Bacteriophage Protein-Protein Interactions

Advances in Virus Research

Volumn 83, Issue , 2012, Pages 219-298

  Häuser, Roman ^a,b   Blasche, Sonja ^b   Dokland, Terje ^c   Haggård Ljungquist, Elisabeth ^d   von Brunn, Albrecht ^e   Salas, Margarita ^f   Casjens, Sherwood ^g   Molineux, Ian ^h   Uetz, Peter ^e,i  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c University of Alabama at Birmingham   (United States)

^d STOCKHOLM UNIVERSITY   (Sweden)

^e UNIVERSITY OF MUNICH   (Germany)

^f CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

^g UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^h UNIVERSITY OF TEXAS AT AUSTIN   (United States)

ⁱ VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Bacteriophages; Cp 1; Dp 1; Host virus interactions; Interactome; Lambda; P2; P22; P4; Phi 29; Protein protein interactions; T7; Yeast two hybrid

Indexed keywords

EID: 84862857332     PISSN: 00653527     EISSN: 15578399     Source Type: Book Series    
DOI: 10.1016/B978-0-12-394438-2.00006-2     Document Type: Chapter

References (436)

1. Abbani M.A., Papagiannis C.V., Sam M.D., Cascio D., Johnson R.C., Clubb R.T. Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly. Proc. Natl. Acad. Sci. USA 2007, 104:2109-2114.
2. Abril A.M., Marco S., Carrascosa J.L., Salas M., Hermoso J.M. Oligomeric structures of the phage phi29 histone-like protein p6. J. Mol. Biol. 1999, 292:581-588.
3. Agarwal M., Arthur M., Arbeit R.D., Goldstein R. Regulation of icosahedral virion capsid size by the in vivo activity of a cloned gene product. Proc. Natl. Acad. Sci. USA 1990, 87:2428-2432.
4. Agirrezabala X., Martin-Benito J., Caston J.R., Miranda R., Valpuesta J.M., Carrascosa J.L. Maturation of phage T7 involves structural modification of both shell and inner core components. EMBO J. 2005, 24:3820-3829.
5. Agirrezabala X., Martin-Benito J., Valle M., Gonzalez J.M., Valencia A., Valpuesta J.M., Carrascosa J.L. Structure of the connector of bacteriophage T7 at 8A resolution: Structural homologies of a basic component of a DNA translocating machinery. J. Mol. Biol. 2005, 347:895-902.
6. Agirrezabala X., Velazquez-Muriel J.A., Gomez-Puertas P., Scheres S.H., Carazo J.M., Carrascosa J.L. Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold. Structure 2007, 15:461-472.
7. Albert A., Munoz-Espin D., Jimenez M., Asensio J.L., Hermoso J.A., Salas M., Meijer W.J. Structural basis for membrane anchorage of viral phi29 DNA during replication. J. Biol. Chem. 2005, 280:42486-42488.
8. Alfano C., McMacken R. Ordered assembly of nucleoprotein structures at the bacteriophage lambda replication origin during the initiation of DNA replication. J. Biol. Chem. 1989, 264:10699-10708.
9. Ali S.S., Beckett E., Bae S.J., Navarre W.W. The 5.5 protein of phage T7 inhibits H-NS through interactions with the central oligomerization domain. J. Bacteriol 2011, 193:4881-4892.
10. Anderson D.L., Hickman D.D., Reilly B.E. Structure of Bacillus subtilis bacteriophage phi 29 and the length of phi 29 deoxyribonucleic acid. J. Bacteriol. 1966, 91:2081-2089.
11. Anderson W.F., Takeda Y., Echols H., Matthews B.W. The structure of a repressor: Crystallographic data for the Cro regulatory protein of bacteriophage lambda. J. Mol. Biol. 1979, 130:507-510.
12. Ang D., Keppel F., Klein G., Richardson A., Georgopoulos C. Genetic analysis of bacteriophage-encoded cochaperonins. Annu. Rev. Genet. 2000, 34:439-456.
13. Asensio J.L., Albert A., Muñoz-Espín D., González C., Hermoso J., Villar L., Jiménez-Barbero J., Salas M., Meijer W.J. Structure of the functional domain of phi29 replication organizer: Insights into oligomerization and DNA binding. J. Biol. Chem. 2005, 280:20730-20739.
14. Atanasiu C., Byron O., McMiken H., Sturrock S.S., Dryden D.T. Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7. Nucleic Acids Res. 2001, 29:3059-3068.
15. Atanasiu C., Su T.J., Sturrock S.S., Dryden D.T. Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme. Nucleic Acids Res 2002, 30:3936-3944.
16. Ayers D.J., Sunshine M.G., Six E.W., Christie G.E. Mutations affecting two adjacent amino acid residues in the alpha subunit of RNA polymerase block transcriptional activation by the bacteriophage P2 Ogr protein. J. Bacteriol. 1994, 176:7430-7438.
17. Backhaus H., Petri J.B. Sequence analysis of a region from the early right operon in phage P22 including the replication genes 18 and 12. Gene 1984, 32:289-303.
18. Badia D., Camacho A., Pérez-Lago L., Escandón C., Salas M., Coll M. The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA. Mol. Cell. 2006, 22:73-81.
19. Ball C.A., Johnson R.C. Efficient excision of phage lambda from the Escherichia coli chromosome requires the Fis protein. J. Bacteriol. 1991, 173:4027-4031.
20. Barrett K.J., Marsh M.L., Calendar R. Interactions between a satellite bacteriophage and its helper. J. Mol. Biol. 1976, 106:683-707.
21. Bartel P.L., Roecklein J.A., SenGupta D., Fields S. A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet. 1996, 12:72-77.
22. Barthelemy I., Salas M. Characterization of a new prokaryotic transcriptional activator and its DNA recognition site. J. Mol. Biol. 1989, 208:225-232.
23. Bazinet C., Benbasat J., King J., Carazo J.M., Carrascosa J.L. Purification and organization of the gene 1 portal protein required for phage P22 DNA packaging. Biochemistry 1988, 27:1849-1856.
24. Bell C.E., Lewis M. Crystal structure of the lambda repressor C-terminal domain octamer. J. Mol. Biol. 2001, 314:1127-1136.
25. Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 1951, 62:293-300.
26. Bertani L.E., Six E. The P2-like phages and their parasite, P4. 1988, 73-143. Plenum Press, New York. R. Calendar (Ed.).
27. Bienkowska-Szewczyk K., Lipinska B., Taylor A. The R gene product of bacteriophage lambda is the murein transglycosylase. Mol. Gen. Genet. 1981, 184:111-114.
28. Blanco L., Gutierrez J., Lazaro J.M., Bernad A., Salas M. Replication of phage phi 29 DNA in vitro: Role of the viral protein p6 in initiation and elongation. Nucleic Acids Res. 1986, 14:4923-4937.
29. Blanco L., Prieto I., Gutierrez J., Bernad A., Lazaro J.M., Hermoso J.M., Salas M. Effect of NH4+ ions on phi 29 DNA-protein p3 replication: Formation of a complex between the terminal protein and the DNA polymerase. J. Virol. 1987, 61:3983-3991.
30. Blanco L., Salas M. Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication. Proc. Natl. Acad. Sci. USA 1984, 81:5325-5329.
31. Botstein D., Waddell C.H., King J. Mechanism of head assembly and DNA encapsulation in Salmonella phage P22. I. Genes, proteins, structures and DNA maturation. J. Mol. Biol 1973, 80:669-695.
32. Bowden D.W., Modrich P. In vitro maturation of circular bacteriophage P2 DNA: Purification of ter components and characterization of the reaction. J. Biol. Chem. 1985, 260:6999-7007.
33. Bowie J.U., Sauer R.T. Equilibrium dissociation and unfolding of the Arc repressor dimer. Biochemistry 1989, 28:7139-7143.
34. Bravo A., Illana B., Salas M. Compartmentalization of phage phi29 DNA replication: Interaction between the primer terminal protein and the membrane-associated protein p1. EMBO J. 2000, 19:5575-5584.
35. Bravo A., Salas M. Initiation of bacteriophage phi29 DNA replication in vivo: assembly of a membrane-associated multiprotein complex. J. Mol. Biol. 1997, 269:102-112.
36. Bravo A., Salas M. Polymerization of bacteriophage phi 29 replication protein p1 into protofilament sheets. EMBO J. 1998, 17:6096-6105.
37. Breg J.N., van Opheusden J.H., Burgering M.J., Boelens R., Kaptein R. Structure of Arc repressor in solution: Evidence for a family of beta- sheet DNA-binding proteins. Nature 1990, 346:586-589.
38. Breitbart M., Salamon P., Andresen B., Mahaffy J.M., Segall A.M., Mead D., Azam F., Rohwer F. Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA 2002, 99:14250-14255.
39. Briani F., Deho G., Forti F., Ghisotti D. The plasmid status of satellite bacteriophage P4. Plasmid 2001, 45:1-17.
40. Broadbent S.E., Davies M.R., van der Woude M.W. Phase variation controls expression of Salmonella lipopolysaccharide modification genes by a DNA methylation-dependent mechanism. Mol. Microbiol. 2010, 77:337-353.
41. Brown B.M., Bowie J.U., Sauer R.T. Arc repressor is tetrameric when bound to operator DNA. Biochemistry 1990, 29:11189-11195.
42. Buchwald M., Murialdo H., Siminovitch L. The morphogenesis of bacteriophage lambda. II. Identification of the principal structural proteins. Virology 1970, 42:390-400.
43. Buchwald M., Siminovitch L. Production of serum-blocking material by mutants of the left arm of the lambda chromosome. Virology 1969, 38:1-7.
44. Buchwald M., Steed-Glaister P., Siminovitch L. The morphogenesis of bacteriophage lambda. I. Purification and characterization of lambda heads and lambda tails. Virology 1970, 42:375-389.
45. Calendar R. "The Bacteriophages" 2006, Oxford University Press, Oxford. 2nd Ed.
46. Calendar R., Lindqvist B., Sironi G., Clark A. Characterization of REP- mutants and their interaction with P2 phage. Virology 1970, 40:72-83.
47. Calles B., Salas M., Rojo F. The phi29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex. EMBO J. 2002, 21:6185-6194.
48. Camacho A., Salas M. Mechanism for the switch of phi29 DNA early to late transcription by regulatory protein p4 and histone-like protein p6. EMBO J. 2001, 20:6060-6070.
49. Camara B., Liu M., Reynolds J., Shadrin A., Liu B., Kwok K., Simpson P., Weinzierl R., Severinov K., Cota E., Matthews S., Wigneshweraraj S.R. T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site. Proc. Natl. Acad. Sci. USA 2010, 107:2247-2252.
50. Campbell A., del-Campillo-Campbell A., Ginsberg M.L. Specificity in DNA recognition by phage integrases. Gene 2002, 300:13-18.
51. Cardarelli L., Lam R., Tuite A., Baker L.A., Sadowski P.D., Radford D.R., Rubinstein J.L., Battaile K.P., Chirgadze N., Maxwell K.L., Davidson A.R. The crystal structure of bacteriophage HK97 gp6: Defining a large family of head-tail connector proteins. J. Mol. Biol. 2010, 395:754-768.
52. Casjens S. Bacteriophage lambda FII gene protein: Role in head assembly. J. Mol. Biol. 1974, 90:1-20.
53. Casjens S. Molecular organization of the bacteriophage P22 coat protein shell. J. Mol. Biol. 1979, 131:1-14.
54. Casjens S. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 2011, in press.
55. Casjens S., Eppler K., Parr R., Poteete A.R. Nucleotide sequence of the bacteriophage P22 gene 19 to 3 region: Identification of a new gene required for lysis. Virology 1989, 171:588-598.
56. Casjens S., Hayden M. Analysis in vivo of the bacteriophage P22 headful nuclease. J. Mol. Biol. 1988, 199:467-474.
57. Casjens S., Horn T., Kaiser A.D. Head assembly steps controlled by genes F and W in bacteriophage lambda. J. Mol. Biol. 1972, 64:551-563.
58. Casjens S.R. Comparative genomics and evolution of the tailed-bacteriophages. Curr. Opin. Microbiol. 2005, 8:451-458.
59. Casjens S.R., Hendrix R.W. Locations and amounts of major structural proteins in bacteriophage lambda. J. Mol. Biol. 1974, 88:535-545.
60. Casjens S.R., Thuman-Commike P.A. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 2011, 411:393-415.
61. Catalano C.E. The terminase enzyme from bacteriophage lambda: A DNA-packaging machine. Cell. Mol. Life Sci. 2000, 57:128-148.
62. Catalano C.E., Tomka M.A. Role of gpFI protein in DNA packaging by bacteriophage lambda. Biochemistry 1995, 34:10036-10042.
63. Cerritelli M.E., Conway J.F., Cheng N., Trus B.L., Steven A.C. Molecular mechanisms in bacteriophage T7 procapsid assembly, maturation, and DNA containment. Adv. Protein Chem. 2003, 64:301-323.
64. Cerritelli M.E., Studier F.W. Assembly of T7 capsids from independently expressed and purified head protein and scaffolding protein. J. Mol. Biol. 1996, 258:286-298.
65. Cerritelli M.E., Studier F.W. Purification and characterization of T7 head-tail connectors expressed from the cloned gene. J. Mol. Biol. 1996, 258:299-307.
66. Cerritelli M.E., Trus B.L., Smith C.S., Cheng N., Conway J.F., Steven A.C. A second symmetry mismatch at the portal vertex of bacteriophage T7: 8-fold symmetry in the procapsid core. J. Mol. Biol. 2003, 327:1-6.
67. Chang C.Y., Kemp P., Molineux I.J. Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell. Virology 2010, 398:176-186.
68. Chang J.R., Poliakov A., Prevelige P.E., Mobley J.A., Dokland T. Incorporation of scaffolding protein gpO in bacteriophages P2 and P4. Virology 2008, 370:352-361.
69. Chang J.R., Spilman M.S., Rodenburg C.M., Dokland T. Functional domains of the bacteriophage P2 scaffolding protein: Identification of residues involved in assembly and protease activity. Virology 2009, 384:144-150.
70. Cheetham G.M., Jeruzalmi D., Steitz T.A. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 1999, 399:80-83.
71. Cheetham G.M., Steitz T.A. Structure of a transcribing T7 RNA polymerase initiation complex. Science 1999, 286:2305-2309.
72. Chen D.H., Baker M.L., Hryc C.F., DiMaio F., Jakana J., Wu W., Dougherty M., Haase-Pettingell C., Schmid M.F., Jiang W., Baker D., King J.A., et al. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc. Natl. Acad. Sci. USA 2011, 108:1355-1360.
73. Chen K.C., Vannais D.B., Jones C., Patterson D., Davidson J.N. Mapping of the gene encoding the multifunctional protein carrying out the first three steps of pyrimidine biosynthesis to human chromosome 2. Hum. Genet. 1989, 82:40-44.
74. Chen Y.C., Rajagopala S.V., Stellberger T., Uetz P. Exhaustive benchmarking of the yeast two-hybrid system. Nature Methods 2010, 7:667-668.
75. Cheng H., Shen N., Pei J., Grishin N.V. Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease. Protein Sci. 2004, 13:2260-2269.
76. Cheng X., Wang W., Molineux I.J. F exclusion of bacteriophage T7 occurs at the cell membrane. Virology 2004, 326:340-352.
77. Cho E.H., Gumport R.I., Gardner J.F. Interactions between integrase and excisionase in the phage lambda excisive nucleoprotein complex. J. Bacteriol. 2002, 184:5200-5203.
78. Cho E.H., Nam C.E., Alcaraz R., Gardner J.F. Site-specific recombination of bacteriophage P22 does not require integration host factor. J. Bacteriol. 1999, 181:4245-4249.
79. Christie G., Anders D., McAlister V., Goodwin T., Julien B., Calendar R. Identification of upstream sequences essential for activation of a bacteriophage P2 late promoter. J Bacteriol 2003, 185:4609-4614.
80. Christie G., Temple L., Bartlett B., Goodwin T. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon. J Bacteriol 2002, 184:6522-6531.
81. Christie G.E., Calendar R. Interactions between satellite bacteriophage P4 and its helpers. Annu. Rev. Genet. 1990, 24:465-490.
82. Clement J.M., Lepouce E., Marchal C., Hofnung M. Genetic study of a membrane protein: DNA sequence alterations due to 17 lamB point mutations affecting adsorption of phage lambda. EMBO J. 1983, 2:77-80.
83. Cone R., Bonura T., Friedberg E.C. Inhibitor of uracil-DNA glycosylase induced by bacteriophage PBS2: Purification and preliminary characterization. J. Biol. Chem. 1980, 255:10354-10358.
84. Cortines J.R., Weigele P.R., Gilcrease E.B., Casjens S.R., Teschke C.M. Decoding bacteriophage P22 assembly: Identification of two charged residues in scaffolding protein responsible for coat protein interaction. Virology 2011, 421:1-11.
85. Court D.L., Oppenheim A.B., Adhya S.L. A new look at bacteriophage lambda genetic networks. J. Bacteriol. 2007, 189:298-304.
86. Crisona N.J., Weinberg R.L., Peter B.J., Sumners D.W., Cozzarelli N.R. The topological mechanism of phage lambda integrase. J. Mol. Biol. 1999, 289:747-775.
87. Crucitti P., Abril A.M., Salas M. Bacteriophage phi 29 early protein p17. Self-association and hetero-association with the viral histone-like protein p6. J. Biol. Chem 2003, 278:4906-4911.
88. Crucitti P., Lazaro J.M., Benes V., Salas M. Bacteriophage phi29 early protein p17 is conditionally required for the first rounds of viral DNA replication. Gene 1998, 223:135-142.
89. d'Herelle F. The Bacteriophage and Its Behavior 1926, Williams & Wilkins, Baltimore, MD, 490-497.
90. Darling P.J., Holt J.M., Ackers G.K. Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding I: Analysis of cro dimerization from nanomolar to micromolar concentrations. Biochemistry 2000, 39:11500-11507.
91. Das A. How the phage lambda N gene product suppresses transcription termination: communication of RNA polymerase with regulatory proteins mediated by signals in nascent RNA. J. Bacteriol. 1992, 174:6711-6716.
92. Datta A.B., Roy S., Parrack P. Role of C-terminal residues in oligomerization and stability of lambda CII: Implications for lysis-lysogeny decision of the phage. J. Mol. Biol. 2005, 345:315-324.
93. Datta I., Banik-Maiti S., Adhikari L., Sau S., Das N., Mandal N.C. The mutation that makes Escherichia coli resistant to lambda P gene-mediated host lethality is located within the DNA initiator Gene dnaA of the bacterium. J. Biochem. Mol. Biol. 2005, 38:89-96.
94. Datta I., Sau S., Sil A.K., Mandal N.C. The bacteriophage lambda DNA replication protein P inhibits the oriC DNA- and ATP-binding functions of the DNA replication initiator protein DnaA of Escherichia coli. J. Biochem. Mol. Biol. 2005, 38:97-103.
95. De Anda J., Poteete A.R., Sauer R.T. P22 c2 repressor. Domain structure and function. J. Biol. Chem 1983, 258:10536-10542.
96. de Beer T., Fang J., Ortega M., Yang Q., Maes L., Duffy C., Berton N., Sippy J., Overduin M., Feiss M., Catalano C.E. Insights into specific DNA recognition during the assembly of a viral genome packaging machine. Mol. Cell. 2002, 9:981-991.
97. de Beus M.D., Doyle S.M., Teschke C.M. GroEL binds a late folding intermediate of phage P22 coat protein. Cell Stress Chaperones 2000, 5:163-172.
98. de Jong R.N., van der Vliet P.C. Mechanism of DNA replication in eukaryotic cells: Cellular host factors stimulating adenovirus DNA replication. Gene 1999, 236:1-12.
99. Deho G., Ghisotti D. The satellite phage P4. 2006, 391-408. Oxford University Press, New York. R. Calendar (Ed.).
100. Deighan P., Diez C.M., Leibman M., Hochschild A., Nickels B.E. The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase. Proc. Natl. Acad. Sci. USA 2008, 105:15305-15310.
101. Demerec M., Fano U. Bacteriophage-resistant mutants in Escherichia coli. Genetics 1945, 30:119-136.
102. Doan D.N.P., Dokland T. The gpQ portal protein of bacteriophage P2 forms dodecameric connctors in crystals. J. Struct. Biol. 2007, 157:432-436.
103. Dodd I.B., Perkins A.J., Tsemitsidis D., Egan J.B. Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev. 2001, 15:3013-3022.
104. Dodson M., Echols H., Wickner S., Alfano C., Mensa-Wilmot K., Gomes B., LeBowitz J., Roberts J.D., McMacken R. Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: Localized unwinding of duplex DNA by a six-protein reaction. Proc. Natl. Acad. Sci. USA 1986, 83:7638-7642.
105. Dokland T. gpO peptidase (Enterobacteria phage P2). Handbook of proteolytic enzymes 2011, Elsevier, Oxford. N.D. Rawlings, G. Salvesen (Eds.).
106. Dokland T., Isaksen M.L., Fuller S.D., Lindqvist B.H. Capsid localization of the bacteriophage P4 Psu protein. Virology 1993, 194:682-687.
107. Dokland T., Lindqvist B.H., Fuller S.D. Image reconstruction from cryo-electron micrographs reveals the morphopoietic mechanism in the P2-P4 bacteriophage system. EMBO J. Eur. Mol. Biol. Organ. J 1992, 11:839-846.
108. Dokland T., Murialdo H. Structural transitions during maturation of bacteriophage lambda capsids. J. Mol. Biol. 1993, 233:682-694.
109. Dokland T., Wang S., Lindqvist B.H. The structure of P4 procapsids produced by coexpression of capsid and external scaffolding proteins. Virology 2002, 298:224-231.
110. Duffy C., Feiss M. The large subunit of bacteriophage lambda's terminase plays a role in DNA translocation and packaging termination. J. Mol. Biol. 2002, 316:547-561.
111. Dufour E., Méndez J., Lázaro J.M., de Vega M., Blanco L., Salas M. An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein. J. Mol. Biol. 2000, 304:289-300.
112. Dunn J.J., Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 1983, 166:477-535.
113. Echols H. Multiple DNA-protein interactions governing high-precision DNA transactions. Science 1986, 233:1050-1056.
114. Elías-Arnanz M., Salas M. Functional interactions between a phage histone-like protein and a transcriptional factor in regulation of phi29 early-late transcriptional switch. Genes Dev. 1999, 13:2502-2513.
115. Eppler K., Wyckoff E., Goates J., Parr R., Casjens S. Nucleotide sequence of the bacteriophage P22 genes required for DNA packaging. Virology 1991, 183:519-538.
116. Eriksson J.M., Haggard-Ljungquist E. The multifunctional bacteriophage P2 cox protein requires oligomerization for biological activity. J. Bacteriol. 2000, 182:6714-6723.
117. Eriksson S.K., Liu T., Haggard-Ljungquist E. Interacting interfaces of the P4 antirepressor E and the P2 immunity repressor C. Mol. Microbiol. 2000, 36:1148-1155.
118. Esposito D., Gerard G.F. The Escherichia coli Fis protein stimulates bacteriophage lambda integrative recombination in vitro. J. Bacteriol. 2003, 185:3076-3080.
119. Frackman S., Siegele D.A., Feiss M. The terminase of bacteriophage lambda: Functional domains for cosB binding and multimer assembly. J. Mol. Biol. 1985, 183:225-238.
120. Franklin N.C. Conservation of genome form but not sequence in the transcription antitermination determinants of bacteriophages lambda, phi 21 and P22. J. Mol. Biol. 1985, 181:75-84.
121. Freire R., Serrano M., Salas M., Hermoso J.M. Activation of replication origins in phi29-related phages requires the recognition of initiation proteins to specific nucleoprotein complexes. J. Biol. Chem. 1996, 271:31000-31007.
122. Friedman D.I., Court D.L. Bacteriophage lambda: Alive and well and still doing its thing. Curr. Opin. Microbiol. 2001, 4:201-207.
123. Frumerie C.M., Eriksson J., Dugast M., Haggard-Ljungquist E. Dimerization of bacteriophage P2 integrase is not required for binding to its DNA target but for its biological activity. Gene 2005, 344:221-231.
124. Fujiki H., Palm P., Zillig W., Calendar R., Sunshine M. Identification of a mutation within the structural gene for the a subunit of DNA-dependent RNA polymerase of E. coli. Mol. Gen. Genet 1976, 145:19-22.
125. Fujisawa H., Shibata H., Kato H. Analysis of interactions among factors involved in the bacteriophage T3 DNA packaging reaction in a defined in vitro system. Virology 1991, 185:788-794.
126. Fujiyama A., Kohara Y., Okazaki T. Initiation sites for discontinuous DNA synthesis of bacteriophage T7. Proc. Natl. Acad. Sci. USA 1981, 78:903-907.
127. Fuller M.T., King J. Assembly in vitro of bacteriophage P22 procapsids from purified coat and scaffolding subunits. J. Mol. Biol. 1982, 156:633-665.
128. Funnell B.E., Inman R.B. Bacteriophage P2 DNA replication: Characterization of the requirement of the gene B protein in vivo. J. Mol. Biol. 1983, 167:311-334.
129. García J.A., Carrascosa J.L., Salas M. Assembly of the tail protein of the Bacillus subtilis phage phi 29. Virology 1983, 125:18-30.
130. Garcia L.R., Molineux I.J. Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli. J. Bacteriol. 1995, 177:4066-4076.
131. Garcia L.R., Molineux I.J. Transcription-independent DNA translocation of bacteriophage T7 DNA into Escherichia coli. J. Bacteriol. 1996, 178:6921-6929.
132. Gascón I., Gutiérrez C., Salas M. Structural and functional comparative study of the complexes formed by viral o29, Nf and GA-1 SSB proteins with DNA. J. Mol. Biol. 2000, 296:989-999.
133. Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dumpelfeld B., Edelmann A., Heurtier M.A., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636.
134. Geisselsoder J., Youdarian P., Deho G., Chidambaram M., Goldstein R., Ljungquist E. Mutants of satellite virus P4 that cannot derepress their bacteriophage P2 helper. J. Mol. Biol. 1981, 148:1-19.
135. Georgopoulos C., Tilly K., Casjens S. Lambdoid phage head assembly. Lambda II 1983, 279-304. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. R. Hendrix, J. Roberts, F.W. Stahl, R. Weisberg (Eds.).
136. Georgopoulos C.P., Hendrix R.W., Casjens S.R., Kaiser A.D. Host participation in bacteriophage lambda head assembly. J. Mol. Biol. 1973, 76:45-60.
137. Ghosh S., Hamdan S.M., Cook T.E., Richardson C.C. Interactions of Escherichia coli thioredoxin, the processivity factor, with bacteriophage T7 DNA polymerase and helicase. J. Biol. Chem. 2008, 283:32077-32084.
138. Ghosh S., Hamdan S.M., Richardson C.C. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex. J. Biol. Chem. 2010, 285:18103-18112.
139. Gilcrease E.B., Winn-Stapley D.A., Hewitt F.C., Joss L., Casjens S.R. Nucleotide sequence of the head assembly gene cluster of bacteriophage L and decoration protein characterization. J. Bacteriol. 2005, 187:2050-2057.
140. González-Huici V., Lázaro J.M., Salas M., Hermoso J.M. Specific recognition of parental terminal protein by DNA polymerase for initiation of protein-primed DNA replication. J. Biol. Chem. 2000, 275:14678-14683.
141. Gottesman M.E., Weisberg R.A. Little lambda, who made thee?. Microbiol. Mol. Biol. Rev. 2004, 68:796-813.
142. Gottesman S., Gottesman M., Shaw J.E., Pearson M.L. Protein degradation in E. coli: The lon mutation and bacteriophage lambda N and cII protein stability. Cell 1981, 24:225-233.
143. Greene B., King J. Binding of scaffolding subunits within the P22 procapsid lattice. Virology 1994, 205:188-197.
144. Greene B., King J. Scaffolding mutants identifying domains required for P22 procapsid assembly and maturation. Virology 1996, 225:82-96.
145. Grimes S., Anderson D. The bacteriophage phi29 packaging proteins supercoil the DNA ends. J. Mol. Biol. 1997, 266:901-914.
146. Grundling A., Smith D.L., Blasi U., Young R. Dimerization between the holin and holin inhibitor of phage lambda. J. Bacteriol. 2000, 182:6075-6081.
147. Guasch A., Pous J., Ibarra B., Gomis-Ruth F.X., Valpuesta J.M., Sousa N., Carrascosa J.L., Coll M. Detailed architecture of a DNA translocating machine: The high-resolution structure of the bacteriophage phi29 connector particle. J. Mol. Biol. 2002, 315:663-676.
148. Guo P., Peterson C., Anderson D. Initiation events in in vitro packaging of bacteriophage phi 29 DNA-gp3. J. Mol. Biol. 1987, 197:219-228.
149. Guo P.X., Erickson S., Xu W., Olson N., Baker T.S., Anderson D. Regulation of the phage phi 29 prohead shape and size by the portal vertex. Virology 1991, 183:366-373.
150. Hadden J.M., Declais A.C., Carr S.B., Lilley D.M., Phillips S.E. The structural basis of Holliday junction resolution by T7 endonuclease I. Nature 2007, 449:621-624.
151. Haggard-Ljungquist E., Halling C., Calendar R. DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. J Bacteriol 1992, 174:1462-1477.
152. Haggard-Ljungquist E., Jacobsen E., Rishovd S., Six E.W., Nilssen O., Sunshine M.G., Lindqvist B.H., Kim K.J., Barreiro V., Koonin E.V., et al. Bacteriophage P2: Genes involved in baseplate assembly. Virology 1995, 213:109-121.
153. Halder S., Datta A.B., Parrack P. Probing the antiprotease activity of lambdaCIII, an inhibitor of the Escherichia coli metalloprotease HflB (FtsH). J. Bacteriol. 2007, 189:8130-8138.
154. Hamada K., Fujisawa H., Minagawa T. Overproduction and purification of the products of bacteriophage T3 genes 18 and 19, two genes involved in DNA packaging. Virology 1986, 151:110-118.
155. Hamdan S.M., Marintcheva B., Cook T., Lee S.J., Tabor S., Richardson C.C. A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor. Proc. Natl. Acad. Sci. USA 2005, 102:5096-5101.
156. Hamdan S.M., Richardson C.C. Motors, switches, and contacts in the replisome. Annu. Rev. Biochem. 2009, 78:205-243.
157. Hang Q., Woods L., Feiss M., Catalano C.E. Cloning, expression, and biochemical characterization of hexahistidine-tagged terminase proteins. J. Biol. Chem. 1999, 274:15305-15314.
158. Häuser R., Sabri M., Moineau S., Uetz P. The proteome and interactome of Streptococcus pneumoniae phage Cp-1. J. Bacteriol. 2011, 193:3135-3138.
159. He Z.G., Rezende L.F., Willcox S., Griffith J.D., Richardson C.C. The carboxyl-terminal domain of bacteriophage T7 single-stranded DNA-binding protein modulates DNA binding and interaction with T7 DNA polymerase. J. Biol. Chem. 2003, 278:29538-29545.
160. He Z.G., Richardson C.C. Effect of single-stranded DNA-binding proteins on the helicase and primase activities of the bacteriophage T7 gene 4 protein. J. Biol. Chem. 2004, 279:22190-22197.
161. Heineman R.H., Bull J.J. Testing optimality with experimental evolution: Lysis time in a bacteriophage. Evolution 2007, 61:1695-1709.
162. Hendrix R., Casjens S. Bacteriophage lambda and its genetic neighborhood. The Bacteriophages 2006, 409-445. Chapter 27, Oxford University Press, Oxford. R. Calendar (Ed.).
163. Hendrix R., Roberts J., Stahl F.W., Weisberg R. Lambda II 1983, 694. CSHL Press, Cold Spring Harbor, NY.
164. Hendrix R.W. Bacteriophages: Evolution of the majority. Theor. Popul. Biol. 2002, 61:471-480.
165. Hendrix R.W. Bacteriophage HK97: Assembly of the capsid and evolutionary connections. Adv. Virus Res. 2005, 64:1-14.
166. Hendrix R.W., Casjens S.R. Protein fusion: A novel reaction in bacteriophage lambda head assembly. Proc. Natl. Acad. Sci. USA 1974, 71:1451-1455.
167. Hendrix R.W., Casjens S.R. Assembly of bacteriophage lambda heads: Protein processing and its genetic control in petit lambda assembly. J. Mol. Biol. 1975, 91:187-199.
168. Hendrix R.W., Duda R.L. Bacteriophage lambda PaPa: Not the mother of all lambda phages. Science 1992, 258:1145-1148.
169. Hendrix R.W., Duda R.L. Bacteriophage HK97 head assembly: A protein ballet. Adv. Virus Res. 1998, 50:235-288.
170. Herman C., Thevenet D., D'Ari R., Bouloc P. The HflB protease of Escherichia coli degrades its inhibitor lambda cIII. J. Bacteriol 1997, 179:358-363.
171. Hermoso J.M., Méndez E., Soriano F., Salas M. Location of the serine residue involved in the linkage between the terminal protein and the DNA of phage phi 29. Nucleic Acids Res. 1985, 13:7715-7728.
172. Hershey A.D. Inheritance in bacteriophage. Ann. N.Y. Acad. Sci 1952, 54:960-962.
173. Ho Y., Rosenberg M. Characterization of the phage lambda regulatory protein cII. Ann. Microbiol. 1982, 133:215-218.
174. Ho Y.S., Pfarr D., Strickler J., Rosenberg M. Characterization of the transcription activator protein C1 of bacteriophage P22. J. Biol. Chem. 1992, 267:14388-14397.
175. Hohn T., Flick H., Hohn B. Petit lambda, a family of particles from coliphage lambda infected cells. J. Mol. Biol. 1975, 98:107-120.
176. Horcajadas J.A., Monsalve M., Rojo F., Salas M. The switch from early to late transcription in phage GA-1: Characterization of the regulatory protein p4G. J. Mol. Biol. 1999, 290:917-928.
177. Hu P., Janga S.C., Babu M., Diaz-Mejia J.J., Butland G., Yang W., Pogoutse O., Guo X., Phanse S., Wong P., Chandran S., Christopoulos C., et al. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 2009, 7:e96.
178. Huang J., Villemain J., Padilla R., Sousa R. Mechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase during different phases of transcription. J. Mol. Biol. 1999, 293:457-475.
179. Huber H.E., Beauchamp B.B., Richardson C.C. Escherichia coli dGTP triphosphohydrolase is inhibited by gene 1.2 protein of bacteriophage T7. J. Biol. Chem 1988, 263:13549-13556.
180. Ibarra B., Valpuesta J.M., Carrascosa J.L. Purification and functional characterization of p16, the ATPase of the bacteriophage phi29 packaging machinery. Nucleic Acids Res. 2001, 29:4264-4273.
181. Illana B., Blanco L., Salas M. Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1: Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. J. Mol. Biol. 1996, 264:453-464.
182. Illana B., Lázaro J.M., Gutierrez C., Meijer W.J., Blanco L., Salas M. Phage phi29 terminal protein residues Asn80 and Tyr82 are recognition elements of the replication origins. J. Biol. Chem. 1999, 274:15073-15079.
183. Isaksen M.L., Dokland T., Lindqvist B.H. Characterization of the capsid associating activity of bacteriophage P4's Psu protein. Virology 1993, 194:647-681.
184. Iwashita S., Kanegasaki S. Enzymic and molecular properties of base-plate parts of bacteriophage P22. Eur. J. Biochem. 1976, 65:87-94.
185. Jackson E.N., Jackson D.A., Deans R.J. EcoRI analysis of bacteriophage P22 DNA packaging. J. Mol. Biol. 1978, 118:365-388.
186. Jeruzalmi D., Steitz T.A. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 1998, 17:4101-4113.
187. Julien B., Lefevre P., Calendar R. The two P2 Ogr-like domains of the delta protein from bacteriophage P4 are required for activity. Virology 1997, 230:292-299.
188. Kageyama Y., Murayama M., Onodera T., Yamada S., Fukada H., Kudou M., Tsumoto K., Toyama Y., Kado S., Kubota K., Takeda S. Observation of the membrane binding activity and domain structure of gpV, which comprises the tail spike of bacteriophage P2. Biochemistry 2009, 48:10129-10135.
189. Kaiser A.D., Jacob F. Recombination between related bacteriophages and the genetic control of immunity and prophage localization. Virology 1957, 4:509-517.
190. Kamtekar S., Berman A.J., Wang J., Lázaro J.M., de Vega M., Blanco L., Salas M., Steitz T.A. The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. EMBO J. 2006, 25:1335-1343.
191. Katsura I. Tail assembly and injection. " Lambda II 1983, 331-346. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. R. Hendrix, J. Roberts, F.W. Stahl, R. Weisberg (Eds.).
192. Katsura I. Mechanism of length determination in bacteriophage lambda tails. Adv. Biophys. 1990, 26:1-18.
193. Katsura I., Tsugita A. Purification and characterization of the major protein and the terminator protein of the bacteriophage lambda tail. Virology 1977, 76:129-145.
194. Kedzierska B., Lee D.J., Wegrzyn G., Busby S.J., Thomas M.S. Role of the RNA polymerase alpha subunits in CII-dependent activation of the bacteriophage lambda pE promoter: identification of important residues and positioning of the alpha C-terminal domains. Nucleic Acids Res. 2004, 32:834-841.
195. Kedzierska B., Szambowska A., Herman-Antosiewicz A., Lee D.J., Busby S.J., Wegrzyn G., Thomas M.S. The C-terminal domain of the Escherichia coli RNA polymerase alpha subunit plays a role in the CI-dependent activation of the bacteriophage lambda pM promoter. Nucleic Acids Res. 2007, 35:2311-2320.
196. Kemp P., Garcia L.R., Molineux I.J. Changes in bacteriophage T7 virion structure at the initiation of infection. Virology 2005, 340:307-317.
197. Kemp P., Gupta M., Molineux I.J. Bacteriophage T7 DNA ejection into cells is initiated by an enzyme-like mechanism. Mol. Microbiol. 2004, 53:1251-1265.
198. Kennaway C.K., Obarska-Kosinska A., White J.H., Tuszynska I., Cooper L.P., Bujnicki J.M., Trinick J., Dryden D.T. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res 2009, 37:762-770.
199. Kennedy W.P., Momand J.R., Yin Y.W. Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase. J. Mol. Biol. 2007, 370:256-268.
200. Kihara A., Akiyama Y., Ito K. Revisiting the lysogenization control of bacteriophage lambda: Identification and characterization of a new host component. HflD. J. Biol. Chem. 2001, 276:13695-13700.
201. Kim K.-J., Sunshine M.G., Lindqvist B.H., Six E.W. Capsid size determination in the P2-P4 bacteriophage system: suppression of sir mutations in P2's capsid gene N by supersid mutations in P4's external scaffold gene sid. Virology 2001, 283:49-58.
202. King J., Casjens S. Catalytic head assembling protein in virus morphogenesis. Nature 1974, 251:112-119.
203. King J., Lenk E.V., Botstein D. Mechanism of head assembly and DNA encapsulation in Salmonella phage P22. II. Morphogenetic pathway. J. Mol. Biol. 1973, 80:697-731.
204. King R.A., Anders D.L., Christie G.E. Site-directed mutagenesis of an amino acid residue in the bacteriophage P2 ogr protein implicated in interaction with Escherichia coli RNA polymerase. Mol. Microbiol. 1992, 6:3313-3320.
205. Kobiler O., Koby S., Teff D., Court D., Oppenheim A.B. The phage lambda CII transcriptional activator carries a C-terminal domain signaling for rapid proteolysis. Proc. Natl. Acad. Sci. USA 2002, 99:14964-14969.
206. Kobiler O., Oppenheim A.B., Herman C. Recruitment of host ATP-dependent proteases by bacteriophage lambda. J. Struct. Biol. 2004, 146:72-78.
207. Kobiler O., Rokney A., Oppenheim A.B. Phage lambda CIII: A protease inhibitor regulating the lysis-lysogeny decision. PLoS One 2007, 2:e363.
208. Kochan J., Carrascosa J.L., Murialdo H. Bacteriophage lambda preconnectors. Purification and structure. J. Mol. Biol. 1984, 174:433-447.
209. Kornitzer D., Altuvia S., Oppenheim A.B. The activity of the CIII regulator of lambdoid bacteriophages resides within a 24-amino acid protein domain. Proc. Natl. Acad. Sci. USA 1991, 88:5217-5221.
210. Lander G.C., Evilevitch A., Jeembaeva M., Potter C.S., Carragher B., Johnson J.E. Bacteriophage lambda stabilization by auxiliary protein gpD: Timing, location, and mechanism of attachment determined by cryo-EM. Structure 2008, 16:1399-1406.
211. Lander G.C., Tang L., Casjens S.R., Gilcrease E.B., Prevelige P., Poliakov A., Potter C.S., Carragher B., Johnson J.E. The structure of an infectious P22 virion shows the signal for headful DNA packaging. Science 2006, 312:1791-1795.
212. LeBowitz J.H., McMacken R. The Escherichia coli dnaB replication protein is a DNA helicase. J. Biol. Chem. 1986, 261:4738-4748.
213. Lee C.S., Guo P. Sequential interactions of structural proteins in phage phi 29 procapsid assembly. J. Virol. 1995, 69:5024-5032.
214. Leffers G.G., Gottesman S. Lambda Xis degradation in vivo by Lon and FtsH. J. Bacteriol. 1998, 180:1573-1577.
215. Lehne B., Schlitt T. Protein-protein interaction databases: Keeping up with growing interactomes. Hum. Genom. 2009, 3:291-297.
216. Lengyel J.A., Goldstein R.N., Marsh M., Calendar R. Structure of the bacteriophage P2 tail. Virology 1974, 62:161-174.
217. Lengyel J.A., Goldstein R.N., Marsh M., Sunshine M.G., Calendar R. Bacteriophage P2 head morphogenesis: cleavage of the major capsid protein. Virology 1973, 53:1-23.
218. Li M., Moyle H., Susskind M.M. Target of the transcriptional activation function of phage lambda cI protein. Science 1994, 263:75-77.
219. Lin L. "Study of Bacteriophage T7 Gene 5.9 and Gene 5.5" 1992, SUNY, Stonybrook, NY.
220. Linderoth N.A., Julien B., Flick K.E., Calendar R., Christie G. Molecular cloning and characterization of bacteriophage P2 genes R and S involved in tail completion. Virology 1994, 200:347-359.
221. Linderoth N.A., Ziermann R., Haggård-Ljungquist E., Christie G.E., Calendar R. Nucleotide sequence of the DNA packaging and capsid synthesis genes of bacteriophage P2. Nucl. Acids Res. 1991, 19:7207-7214.
222. Lindqvist B.H., Deho G., Calendar R. Mechanisms of genome propagation and helper exploitation by satellite phage P4. Microbiol. Rev. 1993, 57:683-702.
223. Little J.W. An exonuclease induced by bacteriophage lambda. II. Nature of the enzymatic reaction. J. Biol. Chem 1967, 242:679-686.
224. Liu Q., Richardson C.C. Gene 5.5 protein of bacteriophage T7 inhibits the nucleoid protein H-NS of Escherichia coli. Proc. Natl. Acad. Sci.USA 1993, 90:1761-1765.
225. Liu T., Renberg S.K., Haggard-Ljungquist E. The E protein of satellite phage P4 acts as an anti-repressor by binding to the C protein of helper phage P2. Mol. Microbiol. 1998, 30:1041-1050.
226. Liu X., Zhang Q., Murata K., Baker M.L., Sullivan M.B., Fu C., Dougherty M.T., Schmid M.F., Osburne M.S., Chisholm S.W., Chiu W. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat. Struct. Mol. Biol. 2010, 17:830-836.
227. Liu Y., Haggard-Ljungquist E. Studies of bacteriophage P2 DNA replication: localization of the cleavage site of the A protein. Nucleic Acids Res 1994, 22:5204-5210.
228. Loeffler J.M., Djurkovic S., Fischetti V.A. Phage lytic enzyme Cpl-1 as a novel antimicrobial for pneumococcal bacteremia. Infect. Immun. 2003, 71:6199-6204.
229. Loeffler J.M., Nelson D., Fischetti V.A. Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase. Science 2001, 294:2170-2172.
230. Longás E., de Vega M., Lázaro J.M., Salas M. Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity. Nucleic Acids Res. 2006, 34:6051-6063.
231. Longás E., Villar L., Lázaro J.M., de Vega M., Salas M. Phage phi29 and Nf terminal protein-priming domain specifies the internal template nucleotide to initiate DNA replication. Proc. Natl. Acad. Sci. USA 2008, 105:18290-18295.
232. Lopez R., Ronda C., Tomasz A., Portoles A. Properties of " diplophage": A lipid-containing bacteriophage. J. Virol. 1977, 24:201-210.
233. Lyakhov D.L., He B., Zhang X., Studier F.W., Dunn J.J., McAllister W.T. Mutant bacteriophage T7 RNA polymerases with altered termination properties. J. Mol. Biol. 1997, 269:28-40.
234. Lyakhov D.L., He B., Zhang X., Studier F.W., Dunn J.J., McAllister W.T. Pausing and termination by bacteriophage T7 RNA polymerase. J. Mol. Biol. 1998, 280:201-213.
235. Makela P.H. Glucosylation of lipopolysaccharide in Salmonella: Mutants negative for O antigen factor 1221. J. Bacteriol. 1973, 116:847-856.
236. Mallory J.B., Alfano C., McMacken R. Host virus interactions in the initiation of bacteriophage lambda DNA replication: Recruitment of Escherichia coli DnaB helicase by lambda P replication protein. J. Biol. Chem. 1990, 265:13297-13307.
237. Marchand I., Nicholson A.W., Dreyfus M. Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase. Mol. Microbiol. 2001, 42:767-776.
238. Marintcheva B., Qimron U., Yu Y., Tabor S., Richardson C.C. Mutations in the gene 5 DNA polymerase of bacteriophage T7 suppress the dominant lethal phenotype of gene 2.5 ssDNA binding protein lacking the C-terminal phenylalanine. Mol. Microbiol 2009, 72:869-880.
239. Marr M.T., Datwyler S.A., Meares C.F., Roberts J.W. Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins. Proc. Natl. Acad. Sci. USA 2001, 98:8972-8978.
240. Marr M.T., Roberts J.W., Brown S.E., Klee M., Gussin G.N. Interactions among CII protein, RNA polymerase and the lambda PRE promoter: Contacts between RNA polymerase and the -35 region of PRE are identical in the presence and absence of CII protein. Nucleic Acids Res. 2004, 32:1083-1090.
241. Marsic N., Roje S., Stojiljkovic I., Salaj-Smic E., Trgovcevic Z. In vivo studies on the interaction of RecBCD enzyme and lambda Gam protein. J. Bacteriol. 1993, 175:4738-4743.
242. Martin A.C., Blanco L., Garcia P., Salas M., Mendez J. In vitro protein-primed initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3' nucleotide of the linear template: A stepwise sliding-back mechanism. J. Mol. Biol. 1996, 260:369-377.
243. Marvik O.J., Dokland T., Nøkling R.H., Jacobsen E., Larsen T., Lindqvist B.H. The capsid size-determining protein Sid forms an external scaffold on phage P4 procapsids. J. Mol. Biol. 1995, 251:59-75.
244. Marvik O.J., Jacobsen E., Dokland T., Lindqvist B.H. Bacteriophage P2 and P4 morphogenesis: assembly precedes proteolytic processing of the capsid proteins. Virology 1994, 205:51-65.
245. Mason S.W., Greenblatt J. Assembly of transcription elongation complexes containing the N protein of phage lambda and the Escherichia coli elongation factors NusA, NusB, NusG, and S10. Genes Dev. 1991, 5:1504-1512.
246. Massad T., Skaar K., Nilsson H., Damberg P., Henriksson-Peltola P., Haggard-Ljungquist E., Hogbom M., Stenmark P. Crystal structure of the P2 C-repressor: A binder of non-palindromic direct DNA repeats. Nucleic Acids Res. 2010, 38:7778-7790.
247. Mattis A.N., Gumport R.I., Gardner J.F. Purification and characterization of bacteriophage P22 Xis protein. J. Bacteriol. 2008, 190:5781-5796.
248. Maxwell K.L., Reed P., Zhang R.G., Beasley S., Walmsley A.R., Curtis F.A., Joachimiak A., Edwards A.M., Sharples G.J. Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange. Proc. Natl. Acad. Sci. USA 2005, 102:11260-11265.
249. Maxwell K.L., Yee A.A., Booth V., Arrowsmith C.H., Gold M., Davidson A.R. The solution structure of bacteriophage lambda protein W, a small morphogenetic protein possessing a novel fold. J. Mol. Biol. 2001, 308:9-14.
250. Mayer J.E., Schweiger M. RNase III is positively regulated by T7 protein kinase. J. Biol. Chem. 1983, 258:5340-5343.
251. McDonnell M., Lain R., Tomasz A. " Diplophage": A bacteriophage of Diplococcus pneumoniae. Virology 1975, 63:577-582.
252. Medina E., Wieczorek D., Medina E.M., Yang Q., Feiss M., Catalano C.E. Assembly and maturation of the bacteriophage lambda procapsid: gpC is the viral protease. J. Mol. Biol. 2010, 401:813-830.
253. Meijer W.J., Horcajadas J.A., Salas M. Phi29 family of phages. Microbiol. Mol. Biol. Rev. 2001, 65:261-287.
254. Meijer W.J., Lewis P.J., Errington J., Salas M. Dynamic relocalization of phage phi 29 DNA during replication and the role of the viral protein p16.7. EMBO J 2000, 19:4182-4190.
255. Meijer W.J., Serna-Rico A., Salas M. Characterization of the bacteriophage phi29-encoded protein p16.7: A membrane protein involved in phage DNA replication. Mol. Microbiol 2001, 39:731-746.
256. Mencía M., Monsalve M., Rojo F., Salas M. Transcription activation by phage phi29 protein p4 is mediated by interaction with the alpha subunit of Bacillus subtilis RNA polymerase. Proc. Natl. Acad. Sci. USA 1996, 93:6616-6620.
257. Mencía M., Monsalve M., Salas M., Rojo F. Transcriptional activator of phage phi 29 late promoter: mapping of residues involved in interaction with RNA polymerase and in DNA bending. Mol. Microbiol. 1996, 20:273-282.
258. Méndez J., Blanco L., Esteban J.A., Bernad A., Salas M. Initiation of phi 29 DNA replication occurs at the second 3' nucleotide of the linear template: A sliding-back mechanism for protein-primed DNA replication. Proc. Natl. Acad. Sci. USA 1992, 89:9579-9583.
259. Méndez J., Blanco L., Salas M. Protein-primed DNA replication: A transition between two modes of priming by a unique DNA polymerase. EMBO J. 1997, 16:2519-2527.
260. Mikawa Y.G., Maruyama I.N., Brenner S. Surface display of proteins on bacteriophage lambda heads. J. Mol. Biol. 1996, 262:21-30.
261. Moak M., Molineux I.J. Role of the Gp16 lytic transglycosylase motif in bacteriophage T7 virions at the initiation of infection. Mol. Microbiol. 2000, 37:345-355.
262. Moak M., Molineux I.J. Peptidoglycan hydrolytic activities associated with bacteriophage virions. Mol. Microbiol. 2004, 51:1169-1183.
263. Molineux I.J. The T7 group. The Bacteriophages 2006, 277-301. Chapter 20, Oxford University Press, Oxford. R. Calendar (Ed.).
264. Molineux I.J. Fifty-three years since Hershey and Chase; much ado about pressure but which pressure is it?. Virology 2006, 344:221-229.
265. Monsalve M., Calles B., Mencía M., Salas M., Rojo F. Transcription activation or repression by phage psi 29 protein p4 depends on the strength of the RNA polymerase-promoter interactions. Mol. Cell. 1997, 1:99-107.
266. Monsalve M., Mencía M., Rojo F., Salas M. Activation and repression of transcription at two different phage phi29 promoters are mediated by interaction of the same residues of regulatory protein p4 with RNA polymerase. EMBO J. 1996, 15:383-391.
267. Monsalve M., Mencía M., Salas M., Rojo F. Protein p4 represses phage phi 29 A2c promoter by interacting with the alpha subunit of Bacillus subtilis RNA polymerase. Proc. Natl. Acad. Sci. USA 1996, 93:8913-8918.
268. Mooney P.Q., North R., Molineux I.J. The role of bacteriophage T7 gene 2 protein in DNA replication. Nucleic Acids Res. 1980, 8:3043-3053.
269. Morais M.C., Choi K.H., Koti J.S., Chipman P.R., Anderson D.L., Rossmann M.G. Conservation of the capsid structure in tailed dsDNA bacteriophages: The pseudoatomic structure of phi29. Mol. Cell. 2005, 18:149-159.
270. Morais M.C., Kanamaru S., Badasso M.O., Koti J.S., Owen B.A., McMurray C.T., Anderson D.L., Rossmann M.G. Bacteriophage phi29 scaffolding protein gp7 before and after prohead assembly. Nat. Struct. Biol. 2003, 10:572-576.
271. Morita M., Tasaka M., Fujisawa H. Analysis of functional domains of the packaging proteins of bacteriophage T3 by site-directed mutagenesis. J. Mol. Biol. 1994, 235:248-259.
272. Morita M., Tasaka M., Fujisawa H. Structural and functional domains of the large subunit of the bacteriophage T3 DNA packaging enzyme: Importance of the C-terminal region in prohead binding. J. Mol. Biol. 1995, 245:635-644.
273. Mosig G., Yu S., Myung H., Haggard-Ljungquist E., Davenport L., Carlson K., Calendar R. A novel mechanism of virus-virus interactions: Bacteriophage P2 Tin protein inhibits phage T4 DNA synthesis by poisoning the T4 single-stranded DNA binding protein, gp32. Virology 1997, 230:72-81.
274. Mount D.W., Harris A.W., Fuerst C.R., Siminovitch L. Mutations in bacteriophage lambda affecting particle morphogenesis. Virology 1968, 35:134-149.
275. Muñoz-Espín D., Daniel R., Kawai Y., Carballido-Lopez R., Castilla-Llorente V., Errington J., Meijer W.J., Salas M. The actin-like MreB cytoskeleton organizes viral DNA replication in bacteria 2009, Proc. Natl. Acad. Sci, USA.
276. Muñoz-Espín D., Holguera I., Ballesteros-Plaza D., Carballido-Lopez R., Salas M. Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid. Proc. Natl. Acad. Sci. USA 2010, 107:16548-16553.
277. Murialdo H. Early intermediates in bacteriophage lambda prohead assembly. Virology 1979, 96:341-367.
278. Murialdo H., Becker A. Head morphogenesis of complex double-stranded deoxyribonucleic acid bacteriophages. Microbiol. Rev. 1978, 42:529-576.
279. Murialdo H., Tzamtzis D. Mutations of the coat protein gene of bacteriophage lambda that overcome the necessity for the Fl gene; the EFi domain. Mol. Microbiol. 1997, 24:341-353.
280. Murphy K.C. Bacteriophage P22 Abc2 protein binds to RecC increases the 5' strand nicking activity of RecBCD and together with lambda bet, promotes Chi- independent recombination. J. Mol. Biol. 2000, 296:385-401.
281. Murray N.E. Type I restriction systems: Sophisticated molecular machines (a legacy of Bertani and Weigle). MMBR 2000, 64:412-434.
282. Nakai H., Richardson C.C. The gene 1.2 protein of bacteriophage T7 interacts with the Escherichia coli dGTP triphosphohydrolase to form a GTP-binding protein. J. Biol. Chem 1990, 265:4411-4419.
283. Nechaev S., Severinov K. Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein. J. Mol. Biol. 1999, 289:815-826.
284. Nemecek D., Gilcrease E.B., Kang S., Prevelige P.E., Casjens S., Thomas G.J. Subunit conformations and assembly states of a DNA-translocating motor: The terminase of bacteriophage P22. J. Mol. Biol. 2007, 374:817-836.
285. Nemecek D., Lander G.C., Johnson J.E., Casjens S.R., Thomas G.J. Assembly architecture and DNA binding of the bacteriophage P22 terminase small subunit. J. Mol. Biol. 2008, 383:494-501.
286. Newlove T., Konieczka J.H., Cordes M.H. Secondary structure switching in Cro protein evolution. Structure (Camb.) 2004, 12:569-581.
287. Nickels B.E., Roberts C.W., Sun H., Roberts J.W., Hochschild A. The sigma(70) subunit of RNA polymerase is contacted by the (lambda)Q antiterminator during early elongation. Mol. Cell. 2002, 10:611-622.
288. Nilsson A.S., Haggård-Ljungquist E. The P2-like bacteriophages. 2006, 365-390. Oxford University Press, New York. R. Calendar (Ed.).
289. Nilsson A.S., Karlsson J.L., Haggård-Ljungquist E. Site-specific recombination links the evolution of P2-like coliphages and pathogenic enterobacteria. Mol. Biol. Evol. 2004, 21:1-13.
290. Nooren I.M., Kaptein R., Sauer R.T., Boelens R. The tetramerization domain of the Mnt repressor consists of two right-handed coiled coils. Nat. Struct. Biol. 1999, 6:755-759.
291. Nuez B., Rojo F., Salas M. Phage phi 29 regulatory protein p4 stabilizes the binding of the RNA polymerase to the late promoter in a process involving direct protein-protein contacts. Proc. Natl. Acad. Sci. USA 1992, 89:11401-11405.
292. Odegrip R., Haggard-Ljungquist E. The two active-site tyrosine residues of the a protein play non-equivalent roles during initiation of rolling circle replication of bacteriophage p2. J Mol Biol 2001, 308:147-163.
293. Odegrip R., Schoen S., Haggard-Ljungquist E., Park K., Chattoraj D.K. The interaction of bacteriophage P2 B protein with Escherichia coli DnaB helicase. J. Virol. 2000, 74:4057-4063.
294. Olia A., Prevelige P., Johnson J., Cingolani G. Three-dimensional structure of a viral genome-delivery portal vertex. Nat. Struct. Mol. Biol 2011, in press.
295. Olia A.S., Al-Bassam J., Winn-Stapley D.A., Joss L., Casjens S.R., Cingolani G. Binding-induced stabilization and assembly of the phage P22 tail accessory factor gp4. J. Mol. Biol. 2006, 363:558-576.
296. Olia A.S., Bhardwaj A., Joss L., Casjens S., Cingolani G. Role of gene 10 protein in the hierarchical assembly of the bacteriophage P22 portal vertex structure. Biochemistry 2007, 46:8776-8784.
297. Oppenheim A.B., Kobiler O., Stavans J., Court D.L., Adhya S. Switches in bacteriophage lambda development. Annu. Rev. Genet. 2005, 39:409-429.
298. Pani B., Ranjan A., Sen R. Interaction surface of bacteriophage P4 protein Psu required for complex formation with the transcription terminator Rho. J. Mol. Biol. 2009, 389:647-660.
299. Parker M.H., Casjens S., Prevelige P.E. Functional domains of bacteriophage P22 scaffolding protein. J. Mol. Biol. 1998, 281:69-79.
300. Parker M.H., Stafford W.F., Prevelige P.E. Bacteriophage P22 scaffolding protein forms oligomers in solution. J. Mol. Biol. 1997, 268:655-665.
301. Parkinson M.J., Lilley D.M. The junction-resolving enzyme T7 endonuclease I: Quaternary structure and interaction with DNA. J. Mol. Biol. 1997, 270:169-178.
302. Parua P.K., Mondal A., Parrack P. HflD, an Escherichia coli protein involved in the lambda lysis-lysogeny switch, impairs transcription activation by lambdaCII. Arch. Biochem. Biophys. 2010, 493:175-183.
303. Pastrana R., Lazaro J.M., Blanco L., Garcia J.A., Mendez E., Salas M. Overproduction and purification of protein P6 of Bacillus subtilis phage phi 29: Role in the initiation of DNA replication. Nucleic Acids Res. 1985, 13:3083-3100.
304. Pedulla M.L., Ford M.E., Karthikeyan T., Houtz J.M., Hendrix R.W., Hatfull G.F., Poteete A.R., Gilcrease E.B., Winn-Stapley D.A., Casjens S.R. Corrected sequence of the bacteriophage p22 genome. J. Bacteriol. 2003, 185:1475-1477.
305. Pell L.G., Liu A., Edmonds L., Donaldson L.W., Howell P.L., Davidson A.R. The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages. J. Mol. Biol. 2009, 389:938-951.
306. Poteete A.R., Botstein D. Purification and properties of proteins essential to DNA encapsulation by phage P22. Virology 1979, 95:565-573.
307. Poteete A.R., Fenton A.C. DNA-binding properties of the Erf protein of bacteriophage P22. J. Mol. Biol. 1983, 163:257-275.
308. Poteete A.R., King J. Functions of two new genes in Salmonella phage P22 assembly. Virology 1977, 76:725-739.
309. Poteete A.R., Sauer R.T., Hendrix R.W. Domain structure and quaternary organization of the bacteriophage P22 Erf protein. J. Mol. Biol. 1983, 171:401-418.
310. Potrykus K., Baranska S., Wegrzyn A., Wegrzyn G. Composition of the lambda plasmid heritable replication complex. Biochem. J. 2002, 364:857-862.
311. Prell H.H., Harvey A.M. P22 antirepressor protein prevents in vivo recA-dependent proteolysis of P22 repressor. Mol. Gen. Genet. 1983, 190:427-431.
312. Prevelige P.E., Thomas D., King J. Scaffolding protein regulates the polymerization of P22 coat subunits into icosahedral shells in vitro. J. Mol. Biol. 1988, 202:743-757.
313. Pruss G.J., Wang J.C., Calendar R. In vitro packaging of covalently-closed circular monomers of bacteriophage DNA. J. Mol. Biol. 1975, 98:465-478.
314. Ptashne M. A Genetic Switch: Phage Lambda Revisited 2004, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Third Ed.
315. Ptashne M. A Genetic Switch. Phage Lambda Revisited 2006, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
316. Putnam C.D., Shroyer M.J., Lundquist A.J., Mol C.D., Arvai A.S., Mosbaugh D.W., Tainer J.A. Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. J. Mol. Biol. 1999, 287:331-346.
317. Qimron U., Marintcheva B., Tabor S., Richardson C.C. Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage. Proc. Natl. Acad. Sci. USA 2006, 103:19039-19044.
318. Radding C.M., Rosenzweig J., Richards J., Cassuto E. Appendix: Separation and characterization of exonuclease, β protein and a complex of both. J. Biol. Chem. 1971, 146:2510-2512.
319. Rahmsdorf H.J., Pai S.H., Ponta H., Herrlich P., Roskoski R., Schweiger M., Studier F.W. Protein kinase induction in Escherichia coli by bacteriophage T7. Proc. Natl. Acad. Sci. USA 1974, 71:586-589.
320. Rajagopala S.V., Casjens S., Uetz P. The protein interaction map of bacteriophage lambda. BMC Microbiol. 2011, 11:213.
321. Ranade K., Poteete A.R. Superinfection exclusion (sieB) genes of bacteriophages P22 and lambda. J. Bacteriol. 1993, 175:4712-4718.
322. Ranade K., Poteete A.R. A switch in translation mediated by an antisense RNA. Genes Dev. 1993, 7:1498-1507.
323. Ray P., Murialdo H. The role of gene Nu3 in bacteriophage lambda head morphogenesis. Virology 1975, 64:247-263.
324. Rennell D., Poteete A.R. Phage P22 lysis genes: Nucleotide sequences and functional relationships with T4 and lambda genes. Virology 1985, 143:280-289.
325. Rennell D., Poteete A.R. Genetic analysis of bacteriophage P22 lysozyme structure. Genetics 1989, 123:431-440.
326. Rezende L.F., Hollis T., Ellenberger T., Richardson C.C. Essential amino acid residues in the single-stranded DNA-binding protein of bacteriophage T7: Identification of the dimer interface. J. Biol. Chem. 2002, 277:50643-50653.
327. Rishovd S., Lindqvist B.H. Bacteriophage P2 and P4 morphogenesis: protein processing and capsid size determination. Virology 1992, 187:548-554.
328. Rishovd S., Marvik O.J., Jacobsen E., Lindqvist B.H. Bacteriophage P2 and P4 morphogenesis: Identification and characterization of the portal protein. Virology 1994, 200:744-751.
329. Roberts C.W., Roberts J.W. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell 1996, 86:495-501.
330. Roberts J.W. Termination factor for RNA synthesis. Nature 1969, 224:1168-1174.
331. Roberts J.W., Yarnell W., Bartlett E., Guo J., Marr M., Ko D.C., Sun H., Roberts C.W. Antitermination by bacteriophage lambda Q protein. Cold Spring Harb. Symp. Quant. Biol. 1998, 63:319-325.
332. Robertson E.S., Aggison L.A., Nicholson A.W. Phosphorylation of elongation factor G and ribosomal protein S6 in bacteriophage T7-infected Escherichia coli. Mol. Microbiol. 1994, 11:1045-1057.
333. Robertson E.S., Nicholson A.W. Protein kinase of bacteriophage T7 induces the phosphorylation of only a small number of proteins in the infected cell. Virology 1990, 175:525-534.
334. Robertson E.S., Nicholson A.W. Phosphorylation of Escherichia coli translation initiation factors by the bacteriophage T7 protein kinase. Biochemistry 1992, 31:4822-4827.
335. Rodriguez-Cerrato V., Garcia P., Del Prado G., Garcia E., Gracia M., Huelves L., Ponte C., Lopez R., Soriano F. In vitro interactions of LytA, the major pneumococcal autolysin, with two bacteriophage lytic enzymes (Cpl-1 and Pal), cefotaxime and moxifloxacin against antibiotic-susceptible and -resistant Streptococcus pneumoniae strains. J. Antimicrob. Chemother. 2007, 60:1159-1162.
336. Rojo F., Mencia M., Monsalve M., Salas M. Transcription activation and repression by interaction of a regulator with the alpha subunit of RNA polymerase: The model of phage phi 29 protein p4. Prog. Nucleic Acid Res. Mol. Biol. 1998, 60:29-46.
337. Rojo F., Salas M. A DNA curvature can substitute phage phi 29 regulatory protein p4 when acting as a transcriptional repressor. EMBO J. 1991, 10:3429-3438.
338. Sabri M., Häuser R., Ouellette M., Liu J., Dehbi M., Moeck G., Garcia E., Titz B., Uetz P., Moineau S. Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. J. Bacteriol. 2011, 193:551-562.
339. Saito H., Richardson C.C. Processing of mRNA by ribonuclease III regulates expression of gene 1.2 of bacteriophage T7. Cell 1981, 27:533-542.
340. Salas M. Protein-priming of DNA replication. Annu. Rev. Biochem. 1991, 60:39-71.
341. Sam M.D., Papagiannis C.V., Connolly K.M., Corselli L., Iwahara J., Lee J., Phillips M., Wojciak J.M., Johnson R.C., Clubb R.T. Regulation of directionality in bacteriophage lambda site-specific recombination: structure of the Xis protein. J. Mol. Biol. 2002, 324:791-805.
342. Sam M.D., Cascio D., Johnson R.C., Clubb R.T. Crystal structure of the excisionase-DNA complex from bacteriophage lambda. J. Mol. Biol. 2004, 338:229-240.
343. Sanger F., Air G.M., Barrell B.G., Brown N.L., Coulson A.R., Fiddes C.A., Hutchison C.A., Slocombe P.M., Smith M. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977, 265:687-695.
344. Sauer B., Ow D., Ling L., Calendar R. Mutants of satellite bacteriophage P4 that are defective in the suppression of transcriptional polarity. J. Mol. Biol. 1981, 145:29-46.
345. Savalia D., Robins W., Nechaev S., Molineux I., Severinov K. The role of the T7 Gp2 inhibitor of host RNA polymerase in phage development. J. Mol. Biol. 2010, 402:118-126.
346. Savva C.G., Dewey J.S., Deaton J., White R.L., Struck D.K., Holzenburg A., Young R. The holin of bacteriophage lambda forms rings with large diameter. Mol. Microbiol. 2008, 69:784-793.
347. Schmitt C.K., Molineux I.J. Expression of gene 1.2 and gene 10 of bacteriophage T7 is lethal to F plasmid-containing Escherichia coli. J. Bacteriol. 1991, 173:1536-1543.
348. Schulz E.C., Dickmanns A., Urlaub H., Schmitt A., Muhlenhoff M., Stummeyer K., Schwarzer D., Gerardy-Schahn R., Ficner R. Crystal structure of an intramolecular chaperone mediating triple-beta-helix folding. Nat. Struct. Mol. Biol. 2010, 17:210-215.
349. Semerjian A.V., Malloy D.C., Poteete A.R. Genetic structure of the bacteriophage P22 PL operon. J. Mol. Biol. 1989, 207:1-13.
350. Serna-Rico A., Munoz-Espin D., Villar L., Salas M., Meijer W.J. The integral membrane protein p16.7 organizes in vivo phi29 DNA replication through interaction with both the terminal protein and ssDNA. EMBO J 2003, 22:2297-2306.
351. Serna-Rico A., Salas M., Meijer W.J. The Bacillus subtilis phage phi 29 protein p16.7, involved in phi 29 DNA replication, is a membrane-localized single-stranded DNA-binding protein. J. Biol. Chem 2002, 277:6733-6742.
352. Serrano M., Gutierrez C., Freire R., Bravo A., Salas M., Hermoso J.M. Phage phi 29 protein p6: A viral histone-like protein. Biochimie 1994, 76:981-991.
353. Serrano-Heras G., Bravo A., Salas M. Phage phi29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase. Proc. Natl. Acad. Sci. USA 2008, 105:19044-19049.
354. Serrano-Heras G., Ruiz-Maso J.A., del Solar G., Espinosa M., Bravo A., Salas M. Protein p56 from the Bacillus subtilis phage phi29 inhibits DNA-binding ability of uracil-DNA glycosylase. Nucleic Acids Res. 2007, 35:5393-5401.
355. Serrano-Heras G., Salas M., Bravo A. A uracil-DNA glycosylase inhibitor encoded by a non-uracil containing viral DNA. J. Biol. Chem. 2006, 281:7068-7074.
356. Severinova E., Severinov K. Localization of the Escherichia coli RNA polymerase beta' subunit residue phosphorylated by bacteriophage T7 kinase Gp0.7. J. Bacteriol 2006, 188:3470-3476.
357. Sevilla-Sierra P., Otting G., Wuthrich K. Determination of the nuclear magnetic resonance structure of the DNA-binding domain of the P22 c2 repressor (1 to 76) in solution and comparison with the DNA-binding domain of the 434 repressor. J. Mol. Biol. 1994, 235:1003-1020.
358. Shotland Y., Shifrin A., Ziv T., Teff D., Koby S., Kobiler O., Oppenheim A.B. Proteolysis of bacteriophage lambda CII by Escherichia coli FtsH (HflB). J. Bacteriol. 2000, 182:3111-3116.
359. Simon M.N., Studier F.W. Physical mapping of the early region of bacteriophage T7 DNA. J. Mol. Biol. 1973, 79:249-265.
360. Simpson A.A., Leiman P.G., Tao Y., He Y., Badasso M.O., Jardine P.J., Anderson D.L., Rossmann M.G. Structure determination of the head-tail connector of bacteriophage phi29. Acta Crystallogr. D Biol. Crystallogr. 2001, 57:1260-1269.
361. Simpson A.A., Tao Y., Leiman P.G., Badasso M.O., He Y., Jardine P.J., Olson N.H., Morais M.C., Grimes S., Anderson D.L., Baker T.S., Rossmann M.G. Structure of the bacteriophage phi29 DNA packaging motor. Nature 2000, 408:745-750.
362. Singleton M.R., Sawaya M.R., Ellenberger T., Wigley D.B. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 2000, 101:589-600.
363. Sippy J., Feiss M. Analysis of a mutation affecting the specificity domain for prohead binding of the bacteriophage lambda terminase. J. Bacteriol. 1992, 174:850-856.
364. Six E.W. The helper dependence of satellite bacteriophage P4: which gene functions of bacteriophage P2 are needed by P4?. Virology 1975, 67:249-263.
365. Six E.W., Sunshine M.G., Williams J., Haggård-Ljungquist E., Lindqvist B.H. Morphopoietic switch mutations of bacteriophage P2. Virology 1991, 182:34-46.
366. Souza L., Calendar R., Six E., Lindqvist B. A transactivation mutant of satellite phage P4. Virology 1977, 81:81-90.
367. Stano N.M., Patel S.S. T7 lysozyme represses T7 RNA polymerase transcription by destabilizing the open complex during initiation. J. Biol. Chem. 2004, 279:16136-16143.
368. Steinbacher S., Miller S., Baxa U., Budisa N., Weintraub A., Seckler R., Huber R. Phage P22 tailspike protein: Crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen recognition and cleavage. J. Mol. Biol 1997, 267:865-880.
369. Steinbacher S., Seckler R., Miller S., Steipe B., Huber R., Reinemer P. Crystal structure of P22 tailspike protein: Interdigitated subunits in a thermostable trimer. Science 1994, 265:383-386.
370. Stellberger T., Häuser R., Baiker A., Pothineni V.R., Haas J., Uetz P. Improving the yeast two-hybrid system with permutated fusions proteins: The Varicella Zoster Virus interactome. Proteome Sci. 2010, 8:8.
371. Stephanou A.S., Roberts G.A., Cooper L.P., Clarke D.J., Thomson A.R., MacKay C.L., Nutley M., Cooper A., Dryden D.T. Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification. J. Mol. Biol. 2009, 391:565-576.
372. Sternberg N., Hoess R.H. Display of peptides and proteins on the surface of bacteriophage lambda. Proc. Natl. Acad. Sci. USA 1995, 92:1609-1613.
373. Sternberg N., Weisberg R. Packaging of coliphage lambda DNA. II. The role of the gene D protein. J. Mol. Biol 1977, 117:733-759.
374. Steven A.C., Trus B.L., Maizel J.V., Unser M., Parry D.A., Wall J.S., Hainfeld J.F., Studier F.W. Molecular substructure of a viral receptor-recognition protein. The gp17 tail-fiber of bacteriophage T7. J. Mol. Biol 1988, 200:351-365.
375. Stone J.C., Miller R.C. Spontaneous temperature-sensitive mutations in bacteriophage T7. J. Virol. 1985, 54:886-888.
376. Studier F.W. Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction system of the host. J. Mol. Biol 1975, 94:283-295.
377. Studier F.W., Movva N.R. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J. Virol. 1976, 19:136-145.
378. Studier F.W. Identification and mapping of five new genes in bacteriophage T7. J. Mol. Biol. 1981, 153:493-502.
379. Summer E.J., Berry J., Tran T.A., Niu L., Struck D.K., Young R. Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. J. Mol. Biol. 2007, 373:1098-1112.
380. Sunshine M., Usher D., Calendar R. Interaction of P2 bacteriophage with the dnaB gene of Escherichia coli. J. Virol. 1975, 16:284-289.
381. Sunshine M.G., Sauer B. A bacterial mutation blocking P2 phage late gene expression. Proc. Natl. Acad. Sci. USA 1975, 72:2770-2774.
382. Susskind M.M., Botstein D. Mechanism of action of Salmonella phage P22 antirepressor. J. Mol. Biol. 1975, 98:413-424.
383. Susskind M.M., Botstein D. Molecular genetics of bacteriophage P22. Microbiol. Rev. 1978, 42:385-413.
384. Szambowska A., Pierechod M., Wegrzyn G., Glinkowska M. Coupling of transcription and replication machineries in λ DNA replication initiation: Evidence for direct interaction of Escherichia coli RNA polymerase and the λ O protein. Nucleic Acids Res. 2010, 39:168-177.
385. Tahirov T.H., Temiakov D., Anikin M., Patlan V., McAllister W.T., Vassylyev D.G., Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature 2002, 420:43-50.
386. Takahashi I., Marmur J. Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis. Nature 1963, 197:794-795.
387. Tang J., Lander G., Olia A., Li R., Casjens S., Prevelige P., Cingolani G., Baker T., Johnson J. Peering down the barrel of a bacteriophage portal: The genome packaging and release valve in P22. Structure 2011, 19:496-502.
388. Tang L., Gilcrease E.B., Casjens S.R., Johnson J.E. Highly discriminatory binding of capsid-cementing proteins in bacteriophage L. Structure 2006, 14:837-845.
389. Tao Y., Olson N.H., Xu W., Anderson D.L., Rossmann M.G., Baker T.S. Assembly of a tailed bacterial virus and its genome release studied in three dimensions. Cell 1998, 95:431-437.
390. Temple L., Forsburg S., Calendar R., Christie G. Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2. Virology 1991, 181:353-358.
391. Tokuno S.I., Gough M. UV sensitivity of a nonrepressor regulatory protein of bacteriophage P22. J. Virol. 1976, 18:65-70.
392. Tran N.Q., Lee S.J., Richardson C.C., Tabor S. A novel nucleotide kinase encoded by gene 1.7 of bacteriophage T7. Mol. Microbiol 2010, 77:492-504.
393. Tsui L., Hendrix R.W. Head-tail connector of bacteriophage lambda. J. Mol. Biol. 1980, 142:419-438.
394. Tsui L.C., Hendrix R.W. Proteolytic processing of phage lambda tail protein gpH: Timing of the cleavage. Virology 1983, 125:257-264.
395. Tye B.K., Huberman J.A., Botstein D. Non-random circular permutation of phage P22 DNA. J. Mol. Biol. 1974, 85:501-528.
396. Uetz P., Rajagopala S.V., Dong Y.A., Haas J. From ORFeomes to protein interaction maps in viruses. Genome Res. 2004, 14:2029-2033.
397. Valpuesta J.M., Fujisawa H., Marco S., Carazo J.M., Carrascosa J.L. Three-dimensional structure of T3 connector purified from overexpressing bacteria. J. Mol. Biol. 1992, 224:103-112.
398. Valpuesta J.M., Sousa N., Barthelemy I., Fernandez J.J., Fujisawa H., Ibarra B., Carrascosa J.L. Structural analysis of the bacteriophage T3 head-to-tail connector. Journal of structural biology 2000, 131:146-155.
399. van der Poll T., Opal S.M. Pathogenesis, treatment, and prevention of pneumococcal pneumonia. Lancet 2009, 374:1543-1556.
400. Vander Byl C., Kropinski A.M. Sequence of the genome of Salmonella bacteriophage P22. J. Bacteriol. 2000, 182:6472-6481.
401. Vershon A.K., Liao S.M., McClure W.R., Sauer R.T. Bacteriophage P22 Mnt repressor: DNA binding and effects on transcription in vitro. J. Mol. Biol. 1987, 195:311-322.
402. Vershon A.K., Liao S.M., McClure W.R., Sauer R.T. Interaction of the bacteriophage P22 Arc repressor with operator DNA. J. Mol. Biol. 1987, 195:323-331.
403. Villafane R., Zayas M., Gilcrease E.B., Kropinski A.M., Casjens S.R. Genomic analysis of bacteriophage epsilon 34 of Salmonella enterica serovar Anatum (15+). BMC Microbiol. 2008, 8:227.
404. Wang J., Hofnung M., Charbit A. The C-terminal portion of the tail fiber protein of bacteriophage lambda is responsible for binding to LamB, its receptor at the surface of Escherichia coli K-12. J. Bacteriol. 2000, 182:508-512.
405. Wang S., Chang J.R., Dokland T. Assembly of bacteriophage P2 and P4 procapsids with internal scaffolding protein. Virology 2006, 348:133-140.
406. Wang S., Palasingam P., Nøkling R.H., Lindqvist B.H., Dokland T. In vitro assembly of bacteriophage P4 procapsids from purified capsid and scaffolding proteins. Virology 2000, 275:133-144.
407. Wang W.F., Cheng X., Molineux I.J. Isolation and identification of fxsA, an Escherichia coli gene that can suppress F exclusion of bacteriophage T7. J. Mol. Biol. 1999, 292:485-499.
408. Warren D., Sam M.D., Manley K., Sarkar D., Lee S.Y., Abbani M., Wojciak J.M., Clubb R.T., Landy A. Identification of the lambda integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation. Proc. Natl. Acad. Sci. USA 2003, 100:8176-8181.
409. Wegrzyn A., Taylor K., Wegrzyn G. The cbpA chaperone gene function compensates for dnaJ in lambda plasmid replication during amino acid starvation of Escherichia coli. J. Bacteriol. 1996, 178:5847-5849.
410. Wegrzyn A., Wegrzyn G. Inheritance of the replication complex: A unique or common phenomenon in the control of DNA replication?. Arch. Microbiol. 2001, 175:86-93.
411. Wegrzyn G., Wegrzyn A. Stress responses and replication of plasmids in bacterial cells. Microb. Cell Fact. 2002, 1:2.
412. Weigele P.R., Sampson L., Winn-Stapley D., Casjens S.R. Molecular genetics of bacteriophage P22 scaffolding protein's functional domains. J. Mol. Biol. 2005, 348:831-844.
413. Werts C., Michel V., Hofnung M., Charbit A. Adsorption of bacteriophage lambda on the LamB protein of Escherichia coli K-12: point mutations in gene J of lambda responsible for extended host range. J. Bacteriol. 1994, 176:941-947.
414. White J.H., Richardson C.C. Gene 18 protein of bacteriophage T7: Overproduction, purification, and characterization. J. Biol. Chem. 1987, 262:8845-8850.
415. Wickner S. DNA-dependent ATPase activity associated with phage P22 gene 12 protein. J. Biol. Chem. 1984, 259:14038-14043.
416. Wickner S.H., Zahn K. Characterization of the DNA binding domain of bacteriophage lambda O protein. J. Biol. Chem. 1986, 261:7537-7543.
417. Wood L.F., Tszine N.Y., Christie G.E. Activation of P2 late transcription by P2 Ogr protein requires a discrete contact site on the C terminus of the alpha subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 1997, 274:1-7.
418. Xiang Y., Leiman P.G., Li L., Grimes S., Anderson D.L., Rossmann M.G. Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol. Cell. 2009, 34:375-386.
419. Xiang Y., Morais M.C., Cohen D.N., Bowman V.D., Anderson D.L., Rossmann M.G. Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail. Proc. Natl. Acad. Sci. USA 2008, 105:9552-9557.
420. Xu J., Hendrix R.W., Duda R.L. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell. 2004, 16:11-21.
421. Yang F., Forrer P., Dauter Z., Conway J.F., Cheng N., Cerritelli M.E., Steven A.C., Pluckthun A., Wlodawer A. Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD. Nat. Struct. Biol. 2000, 7:230-237.
422. Yin Y.W., Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 2002, 298:1387-1395.
423. Yin Y.W., Steitz T.A. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 2004, 116:393-404.
424. Yoshikawa H., Elder J.H., Ito J. Comparative studies on the small Bacillus bacteriophages. J. Gen. Appl. Microbiol. 1986, 155:392-401.
425. Youderian P., Susskind M.M. Identification of the products of bacteriophage P22 genes, including a new late gene. Virology 1980, 107:258-269.
426. Yura K., Yamaguchi A., Go M. Coverage of whole proteome by structural genomics observed through protein homology modeling database. J. Struct. Funct. Genom. 2006, 7:65-76.
427. Zahn K., Blattner F.R. Binding and bending of the lambda replication origin by the phage O protein. EMBO J. 1985, 4:3605-3616.
428. Zahn K., Blattner F.R. Direct evidence for DNA bending at the lambda replication origin. Science 1987, 236:416-422.
429. Zahn K., Landy A. Modulation of lambda integrase synthesis by rare arginine tRNA. Mol. Microbiol. 1996, 21:69-76.
430. Zhang X., Studier F.W. Isolation of transcriptionally active mutants of T7 RNA polymerase that do not support phage growth. J. Mol. Biol. 1995, 250:156-168.
431. Zhang X., Studier F.W. Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme. J. Mol. Biol. 1997, 269:10-27.
432. Zhang X., Studier F.W. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection. J. Mol. Biol. 2004, 340:707-730.
433. Ziermann R., Calendar R. Characterization of the cos sites of bacteriophages P2 and P4. Gene 1990, 96:9-15.
434. Zillig W., Fujiki H., Blum W., Janekovic D., Schweiger M., Rahmsdorf H., Ponta H., Hirsch-Kauffmann M. In vivo and in vitro phosphorylation of DNA-dependent RNA polymerase of Escherichia coli by bacteriophage-T7-induced protein kinase. Proc. Natl. Acad. Sci. USA 1975, 72:2506-2510.
435. Zinder N.D., Lederberg J. Genetic exchange in Salmonella. J. Bacteriol. 1952, 64:679-699.
436. zylicz M., Ang D., Liberek K., Georgopoulos C. Initiation of lambda DNA replication with purified host- and bacteriophage-encoded proteins: The role of the dnaK, dnaJ and grpE heat shock proteins. EMBO J. 1989, 8:1601-1608.