Transformation and Recombination

David Dubnau; Charles M. Lovett

doi:10.1128/9781555817992.ch32

Chapter 32 : Transformation and Recombination

Authors: David Dubnau, Charles M. Lovett

Content Type: Monograph

Publication Year: 2002

Category: Bacterial Pathogenesis

Book DOI: 10.1128/9781555817992

Chapter DOI: 10.1128/9781555817992.ch32

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Transformation and Recombination, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555817992/9781555812058_Chap32-1.gif /docserver/preview/fulltext/10.1128/9781555817992/9781555812058_Chap32-2.gif

Abstract:

This chapter emphasizes competence regulation and the roles of recombination and repair enzymes. More than a dozen genes encoding transformation proteins have been identified in Bacillus subtilis. Orthologs of these proteins have been recognized in other transformation systems, both gram negative and gram positive, and it appears that many aspects of the DNA uptake mechanism are conserved. The contribution of competence and sporulation factor (CSF) to modulating the expression of srfA is relatively minor, exerting only a two-to-threefold effect, but increasing the level of extracellular CSF exerts a profound inhibitory effect on srfA expression, while stimulating sporulation. Homologous recombination in B. subtilis is central to both genetic transformation in competent cells and DNA repair following exposure to agents that damage DNA. Correspondingly, many of the genes that code for recombination proteins are regulated by either ComK or the SOS DNA repair regulon; the critical recombination gene, recA, is regulated by both ComK and the SOS pathway. The current models for homologous recombination in prokaryotes are based primarily on a large body of genetic and biochemical studies in Escherichia coli. More than a dozen genes encoding recombination proteins have been identified in B. subtilis. All but two of these, recS and recU, seem to have functional counterparts in E. Coli; on the other hand, homologs of several known E. Coli recombination genes, including recE, recG, recJ, recT, and ruvC, have not been found in B. subtilis.

Citation: Dubnau D, Lovett C. 2002. Transformation and Recombination, p 453-471. In Sonenshein A, Losick R, Hoch J (ed), Bacillus subtilis and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch32

Key Concept Ranking

Transcription Start Site: 0.5668108
DNA Synthesis: 0.5553502
Genetic Recombination: 0.55414814
Bacterial Proteins: 0.55414706
Holliday Junction Resolvase: 0.45401514

0.5668108

Highlighted Text: Show | Hide

Full text loading...

Figures

Transformation and Recombination

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817992.chap32-1,webId=/content/author/10.1128/9781555817992.chap32-1,properties={foaf_givenname=David, foaf_name=David Dubnau, foaf_surname=Dubnau}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817992.chap32-2,webId=/content/author/10.1128/9781555817992.chap32-2,properties={foaf_givenname=Charles M., foaf_name=Charles M. Lovett, foaf_surname=Lovett}]]

/content/10.1128/9781555817992.chap32.fig32-1

FIGURE 1

Cartoon representation of DNA uptake during transformation of gram-positive and gram-negative bacteria.

10.1128/9781555817992/fig32-1_thmb.gif

10.1128/9781555817992/fig32-1.gif

FIGURE 1

Cartoon representation of DNA uptake during transformation of gram-positive and gram-negative bacteria.

/content/10.1128/9781555817992.chap32.fig32-2

FIGURE 2

The backbone pathway of competence regulation in B. subtilis.

10.1128/9781555817992/fig32-2_thmb.gif

10.1128/9781555817992/fig32-2.gif

FIGURE 2

The backbone pathway of competence regulation in B. subtilis.

/content/10.1128/9781555817992.chap32.fig32-3

FIGURE 3

The quorum-sensing system (see module 1, Fig. 2 ). (A) Genetic map of the quorum-sensing locus. The black and shaded boxes indicate the extent of the N-terminal hydrophobic and linker regions, respectively, of ComP. (B) Diagram of the quorum-sensing pathways. The box represents a cell. The circled + and — symbols indicate positive and negative effects.

10.1128/9781555817992/fig32-3_thmb.gif

10.1128/9781555817992/fig32-3.gif

FIGURE 3

/content/10.1128/9781555817992.chap32.fig32-4

FIGURE 4

Operation of the Mec switch (see module 2, Fig. 2 ). The dotted outlines indicate degradation. The circled + symbol indicates that ComK operates positively on its own promoter. A, C, P, and S represent MecA, ClpC, ClpP, and ComS, respectively.

10.1128/9781555817992/fig32-4_thmb.gif

10.1128/9781555817992/fig32-4.gif

FIGURE 4

/content/10.1128/9781555817992.chap32.fig32-5

FIGURE 5

Additional inputs to the backbone pathway of competence regulation (compare with Fig. 2 ). Genes above and below the backbone act positively and negatively, respectively. The quorum-sensing genes and those involved in the Mec switch are omitted from this figure. ClpP is included because it affects competence independently of its direct function in the Mec switch.

10.1128/9781555817992/fig32-5_thmb.gif

10.1128/9781555817992/fig32-5.gif

FIGURE 5

/content/10.1128/9781555817992.chap32.fig32-6

FIGURE 6

Biochemical model for genetic recombination in Β. subtilis, adapted from reference 92 .

10.1128/9781555817992/fig32-6_thmb.gif

10.1128/9781555817992/fig32-6.gif

FIGURE 6

Biochemical model for genetic recombination in Β. subtilis, adapted from reference 92 .

References

/content/book/10.1128/9781555817992.chap32

1. Albano, M.,, R. Breitling,, and D. Dubnau. 1989. Nucleotide sequence and genetic organization of the Bacillus subtilis comG operon. J. Bacteriol. 171:5386–5404.

2. Albano, M.,, and D. Dubnau. Unpublished results.

3. Albano, M.,, J. Hahn,, and D. Dubnau. 1987. Expression of competence genes in Bacillus subtilis. J. Bacteriol. 169: 3110–3117.

4. Alonso, J. C.,, K. Shirahige,, and N. Ogasawara. 1990. Molecular cloning, genetic characterization and DNA sequence analysis of the recM region of Bacillus subtilis. Nucleic Acids Res. 18:6771–6777.

5. Alonso, J. C.,, A. C. Stiege,, and G. Luder. 1993. Genetic recombination in Bacillus subtilis 168: effect of recN, recF, recH and addAB mutations on DNA repair and recombination. Mol. Gen. Genet. 239:129–136.

6. Alonso, J. C.,, R. H. Tailor,, and G. Luder. 1988. Characterization of recombination-deficient mutants of Bacillus subtilis. J. Bacteriol. 170:3001–3007.

7. Anderson, D. G.,, and S. C. Kowalczykowski. 1997. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner. Cell 90:77–86.

8. Arwert, F.,, and G. Venema. 1973. Transformation in Bacillus subtilis. Fate of newly introduced transforming DNA. Mol. Gen. Genet. 123:185–198.

9. Ayora, S.,, and J. C. Alonso. 1997. Purification and characterization of the RecF protein from Bacillus subtilis 168. Nucleic Acids Res. 25:2766–2772.

10. Ayora, S.,, A. C. Stiege,, R. Lurz,, and J. C. Alonso. 1997. Bacillus subtilis 168 RecR protein-DNA complexes visualized as looped structures. Mol. Gen. Genet. 254:54–62.

11. Bai, U.,, I. Mandic-Mulec,, and I. Smith. 1993. SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction. Genes Dev. 7:139–148.

12. Banky, P.,, V. Mandava,, and C. M. Lovett, Jr. Unpublished results.

13. Bothwell, L.,, S. Canny,, S. Colavito,, S. Fuller,, E. Groban,, L. Hensley,, C. M. Lovett, Jr.,, T. O'Brien,, T. M. O'Gara,, and L. Tomm. Unpublished results.

14. Braedt, G.,, and G. R. Smith. 1989. Strand specificity of DNA unwinding by RecBCD enzyme. Proc. Natl. Acad. Sci. USA 86:871–875.

15. Bresler, S. E.,, R. A. Kreneva,, and V. V. Kushev. 1968. Correction of molecular heterozygotes in the course of transformation. Mol. Gen. Genet. 102:257–268.

16. Burbulys, D.,, K. A. Trach,, and J. A. Hoch. 1991. Initiation of sporulation in B. subtilis is controlled by a multi-component phosphorelay. Cell 64:545–552.

17. Campbell, E. A.,, S. Y. Choi,, and H. R. Masure. 1998. A competence regulon in Streptococcus pneumoniae revealed by genomic analysis. Mol. Microbiol. 27:929–939.

18. Carter, H. L.,, K. M. Tatti,, and C. P. Moran, Jr. 1990. Cloning of a promoter used by sigma H RNA polymerase in Bacillus subtilis. Gene 96:101–105.

19. Chaudhuri, B.,, and C. M. Lovett, Jr. Unpublished results.

20. Chedin, 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.

21. Chedin, 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.

22. Cheo, D. L.,, K. W. Bayles,, and R. E. Yasbin. 1991. Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis. J. Bacteriol. 173: 1696–1703.

23. Chung, Y. S.,, F. Breidt,, and D. Dubnau. 1998. Cell surface localization and processing of the ComG proteins, required for DNA binding during transformation of Bacillus subtilis. Mol. Microbiol. 29:905–913.

24. Chung, Y. S.,, and D. Dubnau. 1998. All seven comG open reading frames are required for DNA binding during the transformation of competent Bacillus subtilis. J. Bacteriol. 180:41–45.

25. Chung, Y. S.,, and D. Dubnau. 1994. ComC is required for the processing and translocation of ComGC, a pilin-like competence protein of Bacillus subtilis. Mol. Microbiol. 15:543–551.

26. Claverys, J. P.,, and S. A. Lacks. 1986. Heteroduplex deoxyribonucleic acid base mismatch repair in bacteria. Microbiol. Rev. 50:133–165.

27. Claverys, J. P.,, M. Prudhomme,, I. Mortier-Barriere,, and B. Martin. 2000. Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity? Mol. Microbiol. 35:251–259.

28. Connolly, B.,, C. A. Parsons,, F. E. Benson,, H. J. Dunderdale,, G. J. Sharpies,, R. G. Lloyd,, and S. C. West. 1991. Resolution of Holliday junctions in vitro requires the Escherichia coli ruvC gene product. Proc. Natl. Acad. Sci. USA 88:6063–6067.

29. Craig, N. L.,, and J. W. Roberts. 1980. E. Coli recA protein-directed cleavage of phage lambda repressor requires polynucleotide. Nature 283:26–30.

30. Danner, D. B.,, R. A. Deich,, K. L. Sisco,, and H. O. Smith. 1980. An eleven-base-pair sequence determines the specificity of DNA uptake in Haemophilus transformation. Gene 11:311–318.

31. de Vos, W. M.,, S. C. de Vries,, and G. Venema. 1983. Cloning and expression of the Escherichia coli recA gene in Bacillus subtilis. Gene 25:301–308.

32. Dixon, D. A.,, and S. C. Kowalczykowski. 1991. Homologous pairing in vitro stimulated by the recombination hotspot, Chi. Cell 66:361–371.

33. Dixon, D. A.,, and S. C. Kowalczykowski. 1993. The recombination hotspot chi is a regulatory sequence that acts by attenuating the nuclease activity of the E. Coli RecBCD enzyme. Cell 73:87–96.

34. Dooley, D. C.,, C. T. Hadden,, and E. W. Nester. 1971. Macromolecular synthesis in Bacillus subtilis during development of the competent state. J. Bacteriol. 108:668–679.

35. Draskovic, I.,, and D. Dubnau. Unpublished results.

36. D'Souza, C.,, M. M. Nakano,, and P. Zuber. 1994. Identification of comS, a gene of the srfA operon that regulates the establishment of genetic competence in Bacillus subtilis. Proc. Nad. Acad. Sci. USA 91:9397–9401.

37. Dubnau, D. 1999. DNA uptake in bacteria. Annu. Rev. Microbiol. 53:214–244.

38. Dubnau, D., 1993. Genetic exchange and homologous recombination, p. 555–584. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology and Molecular Genetics. American Society for Microbiology, Washington, D.C.

39. Dubnau, D., 1976. Genetic transformation of Bacillus subtalis: a review with emphasis on the recombination mechanism, p. 14–27. In D. Schlessinger (ed.), Microbiology—1976. American Society for Microbiology, Washington, D.C.

40. Dubnau, D.,, and C. Cirigliano. 1973. Fate of transforming deoxyribonucleic acid after uptake by competent Bacillus subtilis: nonrequirement of deoxyribonucleic acid replication for uptake and integration of transforming deoxyribonucleic acid. J. Bacteriol. 113:1512–1514.

41. Dubnau, D.,, and C. Cirigliano. 1972. Fate of transforming DNA following uptake by competent Bacillus subtilis. III. Formation and properties of products isolated from transformed cells which are derived entirely from donor DNA. J. Mol. Biol. 64:9–29.

42. Dubnau, D.,, and C. Cirigliano. 1972. Fate of transforming DNA following uptake by competent Bacillus subtilis. IV. The endwise attachment and uptake of transforming DNA. J. Mol. Biol. 64:3l–46.

43. Dubnau, D.,, and M. Roggiani. 1990. Growth medium-independent genetic competence mutants of Bacillus subtilis. J. Bacteriol. 172:4048–4055.

44. Dubnau, D.,, and K. Turgay,. 2000. The regulation of competence in Bacillus subtilis and its relation to stress response, p. 249–260. In G. Storz, and R. Hengge-Aronis (ed.), Bacterial Stress Responses. American Society for Microbiology, Washington, D.C.

45. Dubnau, E.,, J. Weir,, G. Nair,, H. L. Carter III,, C. P. Moran, Jr.,, and I. Smith. 1988. Bacillus sporulation gene spo0H codes for ��30 (��H). J. Bacteriol. 170:1054–1062.

46. Elkins, C.,, C. E. Thomas,, H. S. Seifert,, and P. F. Sparling. 1991. Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence. J. Bacteriol. 173: 3911–3913.

47. Fernandez, S.,, Y. Kobayashi,, N. Ogasawara,, and J. C. Alonso. 1999. Analysis of the Bacillus subtilis recO gene: RecO forms part of the RecFLOR function. Mol. Gen. Genet. 261:567–573.

48. Fernandez, S.,, A. Sorokin,, and J. C. Alonso. 1998. Genetic recombination in Bacillus subtilis 168: effects of recU and recS mutations on DNA repair and homologous recombination. J. Bacteriol. 180:3405–3409.

49. Friedberg, E. C.,, G. C. Walker,, and W. Siede (ed.). 1995. DNA Repair and Mutagenesis. ASM Press, Washington, D.C.

50. Gerth, U.,, E. Kriiger,, I. Derre,, T. Msadek,, and M. Hecker. 1998. Stress induction of the Bacillus subtilis clpP gene encoding a homologue of the proteolytic component of the Clp protease and the involvement of ClpP and ClpX in stress tolerance. Mol. Microbiol. 28:787–802.

51. Gerth, U.,, A. Wipat,, C. R. Harwood,, N. Carter,, P. T. Emmerson,, and M. Hecker. 1996. Sequence and transcriptional analysis of cipX, a class-Ill heat-shock gene of Bacillus subtilis. Gene 181:77–83.

52. Green, W. H.,, T. Jackson,, and C. M. Lovett, Jr. Unpublished results.

53. Grossman, A. D. 1995. Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Annu. Rev. Genet. 29: 477–508.

54. Guillen, N.,, Y. Weinrauch,, and D. Dubnau. 1989. Cloning and characterization of the regulatory Bacillus subtilis competence genes, comA and comB. J. Bacteriol. 171: 5354–5361.

55. Hadden, C.,, and E. W. Nester. 1968. Purification of competent cells in the Bacillus subtilis transformation system. J. Bacteriol. 95:876–885.

56. Hahn, J.,, J. Bylund,, M. Haines,, M. Higgins,, and D. Dubnau. 1995. Inactivation of mecA prevents recovery from the competent state and the partitioning of nucleoids in Bacillus subtilis. Mol. Microbiol. 18:755–767.

57. Hahn, J.,, and D. Dubnau. 1991. Growth stage signal transduction and the requirements for srfA induction in the development of competence. J. Bacteriol. 173:7275–7282.

58. Hahn, J.,, and J. Dubnau. Unpublished results.

59. Hahn, J.,, B. J. Haijema,, and D. Dubnau. Unpublished results.

60. Hahn, J.,, G. Inamine,, Y. Kozlov,, and D. Dubnau. 1993. Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA. Mol. Microbiol. 10:99–111.

61. Hahn, J.,, L. Kong,, and D. Dubnau. 1994. The regulation of competence transcription factor synthesis constitutes a critical control point in the regulation of competence in Bacillus subtilis. J. Bacteriol. 176:5753–5761.

62. Hahn, J.,, A. Luttinger,, and D. Dubnau. 1996. Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis. Mol. Microbiol. 21:763–775.

63. Hahn, J.,, M. Persuh,, R. Berka,, A. Sloma,, and D. Dubnau. Unpublished results.

64. Hahn, J.,, M. Roggiani,, and D. Dubnau. 1995. The major role of Spo0A in genetic competence is to downregulate abrB, an essential competence gene. J. Bacteriol. 177: 3601–3605.

65. Haijema, B. J.,, L. W. Hamoen,, J. Kooistra,, G. Venema,, and D. van Sinderen. 1995. Expression of the ATP-dependent deoxyribonuclease of Bacillus subtilis is under competence-mediated control. Mol. Microbiol. 15:203–211.

66. Haijema, B. J.,, D. van Sinderen,, K. Winterling,, J. Kooistra,, G. Venema,, and L. W. Hamoen. 1996. Regulated expression of the dinR and recA genes during competence development and SOS induction in Bacillus subtilis. Mol. Microbiol. 22:75–85.

67. Hamoen, L.,, B. J. Haijema,, G. Venema,, and C. M. Lovett, Jr. Unpublished results.

68. Hamoen, L.,, M. Marahiel,, and P. Serror. Unpublished results.

69. Hamoen, L. W.,, H. Eshuis,, J. Jongbloed,, G. Venema,, and D. van Sinderen. 1995. A small gene, designated comS, located within the coding region of the fourth amino acid-activation domain of srfA, is required for competence development in Bacillus subtilis. Mol. Microbiol. 15:55–63.

70. Hamoen, L. W.,, A. F. Van Werkhoven,, J. J. Bijlsma,, D. Dubnau,, and G. Venema. 1998. The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix. Genes Dev. 12:1539–1550.

72. Hamoen, L. W.,, A. F. Van Werkhoven,, G. Venema,, and D. Dubnau. 2000. The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 97: 9246–9251.

73. Haseltine-Cahn, F.,, and M. S. Fox. 1968. Fractionation of transformable bacteria from competent cultures of Bacillus subtilis on renografin gradients. J. Bacteriol. 95: 867–875.

74. Havarstein, L. S.,, R. Hakenbeck,, and P. Gaustad. 1997. Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges. J. Bacteriol. 179:6589–6594.

75. Havarstein, L. S.,, and D. A. Morrison,. 1999. Quorum sensing and peptide pheromones in streptococcal competence for genetic transformation, p. 9–26. In G. M. Dunny, and S. C. Winans (ed.), Cell-Cell Signaling in Bacteria. American Society for Microbiology, Washington, D.C.

76. Hegde, S. P.,, M. Rajagopalan,, and M. V. Madiraju. 1996. Preferential binding of Escherichia coli RecF protein to gapped DNA in the presence of adenosine (gamma-thio) triphosphate. J. Bacteriol. 178:184–190.

77. Holliday, A. R.,, R. B. Morris,, and R. P. Sharpley. 1964. Compound 84/F 1983 compared with D-amphetamine and placebo in regard to effects on human performance. Psychopharmacohgia 6:192–200.

78. Hurstel, S.,, M. Granger-Schnarr,, and M. Schnarr. 1988. Contacts between the LexA repressor—or its DNA-binding domain—and the backbone of the recA operator DNA. EMBOJ. 7:269–275.

79. Inamine, G. S.,, and D. Dubnau. 1995. ComEA, a Bacillus subtilis integral membrane protein required for genetic transformation, is needed for both DNA binding and transport. J. Bacteriol. 177:3045–3051.

80. Jaacks, K. J.,, J. Healy,, R. Losick,, and A. D. Grossman. 1989. Identification and characterization of genes controlled by the sporulation-regulatory gene spo0H in Bacillus subtilis. J. Bacteriol. 171:4121–4129.

81. Ji, G.,, R. Beavis,, and R. P. Novick. 1997. Bacterial interference caused by autoinducing peptide variants. Science 276:2027–2030.

82. Ji, G.,, R. C. Beavis,, and R. P. Novick. 1995. Cell density control of staphylococcal virulence mediated by an octapeptide pheromone. Proc. Natl. Acad. Sci. USA 92:12055–12059.

83. Johnson, M.,, and C. M. Lovett, Jr. Unpublished results.

84. Karudapuram, S.,, and G. J. Barcak. 1997. The Haemophilus influenzae dprABC genes constitute a competence-inducible operon that requires the product of the tfoX (sry) gene for transcriptional activation. J. Bacteriol. 179:4815–4820.

85. Karudapuram, S.,, X. Zhao,, and G. J. Barcak. 1995. DNA sequence and characterization of Haemophilus influenzae dprA+, a gene required for chromosomal but not plasmid DNA transformation. J. Bacteriol. 177:3235–3240.

86. Kleerebezem, M.,, L. E. Quadri,, O. P. Kuipers,, and W. M. de Vos. 1997. Quorum sensing by peptide pheromones and two-component signal-transduction systems in Gram-positive bacteria. Mol. Microbiol. 24:895–904.

87. Kong, L.,, and D. Dubnau. 1994. Regulation of competence-specific gene expression by Mec-mediated protein-protein interaction in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 91:5793–5797.

88. Kong, L.,, K. J. Siranosian,, A. D. Grossman,, and D. Dubnau. 1993. Sequence and properties of mecA, a negative regulator of genetic competence in Bacillus subtilis. Mol. Microbiol. 9:365–373.

89. Kooistra, J.,, B. J. Haijema,, and G. Venema. 1993. The Bacillus subtilis addAB genes are fully functional in Escherichia coli. Mol. Microbiol. 7:915–923.

90. 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.

91. Kooistra, J.,, B. Vosman,, and G. Venema. 1988. Cloning and characterization of a Bacillus subtilis transcription unit involved in ATP-dependent DNase synthesis. J. Bacteriol. 170:4791–4797.

92. Kowalczykowski, S. C.,, D. A. Dixon,, A. K. Eggleston,, S. D. Lauder,, and W. M. Rehrauer. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58:401–465.

93. Kruger, E.,, U. Volker,, and M. Hecker. 1994. Stress induction of clpC in Bacillus subtilis and its involvement in stress tolerance. J. Bacteriol. 176:3360–3367.

94. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16:373–384.

95. Lacks, S.,, B. Greenberg,, and M. Neuberger. 1975. Identification of a deoxyribonuclease implicated in genetic transformation of Diplococcus pneumoniae. J. Bacteriol. 123:222–232.

96. Lacks, S.,, B. Greenberg,, and M. Neuberger. 1974. Role of a deoxyribonuclease in the genetic transformation of Diplococcus pneumoniae. Proc. Natl. Acad. Sci. USA 71: 2305–2309.

97. Lacks, S.,, and M. Neuberger. 1975. Membrane location of a deoxyribonuclease implicated in the genetic transformation of Diplococcus pneumoniae. J. Bacteriol. 124:1321–1329.

98. Lacks, S. A., 1999. DNA uptake by transformable bacteria, p. 138–168. In J. K. Broome-Smith,, S. Baumberg,, C.J. Stirling,, and F. B. Ward (ed.), Transport of Molecules Across Microbial Membranes. Cambridge University Press, Cambridge, England.

99. Larson, T. G.,, and S. H. Goodgal. 1992. Donor DNA processing is blocked by a mutation in the com1OlA locus of Haemophilus influenzae. J. Bacteriol. 174:3392–3394.

100. Larson, T. G.,, and S. H. Goodgal. 1991. Sequence and transcriptional regulation of comlOlA, a locus required for genetic transformation in Haemophilus influenzae. J. Bacteriol. 173:4683–4691.

101. Lavery, P. E.,, and S. C. Kowalczykowski. 1992. A postsynaptic role for single-stranded DNA-binding protein in recA protein-promoted DNA strand exchange. J. Biol. Chem. 267:9315–9320.

102. Lazazzera, B. A.,, T. Palmer,, J. Quisel,, and A. D. Grossman,. 1999. Cell density control of gene expression and development in Bacillus subtilis, p. 27–46. In G. M. Dunny, and S. C. Winans (ed.), Cell-Cell Signaling in Bacteria. American Society for Microbiology, Washington, D.C.

103. Lazazzera, B. A.,, J. M. Solomon,, and A. D. Grossman. 1997. An exported peptide functions intracellularly to contribute to cell density signaling in B. subtilis. Cell 89: 917–925.

104. Lee, M. S.,, and K. J. Marians. 1990. Differential ATP requirements distinguish the DNA translocation and DNA unwinding activities of the Escherichia coli PriA protein. J. Biol. Chem. 265:17078–17083.

105. Lee, M. S.,, and D. A. Morrison. 1999. Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J. Bacteriol. 181:5004–5016.

106. Lina, G.,, S. Jarraud,, G. Ji,, T. Greenland,, A. Pedraza,, J. Etienne,, R. P. Novick,, and F. Vandenesch. 1998. Transmembrane topology and histidine protein kinase activity of AgrC, the agr signal receptor in Staphylococcus aureus. Mol. Microbiol. 28:655–662.

107. Little, J. W. 1984. Autodigestion of lexA and phage lambda repressors. Proc. Natl. Acad. Sci. USA 81:1375–1379.

108. Little, J. W.,, and S. A. Hill. 1985. Deletions within a hinge region of a specific DNA-binding protein. Proc. Natl. Acad. Sci. USA 82:2301–2305.

109. Little, J. W.,, and D. W. Mount. 1982. The SOS regulatory system of Escherichia coli. Cell 29:11–22.

110. Little, J. W.,, D. W. Mount,, and C. R. Yanisch-Perron. 1981. Purified lexA protein is a repressor of the recA and lexA genes. Proc. Natl. Acad. Sci. USA 78:4199–4203.

111. Liu, J.,, and P. Zuber. 1998. A molecular switch controlling competence and motility: competence regulatory factors ComS, MecA, and ComK control sigmaD-dependent gene expression in Bacillus subtilis. J. Bacteriol. 180: 4243–4251.

112. Liu, L.,, M. Nakano,, O. H. Lee,, and P. Zuber. 1996. Plasmid-amplified comS enhances genetic competence and suppresses sinR in Bacillus subtilis. J. Bacteriol. 178: 5144–5152.

113. Londofio-Vallejo, J. A.,, and D. Dubnau. 1993. comF, a Bacillus subtilis late competence locus, encodes a protein similar to ATP-dependent RNA/DNA helicases. Mol. Microbiol. 9:119–131.

114. Londofio-Vallejo, J. A.,, and D. Dubnau. 1994. Membrane association and role in DNA uptake of the Bacillus subtilis PriA analog ComF1. Mol. Microbiol. 13:197–205.

115. Londofio-Vallejo, J. A.,, and D. Dubnau. 1994. Mutation of the putative nucleotide binding site of the Bacillus subtilis membrane protein ComFA abolishes the uptake of DNA during transformation. J. Bacteriol. 176:4642–4645.

116. Love, P. E.,, M. J. Lyle,, and R. E. Yasbin. 1985. DNA-damage-inducible (din) loci are transcriptionally activated in competent Bacillus subtilis. Proc. Natl. Acad. Sci. USA 82:6201–6205.

117. Lovett, C. M., Jr.,, K. C. Cho,, and T. M. O'Gara. 1993. Purification of an SOS repressor from Bacillus subtilis. J. Bacteriol. 175:6842–6849.

118. Lovett, C. M., Jr.,, P. E. Love,, and R. E. Yasbin. 1989. Competence-specific induction of the Bacillus subtilis RecA protein analog: evidence for dual regulation of a recombination protein. J. Bacteriol. 171:2318–2322.

119. Lovett, C. M., Jr.,, P. E. Love,, R. E. Yasbin,, and J. W. Roberts. 1988. SOS-like induction in Bacillus subtilis: induction of the RecA protein analog and a damage-inducible operon by DNA damage in Rec+ and DNA repair-deficient strains. J. Bacteriol. 170:1467–1474.

120. Lovett, C. M., Jr.,, T. M. O'Gara,, and J. N. Woodruff. 1994. Analysis of the SOS inducing signal in Bacillus subtilis using Escherichia coli LexA as a probe. J. Bacteriol. 176:4914–4923.

121. Lovett, C. M., Jr.,, and J. W. Roberts. 1985. Purification of a RecA protein analogue from Bacillus subtilis. J. Biol. Chem. 260:3305–3313.

122. Luttinger, A.,, J. Hahn,, and D. Dubnau. 1996. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol. Microbiol. 19:343–356.

123. Macfadyen, L. P.,, I. R. Dorocicz,, J. Reizer,, M. H. Saier, Jr.,, and R. J. Redfield. 1996. Regulation of competence development and sugar utilization in Haemophilus influenzae Rd by a phosphoenolpyruvate:fructose phosphotransferase system. Mol. Microbiol. 21:941–952.

124. Madiraju, M. V.,, and A. J. Clark. 1992. Evidence for ATP binding and double-stranded DNA binding by Escherichia coli RecF protein. J. Bacteriol. 174:7705–7710.

125. Magnuson, R.,, J. Solomon,, and A. D. Grossman. 1994Biochemical and genetic characterization of a competence pheromone. Cell 77:207–216.

126. Mandic-Mulec, I.,, N. Gaur,, U. Bai,, and I. Smith. 1992. Sin, a stage-specific repressor of cellular differentiation. J. Bacteriol. 174:3561–3569.

127. Marciano, D. K.,, M. Russel,, and S. M. Simon. 1999. An aqueous channel for filamentous phage export. Science 284:1516–1519.

128. Mayville, P.,, G. Ji,, R. Beavis,, H. Yang,, M. Goger,, R. P. Novick,, and T. W. Muir. 1999. Structure-activity analysis of synthetic autoinducing thiolactone peptides from Staphylococcus aureus responsible for virulence. Proc. Natl. Acad. Sci. USA 96:1218–1223.

129. McCarthy, C.,, and E. W. Nester. 1967. Macromolecular synthesis in newly transformed cells of Bacillus subtilis. J. Bacteriol. 94:131–140.

130. Mejean, V.,, and J. Claverys. 1988. Polarity of DNA entry in transformation of Streptococcus pneumoniae. Mol. Gen. Genet. 213:444–448.

131. Mejean, V.,, and J. P. Claverys. 1993. DNA processing during entry in transformation of Streptococcus pneumoniae. J. Biol. Chem. 268:5594–5599.

132. Michod, R. E.,, M. F. Wojciechowski,, and M. A. Hoelzer. 1988. DNA repair and the evolution of transformation in the bacterium Bacillus subtilis. Genetics 118:31–39.

133. Miller, M. C.,, J. B. Resnick,, B. T. Smith,, and C. M. Lovett, Jr. 1996. The Bacillus subtilis dinR gene codes for the analogue of Escherichia coii LexA. Purification and characterization of the DinR protein. J. Biol. Chem. 271: 33502–33508.

134. Mohan, S.,, J. Aghion,, N. Guillen,, and D. Dubnau. 1989. Molecular cloning and characterization of cotnC, a late competence gene of Bacillus subtilis. J. Bacteriol. 171: 6043–6051.

135. Mohan, S.,, and D. Dubnau. 1990. Transcriptional regulation of comC: evidence for a competence-specific factor in Bacillus subtilis. J. Bacteriol. 172:4064–4071

136. Msadek, T.,, V. Dartois,, F. Kunst,, M. L. Herbaud,, F. Denizot,, and G. Rapoport. 1998. ClpP is required for competence development, motility, degradative enzyme synthesis, growth at high temperature and sporulation. Mol. Microbiol. 27:899–914.

137. Msadek, T.,, F. Kunst,, D. Henner,, A. Klier,, G. Rapoport,, and R. Dedonder. 1990. Signal transduction pathway controlling the synthesis of a class of degradative enzymes in Bacillus subtilis: expression of the regulatory genes and analysis of mutations in degS and degU. J. Bacteriol. 172:824–834.

138. Msadek, T.,, F. Kunst,, A. Klier,, and G. Rapoport. 1991. DegS-DegU and ComP-ComA modulator-effector pairs control expression of the Bacillus subtilis pleiotropic regulatory gene degQ. J. Bacteriol. 173:2366–2377.

139. Msadek, T.,, F. Kunst,, and G. Rapoport. 1994. MecB of Bacillus subtilis is a pleiotropic regulator of the ClpC AT-Pase family, controlling competence gene expression and survival at high temperature. Proc. Natl. Acad. Sci. USA 91:5788–5792.

140. Msadek, T.,, F. Kunst,, and G. Rapoport,. 1995. A signal transduction network in Bacillus subtilis includes the DegS/DegU and ComP/ComA two-component systems, p. 447–471. In J. A. Hoch, and T. J. Silhavy (ed.), Two-Component Signal Transduction. ASM Press, Washington, D.C.

141. Muniyappa, K.,, S. L. Shaner,, S. S. Tsang,, and C. M. Radding. 1984. Mechanism of the concerted action of recA protein and helix-destabilizing proteins in homologous recombination. Proc. Natl. Acad. Sci. USA 81: 2757–2761.

142. Nakano, M. M.,, L. Xia,, and P. Zuber. 1991. Transcription initiation region of the srfA operon which is controlled by the comP-comA signal transduction system in Bacillus subtilis. J. Bacteriol. 173:5487–5493.

143. Nakano, M. M.,, Y. Zhu,, J. Liu,, D. Y. Reyes,, H. Yoshikawa,, and P. Zuber. 2000. Mutations conferring amino acid residue substitutions in the carboxy-terminal domain of RNA polymerase can suppress clpX and clpP with respect to developmentally regulated transcription in Bacillus subtilis. Mol. Microbiol. 37:869–884.

144. Nakano, M. M.,, and P. Zuber. 1989. Cloning and characterization of srfB, a regulatory gene involved in surfactin production and competence in Bacillus subtilis. J. Bacteriol. 171:5347–5353.

145. Nakano, M. M.,, and P. Zuber. 1991. The primary role of ComA in establishment of the competent state in Bacillus subtilis is to activate the expression of srfA. J. Bacteriol. 173:7269–7274.

146. Nester, E. W.,, and B. A. D. Stocker. 1963. Biosynthetic latency in early stages of deoxyribonucleic acid transformation in Bacillus subtilis. J. Bacteriol. 86:785–796.

147. Ogura, M.,, L. Liu,, M. Lacelle,, M. M. Nakano,, and P. Zuber. 1999. Mutational analysis of ComS: evidence for the interaction of ComS and MecA in the regulation of competence development in Bacillus subtilis. Mol. Microbiol. 32:799–812.

148. Ogura, M.,, Y. Ohshiro,, S. Hirao,, and T. Tanaka. 1997. A new Bacillus subtilis gene, med, encodes a positive regulator of comK. J. Bacteriol. 179:6244–6253.

149. Ogura, M.,, and T. Tanaka. 2000. Bacillus subtilis comZ (yjzA) negatively affects expression of comG but not comK. J. Bacteriol. 182:4992–4994.

150. Otto, M.,, R. Sussmuth,, G. Jung,, and F. Gotz. 1998. Structure of the pheromone peptide of the Staphylococcus epidermidis agr system. FEBS Lett. 424:89–94

151. Otto, M.,, R. Sussmuth,, C. Vuong,, G. Jung,, and F. Gotz. 1999. Inhibition of virulence factor expression in Staphylococcus aureus by the Staphylococcus epidermidis agr pheromone and derivatives. FEBS Lett. 450:257–262.

152. Palmen, R.,, and K. J. Hellingwerf. 1997. Uptake and processing of DNA by Acinetobacter calcoaceticus—a review. Gene 192:179–190.

153. Parsons, C. A.,, A. Stasiak,, R. J. Bennett,, and S. C. West. 1995. Structure of a multisubunit complex that promotes DNA branch migration. Nature 374:375–378.

154. Perego, M., 1999. Self-signaling by Phr peptides modulates Bacillus subtilis development, p. 243–258. In G. M. Dunny, and S. C. Winans (ed.), Cell-Cell Signaling in Bacteria. American Society for Microbiology, Washington, D.C.

155. Persuh, M.,, and D. Dubnau. Unpublished results.

156. Persuh, M.,, K. Turgay,, I. Mandic-Mulec,, and D. Dubnau. 1999. The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch. Mol. Microbiol. 33:886–894.

157. Phizicky, E. M.,, and J. W. Roberts. 1981. Induction of SOS functions: regulation of proteolytic activity of E. Coli RecA protein by interaction with DNA and nucleoside triphosphate. Cell 25:259–267.

158. Piazza, F.,, P. Tortosa,, and D. Dubnau. 1999. Mutational analysis and membrane topology of ComP, a quorum-sensing histidine kinase of Bacillus subtilis controlling competence development. J. Bacteriol. 181:4540–4548.

159. Pozzi, G.,, L. Masala,, F. Iannelli,, R. Manganelli,, L. S. Havarstein,, L. Piccoli,, D. Simon,, and D. A. Morrison. 1996. Competence for genetic transformation in encapsulated strains of Streptococcus pneumoniae: two allelic variants of the peptide pheromone. J. Bacteriol. 178: 6087–6090.

160. Prowedi, R.,, and D. Dubnau. 1998. ComEA is a DNA receptor for transformation of competent Bacillus subtilis. Mol. Microbiol. 31:271–280.

161. Prowedi, R.,, and D. Dubnau. Unpublished results.

162. Puyet, A.,, B. Greenberg,, and S. A. Lacks. 1990. Genetic and structural characterization of EndA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae. J. Mol. Biol. 213:727–738.

163. Ratnayake-Lecamwasam, M.,, and A. L. Sonenshein. Personal communication.

164. Raymond-Denise, A.,, and N. Guillen. 1992. Expression of the Bacillus subtilis dinR and recA genes after DNA damage and during competence. J. Bacteriol. 174: 3171–3176.

165. Raymond-Denise, A.,, and N. Guillen. 1991. Identification of dinR, a DNA damage-inducible regulator gene of Bacillus subtilis. J. Bacteriol. 173:7084–7091.

166. Redfield, R. J. 1988. Evolution of bacterial transformation: is sex with dead cells ever better than no sex at all? Genetics 119:213–221.

167. Redfield, R. J. 1993. Evolution of natural transformation: testing the DNA repair hypothesis in Bacillus subtilis and Haemophilus influenzae. Genetics 133:755–761.

168. Redfield, R. J. 1993. Genes for breakfast: the have-your-cake-and-eat-it-too of bacterial transformation. J. Hered. 84:400–404.

169. Redfield, R. J. 1991. sxy-1, a Haemophilus influenzae mutation causing greatly enhanced spontaneous competence. J. Bacteriol. 173:5612–5618.

170. Roggiani, M.,, and D. Dubnau. 1993. ComA, a phosphorylated response regulator protein of Bacillus subtilis, binds to the promoter region of srfA. J. Bacteriol. 175: 3182–3187.

171. Roggiani, M.,, J. Hahn,, and D. Dubnau. 1990. Suppression of early competence mutations in Bacillus subtilis by mec mutations. J. Bacteriol. 172:4056–4063.

172. Sancar, A.,, and G. B. Sancar. 1988. DNA repair enzymes. Annu. Rev. Biochem. 57:29–67.

173. Sassanfar, M.,, and J. W. Roberts. 1990. Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. J. Mol. Biol. 212:79–96.

174. Schirmer, E. C.,, J. R. Glover,, M. A. Singer,, and S. Lindquist. 1996. HSP1OO/Clp proteins: a common mechanism explains diverse functions. Trends Biochem. Sci. 21:289–296.

175. Schnarr, M.,, J. Pouyet,, M. Granger-Schnarr,, and M. Daune. 1985. Large-scale purification, oligomerization equilibria, and specific interaction of the LexA repressor of Escherichia coli. Biochemistry 24:2812–2818.

176. Serror, P.,, and A. L. Sonenshein. 1996. CodY is required for nutritional repression of Bacillus subtilis genetic competence. J. Bacteriol. 178:5910–5915.

177. Shah, A.,, and C. M. Lovett, Jr. Unpublished results.

178. Shan, Q.,, J. M. Bork,, B. L. Webb,, R. B. Inman,, and M. M. Cox. 1997. RecA protein filaments: end-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins. J. Mol. Biol. 265:519–540.

179. Shibata, T.,, C. DasGupta,, R. P. Cunningham,, and C. M. Radding. 1979. Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc. Natl. Acad. Sci. USA 76: 1638–1642.

180. Singh, R. M. 1972. Number of deoxyribonucleic acid uptake sites in competent cells of Bacillus subtilis. J. Bacteriol. 110:266–272.

181. Slack, F. J.,, P. Serror,, E. Joyce,, and A. L. Sonenshein. 1995. A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon. Mol. Microbiol. 15:689–702.

182. Slilaty, S. N.,, and J. W. Little. 1987. Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism. Proc. Natl. Acad. Sci. USA 84:3987–3991.

183. Smeets, L. C.,, J. J. Bijlsma,, E. J. Kuipers,, C. M. Vandenbroucke-Grauls,, and J. G. Kusters. 2000. The dprA gene is required for natural transformation of Helicobacter pylori. FEMS Immunol. Med. Microbiol. 27:99–102.

184. Smith, H.,, K. Wiersma,, S. Bron,, and G. Venema. 1984-Transformation in Bacillus subtilis: a 75,000-dalton protein complex is involved in binding and entry of donor DNA. J. Bacteriol. 157:733–738.

185. Smith, H.,, K. Wiersma,, S. Bron,, and G. Venema. 1983. Transformation in Bacillus subtilis: purification and partial characterization of a membrane-bound DNA-binding protein. J. Bacteriol. 156:101–108.

186. Smith, H.,, K. Wiersma,, G. Venema,, and S. Bron. 1985. Transformation in Bacillus subtilis: further characterization of a 75,000-dalton protein complex involved in binding and entry of donor DNA. J. Bacteriol. 164:201–206.

187. Smith, I. Personal communication.

188. Smith, I., 1993. Regulatory proteins that control late-growth development, p. 785–800. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D.C.

189. Solomon, J.,, R. Magnuson,, A. Srivastava,, and A. D. Grossman. 1995. Convergent sensing pathways mediate response to two extracellular competence factors in Bacillus subtilis. Genes Dev. 9:547–558.

190. Solomon, J. M.,, and A. D. Grossman. 1996. Who's competent and when: regulation of natural genetic competence in bacteria. Trends Genet. 12:150–155.

191. Solomon, J. M.,, B. A. Lazazzera,, and A. D. Grossman. 1996. Purification and characterization of an extracellular peptide factor that affects two developmental pathways in Bacillus subtilis. Genes Dev. 10:2014–2024.

192. Stasiak, A.,, I. R. Tsaneva,, S. C. West,, C. J. Benson,, X. Yu,, and E. H. Egelman. 1994. The Escherichia coli RuvB branch migration protein forms double hexameric rings around DNA. Proc. Natl. Acad. Sci. USA 91:7618–7622.

193. Strauch, M., 1993. AbrB, a transition state regulator, p. 757–764. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D.C.

194. Tanaka, T.,, and M. Kawata. 1988. Cloning and characterization of Bacillus subtilis iep, which has positive and negative effects on production of extracellular proteases. J. Bacteriol. 170:3593–3600.

195. Tomb, J.-F.,, H. El-Hajj,, and H. O. Smith. 1991. Nucleotide sequence of a cluster of genes involved in the transformation of Haemophilus influenzae RD. Gene 104: 1–10.

196. Tortosa, P.,, M. Albano,, and D. Dubnau. 2000. Characterization of ylbF, a new gene involved in competence development and sporulation in Bacillus subtilis. Mol. Microbiol. 35:1110–1119.

197. Tortosa, P.,, M. Albano,, T. H. Tran,, and D. Dubnau. Unpublished results.

198. Tortosa, P.,, and D. Dubnau. 1999. Competence for transformation: a matter of taste. Curr. Opin. Microbiol. 2:588–592.

199. Tortosa, P.,, and D. Dubnau. Unpublished results.

200. Tortosa, P.,, L. Logsdon,, B. Kraigher,, Y. Itoh,, I. Mandic-Mulec,, and D. Dubnau. 2001. Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system. J. Bacteriol. 183:451–460.

201. Tran, T. H.,, and D. Dubnau. Unpublished results.

202. Tsaneva, I. R.,, B. Muller,, and S. C. West. 1992. ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. Coli. Cell 69:1171–1180.

203. Turgay, K.,, J. Hahn,, J. Burghoorn,, and D. Dubnau. 1998. Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J. 17:6730–6738.

204. Turgay, K.,, L. W. Hamoen,, G. Venema,, and D. Dubnau. 1997. Biochemical characterization of a molecular switch involving the heat shock protein ClpC, that controls the activity of ComK, the competence transcription factor of Bacillus subtilis. GenesDev. 11:119–128.

205. Umezu, K.,, and R. D. Kolodner. 1994. Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein. J. Biol. Chem. 269:30005–30013.

206. Vagner, V.,, J.-P. Claverys,, S. D. Ehrlich,, and V. Mejean. 1990. Direction of DNA entry in competent cells of Bacillus subtilis. Mol. Microbiol. 4:1785–1788.

207. van Sinderen, D.,, R. Kiewiet,, and G. Venema. 1995. Differential expression of two closely related deoxyri-bonucleases, nucA and nucB in Bacillus subtilis. Mol. Microbiol. 15:213–223.

208. van Sinderen, D.,, A. Luttinger,, L. Kong,, D. Dubnau,, G. Venema,, and L. Hamoen. 1995. comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Mol. Microbiol. 15:455–462.

209. van Sinderen, D.,, A. ten Berge,, B. J. Hayema,, L. Hamoen,, and G. Venema. 1994. Molecular cloning and sequence of comK, a gene required for genetic competence in Bacillus subtilis. Mol. Microbiol. 11:695–703.

210. van Sinderen, D.,, and G. Venema. 1994. comK acts as an autoregulatory control switch in the signal transduction route to competence in Bacillus subtilis. J. Bacteriol. 176: 5762–5770.

211. Vosman, B.,, J. Kooistra,, J. Olijve,, and G. Venema. 1987. Cloning in Escherichia coii of the gene specifying the DNA-entry nuclease of Bacillus subtilis. Gene 52:175–183.

212. Vosman, B.,, G. Kuiken,, and G. Venema. 1988. Transformation in Bacillus subtilis: involvement of the 17-kilo-dalton DNA-entry nuclease and the competence-specific 18-kilodalton protein. J. Bacteriol. 170:3703–3710.

213. Walker, G. C. 1984. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev. 48:60–93.

214. 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.

215. Weinrauch, Y.,, N. Guillen,, and D. Dubnau. 1989. Sequence and transcription mapping of Bacillus subtilis competence genes comB and comA, one of which is related to a family of bacterial regulatory determinants. J. Bacteriol. 171:5362–5375.

216. Weinrauch, Y.,, T. Msadek,, F. Kunst,, G. Rapoport,, and D. Dubnau. 1991. Sequence and properties of comQ, a new competence gene of Bacillus subtilis. J. Bacteriol. 173: 5685–5693.

217. Weinrauch, Y.,, R. Penchev,, E. Dubnau,, I. Smith,, and D. Dubnau. 1990. A Bacillus subtilis regulatory gene product for genetic competence and sporulation resembles sensor protein members of the bacterial two-component signal-transduction systems. Genes Dev. 4:860–872.

218. West, S. C. 1996. The RuvABC proteins and Holliday junction processing in Escherichia coli. J. Bacteriol. 178: 1237–1241.

219. Whatmore, A. M.,, V. A. Barcus,, and C. G. Dowson. 1999. Genetic diversity of the streptococcal competence (com) gene locus. J. Bacteriol. 181:3144–3154.

220. Williams, P. M.,, L. A. Bannister,, and R. J. Redfield. 1994 The Haemophilus influenzae sxy-1 mutation is in a newly identified gene essential for competence. J. Bacteriol. 176:6789–6794.

221. Winterling, K. W.,, D. Chafin,, J. J. Hayes,, J. Sun,, A. S. Levine,, R. E. Yasbin,, and R. Woodgate. 1998. The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J. Bacteriol. 180:2201–2211.

222. Winterling, K. W.,, A. S. Levine,, R. E. Yasbin,, and R. Woodgate. 1997. Characterization of DinR, the Bacillus subtilis SOS repressor. J. Bacteriol. 179:1698–1703.

223. Yasbin, R. E. 1977. DNA repair in Bacillus subtilis. II. Activation of the inducible system in competent bacteria. Mol. Gen. Genet. 153:219–225.

224. Yasbin, R. E.,, D. L. Cheo,, and K. W. Bayles. 1992. Inducible DNA repair and differentiation in Bacillus subtilis: interactions between global regulons. Mol. Microbial. 6: 1263–1270.

225. Zulty, J. J.,, and G. J. Barcak. 1995. Identification of a DNA transformation gene required for coml01A+ expression and supertransformer phenotype in Haemophilus influenzae. Proc. Natl. Acad. Sci. USA 92:3616–3620.

Tables

Transformation and Recombination

/content/10.1128/9781555817992.chap32.tab32-1

TABLE 1

Transformation genes of Bacillus subtilis

10.1128/9781555817992/tab32-1_thmb.gif

10.1128/9781555817992/tab32-1.gif

TABLE 1

Transformation genes of Bacillus subtilis

/content/10.1128/9781555817992.chap32.tab32-2

TABLE 2

Competence regulatory proteins of B. subtilis

10.1128/9781555817992/tab32-2_thmb.gif

10.1128/9781555817992/tab32-2.gif

TABLE 2

Competence regulatory proteins of B. subtilis

/content/10.1128/9781555817992.chap32.tab32-3

TABLE 3

B. subtilis recombination genes

a Organisms containing homologs with highest identity; homologs with at least 60% identity are in boldface.

10.1128/9781555817992/tab32-3_thmb.gif

10.1128/9781555817992/tab32-3.gif

TABLE 3

B. subtilis recombination genes

a Organisms containing homologs with highest identity; homologs with at least 60% identity are in boldface.

/content/10.1128/9781555817992.chap32.tab32-4

TABLE 4

Β. subtilis din genes

a Approximate position of center of operator sequence based on locations of putative +1. Only the recA promocer has been mapped.

b Apparent binding constants were determined by quantitative mobility shift assays ( 12 , 13 , 83 ).

c Organisms containing homologs with highest identity; homologs with at least 60% identity are in boldface.

10.1128/9781555817992/tab32-4_thmb.gif

10.1128/9781555817992/tab32-4.gif

TABLE 4

Β. subtilis din genes

a Approximate position of center of operator sequence based on locations of putative +1. Only the recA promocer has been mapped.

b Apparent binding constants were determined by quantitative mobility shift assays ( 12 , 13 , 83 ).

c Organisms containing homologs with highest identity; homologs with at least 60% identity are in boldface.