642
Views
11
CrossRef citations to date
0
Altmetric
Review Article

Bacteriophage-encoded functions engaged in initiation of homologous recombination events

Pages 197-220 | Received 30 Nov 2008, Accepted 20 Apr 2009, Published online: 30 Jun 2009

References

  • Akroyd, JE, Clayson, E, and Higgins, NP 1986, Purification of the gam gene–product of bacteriophage Mu and determination of the nucleotide sequence of the gam gene Nucleic Acids Res 14: 6901–6914
  • Alberts, BM, and Frey, L 1970, T4 bacteriophage gene 32: a structural protein in the replication and recombination of DNA Nature 227: 1313–1318
  • Alonso, JC, Lüder, G, and Trautner, TA 1992, Intramolecular homologous recombination in Bacillus subtilis 168 Mol Gen Genet 236: 60–64
  • Alonso, JC, Lüder, G, and Trautner, TA 1986, Requirements for the formation of plasmid–transducing particles of Bacillus subtilis bacteriophage SPP1 EMBO J 5: 3723–3728
  • Alonso, JC, Lüder, G, Steige, AC, Chai, S, Weise, F, and Trautner, TA 1997, The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1 Gene 204: 201–221
  • Anderson, DG, and Kowalczykowski, SC 1997a, The recombination hotspot χ is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme Genes Dev 11: 571–581
  • Anderson, DG, and Kowalczykowski, SC 1997b, The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a Chi–regulated manner Cell 90: 77–86
  • Appasani, K, Thaler, DS, and Goldberg, EB 1999, Bacteriophage T4 gp2 interferes with cell viability and with bacteriophage lambda red recombination J Bacteriol 181: 1352–1355
  • Araki, H, and Ogawa, H 1981, The participation of T7 DNA–binding protein in T7 genetic recombination Virology 111: 509–515
  • Aravind, L, Makarova, KS, and Koonin, EV 2000, Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories Nucleic Acids Res 28: 3417–3432
  • Ayora, S, Missich, R, Mesa, P, Lurz, R, Yang, S, Egelman, EH, and Alonso, JC 2002, Homologous–pairing activity of the Bacillus subtilis bacteriophage SPP1 replication protein G35P J Biol Chem 277: 35969–35979
  • Beernink, HT, and Morrical, SW 1999, RMPs: recombination/replication mediator proteins TIBS 24: 385–389
  • Beheme, MT, Lilley, GD, and Ebisuzaki, K 1976, Postinfection control by bacteriophage T4 of Escherichia coli recBC nuclease activity J Virol 18: 20–25
  • Bendtsen, JD, Nilsson, AS, and Lehnherr, H 2002, Phylogenetic and functional analysis of the bacteriophage P1 single–stranded DNA–binding protein J Virol 76: 9695–9701
  • Botstein, D, and Matz, MJ 1970, A recombination function essential to the growth of bacteriophage P22 J Mol Biol 54: 417–440
  • Bouchard, JD, and Moineau, S 2004, Lactococcal phage genes involved in sensitivity to AbiK and their relation to single–strand annealing proteins J Bacteriol 186: 3649–3652
  • Bravo, A, and Alonso, JC 1990, The generation of concatemeric plasmid DNA in Bacillus subtilis as a consequence of bacteriophage SPP1 infection Nucleic Acids Res 18: 4651–4657
  • Brister, JR, and Nossal, NG 2007, Multiple origins of replication contribute to a discontinuous pattern of DNA synthesis across the T4 genome during infection J Mol Biol 368: 336–348
  • Brooks, K, and Clark, AJ 1967, Behaviour of lambda bacteriophage in a recombination deficient strain of Escherichia coli J Virol 1: 283–293
  • Brüssow, H, and Desiere, F 2001, Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages Mol Microbiol 39: 213–222
  • Brüssow, H, and Hendrix, RW 2002, Phage genomics: small is beautiful Cell 108: 13–16
  • Burger, KJ, and Trautner, TA 1978, Specific labelling of replicating SPP1 DNA: analysis of viral DNA synthesis and identification of phage DNA–genes Mol Gen Genet 166: 277–285
  • Campbell, A 1994, Comparative molecular biology of lambdoid phages Annu Rev Microbiol 48: 193–222
  • Campbell, A 1988, Phage evolution and speciation In: The bacteriophages, vol 1, ed Calendar, R, 1–14, Plenum Press, New York
  • Carles–Kinch, K, George, JW, and Kreuzer, KN 1997, Bacteriophage T4 UvsW protein is a helicase involved in recombination, repair and the regulation of DNA replication origins EMBO J 16: 4142–4151
  • Casjens, SR 2005, Comparative genomics and evolution of the tailed–bacteriophages Curr Opin Microbiol 8: 451–458
  • Cassuto, E, and Radding, CM 1971, Mechanism for the action of lambda exonuclease in genetic recombination Nat New Biol 229: 13–16
  • Chase, JW, and Williams, KR 1986, Single–stranded DNA binding proteins required for DNA replication Annu Rev Biochem 55: 103–136
  • Choi, M, Miller, A, Cho, NY, and Rothman–Denes, LB 1995, Identification, cloning and characterization of the bacteriophage N4 gene encoding the single–stranded DNA–binding protein J Biol Chem 270: 22541–22547
  • Chopin, A, Bolotin, A, Sorokin, A, Ehrlich, SD, and Chopin, M-Ch 2001, Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations Nucleic Acids Res 29: 644–651
  • Conkling, M, and Drake, J 1984, Thermal rescue of UV–irradiated bacteriophage T4 and biphasic mode of action of the WXY system Genetics 107: 525–536
  • Connelly, JC, and Leach, DR 2002, Tethering on the brink: the evolutionarily conserved Mre11–Rad50 complex Trends Biochem Sci 27: 410–418 Review
  • Copeland, NG, Jenkins, NA, and Court, DL 2001, Recombineering: a powerful new tool for mouse functional genomics Nat Rev Genet 2: 769–779
  • Court, DL, Sawitzke, JA, and Thomason, LC 2002, Genetic engineering using homologous recombination Annu Rev Genet 36: 361–388
  • Court, R, Cook, N, Saikrishnan, K, and Wigley, D 2007, The crystal structure of λ–Gam protein suggests a model for RecBCD inhibition J Mol Biol 371: 25–33
  • Datsenko, KA, and Wanner, BL 2000, One–step inactivation of chromosomal genes in Escherichia coli K–12 using PRC products Proc Natl Acad Sci USA 97: 6640–6645
  • Datta, S, Costantino, N, Zhou, X, and Court, DL 2008, Identification and analysis of recombineering functions from Gram–negative and Gram–positive bacteria and their phages Proc Natl Acad Sci USA 105: 1626–1631
  • Derbise, A, Lesic, B, Dacheux, D, Ghigo, JM, and Carniel, E 2003, A rapid and simple method for inactivating chromosomal genes in Yersinia FEMS Immunol Med Microbiol 38: 113–116
  • Declais, AC, and Lilley, DM 2008, New insight into the recognition of branched DNA structure by junction–resolving enzymes Curr Opin Struct Biol 18: 86–95
  • Derr, LK, and Drake, JW 1990, Isolation and genetic characterization of new uvsW alleles of bacteriophage T4 Mol Gen Genet 222: 257–264
  • Dixon, DA, and Kowalczykowski, SC 1995, Role of the Escherichia coli recombination hotspot, Chi in a RecABCD–dependent homologous pairing J Biol Chem 270: 16360–16370
  • Edgar, RS, Denhardt, GH, and Epstein, RH 1964, A comparative genetic study of conditional lethal mutations of bacteriophage T4D Genetics 49: 635–648
  • El Karoui, M, Ehrlich, D, and Gruss, A 1998, Identification of the lactococcal exonuclease/helicase and its modulation by the putative Chi sequence Proc Natl Acad Sci USA 95: 626–631
  • El Karoui, M, Biaudet, V, Schbath, S, and Gruss, A 1999, Characteristics of Chi distribution on different on different bacterial genomes Res Microbiol 150: 579–587
  • Ellis, HM, Yu, D, DiTizio, T, and Court, DL 2001, High efficiency mutagenesis, repair and engineering of chromosomal DNA using single–stranded oligonucleotides Proc Natl Acad Sci USA 98: 6742–6746
  • Ford, ME, Sarkis, GJ, Belanger, AE, Hendrix, RW, and Hatfull, GF 1998, Genome structure of mycobacteriophage D29: implications for phage evolution J Mol Biol 279: 143–164
  • Formosa, T, and Alberts, BM 1986, Purification and characterization of the T4 bacteriophage uvsX protein J Biol Chem 261: 6107–6118
  • Formosa, T, Burke, RL, and Alberts, BM 1983, Affinity purification of bacteriophage T4 proteins essential for DNA replication and genetic recombination Proc Natl Acad Sci USA 80: 2442–2446
  • Friedman, SA, and Hays, JB 1986, Selective inhibition of E coli recBC activities by plasmid–encoded GamS of phage lambda Gene 43: 255–263
  • Gascón, I, Gutiérrez, C, and Salas, M 2000, Structural and functional comparative study of the complexes formed by viral ϕ29, Nf and GA–1 SSB proteins with DNA J Mol Biol 296: 989–999
  • George, JW, and Kreuzer, KN 1996, Repair of double–strand breaks in bacteriophage T4 by a mechanism that involves extensive DNA replication Genetics 143: 1507–1520
  • George, JW, Stohr, BA, Tomso, DJ, and Kreuzer, KN 2001, The tight linkage between DNA replication and double–strand break repair in bacteriophage T4 Proc Natl Acad Sci USA 98: 8290–8297
  • Hall, SD, and Kolodner, RD 1994, Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein Proc Natl Acad Sci USA 91: 3205–3209
  • Halpern, D, Gruss, A, Claverys, J-P, and El Karoui, M 2004, rexAB mutants in Streptococcus pneumoniae Microbiology 150: 2409–2414
  • Harris, LD, and Griffith, JD 1989, UvsY protein of bacteriophage T4 is an accessory protein for in vitro catalysis of strand exchange J Mol Biol 206: 19–27
  • Hatfull, GF 2008, Bacteriophage genomics Curr Opin Microbiol 11: 447–453
  • Henderson, D, and Weil, J 1975, Recombination–deficient deletions in bacteriophage lambda and their interaction with Chi mutations Genetics 79: 143–174
  • Hendrix, RW, Hatfull, GF, and Smith, MC 2003, Bacteriophages with tails: chasing their origin and evolution Res Microbiol 154: 253–257
  • Hill, SA, Stahl, MM, and Stahl, FW 1997, Single–strand DNA intermediates in phage lambda’s Red recombination pathway Proc Natl Acad Sci USA 94: 2951–2956
  • Hollis, T, Stattel, JM, Walther, DS, Richardson, CC, and Ellenberger, T 2001, Structure of the gene 25 protein, a single–stranded DNA binding protein encoded by bacteriophage T7 Proc Natl Acad Sci USA 98: 9557–9562
  • Hosoda, J, Mathews, E, and Jansen, B 1971, Role of genes 46 and 47 in bacteriophage T4 reproduction I In vivo deoxyribonucleic acid replication J Virol 8: 372–387
  • Huang, Y–J, Parker, MM, and Belfort, M 1999, Role of exonucleolytic degradation in group I intron homing in phage T4 Genetics 153: 1501–1512
  • Husseiny, M I, and Hensel, M 2005, Rapid method for the construction of Salmonella enterica Serovar Typhimurium vaccine carrier strains Infect Immun 73: 1598–1605
  • Iyer, LM, Koonin, EV, and Aravind, L 2002, Classification and evolutionary history of the single–strand annealing proteins, RecT, Redβ, ERF and RAD 52 BMC Genomics 3: 8
  • Jiang, H, Giedroc, D, and Kodadek, T 1993, The role of protein–protein interactions in the assembly of the presynaptic filament for T4 homologous recombination J Biol Chem 268: 7904–7911
  • Jones, CE, Mueser, TC, and Nossal, NG 2000, Interaction of the bacteriophage T4 gene 59 helicase loading protein and gene 41 helicase with each other and with fork, flap, and cruciform DNA J Biol Chem 275: 27145–27154
  • Jones, CE, Mueser, TC, Dudas, KC, Kreuzer, KN, and Nossal, NG 2001, Bacteriophage T4 gene 41 helicase and gene 59 helicase–loading protein: A versatile couple with roles in replication and recombination Proc Natl Acad Sci USA 98: 8312–8318
  • Juhala, RJ, Ford, ME, Duda, RL, Youlton, A, Hatfull, GF, and Hendrix, RW 2000, Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages J Mol Biol 299: 27–51
  • Kaiser, K, and Murray, NE 1980, On the nature of sbcA mutations in E coli K 12 Mol Gen Genet 179: 555–563
  • Kantake, N, Madiraju, MVVM, Sugiyama, T, and Kowalczykowski, SC 2002, Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA–binding protein: a common step in genetic recombination Proc Natl Acad Sci USA 99: 15327–15332
  • Karakousis, G, Ye, N, Li, Z, Chiu, SK, Reddy, G, and Radding, CM 1998, The Beta protein of phage lambda binds preferentially to an intermediate in DNA renaturation J Mol Biol 276: 721–731
  • Karu, AE, Sakaki, Y, Echols, H, and Linn, S 1975, The γ protein specified by bacteriophage λ J Biol Chem 250: 7377–7387
  • Kim, YT, and Richardson, CC 1993, Bacteriophage T7 gene 25 protein: an essential protein for DNA replication Proc Natl Acad Sci USA 90: 10173–10177
  • Kmiec, E, and Holloman, WK 1981, Beta protein of bacteriophage lambda promotes renaturation of DNA J Biol Chem 256: 12636–12639
  • Kodadek, T, Gan, DC, and Stemke–Hale, K 1989, The phage T4 uvsY recombination protein stabilizes presynaptic filaments J Biol Chem 264: 16451–16457
  • Kolodner, R, Hall, SD, and Luisi–DeLuca, C 1994, Homologous pairing proteins encoded by the Escherichia coli recE and recT genes Mol Microbiol 11: 23–30
  • Kong, D, and Richardson, CC 1998, Role of the acidic carboxyl–terminal domain of the single–stranded DNA–binding protein of bacteriophage T7 in specific protein–protein interactions J Biol Chem 273: 6556–6564
  • Kong, D, and Richardson, CC 1996, Single–stranded DNA binding protein and DNA helicase of bacteriophage T7 mediate homologous DNA strand exchange EMBO J 15: 2010–2019
  • Kong, D, Nossal, NG, and Richardson, CC 1997, Role of the bacteriophage T7 and T4 single–stranded DNA–binding proteins in the formation of joint molecules and DNA helicase–catalyzed polar branch migration J Biol Chem 272: 8380–8387
  • Kooistra, J, and Venema, G, 1991, Cloning, sequencing, and expression of Bacillus subtilis genes involved in ATP–dependent nuclease synthesis J Bacteriol 173: 3644–3655
  • Kovall, R, and Matthews, BW 1997, Toroidal structure of λ–exonuclease Science 277: 1824–1827
  • Kowalczykowski, SC 2000, Initiation of genetic recombination and recombination–dependent replication TIBS 25: 156–165
  • Kowalczykowski, SC, Bear, D, and von Hippel, P 1981, Single–stranded DNA binding protein In: The Enzymes, ed Boyer, PD, 373–442, Academic Press, New York
  • Kreuzer, KN 2005, Interplay between DNA replication and recombination in prokaryotes Annu Rev Microbiol 59: 43–67
  • Kreuzer, KN 2000, Recombination–dependent DNA replication in phage T4 TIBS 25: 165–173
  • Kreuzer, KN, Yap, WY, Menkens, AE, and Engman, HW 1988, Recombination–dependent replication of plasmids during bacteriophage T4 infection J Biol Chem 263: 11366–11373
  • Kruger, DH, and Schroeder, C 1981, Bacteriophage T3 and bacteriophage T7 virus–host cell interactions Microbiol Rev 45: 9–51
  • Kusano, K, Takahashi, NK, Yoshikura, H, and Kobayashi, I 1994, Involvement of RecE exonuclease and RecT annealing protein in DNA double–strand break repair by homologous recombination Gene 138: 17–25
  • Kuzminov, A 1999, Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda Microbiol Mol Biol Rev 63: 751–813
  • Kuzminov, A, Schabtach, E, and Stahl, FW 1994, Chi sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating exoV activity of RecBCD nuclease EMBO J 13: 2764–2776
  • Lam, ST, Stahl, MM, McMilin, KD, and Stahl, FM 1974, Rec–mediated recombinational hot spot activity in bacteriophage lambda II A mutation which causes hot spot activity Genetics 77: 425–433
  • Lefebvre, SD, Wong, ML, and Morrical, SW 1999, Simultaneous interactions of bacteriophage T4 DNA replication proteins gp59 and gp32 with single–stranded (ss) DNA J Biol Chem 274: 22830–22838
  • Lehnherr, H, Bendtsen, JD, Preuss, F, and Ilyina, TV 1999, Identification and characterization of the single–stranded DNA–binding protein of bacteriophage P1 J Bacteriol 181: 6463–6468
  • Lesic, B, and Rahme, LG 2008, Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa BMC Molecular Biology 9: 20
  • Li, Z, Karakousis, G, Chiu, SK, Reddy, G, and Radding, CM 1998, The beta protein of phage λ promotes strand exchange J Mol Biol 276: 733–744
  • Little, JW, Lehman, IR, and Kaiser, AD 1967, An exonuclease induced by bacteriophage λ J Biol Chem 242: 672–678
  • Lohman, TM, and Ferrari, ME 1994, Escherichia coli single–stranded DNA–binding protein: multiple DNA–binding modes and cooperativities Annu Rev Biochem 63: 527–570
  • Lucchini, S, Desiere, F, and Brüssow, H 1999, Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory J Virol 73: 8647–8656
  • Luria, SE 1947, Reactivation of irradiated bacteriophage by transfer of self–reproducing units Proc Natl Acad Sci USA 33: 253–264
  • Marsić, N, Roje, S, Stojiljkovićc, I, Salaj–šmic, E, and Trgovcević, Z 1993, In vivo studies on the interaction of RecBCD enzyme and lambda Gam protein J Bacteriol 175: 4738–4743
  • Martínez–Jiménez, MI, Alonso, JC, and Ayora, S 2005, Bacillus subtilis bacteriophage SPP1–encoded gene 341 product is a recombination–dependent DNA replication protein J Mol Biol 351: 1007–1019
  • Melamede, RJ, and Wallace, SS 1977, Properties of the nonlethal recombinational repair x and y mutants of bacteriophage T4 II DNA synthesis J Virol 24: 28–40
  • McAuliffe, O, Mills, S, Fitzgerald, GF, and Ross, RP 2005, Mining the lactococcal genome for genes that respond to phage attack 8th Symposium on lactic acid bacteria Eegmond am See Book of abstracts – L068
  • Miller, ES, Kutter, E, Mosig, G, Arisaka, F, Kunisawa, T, and Rüger, W 2003, T4 genome Microbiol Mol Biol Rev 67: 86–156
  • Monod, C, Repoila, F, Kutateladze, M, Tétart, F, and Krisch, HM 1997, The genome of the pseudo T–even bacteriophages, a diverse group that resembles T4 J Mol Biol 267: 237–249
  • Morimatsu, K, and Kowalczykowski, SC 2003, RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair Mol Cell 11: 1337–1347
  • Mosig, G 1987, The essential role of recombination in phage T4 growth Annu Rev Genet 21: 347–371
  • Mosig, G 1985, Bacteriophage T4 gene 32 participates in excision repair as well as recombinational repair of UV damages Genetics 110: 159–171
  • Mosig, G, Ehring, R, Schliewen, W, and Bock, S 1971, The patterns of recombination and segregation in terminal regions of T4 DNA molecules Mol Gen Genet 113: 51–91
  • Mosig, G, Gewin, J, Luder, A, Colowick, N, and Vo, D 2001, Two recombination–dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer Proc Natl Acad Sci USA 98: 8306–8311
  • Mueller, JE, Clyman, T, Huang, YJ, Parker, MM, and Belfort, M 1996, Intron mobility in phage T4 occurs in the context of recombination–dependent DNA replication by way of multiple pathways Genes Dev 10: 351–364
  • Muniyappa, K, and Radding, CM 1986, The homologous recombination system of phage lambda Pairing activities of Beta protein J Biol Chem 261: 7472–7478
  • Murphy, KC 2007, The λ Gam protein inhibits RecBCD binding to dsDNA ends J Mol Biol 371: 19–24
  • Murphy, KC 2000, 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 296: 385–401
  • Murphy, KC 1998, Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli J Bacteriol 180: 2063–2071
  • Murphy, KC 1994, Biochemical characterization of P22 phage–modified Escherichia coli RecBCD enzyme J Biol Chem 269: 22507–22516
  • Murphy, KC 1991, Lambda Gam protein inhibits the helicase and Chi–stimulated recombination activities of Escherichia coli RecBCD enzyme J Bacteriol 173: 5808–5821
  • Murphy, KC, and Campellone, KG, 2003, Lambda Red–mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E coli BMC Mol Biol 4: 11
  • Murphy, KC, and Lewis, LJ 1993, Properties of Escherichia coli expressing bacteriophage P22 Abc (anti–RecBCD) proteins, including inhibition of Chi activity J Bacteriol 175: 1756–1766
  • Murphy, KC, Campellone, KG, and Poteete, AR 2000, PCR–mediated gene replacement in Escherichia coli Gene 246: 321–330
  • Murphy, KC, Fenton, AC, and Poteete, AR 1987, Sequence of the bacteriophage P22 anti–RecBCD (abc) genes and properties of P22 abc region deletion mutants Virology 160: 456–464
  • Muyrers, JP, Zhang, Y, and Stewart, AF 2001, Techniques: recombinogenic engineering – new options for cloning and manipulating DNA TIBS 26: 325–331
  • Muyrers, JP, Zhang, Y, Buchholz, F, and Stewart, AF 2000, RecE/RecT and Redα/Redβ initiate double–stranded break repair by specifically interacting with their respective partners Genes Dev 14: 1971–1982
  • Muyrers, JP, Zhang, Y, Testa, G, and Stewart, AF 1999, Rapid modification of bacterial artificial chromosomes by ET–recombination Nucleic Acids Res 27: 1555–1557
  • Myers, RS, and Rudd, KE 1998, Mining DNA sequences for molecular enzymology: the Redα superfamily defines a set of recombination nucleases In Proceedings of the 1998 Miami Nature Biotechnology Winter Symposium, 49–50 Oxford University Press, Oxford, United Kingdom
  • Mythili, E, Kumar, K, and Muniyappa, K 1996, Characterization of the DNA–binding domain of Beta protein, a component of phage lambda Red–pathway, by UV catalyzed cross–linking Gene 182: 81–87
  • Nelson, SW, and Benkovic, SJ 2007, The T4 phage UvsW protein contains both DNA unwinding and strand annealing activities J Biol Chem 282: 407–416
  • Noirot, P, Gupta, RC, Radding, CM, and Kolodner, RD 2003, Hallmarks of homology recognition by RecA–like recombinases are exhibited by the unrelated Escherichia coli RecT protein EMBO J 22: 324–334
  • Pacumbaba, R, and Center, MS 1975, Partial purification and properties of a bacteriophage T7 inhibitor of the host exonuclease V activity J Virol 16: 1200 – 1207
  • Pajunen, MI, Elizondo, MR, Skurnik, M, Kieleczawa, J, and Molineux, IJ 2002, Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3 J Mol Biol 319: 1115–1132
  • Pajunen, MI, Kiljunen, SJ, Söderholm, ME–Lotta, and Skurnik, M 2001, Complete genomic sequence of the lytic bacteriophage YeO3–12 of Yersinia enterocolitica serotype O:3 J Bacteriol 183: 1928–1937
  • Park, MS, Ludwig, DL, Stigger, E, and Lee, S-H., 1996, Physical interaction between human RAD52 and RPA is required for homologous recombination in mammalian cells J Biol Chem 271: 18996–19000
  • Paškvan, I, Salaj–šmic, E, Ivančić–Baće, I, Zahradka, K, Trogovčević, ž, and Brčić–Kostić, K 2001, The genetic dependence of RecBCD–Gam mediated double–strand end repair in Escherichia coli FEMS Microbiol Let 205: 299–303
  • Passy, SI, Yu, X, Li, Z, Radding, CM, and Egelman, EH 1999, Rings and filaments of β protein from bacteriophage λ suggests a superfamily of recombination proteins Proc Natl Acad Sci USA 96: 4279–4284
  • Ponticelli, AS, Schultz, DW, Taylor, AW, and Smith, GR 1985, Chi–dependent DNA strand cleavage by RecBCD enzyme Cell 41: 145–151
  • Poteete, AR 2008, Involvement of DNA replication in phage lambda Red–mediated homologous recombination Mol Microbiol 68: 66–74
  • Poteete, AR 2004, Modulation of DNA repair and recombination by the bacteriophage λ Orf function in Escherichia coli K–12 J Bacteriol 186: 2699–2707
  • Poteete, AR 1988, Bacteriophage P22 In: The bacteriophages, vol II, ed Calendar, R, 647–682, Plenum Press, New York
  • Poteete, AR, and Fenton, AC 1993, Efficient double–strand break–stimulated recombination promoted by the general recombination systems of phages lambda and P22 Genetics 134: 1013–1021
  • Poteete, AR, and Fenton, AC 1984, Lambda red–dependent growth and recombination of phage P22 Virology 134: 161–167
  • Poteete, AR, and Fenton, AC 1983, DNA–binding properties of the Erf protein of bacteriophage P22 J Mol Biol 163: 257–275
  • Poteete, AR, Fenton, AC, and Murphy, KC 1988, Modulation of Escherichia coli RecBCD activity by the bacteriophage lambda Gam and P22 Abc functions J Bacteriol 170: 2012–2021
  • Poteete, AR, Fenton, AC, and Nadkarni, A 2004, Chromosomal duplicates and cointegrates generated by the bacteriophage lambda Red system in Escherichia coli K–12 BMC Mol Biol 5: 22
  • Poteete, AR, Fenton, AC, and Semerjian, AV 1991, Bacteriophage P22 accessory recombination function Virology 182: 316–323
  • Radding, CM, Rosenzweig, J, Richards, F, and Cassuto, E 1971, Separation and characterization of exonuclease, Beta protein, and a complex of both J Biol Chem 246: 2510–2512
  • Ranallo, RT, Barnoy, S, Thakkar, S, Urick, T, and Venkatesan, MM 2006, Developing live Shigella vaccines using λ Red recombineering FEMS Immunol Med Microbiol 47: 462–469
  • Rossi, MS, Paquelin, A, Ghigo, JM, and Wandersman, C 2003, Haemophore–mediated signal transduction across the bacterial cell envelope in Serratia marcescens: the inducer and the transported substrate are different molecules Mol Microbiol 48: 1467–1480
  • Rybalchenko, N, Golub, EI, Baoyuan, B, and Radding, CM 2004, Strand invasion promoted by recombination protein Beta of coliphage lambda Proc Natl Acad Sci USA 101: 17056–17060
  • Sadowski, PD, Bradley, W, Lee, D, and Roberts, L 1980, Genetic recombination of bacteriophage T7 DNA in vitro In: Molecular mechanisms of replication and genetic recombination, eds Alberts, B and Fox, CF, 941–952 Academic Press, New York NY
  • Sakaki, Y 1974, Inactivation of the ATP–dependent DNase of Escherichia coli after infection with double–stranded DNA phages J Virol 14: 1611–1612
  • Sawitzke, JA, and Stahl, FW 1992, Phage λ has an analogue of Escherichia coli recO, recR and recF genes Genetics 130: 7–16
  • Sawitzke, JA, Thomason, LC, Costantino, N, Bubunenko, M, Datta, S, and Court, DL 2007, Recombineering: in vivo genetic engineering in E coli, S enterica, and beyond Methods Enzymol 421: 171–199
  • Sharples, GJ, Corbett, LM, and Graham, IR 1998, Lambda Rap protein is a structure–specific endonuclease involved in phage recombination Proc Natl Acad Sci USA 95: 13507–13512
  • Signer, E 1991, General recombination In: The bacteriophage lambda, ed Hershey, AD, 139–174, Cold Spring Harbor, New York
  • Skalka, A 1971, Origin of DNA concatemers during growth In: The bacteriophage lambda, ed Hershey, AD, 535–547 Cold Spring Harbour, New York
  • Smith, GR 1988, Homologous recombination in Prokaryotes Microbiol Mol Biol Rev 52: 1–28 Erratum in: Microbiol Mol Biol Rev 52: 304
  • Smith, GR 1987, Mechanism and control of homologous recombination in Escherichia coli Annu Rev Genet 21: 179–201
  • Smith, GR, Kunes, SM, Schultz, DW, Taylor, A, and Triman, KL 1981, Structure of chi hotspots of generalized recombination Cell 24: 429–436
  • Stahl, FW 1998, Recombination in phage λ: one geneticist’s historical perspective Gene 223: 95–102
  • Stahl, FW, and Stahl, MM 1977, Recombination pathway specificity of Chi Genetics 86: 715–725
  • Stahl, FW, and Stahl, MM 1974, A role for recBC nuclease in the distribution of crossovers along unreplicated chromosomes of phage lambda Mol Gen Genet 131: 27–30
  • Stahl, FW, McMilin, KD, Stahl, MM, and Nozu, Y 1972, An enhancing role for DNA synthesis in formation of bacteriophage lambda recombinants Proc Natl Acad Sci USA 69: 3598–3601
  • Stahl, MM, Thomason, L, Poteete, AR, Tarkowski, T, Kuzminov, A, and Stahl, FW 1997, Annealing vs invasion in phage λ recombination Genetics 147: 961–977
  • Subramanian, K, Rutvisuttinunt, W, Scott, W, and Myers, RS 2003, The enzymatic basis of processivity in lambda exonuclease Nucleic Acids Res 31: 1585–1596
  • Susskind, MM, and Botstein, D 1978, Molecular genetics of bacteriophage P22 Microbiol Mol Biol Rev 42: 385–431
  • Sweezy, MA, and Morrical, SW 1999, Biochemical interactions within a ternary complex of the bacteriophage T4 recombination proteins UvsY and gp32 bound to single–stranded DNA Biochemistry 38: 936–944
  • Sweezy, MA, and Morrical, SW 1997, Single–stranded DNA binding properties of the uvsY recombination protein of bacteriophage T4 J Mol Biol 266: 927–938
  • Szczepańska, AK, Bidnenko, E, Płochocka, D, McGovern, S, Ehrlich, SD, Bardowski, J, Polard, P, and Chopin, M-Ch 2007, A distinct single–stranded DNA–binding protein encoded by the Lactococcus lactis bacteriophage bIL67 Virology 363: 104–112
  • Szostak, JW, Orr–Weaver, TL, Rothstein, RJ, and Stahl, FW 1983, The double–strand break model for recombination Cell 33: 25–33
  • Tarkowski, TA, Mooney, D, Thomason, LC, and Stahl, FW 2002, Gene products encoded in the ninR region of phage λ participate in Red–mediated recombination Genes Cells 7: 351–363
  • Taylor, AF, and Smith, GR 1999, Regulation of homologous recombination: Chi inactivates RecBCD enzyme by disassembly of the three subunits Genes Dev 13: 890–900
  • Taylor, AF, Schultz, DW, Ponticelli, AS, and Smith, GR 1985, RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation–dependence of the cutting Cell 41: 153–163
  • Thomason, LC, Thaler, DS, Stahl, MM, and Stahl, FW 1997, In vivo packaging of bacteriophage lambda monomeric chromosomes J Mol Biol 267: 75–87
  • Thresher, RJ, Makhov, AM, Hall, SD, Kolodner, R, and Griffith, JD 1995, Electron microscopic visualization of RecT protein and its complexes with DNA J Mol Biol 254: 364–371
  • Umezu, K, Chi, N-W, and Kolodner, RD 1993, Biochemical interaction of the Escherichia coli RecF, RecO, and RecR proteins with RecA protein and single–stranded DNA binding protein Proc Natl Acad Sci USA 90: 3875–3879
  • van Kessel, JC, and Hatfull, GF 2007, Recombineering in Mycobacterium tuberculosis Nat Met 4: 147–152
  • van Kessel, JC, Marinelli, LJ, and Hatfull, GF 2008, Recombineering mycobacteria and their phages Nat Rev Microbiol 6: 851–857
  • Vellani, TS, and Myers, RS 2003, Bacteriophage SPP1 Chu is an alkaline exonuclease in the SynExo family of viral two–component recombinases J Bacteriol 185: 2465–2474
  • Viret, JF, Bravo, A, and Alonso, JC 1991, Recombination–dependent concatemeric plasmid replication Microbiol Mol Biol Rev 55: 675–683
  • Weaver, S, and Levine, M 1977, Recombination circularization of Salmonella phage P22 DNA Virology 76: 29–38
  • Webb, MR, Plank, JL, Long, DT, Hsieh, T, and Kreuzer, KN 2007, The phage T4 protein UvsW drives Holliday junction branch migration J Biol Chem 282: 34401–34411
  • Weigel, C, and Seitz, H 2006, Bacteriophage replication modules FEMS Microbiol Rev 30: 321–381
  • Weise, F, Chai, S, Lüder, G, and Alonso, JC 1994, Nucleotide sequence and complementation studies of the gene 35 region of the Bacillus subtilis bacteriophage SPP1 Virology 202: 1046–1049
  • Williams, JG, and Radding, CM 1981, Partial purification and properties of an exonuclease inhibitor induced by bacteriophage Mu–1 J Virol 39: 548–558
  • Womack, FC 1963, An analysis of single–burst progeny of bacteria singly infected with a bacteriophage heterozygote Virology 21: 232–241
  • Yassa, DS, Chou, KM, and Morrical, SW 1997, Characterization of an amino–terminal fragment of the bacteriophage T4 UvsY recombination protein Biochemie 79: 275–285
  • Yonesaki, T, and Minagawa, T 1985, T4 phage gene uvsX product catalyses homologous DNA pairing EMBO J 4: 3321–3327
  • Yu, D, Ellis, HM, Lee, E–C, Jenkins, NA, Copeland, NG, and Court, DL 2000, An efficient recombination system for chromosome engineering in Escherichia coli Proc Natl Acad Sci USA 97: 5978–5983
  • Yu, D, Sawitzke, JA, Ellis, H, and Court, DL 2003, Recombineering with overlapping single–stranded DNA oligonucleotides: testing a recombination intermediate Proc Natl Acad Sci USA 100: 7207–7212
  • Zhang, Y, Buchholz, F, Muyrers, JP, and Stewart, AF 1998, A new logic for DNA engineering using recombination in Escherichia coli Nat Genet 20: 123–128

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.