyses of the tail sheath
protein, gp18, by limited proteolysis, immunoblotting and
immunoelectron microscopy. Biochemistry
29: 5057-5062. UTHSCSA
Atanasova NS, Sencilo A, Peitila MK, Roine E, Oksanen HM, Bamford
DH. 2015. Comparison of lipid-containing bacterial and
archael viruses. Adv Virus Res. 92:1-61.
Autret S, Nair R, Errington J. 2001. Genetic
analysis of the chromosome segregation protein Spo0J of Bacillus
subtilis: evidence for separate domains involved in DNA binding
and interactions with Soj protein. Mol. Micro. 41 (3): 743-755.
Some bkg relevant to the Spo0J system: Spo0J is parB,
and Soj is parA. Spo0J binds multiple loci within
100,000bp of ori and condenses to microscopically visible loci.
Soj is also a negative transcription regulator. Soj required for
efficient formation of these condensed loci. Spo0J also
required to initiate sporulation.
Gives as reviews of plasmid parAB function: Gordon and Wright,
2000, and Gerdes, K., Møller-Jensen, J., and Jensen, R.B. (2000)
Plasmid and chromosome partitioning: surprises from phylogeny.
Mol Microbiol 37: 455–466.
Gerdes et al mostly about subfamilies of parA, but also says
that parB can only be meaningfully aligned within subgroups.
Mutation affecting Soj interaction in N terminal region;
mutations affecting DNA binding in mid to C terminal region,
specifically 138-157 and the C terminal. The C terminal is
thought to be a coiled coil domain effecting dimerization.
Bailey S, Wichitwechkarn J, Johnson D, Reilly BE, Anderson DL,
Bodley JW. 1990. Phylogenetic analysis and secondary
structure of the Bacillus subtilis bacteriophage RNA required for
DNA packaging. J Biol Chem. 265:22365-70. PMID:
Bailly-Bechet M, Vergassola M, and Rocha E. 2007. Causes for the
intriguing presence of tRNAs in phages. Genome Res. 17:1486-1495.
Correlates with codon usage.
Virulent phages have more tRNAs, and greater deviation in
codon usage than temperate ones.
4 different RNA sequences found in 29 different phages.
Formally makes the case for a single ancestral major capsid
protein by comparing X ray structures of HK97 and T4 with
cryoEM of P22, HSV, and phi29?
Compared secondary structures with some porgram called
Jiang, W., M. L. Baker, S. J. Ludtke, and W. Chiu. 2001.
information gap: computational tools for intermediate resolution
interpretation. J. Mol. Biol. 308:1033–1044.
Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C,
Afonine PV, Adams PD, King JA, Jiang W, Chiu W. 2013.
Validated near-atomic resolution structure of bacteriophage
epsilon15 derived from cryo-EM and modeling. Proc. Natl. Acad.
Sci. USA 110: 12301-12306.
Including gp10 head decoration.
Bamford JK, Hanninen AL, Pakula TM, Ojala PM, Kalkkinen N, Frilander
M, Bamford DH. Genome organization of membrane-containing
bacteriophage PRD1. Virology. 1991 Aug;183(2):658-76.
This paper completes the 15 kb sequence.
The virus has a lipid membrane under a protein capsid.
Tectivirus - it's so unusual it has its own class.
I take it there is not much simililarity. Eventually a
relation of the capsid protein to adenovirus was reported.
Baudoux AC Hendrix RW Lander GC Baily X Podell S Paillard C Johnson
JE Potter CS Carrager B Azam F. 2012. Genomic and functional
analysis of Vibrio phage SIO-2 reveals novel insights into ecology
and evolution of marine siphoviruses. Environ. Microbiol.
14:2071-2086. PMID 22225728
Battistuzzi FU, Feijao A, Hedges SB. 2004. A genomic timescale of
prokaryote evolution: insights into the orgin of methaongenesis,
phototrophy, and the colonization of land. BMC
He calibrates the eubacterial tree on the Great Oxidation
Event for which he uses 2.3 Bya citing Holland HD: Volcanic
gases, black smokers, and the Great
Made portal-HOC fusion proteins proposed to tether the portal
to the HOC binding site on the capsid and prevent rotation.
Packaging under these circumstances is argued to mean that
portal rotation is not involved in packaging.
HOC binding sites appear at capsid expansion time. There
seems to be no disruption of packaging at this point with the
portal-HOC fusion proteins.
They note that HOC binding to capsid is tight, surviving
thermal disruption of the phage head or conditions that
This pont may be somewhat exaggerated. Weak interfaces
do not necessarily come apart at 68 degrees. The conditions to
dissociate antibodies were high Mg++ or pH 2. Those are
conditions that would destablilize some interfaces and
stabilize others. We also don't know if the tethered HOC
retains its native binding strength.
They do acknowledge that the HOC might dissocate.
Also attached domains to the C terminus and that didn't
adversely affect packaging.
Last 30 residue deletion was survivable (although apparently
just barely). Contrast to C terminus of portal in other
phages needed for headfull sensing. ???
They have a good review of portal literature.
Hoc is nonessential, but they had some evidence it was
functional in the portal. Both N and C terminal fusions were
Becker SC, Dong S, Baker JR, Foster-Frey J, Pritchard DG, Donovan
DM. 2009. LysK CHAP endopeptidase domain is required for lysis of
live staphylococcal cells. FEMS Microbiol Lett 294:52-60.
Beilstein F, Dreiseikelmann
B. 2005. Bacteriophages of freshwater Brevundimonas vesicularis
isolates. Res. Micro. xxx:xxxx
Isolated 7 phage species: some siphoviridae and some
The Podoviridae have terminal repeats, and may be T7 related.
This is an alpha proteobacteria
Benevides JM, Bondre P, Duda RL, Hendrix RW, Thomas GJ. 2004. Domain
structures and roles in bacteriophage HK97 capsid assembly and
maturation. Biochem. 43: 5428-5436.
Establishes that the N terminal propeptide is in an alpha
helical conformation, and compares this to scaffold structure.
Benkovic SJ, Valentine AM, Salinas F. 2001.
Replisome-mediated DNA replication. Ann. Rev. Biochem.
Reviews replication systems of E. coli, T7, and
Benson SD, Bamford JKH, Bamford DH, Burnett RM. 1999. Viral
evolution revealed by Bacteriophage PRD1 and human adenovirus coat
protein structures. Cell 98:825-833.
Berger B. Shor PW. 1998. On the Structure of the
Scaffolding Core of Bacteriophage T4 and Its Role in Head Length
Determination. J. Struct. Biol. 121(3):285-294.
Disputes traditional arrangement that there are 6 helical
chains of scaffold because it doesn't match the symmetry of the
capsid head protein.
Beumer A, and Robinson JB. 2005. A
broad-host-range, generalized transducing phage (SN-T) acquires 16S
rRNA genes from different genera of bacteria. Appl. Env.Micro.
What kind of phage is this?
Infects gammaproteobacteria: Sflexneri, P. vulgaris, E. coli,
and P. aeruginosa, alpha: R. rubnam, and beta: S. natans.
Bignell C, Thomas CM. 2001. The bacterial ParA-ParB partitioning
proteins. J. Biotechnology 91 (1): 1-34.
ParA is membrane bound ATPase that osicllates in its
localization with different ends of the bacterial.
E coli parA member is minD.
Johanesen,P.A., Crellin,P.K., Cheung,J.K., Katz,M.E., Wright,C.L.,
Haring,V. and Rood,J.I. 1999. Complete nucleotide sequence of the
27-kilobase virulence related locus (vrl) of Dichelobacter
nodosus: evidence for extrachromosomal origin. Infect.
Immun. 67 (3), 1277-1286.
Dichelobacter nodusus is ovine footrot pathogen. Vrl is
virulence locus (a prophage or cryptic prophage)
Number of phage functions identified: In particular vrlC
(although they toyed with the idea of an extracellular location
and then rejected it) has sialidase domains (probably meaning a
tail or other fiber). Note however Copley RR, Russell RB,
Ponting CP. 2001. Prot. Sci. 10(2): 285-292, complicate the
meaning of the "Asp Box" motifs used for this identification.
Binettti AG, Del Rio B, Martin MC,
Alvarez MA. 2005. Detection and characterization of Streptococcus
thermophilus bacteriophages by use of the antireceptor gene
sequence. Appl. Env. Micro. 71: 6096-6103.
PCR amplify VR2, a region of the antireceptor, to predict host
range of a bacteriophage.
orf18 of phiDT1 and phiMD4.
Bjornsti MA, Reilly BE, Anderson DL.1983. Morphogenesis of
bacteriophage phi 29 of Bacillus subtilis: oriented and quantized
in vitro packaging of DNA protein gp3. J Virol. 45:383-96. PMID:
Bjornsti MA, Reilly BE, Anderson DL. 1984. Bacteriophage phi 29
proteins required for in vitro DNA-gp3 packaging. J Virol. 1984
50:766-72. PMID: 6427474
Bjornsti MA, Reilly BE, Anderson DL. 1985, Morphogenesis of
bacteriophage phi 29 of Bacillus subtilis: prohead restoration for
DNA-gp3 packaging and assembly. J Virol. 53:858-61.
Black LW, Peng G. 2006. Mechanistic coupling of bacteriophage T4
DNA packaging to components of the replication-dependent late
transcription machinery. J. Biol. Chem. 281: 25635-25643.
Black LW, Thomas JA. 2012. Condensed Genome Structure. Adv Exp
Med Biol. 2012;726:469-87. doi: 10.1007/978-1-4614-0980-9_21.
Review. PMID: 22297527
Review structure of the packaged DNA in phage virions and
internal virion proteins of phages.
Blackburn, N. T. & Clarke, A. J. (2001). Identification of
four families of peptidoglycan lytic transglycosylases. J Mol Evol
Other families: MltA (pfam03562), MltB, lambda endolysin
(pfam00959, includes T4 lysozyme)
These are mostly bacterial enzymes used to remodel the cell
Slt stands for soluble, and Mlt for membrane bound.
They built their families starting with E. coli genes of which
there are about a half dozen orthologues, and the lambda
endolysin domain. They detected 127 total members.
Apparently many of these are phage encoded, but they didn't
give a list.
Blatny JM, Godager L, Lunde M, and Ness IF. 2004. Compelte genome
sequence of the Lactococcus lactis termperatue phage phiLC3:
coparative analysis of phiLC3 and its relatives in lactococci and
streptococci. Vir. 318:231-244.
73% DNA identity to rlt
Summarized as lysogeny/lysis related to Tuc2009, structure
related to rlt, and a unique replication module.
Blum H, Zillig W, Mallok S, et al. The genome of the archaeal
virus SIRV1 has features in common with genomes of eukaryal
viruses. VIROLOGY 281 (1): 6-9 MAR 1 2001.
Poxviridae, Pycodnaviridae, and Asfarviridae.
The common features is covalent closure of the ends of the
Borriss M, Lombardot T, Glockner FO, Becher D, Albrecht D, Schweder
T. 2007. Genome and proteome characterization of the psychrophilic
Flavobacterium bacteriophage 11b. Extremophiles 11: 95-104.
Botstein D. 1980. A theory of modular evolution for
bacteriophages. Ann. N.Y. Acad. Sci. 354: 484-490.
a ref. for the origin of the modular theory.
The original theory was based on heteroduplex analysis and
genetic analysis between lambda and P22.
It featured exchange of functionally alternative modules by
homologous recombination in regions flanking the modules.
It featured retention of overall genome organization, and
retention of regulatory logic.
Bouchard, J. D. & Moineau, S. (2000). Homologous recombination
between a lactococcal
bacteriophage and the chromosome of its host strain. Virology 270,
A lytic phage acquired two sequences from a chromosomal
Brietbart M, Rohwer F.
2006. Here a virus, there a virus, everywhere the same virus?
Trends in Microbiology 13:xxxx
Describes a "Bank Model" where the most abundant viruses in a
local are active and the remainder are in low abundance and very
diverse. Members of the low abundance class move to the
abundant active class as new host strains expand in the
environment. Room for new hosts may be made by phages
beating down the extant abundant host strains.
Talk about "metagenomes". Is this the group description
of viruses you get from community sequencing?
Brondsted L, Ostergaard S, Pedersen M, et al. 2001. Analysis
of the complete DNA sequence of the temperate bacteriophage
TP901-1: Evolution, structure, and genome organization of
lactococcal bacteriophages. Virol. 283 (1): 93-109.
Belongs in P335 group with temperate r1t and Tuc2009; there
are also virulant members.
Bouet JY, Funnell BE. P1 ParA interacts with the P1 partition
complex at parS and an ATP-ADP switch controls ParA activities.
EMBO J. 18 (5): 1415-1424.
Bkg: parA & parB control partitioning of P1? plasmids into
daughter cells. ParS is DNA site that wraps around
parB. ParA is an ATPase.
This paper shows interaction of parA with the parB/DNA complex
Brenner S. Bacteriophage tales. Current Biology. 7(11):R736, 1997
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead
D, Azam F, and
Rohwer F. (2002) Genomic analysis of uncultured marine viral
communities. PNAS 2002 99: 14250-14255.
Brentlinger KL. Hafenstein S. Novak CR. Fane BA. Borgon R.
McKenna R. Agbandje-McKenna M. 2002. Microviridae, a family divided: isolation,
characterization, and genome sequence of phiMH2K, a bacteriophage
obligate intracellular parasitic bacterium Bdellovibrio
bacteriovorus. J. Bact. 184(4):1089-1094.
Microviridae is single stranded DNA phages.
They say only two subdivisions of Microviridae.
This phage plus others characterized in Chlamydia
form one subdivision.
The prototype for the other group is phiX174.
Briers, Y., Miroshnikov, K.,
Chertkov, O., Nekrasov, A., Mesyanzhinov, V., Volckaert, G., and
Lavigne, R., 2008. The structural peptidoglycan hydrolase gp181 of
bacteriophage phiKZ. Biochem Biophys Res
Commun. 374, 747-751.
In the C-terminal section of this large structural protein,
they show by deletion analysis that residues 1880..2042 can lyse
cells and that 2043..2237 enhances lysis.
They declare this protein a component of the cell puncturing
Brussow, H. & Desiere, F. (2001). Comparative phage genomics
and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol.
lambda-, psiM2-, L5-, Sfi21-, Sfi11-, C31-, sk1- and
TM4- like phages form a "supergroup".
This fuses together 3 different groups from our phylogeny of
fam 2: lambda
fam 1: Sfi21, L5, Tm4, C31, ski,
fam 6: Sfi11, psiM2
Emphasizes multigene modules; Often uses gene order to infer
Sfi21 is a cos site group and Sfi11 is a pac site group.
The modules with the packaging enzymes are not prone to
rearrangment. It contains small and large terminase,
portal protein, scaffold and head proteins.
Lysogeny, lysis, and tail fiber highly prone to insertion and
Two different replicative modules apparent.
The tape measure protein is usually the largest. I'm
getting the impression that T7 gp16 is such a protein, but
because of the small size of the tail it is recessed back into
Bhunchoth A, Blanc-Mathieu R, Mihara T, Nishimura Y, Askora A,
Phironrit N, Leksomboon C, Chatchawankanphanich O Kawasaki T,
Nakano M, Fujie M, Ogata H, Yamada T. 2016. Two asian
jumbo phages, phiRSL2 and phiRSF1, infect RAlstonia solanacearum
and show common features of phiKZ-related phages. Virology
494:56-66; PMID 27081857
Burkal'tseva MV, Krylov VN,
Pleteneve EA, Shaburova OV, Krylov SV, Volkart G, Sykilinda NN,
Kurochkina LP, and Mesyanzhinov VV. 2002. Phenogenetic
characterization of a group of giant phiKZ-like bacteriophages of
Pseudomonas aeruginosa. Russian
J. Genet. 38: 1242-1250. UTHSCSA
Classic review of recombination involving lambda, P22, and
Besides the obvious (P22 is a Podovirus), numerous examples of
recent transfers detected by highly similar patches of DNA
sequence are described.
P22, L, and LP-7 came from Salmonella typhimurium, although
they grow on E. coli.
HK97 it the one with the crosslinked capsid protein.
Carlton RM, Noordman WH, Biswas B, de Meester ED, Loessner MJ.
2005. Bacteriophage P100 for control of Listeria monocytogenes in
foods": Genome sequence, bioinformatic analyses, oral toxicity,
study, and application. Reg. Toxicol. Pharm. 43: 201-312.
Promoting as a preventative bacteriocide against Listeria in
food, which causes Listeriosis.
Mortality rate is 25-30%
Another one in the StaphK group.
Caruthers JM and McKay DB. 2002.Helicase structure and mechanism.
Curr. Opinion in Str. Biol. 12: 123-133.
Casjens, S., Wyckoff, E., Hayden, M., Sampson, L., Eppler, K.,
Randall, S., et al. (1992) Bacteriophage P22 portal protein is
part of the gauge that regulates packing density of intravirion
DNA. J Mol Biol 224: 1055–1074.
Sherwood R. Casjens, Eddie B.
Gilcrease, Wai Mun Huang, Kim L. Bunny, Marisa L. Pedulla, Michael
E. Ford, Jennifer M. Houtz, Graham F. Hatfull, and Roger W. Hendrix.
2004. The pKO2 Linear Plasmid Prophage of Klebsiella oxytoca. J. Bacteriol.
51,602 bp. They actually characterized the prophage
plasmid. It can be observed to make virions, but these
have not been propagated.
N15, and PY54 are other linear prophages. Virion ends
and plasmid ends are not at the same site, and the plasmid had
covalently hairpinned ends..
Says head, tail shaft, and lysis genes not identifiably
homologous to N15, but others are.
They seem to have used a 30% identity threshold
boundary. Many of the genes stated not to be
identifiably similar are also noted to be the same size and in
the same order, so there is obviously a lot of homology
underneath this conservative threshold of detection.
From their figure, it appears that pKO2 is more similar to
N15 than PY54 in most places, but more similar to PY54 in the
head, head connector, and tape measure segments (a continuous
segment bounded by a cos site)
has long non contractile tail with real long tail tip fiber
with segmental coiled coil structure.
Has discussion of dinI and umuD function.
Casjens AR, Gilcrease, EB,
Winn-Stapley DA, Schicklmaier P, Schmieger H, Pedulla ML, Ford ME,
Houtz JM, Hatfull GF, and Hendrix RW. 2005. The generalized
transducing Salmonella Bacteriophage ES18: complete genome
sequence and DNA packaging strategy. J. Bact.
The have a terminase tree and indicate commonality of the
kinds of ends formed with clades. The labels are hard to
read. They are (personal communciation and with some
species indication and gi numbers added for clarification by
comparison to our family tree):
lambda-like 5' extended COS ends
CP-933K (= Ec.|gi|25518216), Fels-1, Gifsy-2, PP02 (=
Pp.KT2440|gi|24984656), WO, Gifsy-1, 21 (= phage 21 = or
very close to Ec.|gi|26107839?), N15, lambda
Chang J, Weigele P, King J. Chiu W, Jiang W. 2006. Cryo-EM
asymmetric reconstruction of bacteriophage P22 reveals organization
of its DNA packaging and infecting machinery. Structure
14:1073-1082. PMID 16730179.
They don't visualize the internal tube.
They imagine the pilot proteins, gp7, 16, 20 in the portal,
and maybe just behind it, with a wisp of intensity behind that
that they label DNA.
Pilot/inject protiens cited to:
Poteete AR, and King J. 1977. Functions of two new genes in
Salmonella phage P22 assembly. Virology 76: 725-739.
7, 16 20 are said to map contiguously by genetic
mapping. Gene numbers are not in order, These are gene
names, not gp numbers.
gene 7 gp 11
gene 20 gp12
gene 16 gp13.
gp16 and 20 are referred to Botstein et al., JMB
Phenotype of all three is said to be similar
gp7 is said to be 15kD. and is required to be injected to
enable phage specific protein synthesis
Bryant JL Jr, and King J. 1984. DNA injection proteins
are targets of acridine-sensitized photoinactivation of
bacteriophage P22. J. Mol. Biol. 180:837-863. PMID 6335533.
Implies that the three proteins are close to the DNA in
Hoffman B and Levine M 1975a. Bacteriophage P22 virion
prtotein which performs an essential early function. II.
J. Virol 16: 1547-1559.
Casjens S. 2003. Prophages and bacterioal genomics: what have we
learned so far? Mol. Microbiol. 49: 277-300.
Discussion about prophage decay.
Table 1 supplementary material tabulates them in many baterial
Casjens SR. 2005. Comparative
genomics and evolution of the tailed-bacteriophages. Curr. Opin.
Micro. 8: 451-458.
Has a discussion with examples of evolutionary issues raised
by phage sequence comparisons.
Claims that there is no single gene found in all tailed phages
that could be the basis of a phylogeny.
Talks about novel joints as a result of recombination followed
by deletion of extraneous regions.
Talks about how some homology may be too distant to recognize,
and cites lack of sufficient structures.
Coins the term "non recognizably homologous" alleles to
discuss genes playing same function but of different ancestry.
Discusses replaceability of lambda side fibers and T4 tail
Discusses the SP6 tail spike move, and the putative
Pseudomonas putida T7 "prophage"
Talks about prophage portion of the viral gene pool.
Mentions phi29 capsid protein structure.
Catalano CE. The terminase enzyme from bacteriophage lambda: a
DNA-packaging machine. Cellular & Molecular Life
Sciences. 57(1):128-48, 2000 Jan 20. UI: 20406133
Cermakian N, Ikeda TM, Miramontes
P, Lang BF, Gray MW, and Cedergren R. 1997. On the evolution of the
single-subunit RNA polymerases.J.
Mol. Evol. 45:671-681.
The T7-like RNA polymerase is distinct from other RNA
polymerases in being composed of only one polypeptide chain.
T7-like RNA polymerase apparently passed through the
mitochondrial endosymbiosis ~ 1.1 Bya.
Found in eucaryotes in mitochondrial linear plasmid
reminiscent of T7 itself.
Also found in the eucaryotic genome, where it is expressed and
imported into either mitochondria or chloroplasts to act as
organelle RNA polymerase.
At the time it was not totally clear if the common ancestor
was a T7-like virus or something else from which T7-like phages
subsequently obtained the gene. However, now it is clear
that T7-like phages with RNA polymerase in place pre-existed the
mitochondrial endosymbosis. eg. see cyanophage P60.
Cerritelli, M.E., Trus, B.L., Smith, C.S., Cheng, N., Conway,
J.F., and Steven, A.C. 2003. A second symmetry mismatch at
the portal vertix of bacteriophage T7: 8-fold symmetry in the
procapsid core. J. Mol. biol. 3327: 1-6. PMID 12614603
Cerritelli ME, Wall JS, Simon MN, Conway JF, Steven AC.
1996. Stoichiometry and domainal organization of the long
tail-fiber of bacteriphage T4: a hinged viral adhesin. J.
Mol. biol. 260:767-780. PMID: 8709154.
Ceyssens PJ, Lavigne R,
Mattheus W, Chibeu A, Hertveldt K, Mast J, Robben J, and Volckaert
G. 2006. Genomic analysis of Pseudomonas aeruginosa phages LKD16
and LKA1: establishment of the phiKMV subgroup with the T7
Bact. 188: 6924-6931.
Ceyssens PJ, Brabban A, Rogge L, Lewis MS, Pickard D, Goulding D,
Dougan G, Noben JP, Kropinski A, Kutter E, Lavigne R.
2010. Molecular and physiological analysis of three
Pseudomonas aeruginosa phages belonging to the "N4-like
viruses". Virology 405:26-30. PMID 20619867.
Define the RNA polymerase gene being adjacent to the
structural genes instead of being on the end as definitive.
Ceyssens PJ, Minakhin L, Van den Bossche A, Yakunina M, Klimuk E,
Blasdel B, De Smet J, Noben JP, Blaisi U, Severiov K, Lavigne
R. 2014. Development of gaint bacteriophage phiKZ is
independent of the host transcription apparatus. J. Virol
88:10501-1-510. PMID 24965474.
Chan JZ-M, Millard AD, Mann NH, and Schafer H. 2014 Comparative
genomics defines the core genome of the growing N4-like phage
genus and identifies N4-like Roseophage specific genes.
Front. Microbiol 10:
Tabulate N4-like viruses, and show a tree.
Chan YW Mohr R Millard AD Holmes AB Larkum AW Whitworth AL Mann
NH Scanlan DJ Hess WR Clokie MR (2011) Discovery of cyanophage
genomes which contain mitochondrial DNA polymerase. Mol.
Biol. Evol. 28:2269-2274. PMID 21335340
A-HIS1 and A-HIS2 are siphoviruses.
They, together with S-TIM5 have the most similar phage-borne
members of the DNA polymerase family found in mitochondria.
The paper only talks about the polymerases. But full
genomic sequences are deposited in GenBank.
Their tree was made from scant sequence that was weakly
aligned. The alignment is given in a supplement.
Their conclusion is OK, but minor details of the tree (e.g.
they had SPO1 wander into the bacterial clade) are not reliable.
Chandry, P. S., Moore, S. C., Boyce, J. D., Davidson, B. E. &
Hillier, A. J. (1997). Analysis
of the DNA sequence, gene expression, origin of replication and
modular structure of the
Lactococcus lactis lytic bacteriophage sk1. Mol Microbiol 26,
Chang B, Miyamoto H,
Taniguchi H, and Yoshida S. 2002. Isolation and Genetic
Characterization of a Novel Filamentous Bacteriophage, a Deleted
Form of Phage f237, from a Pandemic Vibrio parahaemolyticus O4:K68
IMMUNOLOGY 46 (8): 565-569.
Chemla YR, Aathavan K, Michaelis
J, Grimes S, Jardine PJ, Anderson DL, and Bustamante C. 2005.
Mechanism of force generation of a viral DNA packaging motor. Cell
phi29 and optical tweasers to measure force.
cites papers claiming either 5 or 6 terminases per capsid.
Does kinetic measurements in combination with force
They basically fit their kinetic data to the Fujisawa and
Morita translocase model.
They find that the Hill coefficient of ATP binding (and ADP
binding) is ~ 1.
That means no cooperativity in nucleotide binding between
This is cooperativity in the strict sense: ATP bound
to one ATPase can not improve the binding of ATP to another
This does not perclude cooperating in some other sense.
ADP product inhibition is linear with ADP concentration.
This means only one ADP molecule binds per active site.
Binding of a single AMP-PNP (nonhydrolyzable ATP analogue)
in competition with ATP stalls the motor for the residence
time of the inhibitor. Stalling is linearly dependent on
concentration of the inhibitor.
This means that either all ATPase subunits must fire for a
motor cycle to commence, or that they are sequenced such
that no other ATPase can act until the currently engaged one
They note that this does not require a predefined
sequence, only that all must wait for one to act.
Change in velocity with respect to force applied is used to
calculate a "characteristic distance" of 1.1 A (per 6.8 A
They describe this as the distance to the transition state
along the mechanical axis.
As described in their 2001 paper, the assumpition is that
there is a single point in the excursion where a weak
applied back force creates an energy barrier (a transition
state). The back force can be envisionsed at a linearly
rising line in the free energy diagram, which is then added
to the unresisted free energy diagram. The moleucle
will need a kick from thermal energy to clear the barrier.
The distance traversed to clear that barrier is 1.1 A.
Over the rest of the excursion the free energy drop per
increment of distance is enough that the weak back force
will not slow down the movement. As back force is
increased, the 1.1 A distance was relative constant up
to a point. With back preassure approaching the
stall point, (overpowers the net free energy drop) a wider
distance began to prevail. This iimplies a particularly
steep drop over some of the range to keep the overall free
energy The 1.1 A comes from E = F x d, where E
is the height of the activation barrier produced by F, and d
is the distance that must be invoked to make E = F x
d. This distance would correspond to the distance from
the greatest climb found on the curve from any local minimum
to any following local maximum.
This rules out thermal rachet-like behavior for greater
than 1.1 A out of 6.8 A.
For ATP, Vmax/Km at low ATP is force independent. This
means that applying load does not slow down the motor by
causing an increase in hydrolyzed ATP from abortive motor
An informal statement might be that while velocity is
slowed, ATP binding is held up and stays in pace with
completed motor cycles.
For ADP, similarly binding is force independent.
Pi concentration has no effect on force dependent
velocity. This means that Pi is released in the
The conclude that an adjacent terminase engages the DNA (in
what must be the up position of the stroke) before the
preceding uit releases the DNA (in the down position).
They want ATP binding and DNA binding at once, with the
power stroke accompanying P release.
kb (which I think is the ATP binding constant) is force
independent. Hence ATP binding does not power the
power stroke and the power stroke must follow an
irreversible step after ATP binding (presumably ATP
hydrolysis, or the release of ADP or Pi if hydrolysis stores
its energy in a conformational state of the enzyme).
Similary, pausing caused by competition with
nonhydrolyzable ATP is not affecting by applying back
pressure, indicating that ATP binding is dissociated from
the power stroke by an irreversible step.
They say slipage increases as ATP is decreased and is
accelerated as ADP is increased. They interpret this
to mean that an empty site or an ADP bound terminase is not
the form that tightly binds DNA. (By elimination, the DNA is
said to bind the ATP bound form).
What about a model in which the DNA binds not to an ATP
bound terminase, but to an activated ADP bound form
generated by ATP hydrolysis?
They report that gammaSATP binds in two phases, a high
affinity phase that does not dissociate DNA, and a low
affinity phage that does dissociate DNA. They use this
to argue that two terminase subunits are involved in the
mechanism (one handing the DNA off to the other).
Can you interpret this that ATP binding causes release
of the DNA in the cycle?
They say ADP dependence of the motor is not consistent
with force generation coupled to ADP release, and argue that
the ATP hydrolysis step itself does not release the energy,
but rather release of the Pi. Hence they make the
force generating step coincident with the release of Pi.
show dimer, tetramer, hexamer pathway of assembly.
Made two kinds of covalently fused dimers and recovered about
1% packaging activity.
Chen F., and Lu, J. 2002. Genomic sequence and Evolution of Marine
Cyanophage P60: a New insight on lytic and lysogenic phages.
Applied and Environ. Microbiol. 68: 2589-2594.
47,872 bp Podovirus
T7 like genes:
T7 tail poteins
packaging protein split in two?
Some metabolic genes derived from cyanobacteria (how close
They never mention the ends; there are not terminal repeats
listed within the sequence.
Two extensive inverted repeats are in the sequence but not
mentioned in the manuscript:
268..81 matches 30309..30496 perfectly.
10..68 matches 30934..30875 with a frameshift and a base
Fig. 3 has T7, phiYeO3-12, and SIO1 rearranged beyond
Chen Z, and Schneider TD. 2005. Information theory based T7-like
promoter models: classification of bacteriophages and differential
evolution of promoters and their polymerases. NAR 33: 6172-6187.
have some trees
Cheng N, Wu W, Watts NR, Steven AC. 2014. Exploiting
radiation damage to map proteins in nucleoprotein complexes:
The internal structure of bacteriophage T7. J. Struct Biol
Bubblegram on T7
Chevalier, B. S. & Stoddard, B. L. (2001). Homing
endonucleases: structural and functional
insight into the catalysts of intron/intein mobility. Nucleic
Acids Res 29, 3757-3774.
Chibani-Chennoufi S, Bruttin A,
Dillmann M-L, and Brussow H. 2004. Phage-Host Interaction: an
Ecological Perspective. J. Bact.
Describes ecology of phages in marine environment, soil, and
in industrial fermentation.
Describes some examples of polyvalency (infecting more than
Describes lysogenic conversion.
Reference to abi (abortive infection systems) for resisting
Shows prototypical electron micrographs of podo, myo, and
Chibani-Chennoufi S. Canchaya C, Bruttin A., and Brussow H. 2004.
Comparative genomics of the T4-like Escherichia coli Phage JS98:
Implications for the evolution of T4 phages. J. Bact.
The sequence was only finished to the level of several large
contigs, and then these were analyzed by the assumption that
they align in a colinear fashion with T4.
They emphasize the relative lack of idels in alignments of T4
and its related phages, saying that it is much less than for
lambdoid phages over a similar host range. There is a lack
of any quantitative consideration of the amount of time passed,
They point out some cases where mobile introns may have
mobilized adjacent genes.
They review a lot of functional information and diversity
information about several of the genes covered, and have some
nicely color coded figures showing the way gene conservation
varies by function among many of these genes. There is
also some R/S analysis discussed.
Chibani-Chennoufi S, Dillmann
M-L, Marvin-Guy L, Rami-Shojaei S, and Brüssow H.
2004. Lactobacillus plantarum Bacteriophage LP65: a New Member of
the SPO1-Like Genus of the Family Myoviridae. J. Bact.
Their frame prediction used frameD (Toulouse Bioinfo INRA with
ATG, GTG, TTG and length >= 30.
The large terminase had a HNH insertion in it.
They didn't sequence the ends. Did they stop at the
They note that the head and tail genes seem to line up in a
gene order like Sfi11 (a siphoviridae), whereas this is not the
case for T4. They suggest that the contractile tail in
this group evolved by convergent evolution from a siphoviral
ancestor, not from a common ancestor with myovirus T4. To
make this argument, they seemed to be equating lots of genes
without detectable sequence similarity and not particularly even
the same size and without demonstrated analogous function.
Choi KH, McPartland J, Kaganman I, Bowman VD, Rothman-Denes LB,
Rossmann MG. 2008. Insight into DNA and protein transport in
double-stranded DNA viruses: the structure of bacteriophage
Escherichia phage N4 is NC_008720; not to be confused with
Vibrio phage N4 (a T7-like podovirus)
It's also called Enterobacteria phage N4 at GenBank, and is
the prototype for a kind of podovirus that is structurally
substantially different from T7, has an internal RNAP instead of
the T7-like internal virion proteins, or the T7-like RNAP, and
has a genome size just over 70 kD.
Quasi T=9 symmetry; 535 capsid proteins (540 -5).
may have location of vRNAP in virion, based on decreased
intensity of inner core just above portal in vRNAP- mutants
The presume that vRNAP goes in first with 500 nt of genome,
and then participates in bringing in the rest of the DNA.
Has a non contractile tail sheath and a tail tube.
Apparently this is not typical of Podoviruses
the side fibers are gp66. There are twelve of them, and
they have more of a ribbon appearance than the coiled coil
appearance of T7.
the non-contractile sheath surrounding the short tail tube is
had head decorating protein gp17; binds at pseudo 3fold axes,
but as monomer; has Ig fold.
major capsid is gp56
vRNAP is gp50
sheath is gp65, and constains an antireceptor
portal is gp59
appendages are 66
The paper is noncommital about which protein is the tail tube,
and which protein supplies the 'plug', -- a density seen at the
end of the tube that appears to block it off.
Chopin A, Bolotin A, Sorokin A, et al. Analysis of six
prophages in Lactococcus lactis IL1403: different genetic
structure of temperate and virulent phage populations.
NUCLEIC ACIDS RES 29 (3): 644-651 FEB 1 2001.
Suggests that lytic phages have less rearranging and
recombining going on than temperate ones.
Virulant Lactococcal phages belong to two groups
936 (bIL60, bIL170?)
Temperate phages refered to as P335 group
large genome group (33–42 kb; bIL285, bIL286, bIL309,
Tuc2009 and r1t)
small genome group (14–15 kb; bIL310, bIL311 and bIL312)
TP901-1 and BK5-T were partially sequenced lactococcal
prophages at the time.
Christiansen, B., Brondsted, L., Vogensen, F. K. & Hammer, K.
(1996). A resolvase-like protein is required for the site-specific
integration of the temperate lactococcal bacteriophage TP901-1. J
Bacteriol 178, 5164-5173.
An integration system without int.
Orf1 is 485 residues; 1st 180 are 35% to resolvase. This
is the only protein required for integration.
Presumably there is a repressor and an excisase?
Other family members mentioned are Cin, Hin, Gin, Bin, Tn2501,
Tn21, Tn3, Tn1000, Tn501.
From CD-search: gnl|Pfam|pfam00239, resolvase, Resolvase, N
terminal domain. The N-terminal domain of the resolvase family
(this family) contains the active site and the dimer interface.
The extended arm at the C-terminus of this domain connects to
the C-terminal helix-turn-helix domain of resolvase - see
Although VpV orf 33 matches this family, it is a much better
match to the polymerase associated exo domain; apparently
this family is derived from the same exo domain.
Chung YB, Nardone C, Hinkle DC. 1990. Bacteriophage T7
DNA packaging. III. A "hairpin" end formed on T7 concatemers may be
an intermediate in the processing reaction. J Mol
The following concatermic genome is replaced by a duplicated
segment ending in a hairpin by synthesis initiated at an
inverted repeat 190 bp to left of mature left end, in a process
that does not require gp 19, 18, or 10.
Rifampicin resistant RNA synthesis occurs after PBS2
They purified a 4 subunit RNA polymerase not matching any of
the subunits of B. subtilis RNA polymerase.
Subunit sizes were I 80 Kdal, II 76 Kdal, III 58 Kdal, and IV
Growth was rifampicin resistant from outset, so polymerase may
be in capsid.
Clark AJ. Inwood W. Cloutier T. Dhillon TS. Nucleotide sequence of
coliphage HK620 and the evolution of lambdoid phages. Journal of
Molecular Biology. 311(4):657-79, 2001
Most similar to P22; essentially this is a E. coli version of
P22 (which infects Salmonella). However, terminase and
capsid are indicated to not be P22-like. That agrees with
our terminase tree which has HK620 and a small group essentially
separate from anything else.
Has an outlier gene to APSE-1 that they figure is 200 Myr out
(based on divergence of the host species; ie. the unnamed host
of APSE-1 clusters with E. coli and Proteus vulgaris; The
unnamed host is called the secondary endosympiont of peas.).
They say that the metabolic domain is highly mosaic.
They say that P22-like phages (of which APSE-1 is one) are
morphologically Podoviruses, but genome structure and sequence
is lambdoid. These can make viable hybrids with lambda.
They expand on Botstein's modular exchange module in which non
homologous segments are flanked by homologous "linker" segments
that mediate reassortment within group by homologous
Cohen DN, Sham YY, Haugstad GD, Xiang Y, Rossmann MG, Anderson DL,
Popham DL. 2009. Shared catalysis in virus entry and
bacterioal cell wall depolymerization. J. Mol. Biol.
387: 607-618. PMID 19361422.
Worked out mechanism of LytM, and gp13 of phi29.
Comeau AM, and Krisch HM.
2005. War is peace - dispatches from the bacterial and phage killing
fields. Curr. Opin. Microbiol. 8: 488-494.
Discusses the problem of virulent phages and the coadaptive
struggle with their hosts.
Cites numerous papers about host resistance.
Talks about phage replacing antireceptors to counter receptor
Reviews phage functions to defeat host restriction systems.
Discusses internal proteins (IPs) injected with DNAs and
proposed to defeat host defenses.
Talks about hyperplastic phage genomic regions.
Talks about S-PM2 and encoded photoproteins, and S
adenosylmethionine decarboxylase involved in biosynthesis of
polyamines involved in photo processes.
Talks about phage tail fibers coopted for host functions.
Cites cases of cellular recruitement of phage replication
Touches on phage bacterial coevolution as a generator of
functions and diversity some of which becomes fixed into
Comeau AM., Bertrand C, Letarov A, Tetart F, and Kirsch HM. 2007.
Molecular architecture of the T4 phage superfamily: A conserved core
genome and a plastic periphery. Virology
Talks about hyperplastic regions, hyperplascicity of tail
fibers, and internal proteins that are injected to alter the
Replicative modules are also conserved in T4-like phages.
Cites Hambly et al. Proc. Natl. Acad. Sci. U.S.A. 98,
11411–11416. and Tétart et al, J. Bacteriol. 183, 358–366 to say
the T4-like phage have significant morphology differences. But
this turns out to be just about head shape. However, the
Hambly article has an EM that looks like it could be real
different, but they only comment on symmetry in the head and the
Shows a comparison of structural modules (pasted together but
I notice that the hub and tail fibers are not in it).
Increased in larger genome versions of T4 only by about 30%.
Shows a nice figure of the tail fiber gene arrangement showing
that the proximal fiber is clearly constant, and then things get
Attributed most of the extra genes in the larger genome
variants of the T4-like phages to specific processes relative to
the phages environmnet. Ie. PSM2 has photosynthesis
Conway JF, Wikoff WR, Cheng N, Duda
RL, Hendrix RW, Johnson JE, Steven AC. 2001. Virus maturation
involving large subunit rotations and local refolding. Science
cyroEM and X ray fitting of the HK97 capsid protein before and
after capsid expansion.
The N-arm, containing the cleavage site for the delta peptide
is one of the units that has to be refolded. They assume
the N terminus remains inside, but can't really locate it.
It is near the subunit interface, so could thread through to be
exposed to the outside.
One participant in the cross link is the E-loop, which is
clearly on the exterior as demonstrated by trypsin cleavage.
Crutz-Le Coq AM, Cesselin B, Commissaire J, and Anba J. 2002.
Sequence analysis of the lactococcal bacteriophage bIL170:
insights into structural proteins and HNH endonucleases in dairy
phages. Microbiology 148(4): 985-1001.
Siphoviridae: 3 groups in Lactococcus: c2, 936, and P335
(contains termperate members)..
Other completely sequenced 936 group member is ski; 84% nt
F4-1 and bIL41 also in this group
Early and replicative region has much heavier density of
indels. Refers to Lubbers et al., for the similar
characterization of the c2 group.
Gives an extensive analysis of domain structure in putative
Gives an analysis of transglycosylase domains in a number of
genes. Says T7 gp16 has one.
Often either the C terminal of the tape measure protein or
an auxilliary tail protein has transglycosylase of the EmtA
T7 gp16 and PRD1 gp7 and SPbeta Yomi have an Slt
subtype. The T7 domain is on the N terminal. See
Moak & Molineux, 2000. This is pfam01464, and is
detected by CD-search on T7 gp16.
Cuervo A, Pulido-Cid M, Chagoyen M, Arranz R, Gonzalez-Garcia VA,
Garcia-Doval C, Caston JR, Valpuesta JM, van Raaij MJ, Martin-Benito
J. and Carrascosa JL. Structural characterization of the
bacteriophage T7 tail machinery. J. Biol. Chem.
288:26290-26299. PMID 23884409
cryoEM of T7.
Talks of all the podoviruses, including phi29, N4, P22, as
having a nozzel structure the way T7 does.
Claims gatekeepr is similar to long tailed phages citing: Olia
et al., Nat. Struct. Mol. Biol. 18:597-603.
propose structural change by portal releases terminase and
brings on gp11 (T7 nomenclature).
reconstruction if gp12 (nozzel) suggests that the central
domain is the upper part of the DNA channel. one end domain (N
ter?) flairs out to give the nozzle the cone shape, and the
other end extends the channel and closes it off.
Said P22 gp4 and T7 gp11 have similar location and may share
structure features, although no sequence homology was found.
The Xray structure of P22 gp4 is in Nat. Struct. Biol. 18:
for gp11, they did some kind of structure alignment with P22
gp4 and Sf6 gp6. It was based on 4 helixes, with helix 4
positioned on the inside of the channel.
Davey MJ, Funnell BE. 1997. Modulation of the P1 plasmid partition
protein ParA by ATP, ADP, and P1 ParB. J. Biol. Chem. 272 (24):
ParA ATPase activity is stimulated by ParB.
ATP binding stimulates binding of ParA to the promoters it
regulates. ATP hydrolysis inhibits DNA binding.
Davidson, A. & Gold, M. (1992). A novel in vitro DNA packaging
system demonstrating a direct role for the bacteriophage l FI gene product. Virology,
gpFI required for maximal packaging activity.
fin mutants that escape this requirement map to temrinase, but
were not sequenced as of writing this paper.
Davidson, A. & Gold, M. (1992). Mutations abolishing the
endonuclease activity of bacteriophage l terminase
lie in two distict regions of the A gene,
one of which may encode a leucine zipper DNA binding domain. Virology
E586K (at the RNE) has strong effect on killing endo
activity. They interpreted this as disrupting a bZIP
(coiled coil) interaction, but its now recognized as a catalytic
I600S is a spontaneous ts. They recognized it as outside
the zipper, and inconsistent with free standing coiled
coil. It makes perfect sense in the ruvC fold.
D401G (at conserved res 1) is strong endo -
An insertion in this region kill endo
Many substitutiosn at Q403 kill endo
Q426 and W421 (many mutations) have weak effect.
Depping R, Lohaus C, Meyer HE, Ruger W. 2005. The
mono-ADP-ribosyltransferases Alt and ModB of bacteriophage T4:
Target proteins identified. BBRC 335: 1217-1223.
Targets include E. coli trigger factor (a chaperone), GroEL,
There is also a ModA.
Several proteins hit by Alt and ModB.
RNA polymerase alpha is the long known target of both Alt and
ModB, with Alt adenylsylation increasing activity on T4 early
promoters and ModB adenylsylation repressing it (and maybe
targetting middle promoters).
Desiere, F., Lucchini, S. & Brussow, H. (1998). Evolution of
bacteriophage genomes by modular exchanges followed by point
mutations and small deletions and
insertions. Virology 241, 345-356.
Desiere F. Lucchini S. Brussow
H. 1999. Comparative sequence analysis of the DNA
packaging, head, and tail morphogenesis modules in the temperate
cos-site Streptococcus thermophilus bacteriophage
Says gene map similar to lambda phage is absence of sequence
Contains a ClpP protease family member.
Desiere F, Pridmore RD, and Brussow H. 2000. Comparative Genomics
of the Late Gene Cluster from Lactobacillus Phages.
Virology 275, 294-305.
About 3 prophages from Lactobacillus johnsoni
Lj965 - like pac site Streptococcus thermophilus phages
delbrueckii phage LL-H/Lactobacillus plantarum phage
phig1e/Listeria monocytogenes phage A118
With Bacillus subtilis SPP1 as an outgroup.
Says similarity to gram negative lambdoid phages weak or
Our large terminase tree has those all together in fam 6
(including SPP1), except TP901-1 is in fam 5.
Defines independent cos-site clade with Lactobacillus gasseri
phage adh, and gram neg. Pseudomonas aeruginosa phage D3
Lactobacillus casei phage A2 is cos site phage
Our large terminase fam 1 has adh, D3, as well as A2, and
many others including Sfi21.
Has a comparison of pac and cos structure cassettes.
cos generally have a small term - large term - minor head -
scaffold - major head gene order.
pac generally have a small term - large term - ClpP protease -
major head (from which scaffold is cleaved by protease)
Tree of phage ClpP proteases have a separate phage clade with
a deep, though probably eubacterial origin.
They rate looks a little high (< 2x) in the phage clade,
but it's hard to figure out what saturation will have done in
terms of damping out a bigger difference.
Desiere F, Mahanivong C, Hillier AJ, et al. Comparative genomics of
lactococcal phages: Insight from the complete genome sequence of
Lactococcus lactis phage BK5-T. VIROLOGY 283 (2): 240-252 MAY 10
Compares BK5-T and Sfi21.
Both are temperate phages of Lactococus lactis
Lactococcus lactis is a low GC gram positive.
Other low GC gram positives are: Staphylococcus,
Lactobacillus (may be polyphyletci group with members from
both high and low GC gram positives), Streptococcus, Bacillus,
Clostridium, Sporosarcina, Heliobacterium, Mycoplasmas
The high/low GC split based on 16S rRNA appears to be about
90% of the way back to gram +/- split (although I need to
research how well this is corrected for coincidence).
Gram +/- is estimated anywhere from 1.7 to 2.4 Bya, so
high/low GC crudely is 1.5 - 2.2 Bya.
Belong to Siphoviridae: long non contractile tailed phage.
Although lambda is the namesake for these phages, I think lambda
itself is really in a group much further diverged than gram +/-
split, and it never makes an appearance in these papers.
Also compared more distantly related lactococcal phages ski,
Generally more divergent if from more divergent hosts, but
some evidence of chimerism and horizontal transfer.
They say rlt more closely related to mycophages.
They have a large terminase tree in fig 6. Their point
is that it is consistent with their impressions of similarity
based on gene order. They were hampered by using Clustal
W, which loses power over the deeper splits, and these were
drawn with horrible bootstrap values and not interpreted
much. By comparison to our large terminase tree:
They mainly wanted to coorelate that Sfi21, BK5-T, and adh
were closer to each other than to (A2,PVL), which were closer
than other stuff, with (rlt,TM4) being particularly far
out. We agree with that.
We find a radiation not distinguishable by bootstrap (at
least not as of pfra) that encompases both gram +/- split and
high GC/low GC split, with the rlt group further out than
that. If we flatten out their bad bootstrap values, it
essentially comes to that, except we resolve that rlt group is
inside of the other outgroups (specifically more like the
other fam 1 genes just mentioned than like the P2-like phages)
but apparently diverged prior to the gram +/- split.
Hélène Deveau, Rodolphe Barrangou,
Josiane E. Garneau, Jessica Labonté, Christophe Fremaux, Patrick
Boyaval, Dennis A. Romero, Philippe Horvath, and Sylvain Moineau.
2008. Phage Response to CRISPR-Encoded Resistance in Streptococcus
thermophilus. J Bacteriol. 2008 February; 190(4): 1390–1400
Dittmer A, Drach JC, Townsend LB,
Fischer A, and Bogner E. 2005. Interaction of the putative human
cytomegalovirus portal protein pUL104 with the large terminase
subunit pUL56 and its inhibition by benzimidazole-D-ribonucleosides.
VIROLOGY 79 (23): 14660-14667. UTHSCSA
Colocalize in the nucleus.
Djordjevic GM, Klaenhammer TR. 1997. Bacteriophage-triggered
defense systems: Phage adaptation and design improvements. APPL
ENVIRON MICROB 63 (11): 4370-4376.
A suicide defense system; is this a natural system? *
Dobbins AT, Matthew G Jr., Basham DA, Ford ME, Houtz JM, Pedulla ML,
Lawrence JG, Hatfull GF, and Hendrix RW. 2004. Complete
genomic sequence of the virulent Salmonella bacteriophage SP6.
J. Bact 186: 1933-1944.
T7-like, but with a 5 kb novel segment.
Has a format of diagram that coordinates 5 member unrooted
trees along the genome and points out where T7/T3/phiYeO
Cites a temperate version of t7 in Psuedomonas Putida (Nelson
et al., Env. Microbiol. 4:799-808.
Has replicative direction mapped by skew.
Domotor D Becsagh P Rakhely G Schneider G Kovacs T 2012.
Complete genomic sequence of Erwinia amylovora phage phiEaH2. J.
Virol. 86: 10899. PMID 22966191.
Edgar R, Chattoraj DK, Yarmolinsky M. 2001. Pairing of P1
plasmid partition sites by ParB. Mol. Micro. 42 (5): 1363-1370.
Effantin G, Boulanger P, Neumann E, Letellier L, Conway JF. 2006.
Bacteriophage T5 structure reveals similarities with HK97 and T4
suggesting evolutionary relationships. J.
Mol. Biol. 361:993-1002.
Cryo EM on T5 head
Similar to HK97 and T4
Has a head decoration protein on each hexamer. pb10, 164
Baseplate (or at least the fibers coming from it) have a 3
fold symmetry instead of 6 fold
Tail tube is trimeric instead of hexameric.
Thinks the tape measure is 5 or 6 fold and extends out the
tail tip to form a host recognition fiber. Is partially
Thinks the delta domain controls the geometry (T number)
10,160 bp direct repeats.
Endy D, You L, Yin J, and Molineux IJ. 2000. Computation,
prediction, and experimental tests of fitness for bacteriophage T7
mutants with permuted genomes. Proc. Natl. Acad. Sci. USA. 97:
T7 DNA enters relatively slowly and this partially controls
Made mutants with RNAP gene out of place.
Entenza JM, Loeffler JM,
Grandgirard D, Fischetti VA, Moreillon P. 2005. Therapeutic
effects of bacteriophage Cp1-1 Lysin against Streptococcus
pneumoniae endocarditis in rats. Antimicrob. Agents and
Chemotherapy 49: 4789-4792.
Esposito D. Fitzmaurice WP. Benjamin RC. Goodman SD. Waldman AS.
Scocca JJ. The complete
nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids
Research. 24(12):2360-8, 1996.
Can recognize the last two structures (D5,D6) with Rfam
ORF not always there, but when there is in D4
5' splice site defined by end of complementarity to two
internal loops (EBS1, EBS2)
Filchikov MV, Osmakov DI, Logovskaya LV, Sykilinda NN, Kadykov
VA, Kurochkina LP, Mesyanzhinov VV, Bernal RA, Miroshnkkov KA.
2009. Pseudomonas aeruginosa bacteriophage SN: 3D-reconstruction
of the capsid and identification of surface proteins by electron
microscopy. Russian J. of Bioorganic Chemistry 35:728-733 link.
Filée J, Forterre P & Laurent J. 2003. The role played by
viruses in the evolution of their hosts: a view based on
informational protein phylogenies. Res. Microbiol.
154:237-243. PMID: 12798227. UTHSCSA
Filée J Forterre P Tang S-L Laurent J (2002) Evolution if DNA
polymerase families: Evidences for multiple gene exchange between
cellular and viral proteins. J. Mol. Evol. 54: 763-773. PMID 12029358.
PolA family separate between cellular and phage, except
mitochondria recruited a phage polymerase.
PolB family separate between cellular and phage.
SPBc2 has a Y family DNA polymerase.
Filee J, and Forterre P. 2005.
Viral proteins functioning in organelles: a cryptic origin?
Trends. Microbiol. 13: 510-513.
Reviews data about mitochondrial RNA polymerase, DNA
polymerase, and DNA primase being of T7-like origin.
Notes cryptic fragments of T7-like phages in several genomes
and proposes that cryptic fragments were the transfer agent
rather than a phage genome itself.
Filée, J., Bapteste, E., Susko, E. and
Krisch, H.M. (2006) A selective barrier to horizontal gene transfer
in the T4-type bacteriophages that has preserved a core genome with
the viral replication and structural genes. Mol
Biol Evol. 23:1688-96. PMID: 16782763. UTHSCSA
Emphasizes congruency of trees for major proteins and draws a
tree from joined sequence.
Says there is no lateral transfer into these conserved core
modules, but it is unclear if he hasn't pruned out extra
Cites that the cyano T4s got the ThyX version of thymidylate
synthetase apparently from cyanobacteria, while all the others
have the ThyA version.
Says that there is frequent lateral transfer of the
nonubiquitous T4 genes. Isn't that circular statement?
He argues that the cyano T4s to T4s are even more diverged
than gram negatives to cyanobacteria because genes like DNAb and
RecA are more divergent phage to phage than host to host.
He claims 2.5 to 3.2 Bya citing Battistuzzi et al. 2004
Argues at length that the conservation of gene clustering (he
doesn't say order, but the order is also conserved) has to do
with protein-protein interactions, complexes, macroassemblies,
nanomachines, etc. Never quite gets around to saying
"coadapted", but that is the implication.
Firczuk M, Mucha A, Bochtler. 2005.
Crystal structures of active LytM. J. Mol. Biol. 254:578-590.
Aka lysostaphin-type enzymes, metalloendopeptidases that
cleave the pentaglycine crossbridge.
Cellular ones secreted as proenzymes that require cleavage for
Different domains attached to different enzymes
They solved more structures at different pH's and with
Bkg: CRISPR arrays in bacterial chromosomes have short
segments of DNA derived from phages, and resist infection by
phages matching those sequences.
CRISPR refers to a conserved repeating sequence bounding each
The phages sequences themselves are called "spacers".
In the phage itself, they are called "proto-spacers".
The arrays are usually oriented so that they are transcribed
from right to left. The promoter is called a "leader".
New spacers accrue at the leader-proximal end of the array.
Spacers are found to match phages, plasmids, and even some
chromosomal loci claimed to be derived by conjugation.
The method of capture is unkown at this time.
Some genes usually nearby, called CAS genes, are involved.
For a given array, the protospacers are followed by a
characteristic sequence called a PAM, which is usually 2 bp and
may be 0 or 1 bp off the end. It's not clear to me if
these are required for the recognition at attack time, or just a
signature left from capture.
Mojica argues that attack is against DNA, because there is no
strand bias for the transcripts.
Refers to Makarova et al. (Biol Direct 1, 7; 2006) for the
RNA driven counter hypothesis.
Strictly speaking, the bias only says that the capture
doesn't involve RNA. But if the arrays persist long
enough for selective effects to enrich for effective spacers,
then it would also say that the attack does not involve RNA.
Cites a case where a new spacer was acquired during a phage
challenge (Horvath et al.,
2008; J Bacteriol 190, 1401–1412.). This implies that they
can be acquired during lytic challenge and do not require the
phages to be temperate. However, most identified
protospacers are to temperate phages. A511 was cited as a
counter example. One spacer isn't a very strong
argument. The example would have to be examined carefully.
Mojica tabulates protospacers down to 90% matches, but cites a
paper that says mutating one base destroys function.
Most spacers don't match anything. Mojica blamed this on
phage diversity. Keep in mind that genes that were easily
identifiable by protein similarity might not be identifiable in
as 27-72 nt DNA sequences.
Fokine A, Battisti AJ, Bowman VD,
Efimov AV, Kurochkina LP, Chipman PR, Mesyanzhinov VV, Rossmann MG.
2007. Cryo-EM study of the Pseudomonas Bacteriophage phiKZ. Structure
Identifies gp29 as the sheath protein, and says T4 gp18 and
this protein can coassemble.
Sheath is ~ 44 rings.
Identifies gp181 as probable component of cell puncturing
Other than capsid protein, does not identify any other genes
with the cryoEM densities.
Fokine A, Leiman PG, Shneider MM,
Ahvazi B, Boeshans KM, Steven AC, Black LW, Mesyanzhinov VV,
Rossmann MG. 2005. Structural and functional similarities
between the capsid proteins of bacteriophages T4 and HK97
point to a common ancestry. PNAS 102:
Fokine A, Kostyuchenko VA, Efimov
AV, Kurochkina LP, Sykilinda NN, Robben J, Volckaert G, Hoenger A,
Chipman PR, Battisti AJ., Rossmann MG, Mesyanzhinov VV. 2005. A
three-dimensional cryo-electron microscopy structure of the
bacteriophage phiKZ head. J.
Mol. Biol. 352:117-124. UTHSCSA
gp120 is the major capsid protein.
T=27, which means copy number = (27-1) * 60 = 1560
First 163 residues cleaved off.
There is an inserted endothiapepsin domain that also has
Proposed soc in T4 plays same role as the insertion in phiKZ
Say a single vertex (of which there are 55) is composed of
domains adding up to 208kD (That's for one; There
would be 5 each of each component). There is no protein
big enough, so there should be several gene making proteins with
copy number 55 and adding up to 208kD. A breakdown of
"domains" was 25, 30, 27, 33, 35, 33, 40, 35kD.
The show the outlines of what they called the "inner core", or
their version of the inner head body. It seemed to be less
that 2x the volume of the protal, and mounted on the
Fokine A, Battisti AJ, Kostyuchenko VA, Black LW, Rossmann MG.
2006. Cryo-EM structure of a bacteriophage T4 gp24 bypass
mutant: The evolution of pentameric vertex proteins in icosahedral
viruses. J Struct Biol. 2006 Feb 21; [Epub ahead of print]
Fokine A, Miroshnikov KA, Shneider
MM, Mesyanzhinov W, Rossmann MG. 2008. Structure of the
bacteriphage phiKZ lytic transglycosylase gp144. J. Biol. Chem.
They define "transglycosylase" to mean cleavage of the
glycosidic link to produce 1,6-anhydromuramic acid. This
is further clarified to be a new glycosidic bond between O-6
and C-1, whereas lysozymes hydrolyze using water.
This one cleaves A1gamma peptidoglycans, an is classified to
a family called family 1 lytic transglycosylase.
They defined a 70 residue peptidoglycan binding domain on
the N terminus, and 190 residues of catylatic domain.
But the fold of the transglycosylase doesn't really start till
residue 86. 70..86 is a proline rich linker region.
Ford ME. Stenstrom C. Hendrix RW. Hatfull GF. Mycobacteriophage
TM4: genome structure and gene expression.
Tubercle & Lung Disease. 79(2):63-73, 1998.. UI: 20110038.
Forterre P. New viruses for the new millennium. TRENDS MICROBIOL
9 (3): 114-114 MAR 2001.
Reviews links between eucaryotic and procaryotic viruses:
genome structure of archael virus SIRV and poxviruses.
structural similarities between RNA phage and reoviruses.
capsid protein between phage PRD1 and adenovirus.
Forterre P. 2002. The origin of DNA genomes and DNA replication
proteins. Curr. Opin. in Microbiol. 5:525-532. UTHSCSA
Forterre P. 2006. The origin of viruses and their possible roles
in major evolutionary transitions. Virus Research 117:
Reviews previous commentary on viruses before cells, viruses
from degenerated cells, and viruses from escaping cellular
Discusses viruses as originators of DNA, and reviews the
paradox of two different replicative systems in bacteria vs.
eucaryotes and archae.
Foschino R, Venturelli E, Picozzi C. 2005. Isolation and
characterization of a virulent Lactobacillus sanfranciscensis
Bacteriophage and Its impact on microbial population in sourdough.
Curr. Microbiol. 51: 413-418.
32 Kb pac type phage.
Apparently the physical nature of the dough prevents rampant
amplification of the phage.
RB69 DNA polymerase: 3'-5' exo domain is pdb: d1ih7a1, and
polmyerase domain is pdb: d1ih7a2
They refer to this as an alpha polymerase (aka. family B)
meaning more like human DNA polymerase alpha than like E. coli
N ter domain 1-382 includes exo domain at 109-339. Pol
domain is divided to palm (383-468, 573-729), fingers (469-572)
and thumb (730-903).
Fraser JS, Yu Z, Maxwell KL, Davidson AR. 2006. Ig-like
domains on bacteriophages: a tail of promiscuity and deceit.
J. Mol. Biol. 359:496-507. PMID 16631788.
Tabulates Ig-like domains in bacteriophages
Organizes into three families.
They say that the major capsid protein frameshift extension on
T3 is Ig-like, but in T7 it is not. I identified the T7
extension as an endosialidase.
The recognized the Ig domain decorating the tail tube of
lambda and other phages.
They explicitly describe a postulated analogy to the role of
selectins in blood cell binding to capillary walls.
I got into this paper because I was interested in gp17 head
decoration protein on N4, which is said to be Ig-like.
Others of interest to the podovirus story:
Frick DN, Richardson CC. 2001. DNA primases. Ann. Rev.
Biochem. 70: 39-80.
Frick DN, Richardson CC. 1999. Interaction of bacteriophage
T7 gene 4 primase with its template recognition site. J. Biol.
Chem. 274 (50): 35889-35898.
Gives recognition sites as 5'-GGGTC-3', 5'-TGGTC-3',
5'-GTGTC-3', or 5'-TTGTC-3'.
Fuhrman JA. 1999. Marine viruses and their biogeochemical and
ecological effects. Nature 399: 541-548.
Virus count exceeds bacteria count by 2-5 in all segments of
Cites for high count: Bergh, O., Børsheim, K. Y., Bratbak, G.
& Heldal, M. High abundance of viruses found in aquatic
environments. Nature 340, 467–468 (1989), plus many followup
studies showing consistency of result in various segments of the
Cites Wommack, K. E., Ravel, J., Hill, R. T., Chun, J. S.
& Colwell, R. R. Appl. Environ. Microbiol. 65, 231–240
(1999) for diversity as measured by pulsed field electrophoresis
of genomic DNAs.
Virus count tends to fluctuate with bacteria, suggesting they
are mainly bacteriophages. Viruses affecting other
microorganisms are also featured in the review.
Cites for killing of host populations: Proctor, L. M. &
Fuhrman, J. A. Viral mortality of marine bacteria and
cyanobacteria. Nature 343, 60–62 (1990).
Cites range of estimates for fraction of bacterial mortality
due to viruses in aerobic waters as 10-50%.
Supplies a list of ecological processes that viruses may
Puzzles over why resistance isn't more common.
Discusses pseudolysogeny, in which a host transiently survives
a lytic infection.
Cites Jiang, S. C. & Paul, J. H. Microb. Ecol. 35,
235–243 (1998) for 40% of cultured marine bacterial being
Only a brief discussion of genetic exchange, featuring how the
very rare events would be amplified due to high population sizes
in ocean and effective mixing. Cites oceanic bacterial
generation time as about a day.
Fu X, Walter MH, Paredes A, Morais MC, Liu J. 2011. The
mechanism of DNA ejection in the Bacillus anthracis spore-binding
phage 8a revealed by cryo-electron tomography. Virology
421:141-148. PMID 22018785.
Propose that the rotation involved in sheath contraction also
rotates something in the neck gating DNA passage.
Fu C, Johnson JE. 2012. Structure and cell biology of archael
virus STIV. Curr. Opin. Virol. 2:122-127.
Much more obvious than PRD1 paper in how the proteins are
oriented relative to the exterior.
20484 partial sequence, AB161975 (nearly full length); aka
This is in-the-coat nondefective viral DNA corresponding to
the defective WO prophage previously reported.
No typical replicative module indicated although there is a
Has lambda-like head structure and identifiable baseplate and
They say the ends could not be cloned.
Annotate VrlC homologues as probable secreted proteins.
Elsewhere I noted that it had a sialidase domain and figured it
to be tail tip fiber. The nature of these Vrl genes is
currently problematical. They fall in a "virulence" locus
that looks like a prophage. Which gene in the prophage is
the virulence gene is completely unclear to me.
Gadaleta P, Zorzopulos J. 1997. Kluyvera bacteriophage Kvp1: a new
member of the Podoviridae family phylogenetically related to the
coliphage T7. Virus Res. 51 (1): 43-52.
Gaidelyte A, Cvirkaite-Krupovic V, Daugelavicius R, Bamford JKH,
Bamford DH. 2006. The entry mechanism of membrane-containing phage
Bam35 infecting Baillus thuringiensis. J. Bact 188: 5925-5934.
16 kb genome with viral particle like PRDI.
Gan HM, Sieo CC, Tang SGH, Omar AR, and Ho YW. 2013. The
complete genome sequence of EC1-UPM, a novel N4-like bacteriophage
that infects Escherichia coli O78:K80. Virol. J. 10:308. PMID
Gan L, Speir JA, Conway JF, Lander G, Cheng N, Firek BA, Hendrix RW,
Duda RL, Liljas L, and Johnson JE. 2006. Capsid conformational
sampling in HK97 maturation visualized by X-ray crystallography and
Mutants trap the HK97 capsid expansion in an intermediate
Garcis LR Molineux IJ (1995) Rate of translocation of bacteriophage
T7 DNA across the membranes of Escherichia coli. J. Bacteriol.
T7 RNA polymerase does it.
Note: They later had a paper where mutants of gp16
allowed the DNA to get in without transcription, but still
claimed to be "enzymatically catalyzed".
Gilcrease EB, Winn-Stapley DA,
Hewitt FC, Joss L, Casjens SR. 2005. Nucleotide sequence of the
head assembly gene cluster of bacteriophage L and decoration
protein characterization. J. Bact. 187:2050-2057.
Dec, present in L but not P22 which is otherwise very close,
is a trimer that binds the head like lambda gpD.
Gipson, P, Baker ML, Raytcheva D,
Haase-Pettingell C, Piret J, King JA, and Chiu W. 2013.Protruding knob-like
proteins violate local symmetries in an icosahedral marine virus.Nat. Commun. 5:4278.
They don't comment on tail or core proteins, but tubeA, tubeB,
IVP B and D are obvious by psiblast to P-SSP7. IVP C is
orphaned for P-SSP7.
Goodridge, LD. 2004. Bacteriophage biocontrol of plant
pathogens: fact or fiction? Trends Biotechnol 22: 384-385.
Comments on a paper by Gill and Abedon that indicates some
further investigation is required.
Guash A, Pous J, Ibarra B, Gomis-Ruth
FX, Valpuesta JM, Sousa N, Carrascosa JL, coll M. 2002 Detaild
architecture of a DNA translocating machine: the high-resolution
structure of the bacteriphage phi 29 connector particle. J.
Mol. Biol. 315, 663-676.
3D structure of phi29 portal
Notes N ter 13 residues is where packaging ATPase interacts.
Channel is 35 A wide; DNA is 23 A wide
They have a spinning portal drive model with a 6 mer ATPase
driving a 12mer portal producing 12 degress retrograde rotation
on the DNA That's geometrically wrong. It would have
to be a 5 mer ATPase to produce the 12 degree rotation.
Girons,I.S., Bourhy,P., Ottone,C., Picardeau,M., Yelton,D.,
Hendrix,R.W., Glaser,P. and Charon,N. 2000. The LE1 bacteriophage
replicates as a plasmid within Leptospira biflexa: construction of
an L. biflexa-Escherichia coli shuttle vector. J. Bact. 182 (20),
A larger segment of sequence is reported in BX571876,
attributed to Bourhy,P., Frangeul,L., Glaser,P. and Saint
Gonzales-Huici V, Sala M, Hermoso JM. 2004. The push-pull mechanism
of bacteriophage Phi29 DNA injection. Mol. Microbiol 52: 529-540.
Goodrich-Blair H, Scarlato V, Gott JM, Xu MQ, Shub DA. 1990. A
self-splicing group I intron in the DNA polymerase gene of
Bacillus subtilis bacteriophage SPO1. Cell. 63(2):417-24.
Gordon GS, Wright A. 2000. DNA segregation in bacteria. Ann. Rev.
Micro. 54: 681-708.
The ori's of bacterial chromosomes are seggregated as
replication begins, and the rest of the chromosome is pulled
into the developing daughter cells by a condensation process.
Lists plasmids that use the par system as F, P1, and R1.
Guan C, and Kumar S. 2005. A single catalytic domain of the
junction-resolving enzyme T7 endonuclease I is a non-specific
nicking endonuclease. NAR 33: 6225-6234.
T7 endo I resolves holliday junctions.
Is a homodimer
Conclude that monomers would prefer to nick ordinary ds DNA,
but the two active sites in the homodimer are juxtaposed to make
it recognize a holliday structure.
There is a 3D structure: Hadden et al. 2001. Nat. Str. Biol:
Guo F, Liu Z, Vago F, Ren Y, Wu W, et
al. Visualization of uncorrelated, tandem symmetry mismatches in
the internal genome packaging apparatus of bacteriophage T7. Proc Nat'l Acad Sci USA. 2013;110:6811–6. PMID: 23580619.
Gives the 12 fold, 8 fold, 4 fold numbers to core porteins.
Core has a small tilt.
Guo P, Zhang C, Chen C, Trottier M, Garver K. Inter-RNA interaction
of phage phi29 pRNA to form a hexameric complex for viral DNA
transportation. Mol Cell 1998; 2: 149–155.
Guo, P., Erickson, S., and
Anderson, D.L. (1987). A small viral RNA is required for in vitro
packaging of bacteriophage phi 29 DNA. Science
236: 690–694. UTHSCSA
First 120 of 174 nt essential for packaging.
Haggard-Liungquist E, Jacobsen E,
Rishovd S, Six EW, Nilssen O, Sunshine MG, Lindqvist BH, Kim K-J,
Barreiro V, Koonin EV, Calendar R. 1995. Bacteriophage P2: Genes
Involved in Baseplate Assembly. Vir.
213: 109-121. UTHSCSA
By immuno gold staining, gpV is tail spike (a short central
tip to the tail), and gpJ is exposed at the periphery of the
Hambly E, Tetart F, Desplats C, Wilson WH, Krisch HM, Mann NH.2001.
A conserved genetic module that encodes the major virion components
in both the coliphage T4 and the marine cyanophage S-PM2. Proc
Natl Acad Sci U S A. 98(20):11411-6.
EM shows an icosohedral head and longer tail than T4.
Baseplate and fibers may be different than T4, but they do not
comment on this.
Show a chewed up looking alignment of the tail sheath across
T4-like and even P2 using McCaw.
Comparison of head cassette shows a small frame or two
Handa N, and Kobayashi I. 2005 Type III Restriction is alleviated
by bacteriophage (RecE) homologous recombination function but
enhanced by bacterial (RecBCD) function. J. Bact. 187: 7362-7373.
EcoPI or EcoP15 were enhanced by RecET in rac prophage
RecT becomes required if in RecA- background.
Discusses idea that restriction modification systems are
selfish gene systems, and exhibit selfish molecular drive during
Cites numbers of strategies used by phages to avoid
Hang JQ, Tack BF, Feiss M. 2000. ATPase center of bacteriophage
lambda terminase involved in post-cleavage stages of DNA
packaging: Identification of ATP-interactive amino acids. J.
Mol. Biol. 302: 777-795.
Bkg: lambda also has large and small packaging enzymes, in
this case called a terminase.
gpA is the large subunit, and is an ATPase.
This paper explores ATPase active site residues by in vitro
Y46 and K84 interact with 8-aza-ATP. Mutagenesis kills
J, Catalano C, Feiss M. 2001. The functiona asymmetry of cosN,
the nicking site for bacteriophage lambda DNA packaging, is
dependent on the terminase binding site, cosB. Biochem.
These results also reviewed in the Packaging Machines book.
They are 3' recessed ends.
5'TTACG^GGGGGCGGCGACCT^CGCGG 3' - the part of the DNA
that will first enter capsid.
This is called the l strand, and is in the usual orientation
written for lambda (left end on the left).
The cleavage in NL is called N2, the one in NR is called N1.
Mutations in NL affect N2, mutations in NR affect N1.
mutations in NL (ends up connected to right end) block
mutations in NR (ends up connected to left end) do not block
cleavage unless there are also problems in cosB.
Harcombe WR, Bull JJ. 2005. Impact of phages on two-species
bacterial communities. Appl. Env. Microbiol. 71: 5254-5259.
Has some citations about interest in phage therapy and phage
Notes that resistant bacteria always rebound when you attack a
monoculture with phage.
In competition between E. coli and Salmonella, T7 or T5 could
severly depress or extinguish E. coli, but Salmonella would
rebound from SP6.
Hardies SC, Comeau AM, Serwer P,
and Suttle CA. 2003.The complete sequence of marine bacteriophage
VpV262 infecting Vibrio parahaemolyticus indicates that an
ancestral component of a T7 viral supergroup is widespread in the
310 (2), 199-372.
Structural proteins of VpV262 as well as Roseophage SIO1 are
distantly related to T7.
Unlike SIO1, VpV262 does not have a T7-like replicative module
Like SIO1, VpV262 has 2 major converging transcription units.
R, Lapidus A, Kogan Y, Vlcek C, Paces J, Paces V, Ulbrich P,
Pecenkova T, Rebrekov D, Milgram A, Mazur M, Cox R, Kyrpides N,
Ivanova N, Kapatral V, Los T, Lykidis A, Mikhailova N, Reznik G,
Vasieva O, Fonstein M. 2001. Photosyn. Res. 70: 43-52.
6-7 cryptic phages.
Thinks from codon usage that the phages are recent
Genetic analysis in R. capsulatus is through the use of a
defective phage called "Gene Transfer Agent".
This species does photosynthesis and nitrogen fixation.
R. sphaeroides and R. palustris genomes also available?
Heineman RH, Molineux IJ, Bull JJ.
2005. Evolutionary robustness of an optimal phenotype: re-evolution
of lysis in a bacteriophage deleted for its lysin gene. J.
Mol. Evol. 61: 181-191.
Deleted T7 lysozyme and observed the muramidase in internal
protein p16 to become modified to compensate.
Helgstrand C, Wikoff W, Duda RL,
Hendrix RW, Johnson JE, and Liljas L. 2003. The refined structure of
a protein catenane: The KH97 bacteriophage capsid at 3.44 A
Mol. Biol. 334: 885-899.
The penultimate end of the N arm adds a beta strand to the
beta finger of the E-loop.
The strand is 119-125 in HK97.
The N terminus then proceeds through the interface and is
exposed on the exterior of the capsid.
Structure is PDB 1OHG
Hendrix, R.W. (1978) Symmetry mismatch and DNA packaging in large
bacteriophages. Proc Natl Acad Sci USA 75: 4779–4783.
Reviews the Benson et al result that PRD1 capsid protein has
similarity to adenovirus capsid at the structural level
Leaves it as uncertain whether it was horizontal transfer or
dates prior to euk/prok/archae split.
Say 50 virus capsid high res. structures compiled at
http://mmtsb.scripps.edu/viper/viper.html. (HK97 is the only ds
DNA phage there; PRD1 isn't there yet). They are mostly
Says of these 50, most have a 8 stranded beta jelly roll.
Suggests that maybe all the jelly role capsid proteins are
related by descent (would include phiX174), but PRD1 and
adenovirus capsid have some additional structural similarities.
Reviews some similarities in assembly of T4 and Herpes virus,
including a "hint" of similarity between the terminases.
Mentions that ds RNA Reoviruses and the ds RNA phage phi6
share unusual symmetry in the assembly of their capsids.
He prefers horizontal transfer to explain sequence
similarities between Archaeal phage and Bacteriophage, but
prefers ancient origin for structural similarities between phage
and Eucaryotes; But he admits that its just a guess, and
acknowledges the lack of timing information.
minireview of DNA transport during phage packaging.
Goes through annular ring of 12-13 portal proteins.
Citing lambda terminase in particular: terminase binds
concatemer, makes first cleavage, and leads DNA to
prohead. DNA threads past terminase until it makes 2nd
cleavage. Then terminase plus bound concatemer associate
with a new prohead.
Terminase burns one ATP per 2 bp transported.
Citing Guo, P., Erickson, S., and Anderson, D.L. (1987).
Science 236, 690–694, working in phi29, a 174 nt RNA is required
which is phage encoded and present in 6 copies per capsid.
It is not present in mature virions.
For original idea of composing phage by combining parts,
cites: Campbell, A. and Botstein, D. (1983) Evolution of the
lambdoid phages. In Lambda II (Hendrix, R. et al., eds), pp.
365–380, Cold Spring Harbor Laboratory Press.
Reviews the transition from thinking about homologous
recombination to non-homologous recombination.
Proposes major role in virus evolution is single gene
additions ("morons"). Gives a substantial compilation of
Goes so far as to propose how a virus could be built from
nothing, one gene at a time.Their postulated protoviral gene
would be a single capsid gene that functioned by itself as an
agent of horizontal transfer. However, it is not obvious
if any of their examples are recuitments of host genes as
opposed to acquisition from other viruses or prophage.
Strongly features the statement that phage do not have equal
access to the pool. They clarify this as an issue of host
This is the citation that Hendrix gives to justify deeper
relationships among phage types than the impression given by
frequent isolation of phages with little sequence similarity.
More literature on mosaic tail fibers:
Haggard-Ljungquist, E., Halling, C. & Calendar, R.
(1992) J. Bacteriol. 174, 1462-1477.
Sandmeier, H., Iida, S. & Arber, W. (1992) J.
Bacteriol. 174, 3936-3944.
Tetart, F., Repoila, F., Monod, C. & Krisch, H. M.
(1996) J. Mol. Biol. 258, 726-731.
Monod, C., Repoila, F., Kutateladze, M., Tetart, F. &
Krisch, H. M. (1997) J. Mol. Biol. 267, 237-249.
Shows homology relationships among the groups lambdoid
(lambda, HK97, HK022), phi C31 (of Streptomyces),
mycophages (L5, D29), crytpic mycophages (phi Rv1, phi Rv2),
and phi flu (of Haemophilus).
Notes that the coli lambdoid group was not recognized to
have affinity with the mycophages until phi C31 showed up with
strong affinities to both (although apparently in different
sets of genes).
Shows a few relations to genes in other phage:
TM4 primase to mycophage and phi C31.
Also P4 primase to phi C31.
T4 nucleotide kinase to phi C31.
T4 and P2 tail fibers to lambdoid group.
HP1 tail fiber to phi flu.
SPP1 and PBSX terminases to phi flu.
Sfi21 anti repressor to phi flu.
TM4 L5 and tail proteins to mycophages.
rlt and TM4 portal protein to mycophages.
Other than T4, are any of these not temperate?
For method of horizontal exchange, cites 16k per Mya
acquired by E. coli by horizontal transfer, citing Lawrence,
J. G. & Ochman, H. (1998) Proc. Natl. Acad. Sci. USA 95,
9413-9417; hence their model is strongly biased towards
temperate phage. They think exhange by coinfection is
vigorous, but confined along host lines.
Hertveldt K, Lavigne R, Pleteneva
E, Sernova N, Kurochkina L, Korchevskii R, Robben J, Mesyanzhinov V,
Krylov VN, and Volckaert G. 2005. Genome comparison of Pseudomonas aeruginosa large
Mol. Biol. 354:536-545. UTHSCSA
1/3 of gene matched to phiKZ, but only 14 identified with a
homologue of known function.
Notes gp11,25,39,40,166,185 are homing endonucleases, but does
not map out mobile introns.
At another point says 11, 39, 40, 166 are inteins.
Hertwig,S., Klein,I., Schmidt,V., Beck,S., Hammerl,J.A. and
Appel,B. 2003. Sequence analysis of the genome of the
temperate Yersinia enterocolitica phage PY54. J. Mol. Biol. 331,
Grows as linear plasmid with closed ends (like N15);
releases phages as it grows and is highly lysogenic.
In phage head (also N15) DNA has cohesive ends and is ~ 50%
permuted relative to plasmid form.
NC_005069; 46,339 bp.
Most proteins identified: large and small terminase, major and
minor capsid proteins, major tail, tape measure, tail-host
specificity protein, tail fiber, partitioning SpyA and B,
several reperssors (immunity repressor known)and
antiterminators, protelomerase, recombination protein RdgC, exo
VIII, DNA 2 adenine methylases, lysin, holin, and several
homologues of unidentified phage gene families. Discusses
some other possible gene assignments in text.
Cos sites identified
Did some mutagenesis and some transcription studies.
Hoeprich, S. & Guo, P. (2002). Computer modeling of
three-dimensional structure of DNA-packaging RNA(pRNA) monomer.
Dimer, and hexamer of
Phi29 DNA packaging motor. J. Biol. Chem. 277, 20794–20803.
Hollis T, Stattel JM, Walther DS, Richardson CC, Ellenberger T.
2001. Structure of the gene 2.5 protein, a single-stranded DNA
binding protein encoded by bacteriophage T7. PNAS 98 (17):
C terminal flexible acidic region - may be for T7 polymerase
or primase/helicase interaction.
Homa FL. Brown JC. Capsid assembly and DNA packaging in herpes
Reviews in Medical Virology. 7(2):107-122, 1997.
Reviews phage resistance mechanisms, including 22 abi systems
that cause cells to commit suicide.
Many phage resistance determinants are carried on plasmids.
Hu B Margolin W Molineux IJ Liu J (2013) The bacteriophage t7
virion undergoes extensive structural remodeling during
infection. Science 339:576-579. PMID 23306440.
Hwang, Y., Catalano, C. E. & Feiss, M. (1996). Kinetic and
mutational dissection of the two ATPase activities of terminase,
the DNA packaging enzyme
of bacteriophage l. Biochemistry,
35, 2796-2803. UTHSCSA
attributes finding that ATP required to bind but not
hydrolyze for cos cleavage to (Higgins et al., 1988; Cue &
Feiss, 1993a; Higgins& Becker, 1994a,b
but ATP hydrolysis required for separation of ends to
Higgens et al., 1988. Cell 54, 765-
Review preceeding and contradictory evidence indicating 2
ATPase activities, one high affinity and one low affinity.
Made several mutations at K497 in lambda large terminase,
which they thought was a P-loop.
More recent information indicates it's actually in a DNA
binding loop of the ruvC fold.
Also mutated putative P-loop in gpnu1, which they subsequently
have concluded based on the structure is not a P-loop.
They measure a high ATP affinity ATPase and a low affinity
Mutations in K35 in small terminase reduced the low affinity
activity, but it could be restored with higher DNA
concentration. They interpreted this to mean that the
small terminase was a low affinity ATPase. Since they no
longer believe that, I presume that the small terminase is
stimulating a low affinity ATPase activity of the true P-loop
ATPase in a DNA dependent fashion.
Mutations in K497 reduce the high affinity ATPase
activity. Since we now think there is no ATPase in this
domain, I presume that DNA binding to the endo domain is
required to supplement the small terminase binding and get the
full allosteric effect of engaging the DNA upon ATPase
This paper also talked about 8azaATP crosslinking as an
alternative means to detect ATP binding sites and their
affinity, but the actual residues crosslinked were mapped later
into the N terminus.
Isidro A, Henriques AO, and Tavares
P. 2004. The portal protein plasy essential roles at different
steps in the SPP1 DNA packaging process. Virology
In gp15 mutants, the DNA escapes after packaging.
There is a portal mutant in the vicinity of the gp15 contacts
that has the same phenotype
In both cases, the DNA is properly cleaved before release.
What holds the DNA in place for cleavage?
Iyer, L.M., Makarova, K.S., Koonin,
E.V., and Aravind, L. (2004) Comparative genomics of the FtsK-HerA
superfamily of pumping ATPases: implications for the origins
of chromosome segregation, cell division, and viral capsid
packaging. Nucleic Acids Res 32: 5260–5279.
FtsK-HerA superfamily proposed to contain P-loop domains of
FtsK, associates with septal ring and thought to translocate
DNA during bacterial cell division. Somehow associates
with Xer recombinases.
Related proteins that pump peptides in gram positives.
VirD4 and VirB4, T plasmid transfer proteins.
TrwB; congugative plasmid transfer. Has a crystal
Says AAA+ and the RecA/DnaB-like classes are also hexameric.
Archeal HerA (5'->3' and 3' ->5' helicase). associated
with nur (5'->3' nuclease), essentially FtsK in archaea.
These are structural (or predicted structural) similarities
used to create classifications..
He lumps terminases in because they have a beta 3, along with
recA, a family he calls helicase N, and pilT and the FtsK/HerA
Has AdIVA2 lumped next to terminases.
Talks about a conserved "arginine finger" traversing to
another subunit's ATP site and composing a hexameric interface.
Notes that a lot of these are associated with a nuclease,
although apparently not an orthologous one.
Iyer LM, Koonin EV, Leipe DD, Aravind L.
2005. Origin and evolution of the archaeo-eukaryotic primase
superfamily and related palm-domain proteins: structural insights
and new members. Nucl.
Res. 15: 3875-3876.
Fold relationship to polymerases and cyclases through a palm
domain with an RRM fold.
A primase domain found in following various
combinations: Sequence motifs distinguishing various
functions are given.
Works as a replication primase in eucaryotes, archae, and
baculoviruses (and maybe other viruses?).
The phBC6A51 gene is a recognized member of this group.
Examples adjacent to DnaB genes are known.
Many are associated with the large primase subunit family
(I think the MCM domain on the phBC6A51 gene is such a
But some examples with no associated large primase subunit
Works with Ku protein, and ATP-dependent DNA ligases in
non-homologous end-joining DNA repair in bacteria.
prim-pol in crenarchaeal and Gram positive plasmids.
Have a polymerase domain? Often fused to or adjacent to a
helicase. Initiate plasmid replication.
Herpes UL52-like primases
N terminal domains of D5-like protein of NCLDV and phages
RepA-like primases of ColE2 plasmids.
Several primase-helicase proteins from bacteriophages.
Associated with an endonuclease to start rolling circle
Jang HB Fagutao FF Nho SW Park SB Cha IS Yu JE Lee JS IM SP Aoki
T Jung TS. 2013. Phylogenomic network and comparative
genomics reveal a diverged member of the phiKZ-related group,
Marine Vibrio phage JM-2012. J. Virol 87: 12866-12878.
Jardine PJ and Anderson DL. 2006. DNA packaging in
double-stranded phages. In The Bacteriophages (R. Calendar),
Oxford Univ. Press, New York.
Gives a useful succinct summary of the different packaging
Notes T4 is unique in not having even pac site specificity
Notes that in some pac phages, the site is recognized by the
cleavage is nonspecific (Mu; cleaves 56 - 144 bp away in flanking
host DNA), or semi-specific (P22 - ~ 120 bp away).
Jardine PJ, Coombs DH. 1998. Capsid expansion follows the initiation
of DNA packaging in bacteriophage T4. J. Mol. Biol.
Jiang W, Chang J, Jakana J, Weigele
P, King J, and Chiu W.2006. Structure of epsilon15 bacteriophage
reveals genome organization and DNA packaging/injection
439 (7076): 612-616. UTHSCSA
Cryo EM of mature particale, with details on the DNA packing.
~90 nt protruding through the portal.
They note the agreement with SPP1.
Elaborate on similarities of capsid structures.
Johnson JE, and Chiu W. DNA packaging and delivery machines in
tailed bacteriophages. Curr. Opin. Struct. Biol. 17: 237-243.
Reviews structures available at the time: mostly from
P22, T4, phi29, and the HK97 capsid protein
Full cryoEM shown for T4, T7, P22, epsilon15, phi29
emphasizes universality of capsid fold.
emphasizes DNA presumed to be in portal of epsilon15.
That's problematic. How do the internal virion proteins
Juhala RJ. Ford ME. Duda RL. Youlton
A. Hatfull GF. Hendrix RW. 2000. Genomic sequences of
bacteriophages HK97 and HK022: pervasive genetic mosaicism in the
lambdoid bacteriophages. J.
Mol. Biol. 299:27-51.
host: E. coli.
Comparted with lambda and P22 (from Salmonella).
These are all temperate.
I take it they are all closely related.
They define both homologous and non homologous recombination
events from the comparisons.
They introduce something they call a "moron": apparent
recently derived insertion elements with a protein encoding gene
and their own promoter and terminator enabling the protein to be
expressed from inside a repressed operon during lysogeny.
Kakikawa, M., Oki, M., Tadokoro, H., Nakamura, S., Taketo, A.
& Kodaira, K. (1996).
Cloning and nucleotide sequence of the major capsid proteins of
Lactobacillus bacteriophage phi
gle. Gene 175, 157-165.
P4 is the packaging ATPase from phi6 and related ds RNA
Kanamaru S, Leiman PG, Kostyuchenko
VA, Chipman PR, Mesyanzhinov VV, Arisaka F, Rossman MG..
2002. The structure of the bacteriophage T4 cell-puncturing
415: 553-557. UTHSCSA
gp27 is a trimer.
gp5 is the lysozyme. It has a C terminal domain that
forms the puncturing needle, a middle lysozyme domain, and an N
terminal docking domain for gp27. They thought that the
DNA might go through the gp27.
43% id to cytoplasmic T4 lysozyme.
C terminal domain of gp5 is cleaved during maturation, but
remains present. Rich in beta structure and has 11
VxGxxxxx repeats. They think this domain trimerizes the
entire gp5/gp27 complex.
Domains inhibit packaging by full length terminase.
They depict the terminase as a pentamer, but say this is
They have the small terminase going away upon joining of the
preassembled motor to the capsid.
Kaneko J. Kimura T. Narita S. Tomita T. Kamio Y. Complete
nucleotide sequence and molecular
characterization of the temperate staphylococcal bacteriophage
phiPVL carrying Panton-Valentine leukocidin genes. Gene
Karttunen J, Mantynen S, Ihalainen TO, Bamford JK, Osanen HM.
2015. Non-structural proteins P17 and P33 are involved in
the assembly of the internal membrane-containing virus PRD1.
Virology 482:225-233. PMID 25880114.
GroES involvement in phage assembly, and phage-encoded
Kashlev M, Nudler E, Goldfarb A, White T, Kutter E. (1993).
Bacteriophage-T4 alc protein - A transcription termination factor
sensing local modification of DNA. CELL 75: 147-154.
Alc shuts down host transcription during T4 infection.
Alc terminates host transcription at alc sites, which are
T4 transcription pauses because of the modified DNA.
Somehow this prevents alc termination of T4 transcription.
Katsura, I. & Hendrix, R. W. (1984). Length determination in
bacteriophage lambda tails. Cell
Kazmierczak KM, Davydova EK,
Mustaev AA, Rothman-Denes LB. 2002. The phage N4 virion RNA
polymerase catalytic domain is related to single-subunit RNA
J. 21: 5815-5823.
This is not RNA Pol II encoded by 2 polypeptides reported by
Willis et al., but a different gene whose gene product is
packaged in the virion.
They show a tree with both the N4 polymerases, described as
made from conserved sequence blocks and puzzling.
They only committed themselves to the major clusters and noted
that both N4 enzymes and P60 joined within the mitchondrially
encoded cluster. They cited Cermakian's reluctance to
commit to a particular ancestor.
Kim YW, Jang SH, Hong BS, Lim WJ, Kim CW, Sung HC, Chang HI.
Circular permutation of the DNA genome of temperate bacteriophage
phi FC1 from Enterococcus faecalis KBL703.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY 9 (4): 457-463 AUG 1999.
Identifies terminases, vortex protein, and pac site for this
Kemp P, Garcia LR, and Molineux IJ. 2005. Changes in
bacteriophage T7 virion structure at the initiation of infection.
Gives copy numbes for internal core proteins.
Thinks they snake out through the portal.
Kiljunen S Hakala K Pinta E Huttenen S Pluta P Gador A Lonnberg H
Skurnik M. 2005. Yersiniophage phiR1-37 is a tailed bacteriophage
having a 270 kb DNA genome with thymidine replaced by
deoxyuridine. Microbiology 151 (PT12): 4093-4102. PMID 16339954.
Klimuk E, Akulenko N, Makarova KS, Ceyssens PJ, Volchenkov, I,
Lavigne R, Severinov K. 2013. Host RNA polymerase
inhibitors encoded by phiKMV-like phages of Pseudomonas. Vir.
436:67-74. PMID 23127595.
A T7 gp2-like protein encoded in some phiKMV-like phages.
Kimura M and Hisao Fujisawa H. 1991. Dissection of functional
domains of the packaging protein of bacteriophage T3 by
site-directed mutagenesis. Vir.
180: 709-715. UTHSCSA
Mutants made in this paper discussed further in Morita et al.
Kimura K. and Itoh Y. 2003.
Characterization of Poly-gamma-Glutamate Hydrolase Encoded by a
Bacteriophage Genome: Possible Role in Phage Infection of Bacillus
subtilis Encapsulated with Poly-gamma-Glutamate. Appl. Environ.
Microbiol. 69 (5), 2491-2497.
Found in B. subtilis phage phiNIT1.
Demonstrates role in penetrating capsular material apparently
deployed as a shield against phage infection.
Cites role of endo-N-acetylneuraminidase in other phages to
breach capsular materials. However, in those cases the
degradative activity was part of the capsid, whereas in this
case it is not. It is presumed to be released during cell
lysis and have a collateral effect on promoting infection of
other cells in the culture. It actually decreases the
viscoisity of the culture.
There are unannotated genes to the right and left of the
poly-gamma-glutamate hydrolase (PghP).
The upstream gene matches at 85% na similarity an
orf in phageD., which is a pectin lyase probably with a
The PghP gene itself matches the next
gene in phageD at 85% similarity, establishing recent
transfer of a capsular degrading cassette.
Kondabagil KR, Rao VB. 2006. J. Mol. Biol. 358: 67-82. A critical
coiled coil motif in the small terminase, gp16, from bacteriophage
T4: Insights into DNA packaging initiation and assembly of packaging
Mol. Biol. 358: 67-82.
Proposes that a coiled coil motif is found widely in small
terminases, including in bacteriophage lambda.
Kondabaqil KR, Zhanq Z, Rao VB. 2006. The DNA Translocating ATPase
of Bacteriophage T4 Packaging Motor. JMB Aug 25 2006, Epub ahead
Kira S Makarova,
Nick V Grishin, Svetlana A Shabalina,
Yuri I Wolf and Eugene V Koonin. A
putative RNA-interference-based immune system in prokaryotes:
computational analysis of the predicted enzymatic machinery,
functional analogies with eukaryotic RNAi, and hypothetical
mechanisms of action. Biology
Direct 2006, 1:7doi:10.1186/1745-6150-1-7
Kostyuchenko VA, Leiman PG,
Chipman PR, Kanamaru S, van Raaij MJ, Arisaka F, Vadim V
Mesyanzhinov VV, Michael G Rossmann MG. 2003.
Three-dimensional structure of bacteriophage T4
Biol. 10, 688–693. UTHSCSA
Shows gp48 and gp54 above the baseplate and attaching to it.
gp27 and gp5 lined up in the hub
gp6, 25, 53 are the inner cyllinder of the slider.
gp7, 8, 9, 10,11, 12 are localized.
gp10 makes a contact with gp5, 53 underneath the plate, and
this could help hold the lower aspect together prior to
Cites evidence that attachment of gp12 requires prior
attachment of gp11.
Kostyuchenko VA, Chipman PR, Leiman PG, Arisaka F, Mesyanzhinov
VV, Rossmann MG. 2005. The tail structure of bacteriophage T4 and
its mechanism of contraction. Nat Struct. Mol.
Koti JS, Morais MC, Rajagopal R, Owen BA, McMurray CT, Anderson
DL. 2008. DNA packaging motor assembly intermediate of
bacteriophage phi29. J. Mol. Biol. 381:1114-1132. PMID
Kovalyova,I.V. and Kropinski,A.M. 2003. The complete
genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas
putida-evidence for close relationship to the T7 group. Virology
311 (2), 305-315.
37319 bp with 216 bp direct repeats. AF493143, NC_004665
Has essentially the same genes as T7 in the same order with
the following exceptions:
Of these, 0.3 mediates anti-restriction, and 0.7 mediates
host polymerase shutdown, 5.5 is highly expessed and
inhibits nucleod protein H-NS. See Liu and Richardson
1993 PNAS 90, 1761-1765.
The potential to frameshift the capsid protein (gp10) to
tack on the extra domain in 10B is absent.
Has extra small frames: orf 1..11.
Of these, orf3 may be a deoxynucleoside monophosphate
kinase with homology to phiC31 gp52.
Polymerase recognition sequences conserved and late promoter
positions conserved. Early promoters a bit more variable
in position. The 2 terminators of T7 are conserved in
position, although there is a 3rd.
Comments on the variability of the C terminal domain of gp17
which is a cellular receptor.
Comments on the anti mosaic character of the T7 family sensu
stricto, and cites Woese 2002, PNAS 99, 8742–8747, for the
concept of an evolutionary threshold beyond which horizontal
exchange falls off.
But for some reason does not want to put P60 in T7 sensu
Kropinski AM. Sequence of the genome of the temperate,
serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J
BACTERIOL 182 (21): 6066-6074 NOV 2000.*
similar to lambda phages.
Krupovic M, Forterre P, Bamford DH (2010) Comparative analysis of
the mosaic genomes of tailed archaeal viruses and proviruses
suggests common themes for virion architecture and assembly with
tailed viruses of bacteria. J Mol Biol 397(1):144–160. PMID 20109464.
Krupovic M, Spang A, Gribaldo S, Forterre P, Schleper C (2011) A
thaumarchaeal provirus testifies for an ancient association of
tailed viruses with archaea. Biochem Soc Trans 39(1):82–88. PMID 21265751.
Working mostly from proviral sequences.
Notes that there is a higher morphological diversity of phages
among Archae, but the 3 classic forms are represented.
It's a Mu-like myovirus
They give an accounting of the Archae groups with a "tailed"
Krylov VN, Smirnova TA, Minenkova IB, Plotnikova TG, Zhazikov IZ,
and Khrenova EA. 1984. Pseudomonas bacteriphage phiKZ contains an
innter body in its capsid. Can. J. Microbiol 30: 758-762.
Not on line
The report a helical looking large cylinder of 35nm diameter
and 90 nm length that goes away upon infection.
They indicate that it might include DNA.
This is much larger than the inner head body discussed by
Fokine et al., 2005.
Krylov VN, Bourkaltseva MV, Sykilinda NN, Pleteneva EA, Shaburova
OV, Dadykov VA, Miller S, Beibl M. 2004. Comparisons of the genomes
of new giant phages isolated from environmental Pseudomonas
aeruginosa strains of different regions. Russian J. Genet. 40:
By restriction analysis and some immunoblotting.
Krylov VN, Pleteneva EA, Lavigne R,
Hertveldt K, Volckaert G, Sernova NV, Georgopoulos C, Korchevskii
RV, Kurochkina LP, and Mesyanzhinov VV. 2005 Comparison of the
genome for phylogentically related bacteriophages phiKZ and EL of
Pseudomonas aeruginosa: Evolutionary aspectes and minimal genome
J. Genet. 41:356-365.
Kulikov E, Kropinski AM, Golomidova A, Linqohr E, Govorun V,
Serebryakova M, Prokhorov N, Letarova M, Manykin A, Stroskaya A,
Letarov A. 2012. Isolation and characterization of a
novel indigenous intestinal N4-related coliphage vB_EcoP_G7C.
Virology 426:93-99. PMID 22341309.
"Proteome" just means gene predictions. They did not do
PT1028, 66, 44AHJD, P68 in 15-18kb range, and presumably
187, 69, 53, 85, 2638A, 77, 42e, 3A, 47, 37, EW, 96, ROSA, 71,
55, 29, 52A, 88, 92, X2 in 40-45 Kb range and have a lot of
similarity to each other.
K, G1, Twort in 127-140 Kb range and real similar to each
K is the same as staphK from O'Flaherty
et al., which is not actually sequenced to the ends.
(they still cite same length).
K to G1 is 90% identical at nucleotide level,
Twort to K and G1 is ~50% identical at nucleotide level.
Criterion for "completion" not given. K, G1, and twort
are all presented in a circular map, even though K is clearly
not complete. Size range for genomes is said to be
178-217 kb in abstract, but only 127,395, 138,715, and 130,706
in the sequence summary table. ??? The supplementary
information at the PNAS site says that they have not "mapped"
G is NC_007006; twort is NC_007021.
Although they have a table giving different (from O'Flaherty
et al) gene names, coordinates for phage K on the PNAS
website, they don't seem to have any actual GenBank entries
visible at this time (5/25/5). Perhaps they are hung up
with the NCBI annotators trying to sort out the discrepencies
with NC_005880. The column labeled GenBank names contain
the O'Flaherty orf names. Those are blank for extra orfs
that Kwan et al. called.
Some of these phages came from Hans, and he says two of them
are mixed up and one is a contaminant, and 3 were mislabeled.
They have phiKZ again and something 99% identical. The
others are small.
Lander GC, Tang L, Casjens SR, Gilcrease EB, Prevelige P, Poliakov
A, Potter CS, Carragher B, Johnson JE. 2006. The structure of an
infectious P22 virion shows the signal for headful DNA packaging.
Science 312: 1791-1795.
They think the DNA ends up wrapped around the portal complex
on the inside.
Lander GC, Khayat R, Li R, Prevelige PE, Potter CS, Carragher B,
Johnson JE. 2009. The P22 tiail machine at subnanometer
resolution reveals the architecture of an infection conduit.
Structure 17: 789-799.
Lander GC Baudoux AC Azam F Potter CS Carragher B Johnson
JE. 2012. Capsomer dynamics and stabilization in the
T=12 marine bacteriophage SIO-2 and its procapsid studied by
CryoEM. Structure 20:498-503. PMID 22405008
Landthaler,M. and Shub,D.A. 1999. Unexpected abundance of
self-splicing introns in the genome of bacteriophage Twort:
introns in multiple genes, a single gene with three introns, and
exon skipping by group I ribozymes. Proc. Natl. Acad. Sci. U.S.A.
96 (12), 7005-7010.
Detected by GTP-labeled RNA.
Notes that phage group I introns are of group IA2 citing
Michel F & Westhof E. 1990. JMB 216:585-610. Says only
introns in bacteria are in prophages or in tRNA (group
IC3). Says only the T4 introns in gram negative phages,
but many more in low GC gram positives. Twort is in
Staphylococcus (low GC gram positive).
Only a few segments of the Twort sequence are reported.
Lavigne R, Noben JP, Hertveldt K,
Ceyssens PJ, Briers Y, Dumont D, Roucourt B, Krylov VN, Mesyanzhinov
VV, Robben J, Volckaert G. 2006. The structural proteome
of Pseudomonas aeruginaso bacteriophage phiKMV. Microbiology
152(Pt 2): 529-534.
Str. proteins are :
gp 30 (portal), gp32 (capsid, no frameshift), gp33 tail A,
gp34 tail B, gp 35 (like T7 gp13 internal virion?, but not
found by ms) gp36 (fusion of T7 gp14/15 and has lysozyme on
C ter), gp37 (like T7 gp16 internal virion),
Probable tail fibers based on position: gp 38, 39, 40 (was
39 found by ms?)
Novel to phiKMV-like phages: gp47, 48 (on end of genome),
gp29 (right before portal).
Notes that phiKMV, SP6 and others have lysozyme domain at C
ter of T7 gp15 homolog, whereas T7 has transglycosylase at N
terminus of gp16.
gp47 and 48 were not identified with a Coomassie staining
Lavigne R Seto D Mahadevan P Ackermann HW Kropinski AM (2008)
Unifying classical and molecular taxonomic classification: analysis
fo the Podoviridae using BLASTP-based tools. Res. Microbiol.
Defined Autographivirnae and Picovirinae.
Lavigne R, Burkal'tseva MV, Robben J,
Sykilinda NN, Kurochkina LP, Grymonprez B, Jonckx B, Krylov VN,
Mesyanzhinov VV, Volckaert G. 2003. The genome of bacteriophage
phiKMV, a T7-like virus infecting Pseudomonas aeruginosa. Virology.
On our terminase tree, this phage terminase clusters with 100%
bootstrap with the T7 clade, but is further out that P60.
This phage is clearly T7-like, including an RNA polymerase.
Talks about different species concepts, and illustrates
effects of horizontal exchange.
Discusses methods of horizontal exchange.
Phrases it in terms of heirarchical classification failure.
Lazarevic V. Dusterhoft A. Soldo B. Hilbert H. Mauel C. Karamata
D. 1999. Nucleotide sequence of the Bacillus subtilis
temperate bacteriophage SPbetac2. Microbiology. 145 ( Pt
Dusterhoft,A., Hilbert,H., Mauel,C. and Karamata,D. 1998.
Introns and intein coding sequence in the ribonucleotide reductase
genes of Bacillus subtilis temperate bacteriophage SPbeta. Proc.
Natl. Acad. Sci. U.S.A. 95 (4), 1692-1697.
Large and small subunits of ribonucleotide reductase in SPb
(c2?) each have an intron. They call them bnrdE and
bnrdF. bnrdE also has an intein.
Cites as background E. coli gene names nrdA/B (aerobic
essential), nrd E/F (aerobic nonessential), and rnd D/G
(anaerobic). Notes two enzymes encoded in T4, with two of
the subunit genes interrupted by introns.
Lebedev, AA ; Vagin, A ; Orlova, EV ; Dodson, EJ ; Tavares, P. 2005.
Crystal structure of the portal protein from bacteriophage SPP1 and
model for DNA translocation FEBS JOURNAL 272: 334-334 Suppl.
Meeting abstract, apparently not on line.
Lecoutere E, Ceyssens PJ,
Miroshikov KA, Mesyanzhinov VV, Krylov VN, Noben JP, Robben J,
Hertveldt K, Volckaert G, Lavigne R. (2009) Identification and
comparative analysis of the structural proteiomes of phiKZ and EL,
two giant Pseudomonas aeruginosa bacteriophages. Proteomics
Lee, J.-H., J. Bai,
H. Shin, Y. Kim, B. Park, S. Heu and S. Ryu (2016). "A Novel
Bacteriophage Targeting Cronobacter sakazakii Is a Potential
Biocontrol Agent in Foods." Applied and Environmental
myovirus with good EM. Relationship to SPN3US and
phiEaH2 in RNAP is emphasized.
CR5 is very close to SPN3US. DNA pol is 99% identical.
Leffers G, Rao VB.
Biochemical characterization of an ATPase activity associated with
the large packaging subunit gp17 from bacteriophage T4.
JOURNAL OF BIOLOGICAL CHEMISTRY 275 (47): 37127-37136
NOV 24 2000.
Background: 3 componenets of packaging machine are the large
and small subunit packaging enzymes and the portal protein.
gp17 is the large subunit in T4; gp16 is the small subunit.
This paper reports that gp17 is an ATPase whose ATPase
activity is greatly increased by association with the small
Lehman SM, Kropinski AM, Castle AJ, Svircev AM: Complete genome of
the broad-host-range Erwinia amylovora phage fEa21-4 and its
relationship to Salmonella phage felix O1.
Applied & Environmental Microbiology 2009, 75:2139-2147.
Leiman PG, Battisti AJ, Bowman VD, Stunmeyer K, Muhlenhoff M,
Gerardy-Schahn R, Scholl D, Molineux IJ. 2007. The
structure of bacteriophages K1E and D1-5 esplain processive
degradation of polysaccharide capsules and evolution of new host
specificities. J. Mol. Biol. 371:836-849. PMID 17585937.
gp37 binds tubeA/B. Two adhesins bind to gp37. The
N-terminal of gp37 is homologous to N terminal of T7 gp17.
gp37 is trimeric, although they never say coiled coil.
Leiman PG, Shneider MM, Kostyuchenko
VA, Chipman PR, Mesyanzhinov VV, Rossmann MG. 2003. Structure and
location of gene product 8 in the bacteriophage T4 baseplate. J.
Mol. Biol. 328: 821-833.
Shown as six dimers distributed underneath the outer layer of
Compared to Leiman et al, 2004, they appear to be mounted on
an inner ring mainly composed of gp6, and maybe gp25, and
surrounded by an outer ring mainly contacting gp7.
The proposed homologue in phageD is missing one extruding
domain, which on fig 7a would appear on the bottom left
projecting out of the page, and on the upper right projecting
back into the page. This would appear to be a zone where
there is not intimate contact with the other proteins.
Leiman PG, Chipman PR, Kostyuchenko
VA, Mesyanzhinov VV. 2004. Three-dimensional rearrangements of
proteins in the tail of bacteriophages T4 on infection of its
Baseplate changes from hexagonal to star shape with tail
contraction. Triggered by contact with host, or 3M urea.
gp19 is the tail tube, and gp 18 is the surrounding tail
Baseplate is 270 x 500 A.
gp13,15 at the proximal (head) end of the tail stabilize the
polymerized tail sheath, and connect through gp 13 and 14 to
the portal ring.
350 A neck wiskers are trimers of gp wac.
tail fibers are 700 A trimer of gp34, followed by hinge
(gp35), and then a 700 A trimer of gp35 and gp37.
Cyro EM of baseplate; see Kostyuchenko et al., 2003.Nat.
Struct. Biol. 10, 688–693.
This paper follows on the baseplate cryoEM by extending the
model to a cryoEM model of the contracted tail.
The inner ring of baseplate proteins that slides on the tail
tube is composed of hexameric rings of gp 6, 25, and 53
positioned one on top of the other in the order indicated from
the head towards tail.
gp48 and 54 are on top of this ring in the non contracted
structure, and are considered part of the tail tube (the plug)
Mounted on this is an outer ring composed of a hexamer of
gp7 [3 domains organized in a sprial like way composing most
of the mass] plus gp8 [underneath and mediating contact
between gp7 domain B and and adjacent domain C..
Each of these units is bound outwards facing by a molecule
of gp9 which forms the socket for the mounting of the tail
Underneath this ring is an outer hexameric ring composed of
gp 10 and 11 (trimers) and an elongated gp 12 (also
called short tail fibers); gp 12 wraps underneath the
structure tying it off in the hexameric form, but is released
and dangles down in the sprung structure. These are
thought to associate with cellular receptors in the outer
membrane. This is associated with substantial rotation
of the gp10,11 ring components, and a lesser rotation of the
upper components but with an angular change in the approach of
the tail fibers. The reorganization exposes the C terminal
domain of gp11 which now projects outwards and upwards tucked
underneath the tail fiber projections, where it is proposed to
stabilize the contracted configuration.. gp11 in associated
with the underlying gp 10 and gp7 have been referred to as
In the closed form, gp 5 and 27 form a central spike, [which
presumably stays associated with the tail tube end upon
extension?]. gp5 on the tip of this structure is the tail
lysozyme. [There seems to be a problem in exactly how gp5,27,
gp 48, and 54 interact with each other and the tail tube].
Further definition in the head neck region is also provided.
Tail sheath monomer (gp18) is pictured as S shaped with one
end of S in towards the tube and mediating most of the contacts,
while the other end sticks out radially away from the
tube. Although they attribute important contacts to the N
terminus, and say no interaction with the tube itself.
Looks like the portions from the tube out are crudely 30%,
45%, and 25% of the mass.
gp6, gp25, gp53 form platform under sheath easily confused
with another layer of the sheath.
Larger and more exposed lobe is N terminal (82-320) and
other two lobes correspond to C terminus (361-659).
Process starts within a few seconds of attachments.
T4 crosses in 30 sec; 4000 bp/s
T7: 850 bp transferred passively, Host RNA polymerase pulls in
next 20%. T7 RNApolymerase brings in the rest.
Takes 10 minutes at 30 C.
Non transcribing mutants can be internalized if there are
mutations to the internal protein gp16.
gp16 enters the cell wall
T5 ( a non contractile tail).
8% enters (passively?); then pause of 4 min.
Proteins A1 and A2 are synthesized.
These pull in rest.
Total time is 6 min.
So? of 121 kb, 112 kb in 2 minutes or 56
kb/min. About 1000 nt /sec ?
The tape measure protein spans the membrane.
Notes that both T5 straight tail fiber (pb2) and
lambda gpH are both proteolytically processed during
Says for both C terminal is distal and N terminal proximal
to head tail connector.
He thinks the protein expands from 20 to 40 nm outer
diameter, pins the outer membrane to the inner membrane, and
acts as a channel for the DNA to follow.
Lin H, Rao VB, Black LW. 1999. Analysis of capsid portal protein
and terminase functional domains: interaction sites required for
DNA packaging in bacteriophage T4. J
Mol Biol. 1999 Jun 4;289(2):249-60.
Define C terminus and a second site as interacting between
portal and terminase by suppressor mutations.
The second site is in the hinge region.
Lingohr EJ, Villegas A, She YM, Ceyssens PJ, and Kropinski AM. 2008.
The genome and proteome of the Kluyvera bacteriophage Kvp1 --
another member of the T7-like Autographivirinae. Virol J.
The kinetic model in support of structural work reported in
Mancini et al. Cell 118: 744-755.
The packaged nucleic acid is ssRNA, which is converted to
dsRNA within the capsid.
This is basically a ss translocase model where the
conformationally active helix 6 (our alpha 5) and an associated
loop appendage with an RNA binding motif face inwards and
directly engage the ssRNA and move it into the capsid.
ATP hydrolysis stimulated by RNA binding.
3 subunits of hexameric ATPase are cooperative.
Hydrolysis concommitant with translocation.
Lisal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall
AG, Tuma R. 2006. Interaction of packaging motor with the
polymerase complex of dsRNA bacteriphage. Virology
351: 73-79. UTHSCSA
hexameric motor associates with several vertexes.
The packaged moiety is ssRNA, which is converted to dsRNA by
polymerase within the capsid.
motor subunits are a P-loop domain connected to capsid protein
with C terminus.
The motor ATPase is called P4. There is an RNA binding
accessory protein called P1.
associated polymerase shuts off P4 ATPase, and may provide
alternative packaging force.
There is structure and mechanism proposed in
Lisal and Tuma, 2005. JBC 280, 23157
Mancini et al 2004a, Cell 118: 744-755.
Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT,
Schmid MF, Osburne MS, Chisholm SW, and Chiu W. 2010.
Structural changes in a marine podovirus associated with release of
its genome into Prochlorococcus. Nat. Str. & Mol. Biol.
cryoEM shows head and tail.
no internal core.
Only a little bit of side fiber shown.
There are no head decoration proteins.
On infection , weakly visualized core disappears, fiber angle
of approach changes, and there is some change in the density
around the nozzel.
Some speculation about Q rich motifs in C terminus of portal
being involved in reversible transitions related to the core
proteins or DNA positioning.
They seem to show the DNA in the portal such that the core
proteins would have to come out with the DNA embedded within
They have tomography of the phage on the cell, but you can't
really make out the extended tube.
They say 8 beta sheets in the nozzel protein
Going back to the GenBank entry, tube A and B were recognized,
but the internal virion proteins were assumed by size and
Loessner MJ, Wendlinger G,
and Scherer S. 1995. Heterogeneous endolysins in Listeria
monocytogenes bacteriophages: a new class of enzymes and evidence
for conserved holin genes within the siphoviral lysis cassettes. Mol.
Microbiol. 16 (6), 1231-1241.
Not yet on line.
Had endolysins adjacent to a holin for A188 and A500, and a
lysin domain for A511.
Referred to these as siphoviridae, although A511 clearly has a
contractile tail sheath.
They said the A511 protein was an N-acetylmuramoyl-L-alanine
amidase, whereas the A500 and A188 proteins were
Applied exogenously, they appear to specifically lyse
Listeria, which is attributed to other domains in the protein.
Loessner MJ, and Scherer S. 1995. Organization and Transcriptional
Analysis of the Listeria Phage A511 Late Gene Region
Comprising the Major Capsid and Tail Sheath Protein Genes cps and
Bact. 177: 6601-6609.
10152 bp sequenced segment. Tail sheath and capsid
proteins very divergent from other phages at the time, and were
identified by biochemical means.
Capsid cleaved after Lys 23 during maturation.
Subsequently this structural module found in Staphlococcus
phageK and B. subtilis phageD.
Host is Listeria monocytogenes.
Included biochemical analysis of promters, and definition of a
TGCTAGATTATAG -10 box for late transcription in this phage.
Loessner MJ, Inman RB, Lauer P, et al. Complete nucleotide
sequence, molecular analysis and genome structure of bacteriophage
A118 of Listeria monocytogenes: implications for
phage evolution MOL MICROBIOL 35 (2): 324-340 JAN 2000.
terminally redundant, and circularly permuted.
Extensive homologies to the other lamda-like phage.
Lopez R. 2004. Streptococcus pneumoniae and its bacteriophages: one
long argument. Int. MicroBiology 7: 163-171.
Starts with the different capsular synthesis operons in
different serotypes of Strep, and then switchs to lysins that
attack the peptditogylcan.
Endogenous (autolysins) are required for normal cellular
growth, but apparently their presence enhances the lytic effect
of beta lactam antibiotics.
Classified as LytA, B,C where A is an amidase cleaving the N
acetyl glucosamine side chain linkage, and B and C cleave the
two inter saccharide linkages in the NAM, NAG backbone.
Additional cell wall cleaving enzymes not found in strep are
endopeptidases and transglycosylases.
In strep, the NAM units are decorated by a polymer of
lipoteichoic acid which has bound choline. The strep cell
wall hydrolyzing enzymes have repeating choline binding domains
[C ter on lytA, N or C ter on others] to recognize the cell
wall. To attack this structure, there is also a phosphoryl
choline esterase, which has the choline binding domains.
The phage Cp1 lysozyme (Cp1-1) shares the choline binding
domains (but has a different catalytic domain).
Some streptococcal phages (eg. Dp-1) require the choline for
absorption. Dp-1 orf53 (receptor binding) has the choline
Cp-7 lysin does not recognize choline and has a different
repeating motif carrying out cell wall recognition.
Phage Pa1 has an amidase for a lysin recombined with the
cholin recognition domains.
Lossoarn J Nesbe CL Mercier C Zhaxybayeva O Johnson MS Charchuck
R Farasin J Bienvenu N Baudoux AC Michoud G Jebbar M Gelin
C. 2015. Menage a trios: a selfish genetic element
uses a virus to propagate within Thermotogales. Environ
Microbiol 1111:1462-2920. PMID 25630351
MPV1 - termperate Siphovirus.
Carries a plasmid
Lubbers, M. W., Waterfield, N. R., Beresford, T. P., Le Page, R.
W. & Jarvis, A. W. (1995). Sequencing and analysis
of the prolate-headed lactococcal bacteriophage c2 genome and
identification of the structural genes. Appl Environ Microbiol
Lubbers MW, Schofield K, Waterfield NR, Polzin KM. 1998.
Transcription analysis of the prolate-headed lactococcal
bacteriophage c2. J. Bact. 180:4487-4496.
Lucchini, S., Desiere, F. & Brussow, H. (1998). The
structural gene module in Streptococcus
thermophilus bacteriophage phi Sfi11 shows a hierarchy of
relatedness to Siphoviridae from a
wide range of bacterial hosts. Virology 246, 63-73.
Lucchini S, Desiere F, Brussow H
Comparative genomics of Streptococcus
thermophilus phage species supports a modular evolution theory
J VIROL 73 (10): 8647-8656 OCT 1999.
Evidence of interchange among 5 phages, some lytic and some
Indels flanked by DNA repeats.
Host range corresponds only to tail fiber.
Describes tail fibers as glycine rich (G-X-Y?) domains
interspersed with variable domains. Says same as for T4
Proposes that lytic phages are "selfish" spinnoffs of
Luneberg E, Mayer B, Daryab N, Kooistra O, Zahringer U, Rohde M,
Swanson J, and Frosch M. 2001. Chromosomal insertion and
excision of a 30 kb unstable genetic element is responsible for
phase variation of lipopolysaccharide and other virulence
determinants in Legionella pneumophila. Mol. Microbiol. 39 (5),
An apparnent cryptic prophage.
Two opposite transcription units.
RecE, RecT, RusA homologues.
orfL homologous to T7 internal virion protein D.
orfW homologous to T7 vhtJ (head to tail joining protein).
RecE and T in the short transcription unit; others in the long
unit. RusA close to junction.
DNA sequence for the element: AJ277755, LPN277755
Lurz R, Orlova EV, Gunther D, Dube P,
Droge A, Weiss F, van Heel M, and Tavares P. 2001. Structural
Organisation of the Head-to-tail interface of a bacterial Virus. J.
Mol. Biol. 310: 1027-1037. UTHSCSA
About SPP1 portal protein.
Shows that SPP1 portal in capsid is a 12 mer in spite of their
earlier paper showing it
assembles in solution to a 13 mer.
Also show gp15, and then gp16 assemble on top of the portal
forming a connection that seals in the DNA and makes a stup to
connect the tail.
There is some proteolytic processing of gp16 associated with
Think that 55-67 bp of DNA is in the "interface", meaning
portal plus gp15/16. Looks like a maximum of 85 A inside
gp15/16, although some of that taken up by the cap on gp16.
Further elaborates their postulate that portal senses
head-full and clamps down on the DNA. They further propose
that signals are sent to the terminase to stop it from packaging
and initiate cleavage.
There modelling of interaction with capsid has the contacts
nearer the external end than does the herpes or phi29 work.
Malys N, Chang DY, Baumann RG, Xie D, Black LW. 2002. A
bipartite bacteriophage T4 SOC and HOC randomized peptide display
library: detection and analysis of phage T4 terminase (gp17) and
late sigma factor (gp55) interaction. J
Mol Biol. 319(2):289-304.
By biopanning, propose interactions of gp17 with portal, small
terminase, self, capsid, ssDNA binding protein, gp45 (sliding
clamp), gp44 (clamp loader), gp2 (DNA end protein), and gp55
(late sigma factor).
Shows that without sigma factor, in vitro packaging 100 x less
gp55 residues 111-136.
Markine-Goriaynoff N, Gillet L, Van Etten JL, Korres H, Verma N, and
Vanderplasschen A. 2004. Glycosyltransferases encoded by viruses. J.
Gen. Vir. 85: 2741-2754.
Review covers both eucaryotic and procaryotic viruses.
Among phages notes glycosylation of DNA to avoid restriction
and glycosyltransferases affecting the cell wall after
lysogenization that changes serotype (hence altering
alpha (T4,6,2) and beta (T4) glucosyltransferases to HMC DNA
(defined by making alpha or beta linkages).
citation given to structural studies on Beta gt of T4.
Cited list of reviews about pathogenic conversion.
Reviews prototypical example of genes altering the O
antigen of Shigella. flexneri, from several prophages and
phages, and some apparently derived by transfer from a
different genome as judged by %GC.
Is a 3 gene cassette; with GtrB synthesising UndP-glucose
precursor, and GtrA flipping it to the periplasmic side of
the membrane, then a serotype specific Gtr<serotype>
gene that modifies a specific moiety on O antigen (a tetra
There are also modifications by acetylation of the O
Notes that since O antigen is the phage receptor, the
conversion also provides immunity to superinfection, which
may be the more direct biological selection. The
propose that immunity to superinfection may play a role in
lytic phages by preventing absorbtion of the progeny phages
to cell debris on the way out.
Martin AC. Lopez R. Garcia P. Analysis of the complete nucleotide
sequence and functional organization of
the genome of Streptococcus pneumoniae bacteriophage Cp-1. Journal
of Virology. 70(6):3678-87, 1996
Marvik OJ, Jocobsen E, Kokland T,
Lindqvist BH. 1994. Bacteriophage P2 and P4 Morphogenesis:
Assembly precedes proteolytic processing of the capsid proteins. Vir.
205: 51-65. UTHSCSA
gpO (scaffold), gpN (capsid) and gpQ (portal) are all cleaved.
As of this paper, they do not recognize that gpO is also a
There are statements to the effect that gpO stimulates but is
not required for cleavage of gpN.
Masui S, Kamoda S, Sasaki T. and Ishikawa H. 2000. Distribution
and evolution of bacteriophage WO in Wolbachia, the
endosymbiont causing sexual alterations in arthropods J. Mol.
Evol. 51 (5), 491-497 (2000).
Terminase and some other presumably structural genes
Matsko N, Klinov D, Manykin A, Demin V, and Klimenko S. 2001. Atomic
force microscopy analysis of bacteriophages phiKZ and T4. J.
Electron Micros. 50: 417-422. UTHSCSA
They have two views of the inner phiKZ body, one of which
makes it look small like the outline in the Fokine paper,
the other of which makes it look more substantial. The
smaller look is probably the higher resolution look.
Matsuzake S, Kuroda M, Kimura
S, and Tanaka S. 1999. Major capsid proteins of certian Vibrio and
Aeromonas phages are homologous to the equivalent protein gp23*, of
coliphage T4. Arch
Virol. 144: 1647-1651.
Vibrio T4-like phages were KVP20, KVP40, and nt-1.
Aeromonas phages were Aeh1 and phage 65.
Gave N terminal sequence determination on mature virion
Mattila S, Oksanen HM, Bamford JK. 2015. Probing protein
interactions in the membrane-containing virus PRD1. J. Gen
McGrath S, Fitzgerald GF, and van Sinderen D. 2002. Identification
and characterization of phage-resistance genes in temperate
lactococcal bacteriophages. Mol. Microbiol. 43(2) 509.
McPartland J, Rothman-Denes LB. 2009. The tail sheath of
bacteriophage N4 interacts with the Escherichia coli
receptor. J. Bact. 191:525-532. PMID 19011026.
Mediavilla J. Jain S. Kriakov J. Ford ME. Duda RL. Jacobs WR Jr.
Hendrix RW. Hatfull GF. Genome organization
and characterization of mycobacteriophage Bxb1. Molecular
Microbiology. 38(5):955-70, 2000. UI: 20572070
host is Mycobacterium smegmatis.
Structural genes weakly related to mycobacteriophages L5 and
This is the primary sequence reference for GA-1 (NC_002649),
and an compares it thoroughly to phi29 and B103.
This is a good place to look for identities and functions of
phi29-like genes such as they are known.
Comparative transcriptional maps given.
Protein-primed replication off the terminal protein (gene 3)
Notes also for Cp-1 and PRD1
Notes functionally specialized motifs in DNA polymerases
that do protein priming.
Members of B type polymerase class
Two accessory proteins are a SSB protein (gene5) and a
Double stranded DNA binding protein (gene 6; DBP)
N ter (to 71) of TP are a DNA binding site.
TP may make a coiled coil interaction to self associate.
gene1 is membrane associated and may anchor replication
gene17 thought to stimulate replication.
gene16.7 may space replicating sites around the cell.
gene 8.5 is a head fiber. It is not required for
infectivity, and GA-1 doesn't have one.
gene8 is the major capsid protein
gene 7 is the scaffold protein
p10 is head tail connector (which would be called portal in
other phages), and is proposed to rotate as a ring relative to
the head. Also called upper collar.
gene 16 is the packaging protein (which would be called large
Their discussion of packaging mainly describes the rotary
there is nothing called small terminase. There is no
cleavage involved, since the DNA does not replicate to form a
There is a ring formed by phage encoded RNA that associates
with p16 (terminase).
The pRNA is also thought to interact with the portal and
specifically with the DNA.
gene 11 is lower collar (essentially the tail) and 6 copies
are incorporated per capsid.
p9 is tail knob (there are no tail fibers). It keeps DNA
p12 is preneck appendage. 12 appendages form on the tail
detectabley below the head, each a dimer of p12.
Site of attachment thought to be interface of p10 and p11
p9 is also required.
Gene 14 is a class I holin
Gene 15 is a lysin (peptidoglycan hydrolase; ).
Gives for classification of peptidoglycan hydrolases
(Ackermann, H.-W. 1998, Adv. Virus Res. 51:135-201)
muramidases (p15 of B103 and phi29 is a muramidase)
amidases (p15 of GA-1 is an amidase, possibly of host
Merabishvilli M, Vandenheuvel D, Kropinski AM, Mast J, De Vos D,
Verbeken G, Noben JP, Lavigne R, Vaneechouffe M, Pirnav JP.
2014. Characterization of newly isolated lytic bacteriophages
active against Acinetobacter baumannii. PLoS One
9:e104853. PMID 25111143.
podovirus vB_AbaP_Acibe1007 (phiKMV-like)
Mesyanzhinov VV, Leiman PG, Kostyuchenko VA, Kurochkina LP,
Miroshnilov KA, Sykilinda NN, and Shneider MM. 2004. REVIEW:
Molecular Architecture of Bacteriophage T4. Biochemistry
Mesyanzhinov VV, Robben J,
Grymonprez B, Kostyuchenko VA, Bourkaltseva MV, Sykilinda NN, Krylov
VN, and Volckaert G. 2001. The genome of bacteriophage phiKZ of Pseudomonas
Mol. Biol. 317:1-19. UTHSCSA
At 280334 bp, it takes over from T4 as the largest phage
Only 59 of 306 ORFs have sequence similarity.
There is essentially no sequence similarity to T4, but they
note similar cleavage patterns during assembly.
Has a number of tRNAs, and several HNH nucleases.
Concludes that there are mobile introns, but doesn't show
evidence beyond NHN nucleases, which are often not part of
HNH genes are gp56, 72, 179, 296. We find that there
is a mobile intron interrupting KZ055/KZ056_1.
Wants to make it a new phage group (genus, I presume).
Current best overall reference for T4 genome and gene
Mentions compact frame organization, overlapping start and
stop codons, and more extensively overlapping genes.
Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A,
Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szcypinksi B,
and Fraser CM. 2003. Complete genome sequenceof the broad-host-range
vibriophage KVP40: Comparative genomics of a T4-related
Has 25 tRNAs and 5 pseudo tRNAs.
Notes that it has a larger capsid than T4, and may be more
tolerant of junk DNA.
They found lots of T4 homologues, but not hub gp27; SAM
recognized it as their gene 334.
Mindich L, Qiao X, Qiao J, Onodera S, Romantschuk M, and Hoogstraten
D. 1999. Isolation of additional bacteriophagees with genomes of
segmented double-stranded RNA. J. Bact 181:
Apparently all from Pseudomonas, although can establish a
"carrier" state (nonlytic but produces virus) in Escherichia and
There were several "close" relatives (primed with same end PCR
primers) and 3 "distant" relatives promised to be reported upon
All have 3 genomic segments of similar size to phi6
(2.9, 4.1, 6.4 kb).
Some require pilus for infection (like phi6) and some do not.
Mindich L. 2004. Packaging,
replication and recombination of the segmented genomes of
bacteriophage phi6 and its relatives. Virus.
Res. 101: 83-92.
Mainly devoted to arguing a model for how 1 copy each of 3
genomic segments gets packaged, but is also a good general
review of the segmented dsRNA phages (Cystoviridae).
Cystoviridae are only RNA viruses that package RNA into
3 ss RNAs (+ strand) are packaged, and then converted to ds
RNA within the capsid.
P1,2,4,7 compose the inner core of the capsid. P2 is the RNA
dependent RNA polymerase.P1 is major capsid protein. P4 is
hexameric helicase that does the packaging. There is no
tail. There appear to be numerous packaging ports on the
Do I understand correctly that there is then additional +
strand made in the capsid? See Frilander et al., 1992. J.
Vir. 66: 5013-5017.
There is an 18 base identity at 5' end and a pac region about
50 nt inside that required for packaging.
There is also a 3' secondary structure required for
Cites Mindich I., 1999. Microbiol. Mol. Biol. Rev. 63: 149-160
for more isolates in this Genus.
Mirold, W. Rabsch, M. Rohde, S. Stender, H. Tschape, H. Russmann
et al., Isolation of a
temperate bacteriophage encoding the type III
effector protein SopE from an epidemic Salmonella
typhimurium strain. Proc. Natl Acad. Sci. USA
96 (1999), pp. 9845–9850.
What is terminase gene?
MIKKONEN M, ALATOSSAVA T.
CHARACTERIZATION OF THE GENOME REGION ENCODING STRUCTURAL PROTEINS
OF LACTOBACILLUS-DELBRUECKII SUBSP LACTIS
GENE 151 (1-2): 53-59 DEC 30 1994.
A gp19 was described from this partially sequenced phage
genome. Wasn't cleaer from abstract if that was meant as a
homologue to T7 gp19. The protein ref was to small subunit
Mitchell MS, Matsuzaki S, Imai S,
Rao VB. 2002. Sequence analysis of bacteriophage T4 DNA packaging
terminase genes 16 and 17 reveals a common ATPase center in the
large subunit of viral terminases. Nucleic
Acids Res. 30: 4009-4021.
Mitchell MS, Rao VB. 2004. Novel
and deviant Walker A ATP-binding motifs in bacteriophage large
terminase-DNA packaging proteins. Virology 321: 217-221.
Moak, M. & Molineux, I. J. 2000. Role of the Gp16 lytic
transglycosylase motif in bacteriophage T7 virions at the
initiation of infection. Mol. Microbiol 37, 345-355.
Citing Molineux (1999) The T7 family of bacteriophages. In
Encyclopedia of Molecular Biology. Creighton TE, ed. NY, John
Wiley & Col, pp. 2495-2507: The three internal
proteins are ejected forming an extensible tail that reaches to
the peptidoglycan layer. The N terminal of gp16 is a
transglycosylase that attacks the peptidoglycan.
Cites Serwer (1978) Observatio of DNA by negative staining:
phage T7: DNA-capsid complexes. Ninth International Congress on
Electron Microscopy II: 228-229: for images of an extended tail.
Shows alignment of 2..143 from T7 gp16 with E. coli SltY
443..592. (the soluble transglycosylase used by E. coli
for remodelling the peptidoglycan).
Inactivating mutation to gp16 transglycosylase domain slowed
infection more at high density than low density. E. coli
known to have denser peptidoglycan layer when grown to high
Overexpression of SltY complements.
Moldovan R, Chapman-McQuiston E, Wu XL. 2007. On kinetics of phage
adsorption. Biophys J. 93:303-315. PMID 17434950.
Molineux IJ. 2006. Fifty-three years since Hershey and Chase; much
ado about pressure but which pressure is it?
VIROLOGY 344 (1): 221-229.
About injection mechanisms.
Molineux IJ, Panja D. 2013 Popping the cork: Mechanisms of phage
genome ejection. Nat. Rev. Microbiol. 11:194-204. PMID 23385786.
Mondigler M, Holtz T, Heller KJ. 1996. Identification of the
receptor-binding regions of pb5 proteins of bacteriophages T5 and
Reviews the positions of host recognition domains on a number
of phages using different strategies.
Moore SD. Prevelige PE. DNA packaging: a new class of molecular
Biology. 12(3):R96-8, 2002
Monson R Foulds I Foweraker J Welch M Salmond GPC. (2011) The
Pseudomonas aeruginosa generalized transducing phage phiPA3 is a
new member of the phiKZ-like group of 'jumbo' phages, and infects
model laboratory strains and clinical isolates from cystic
fibrosis patients. Microbiol
A temporary accession HQ630627 was given in the manuscript,
but does not appear in GenBank.
Morgan GJ. Hatfull GF. Casjens S.
Hendrix RW. Bacteriophage Mu Genome Sequence: Analysis and
Comparison with Mu-like Prophages in Haemophilus, Neisseria and
Deinococcus. J. Mol. Biol. 317(3):337-59, 2002 Pubmed 11922669
By comparison to what will now be discussed as a Mu-like
group, the introduction recognizes
A lambdoid group composed of lambda, 933W, N15, VT2-Sa,
APSE-1, HK022, HK97, P22, HK620, and other unspecified
prophages of E. coli.
A P2-like proteobacterial phage group with P2, phage 186,
phiCTX, HP1, SopEphi, RAP401
An unnamed mycobacterial group including L5, D29 and Bxb1.
Desiere et al.'s low G+C gram positive group.
They refer to Mu-like phages Sp18 (in E. coli O157 genome),
FluMu, The Neisseria meningitidis genome papers for 3 mu-like
prophages from phage Neisseria meningitidis serogroup A strain
Z2491 called Pnm 1,2,3, and 2 from Neisseria meningitidis
serogroup B strain MC58 called (by Morgan et al) NeisMu1 and 2,
a mu-like prophage of Deinococcus radiodurans R1 that they call
RadMu, D108 (E. coli), dVcA1 (Vibrio cholerae), D3112, B3, B39
and PM69 of Pseudomonas aeruginosa, and fragmentary sequences in
Vibrio, Campylobacter, Pasteurella, Shigella and Haemophilus.
The paper reports the sequence of Mu and gives much
comparative information specifically with FluMu, pnm1, Sp18, and
RadMu. pnm 2 and 3 and NiesMu1 and 2 are described in text
as allelic between the two strains, and truncated, whereas pnm1
is described as possibley intact and active and without a
corresponding prophage in strain MC58. RadMu is described
as intact and possibley active.
The paper is a good source of detailed examples of mosaicism
within this group and by reference to other groups.
They discuss some assignments between mu-like structural
elements and lambdoid ones.
Morais MC, Choi KH, Koti JS, Chipman PR, Anderson DL. 2005.
Conservation of the capsid structure in tailed dsDNA bacteriophages:
the pseudoatomic structure of f29. Mol.
Cell 18: 149-159. UTHSCSA
Also has refined structure of prohead with pRNA.
They claim to refute the argument that the prior pRNA
observation was mistaken for head fibers, because these preps
were without fibers.
They hold firm to the observation that the pRNA itself is a
Morais MC, Tao Y, Olson NH, Grimes S, Jardine PJ, Anderson DL, Baker
TS, Rossmann MG. 2001. Cryoelectron-microscopy image reconstruction
of symmetry mismatches in bacteriophage phi29. J. Str. Biol.
Morais MC, Koti JS, Bowman VD, Reyes-Aldrete E, Anderson DL, and
Rossmann MG. 2008. Defining molecular and domain boundaries in
the bacteriophage phi29 DNA packaging motor. Structure 16:
1267-1274. PMID 18682228.
cryo EM pretty much showing the motor the way I'd figured it.
Their model is that the ATPase pushes on the DNA but the
connector holds it between pushes.
Doesn't show the mature tail.
Morita M, Tasaka M, Fujisawa H. 1994. Analysis of functional
domains of the packaging proteins of bacteriophage-T3 by
site-directed mutagenesis. J. Mol. Biol. 235: 248-259.
They speak of pac and non-pack ATPase. pac ATPase is
stimulated by specific T7 DNA, and inhibited by
actinomycin. nonpac is stimulated by any nucleic acid,
and not inhibited by actinomycin. Hamada et al., 1987,
Virology, 159, 244-249.
They also speak of non specific endonuclease activity that
is suppressed by gp18 or ATP.
Fujisawa, H., Kimura, M. & Hashimoto, C. (1990). In
vitro cleavage of the concatemer joint of bacteriophage
T3 DNA. Virology, 174, 26-34.
Note, in order for gp18 DNA complex to join gp19, ATP is
needed. Shibata et al., 1987 Vir 159: 250; Also gp19
preassociates with prohead: 6 if ATP present, but 20 if not.
Fujisawa et al., 1991, Virology, 185, 788-794.
G61D inactivates the ATPase
FYI: This is 2 residues prior to P-loop GK and has limited
range of GRKQASPT in all terminases.
G61D also prevents ATP binding as evidenced by assembly of
20 gp19 onto prohead.
G61D prevents pac cleavage, but not nonpack
cleavage. FYI: This indicates that the configuration
of the unassembled gp19 monomer is not like the closed motor
conformation, otherwise the endo site would be blocked.
G63D has no packaging activity on concatemers, and weak
activity on mature DNA.
FYI: Is G of P-loop motif. Not completely
invariant: SPP1 and a few others have A, A118 group
has M, K, or F, but also use the alternate K motif., VpV262
I wonder if the recovered activity in the in vitro system
(mature DNA) has anything to do with mature DNA, or perhaps
they just loaded it up with enough ATP to overcome a
Seemed completely wild type.
Since this is the supposed beta phosphate ligand, that's
kind of a shocker, but they did put in a conservative change
that shouldn't interfere with ATP binding.
FYI: Essentially all have a K, unless they have it in the
alt. position. When it is in the alternate position,
then various and bulky residues appear here, suggesting that
steric hindrance isn't a problem from this residue.
This is the only other mutant that wouldn't package either
in extract (concatemers) or in vitro (mature DNA).
It associates in excess with prohead, indicating that ATP
did not bind.
non pac DNAse activity is retained, but pac DNAse activity
FYI. 12 residues before the beginning of ruvC fold,
in about a 30 residue excess region found in T7-like but
also Mu like phages and some others. This is just
enough to make it back across the top of the ruvC fold and
get involved in the interface.
I think this means that not only does ATP binding force
the hinge open, but that the hinge has to be in certain
prescribed configurations for ATP to bind.
Did not package concatemers, but was normal on mature DNA
and in other assays.
FYI: position: see above.
Apparently manipulates the hinge region such that it will
work with the motor, but will not properly position the
endonuclease for specific cleavage.
G367D, G369D, G424E; packaging stops with left end in
position to cleave, but cleavage does not occur.
also lost the non pac activity.
FYI: 367, 369 are in the betaA, betaB loop; 424 is 4
residues beyond the acidic residue at the end of betaD.
Morita M, Tasaka M, and Fujisawa H. 1995. Analysis of the
fine-structure of the prohead binding domain of the packaging
protein of bacteriophage-T3 using a hexapeptide, an analog of a
prohead binding-site. Vir. 211: 516-524.
Residues 571-576 in C terminal (region I) of T3 gp19 maturase
B required for binding to the prohead.
Morita M, Tasaka M, and Fujisawa H. 1995. Structural and functional
domains of the large subunit of the bacteriophage-T3 DNA packaging
enzyme - Importance of the C-terminal region in prohead binding. J.
Mol. Biol 245: 635-644.
Morozova O, Marra MA. 2008. Application sof next-generation
sequencing technologies in functional genomics. Genomics 92:255-264.
A review of the 454, Solixa, Solid, and Helicos methods as of
Moscoso M, Eritja R, Espinosa M. 1997. Initiation of replication
of plasmid pMV158: mechanisms of DNA strand-transfer reactions
mediated by the initiator RepB protein. J Mol Biol
RepB is a parB family member.
has a nicking-closing topoI-like activity.
This is apparently how pfam lables the domain as "parB
nuclease domain", although usually parB members are just
described as DNA binding.
Mrazek, J. & Karlin, S. (1998). Strand compositional asymmetry
in bacterial and large viral
genomes. Proc Natl Acad Sci USA 95, 3720-3725.
Mullaney JM, Thompson RB, Gryczynski Z, Black LW. 2000. Green
fluorescent protein as a probe of rotational mobility within
J Virol Methods. 88(1):35-40.
Measured mobility inside the phage head.
Muller JJ, Barbitz S, Heinie K, Freiberg A, Seckler R, Heinemann
U. 2008. An intersubunit active site between supercoiled
parallel beta helices in the trimeric tailspike endorhamnosidase of
Shigella flexneri Phage Sfi6. Structure 16: 766.
Doesn't have the top
Muniesa M, Recktenwald J, Bielaszewska M, Karch H, Schmidt H
Characterization of a Shiga toxin 2e-converting bacteriophage from
an Escherichia coli strain of human origin.
INFECTION AND IMMUNITY 68 (9): 4850-4855 SEP 2000
Narita S, Kaneko J, Chiba J, et al.
Phage conversion of Panton-Valentine leukocidin in Staphylococcus
aureus: molecular analysis of a PVL-converting phage, phi
268 (1-2): 195-206 MAY 2 2001.
Sequence was determined.
Two genes lukS-PV, lukF-PV, make a toxin virulance factor in
Found on this phage, and on a previous Staph phage, phi PVL.
They emphasize that these two are quite different phages that
picked up the same virulance genes.
These two phage seem to have homology generally into the
broader lambdoid group.
Gives following list of toxins transduced by phage:
PVL (Panton-Valentine leukocidin) as above.
diphtheria toxin in Corynebacterium diphtheriae
(Uchida et al., 1971; Nat. New. Biol. 233: 8-11).
pyrogenic toxins A and C in group A Streptococcus
(Johnson et al., 1986; J. Bact. 166: 623-627).
neurotoxin in Clostridium botulinum (Inoue and Iida,
1970; Jpn. J. Microbiol. 14:
Shiga-like toxins in Escherichia coli (Scotland
Lancet ii, p. 216; and O'Brian et al. 1984; Science 226:
cytolysin in Pseudomonas aeruginosa (Hayashi et al.,
1990; Mol. Microbiol. 4: 1703-1709).
cholera toxin in Vibrio cholerae (Waldor and
Mekalanos, 1996; Science 272: 1910-1914; this was a
Nelson SW, Benkovic SJ. (2007) The T4 Phage UvsW Protein Contains
Both DNA Unwinding and Strand Annealing Activities. J Biol Chem.
282:407-16. PMID: 17092935
Newcomb, W. W., R. M. Juhas, D.
R. Thomsen, F. L. Homa, A. D. Burch, S. K. Weller, and J. C.
Brown. 2001. The UL6 gene product forms the portal
for entry of DNA into the herpes simplex virus capsid. J. Virol.
They give a predicted secondary structure model, and discuss
it as similar to phi29, but the comparison is at the level of
just noting that there are alpha helixes in it.
Found at only one of the phage vertices.
Neve H, Zenz KL, Desiere F, Koch A, Heller KJ, and Brussow H. 1998.
Comparison of the lysogeny modules from the termperatue Streptococcus
thermophilus bacteriophages TP-j34 and Sfi21: Implications for
the modular theory of phage evolution. Virology 241: 61-72.
Cited as suggesting modules can be single genes.
Nilsson AS, Haggard-Ljungquist E. 2001. Detection of
homologous recombination among bacteriophage P2 relatives. MOL
PHYLOGENET EVOL 21 (2): 259-269.
Nolan JM, Petrov V, Bertrand C, Krisch HM, Karam JD. 2006.
Genetic diversity among five T4-like bacteriophages. Virol
2006 May 23;3(1):30
T4, RB43, RB49, RB69, 44RR2.8t, Aeh1
Conserved genes, and lots of "non conserved" genes drawn from
diverse gene pool.
Lots of homologous recombination iin structure module in
population sampled world wide over a decade and averaging 96%
Nossal NG, Makhov AM, Chastain PD 2nd, Jones CE, Griffith JD.
(2006) Architecture of the bacteriophage T4 replication
complex revealed with nanoscale biopointers. J Biol Chem. 2006 Nov
13; [Epub ahead of print] PMID: 17105722
Nunez-Ramirez R, Robledo Y, Mesa P, Ayora S, Alonso JC, Carazo
JM, Donate LE. 2006. Quaternary polymorphism of replicateve
helicase G40P: Structural mapping and domain rearrangement. J.
Mol. Biol 357: 1063-1076.
This is the SPP1 replicative helicase.
They find structural polymorphism, which they propose to be
important to the mechanism.
Obregon,V., Garcia,J.L., Garcia,E., Lopez,R. and Garcia,P. 2003.
Genome organization and molecular analysis of the temperate
bacteriophage MM1 of Streptococcus pneumoniae. J. Bact. 185 (7),
40,248 bp; NC_003050
Circularly permuted, terminally redundant.
Most genes have identified homologues.
S. O’Flaherty, A. Coffey, R.
Edwards, W. Meaney, G. F. Fitzgerald and R. P. Ross. 2004. Genome
of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting
Gram-Positive Bacteria with a Low G+C Content. J.Bact 186:
Broad host range against Staphylococcus. May be identical to
phages Au, and phi 812.
They want to declare it as a new genus based on failing to
classify into a "proteomic tree" which summarizes numbers of
detectable homologues among different phages.
127,395 bp; NC_005880; said "extreme ends could not be
sequenced"; suspect terminal redundancy; so look
out, the unsequencable gap may not represent the ends?
118 orfs named, but ignored those < 100 or without
rbs. 33 contiguous in 1 direction, then rest in the other.
No GATC subsequences. (cite Molineau et al 1993 Appl Env
Microbiol. 59:197–202. for precedent) %G+C is 30.6, even lower
than staphylococcus genome.
3 mobile introns; 2 with HNH nucleases and one with an unknown
structural genes similar to A511 (they say that's surprising -
why? They embrace modularity.).
Indicate leftwards and rightwards major promoters separated by
2kb with only 3 tRNA genes. Another tRNA gene is in
leftwards unit (the 33 genes) which have only lysis genes
identified + ligase, RNAse H, and a protein phosphorylase.
Rightwards operon has head and tail structural genes; The A511
segment has capsid, orf 3,4,5,6, tail sheath, 8,9.
Then a typical replicative region, although possibly more than
one DNA polymerases.
Ojha A, Anand M, Bhatt A, Kremer L, Jacobs WR Jr, and Hatfull GF.
2005. GroEL1: A dedicated chaperone involved in mycolic acid
biosynthesis during biofilm formation in mycobacteria. Cell 123:
Phage bxb1 integrates in groEL1 making lysogens unable to make
GroEL2 carries out housekeeping chaperone functions.
GroEL1, 2 are hsp60
GroEL1 required for (or alters?) function of KasA, a component
of fatty acids synthase making mycolic acid.
Mycolic acid is the peculiar cell wall component of
How is cell wall related to biofilm elaboration?
Olia AS, Prevelige PE, Honhson JE, Cingolani G. 2011.
Three-dimensional structure of a viral genome-delivery portal
vertex. Nat. Struct. Mol. Biol. 18: 597-603. PMID 21499245.
Have a crystal structure of P22 gp4 (tubular tail A) in
complex with the portal protein.
See Lander et al., Structure 17:789-799 (2009) for the
Claims that P22 extended C terminal helical segment on the
portal (gp1) forms an exended helical barrel deep into the
capsid.. The in vitro assembled portal has a continuous
cylindrical intensity there, and they modeled a helical coiled
configuration to go there.
Show a structural alignment P22 gp4 and siphoviruses HK97
(gp6) and SPP1 (gp18).
Tavares P, Lurz R, Steige A, Rckert B, and Trautner TA, JMB
264: 954-967 (1996)
Black LW, Annu Rev Micro. 43: 267-292 (1989)
Float the model that the portal does the cleavage.
Also did structure of sizA mutant that packages shorter
Has smaller tenticals
Ortega ME, Catalano CE. 2006. Bacteriophage lambda gpNu1 and
Escherichia coli IHF proteins cooperatively bind and bend viral DNA:
implications for the assembly of a genome-packaging motor. Biochem.
Paddison P, Abedon ST,
Dressman HK, Gailbreath K, Tracy J, Mosser E, Neitzel J, Guttman
B, Kutter E. (1998)
The roles of the bacteriophage T4 r genes in lysis inhibition and
fine-structure genetics: A new perspective. Genetics
About T4 rI, rIIA, rIIB genes.
rI,II,III mutants are rapid lysis mutants.
Mutants in rI, rIIA,B lose lysis inhibition (LIN) -- delayed
lysis if related phages are trying to superinfect.
T4 complete genome is NC_000866.
rIIA is complement(12..2189); rIIB is
complement(167965..168903); The circularly permuted genome of T4
is broken between these two genes in NC_000866.
rI is identified as tk.-2 (meaning 2 frames before thimidine
kinase); aka mobD.8.; It's a small frame.
Say rI is widely conserved among T4 relatives. Does that
mean slow to change in sequence, or just that it's there?
Propose that rI regulates holin in an adaptive response to
superinfection, whereas rIIA,B interact with various prophage
genes, apparently to prevent some [abberant?] early lysis
Note: holins are membrane proteins that accumulate in a timed
fashion to create pores allowing endolysins to exit to the
periplasm and digest the murein. See Wang et al.,
2000. T4 holin is called t protein or T. See
Ramanculov & Young (2001) Gene 265: 25-36 for
domain mapping of T4 holin.
Pajunen MI, Kiljunen SJ, Soderholm MEL, et al. Complete
genomic sequence of the lytic bacteriophage phi YeO3-12 of
Yersinia enterocolitica serotype O : 3. J
Parker ML, Eiserling FA. 1983. Bacteriophage SPO1 Structure and
Morphogenesis. I. Tail Structure and Length Regulation. J. Vir.
Parker ML, Eiserling FA. 1983. Bacteriophage SPO1 Structure and
Morphogenesis. II. Head Structure and DNA Size. J. Vir. 46:
Parker ML, Eiserling FA. 1983.
Bacteriophage SPO1 Structure and Morphogenesis. III. SPO1 Proteins
and Synthesis. J. Vir. 46: 260-269.
Note: visualized by radiolabeling, so number of Met residues
will affect intensity
H1 112.0 faint, obscured by BP2
H2 (N1) 53.7 faint
H3 (H*) 45.7 major capsid 47.7 precursor
H4 30.2 very faint
H5 29.5 very faint
H6 28.2 medium
H7 26.9 faint
H8 (N5) 26.3 medium
H9 25.1 faint
H10 (N6) 24.5 medium
H11 18.2 medium-heavy
H12 14.1 very faint
H13 (N7) 11.7 very faint
H14 11.0 medium-heavy (internal, meaning DNA bound?)
H15 10.5 medium-heavy
H16 10.2 faint
T1 95.5 faint
T2 69.2 very faint (not in wild type phage?)
T3 60.3 (sheath) heavy
T4 58.9 heavy (not in wild type phage?)
T5 33.1 heavy
T6 12.3 (core) very heavy
N1 (H2) 53.7 medium
N2 53.0 medium (do not appear in intact phage?)
N3 53.5 medium (do not appear in intact phage?)
N4 45.7 heavy
N5 (H8) 26.3 medium
N6 (H10) 25.1 medium-heavy
N7 (H13) 12.0 very faint
BP1 148.0 faint
BP2 112.0 heavy
BP3 98.0 heavy
BP4 93.0 very faint
BP5 74.0 medium
BP6 67.5 faint
BP7 60.2 heavy
BP8 58.8 faint
BP9 57.5 heavy
BP10 45.7 very faint
BP11 44.6 very faint
BP12 43.6 heavy, dblt with BP13
BP13 42.6 heavy, dblt with BP12
BP14 40.7 heavy
BP15 36.3 faint
BP16 35.5 medium, dblt with BP17
BP17 31.6 medium, dblt with BP16
BP18 30.2 medium
BP19 29.5 medium
BP20 24.0 medium
BP21 15.8 medium
BP22 15.5 medium-heavy
BP23 12.3 faint
BP24 11.7 faint
BP25 11.0 faint
BP26 10.6 faint, dblt with BP27
BP27 10.2 faint, dblt with BP16
BP28 8.8 very faint
Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson
NR, Quail M, Smithh F, Walter D, Libberton B, Fenton A, Hall N,
Brockhurst MA. 2010. Antagonistic coevolution accelerates molecular
evolution. Nature 464:275-278. PMID:
Payne M, Oakey J and Owens L. 2004. The ability of two
different Vibrio spp. bacteriophages to infect Vibrio harveyi,
Vibrio cholerae and Vibrio mimicus. J. Appl.
Microbiol. 97: 663.
Pedersen M, Østergaard S, Bresciani J, and Vogensen FK.
2000. Mutational Analysis of Two Structural Genes of
the Temperate Lactococcal Bacteriophage TP901-1 Involved in Tail
Length Determination and Baseplate Assembly. Virology
Gives a good accounting with some experimental evidence of how
to map TP901-1 tail genes onto the lambda tail operon.
Pedulla ML. Ford ME. Houtz JM.
Karthikeyan T. Wadsworth C. Lewis JA. Jacobs-Sera D. Falbo J.
Gross J. Pannunzio NR. Brucker W. Kumar V. Kandasamy J. Keenan L.
Bardarov S. Kriakov J. Lawrence JG. Jacobs WR Jr. Hendrix RW.
Hatfull GF. Origins of highly mosaic mycobacteriophage genomes. Cell.
Fractions of genes with no homologues listed:
L5 10/89 (mostly real small) 11%
D29 5/89 (mostly real small) 6%
Bxz2 6/88 (mostly real small) 7%
Omega 134/238 56%
BxB1 30/86 35%
Rosebush 65/90 72%
Che9D 27/111 24%
Bxz1 161/251 64%
Cjw1 76/144 53%
Che8 19/112 17%
Corndog 51/121 42%
Che9c 36/84 43%
TM4 55/92 60%
Barnyard 83/109 76%
Mycobacteria are GC rich gram positive bacteria.
Pecenkova T. Benes V. Paces J. Vlcek C. Paces V. Bacteriophage
B103: complete DNA sequence of its
genome and relationship to other Bacillus phages. Gene.
Petrov AS, Boz MB, Harvey SC. 2007. The conformation
of double-stranded DNA inside bacteriphages depends on capsid size
and shape. J. Struct. biol. 160:241-248. PMID 17919923.
Molecular dynamics simulations.
Petrov VM and Ratnayaka S and Karam JD. 2010. Genetic
insertions and diversifications of the PolB-type DNA polymerase
(gp43) of T4-related phages. J.
Mol. Biol. 395: 457-474.
Petrov VM Rathnayaka S Nolan JM Miller ES Karam JD. 2010. Genomes
of the T4-related bacteriophages as windows on microbiobial genome
evolution. Virol J. 7:292. PMID 21092436
Petrov VM, Nolan JM, Bertrand C, Levy D, Desplats C, Krisch HM,
Karam JD. 2006.Plasticity of the gene functions for DNA
replication in the T4-like phages. J. Mol. Biol.
They show that T4-like gp43 generally has a bigger finger
domain than archaeal polB type DNA polymerases.
4 Aeromonas T4-like phages and an Acinetobacter johnsonnii
phage has the gp43 split to two genes with the break in the
They discuss some bacterial split polB genes and the split
gene in RM378, which are broken at different sites.
They have nice 3D structure pictures of it.
Petrov, V.M., Nolan, J.M., Bertrand, C., Levy, D., Desplat, C.,
Krisch H.M. and Karam, J. D. (2006) Plasticity of the gene
functions for DNA replication in the T4-like phages.J
Mol Biol. 2006 361:46-68. PMID: 16828113.
A lot of conserved gene order.
Discussed evolution of gp43 (DNA polymerase).
Pietila MK, Laurinmaki P, Russell DA, Ko CC, Jacobs-Sera, D,
Hendrix RW, Bamford DH, and Butcher SJ. 2013.
Structure of the archaeal head-taiuled virus HSTV-1 completes the
HK97 fold story. PNAS 110:10604-10609. PMID 23733949.
Genome sequence of HSTV-1 thought to be a podovirus.
Structure shows HK97 fold.
Pindeda M, Gregory BD, Szczypinski B, Baxter KR, Hochschild A,
Miller ES, and Hinton DM. 2004. A family of anti-sigma 70 proteins
in T4-type phages and bacteria that are similar to AsiA, a
transcription inhibitor and co-activator of bacteriophage
T4. J. Mol. Biol. 344: 1183-1197.
In T4 AsiA binds sigma 70 and inhibits transcription from
promoters with sigma 70 -35 box.
Together with MotA, will promote transcrition for middle T4
promoters with MotA box at -30 instead of sigma 70 box at -35.
Propose family including AsiA, its homologues in RB69, 44RR,
KVP40, and Aeh1, as well as E. coli Rsd and Pseudomonas
Though MotA homologue in KVP40 not yet identified, MotA itself
activates KVP40 promoters in an analogous fashion.
Ponchon L, Mangenot S, Boulanger P, and Letellier L. 2005.
Encapsidation and transfer of phage DNA into host cells: From in
vivo to single particles studies. Biochim
Biophys. Acta. 1724: 255-261.
Ponchon L, Boulanger P, Labesse G,
Letellier L. 2005. The endonuclease domain of bacteriophage
terminases belongs to the resolvase/integrase/ribonuclases H
superfamily: A bioinformatics analysis validated by a functional
study on bacteriophage T5. J. Biol. Chem.
Pontarollo RA, Rioux CR, and Potter AA. 1997. Cloning and
characterization of bacteriophage-like DNA from Haemophilus somnus
homologous to phages P2 and HP1. J. Bacteriol. 179: 1872–1879.
What is terminase gene in our alignment?
Pope WH, Weigele PR, Chang J, Pedulla
ML, Ford ME, Houtz, JM, Jiang W, Chiu W, Hatfull GF, Hendrix RW, and
King J. 2007. Genome sequence, structural proteins, and capsid
organization of the cyanophage syn5: A "horned" bacteriophage of
Marine Synechococcus. J. Mol. Biol.
A T7-like sensu latto phage
In phage TbilisiNK25, we matched their gp47, also at the head
of a lysis operon and preceeding the holin gene. They
called it a late expressed non structural protein.
Prangishvili D, Garrett RA, and Koonin EV. 2006.
Evolutionary genomics of archaeal viruses: Unique viral genomes in
the third domain of life. Virus Res. 117:52-67. UTHSCSA
Proctor, L.M. 1997. Advances in the study of marine viruses.
Microsc. Res. Tech. 37: 136-161.
Reviews a substantial number of surveys with electron
microscopy of viral abundance in sea water.
Notes higher variation in viral abundance than bacterial
abundance, including temporal blooms.
Reviews degree of morphological variation.
Expresses concerns about defective virions and extraneous
particles inflating the abundance measurements.
Notes that most marine bacteria still can not be cultured.
Reviews studies that measure the fraction of bacteria with
phage particles inside of them as a measure of the extent of
Reviews cultured host-virus systems
Reviews cyanobacterial phages and viruses infecting eukaryotic
Whereas others propose that most marine viruses are
bacteriophages, Proctor argues for a more substantial eukaryotic
Advocates molecular characterization, meaning protein gels and
Southern blots. Not a word is devoted to DNA sequence.
Putnam CD, Clancy SB, Tsuruta H, Gonzalez S, Wetmur JG, and Tainer
JA. 2001. Structure and mechanism of the RuvB holliday junction
branch migration motor. J.
Mol. Biol. 311: 297-310.
A hexameric double stranded DNA translocase.
P-loop domain forms a ring around the DNA.
Has a conformationally dynamic interface to an 80 residue 4
Przech, A. J., Yu, D., and Weller, S. K. (2003) Point Mutations in
Exon I of the Herpes Simplex Virus Putative Terminase Subunit,
UL15, Indicate that the Most Conserved Residues Are Essential for
Cleavage and Packaging. J. Virol. 77:
Lethal (non complementing) mutants made a conserved places:
L120N, Q205E, G263A, Y285S, but the mutants did associate with
Show alignment among HSV large terminases.
G263 is the G of the P-loop motif
Q205 is the Ad. binding motif.
L120 should be around the small terminase binding site.
Y286 is in middle of beta2; curiously HSV appears to have a
G also in the middle of beta 2.
Sequence and numbers appear to correspond to
gi|9629397|ref|NP_044616.1| Gene info UL15 [Human herpesvirus
1], although Y285S appears to actually be Y286S.
In HSV, UL15 is large terminase, UL28 is small terminase,
UL6 is portal, UL17 and UL32 stabilize DNA in capsid, UL23
binds the terminase and has unknown function.
UL28 recognizes a pac site.
Purohit P, Kondev J, Phillips R. 2003. Mechanics of DNA packaging in
viruses. Proc. Natl. Acad. Sci. USA 100:3173-3178.
A highly mathematical approach to forces in the capsid.
Rabkin SD, and Richardson CC. 1988. Initiation of DNA replication at
cloned origins of bacteriophage T7. J. Mol. Biol. 204: 903-916.
Cites Tamanoi et al., (1980) for identifying the primary ori
to a 129 bp fragment at 14.75-15.0.
Involvies T7 RNA polymerase promoters phi 1.1A and phi 1.1B
followed by a 61 bp 79% A+T segment with 7 copies of TTAA, and a
single 3' CTGGG 5' primase recognition site.
This paper characerizes secondary origins, defined as origins
that begin to function if the primary origin is deleted.
The CTGGG is not required.
The AT block is required.
Radanya EH, Malanoskib G, Nicholas
P. Ambulos NP Jr, Friedbergd EC. and Yasbin RE. 1997. Transfection
enhancement in Bacillus subtilis displays features of a novel DNA
repair pathway. I: DNA base and nucleolytic specificity. Mutation
Research/DNA Repair 384: 107-120.
Place to start looking into inhibition of uracil-DNA
glycosylase by phage PBS2 (which has uracil in its DNA).
Place to start looking into the ability of SPO1 to inhibit
attack against its HMU DNA upon infection, but not transfection.
Rajagopal BS, Reilly BE, Anderson DL. 1993 Bacillus subtilis mutants
defective in bacteriophage phi 29 head assembly. J Bacteriol.
175:2357-62. PMID: 8096839
Ramanculov E. Young R. An ancient player unmasked: T4 rI encodes
a t-specific antiholin.
Molecular Microbiology. 41(3):575-83, 2001
Rao VB, Mitchell MS. 2001. The N-terminal ATPase site in the
large terminase protein gp17 is critically required for DNA
packaging in bacteriophage T4. J. Mol. Biol. 314 (3):
Rao VB & Feiss M. 2008. The bacteriphage DNA packaging
motor. Ann. Rev. Genet. 42: 647-681. PMID: 18687036 UTHSCSA
Didier Raoult, Stéphane Audic, Catherine Robert, Chantal Abergel,
Patricia Renesto, Hiroyuki Ogata, Bernard La Scola, Marie Suzan,
and Jean-Michel Claverie. 2004. The 1.2-Megabase Genome Sequence
of Mimivirus. Science
Ravin V. Ravin N. Casjens S. Ford ME. Hatfull GF. Hendrix RW.
Genomic sequence and analysis of the atypical
temperate bacteriophage N15. Journal of Molecular Biology.
299(1):53-73, 2000. UI: 20328599.
temperate.host: E. coli.
replicates as a linear molecule with hairpins at the telomers.
structural genes similar to bacteriophage lambda.
has lots of stuff apparently derived from plasmids.
They argue for "a much greater diversity of [phage] genomic
architectures than was previously recognized".
Recktenwald J, Schmidt H. 2002 The nucleotide sequence of Shiga
toxin (Stx) 2e-encoding phage phi P27 is not related to other Stx
phage genomes, but the modular genetic structure is conserved.
Infect. Immun. 70 (4): 1896-1908.
Rentas FJ, Rao VB. 2003. Defining
the bacteriophage T4 DNA packaging machine: Evidence for a
C-terminal DNA cleavage domain in the large terminase/packaging
protein gp17. J.
Mol. Biol 334: 37-52. UTHSCSA
D401, E404, G405, D409 required for cleavage
Also H436 - see Kuebler, D. & Rao, V. (1998). Functional
analysis of the DNA packaging/terminase protein gp17 from
bacteriophage T4. J. Mol. Biol. 281(5), 803–814.
They killed a model for a histidine coordinated metal binding
center, but two of the residues tested only tolerated short
aliphatic side chains: H411, and C402. In summary in the
sequence DCsEGrgqDyH, The 2 D positions could not be
changed. The G could not be changed. The others
showed a restricted degree of tolerance consistent with
influencing the structural positioning of the loop.
D401 mutants deficient in initiation cutting but not
Refer to K. Kondabagilu & V.B.R., unpublished data). for
FYI: This is the betaA - betaB loop. D401 is the well
established ruvC active site Mg ligand discussed by Ponchon et
al., 2006, and D409 is conserved in about half of all
terminases. T4 and relatives have a few extra residues in
the region, which probably makes a tight fit explaining the
invariant G residue.
Rizzo AA, Suhanovsky MM, Baker ML, Fraser LC, Jones LM, Rempel
DL, Gross ML, Chiu W. Alexandrescu AT, Teschke CM.
2014. Multiple functional roles of the accessory I-domain of
bacteriophage P22 coat protein revealed by NMR structure and
cryoEM modeling. Structure 22:830-841. PMID 24836025.
I domain is S223 - V345 (STAT...ILNY).
Rodriguez-Casado A. Moore SD. Prevelige PE Jr. Thomas GJ Jr.
Structure of bacteriophage P22 portal protein in relation to
assembly: investigation by Raman spectroscopy. Biochemistry.
Segall A, Steward G, Seguritan V, Breitbart M, Wolven F, and Azam
F. 2000. The complete genomic sequence of the marine phage
Roseophage SIO1 shares homology with nonmarine phages Limnol.
Oceanog. 45: 408-418.
Classifies as T7-like based on closer affinities of the DNA
polymerase and a few other replicative genes to T7 genes.
Finds no RNA polymerase.
Finds two gene-sized segments repeated non tandemly and not as
a terminal repeat.
The sequence as reported does not have any of the traditional
arrangements of bacteriophage genome ends, and they may not have
actually determined end points.
The presumed late transcription unit was oriented in reverse
to the replicative gene transcription unit, in contrast to T7
and its closest relatives.
No simililarities were reported, nor could we find them with
Psi-blast and the database as of 7/17/01, for the presumed
morphogenic and structural genes.
This is the genome that vpv262 most often matches.
The affinity of vpv262 for SIO1 seems confined to some of
the presumed structural and morphogenesis genes.
vpv262 DNA polymerase, helicase, and primase do not have
close affinity for SIO1 (or T7).
Comparison with vpv262 clarifies that 3 orfs that are tied
up in one of the duplicated regions are rearranged versions of
a T7-like maturase B large subunit packaging protein.
Another 2 orfs tied up in the duplicated region are a
rearranged version of the adjacent vpv262 gene, currently of
vpv262 shares the inversion of the presumed late
transcription unit relative to the replicative transcription
vpv262 also doesn't seem to have an RNA polymerase.
Rohwer F, and Edwards R. 2002. The phage proteomic tree: a
genome-based taxonomy for phage. J. Bact. 184:4529-4535.
PMID: 12142423. UTHSCSA
Romero P, Lopez R, Garcia E. 2004. Genomic organization and
molecular analysis of the inducible prophage EJ-1, a mosaic
myovirus from an atypical pneumococcus. Vir.322 (2): 239-252.
Myoviridae by tail morphology.
Incuded from Streptococcus pneumoniae strain 101 with
Head cassette like Lj965; tail cassette like PBSX; others
noted most similar to DT1/Sfi11 or phiSF370.3
Rossmann MG, Arisaka F, Battisti AJ, Bowman VD, Chipman PR, Fokine
A, Hafenstein S, Kanamaru S, Kostyuchenko VA, Mesyanzhinov VV,
Shneider MM, Morais MC, Leiman PG, Palermo LM, Parrish CR, Xiao C.
(2007) From structure of the complex to understanding of the
biology. Acta Crystallogr D Biol Crystallogr. 63(Pt 1):9-16. PMID:
Sabehi G Shaulov L Silver DH Yanai I Harel A Lindell D. (2012) A
novel lineage of myoviruses infecting cyanobacteria is widespread
in the oceans. PNAS 109:2037-2042. PMID 22308387.
S-TIM5 is a myovirus.
It has a DNA polymerase more like mitochondrial DNA polymerase
than does T7. There is a tree in the paper.
Sandegren L, Sjoberg BM. (2006)vSelf-splicing of the
bacteriophage T4 group I introns requires efficient translation of
the pre-mRNA in vivo and correlates with the growth-state of the
infected bacterium. J Bacteriol. 2006 Nov 22; [Epub ahead of
print] PMID: 17122344
Saint Girons I, Bourhy P, Ottone C, et al. The LE1
bacteriophage replicates as a plasmid within Leptospira
biflexa: Construction of an L. biflexa-Escherichia coli
shuttle vector J BACTERIOL 182 (20): 5700-5705 OCT 2000.
Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI,
Grimes JM. 2006. The structure of an RNAi polymerase links RNA
silencing and transcription. Plos
Biol. 4: e434.
The RNAi RNA-directed RNA polymerase of RNA interference
silencing has a catalytic domain fold like that of RNA
polymerase beta prime.
We have one of these genes in phage 0305phi8-36, which we
presume to be a DNA-directed RNA polymerase.
pdb entries 2j7n and 2j7o
Has two double psi beta barrel domains (one is the catalytic
domain). In bacterial RNA polymerases, beta has one and
beta prime has one, and they are distributed in the same way in
Functions as a dimer?
They refer to 3 families based on this fold: pol beta, right
handed (T7 and klenow, reverse transcriptase), and the double
barrel polymerases (this one, and also the beta, beta prime
Savva CGW, Holzenburg A., Bogner. 2004. Insights into the
structure of human cytomegalovirus large terminase subunit pUL56.
Lett. 564: 135-140.
Cryo EM of an apparent head to tail dimer of large terminase.
They interpret it as a head to tail dimer, with each monomer
forming a ring.
To fit our mode, I assume instead that the dimerization alongn
the other axis, hinge to hinge. Then both N ter motor domain and
the endo domain are about the right thickness, protrude to about
the same depth from the hinge, and have a hook to the same side
on the end, probably away from the DNA annulus. In this
interpretation the head to tail dimer would be an artificial
configuration that happens to make and endo and a P-loop hook
approach each other giving the appearance of a hinge. The endo
and the N ter motor domain form a U separated about 25 A by the
thin rigid hinge. It's unclear if this is an open or
closed complex or somewhere in between that just happens to be
stabilized by the head to tail organization. But it seems
unlikely that the two domains contact each other directly, and
it seems likely that the endo domain (presumably the slightly
smaller one) can form a solid ring.
Scheffczik H, Savva CGW, Holzenburg A, et al. 2002. The terminase
subunits pUL56 and pUL89 of human cytomegalovirus are
DNA-metabolizing proteins with toroidal structure. Nucl.
Acids Res. 30 (7): 1695-1703.
The larger terminase hexamer appears to be only 110 A in
diameter in this study.
In the presence of DNA they see one of the hexamer units as a
"cleft", which we would interpret as being the one in the closed
The estimate the central opening as 30 to 40 A, but it looks
more like 20-30 A to me. The edge is fuzzy, so it depends
on where you draw your threshold.
They have only top and bottom views, so you can't see anything
about the thickness.
Scholl,D., Adhya,S. and Merril,C.R. 2002. Bacteriophage SP6
Is Closely Related to Phages K1-5, K5, and K1E but Encodes a Tail
Protein Very Similar to That of the Distantly Related P22. J.
Bacteriol. 184 (10), 2833-2836.
SP6 is a T7-like phage with a single P22-derived tail spike
gene that alters host range.
The tail spike gene has the organization of a moron.
Searls T, Chen DL, Lan T, McLaughlin LW. 2000. Nucleoside
analogue substitutions in the trinucleotide DNA template recognition
sequence 3 '-(CTC)-5 ' and their effects on the activity of
bacteriophage T7 primase. Biochem. 39 (15):4375-4382.
As bgk gives that primers are pppACC(C/A) and pppACAC from
3'-CTGG(G/T)-5' and 3'-CTGTG-5'.
Seegers JF, McGrath S, O'Connell-Motherway M, Arendt EK, van de
Guchte M, Creaven M, fitzgerald GF, van Sinderen D. 2004. Molecular
and trnascriptional analysis of the temperate lactococcal
bacteriophage Tuc2009. Vir. 239:40-52.
Selivanov NA, Prilipov AG, Efimov VP, Marusich EI, Mesyanzhinov
VV. 1990. Cascade of overlapping late genes in bacteriophage T4.
Biomed. Sci. 1: 55-62.
Talks about overlapping frames, and a frameshifted arrangement
between T4 9 and 10.
Sergueev K, Court D, Reaves L,
Austin S. 2002. E. coli cell-cycle regulation by bacteriophage
Mol. Biol. 324:297-307.
lambda Ea8.5 and Ea22 function to block E. coli replication
Serwer, P. (2003). Models of bacteriophage DNA packaging motors. J.
Struct. Biol. 141, 179-188.
An update of the Serwer osmotic pump model.
Serwer P, Hayes SJ, Zaman S, Lieman K,
Rolando M, and Hardies SC. 2004. Improved isolation of undersampled
bacteriophages: finding of distant terminase genes. Vir.
Shaburova OV Hertveldt K de la Cruz DMA Krylov SV Pleteneva EA
Boukaltseva MV Lavigne R Volckaert G and Krylov VN
(2006) Comparison of new giant bacteriophages OBP and
Lu11 of soil Pseudomonads with bacteriophages of the φKZ-supergroup
of Pseudomonas aeruginosa. Russian Journal of
Genetics. 42: 877-885.
Shen PS Domek MJ Sanz-Garcia E Makaju A
Taylor RM Hoggan R Culumber M Oberg C Breakwell DP Prince JT Belnap
DM. 2012. Sequence and structural characterization of
great salt lake bacteriophage CW02, a member of the T-like
supergroup. J. Virol. PMID 22593163.
Has a head decoration like RIO1 gp47, and then a pentameric
head decoration I can track toVpV262, but different from RIO1.
Didn't visualize the tail or the internal core.
Did have mass spec data that was added to the CW02 database.
Shibata H, Fujisawa H, and Minagawa T. 1987. Early events in DNA
packaging in a defined in vitro system of bacteriophage T3. Vir.
Basically defines small terminase + DNA makes a complex that
associates with a large terminase 6 mer already on the prohead.
This is in vitro when fed mature DNA. So in vivo the
concatemer must have encountered dimeric large terminase in
order to get the right end cleaved in the first place.
Shin H, Lee JH, Ahn CS, Ryu S, Cho BC. 2014. Complete
genome sequence of marine bacterium Pseudoalteromonas phenolica
bacteriophage TW1. Arch. Virol. 159:159-162. PUBMED 23851651.
Called a sipho, EM looks like a myovirus except tail sheath
seems too narrow.
Filed in c:\sch\TW1\lit.
Shimizu-Kadota M, Kiwaki M, Sawaki S, et al. 2000. Insertion of
bacteriophage phi FSW into the chromosome of Lactobacillus casei
strain Shirota (S-1): Characterization of the attachment sites and
the integrase gene. Gene 249 (1-2): 127-134.
Shingaki R, Kasahara Y, Inoue T, Kokeguchi S, Fukui K.
2003. Chromosome DNA fragmentation and excretion caused by
defective prophage gene expression in the early-exponential-phase
culture of Bacillus subtilis. Canadian J.
Microbiol. 49 (5): 313-325.
Showe MK, Isobe E, Onorato L. 1976. Bacteriophage T4
prehead proteinase. II. Its cleavage from the product of
gene 21 and regulation in page-infected cells. J. Mol. Biol.
A few inactivated fragments are found in mature virions.
It apparently autoproteolyzes itself to death.
D. Shu and P. Guo, Only one pRNA hexamer but multiple copies of
the DNA-packaging protein gp16 are needed for the motor to package
bacterial virus phi29 genomic DNA. Virology 309 (2003), pp.
The hexameric pRNA ring remains stably bound during packaging,
but p16 (the homologue of terminase) does not.
The result is just that they can recover partially packaged
complexes that will finish if they add gp16 and ATP.
I don't know how this means "multiple copies of gp16". I
think it just means gp16 can dissociate without the rest of the
complex falling apart. This essentially means that the
pRNA and portal can form a locked state in the absence of gp16
so that the DNA doesn't eject. This is essentially what
you expect from a rachet, although I suppose you can invent a
rotary rachet such that the portal is inhibited from reverse
spinning in the absence of p16, or inhibited in passing the DNA.
Sickmier EA. Zhang R. Joachimiak A. White SW. The MotA transcription
bacteriophage T4 contains a novel DNA-binding domain: the 'double
wing' motif. Molecular Microbiology.
Simpson AA, Tao YZ, Leiman PG, Badasso MO,
He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL,
Baker TS,Rossmann MG. 2000. Structure of the bacteriophage
phi 29 DNA packaging motor.
Cyro EM showing a 5 fold symetrical pRNA that appears to send
struts up away from the portal. They show a potential
contact with the lip of the portal protein. CryoEM appears
to show the packaging ATPase perched atop the pRNA struture and
projecting inwards slightly clockwise of radial symmetry.
They then postulate a portal rotary drive model (the original
I think) with the pRNA mounted on the capsid and the terminase
mounted on the pRNA and interacting with the portal.
Wide end inside mostly made of beta sheet and has the C
Long 3 helix region inapproximately coiled coil configuration
composed of the N terminus, and an out and back excursion of the
The part exposed at the portal opening is a simple hook out
The monomer is inclined relative to the 12 fold symmetry axis.
There is some deviation from radial symmetry in the wise ends.
Side to side contacts feature a positively charged surface
juxtaposed to a negatively charged surface.
Oily surface to contact the capsid is part of wide domain and
part of central helical region.
Smith, M. C. M., Burns, R. N., Wilson, S. E. & Gregory, M. A.
(1999). The complete genome sequence of the Streptomyces temperate
phage phi C31: evolutionary relationships to other viruses. Nucl.
Acids Res. 27, 2145-2155.*
Smith MC. Burns N. Sayers JR. Sorrell JA. Casjens SR. Hendrix RW.
Bacteriophage collagen. [letter; comment].
[Comment. Letter] Science. 279(5358):1834, 1998. UI: 98201874.
Notes G-X-Y where X & Y often P for some phage tail fiber
Lengths run from 6..51 repeats.
Most impressive example given is phage 933W.
PRD1 (E. coli) has short example in non tail fiber
Notes that tail fibers are thought to be triple stranded.
A response by Jurgen Engel argues against the idea that these
are related to the collagen triple helix by pointing out the
absence of evidence for proline hydroxylation, and that the
repeats are relatively short to be stable, particularly without
I think that some regions that were permissive of a triple
helix but weren't independently stable might be just the thing
to impose a three stranded structure on tail fibers and keep
them in some register. This would sure help explain the
heterogeneity in length and the apparent fluid unequal
recombination that you see in these genes.
Smith, D.E., Tans, S.J., Smith, S.B., Grimes, S., Anderson, D.L.,
and Bustamante, C. (2001) The bacteriophage straight phi29 portal
motor can package DNA against a large internal force. Nature
413: 748–752. UTHSCSA
Source of the 60 pN force observation.
Observe a slow down near the end of packaging corresponding to
14 pN of back pressure.
Dependence of velocity of force applied used to calculate a
"characteristic distance" associated with the force induced
activation barrier of 1.1 A (per 6.8 A of movement).
This means that the free energy drop over the tranlocation
stroke is not a constant. Over 1.1 A, it is shallow or
nonexistant such that application of a small force converts
this portion of the excursion into an activation barrier (ie a
transition state requiring thermal energy to kick the molecule
over it). The rest of the excursion features enough of a
free energy drop per increment that the back force applied
does not cause resistance to motion. This situation
prevailed over a fair rang of forces, but at high back force
the situation started to change into resistance over a wider
distance. Then, of course, when the net drop in free
energy is overpowered, the motor stalls.
Steinbacher S, Miller S, Baxa U, Budisa N, Weintraub A, Seckler
R, Hber R. 1997. Phage P22 tailspike protein: crystal
structure of the head-binding domain at 2.3 A, fully refined
structure of the endorhamnoseidase at 1.56 A resolution, and the
molecular basis of O-antigen recognition and cleavage. J.
Mol. Biol. 267:85-880. PMID 9135118.
Headgroup has 8 beta strands.
Stummeyer K, Schwarzer D, Claus H, Vogel U, Gerardy-Schahn R, and
Muhlenhoff M. 2006. Evolution of bacteriophages infecting
encapsulated bacteria: lessons from Escherichia coli K1-specific
phages. Mol. Microbiol. 60:1123-1135.
Talks about the same tailspike (an endosialidase) transferring
onto a T7-like (K1F), and SP6-like K1E, K1-5), and a P22-like
Talks about a degenerate tail spike becoming an adapter for
attachement of an unrelated tailspike.
Seems to imply that other than the side fiber, the tail
structures are all homologous among T7, K1F, SP6, K1E, and
Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D,
Loessner MJ, Stetter KO, Weber-Ban E, and Ban N. 2008.
Structural basis of enzyme encapsulation into a bacterial
nanocompartment Nat. Struct. Mol. Biol 15: 939-947. PMID 19172747.
The reconginze that encapsulin has an HK97 capsid protein
Siponen M, Sciara G, Villion M,
Spinelli S, Lichiere J, Cambillau C, Moineau S, Campanacci V.
2009. Crystal structure of ORF12 from Lactococcus lactis phage p2
identifies a tape measure protein chaperone. J. Bact.
The lambda G homolog forms a spiral that wraps around the tape
Spelbrink JN, Li FY, Tiranti V, Nikali K, Yuan QP, Tariq M,
Wanrooij S, Garrido N, Comi G, Morandi L, Santoro L, Toscano A,
Fabrizi GM, Somer H, Croxen R, Beeson D, Poulton L, Suomalainen A,
Jacobs HT, Zeviani M, Larsson C. 2001. Human mitochondrial DNA
deletions associated with mutations in the gene encoding Twinkle,
a phage T7 gene LF-like protein localized in mitochondria. Nat.
Genetics. 28 (3): 223-231.
Twinkle is related to T7 primase/helicase.
Springman R, Badgett MR, Molineux IJ, Bull JJ. 2005. Gene order
constrains adaptations in bacteriophage T7. Vir. 341:141-52.
Mutants with gene 1 out of place evolve to partially recover
Stanley E. Fitzgerald GF. Le Marrec C. Fayard B. van Sinderen D.
Sequence analysis and characterization
of phi O1205, a temperate bacteriophage infecting Streptococcus
thermophilus CNRZ1205. Microbiology.
143 ( Pt 11):3417-29, 1997.
Steven, A.C., Heymann, J.B., Cheng, N., Trus, B.L., and Conway,
J.F. (2005) Virus maturation: dynamics and mechanism of a
stabilizing structural transition that leads to infectivity. Curr
Opin Struct Biol 15: 227–236.
Has reference to a coiled coil structure of a scaffold
Steven AC, Trus BL, Maizel JV, Unser M, Parry DAD, Wall JS, Hainfeld
JF, Studier FW. 1988. Molecular substructure of a viral
receptor-recognition protein; The gp17 tail-fiber of bacteriophage
T7. JMB 200:351-365. PMID 3259634.
They have an EM even at this early date with the fibers tucked
up sideways under the virion.
The fibers look like a bent tube.
Stewart CR, Gaslightwala I, Hinata
K, Krolikowski KA, Needleman DS, Peng AS-Y, Peterman MA, Tobias A,
and Wei P. 1998. Genes and Regulatory Sites of the
‘‘Host-Takeover Module’’ in the Terminal Redundancy of Bacillus
subtilis Bacteriophage SPO1. Virology
First 11.5 kb of a 12.4 kb terminal redundancy is called host
PhageD matches a single 35 AA gene in this region, then a
second gene on focused searching.
Large number of unusually active early promoters.
Although SPO1 is not completely sequenced, this 11.5 kb region
is reported in AF031901.
12 characterized promoters, all with TTGAC[AT] at -35, a TG
before the TATAA box (eg. TGCTAATAT), and an oligo A run
spanning pos -42 often with others. These are characteristic of
Bacillus subtilis sigma A promoters.
15 rho independent terminators
6 hairpin structures thought to be RNAse III cleavage sites
There are small bits of sequence from closely related phages
SP82, and 2C in this region
Stewart CR, Casjens SR, Cresawn SG, Houtz JM, Smith AL, Ford ME,
Peebles CL, Hatfull GF, Hendrix RW, Huang WM, Pedulla ML. 2009. The
genome of Bacillus subtilis bacteriophage SPO1. J. Mol. Biol.
Stone, R. 2002. Stalin's Forgotten
Cure. Science 298:728-731.
A news article about phage therapy reviewing the history, and
recent interest. Includes mention of agricultural
uses. Includes mention of a variety of companies pursuing
phage therapy, as well as regulatory issues.
Strauch E, Lurz R, Beutin L. 2001. Characterization of a Shiga
toxin-encoding temperate bacteriophage of Shigella sonnei
Infect. Immun. 69 (12): 7588-7595.
Stromsten NJ, Bamford DH,
Bamford JK.2005. In vitro DNA packaging of PRD1: a common
mechanism for internal-membrane viruses. J
Mol Biol. 348:617-29. PMID: 15826659. UTHSCSA
Stortelder A, Hendriks J, Buijs JB, Bulthuis J, Gooijer C, van
der Vies SM, van der Zwan G. (2006) Hexamerization of the
bacteriophage T4 capsid protein gp23 and its W13V mutant studied
by time-resolved tryptophan fluorescence. J Phys Chem B Condens
Matter Mater Surf Interfaces Biophys. 110:25050-8. PMID: 17149929
Sturrock SS. Dryden DT. Atanasiu C. Dornan J. Bruce S. Cronshaw
A. Taylor P. Walkinshaw MD.
Crystallization and preliminary X-ray analysis of ocr, the product
of gene 0.3 of bacteriophage T7. Acta
Crystallographica Section D-Biological Crystallography. 57(Pt
Sugden A, Stone R, and Ash C. 2004.
Ecology in the Underworld. Science
Introduction to a special section about ecology of soil.
Diversity and complexity of the food web is featured (in the
section in general), but the role of bacteriophages is not
Sulakvelidze A. Alavidze Z. Morris JG Jr. Bacteriophage therapy.
Antimicrobial Agents & Chemotherapy. 45(3):649-59, 2001. UI:
Very readable minireview giving the history of phage therapy,
and then focusing on reviewing non English papers from Russia
and Eastern Europe where phage therapy has been most commonly
Cites additional reviews:
Alisky J et al., J. Infect. 36:5-15 (1999).
Barrow PA, and Soothill JS, Trends Microbiol. 7: 268-271
For history of subject: Summers WC, Felix d'Herelle and the
origins of molecular biology. Yale Univ. Press., (1999).
Administration of lytic phage preparations as bacteriocidal
therapy was practiced in the West prior to the introduction of
antibiotics, and was continued in the Soviet Union and Eastern
Apparently there is a resurgence of interest for treatment of
multi-drug resistant infections.
Many clinical trials reviewed that were generally glowing
although apparently not well controlled. With that
somewhat serious caveat, cure rates comparable to antibiotics
were consistently reported.
It only works if you culture the offending bacteria and
determine that you have a phage preparation specific to that
bacteria. - ie. there are no broad spectrum phages.
Cites successful treatments of infected surgical wounds,
dysenteric diseases, meningitis, respiratory infections,
and infections of the perionatal cavity or of the eye.
Most common routes of administration described are topical or
oral after bicarb. States that phage gain access to the blood
stream after oral administration. (It wasn't clear to me if this
was in patients compromised by dysenteric disease, or if this
was in the context of a reliable way to deliver the phage to
internal sites.) Intravenous administration was also
described, apparently without adverse consequences.
Phage therapy is also subject to microbial resistance, but
states advantage of phage therapy is that phage can easily be
selected to circumvent resistance.
States that multiple resistance doesn't occur; ie. resistance
to one phage isn't accompanied by resistance to others.
[However, plasmid borne EcoRI; and phage borne P1 restriction
systems would seem to exemplify that multiple resistance does
occur, and can spread just like multiple antibiotic resistance.]
Summer EJ, Berry J, Tran TA, Niu L, Struck DK, Young R. 2007. Rz/Rz1
lysis gene equivalents in phages of Gram-negative hosts. J. Mol. Biol.
Summer EJ, Gonzalez CF, Carlisle T,
Mebane LM, Cass AM, Savva CG, LiPuma JJ, and Young Ry. 2004.
Burkholderia cenocepacia Phage BcepMu and a Family of Mu-like
Phages encoding potential pathogenesis factors. J. Mol. Biol.
36,748 bp completely sequenced
Capsid assembly related to Mu; tail related to P2.
Used some cI fusion system to demonstrate homotypic
interacting domains. This method demonstrates that a
domain folds and can confer dimerization (or higher order) on a
Noted colinear prophages from Salmonella typhi (SalMu, aka
Sti3), Photorhabdus luminescens (PhotoMu), and Chromobacterium
violaceum (ChromoMu). Homology detected at the DNA level
except for about 3 kb at each end.
Has a different transposase than Mu, and and inverted
structure relative to Mu. Actually Mu and BcepMu both have
members of the Tn522-IS1604 transposase family, but they believe
that Mu transposase (TnpA) is less tightly related to
other family members than is the BcepMu transposase. Needs
a tree analysis.
May have a couple of pathogenecity factors.
Burkholderia cenocepacia not usually pathogenic to humans, but
certain strains are major pathogen of cystic fibrosis patients.
The EM seemed to show some odd large structure at the end of
the tail tube (contracted and non contracted), and no obvious
baseplate. Should compare to Mu.
There is heterogeneous host DNA attached to both ends of the
ds linear DNA in the virion.
Cite 31 for statement that gram - phages usually have a holin,
antiholin, and endolysin and an Rz/Rz1 "equivalent" of which
only the endolysin is easily identifiable by homology.
See Wang, Smith, Young. 2000. Ann. Rev. Microbiol. 54:
They note in contrast a protein with a soluble lytic
transglycosylase (slt) domain, and containing an N terminal
transmembrane domain related to SAR sequences in P1 Lyz
endolysin. This kind of transmembrane sequence is found
in a number of phage glycosidase endolysins and us used to
position in the membrane prior to release by holin activation.
Rz/Rz1 is a system (in lambda) of two overlapping genes, one
completely embedded out of frame within the other. Both
have a signal peptide cleavage site. The second is a
proline rich lipoprotein. The pair attacks outer
membrane or inner/outer membrane links during lysis. They are
able to detect a pair of genes with these properties, although
not by homology. See:
Kedzierska et al., 1996, Gene 168:1-8.
Young et al., (1979) JMB 132: 307-322
Zhang and Young. 1999. Mol. Gen. Gen. 262:659-667.
Note that the tape measure protein has potential frame shift
to produce alternative C termini, which is the rule for Mu (41
& 41.5), lambda (G & T) and P2 (E and E').
They discuss the side tail fibers as 18 aa residue repeats in
N terminal half of about 780 residue protein separated by
proline runs with GlyXX motifs.
See Smith et al., 1998. Science 279: 1834.
They assume this is some kind of trimerization motif.
Notes that among transposase based phages that are not
Mu-like, most are in Pseudomonas and are like one of two type
members D3112 and B3.
Tail fiber is gp52, and matches P2gpH on the N terminus.
Sun S, Kondabagil K, Gentz PM, Rossmann MG, Rao VB. 2007. The
structure of the ATPase that powers DNA packaging into
bacteriophage T4 procapsids. Mol.
Cell 25: 943-949. UTHSCSA
Gives crystal structure of the T4 gp17 P-loop domain, and what
they call subdomain II, which is what we call the hinge.
They repeat the 2 bp/ATP arguement and discuss the motor as if
it were a pentamer.
Talk about an inchworm mechanism, postulating two sites of DNA
contact. They site unpublished results that gp17 binds to
DNA in the N terminus (curiously not the C terminus). They
ponder what the 2nd site might be, speculating that maybe two
different subunits bind to the DNA. Their model for the
"inchworm" mechanism is Velanker's PCRA monomeric helicase
They show the conformationally active loop in contact with
They did not consider a relation to hexameric helicases, and
did not comment on any structural similarity of subdomain II to
They used a DEAD box mutant.
PDB entries are 2O0H (w ATP), 2O0J (w ADP), 2O0K (apo)
Their structure appears to include the N terminal sm sub
binding domain occupying the DNA binding site and looped back
over the hinge region. This suggests a conformational
complexity whereby small terminase DNA binding is necessary to
uncover the DNA binding site on the Ploop itself.
Surtees JA, Funnell BE. 2001. The DNA binding domains of P1 ParB and
the architecture of the P1 plasmid partition complex. J. Biol. Chem.
276 (15): 12385-12394.
First 141 residues of ParB not required for interaction with
Wolcott's clinical trail was for safety. There were no
safety concerns turned up.
However, efficacy was no better than control.
FDA stuck him with a mixture of just a few phages not matched
to the infections. These infections are with multiple
strains of bacteria, so there's no wonder.
FDA is currently requiring a separate clinical trial for each
phage or mixture of phages, so that the flexible mixtures that
work on patients about to have amputations, and on patients in
Tbilisi can't really be tried in the U.S.
Regulations also specify that if phages are observed to mutate
or recombine in a clincial trial, that the trial should be
scraped, even if the mutations cause no harm.
British biotech firm Biocontrol completed phage II study
against P. aeruginosa with encouraging results.
Sycheva LV Shneider MM Sykilinda NN Ivanova MA Miroshnikov KA
Leiman PG. 2012. Crystal structure and location of
gp131 in the bacteriophage phiKZ virion. Virology
Takeda S, Arisaka F, Ishii S, and Kyogoku Y. 1990. Structural
studeis of the contractile tail sheath protein of bacteriophage
T4. 1. Conformational change of the tail sheath upon contraction
as probes by differential chemical modification. Bioch. 29:
Takeda S, Sasaki T, Ritani A, Howe
MM, Arisaka F. 1998. Discovery of the tail tube gene of
bacteriophage Mu and sequence analysis of the sheath and tube
Bkg: L, M, Y, N, P, Q, V, W, and R are tail genes by
They identified orf2 at tail tube (not one of previously named
frames) based on matching N terminal sequence of 2nd abundant
protein in Mu tail (after the sheath which is identified as
gpL. Note: T4 tail tube monomer (gp19) is also small (19
Tang L, Gilcrease EB, Casjens SR, Johnson JE. 2006. Highly
discriminatory binding of capsid-cementing proteins in bacteriophage
L. Structure 14:837-45.
Dec (aka orf134) and another protein not yet identified with a
Each bind as a homotrimer at a different place on the phage
C terminal region of Dec similar to they say 5 regions in the
long T4 tail fiber.
Tang J, Lander GC, Olia A, Li R, Casjens S, Prevelige P Jr,
Cingolani G, Baker TS, Johnson JE. 2011. Peering down
the barrel of a bacteriphage portal: The genome packaging and
release valve in P22. Structure 19:496-502. PMID 21439834.
A rendition of the internal barrel with the DNA envisioned in
the barrel and the pilot proteins envisioned in the portal.
Works over changes in the conformation of the portal.
Give list of podoviruses having the C terminal barrel on the
portal, suggesting that they are not a phylogenetic group.
The list includes T4. It was just made by running COILS on
the portal sequence.
Tétart, F., Desplats, C.,
Kutateladze, M., Monod, C., Ackermann, H.-W., Krisch, H. M.
(2001). Phylogeny of the
Major Head and Tail Genes of the
Wide-Ranging T4-Type Bacteriophages. J. Bacteriol.
Identifies T4-like phages by homology in gene 23 (capsid),
gene 18 (tail sheath), and gene 19 (tail tube).
Notes greater divergence for hosts of greater distance, but
Generally: T-even (enterobacteria, < 20% diverged), Pseudo
T-even (< 30% diverged), still mostly enterobacteria, and
Schizo T-even, other gamma proteobacteria (Aeromonas,
vibrio). <50% diverged.
Tetart F, Desplats C, Krisch HM
Genome plasticity in the distal tail fiber
locus of the T-even bacteriophage: Recombination between conserved
swaps adhesin specificity
J MOL BIOL 282 (3): 543-556 SEP 25 1998.
Describes recombining the adhesion domains among the phages
T4, T2, T3, and Ac3.
Sometimes adhesion domain is in C-terminal of tail fiber gene
(ie. T4 gene 37), and sometimes is a separate gene (ie. T2 gene
Thoma C, Borst E, Messerle M, Rieqer M, Hwang JS, Bogner E. 2006.
Identification of the interaction domain of the small terminase
subunit pUL89 with the large subunit pUL56 of human cytomegalovirus.
Thomassen E, Gielen G, Schutz M, Schoehn G, Abrahams, JP, Miller
S, and van Raaij MJ. 2003. The structure of the
receptor-binding domain of the bacteriophage T4 short tail fibre
reveals a knitted trimeric metal-binding fold. J. Mol. Biol.
Long fibers recognize ompC and/or LPS associated with ompC.
Short fibers recognize LPS.
Tremblay DM. Moineau S. Complete genomic sequence of the lytic
bacteriophage DT1 of Streptococcus
thermophilus.Virology. 255(1):63-76, 1999
Trojet SN, Caumont-Sarcos A, Perrody E, Comeau AM, Krisch
HM. 2011. The gp38 adhesins of the T4 superfamily: a
complex modular determinant of the phages's host
specificity. Genome Biol. Evol 3:674-686.
Traub, F., and Maeder, M., 1984. Formation of the prohead core of
bacteriophage T4 in vivo. J. Virol. 49:892.
Truniger V, Lazaro JM, Esteban FJ, et al. 2002. A positively
charged residue of phi 29 DNA polymerase, highly conserved in DNA
polymerases from families A and B, is involved in binding
the incoming nucleotide. Nucl. Acids Res. 30 (7): 1483-1492.
Trus, B. L., N. Q. Chen, W. W.
Newcomb, F. L. Homa, J. C. Brown, and A. C. Steven. 2004.
Structure and polymorphism of the UL6 portal protein of herpes
simplex virus type 1. J. Virol.
EM of a 12 mer ring at 16 A.
Notes 12, 13, 14mers assemble. Also notes other than 12
mers for various phages.
Somewhat problematical in terms of how it fits into the
vertex. They seem to suggest that the wide end of the phi
29 like model folds back and now occupies all of the contact
with the capsid protein, while the alpha helical shank is now
enveloped inside of that.
Turnquist S, Simon M, Egelman E, Anderson D. 1992. Supercoiled DNA
wraps around the bacteriophage phi 29 head-tail connector.
The beginning of the thread that the motor works by wrapping
DNA around the outside of the portal.
Uchiyama J, Rashel M, Maeda
Y, Takemura I, Suqihara S, Akechi K, Muraoka A, Wakiquchi H,
Matsuzaki S. 2008. Isonation and characterization of a novel
Enterococcus faecalis bacteriophage phiEF24C as a therapeutic
Microbiol Lett 278:200-6. UTHSCSA
Sequence is NC_009904;
142072 bp reported as a circular sequence but a linear genome
Has lots of similarity with StaphK, LP65, twort, phageD, etc.
A little closer to the Listeria phages A511 and P100.
Valentine AM, Ishmael FT, Shier VK, Benkovic SJ. 2001. A zinc
ribbon protein in DNA replication: Primer synthesis and
macromolecular interactions by the bacteriophage T4 primase.
BIOCHEMISTRY 40 (50): 15074-15085.
Gene 61 from bacteriophage T4.
Van de Peer Y, and De Wachter R. 1997. TREECON for Windows: a
software package for the construction and drawing of evolutionary
trees. Comput. Appl. Biosci. 10: 569-570.
A result using this program for phage phylogeny based on
multiple proteins was shown in German GJ, Misra R, and Kropinski
AM., Ch. 17, The Bacteriophages, (edited by R Calander), 2006,
Oxford Univ. Press, New York.
van der Wilk F, Dullemans AM, Verbeek M, et al. 1999. Isolation
and characterization of APSE-1, a bacteriophage infecting the
secondary endosymbiont of Acyrthosiphon pisum. Vir. 262
(1): 104-113. *
Infects a bacterial endosymbiont of an aphid.
van Regenmortel MHV, Fauquet CM, Bishop DHL, Carsetns EB, Estes MK,
Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, and Wichner
(eds.) 2000. Virus Taxonomy; Seventh report of the international
committee on taxonomy of viruses. Academic Press, New York.
Mainly a hugh compendium of different viruses giving the
criteria by which they have been classified as to order, family,
genus, and species
Opening chapter about what constitutes a species by van
Basically, if population sequence data were to exist, a
group of viruses for which the full distribution of pairwise
divergences can be recovered from the population would all be
called the same species.
The data doesn't exist to operate that definition for the
vast numer of viruses. Operationally, viruses that are
diverged beyond what one might intuit to be a population
distribution get separate species names. Gain or loss of
genes, it would appear, would necessitate a new species name;
at least in the presence of sequence divergence also.
Above the genus level, criteria are morphological.
Specifically relative to the tailed phages:
The order is Caudovirales which includes all dsDNA
The families are divided up partly on morphological
criteria, and partly on host range falling in different parts
of the biological kingdom. The major families infecting
bacteria are Myoviridae (long contractile tails,
T4-like phages could be considered the prototypical genus), Siphoviridae
(long non-contractile tails, lambda-like phages could be
considere the prototypical genus), and Podoviridae
(short non-contractile tails, T7 could be considered the
The concept of a type-genus isn't officially used, although
the concept of a type-species is central to defining genera.
The language "enough common morphological and replicative
features survive to indicate their fundamental relatedness"
applied loosely to these three families states the assumption
that at least some of the characteristic genes are related by
currently named genera are T7-like, P22-like, and
Criteria for genus status is stated to be "genome
organization, mechanisms of DNA packaging, and presence or
absence of DNA or RNA polymerase". Operationally, it
seems more like size and sharing similar genes with the type
Distinguishing properties of T7-like viruses are given as
genome being non-permuted and terminally redundant and
encoding DNA and RNA polymerase.
van Sinderen D. Karsens H. Kok J. Terpstra P. Ruiters MH. Venema G.
Nauta A. 1996. Sequence analysis and
molecular characterization of the temperate lactococcal
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Vanloock MS, Chen YJ, Yu X, Patel SS, Egelman EH. 2001. The
primase active site is on the outside of the hexameric bacteriophage
T7 gene 4 helicase-primase ring. J. Mol. Biol 311 (5): 951-956.
Bkg: T7 gene 4 is helicase/primase; makes hexameric ring,
translocates by cleaving dTTP.
Valpuesta, J.M., and Carrascosa, J.L. (1994) Structure of viral
connectors and their function in bacteriophage assembly and DNA
packaging. Q Rev Biophys 27: 107–155.
Van den Bossche A, Ceyssens PJ, De Smet J, Hendrix H, Belfon H,
Leimer N, Wagemans J, Delattre AS, Cenes W, Aertsen A, Laduyt B,
Minakhin L, Severinov K, Noben JP, Lavigne R. 2014.
Systematic identification of hypothetical bacteriophage proteins
targeting key protein complexes of Pseudomonas aeruginosa.
J. Proteome Res. 13:4446-4456. PMID 25185497.
Affinity purify known protein regulatory complexes and used
mass spec to ID phage proteins bound to them.
Villarreal LP, DeFilippis VR. (2000). A hypothesis for DNA
viruses as the origin of eukaryotic replication proteins. J.
Vir. 74 (15): 7079-7084.
Based on greater similarity of phage DNA polymerases to
eucaryotic DNA polymerases.
Villegas A, She Y-M, Kropinski AM Lingohr E Mazzocco A,Ojha S,
Waddell TE, Ackermann W, Moyles DM, Ahmed R, and Johnson RP.
The genome and proteome of a virulent Escherichia coli O157:H7
bacteriophage closely resembling Salmonella phage Felix O1.
Virol J. (2009) 6:41.
wV8; about 92% identical at nucleotide level. Made
special point about tail fiber.
Voelker LL. Dybvig K. Sequence analysis of the Mycoplasma
arthritidis bacteriophage MAV1 genome
identifies the putative virulence factor. Gene. 233(1-2):101-7, 1999
Vybiral D Takac M Loessner M Witte A von Ahsen U and Blaesi U.
Complete nucleotide sequence and molecular characterization of two
lytic Staphylococcus aureus phages: 44AHJD and P68. FEMS
Microbiol. Lett. 219 (2), 275-283 (2003).
terminal protein is gp11; says homology to other terminal
proteins not detected.
Wagemans J, Blasdel BG, Van den Bossche A, Uytterhoeven B, De Smet
J, Paeshuvse J, Cenens W, Aertsen A, Uetz P, Delattre AS, Ceyssens
PJ, Lavigne R. 2014. Functional elucidation of antibacterial
pahge ORFans targeting Pseudomonas aeruginosa. Cell Microbiol,
in press. PMID 25059764.
Characterized a bunch of early small proteins in a Pseudomonas
Waldor, M.K., and Mekalanos, J.J. (1996) Lysogenic conversion by a
filamentous phage encoding cholera toxin. Science 272,
Introduces phage CTXphi, which is filamentous. See
Waldor et al., 1997 below for specifics of integrative
Waldor MK, Rubin EJ, Pearson GDN, Kimsey H, Mekalanos JJ.
1997. Regulation, replication, and integration functions of
the Vibrio cholerae CTX phi are encoded by region RS2. Mol.
Microbiol. 24(5): 917-926.
Describes the integrative cassette in the cholera toxin
transducing filamentous phage CTXphi as consisting of 3 genes: a
replicative gene, a site specific integrase, and a repressor.
The integrase is said to not be homologous to other phage
The integrase (rstB2) is only 126 residues long, and still
doesn't match anything.
Also discusses a flanking region called RS1 that has the same
3 genes and a 4th gene in place of the virial component.
It is surrounded by TSDs as if integrated like a transposon.
Wang IN, Smith DL, Young R. (2000). Holins: The protein clocks of
bacteriophage infections. Ann Rev Microbiol. 54: 799-825.
Holins accumulate in membrane and time the release of
endolysins (which degrade peptidoglycan).
Family of over 100 members.
Regulatory interactions with other proteins.
Wang J Sattar KMA Wang CC Karam JD
Konigsberg WH Steitz TA. 1997. Crystal structure of a pol alpha
family replication DNA polymerase from bacteriophage RB69.
Cell 89:1087-1099. PMID 113889835
Weisberg RA. Gottesmann ME. Hendrix RW. Little JW. Family values in
the age of genomics: comparative analyses of
temperate bacteriophage HK022. Annual Review of Genetics.
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Westblade LF, Minakhin L, Kuznedelov K, Tackett AJ, Chang, EJ,
Mooney RA, Vvedenskaya I, Wang, QJ, Fenyo D, Rout MP, Landick R,
Chait BT, Severinov K, and Darst SA. 2008. Rapid isolation and
identification of badteriophage T4-encoded modifications of
Escherichia coli RNA polymerase: A generic method to study
bacteriophage/host interactions. J.
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Whichard JM. (2000) Bacteriophage
felix O1: Genetic characterization and Bioremedial
Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory
S, Greenberg (2001) Gene expression in Pseudomonas aeruginosa
fd like phage are induced. Phage remnants in general are
induced. rpoS (sigma factor) is suppressed. rpoS
downregulation enhances antibiotic resistance.
Wikoff WR, Conway JF, Tang J, Lee KK, Gan L, Chen N, Duda RL,
Hendrix RW, Steven AC, Jonhsn JE. 2006. Time-resolved molecular
dynamics of bacteriophage HK97 capsid maturation interpreted by
electron cryo-microscopy and X-ray crystallography. J.
Str. Biol. 153: 300-306.
Phages below 30 cm may survive over 50 years and be
reintroduced into surface layer by violent storms.
Most phages in surface layer directly produced in surface
Carbon in the form of bacteria is destined to leave the
surface layer, whereas carbon released by lysis is recycled
within surface layer.
Phages generally specific to bacteria within a bacterial
species, and usually to only one or a few strains within a
Carter,R.H. and Rothman-Denes,L.B. 2002. N4 RNA Polymerase II,
a Heterodimeric RNA Polymerase with Homology to the Single-Subunit
Family of RNA Polymerases J. Bacteriol. 184
Two genes in coliphage N4 (p7, p4) correspond to the N and C
terminal parts of T7 RNA polymerase. 2ndary struture and
motif alignments are given in the paper.
A fusion protein of the two works.
N4 is not completely sequenced, so its overall relation to T7
is difficult to ascertain.
Suggests that single chain T7 RNA polymerase may have been
created by a fusion, or vice versa.
N4 gp17 is a ssDNA binding protein required for the RNA
polymerase to function.
In earlier papers by this group: N4 is 72,000 bp linear, with
terminal repeats and variable sticky ends.
An early paper about N4 is Schito GC. The genetics and
physiology of coliphage N4. Virology. 55(1):254-65, 1973.
Wills E, Scholtes L, Baines JD. 2006. The Herpes Simplex Virus 1
DNA packaging proteins encoded by UL6, UL15, UL17, UL28, and UL33
are located on the external surface of the viral capsid. J. Vir.
Aug 18 Epub ahead of print..
Wojciak JM. Sarkar D. Landy A. Clubb RT. Arm-site binding by
lambda -integrase: solution structure
and functional characterization of its amino-terminal domain.
Proceedings of the National Academy of
Sciences of the United States of America. 99(6):3434-9, 2002.
Wommack KE, and Colwell, RR. 2000. Virioplankton: Viruses in
Aquatic Ecosystems. Microbiol. and Mol. Biol. Rev. 64:
Reviews EM studies of abundance of viral particles in seawater
with attention to temporal variation.
Give special attention to virus:bacteria rations (generally
3:1 to 10:1).
Reviews theoretical considerations about what factors may
affect the dynamics of the system.
Small bacterial have lower encounter probability, so viruses
may select for small cell volume.
Burst size is key factor for relating viral abundance to
Viral survival and repair of VU induced DNA damage are key
Notes phage-encoded DNA repair systems: T4 denV, Chlorella
virus PBCV-1 A50L, P. aeroginosa phage UNL-1.
Notes that marine bacteria usually are in stationary
phase. Describes a dynamic where viruses infect a
stationary cell and then lie latent until replication
ensues. Later gives an extensive review of
pseudolysogeny. It's not clear if they consider these
two ideas as the same thing. I get the impression that
there are experimentally determined cases of unstable lysogeny
(meaing phage gets lost without lysis), but it is not clear
why that happens..
Notes that most sampled marine viruses are species or
even strain specific, but reviews a few broad host range
Cites Ackerman HW and DuBow MS (1987; Viruses of prokaryoties:
natural gropus of bacteriphages. CRC Press, Inc. Boca Raton
Fla.) for idea that Enterobacteria are split more finely in
their classification. This artificially makes coliphage seem to
have broader host range.
Reviews consequences of lysogeny.
Runs through dynamic models. They feature a model where
host-specific phages prevent domination by any particular host
species, hence promoting bacterial diversity.
Discusses the impact of viral resistance. Whereas
Fuhrman thought there was less demonstrated than should be
there, these authors assume that it is there. So Fuhrman
sees a paradox as to why there isn't more resistance, whereas
they see a paradox as to why there is so much virus assuming
that resistance is present and maintained by selection.
These authors think that multiplicity of viruses infecting a
single host is key to overcoming resistance, but they really
don't articulate coadaption by viruses as a key to overcoming
Talks about lateral transfer, but mostly from the standpoint
of phage mediating general transduction of bacteria. They
cite lateral transfer in evolution of phage genomes, but really
don't incorporate it into their thinking.
Woods DE, Jeddeloh JA, Fritz DL, and DeShazer D. 2002. Burkholderia
thailandensis E125 harbors a temperate bacteriophage specific for
Burkholderia mallei. J. Bacteriol. 184 (14), 4003-4017
Woods L, Catalano CE.
Kinetic characterization of the GTPase activity of phage lambda
terminase: Evidence for communication between the two "NTPase"
catalytic sites of the enzyme.
BIOCHEMISTRY 38 (44): 14624-14630 NOV 2 1999.
Bkg: the small subunit of the lambda packaging enzymes is
An ATPase site is present on both large and small subunits.
This paper characterizes an additional GTPase activity.
The GTPase depends on the presence of DNA.
Wright A, Hawkins CH, Anggard EE, & Harper DR.
(2009) A controlled clinical trial of a therapeutic
bacteriophage preparation in chronic otitis due to
antibiotic-resistant Pseudomonas aeruginosa; a preliminar report of
Otolaryngology 34: 349-357.
Xiang Y, Leiman PG, Li L, Grimes S, Anderson DL, Rossmann
MG. 2009. Crystallographic insights into the autocatalytic
assembly mechanism of a bacteriophage tail spike. Mol. Cell
34:375-386. PMID 19450535.
gp12 of phi29
Has a Cterminal autochaperonin that is cleaved off during
Has separate domains to digest teichoic acid and to bind
irreversibly to cell wall.
teichoic acid binding is up on the side actually.
Cites Adams 1959 for phage first binding reversibly and later
irreversibly. Bacteriophages (New York: Wiley
Weigele et al., 2003 cited for tail spikes being homotrimers,
tripple beta helix str. and degrading cell wall glycopolymers.
For processing and release of C ter domains of other tail
Gage MJ and Robinson AS 2003. C-terminal hydrophobic
interactions play a critical role in oligomeric assembly of
the P22 tailspike trimer Protein Sci. 12:2732-2747.
Muhlenhoff M, Stummeyer K, Grove M, Sauerborn M,
Gerardy-Schahn R, 2003 Proteolytic processing and
oligomerization of bacteriophage-derived endosialidases. J.
Biol. Chem. 278? 12634-12644.
Schwarzer D, Stummeyer K, Gerardy-Schahn R, and Muhlenhoff
M. , 2007. Characterization of a novel intramolecular
chaperone domain conserved in endosialidases and otehr
bacteriphage tail spke and fiber proteins. J. Biol. Chem
75 kD gp12* cleavage cited to
Carrascosa J, Camacho A, Vinuela E, Salas M. FEBS Lett 44:
Tosi ME, Reilly Be, and Anderson DL., 1975. Morphogenesis of
bacteriophage phi29 of Bacillus subtilis: cleavage and
assembly of the neck appendage protein. J. virol. 16:
Xiang Y, Morais MC, Battisti AJ, Grimes S, Jardine PJ, Anderson
DL, Rossmann MG: 2006. Structural changes of bacteriophage phi29
upon DNA packaging and release. EMBO J 25:5229-5239. PMID 17053784.
cryoEM of mature and emptied head.
Say side fibers str. homologous to P22 side
fibers. It's in the C terminal binding domains. The
side fibers bind a bulge in the top of the lower connector. If
there is any homology to tubeA and B, lower collar must have
both A and the parts of B other than the C terminal cap.
Says two of side fibers arrayed differently, perhaps
determined by symmetry of head.
Thinks head rotates around tail on initiation of infection.
gp3 (DNA terminal protein) is lodged in the portal.
Their presentation is confusing as to whether it is in the
portal itself, in the lower connector, or moves.
Xiang Y, Rossmann MG. 2011. Structure of
bacteriophage phi29 head fibers has a supercoiled triple repeating
helix-turn-helix motif.. PNAS 108:4806-4810. PMID 21383126.
Xiao, F., Moll, D., Guo, S. & Guo, P. (2005). Binding of pRNA
to the N-terminal amino acids of connector protein of bacterial
phage phi29. Nucl. Acids Res. 33: 2640–2649.
There is a supplemental table with accession number.
On Mu the shift is -2.
Yang K, Baines JD. 2006. The putative terminase subunit of herpes
simplex virus 1 encoded by UL28 is necessary and sufficient to
mediate interaction between pUL15 and pUL33. J. Vir. 80: 5733-5739.
Yang Q, Berton N, Manning MC, Catalano CE.
Domain structure of gpNu1, a phage lambda DNA packaging protein.
BIOCHEMISTRY 38 (43): 14238-14247 OCT 26 1999.
Yakunina M Artamonova T Borukhov S Makarova KS Severinov K
Minakhin L. 2015. A non-canonical multisubunit RNA
polymerase encoded by a giant bacteriophage. Nucl. Acids
Res. 43:10411-10420. PMID 26490960.
Yang F, Forrer P, Dauter Z, Conway JF, Cheng N, Cerritelli ME,
Steven AC, Pluckthun A, Wlodawer A. 2000. Novel fold and
capsid-binding properties of the lambda-phage display platform
protein gpD. Nat. Str. Biol.7:230-237. PMID 10700283.
X-ray structure: trimer 1C5E.
They note that gpD not needed for prohead assembly. gpD-
can accommidate 80% of the normal lambda genome.
Locates it at the pseudo three fold axis.
Yoshikawa H, Garvey KJ, Ito J. 1985. Nucleotide sequence analysis
of DNA replication origins of the small Bacillus bacteriophages:
evolutionary relationships. Gene. 37:125-30.
Young R, Wang I-N, and Roof WD. 2000. Phages will out; strategies
of host cell lysis. Trends Microbiol. 8: 120-128.
Young R. Bacteriophage holins: deadly diversity. Journal of
& Biotechnology. 4(1):21-36, 2002.
Zafar, N., R. Mazumder and D. Seto (2002). "CoreGenes: A
computational tool for identifying and cataloging "core" genes in
a set of small genomes." BMC Bioinformatics3(1):
Zajanckauskaite A, Malys N, Nivinskas R. 1997. A rare type of
overlapping genes in bacteriophage T4: gene 30.3' is completely
Zhang Z, Greene B, Thuman-Commike PA, Jakana J, Prevelige PE Jr,
King J, Chiu W. (2000) Visualization of the maturation transition
in bacteriophage P22 by electron cryomicroscopy. J Mol Biol
297:615–626. PMID 10731426.
cryoEM of capsid and procapsid.
gene 30.3 by one position downstream. Gene 194: 157-162.
Zhang, F., Lemieux, S., Wu, X., St.-Arnaud, S., McMurray, C. T.,
Major, F. & Anderson, D. (1998). Function of hexameric RNA in
packaging of bacteriophage phi29 DNA in vitro. Mol.
Cell, 2, 141–147. UTHSCSA
Validates base pairing between two different loops by
compensatory mutations to the two loops.
Among other roles, T7 RNA polymerase pauses on the right end
cleavage sequence and this pause is extended by presence of
lysozyme. This presumably explains why transcription is
required for packaging in T7. This is the initiating
Although they didn't comment on it, Since gp18 (small
terminase) is known to bind the DNA prior to association with
gp19 (large terminase) in T7, it probably works by positioning
Note also that VpV262 and other phage do the T7-like packaging
but do not have a T7-like RNA polymerase. So this is a
refinement, probably replacing a more typical pac site
Zheng H, Olia AS, Gonen M, Andrews S, Cingolani G, and Gonen T.
2007. A conformational switch in bacteriophage P22 portal
protein primes genome injection. Mol. Cell. 29:376-383. UTHSCSA
Zhou ZH, Hiu WH, Shah S, Hih J, O'Connor CM, Sherman MB, Kedes DH,
Schein S. 2014. Four levels of heirarchical
organization, including noncovalent chainmail, brace the mature
tumor herpesvirus capsid against pressurization. Structure 22:
1385-1398. PMID 25220471.
Now setting links as http://ncbi.nlm.nih.gov/pubmed/[pubmed id]
Last update 12/10/2014 - Stephen C. Hardies