Initial cos cleavage of bacteriophage λ concatemers requires proheads and gpFI in in vivo

Molecular Microbiology

Volumn 52, Issue 2, 2004, Pages 501-513

  Sippy, Jean ^a   Feiss, Michael ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; BACTERIOPHAGE; BACTERIOPHAGE GAMMA; CHROMOSOME SIZE; CONTROLLED STUDY; DNA CLEAVAGE; DNA REPLICATION; DNA VIRUS; GENE DELETION; GENE MUTATION; GENETIC CODE; NONHUMAN; PRIORITY JOURNAL; VIRUS CAPSID;

BACTERIOPHAGE LAMBDA; BINDING SITES; CAPSID; DNA, CONCATENATED; DNA, VIRAL; ENDODEOXYRIBONUCLEASES; MODELS, GENETIC; MUTATION; PLASMIDS; VIRAL PROTEINS;

BACTERIOPHAGE 21; BACTERIOPHAGE GAMMA; BACTERIOPHAGE LAMBDA; DNA VIRUSES; UNIDENTIFIED BACTERIOPHAGE;

EID: 1942436909     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2004.03990.x     Document Type: Article

References (74)

1. Arber, W., Enquist, L., Hohn, B., Murray, N.E., and Murray, K. (1983) Experimental methods for use with lambda. In Lambda II. Hendrix, R.W., Roberts, J.W., Stahl, F.W., and Weisberg, R.A. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 433-366.
2. Bear, S., Court, D., and Friedman, D. (1984) An accessory role for Escherischia coli integration host factor: characterization of a lambda mutant dependent upon integration host factor for DNA packaging. J Virol 52: 966-972.
3. Becker, A., and Murialdo, H. (1990) Bacteriophage lambda DNA: the beginning of the end. J Bacteriol 172: 2819-2824.
4. Becker, A., Marko, M., and Gold, M. (1977) Early events in the in vitro packaging of bacteriophage DNA. Virology 78: 291-305.
5. Becker, A., Murialdo, H., Lucko, H., and Morell, J. (1988) Bacteriophage lambda DNA packaging. The product of the Fl gene promotes the incorporation of the prohead to the DNA-terminase Complex. J Mol Biol 199: 597-607.
6. de Beer, T., Meyer, J., Ortega, M., Yang, Q., Maes, L., Duffy, C., Berton, N., et al. (2002) Insights into specific DNA recognition during assembly of a viral genome packaging machine; structure and genetics of the DNA binding domain of gpNu1. Mol Cell 9: 981-991.
7. Bowden, D.W., and Modrich, P. (1985) In vitro maturation of the circular bacteriophage P2 DNA. Purification of ter components and characaterization of the reaction. J Biol Chem 260: 6999-7007.
8. Casjens, S., Hohn, T., and Kaiser, A.D. (1970) Morphological proteins of phage lambda: identification of the major head protein as the product of gene. E Virol 42: 496-507.
9. Catalano, C.E. (2000) The terminase enzyme from bacteriophage lambda: a DNA packaging machine. Cell Mol Life Sci 57: 128-148.
10. Catalano, C.E., and Tomka, M.A. (1995) Role of gpFl protein in DNA packaging by bacteriophage lambda. Biochemistry 34: 10036-10042.
11. Catalano, C.E., Cue, D., and Feiss, M. (1995) Virus DNA packaging: the strategy used by phage lambda. Mol Micro 16: 1075-1076.
12. Chai, S., Bravo, A., Lüder, G., Nedlin, A., Trautner, T.A., and Alonso, J.C. (1992) Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1-6. J Mol Biol 224: 87-102.
13. Cue, D., and Feiss, M. (1992) Genetic analysis of cosB, the binding site for terminase, the DNA packaging enzyme of bacteriophage lambda. J Mol Biol 228: 58-71.
14. Cue, D., and Feiss, M. (1993a) A site required for the termination of packaging of the phage λ chromosome. Proc Natl Acad Sci USA 90: 9290-9294.
15. Cue, D., and Feiss, M. (1993b) The role of cosB, the binding site for terminase, the DNA packaging enzyme of bacteriophage lambda, in the nicking reaction. J Mol Biol 234: 594-609.
16. Cue, D., and Feiss, M. (1998) Termination of packaging of the bacteriophage lambda chromosome: cosQ is required for nicking the bottom strand of cosN. J Mol Biol 280: 11-29.
17. Daniels, D., Schroeder, J., Szybalski, W., Sanger, F., Coulson, A., Hong, G., et al. (1983) Completed annotated lambda sequence. In Lambda II. Hendrix, R.W., Roberts, J.W., Stahl, F.W., and Weisberg, R.A. (eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 519-676.
18. Datsenko, K., and Wanner, B. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97: 6640-6645.
19. Davidson, A., and Gold, M. (1987) A novel in vitro DNA packaging system demonstrating a direct role for the bacteriophage λ Fl gene product. Virology 161: 305-315.
20. Davidson, A., and Gold, M. (1992) Mutations abolishing the endonuclease activity of bacteriophage λ terminase lie in two distinct regions of the A gene, one of which may encode a leucine zipper DNA binding domain. Virology 161: 305-315.
21. Dove, W.F. (1966) Action of the lambda chromosome. I. Control of functions late in bacteriophage development. J Mol Biol 19: 187-197.
22. Emmons, S.W. (1974) Bacteriophage lambda derivatives carrying two copies of the cohesive end site. J Mol Biol 83: 511-525.
23. Feiss, M. (1986) Terminase and the recognition, cutting and packaging of λ chromosomes. Trends Gen 2: 100-104.
24. Feiss, M., Fisher, R.A., Siegele, D.A., Nichols, B.P., and Donelson, J.E. (1979) Packaging of the bacteriophage lambda chromosome: a role for base sequences outside cos. Virology 92: 56-67.
25. Feiss, M., Sippy, J., and Miller, G. (1985) Processive action of terminase during sequential packaging of bacteriophage lambda chromosomes. J Mol Biol 186: 759-771.
26. Frackman, S., Siegele, D.A., and Feiss, M. (1984) A functional domain of bacteriophage lambda terminase for prohead binding. J Mol Biol 180: 283-300.
27. Frackman, S., Siegele, D.A., and Feiss, M. (1985) The terminase of bacteriophage lambda. Functional domains for cosB binding and multimer assembly. J Mol Biol 183: 225-238.
28. Furth, M.E., and Wickner, S.H. (1983) Lambda DNA replication. In Lambda II. Hendrix, R.W., Roberts, J.W., Stahl, J.W., and Weisberg, R.A. (eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 145-173.
29. Georgopoulos, C., Tilly, K., and Casjens, S. (1983) Lambdoid phage head assembly. In Lambda II. Hendrix, R.W., Roberts, J.W., Stahl, J.W., and Weisberg, R.A. (eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 279-304.
30. Guo, P., Peterson, C., and Anderson, D.C. (1987) Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage φ29. J Mol Biol 197: 229-236.
31. Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166: 557-580.
32. Hang, Q., Tack, B., and Feiss, M. (2000) An ATPase center of bacteriophage λ terminase involved in post-cleavage stages of DNA packaging: identification of ATP-interactive amino acids. J Mol Biol 302: 777-795.
33. Hendrix, R.W., and Casjens, S.R. (1975) Assembly of bacteriophage lambda heads: protein processing and its genetic control in petit lambda assembly. J Mol Biol 91: 187-199.
34. Higgins, R.R., Lucko, H.J., and Becker, A. (1988) Mechanism of cos DNA cleavage by bacteriophage lambda terminase: multiple roles of ATP. Cell 54: 765-775.
35. Homa, F.L., and Brown, J. (1997) Capsid assembly and DNA packaging in herpes simplex virus. Rev Med Virol 7: 107-122.
36. Hwang, Y., and Feiss, M. (1995) A defined system for in vitro lambda DNA packaging. Virology 211: 367-376.
37. Hwang, Y., and Feiss, M. (1996) Mutations affecting the high affinity ATPase center of gpA, the large subunit of bacteriophage lambda terminase, inactivate the endonuclease activity of terminase. J Mol Biol 261: 524-535.
38. King, R.A., Anders, D.L., and Christie, G.E. (1992) Site-directed mutagenesis of an amino acid residue in the bacteriophage P2 Ogr protein implicated in interaction with Escherichia coli RNA polymerase. Mol Microbiol 6: 3313-3320.
39. Kochan, J., and Murialdo, H. (1983) Early intermediates in bacteriophage lambda prohead assembly. II. Identification of biologically active intermediates. Virology 131: 100-115.
40. Kochan, J., Carrascosa, J.L., and Murialdo, H. (1984) Bacteriophage lambda preconnectors: purification and structure. J Mol Biol 174: 433-447.
41. Kuzminov, A., Schabtach, E., and Stahl, F.W. (1994) Chi sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating the ExoV activity of RecBCD nuclease. EMBO J 13: 2764-2776.
42. Lanski, F., and Jackson, E.N. (1982) Maturation cleavage of bacteriophage P22 DNA in the absence of DNA packaging. J Mol Biol 154: 565-579.
43. MacKinlay, A.G., and Kaiser, A.D. (1969) DNA replication in head mutants of bacteriophage 1. J Mol Biol 39: 679-683.
44. McClure, S.C., Lorne, C.M., and Gold, M. (1973) A sedimentation analysis of DNA found in Escherichia coli infected with phage 1 mutants. Virology 54: 1-18.
45. Merril, C.R., Biswas, B., Carlton, R., Jensen, N.C., Creed, G.J., Zullo, S., and Adhya, S. (1996) Long-circulating bacteriophage as antibacterial agents. Proc Natl Acad Sci USA 93: 3188-3192.
46. Murialdo, H. (1979) Early intermediates in bacteriophage lambda prohead assembly. Virology 96: 341-367.
47. Murialdo, H. (1991) Bacteriophage lambda DNA maturation and packaging. Annu Rev Biochem 60: 125-153.
48. Murialdo, H., and Fife, W.L. (1984) The maturation of coliphage lambda DNA in the absence of its packaging. Gene 30: 183-194.
49. Murialdo, H., and Fife, W.L. (1987) Synthesis of a transacting inhibitor of DNA maturation by prohead mutants of phage 1. Genetics 115: 3-10.
50. Murialdo, H., and Ray, P.N. (1975) Model for arrangement of minor structural proteins in the head of bacteriophage 1. Nature (London) 257: 815-817.
51. Murialdo, H., and Tzamtzis, D. (1997) Mutations of the coat protein gene of bacteriophage 1 that overcome the necessity for the Fl gene. The EFi domain. Mol Microbiol 24: 341-353.
52. Murialdo, H., Fife, W., Becker, A., Feiss, M., and Yochem, J. (1981) Bacteriophage lambda DNA maturation. The functional relationships among the products of genes Nul, A and Fl. J Mol Biol 145: 375-404.
53. Murialdo, H., Tzamtzis, D., Berru, M., Fife, W.L., and Becker, A. (1997) Mutations in the terminase genes of bacteriophage λ that bypass the necessity for Fl. Mol Microbiol 24: 937-952.
54. Newcomb, W.W., Juhas, R.M., Thomsen, D.R., Homa, F.L., Burch, A.D., Weller, S.K., and Brown, J.C. (2001) The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid. J Virol 75: 10923-10932.
55. Pal, S.K., and Chattoraj, D.K. (1988) P1 plasmid replication: initiator sequestration is inadequate to explain control by initiator-binding sites. J Bacteriol 172: 2819-2824.
56. Parkinson, J.S. (1968) Genetics of the left arm of the chromosome of bacteriophage lambda. Genetics 59: 311-325.
57. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
58. Sanger, F., Coulson, A.R., Hong, G.F., Hill, D.F., and Petersen, G.B. (1982) Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 162: 729.
59. Shinder, G., and Gold, M. (1988) The Nu1 subunit of bacteriophage lambda terminase binds to specific sites in cos DNA. J Virol 62: 387-392.
60. Shinder, G., and Gold, M. (1989) Integration host factor (IHF) stimulates binding of the gpNu1 subunit of λ terminase to cos DNA. Nucleic Acids Res 17: 2005-2022.
61. Siegele, D.A., Frackman, S., Sippy, J., Momany, T., Howard, T.M., Tilly, K., et al. (1983) The head genes of bacteriophage 21. Virology 129: 484-489.
62. Sippy, J., and Feiss, M. (1992) Analysis of a mutation affecting the specificity domain for prohead binding of the bacteriophage lambda terminase. J Bacteriol 174: 850-856.
63. Six, E., and Klug, C.A.C. (1973) Bacteriophage P4: a satellite virus depending on a helper such as prophage P2. Virology 51: 327-344.
64. Smith, M.P., and Feiss, M. (1993a) Sequence analysis of the phage 21 genes for prohead assembly and head completion. Gene 126: 1-7.
65. Smith, M.P., and Feiss, M. (1993b) Sites and gene products involved in lambdoid phage DNA packaging. J Bacteriol 175: 2393-2399.
66. Sternberg, N. (1976) A genetic analysis of bacteriophage λ head assembly. Virology 71: 568-582.
67. Tomka, M.A., and Catalano, C.E. (1993) Physical and Kuietic characterization of the DNA packaging enzyme from bacteriophage lambda. J Biol Chem 268: 3056-3065.
68. Tsui, L., and Hendrix, R.W. (1980) Head-tail connector of bacteriophage lambda. J Mol Biol 142: 419-438.
69. Walker, J.E., Aufferet, A.D., Carne, A., Gurnett, A., Hanisch, P., Hill, D., and Saraste, M. (1982a) Solid-phase sequence analysis of polypeptides eluted from polyacrylamide gels: An aid to interpretation of DNA sequences as exemplified by Escherichia coli unc operon and bacteriophage lambda. Euro J Biochem 123: 23-260.
70. Walker, J.E., Saraste, M., Runswick, M., and Gay, N. (1982b) Distantly related sequences in the α-and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 8: 945-951.
71. Wu, W.-F., Christiansen, S., and Feiss, M. (1988) Domains for protein-protein interactions at the N and C termini of the large subunit of bacteriophage lambda terminase. Genetics 119: 477-484.
72. Yeo, A., and Feiss, M. (1995a) Specific interaction of terminase, the DNA packaging enzyme of bacteriophage lambda, with the portal protein of the prohead. J Mol Biol 245: 141-150.
73. Yeo, A., and Feiss, M. (1995b) Mutational analysis of the prohead binding domain of the large subunit of terminase, the bacteriophage lambda DNA packaging enzyme. J Mol Biol 245: 126-140.
74. Yu, D., Ellis, H.M., Lee, E.-C., Jenkins, N.A., Copeland, N.G., and Court, D.L. (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci USA 97: 5978-5983.