The recombination genes addAB are not restricted to gram-positive bacteria: Genetic analysis of the recombination initiation enzymes RecF and AddAB in Rhizobium etli

Journal of Bacteriology

Volumn 186, Issue 23, 2004, Pages 7905-7913

  Zuñiga Castillo, Jacobo ^a   Romero, David ^a   Martínez Salazar, Jaime M ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; MITOMYCIN C; NALIDIXIC ACID; PROTEIN ADDAB; RECF PROTEIN; UNCLASSIFIED DRUG;

ADDAB GENE; ARTICLE; BACTERIAL GENE; DNA DAMAGE; GENE DELETION; HOMOLOGOUS RECOMBINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RECF GENE; RHIZOBIUM ETLI; ULTRAVIOLET IRRADIATION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DNA-BINDING PROTEINS; EXODEOXYRIBONUCLEASES; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; RHIZOBIUM ETLI;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA; RHIZOBIUM ETLI; TRIXIS;

EID: 9244236007     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.23.7905-7913.2004     Document Type: Article

References (66)

1. Alonso, J. C., R. H. Tailor, and G. Lüder. 1988. Characterization of recombination-deficient mutants of Bacillus subtilis. J. Bacteriol. 170:3001-3007.
2. Alonso, J. C., G. Lüder, and R. H. Tailor. 1991. Characterization of Bacillus subtilis recombinational pathways. J. Bacteriol. 173:3977-3980.
3. Bi, X., and L. F. Liu. 1994. recA-independent and recA-dependent intramolecular plasmid recombination: differential homology requirement and distance effect. J. Mol. Biol. 235:414-423.
4. Biswas, I., E. Magin, S. D. Ehrlich, and A. Gruss. 1995. A 7-base-pair sequence protects DNA from exonucleolytic degradation in Lactococcus lactis. Proc. Natl. Acad. Sci. USA 92:2244-2248.
5. Bork, J. M., M. M. Cox, and R. B. Inman. 2001. The RecOR proteins modulate RecA protein functions at the 5′-ends of single-strand DNA. EMBO J. 20:7313-7322.
6. Brom, S., A. García de los Santos, T. Stepkowsky, M. Flores, G. Dávila, D. Romero, and R. Palacios. 1992. Different plasmids of Rhizobium leguminosarum bv. phaseoli are required for optimal symbiotic performance. J. Bacteriol. 174:5183-5189.
7. Chédin, F., P. Noirot, V. Biaudet, and S. D. Ehrlich. 1998. A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis. Mol. Microbiol. 29:1369-1377.
8. Chédin, F., S. D. Ehrlich, and S. C. Kowalczykowski. 2000. The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate chi sequence in vitro. J. Mol. Biol. 298:7-20.
9. Chédin, F., and S. C. Kowalczykowski. 2002. A novel family of regulated helicases/nucleases from Gram-positive bacteria: insights into the initiation of DNA recombination. Mol. Microbiol. 43:823-834.
10. Cohen, A., and A. Laban. 1983. Plasmidic recombination in Escherichia coli K-12: the role of recF gene function. Mol. Gen. Genet. 189:471-474.
11. Cox, M. M. 2001. Recombinational DNA repair of damaged replication forks in Escherichia coli. Annu. Rev. Genet. 35:53-82.
12. Dillingham, M. S., M. Spies, and S. C. Kowalczykowski. 2003. RecBCD enzyme is a bipolar DNA helicase. Nature 423:893-897.
13. Eisen, J. A., and P. C. Hanawalt. 1999. A phylogenomic study of DNA repair genes, proteins and process. Mutat. Res. 435:171-213.
14. El Karoui, M., S. D. Ehrlich, and A. Grass. 1998. Identification of the lactococcal exonuclease/recombinase and its modulation by the putative chi sequence. Proc. Natl. Acad. Sci. USA 95:626-631.
15. El Karoui, M., V. Biaudet, S. Schbath, and A. Gruss. 1999. Characteristics of chi distribution on different bacterial genomes. Res. Microbiol. 150:579-587.
16. Felsenstein, J. 1995. PHYLIP (Phylogeny Inference Package) version 3.57c. Department of Genetics, University of Washington, Seattle, Wash.
17. Fernández, S., S. Ayora, and J. C. Alonso. 2000. Bacillus subtilis homologous recombination: genes and products. Res. Microbiol. 151:481-486.
18. Feschenko, V. V., L. A. Rajman, and S. T. Lovett. 2003. Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases. Proc. Natl. Acad. Sci. USA 100:1134-1139.
19. Girard, M. L., M. Flores, S. Brom, D. Romero, R. Palacios, and G. Dávila. 1991. Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli. J. Bacteriol. 173:2411-2419.
20. Haijema, B. J., R. Meima, J. Kooistra, and G. Venema. 1996. Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus subtilis AddAB enzyme activities. J. Bacteriol. 178:5130-5137.
21. Horii, Z., and A. J. Clark. 1973. Genetic analysis of the RecF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J. Mol. Biol. 80:327-344.
22. James, A. A., P. T. Morrison, and R. Kolodner. 1982. Genetic recombination of bacterial plasmid DNA: analysis of the effect of recombination-deficient mutations on plasmid recombination. J. Mol. Biol. 160:411-430.
23. Kokotek, W., and W. Lotz. 1991. Construction of a mobilizable cloning vector for site-directed mutagenesis of gram-negative bacteria: application to Rhizobium leguminosarum. Gene 98:7-13.
24. Kooistra, J., B. Vosman, and G. Venema. 1988. Cloning and characterization of a Bacillus subtilis transcription unit involved in ATP-dependent nuclease synthesis. J. Bacteriol. 170:4791-4797.
25. Kooistra, J., and G. Venema. 1991. Cloning, sequencing, and expression of Bacillus subtilis genes involved in ATP-dependent nuclease synthesis. J. Bacteriol. 173:3644-3655.
26. Kooistra, J., B. J. Haijema, and G. Venema. 1993. The Bacillus subtilis addAB are functional in Escherichia coli. Mol. Microbiol. 7:915-923.
27. Kooistra, J., B. A. Haijema, A. Hesseling-Meinders, and G. Venema. 1997. A conserved helicase motif of the AddA subunit of the Bacillus subtilis ATP-dependent nuclease (AddAB) is essential for DNA repair and recombination. Mol. Microbiol. 23:137-149.
28. Kovach, M. E., P. H. Elzer, D. S. Hill, G. T. Robertson, M. A. Farris, R. M. Roop II, and K. N. Peterson. 1995. Four derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175-176.
29. Kowalczykowski, S. C., D. A. Dixon, A. K. Eggelston, S. D. Lauder, and W. M. Rehrauer. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58:401-465.
30. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25:156-165.
31. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage λ. Microbiol. Mol. Biol. Rev. 63:751-813.
32. Laban, A., and A. Cohen. 1981. Interplasmidic and intraplasmidic recombination in Escherichia coli K-12. Mol. Gen. Genet. 184:200-207.
33. Lam, S. T., M. M. Stahl, K. D. McMilin, and F. W. Stahl. 1974. Rec-mediated recombinational hot spot activity in bacteriophage lambda. II. A mutation which causes hot spot activity. Genetics 77:425-433.
34. Lovett, S. T., P. T. Drapkin, V. A. Sutera, Jr., and T. J. Gluckman-Peskin. 1993. A sister-strand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherichia coli. Genetics 135:631-642.
35. Lovett, S. T., T. J. Gluckman, P. J. Simon, V. A. Sutera, Jr., and P. T. Drapkin. 1994. Recombination between repeats in Escherichia coli by a recA-independent, proximity-sensitive mechanism. Mol. Gen. Genet. 245:294-300.
36. Lovett, S. T., R. L. Hurley, V. A. Sutera, Jr., R. H. Aubuchon, and M. A. Lebedeva. 2002. Crossing over between regions of limited homology in Escherichia coli: RecA-dependent and RecA-independent pathways. Genetics 160:851-859.
37. Luisi-DeLuca, C., S. T. Lovett, and R. D. Kolodner. 1989. Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12. Genetics 122:269-278.
38. Martinez-Salazar, J. M., and C. Gómez-Eichelmann. 1987. Molecular rearrangements between two different plasmids of the FII incompatibility group in different recombination-deficient Escherichia coli strains. Plasmid 18:237-245.
39. Martínez-Salazar, J. M., D. Romero, M. L. Girard, and G. Dávila. 1991. Molecular cloning and characterization of the recA gene of Rhizobium phaseoli and construction of recA mutants. J. Bacteriol. 173:3035-3040.
40. Martínez-Salazar, J. M., and D. Romero. 2000. Role of ruvB gene in homologous and homeologous recombination in Rhizobium etli. Gene 243:125-131.
41. Mavingui, P., M. Flores, X. Guo, G. Dávila, X. Perret, W. J. Broughton, and R. Palacios. 2002. Dynamic of genome architecture in Rhizobium sp. strain NGR234. J. Bacteriol. 184:171-176.
42. Miranda, A., and A. Kuzminov. 2003. Chromosomal lesion suppression and removal in Escherichia coli via linear DNA degradation. Genetics 163:1255-1271.
43. Morimatsu, K., and S. C. Kowalczykowski. 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.
44. Motamedi, M. R., K. S. Szigety, and M. Rosenberg. 1999. Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo. Genes Dev. 13:2889-2903.
45. Myers, R. S., and F. W. Stahl. 1994. Chi and the RecBCD enzyme of Escherichia coli. Annu. Rev. Genet. 28:49-70.
46. Page, R. D. M. 1996. Tree View: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
47. Quandt, J., and M. F. Hynes. 1993. Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria. Gene 127:15-21.
48. Quiberoni, A., I. Biswas, M. El Karoui, L. Rezaïki, P. Tailliez, and A. Gruss. 2001. In vivo evidence of two active nuclease motifs in the double-strand break repair enzyme RexAB of Lactococcus lactis. J. Bacteriol. 183:4071-4078.
49. Quiberoni, A., L. Rezaïki, M. El Karoui, I. Biswas, P. Tailliez, and A. Gruss. 2001. Distinctive features of homologous recombination in an "old" microorganism, Lactococcus lactis. Res. Microbiol. 152:131-139.
50. Quinto, C., H. De la Vega, M. Flores, J. Leemans, M. A. Cevallos, M. A. Pardo, R. Azpiroz, M. L. Girard, E. Calva, and R. Palacios. 1985. Nitrogenase reductase: a functional multigene family in Rhizobium phaseoli. Proc. Natl. Acad. Sci. USA 82:1170-1174.
51. Rodríguez, C., and D. Romero. 1998. Multiple recombination events maintain sequence identity among members of the nitrogenase multigene family in Rhizobium etli. Genetics 149:785-794.
52. Romero, D., S. Brom, J. M. Martínez-Salazar, M. L. Girard, R. Palacios, and G. Dávila. 1991. Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli. J. Bacteriol. 173:2435-2441.
53. Romero, D., J. M. Martínez-Salazar, M. L. Girard, S. Brom, G. Dávila, R. Palacios, M. Flores, and C. Rodríguez. 1995. Discrete amplifiable regions (amplicons) in the symbiotic plasmid of Rhizobium etli CFN42. J. Bacteriol. 177:973-980.
54. Romero, D., and R. Palacios. 1997. Gene amplification and genomic plasticity in prokaryotes. Annu. Rev. Genet. 31:91-111.
55. Sam brook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
56. Simon, R., U. Priefer, and A. Pühler. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Biotechnology. 1:784-791.
57. Sourice, S., V. Biaudet, M. El Karoui, S. D. Erlich, and A. Gruss. 1998. Identification of the Chi site of Haemophilus influenzae as several sequences related to the Escherichia coli Chi site. Mol. Microbiol. 27:1021-1029.
58. Sugino, A., C. L. Peebles, K. N. Kreuzer, and N. R. Cozzarelli. 1977. Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc. Natl. Acad. Sci. USA 74:4767-4771.
59. Taylor, F. A., and G. R. Smith. 2003. RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature 423:889-893.
60. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
61. Umezu, K., N. W. Chi, and R. Kolodner. 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.
62. Valencia-Morales, E., and D. Romero. 2000. Recombination enhancement by replication (RER) in Rhizobium etli. Genetics 154:971-983.
63. Webb, B. L., M. M. Cox, and R. B. Inman. 1997. Recombinational DNA repair: the RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps. Cell 91:347-356.
64. Webb, B. L., M. M. Cox, and R. B. Inman. 1999. ATP hydrolysis and DNA binding by the Escherichia coli RecF protein. J. Biol. Chem. 274:15367-15374.
65. Xu, B., C. Paszty, and P. F. Lurquin. 1988. A plasmid-based method to quantitate homologous recombination frequencies in gram-negative bacteria. BioTechniques 6:752-760.
66. Zaman, M. M., and T. C. Boles. 1996. Plasmid recombination by the RecBCD pathway of Escherichia coli. J. Bacteriol. 178:3840-3845.