Literature relative to phage sequence analysis.

This page is a gathering point for links from our phage sequence database system into the literature. We accumulate various notes here about the contents of papers that we have had reason to refer to from inside the database system. This page is not intended to be a comprehensive review of phage literature, although if it is helpful to anyone, they are welcome to use it. -- Stephen C. Hardies

Abbasifar R, Griffiths MW, Sabour PM, Ackermann HW, Vandersteegen K, Lavigne R, Noben JP, Alanis Villa A, Abbasifar A, Nash JH, Kropinksi AM.  2014.  Supersize me: Cronobacter sakazakii phage GAP32.  Vir. 460-461: 138-146.  PMID 25010279.

Abrescla NGA Cockburn JJB Grimes JM Sutton GC Dipros JM Butcher SJ Fuller SD San Martin C Burnett RM Stuart DI Bamford DH Bamford JKH. Insights into assembly from structural analysis of bacteriophage PRD1.  Nature 432:68-74.
Abrescia NG, Bamford DH, Grimes JM, and Stuart DI. 2012. Structure unifies the viral universe Annu. Rev. Biochem 81: 796-822. PMID 22482909.

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

Adriaenssens EM Ackermann H-W Anany H Blasdel B Connerton IF Goulding D Griffiths MW Hooton SP Kutter EM Kropinski AM Lee J-H Maes M Pickard D Ryu S Sepehrizadeh Z Shahrbabak SS Toribio AL Lavigne R.  (2012) A suggested new bacteriophage genus: "Viunalikevirus".  Arch Virol 157:2035-2046. PMID 22707403.

Agirrezabala X, Martin-Benito J, Caston JR, Miranda R, Valpuesta M, and Carrascosa JL. 2005. Maturation of phage T7 involves structural modification of both shell and inner core components.  EMBO J. Agirrezabala, X., Martin-Benito, J., Valle, M., Gonzalez, J.M., Valencia, A., Valpuesta, J.M., and Carrascosa, J.L. (2005) Structure of the connector of bacteriophage T7 at 8A resolution: structural  homologies of a basic component of a DNA translocating machinery. J Mol Biol 347: 895–902.

Aksyuk AA, Leiman PG, Shneider MM, Mesyanzhinov VV, Rossmann MG.  2009.  The structure of gene product 6 of bacteriphage T4, the hinge-pin of the baseplate. Structure 17: 800-808

Akita F, Chong KT, Tanaka H, Yamashita E, Miyazaki N, Nakaishi Y, Suzuld M, Namba K, Ono Y, Tsukihara T, and Nakagawa A. 2007.  the crstal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosius provides insight into the evolution of viruses.  J. Mol. Biol. 268: 1469-1483. PMID 17397865.

Aksyuk AA, Leiman PG, Kurochkina LP, Shneider MM, Kostyuchenko VA, Mesyanzhinov VV, Rossman MG. 2009. The tail sheath structure of bacteriphage T4: a molecular machine for infecting bacteria. EMBO J. 28:821-9.

Aksyuk AA, Bowman VD, Kaufmann , Fields C, Klose T, Holdawayt HA,.Fischetti VA, Rossmann MG. 2012.  Structural investigation sof a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry.  PNAS 109:14001-14006. PMID 22891295.

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.

Allison GE. Angeles D. Tran-Dinh N. Verma NK. 2002.  Complete Genomic Sequence of SfV, a Serotype-Converting Temperate Bacteriophage of Shigella flexneri. J.Bact.184:1974-87. Altermann, E., Klein, J. R. & Henrich, B. (1999). Primary structure and features of the genome of the Lactobacillus
gasseri temperate bacteriophage phi adh. Gene 236; 333-346. Andrews D, Butler JS, Al-Bassam J, Joss L, Winn-Stapley DA, Casjens S, and Cin golani G. 2004. Bacteriophage P22 tail accessory factor GP26 is a long triple-stranded coiled-coil.  J. Biol. Chem. Dec. 27 in press. Aravind, L., Makarova, K. S. & Koonin, E. V. (2000). Survey and summary. Holliday junction
resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary
trajectories. Nucleic Acids Res 28, 3417-3432.

Arisaka F, Takeda S, Funane K, Nishijima N, and Ishii S. 1990. Structural studies of the contractile tail sheath protein of bacteriophage T4. 2. Structural analyses of the tail sheath protein, gp18, by limited proteolysis, immunoblotting and immunoelectron microscopy. Biochemistry 29: 5057-5062. UTHSCSA Link.

Atanasova NS, Sencilo A, Peitila MK, Roine E, Oksanen HM, Bamford DH.  2015.  Comparison of lipid-containing bacterial and archael viruses.  Adv Virus Res.  92:1-61.

Autret S, Nair R, Errington J. 2001. Genetic analysis of the chromosome segregation protein Spo0J of Bacillus subtilis: evidence for separate domains involved in DNA binding and interactions with Soj protein. Mol. Micro. 41 (3): 743-755.

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.

Baker ML, Jiang W, Rixon FJ, and Chiu W. 2005. Common Ancestry of Herpesviruses and Tailed DNA Bacteriophages. J. Vir. 79: 14967-14970. UTHSCSA Link. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W.  2013.  Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.  Proc. Natl. Acad. Sci. USA 110: 12301-12306.

Bamford JK, Hanninen AL, Pakula TM, Ojala PM, Kalkkinen N, Frilander M, Bamford DH. Genome organization of membrane-containing bacteriophage PRD1. Virology. 1991 Aug;183(2):658-76. Baudoux AC Hendrix RW Lander GC Baily X Podell S Paillard C Johnson JE Potter CS Carrager B Azam F. 2012. Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses.  Environ. Microbiol. 14:2071-2086.  PMID 22225728

Battistuzzi FU, Feijao A, Hedges SB. 2004. A genomic timescale of prokaryote evolution: insights into the orgin of methaongenesis, phototrophy, and the colonization of land. BMC Evol. Biol 4:44.

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

Bartlett DH. Azam F. 2005. Chitin, Cholera, and competence (Science Perspective). Sci. 310: 1775-1777. Baumann RG, Black LW.  2003.  Isolation and characterization of T4 bacteriophage gp17 terminase, a large subunit multimer with enhanced ATPase activity.
J Biol Chem. 278(7):4618-27.

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.

Becker SC, Foster-Frey, J, Stodola AJ, Anacker D, Donovan DM. (2009) Differentially conserved staphylococcal SH3b_5 cell wall binding domains confer increased staphylolytic and streptolytic activity to a streptococcal prophage endolysin domain.  Gene 443: 32-41.

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

Benevides JM, Bondre P, Duda RL, Hendrix RW, Thomas GJ. 2004. Domain structures and roles in bacteriophage HK97 capsid assembly and maturation. Biochem. 43: 5428-5436.

Benkovic SJ, Valentine AM, Salinas F.  2001. Replisome-mediated DNA replication. Ann. Rev. Biochem.

Benson SD, Bamford JKH, Bamford DH, Burnett RM. 1999. Viral evolution revealed by Bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98:825-833.

Berger B. Shor PW. 1998.  On the Structure of the Scaffolding Core of Bacteriophage T4 and Its Role in Head Length Determination. J. Struct. Biol. 121(3):285-294.

Beumer A, and Robinson JB. 2005. A broad-host-range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria. Appl. Env.Micro. 71:8301-8304.

Bignell C, Thomas CM. 2001. The bacterial ParA-ParB partitioning proteins. J. Biotechnology 91 (1): 1-34.

Billington,S.J., Huggins,A.S., Johanesen,P.A., Crellin,P.K., Cheung,J.K., Katz,M.E., Wright,C.L., Haring,V. and Rood,J.I. 1999. Complete nucleotide sequence of the 27-kilobase virulence related  locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal  origin.  Infect. Immun. 67 (3), 1277-1286. Binettti AG, Del Rio B, Martin MC, Alvarez MA. 2005. Detection and characterization of Streptococcus thermophilus bacteriophages by use of the antireceptor gene sequence.  Appl. Env. Micro. 71: 6096-6103.

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.

Black LW, Thomas JA. 2012. Condensed Genome Structure. Adv Exp Med Biol. 2012;726:469-87. doi: 10.1007/978-1-4614-0980-9_21. Review. PMID: 22297527

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

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.

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.

Borriss M, Lombardot T, Glockner FO, Becher D, Albrecht D, Schweder T. 2007. Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b. Extremophiles 11: 95-104.

Botstein D. 1980. A theory of modular evolution for bacteriophages. Ann. N.Y. Acad. Sci. 354: 484-490.

Bouchard, J. D. & Moineau, S. (2000). Homologous recombination between a lactococcal
bacteriophage and the chromosome of its host strain. Virology 270, 65-75.

Brietbart M, Rohwer F. 2006.  Here a virus, there a virus, everywhere the same virus? Trends in Microbiology 13:xxxx

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.

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.

Brenner S. Bacteriophage tales. Current Biology. 7(11):R736, 1997

Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, and
Rohwer F. (2002) Genomic analysis of uncultured marine viral communities. PNAS 2002 99: 14250-14255.

Brentlinger KL. Hafenstein S. Novak CR. Fane BA. Borgon R. McKenna R. Agbandje-McKenna M. 2002.
Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the
obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. J. Bact. 184(4):1089-1094.

Briers, Y., Miroshnikov, K., Chertkov, O., Nekrasov, A., Mesyanzhinov, V., Volckaert, G., and Lavigne, R., 2008. The structural peptidoglycan hydrolase gp181 of bacteriophage phiKZ. Biochem Biophys Res Commun. 374, 747-751.

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

Bhunchoth A, Blanc-Mathieu R, Mihara T, Nishimura Y, Askora A, Phironrit N, Leksomboon C, Chatchawankanphanich O Kawasaki T, Nakano M, Fujie M, Ogata H, Yamada T.  2016.  Two asian jumbo phages, phiRSL2 and phiRSF1, infect RAlstonia solanacearum and show common features of phiKZ-related phages.  Virology 494:56-66;  PMID 27081857

Burkal'tseva MV, Krylov VN, Pleteneve EA, Shaburova OV, Krylov SV, Volkart G, Sykilinda NN, Kurochkina LP, and Mesyanzhinov VV. 2002. Phenogenetic characterization of a group of giant phiKZ-like bacteriophages of Pseudomonas aeruginosa. Russian J. Genet. 38: 1242-1250. UTHSCSA Link. Butcher SJ, Manole V, Karhu NJ.  2012 Lipid-containing viruses: bacteriphage PRD1 assembly.  Adv Exp Med Biol 726:365-377.

Campbell A. 1994. Comparative molecular biology of lambdoid phages. Annu Rev. Microbiol. 48:193-222UTHSCSA Link.

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.

Caruthers JM and McKay DB. 2002.Helicase structure and mechanism. Curr. Opinion in Str. Biol. 12: 123-133.

Casjens, S., Wyckoff, E., Hayden, M., Sampson, L., Eppler, K., Randall, S., et al. (1992) Bacteriophage P22 portal protein is part of the gauge that regulates packing density of intravirion DNA. J Mol Biol 224: 1055–1074.

Sherwood R. Casjens, Eddie B. Gilcrease, Wai Mun Huang, Kim L. Bunny, Marisa L. Pedulla, Michael E. Ford, Jennifer M. Houtz, Graham F. Hatfull, and Roger W. Hendrix. 2004. The pKO2 Linear Plasmid Prophage of Klebsiella oxytoca. J. Bacteriol. 186: 1818-1832.

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.

Chang J, Weigele P, King J. Chiu W, Jiang W. 2006.  Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery.  Structure 14:1073-1082.  PMID 16730179.

Casjens S. 2003. Prophages and bacterioal genomics: what have we learned so far? Mol. Microbiol. 49: 277-300.

Casjens SR. 2005. Comparative genomics and evolution of the tailed-bacteriophages. Curr. Opin. Micro. 8: 451-458.

Catalano CE. The terminase enzyme from bacteriophage lambda: a DNA-packaging machine.  Cellular & Molecular Life Sciences. 57(1):128-48, 2000 Jan 20. UI: 20406133

Cermakian N, Ikeda TM, Miramontes P, Lang BF, Gray MW, and Cedergren R. 1997. On the evolution of the single-subunit RNA polymerases.J. Mol. Evol. 45:671-681.

Cerritelli, M.E., Trus, B.L., Smith, C.S., Cheng, N., Conway, J.F., and Steven, A.C.  2003. A second symmetry mismatch at the portal vertix of bacteriophage T7: 8-fold symmetry in the procapsid core.  J. Mol. biol. 3327: 1-6.  PMID 12614603

Cerritelli ME, Wall JS, Simon MN, Conway JF, Steven AC.  1996. Stoichiometry and domainal organization of the long tail-fiber of bacteriphage T4: a hinged viral adhesin.  J. Mol. biol. 260:767-780.  PMID: 8709154.

Ceyssens PJ, Lavigne R, Mattheus W, Chibeu A, Hertveldt K, Mast J, Robben J, and Volckaert G. 2006. Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the phiKMV subgroup with the T7 supergroup. J. Bact. 188: 6924-6931.

Ceyssens PJ, Brabban A, Rogge L, Lewis MS, Pickard D, Goulding D, Dougan G, Noben JP, Kropinski A, Kutter E, Lavigne R.  2010.  Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the "N4-like viruses".  Virology 405:26-30.  PMID 20619867.

Ceyssens PJ, Minakhin L, Van den Bossche A, Yakunina M, Klimuk E, Blasdel B, De Smet J, Noben JP, Blaisi U, Severiov K, Lavigne R.  2014.  Development of gaint bacteriophage phiKZ is independent of the host transcription apparatus.  J. Virol 88:10501-1-510.  PMID 24965474.

Chan JZ-M, Millard AD, Mann NH, and Schafer H. 2014 Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes.  Front. Microbiol 10:

Chan YW Mohr R Millard AD Holmes AB Larkum AW Whitworth AL Mann NH Scanlan DJ Hess WR Clokie MR (2011) Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.  Mol. Biol. Evol. 28:2269-2274.  PMID 21335340

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.

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.

Chen F., and Lu, J. 2002. Genomic sequence and Evolution of Marine Cyanophage P60: a New insight on lytic and lysogenic phages.  Applied and Environ. Microbiol. 68: 2589-2594.

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.

Cheng N, Wu W, Watts NR, Steven AC.  2014.  Exploiting radiation damage to map proteins in nucleoprotein complexes:  The internal structure of bacteriophage T7.  J. Struct Biol 185:250-256.

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.

Chibani-Chennoufi S. Canchaya C, Bruttin A., and Brussow H. 2004. Comparative genomics of the T4-like Escherichia coli Phage JS98: Implications for the evolution of T4 phages.  J. Bact. 186:827-8286.

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.

Choi KH, McPartland J, Kaganman I, Bowman VD, Rothman-Denes LB, Rossmann MG. 2008. Insight into DNA and protein transport in double-stranded DNA viruses: the structure of bacteriophage N4.  JMB 378:726-736.

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.

Christiansen, B., Brondsted, L., Vogensen, F. K. & Hammer, K. (1996). A resolvase-like protein is required for the site-specific integration of the temperate lactococcal bacteriophage TP901-1. J Bacteriol 178, 5164-5173. Chung YB, Nardone C, Hinkle DC.  1990.  Bacteriophage T7 DNA packaging. III. A "hairpin" end formed on T7 concatemers may be an intermediate in the processing reaction.  J Mol Biol.216:939-48. Clark S, Losick R, Pero J. 1974. New RNA polymerase from Bacillus subtilis infected with phage PBS2. Nature 252:21-24. UTHSCSA Link. Clark AJ. Inwood W. Cloutier T. Dhillon TS. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. Journal of Molecular Biology. 311(4):657-79, 2001 Cohen DN, Sham YY, Haugstad GD, Xiang Y, Rossmann MG, Anderson DL, Popham DL.  2009.  Shared catalysis in virus entry and bacterioal cell wall depolymerization.  J. Mol. Biol. 387:  607-618. PMID 19361422.
Comeau AM, and Krisch HM. 2005. War is peace - dispatches from the bacterial and phage killing fields. Curr. Opin. Microbiol. 8: 488-494. Comeau AM., Bertrand C, Letarov A, Tetart F, and Kirsch HM. 2007. Molecular architecture of the T4 phage superfamily: A conserved core genome and a plastic periphery. Virology 362:384-396,UTHSCSA Link.

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.

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.

Cuervo A, Pulido-Cid M, Chagoyen M, Arranz R, Gonzalez-Garcia VA, Garcia-Doval C, Caston JR, Valpuesta JM, van Raaij MJ, Martin-Benito J. and Carrascosa JL.  Structural characterization of the bacteriophage T7 tail machinery.  J. Biol. Chem. 288:26290-26299. PMID 23884409
Davey MJ, Funnell BE. 1997. Modulation of the P1 plasmid partition protein ParA by ATP, ADP, and P1 ParB. J. Biol. Chem. 272 (24): 15286-15292. Davidson, A. & Gold, M. (1992). A novel in vitro DNA packaging system demonstrating a direct role for the bacteriophage l FI gene product. Virology, 161, 305-315.

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.

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.

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.

    Desiere F, Mahanivong C, Hillier AJ, et al. Comparative genomics of lactococcal phages: Insight from the complete genome sequence of Lactococcus lactis phage BK5-T. VIROLOGY 283 (2): 240-252 MAY 10 2001. Desplats C, Krisch HM. 2003. The diversity and evolution of the T4-type bacteriophages. Research in Microbiology 154: 259-267. UTHSCSA Link.
  • Adds the exo-T evens to the schizo T-evens, etc.
  • Hélène Deveau, Rodolphe Barrangou, Josiane E. Garneau, Jessica Labonté, Christophe Fremaux, Patrick Boyaval, Dennis A. Romero, Philippe Horvath, and Sylvain Moineau. 2008. Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus. J Bacteriol. 2008 February; 190(4): 1390–1400
    Dittmer A, Drach JC, Townsend LB, Fischer A, and Bogner E. 2005. Interaction of the putative human cytomegalovirus portal protein pUL104 with the large terminase subunit pUL56 and its inhibition by benzimidazole-D-ribonucleosides. JOURNAL OF VIROLOGY 79 (23): 14660-14667UTHSCSA Link. Djordjevic GM, Klaenhammer TR. 1997.  Bacteriophage-triggered defense systems: Phage adaptation and design improvements. APPL ENVIRON MICROB 63 (11): 4370-4376. Dobbins AT, Matthew G Jr., Basham DA, Ford ME, Houtz JM, Pedulla ML, Lawrence JG, Hatfull GF, and Hendrix RW.  2004. Complete genomic sequence of the virulent Salmonella bacteriophage SP6.  J. Bact 186: 1933-1944. Domotor D Becsagh P Rakhely G Schneider G Kovacs T  2012.  Complete genomic sequence of Erwinia amylovora phage phiEaH2. J. Virol. 86: 10899.  PMID 22966191.

    Draper B, Rao VB. 2007. An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests an inchworm-type translocation mechanism. J. Mol. Biol. 369:79-94. UTHSCSA Link.

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

    Duda A, Hendrix RW, Huang WM, Conway JF.  2006. Shared architecture of bacteriophage SPO1 and herpesvirus capsids.  Curr. Biol. 16: 440.

    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.

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

    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.

    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.

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  • The original rotating portal observation.
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  • 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.
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  • 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.
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    Willis,S.H., Kazmierczak,K.M., Carter,R.H. and Rothman-Denes,L.B. 2002.  N4 RNA Polymerase II, a Heterodimeric RNA Polymerase with Homology to the Single-Subunit Family of RNA Polymerases J. Bacteriol. 184 (18), 4952-4961.
  • 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.

    Woods DE, Jeddeloh JA, Fritz DL, and DeShazer D. 2002. Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei. J. Bacteriol. 184 (14), 4003-4017

    Woods L, Catalano CE.
    Kinetic characterization of the GTPase activity of phage lambda terminase: Evidence for communication between the two "NTPase" catalytic sites of the enzyme.
    BIOCHEMISTRY  38 (44): 14624-14630 NOV 2 1999.

    Wright A, Hawkins CH, Anggard EE, & Harper DR.  (2009)  A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminar report of efficacy.  Clinical Otolaryngology 34: 349-357.

    Xiang Y, Leiman PG, Li L, Grimes S, Anderson DL, Rossmann MG.  2009. Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike.  Mol. Cell 34:375-386.  PMID  19450535.

    Xiang Y, Morais MC, Battisti AJ, Grimes S, Jardine PJ, Anderson DL, Rossmann MG: 2006. Structural changes of bacteriophage phi29 upon DNA packaging and release. EMBO J 25:5229-5239.  PMID 17053784.

    Xiang Y, Rossmann MG.  2011.  Structure of bacteriophage phi29 head fibers has a supercoiled triple repeating helix-turn-helix motif..  PNAS 108:4806-4810.  PMID 21383126.

    Xiao, F., Moll, D., Guo, S. & Guo, P. (2005). Binding of pRNA to the N-terminal amino acids of connector protein of bacterial phage phi29. Nucl. Acids Res. 33: 2640–2649.

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

    Yang K, Baines JD. 2006. The putative terminase subunit of herpes simplex virus 1 encoded by UL28 is necessary and sufficient to mediate interaction between pUL15 and pUL33. J. Vir. 80: 5733-5739.

    Yang Q, Berton N, Manning MC, Catalano CE.
    Domain structure of gpNu1, a phage lambda DNA packaging protein.
    BIOCHEMISTRY  38 (43): 14238-14247 OCT 26 1999.

    Yakunina M Artamonova T Borukhov S Makarova KS Severinov K Minakhin L.  2015.  A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage.  Nucl. Acids Res. 43:10411-10420.  PMID 26490960.

    Yang F, Forrer P, Dauter Z, Conway JF, Cheng N, Cerritelli ME, Steven AC, Pluckthun A, Wlodawer A.  2000. Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD.  Nat. Str. Biol.7:230-237. PMID 10700283.

    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.

    Zafar, N., R. Mazumder and D. Seto (2002). "CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes." BMC Bioinformatics 3(1): 12.  PMID 11972896

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

    Zhang Z, Greene B, Thuman-Commike PA, Jakana J, Prevelige PE Jr, King J, Chiu W. (2000) Visualization of the maturation transition in bacteriophage P22 by electron cryomicroscopy. J Mol Biol 297:615–626. PMID 10731426.

    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.

    Zhang X, and Studier FW. 2004. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection.  J. Mol. Biol. 340: 707-730. UTHSCSA Link. Zheng H, Olia AS, Gonen M, Andrews S, Cingolani G, and Gonen T. 2007.  A conformational switch in bacteriophage P22 portal protein primes genome injection.  Mol. Cell. 29:376-383. UTHSCSA Link.

    Zhou ZH, Hiu WH, Shah S, Hih J, O'Connor CM, Sherman MB, Kedes DH, Schein S.  2014.  Four levels of heirarchical organization, including noncovalent chainmail, brace the mature tumor herpesvirus capsid against pressurization.  Structure 22: 1385-1398.  PMID 25220471.

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