Literature relative to phage sequence analysis.

• 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

• 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

• 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.

•  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

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

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

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.

• 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.

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.

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.

• 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.

• 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 discrepen