Literature relative to phage sequence analysis.

Abuladze NK, Gingery M, Tsai J, Eiserling FA. 1994. Tail Length Determination in Bacteriophage T4.  Vir. 199:301-310.

• 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.

• 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

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 binding domain.

• 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).

• Cohesive ends.
• Has a ClpP protease and discussion of that function.

• Background:
• 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 viruses?
• 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 for T7?]
• 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 proteins".
• 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 elongated  trimer.
• Coiled coil pattern looks like several genes in phageD and others.
• 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, 777-810.
• See also: Del Angel, V. D., Dupuis, F., Mornon, J. P., and Callebaut, I. (2002) Biochem Biophys Res

Commun 293, 1153-1160

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 Link.

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.

• 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 foldhunter
• Jiang, W., M. L. Baker, S. J. Ludtke, and W. Chiu. 2001. Bridging the

information gap: computational tools for intermediate resolution structure
interpretation. J. Mol. Biol. 308:1033–1044.

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: 2125049

Bailly-Bechet M, Vergassola M, and Rocha E. 2007. Causes for the intriguing presence of tRNAs in phages. Genome Res. 17:1486-1495. UTHSCSA Link.

• 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.
• Secondary structure model.

• 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.

• 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

Oxidation Event. Geochimica et Cosmochimica Acta 2002, 21:3811-3826.
• His tree has cyanobacteria to gram positives at 3.0 Bya.
• Low GC at 2.7 Bya
• Strep, Listeria, Bacillus at 1.9 Bya
• Gram positives to gram negatives at 3.2 Bya
• Proteobacterial diversification at 2.7 Bya
• Gamma to alpha at 2.5 Bya
• Origin of life at 4.2 Bya
• E. coli/Salmonella 0.1 Bya, supported by a study of host evolution.
• Vibrio 0.8 bya
• Pseudomonas 1.3 Bya
• Xanthomonas 1.9 Bya
• Unfortunately does not have chloroplastic or mitochondrial endosymbiosis on the tree.
• He thinks bacteria invaded land before oxygen evolution.
• Seems problematically compressed in early periods to me, but the key problem is when was GOE.
• S.B. Hedges, J.E. Blair, M.L. Venturi, J.L. Shoe, A molecular time

scale of eukaryote evolution and the rise of complex multicellular life
BMC, Evol. Biol. 1 (2001) 4.
• Eucaryotes to eubacteria 2.7 Bya
• Mitochondria 1.8 Bya
• SB Hedges is the guy to search on for absolute rates.
• They have a web site with a calculator, but there is not much to it yet. http://www.timetree.net/

Bartel PL, Roecklein JA, SenGupta D, Fields S. 1996. A protein linkage map of Escherichia coli bacteriophage T7. Nat Genetics 12 (1): 72-77.

• By yeast 2 hybrid interaction.
• Says some genes that are overlapping frames interact.

• A short Perspective that reviews the following information:
• V. cholerae feeds on chitin, and forms biofilms on chitin-containing plankton.
• In this configuration, the bacteria are more infectious
• Chitin stimulates transformation by DNA.
• Speculate that V. vulnificans ("major cause of seafood-related fatalities") may behave similarly
• V. cholerae secretes a chitin binding protein involved in colonizing human epithelial cells.
• Chitin is most abundant polymer after cellulose, and most abundant marine polymer.

Baumann RG, Mullaney J, Black LW. 2006. Portal fusion protein constraints on function in DNA packaging of bacteriophage T4. Mol. Micro. 61: 16-32. UTHSCSA Link.

• 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 dissociate antibodies.
• 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 used.
• More info on Hoc fusions and Hoc
• Ren et al., 1997 Gene 195: 303-311
• Fokine et al., 2004, PNAS 101: 6003
• Iwasaki et al., 2000 Vir. 271: 321
• Olson et al., 2001 Vir 279:385-391
• 
  

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 Podoviridae
• The Podoviridae have terminal repeats, and may be T7 related.
• This is an alpha proteobacteria

• 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 T4.

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.

• 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.

• Reveiw
• ParA is membrane bound ATPase that osicllates in its localization with different ends of the bacterial.
• E coli parA member is minD.

• 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.

• 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: 6185695

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.  PMID: 3919187

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.

Blackburn, N. T. & Clarke, A. J. (2001). Identification of four families of peptidoglycan lytic transglycosylases. J Mol Evol
52, 78-84.

• LysG family (all pfam01464?); subfamilies: slt (pfam01464), MltC, EmtA, MltD, VfhD
• Other families: MltA (pfam03562), MltB, lambda endolysin (pfam00959, includes T4 lysozyme)
• These are mostly bacterial enzymes used to remodel the cell wall.
• 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.

• 32,172 bp
• 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 linear DNA.

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, 65-75.

• A lytic phage acquired two sequences from a chromosomal prophage.

• review
• 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.

• Siphoviridae
• 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

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 of the
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.

Brussow, H. & Desiere, F. (2001). Comparative phage genomics and the evolution of
Siphoviridae: insights from dairy phages. Mol. Microbiol. 39, 213-223.

•  lambda-, psiM2-, L5-, Sfi21-, Sfi11-, C31-, sk1- and TM4- like phages form a "supergroup".
• This fuses together 3 different groups from our phylogeny of large terminases:
• fam 2: lambda
• fam 1: Sfi21, L5, Tm4, C31, ski,
• fam 6: Sfi11, psiM2
• Emphasizes multigene modules; Often uses gene order to infer common ancestry.
• 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 deletion.
• 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 the capsid.

• Did the N terminal sequencing for phiEL

• Classic review of recombination involving lambda, P22, and phage21.
• 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%
• 131,384 bp.
• Another one in the StaphK group.
• Accession number?

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.

• Headfull sensor.

• NC_005857
• 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. 187: 1091-1104.

• 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):
• VP16T, VHML
• 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
• TP901-1, Aaphi23
• Mu-like headful
• RadMu, MuSo1, FluMu, Sp18, Mu
• 933W
• P2-like 5' extended COS ends
• K139, HP1, Fels-2, 186, L-413C, P2, XccP1, phiCTX,
• T4-like headful
• KVP40, Aeh1, RB49, T4
• Bcep22,, PBC5
• 3'-extended COS ends
• VWB, D29, L5, phiBT1, phiC31, Xp10, Meso2, CP-933N, P, V, bIL67, c2, lambdaSa2, bIL170, P008, ski, phiadh, BK5-T, Sfi19, Sfi21, A2, phiPVL, phi13, LisI6, bIL285, Clth1, lambdaSo, HK022, HK97, Clo2, lambda Ba02, phiSa2MW, phiSLT, Flex5, Ps7, phi105, phi3626, PP04, D3, phiE125, phi P27, ST64B, SfV, PY54, phiK02
• GTA headful (gene transfer agents like that in Rhodobacter capsulatus)
• Cc1, Rhodo GTA, Tum2, Bruc1
• T7-like direct terminal repeats
• SP6, phiKMV, PP03, gh-1, A1122, T7, phiYeO3-12, T3
• P22-like headful
• LP7, ST64T,L, P22, phiETA, phiO1205, Sfi11, Lj965, Cpt1, EJ1-1, phi8382.3, SPP1, PBSX, SKIN, A118, MM1, LL-H, phig1e
• APse-1, phiFlu, HK620, Sf6, phiHSIC, Plu10, ES18.

• Discussion about prophage decay.
• Table 1 supplementary material tabulates them in many baterial sequences.

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 fibers.
• 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

• Review

• 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.

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, 49-64.

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 Strain.  MICROBIOLOGY AND 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 122: 683-692.

• phi29 and optical tweasers to measure force.
• cites papers claiming either 5 or 6 terminases per capsid.
• Does kinetic measurements in combination with force measurements.
• 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 ATPase subunits.
• This is cooperativity in the strict sense:  ATP bound to one ATPase can not improve the binding of ATP to another subunit.
• 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 acts.
• 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 stroke).
• 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 cycles.
• 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 irreversible step.
• 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.

Chen, C., Sheng, S., Shao, Z. & Guo, P. (2000). A dimer as a building block in assembling RNA. A hexamer that gears bacterial virus phi29 DNA translocating
machinery. J. Biol. Chem. 275, 17510–17516. UTHSCSA Link.

• show dimer, tetramer, hexamer pathway of assembly.
• Made two kinds of covalently fused dimers and recovered about 1% packaging activity.

• 47,872 bp Podovirus
• T7 like genes:
• RNA polymerase
• primase-helicase
• DNA polymerase
• T7 tail poteins
• packaging protein split in two?
• portal protein
• SIO1 genes:
• gp7
• Some metabolic genes derived from cyanobacteria (how close really?)
• 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 substitution.
• Fig. 3 has T7, phiYeO3-12, and SIO1 rearranged beyond recognition.

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

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. 186:3677-3686.

• Review
• Describes ecology of phages in marine environment, soil, and in industrial fermentation.
• Describes some examples of polyvalency (infecting more than one species).
• Describes lysogenic conversion.
• Reference to abi (abortive infection systems) for resisting infections.
• Shows prototypical electron micrographs of podo, myo, and siphoviruses.

• 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, however.
• 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. 186: 7069-7083.

• For comparison, they note a preliminary version of SPO1 at http://pbi.bio.pitt.edu.
• 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 circular stage?
• 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.

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?)
• c6a
• 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.

• 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.
• CAA59475; NP112664
• 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 pfam02796.
• 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.

• 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.

• PBS2 is a clear plaque mutant of PBS1.
• Rifampicin resistant RNA synthesis occurs after PBS2 infection.
• 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 48 Kdal
• Growth was rifampicin resistant from outset, so polymerase may be in capsid.

• 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 recombination.

• 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 mutation
• 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 genes.
• Touches on phage bacterial coevolution as a generator of functions and diversity some of which becomes fixed into bacterial genomes.

• Talks about hyperplastic regions, hyperplascicity of tail fibers, and internal proteins that are injected to alter the host.
• 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 tail length.
• 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 really variable.
• 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 related genes.

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 27: 744-748.

• 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.

• bIL170 = AF009630; bIL120=AY054975; bIL15=AY054976; bIL191=AY054977; bIL77=AY054978
• 31754 bp, cohesive ends.
• Siphoviridae: 3 groups in Lactococcus: c2, 936, and P335 (contains termperate members)..
• Other completely sequenced 936 group member is ski; 84% nt identity.
• 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 fiber genes.
• 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 subtype
• 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.

• ParA ATPase activity is stimulated by ParB.
• ATP binding stimulates binding of ParA to the promoters it regulates. ATP hydrolysis inhibits DNA binding.

• 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 189, 21-30.

• 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 residue.
• 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, and EF-Tu.
• 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 Streptococcus thermophilus
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 Sfi21.Virology. 260(2):244-53.

Says gene map similar to lambda phage is absence of sequence similarity.

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 (sfi11)
• Lj928
• Lj771
• Defines two pac site clades in gram positives:
• Lj965/S. thermophilus phage Sfi11/Lactococcus lactis phage TP901-1
• Lactobacillus

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 undetectable.
• 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.

• 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
• High GC gram positives are: Corynebacterium, Arthrobacter, Propionibacterium, Mycobacterium, Streptomyces, Actinomyces.
• 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, c2, rlt.
• 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.

Addes the exo-T evens to the schizo T-evens, etc.

• Colocalize in the nucleus.

• A suicide defense system; is this a natural system? *

• T7-like, but with a 5 kb novel segment.
• 43,769 bp
• Has a format of diagram that coordinates 5 member unrooted trees along the genome and points out where T7/T3/phiYeO recombination occcurred.
• Cites a temperate version of t7 in Psuedomonas Putida (Nelson et al., Env. Microbiol. 4:799-808.
• Has replicative direction mapped by skew.

Duda RL, Martincic K, and Hendrix RW. 1995. Genetic basis of bacteriophage HK97 prohead assembly. J. Mol. Biol. 247: 636-647.

• Describes the crosslinking of the capsid protein, and marks a crosslink site in the capsid protein.
• Marks the major capsid protein cleavage site after K103.

• SPO1 and herpes have T=16 capsids, whereas Most tailed phages have T=25.
• Some cryo EM shown.

Duffy C. Feiss M. 2002. The Large Subunit of Bacteriophage lambda's Terminase Plays a Role in DNA
Translocation and Packaging Termination. J. Mol. Biol. 316(3):547-61.

• G18E disrupts small terminase interaction site.
• K76R in P loop; no packaging
• N166Y was inefficient in all aspects of terminase function; located in alpha 3
• R225H (alpha 5), T328I and D349G (hinge) package and cleave, but fail to complete assembly.  DNA remains DNAse sensitive.
• L180F in DExx box; stalls
• G191S DExx loop; no packaging
• T194M DExx loop; slow
• G212S adjacent to sensor residue; stalls

Duplessis M, Moineau S . 2001. Identification of a genetic determinant responsible for host specificity in Streptococcus thermophilus bacteriophages. Mol. Micro. 41 (2): 325-336.

• In the C-terminal region of the ~850 collagen-like repeat containing fibers.  Actually about 150 residues that is about 100 residues removed from the C terminus.
• orf18 of DT1 is prototype.
• These are gram positives.
• Background cited:
• For T4 it's the C ter of orf37
• For lambda J it's the 249 C terminal amino acids
• Host specificity domain also called "anti receptor" domain.

Duplessis M, Russell WM, Romero DA, Moineau S. 2005. Global gene expression analysis of two Streptococcus thermophilus bacteriophages using DNA microarray.  Vir. 340: 192-208.

• Did DT1 (cos) and 2972 (pac).
• Comparted to existing data from Sfi19 and 21.
• There are some switches between middle and late for certain modules, and between early and middle.

Ebersbach G, Gerdes K. 2001. The double par locus of virulence factor pB171: DNA segregation is correlated with oscillation of ParA. PNAS 98 (26): 15078-15083.

• Shows evidence that oscillation is relevant.

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.

• Siphovirus
• Cryo EM on T5 head
• Similar to HK97 and T4
• Has a head decoration protein on each hexamer. pb10, 164 residues.
• 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 coiled coil.
• Thinks the delta domain controls the geometry (T number)
• 10,160 bp direct repeats.

• T7 DNA enters relatively slowly and this partially controls gene expression.
• 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.

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 Link.

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.
• No trees
• 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.

• 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 domains.
• 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.

• Aka lysostaphin-type enzymes, metalloendopeptidases that cleave the pentaglycine crossbridge.
• Cellular ones secreted as proenzymes that require cleavage for activation.
• Different domains attached to different enzymes
• They solved more structures at different pH's and with substrate analogues.

• Good reference for structure of gram positive lysins.

• 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 device.
• Other than capsid protein, does not identify any other genes with the cryoEM densities.

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 Link.

• 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 structural connections.
• 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 portal. 
  
• 
  

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. 2006. The origin of viruses and their possible roles in major evolutionary transitions.  Virus Research 117: 5-16.  UTHSCSA Link.

• Reviews previous commentary on viruses before cells, viruses from degenerated cells, and viruses from escaping cellular genes.
• 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.

• EV3
• 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 pol I.
• 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).

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'.

• Review
• Virus count exceeds bacteria count by 2-5 in all segments of marine environment.
• 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 marine environment.
• 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 affect.
• 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 lysogens.
• 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.

• 20484 partial sequence, AB161975 (nearly full length); aka bacteriophage WOcauB1
• 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 putative transposase.
• Has lambda-like head structure and identifiable baseplate and tail genes.
• 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.

• Mutants trap the HK97 capsid expansion in an intermediate state.

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.

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), 5700-5705.

• A larger segment of sequence is reported in BX571876, attributed to Bourhy,P., Frangeul,L., Glaser,P. and Saint Girons,I., unpublished.

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.

• Review
• 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.

• 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: 8: 62-67.
• 
  

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 link.

• Called pRNA
• First 120 of 174 nt essential for packaging.

• By immuno gold staining, gpV is tail spike (a short central tip to the tail), and gpJ is exposed at the periphery of the baseplate.

• 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 inserted.

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 background
• RecT becomes required if in RecA- background.
• Discusses idea that restriction modification systems are selfish gene systems, and exhibit selfish molecular drive during horizontal transfer.
• Cites numbers of strategies used by phages to avoid restriction systems.

• 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 mutagenesis.
• Y46 and K84 interact with 8-aza-ATP.  Mutagenesis kills ATPase.

• 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 cleavage.
• 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 bacteriocides.
• 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 marine environment.Virology 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.

• 6-7 cryptic phages.
• Thinks from codon usage that the phages are recent horizontal transfers.
• 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?

• Deleted T7 lysozyme and observed the muramidase in internal protein p16 to become modified to compensate.

• 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.

The original rotating portal observation.

• 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 eucaryotic.
• 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.

Hendrix R.W. (1998) Bacteriophage DNA Packaging: RNA Gears in a DNA Transport Machine. Cell 94:147-150. UTHSCSA link.

• 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.

Hendrix RW. Lawrence JG. Hatfull GF. Casjens S. 2000, The origins and ongoing evolution of viruses. Trends in Microbiology. 8(11):504-8.

• 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 them.
• 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.
• Calls the model "moron accretion".

Hendrix RW. Smith MC. Burns RN. Ford ME. Hatfull GF. 1999. Evolutionary relationships among diverse bacteriophages
and prophages: all the world's a phage.  Proceedings of the National Academy of Sciences of the United
States of America. 96(5):2192-7. UI: 99162580.  UTHSCSA Link.

Strongly features the statement that phage do not have equal access to the pool.  They clarify this as an issue of host range.

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.

• phage phiEL
• 1/3 of gene matched to phiKZ, but only 14 identified with a homologue of known function.
• Myoviridae
• Says is first with a groEL
• At NCBI is NC_007623, and AJ697969
• 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, 605-622.

• 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.

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): 9557-9562.

• Crystal structure.
• OB fold.
• C terminal flexible acidic region - may be for T7 polymerase or primase/helicase interaction.

Hoskisson PA, and Smith MCM. (2007) Hypervariation and phase variation in the bacteriophage 'resistome'.  Curr. Opin. in Microbiol. 10:396-400. UTHSCSA Link.

• Reviews phage resistance mechanisms, including 22 abi systems that cause cells to commit suicide.
• Many phage resistance determinants are carried on plasmids.

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 Link.

• Bkg:
• 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-

775
• 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 ATPase
• 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 activity.
• 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 322: 253-263.

• 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?

• 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 struture; hexamer.
• 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.
• terminases
• 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 group.
• 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.

• 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 domain).
• But some examples with no associated large primase subunit are known.
• 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 replication (RCR)

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 strategies.
• 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).

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 apparatus  NATURE 439 (7076): 612-616. UTHSCSA Link.

• 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.

 

 
 
 

John van der Oost, Matthijs M. Jore, Edze R. Westra, Magnus Lundgren and Stan J. J. Brouns. 2009. CRISPR- based adaptive and heritable immunity in prokaryotes.
PMID: 19646880

• Rotem Sorek, Victor Kunin and Philip Hugenholtz. 2008. CRISPR- a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature PMID: 18157154


Juhala RJ. Ford ME. Duda RL. Youlton A. Hatfull GF. Hendrix RW. 2000.  Genomic sequences of bacteriophages HK97

• 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.

• Temperate; 42.5 Kb

• P4 is the packaging ATPase from phi6 and related ds RNA bacteriophages.

• 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.

Kanamaur S, Kondabaqil K, Rossmann MG, Rao VB. 2004. The functional domains of bacteriophage T4 terminase. J. Biol. Chem. 279: 40795-40801.

• Separated N and C terminal domains.
• Only found ATPase in N terminal domain.
• Domains inhibit packaging by full length terminase.
• They depict the terminase as a pentamer, but say this is arbitrary.
• 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 215(1):57-67, 1998

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 frequent.
• T4 transcription pauses because of the modified DNA.  Somehow this prevents alc termination of T4 transcription.

Kazmierczak KM, Davydova EK, Mustaev AA, Rothman-Denes LB. 2002. The phage N4 virion RNA polymerase catalytic domain is related to single-subunit RNA polymerases.  EMBO 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 phage.

• Mutants made in this paper discussed further in Morita et al.

• 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.
• Nucleotide entry is AB091475.
• 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 similar function.
• The PghP gene itself matches the next gene in phageD at 85% similarity, establishing recent transfer of a capsular degrading cassette.

• 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 of print.

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
baseplate. Nat. Str. Biol. 10, 688–693.  UTHSCSA link.

• 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 triggering.
• Cites evidence that attachment of gp12 requires prior attachment of gp11.
• 
  

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:
• Missing 0.3, 0.5, 0.7, 1.5, 4.2, 4.7, 5.3, 5.5, 17
• 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 stricto.  why?

Kropinski AM. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J BACTERIOL 182 (21): 6066-6074 NOV 2000.*

• temperate.
• similar to lambda phages.

• 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.
  

• By restriction analysis and some immunoblotting.

Kuebler D, Rao VB. 1998. Functional analysis of the DNA-packaging/terminase protein gp17 from bacteriophage T4. J. Mol. Biol. 281: 803-814. UTHSCSA Link.

• H436R, and other mutants at H436 kill both the endonuclease activity and the ability to package mature T4 DNA, (which does not require the endo activity).
• FYI: H436 is at the beginning of alpha a in the ruvC fold.

Kurochkina LP, Vishnevskiy AY, Zhemaeva LV, Sykilinda NN, Strelkov SV, Mesyanzhinov VV.2006.  Structure, stability, and biological activity of bacteriophage T4 gene product 9 probed with mutagenesis and monoclonal antibodies. J Struct Biol. 2006 May;154(2):122-9.

• study of gp9, which connects to the long tail fibers.

• As bkg: T7, T4, E. coli (dnaG) primases all have zinc fingers and recognize 3'-CTG, T(C/T)G, and GTC, respectively.
• They swapped zinc fingers but the chimeras recognized yet again other sequences, so zinc finger is not only determinant.

• Summary of the state of understanding of the T4 genome as of 1995.
• Commonly used reference to the complete sequence of T4.
• See Miller et al., 2003.

• "Proteome" just means gene predictions.  They did not do proteomics.
• PT1028, 66, 44AHJD, P68 in 15-18kb range, and presumably phi29-like?
• 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 other.
• 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" the ends.
• 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.

• They think the DNA ends up wrapped around the portal complex on the inside.

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.

• 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 5):1055-67. *

Lazarevic,V., Soldo,B., 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.
• Note: SPBetac2 is a live inducible prophage.
• NC_001884.

• Meeting abstract, apparently not on line.

Lee TJ, Guo PX. 2006. Interaction of gp16 with pRNA and DNA for genome packaging by the motor of bacterial virus phi29
J. Mol. Biol. 356: 589-599. UTHSCSA LINK.

• Summarize their model as torque on a bolt.
• gp16 binds DNA nonspecifically.
• gp16 binds procapsid with pRNA more tightly than just procapsid.
• They have gp16 as the DNA contacting component of the motor.
• They are saying 5 or 6 for the radial symmetry.
• They give references to the argument that pRNA is a hexamer.

• 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 subunit.

• Shown as six dimers distributed underneath the outer layer of baseplate proteins.
• 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 host.  Cell 118: 419-429.

• Bkg:
• 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 sheath.
• 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 fibers.
• 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 tail "pins".
• 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).
• Arisaka et al, 1990. Biochemistry 29: 5057-5062
• Takeda et al., 1990. Biochemistry 29: 5050-5056.

• gp10, 11, 12 are structurally similar.

• Review of injection problem.
• 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 assembly.
• 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.

Lisal J, Tuma R. 2005. Cooperative Mechanism of RNA Packaging Motor.J. Biol. Chem. 280: 23157-23164.  UTHSCSA link.

• The kinetic model in support of structural work reported in Mancini et al. Cell 118: 744-755.
• phi 12
• 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 link.

• bacteriophage P12.
• 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.

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 L-alanoyl-D-glutamate peptidases.
• Applied exogenously, they appear to specifically lyse Listeria, which is attributed to other domains in the protein.

X91069

Recognized as a myovirus.

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.

• temperate, 40.8Kb.
• terminally redundant, and circularly permuted.
• Extensive homologies to the other lamda-like phage.

• Reveiw:
• 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 binding domains.
• 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.

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
61, 4348-4356.

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 temperate.
• 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 group.
• Proposes that lytic phages are "selfish" spinnoffs of temperate phages.

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), 1259-1271.

• 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

• 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 tail attachment.
• 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.

Lysenko EA, Kusnetsov VV. 2005. Plastid RNA polymerases. Mol. Biol. 39 (5): 762-775.

• Review
• Has a tree, but top sections not resolved.

Maluf NK, and Feiss M. (2006). MicroCommentary: Virus DNA translocation: progress towards a first ascent of Mount Pretty Difficult.  Mol. Micro. 61:1-4.

• Commentary on Baumann et al., 2006 experiment tethering portal to the capsid in T4.

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 efficient.
• gp55 residues 111-136.

• 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 pathogenicity).
• 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 oligosaccharide).
• There are also modifications by acetylation of the O antigen.
• 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 Link.

• gpO (scaffold), gpN (capsid) and gpQ (portal) are all cleaved.
• As of this paper, they do not recognize that gpO is also a protease.
• 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 sequenced.

• 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.
  

• Vibrio T4-like phages were KVP20, KVP40, and nt-1.
• Aeromonas phages were Aeh1 and phage 65.
• Gave dendogram
• Gave N terminal sequence determination on mature virion proteins.

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

• temperate.
• host is Mycobacterium smegmatis.
• Structural genes weakly related to mycobacteriophages L5 and D29.
• Different integration cassette.

• 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) is described.
• 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 apparatus.
• 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 terminase elsewhere)
• Their discussion of packaging mainly describes the rotary motor model.
• there is nothing called small terminase.  There is no cleavage involved, since the DNA does not replicate to form a concatemer.
• 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 from exiting.
• 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 origin)
• peptidases
• transglycosylases

• At 280334 bp, it takes over from T4 as the largest phage completely sequenced.
• 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 mobile introns??
• 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).
• Says genome terminally redundant "like T4".

• Current best overall reference for T4 genome and gene properties.
• Mentions compact frame organization, overlapping start and stop codons, and more extensively overlapping genes.

• T4 like.
• 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.

• Apparently all from Pseudomonas, although can establish a "carrier" state (nonlytic but produces virus) in Escherichia and Salmonella.
• There were several "close" relatives (primed with same end PCR primers) and 3 "distant" relatives promised to be reported upon later.
• 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 preformed structure.
• 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 virion.
• 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 stabilization.
• 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.

• SopEphi
• What is terminase gene?

MIKKONEN M, ALATOSSAVA T.
CHARACTERIZATION OF THE GENOME REGION ENCODING STRUCTURAL PROTEINS OF  LACTOBACILLUS-DELBRUECKII SUBSP LACTIS BACTERIOPHAGE-LL-H.
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 terminase.

Mitchell MS, Rao VB. 2004. Novel and deviant Walker A ATP-binding motifs in bacteriophage large terminase-DNA packaging proteins. Virology 321: 217-221.

Mitchell MS, Rao VB 2006. Functional analysis of the bacteriophage T4 DNA-packaging ATPase motor.  J Biol Chem. 2006 Jan 6;281(1):518-27.

• Mutagenesis around the DExx box.

• 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 density.
• Overexpression of SltY complements.

• About injection mechanisms.

• 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 motors. Current
Biology. 12(3):R96-8, 2002

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

• 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.

• 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 pentamer.

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.

Morita M, Tasaka M, Fujisawa H. 1994. Analysis of functional domains of the packaging proteins of bacgteiophage T3 by site-directed mutagenesis. J. Mol. Biol. 235: 248-259.  UTHSCSA Link.

• Bkg:
• gp18 is small terminase; gp19 is large terminase
• 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.
• 
  
• in gp19
• 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
• 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 has Q,
• 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 degraded Km.
• K64T
• 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.
• H344D
• 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 is precluded.
• 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.
• H347R
• 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.

• A review of the 454, Solixa, Solid, and Helicos methods as of 2008.
  

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 268(5):840-56.

• 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.
• 
  

Mullaney JM, Thompson RB, Gryczynski Z, Black LW. 2000. Green fluorescent protein as a probe of rotational mobility within bacteriophage T4.
J Virol Methods.  88(1):35-40.

• Measured mobility inside the phage head.

• phi P27

• Sequence was determined.
• temperate.
• Two genes lukS-PV, lukF-PV, make a toxin virulance factor in Staph infections.
• 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:

87-89).
• Shiga-like toxins in Escherichia coli (Scotland Lancet ii, p. 216; and O'Brian et al. 1984; Science 226: 694-696).
• 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 filamentous phage.)

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. 75:10923–10932.  UTHSCSA Link.

• 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.

• Cited as suggesting modules can be single genes.

Nolan JM, Petrov V, Bertrand C, Krisch HM, Karam JD.  2006. Genetic diversity among five T4-like bacteriophages. Virol J. 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% identity.

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.

Oakey HJ Cullen BR and Owens L. 2002. The complete nucleotide sequence of the Vibrio harveyi
 bacteriophage VHML. J. Appl. Microbiol. 93 (6), 1089-1098.

• NC_004456,  43198 bp; Myoviridae

• 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: 2862-2871.

• 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 cargo.
• 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.

• Phage bxb1 integrates in groEL1 making lysogens unable to make biofilm.
• 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 mycobacteria.
• How is cell wall related to biofilm elaboration?

• by cryoEM the portal is pretty clearly 13 fold.  In a later paper, they say that portal is a 12 mer in the capsid, and the 13 mer only forms if it oligomerized free of the capsid.
• 35 A pore, narrow part of channel is towards the tail.
• They speak of "tenticals" in the pore approaching the DNA in the capsid side of the channel
• They cite for the portal being the headful sensor:
• Streisinger G, Emrich J, and Stahl MM. PNAS 57: 292-295 (1967)
• Tye BK, Huberman JA, and Botstein DJ. JMB 85: 501-532 (1974)
• 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 headfuls.
• Has smaller tenticals

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  148: 1539-1550.

• 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 pathway.

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. 46: 239-249.

Parker ML, Eiserling FA. 1983. Bacteriophage SPO1 Structure and Morphogenesis. II. Head Structure and DNA Size. J. Vir. 46: 250-259.

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
• Head proteins:
• 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
• Tail
• 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
• Neck
• 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
• Baseplate
• 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

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 276:315-328.

• 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. 113(2):171-82, 2003.

• 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. 199(1-2):157-63, 1997.

Petrov VM, and Karam JD. 2004. Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages.  Biochem. (Mosc.) 69: 1489-1496. UTHSCSA Link

• 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 finger region.
• 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).

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.

• Bkg:
• 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 AlgQ.
• Though MotA homologue in KVP40 not yet identified, MotA itself activates KVP40 promoters in an analogous fashion.

• General review

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.

• RAP401
• What is terminase gene in our alignment?

• 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 Link.

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 infection.
• Reviews cultured host-virus systems
• Reviews cyanobacterial phages and viruses infecting eukaryotic phytoplankton
• Whereas others propose that most marine viruses are bacteriophages, Proctor argues for a more substantial eukaryotic virus component.
• Advocates molecular characterization, meaning protein gels and Southern blots.  Not a word is devoted to DNA sequence.

• 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 helix domain.

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: 9613–9621.

• Lethal (non complementing) mutants made a conserved places: L120N, Q205E, G263A, Y285S, but the mutants did associate with the capsid.
• 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.
• Bkg:
• 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.

• A highly mathematical approach to forces in the capsid.

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.

• 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.
• See also pp 121-134.

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): 401-411.

Rao VB & Feiss M. 2008.  The bacteriphage DNA packaging motor.  Ann. Rev. Genet. 42: 647-681. PMID: 18687036 UTHSCSA Link.

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 306: 1344-1350.

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.

• has lots of stuff apparently derived from plasmids.
• They argue for "a much greater diversity of [phage] genomic architectures than was previously recognized".

Ren Z, Black LW. 1998. Phage T4 SOC and HOC display of biologically active, full-length proteins on the viral capsid.
Gene. 1998 Jul 30;215(2):439-44.

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 Link.

• 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 termination cutting.
• Refer to K. Kondabagilu & V.B.R., unpublished data). for R406 mutagenesis.
• 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.

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. 40(45):13583-91, 2001

Rohwer F, 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 unidentified function.
• vpv262 shares the inversion of the presumed late transcription unit relative to the replicative transcription unit.
• 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 Link.

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 mitomycin C.
• Circularly permuted.
• Head cassette like Lj965; tail cassette like PBSX; others noted most similar to DT1/Sfi11 or phiSF370.3

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 space.
• 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 arrangement?).

Savva CGW, Holzenburg A., Bogner. 2004. Insights into the structure of human cytomegalovirus large terminase subunit pUL56. FEBS 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 complex.
• 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.

• As bgk gives that primers are pppACC(C/A) and pppACAC from 3'-CTGG(G/T)-5' and 3'-CTGTG-5'.

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.

• An update of the Serwer osmotic pump model.

Shibata H, Fujisawa H, and Minagawa T. 1987. Early events in DNA packaging in a defined in vitro system of bacteriophage T3. Vir. 159:250-258.

• 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.
• 
  

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.

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. 108–113.

• 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.

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. NATURE 408:745-750.

• 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.

• Crystal structure of the phi29 portal protein.
• Wide end inside mostly made of beta sheet and has the C terminus.
• Long 3 helix region inapproximately coiled coil configuration composed of the N terminus, and an out and back excursion of the chain.
• The part exposed at the portal opening is a simple hook out and back.
• 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.
• PDB 1ijg.
• 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 genes.
• Lengths run from 6..51 repeats.
• Most impressive example given is phage 933W.
• PRD1 (E. coli) has short example in non tail fiber gene.
• 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 proline hydroxylation.
• 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.

• 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.

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.

• Mutants with gene 1 out of place evolve to partially recover fitness.

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 protein.

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 246:329-340.

• First 11.5 kb of a 12.4 kb terminal redundancy is called host takeover module.
• 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

• 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.

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 Link.

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 11):1652-4, 2001

Sugden A, Stone R, and Ash C. 2004. Ecology in the Underworld. Science 304:1613.

• 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 mentioned.

• 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 applied.
• Cites additional reviews:
• Alisky J et al., J. Infect. 36:5-15 (1999).
• Barrow PA, and Soothill JS, Trends Microbiol. 7: 268-271 (1997).
• Calrton RM. Arch Immunol. Ther. Exp. 5:267-274. (1999).
• For history of subject: Summers WC, Felix d'Herelle and the origins of molecular biology. Yale Univ. Press., (1999). posted at (http://www.evergreen.edu/user/t4/phagetherapy/phagethra.html).
• 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 Europe.
• 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, 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. 340: 49-65.

• Myovirus
• 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 linked domain..
• 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: 799-825.
• 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.
• 
  

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 Link

• 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 model.
• They show the conformationally active loop in contact with subdomain II.
• They did not consider a relation to hexameric helicases, and did not comment on any structural similarity of subdomain II to anything.
• 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.

• First 141 residues of ParB not required for interaction with ParS.
• Model for how ParB dimer binds ParS.

• 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.

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: 5050-5056.

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 genes.  BBA 1399:88-92.

• Bkg: L, M, Y, N, P, Q, V, W, and R are tail genes by mutagenesis.
• 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 Kd).

• Dec (aka orf134) and another protein not yet identified with a phage gene.
• Each bind as a homotrimer at a different place on the phage surface.
• C terminal region of Dec similar to they say 5 regions in the long T4 tail fiber.

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. 183: 358-366.

• 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 some chimeras.
• 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.

• 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 38).

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. 331:361-373.

• 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

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. 78:12668–12671. UTHSCSA Link.

• 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.

• 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 candidate. FEMS Microbiol Lett 278:200-6. UTHSCSA Link.

• 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.

• 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.

• 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 Regenmortel.
• 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 viruses.
• 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 prototypical genus).
• 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 descent.
• For Podoviridae:
• currently named genera are T7-like, P22-like, and phi29-like.
• 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 species.
• Distinguishing properties of T7-like viruses are given as genome being non-permuted and terminally redundant and encoding DNA and RNA polymerase.

Vander Byl C, Kropinski AM. 2000. Sequence of the genome of Salmonella bacteriophage P22. J. Bact. 182 (22): 6472-6481. UTHSCSA Link.

• temperate.

sequences mostly similar to other phages.

• 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.

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.

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).

• phi29-like phages
• terminal protein is gp11; says homology to other terminal proteins not detected.

• Introduces phage CTXphi, which is filamentous.  See Waldor et al., 1997 below for specifics of integrative mechanism.

• 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 integrases.
• 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.

• Holins accumulate in membrane and time the release of endolysins (which degrade peptidoglycan).
• Family of over 100 members.
• Regulatory interactions with other proteins.

• Review

Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg (2001) Gene expression in Pseudomonas aeruginosa biofilms. Nature 413: 860-864.

• 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.

Wilhelm SW and Suttle CA. 1999. Viruses and nutrient cycles in the sea. Biosience 49: 781-788.

• Review.
• 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 layer.
• 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 species.

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: 69-114.

• 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 host mortality.
• Viral survival and repair of VU induced DNA damage are key factors.
• 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 viruses.
• 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 resistance.
• 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.

• phi-E125

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 gpNu1.
• 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.

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.

Xu J, Hendrix RW, Duda RL. 2004. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell. 16:11-21.

• Bkg:
• In lambda gp GT is encoded including a -1 frameshift.  This is a tail assembly gene not found in final structure.
• In XXXYYYZ (Y is either an A or a T), slips back -1 to put YYY in frame.
• Found it in other phages, in modular context between major tail protein and tape measure.
• Verified for HK97, HK022, Mu, L5, TM4, and phiC31
• Predicted for: P2, SPP1, PBSX, psiM2, TP901-1, rlt, c2, phich1, phi105, PSA, SfV, phihalo1 pro, F pyocin, PVL, 01205, Sfi19, L10, HP1, Yersinia lambda, DeiPro, Borreliapro,
• There is a supplemental table with accession number.
• On Mu the shift is -2.

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.

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.  PMID: 3932129

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 Molecular Microbiology
& Biotechnology. 4(1):21-36, 2002.

Zajanckauskaite A, Malys N, Nivinskas R. 1997. A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within 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 Link.

• Validates base pairing between two different loops by compensatory mutations to the two loops.
• Sys sees a hexamer by ultracentrifugation.

• 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 packaging event.
• 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 gp18.
• 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 mechanism.

Now setting links as http://ncbi.nlm.nih.gov/pubmed/[pubmed id]
Last update 04/30/2009 - Stephen C. Hardies

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