Chapter 22 : Natural Transformation, Recombination, and Repair

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

Preview this chapter:
Zoom in

Natural Transformation, Recombination, and Repair, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818005/9781555812133_Chap22-1.gif /docserver/preview/fulltext/10.1128/9781555818005/9781555812133_Chap22-2.gif


Three mechanisms of horizontal gene transfer are commonly observed: natural transformation, conjugation, and transduction. Natural transformation and other mechanisms of horizontal gene transfer are dependent on DNA recombination. The latter mechanism is probably the most important function in postreplicative DNA repair. All organisms respond to the continuous damaging of their DNA by exogenous or endogenous factors with several, possibly redundant, systems of DNA repair. The number of different systems seems to vary considerably between organisms, although this does not necessarily imply altered mutation rates. Natural transformation of , together with DNA recombination and repair, is discussed in this chapter to underline the interdependence of these cellular functions. Natural transformation competence in most gram-negative bacteria is associated with production of type IV pili. The importance of recombination for natural transformation competence is mentioned, but (homologous) recombination is also possible during all other states of transient or permanent diploidy, i.e., during conjugation or transduction or after DNA replication. Branch migration and junction resolution can also be performed by RecG, but both systems may have different functions in (recombinational) DNA repair. The resolution of some Holliday junctions during recombinational repair results in the formation of chromosomal dimers, which have to be resolved by the XerCD site-specific recombinases found in many organisms.

Citation: Fischer W, Hofreuter D, Haas R. 2001. Natural Transformation, Recombination, and Repair, p 249-257. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch22

Key Concept Ranking

Microbial Evolution
Chromosomal DNA
DNA Polymerase V
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Arrangement of gene loci involved in transformation competence. Gene arrangement of the four loci that to date have been shown to be necessary for transformation competence. Gene orientations, numbers, and designations are shown according to the genome sequence of strain J99. Localizations and putative functions of the encoded proteins are indicated. Abbreviations: IM, inner membrane; PP, periplasmic space; CY, cytoplasm. The proteins marked by an asterisk are associated with membrane fractions as well. For the DprA and ComH proteins, no experimental data are available.

Citation: Fischer W, Hofreuter D, Haas R. 2001. Natural Transformation, Recombination, and Repair, p 249-257. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch22
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Aim, R. A.,, L. S. Ling,, D. T. Moir,, B. L. King,, E. D. Brown,, P. C. Doig,, D. R. Smith,, B. Noonan,, B. C. Guild,, B. L. dejonge,, G. Carmel,, P. J. Tummino,, A. Caruso,, M. Uria-Nickelsen,, D. M. Mills,, C. Ives,, R. Gibson,, D. Merberg,, S. D. Mills,, Q. Jiang,, D. E. Taylor,, G. F. Vovis,, and T. J. Trust. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176180.
2. Ando, T.,, D. A. Israel,, K. Kusugami,, and M. J. Blaser. 1999. HP0333, a member of the dprA family, is involved in natural transformation in Helicobacter pylori. J. Bacteriol. 181: 55725580.
2a.. Ando, T.,, Q. Xu,, M. Torres,, K. Kusugami,, D. A. Israel,, and M. J. Blaser. 2000. Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer. Mol. Microbiol. 37:10521065.
3. Aravind, L.,, D. R. Walker,, and E. V. Koonin. 1999. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27:12231242.
4. Biswas, G. D.,, K. L. Burnstein,, and P. F. Sparling. 1986. Linearization of donor DNA during plasmid transformation in Neisseria gonorrhoeae. J. Bacteriol. 168:756761.
5. Bohne, J.,, A. Yim,, and A. N. Binns. 1998. The Ti plasmid increases the efficiency of Agrobacterium tumefaciens as a recipient in virB-mediated conjugal transfer of an IncQ plasmid. Proc. Natl. Acad. Sci. USA 95:70577062.
6. Bukanov, N. O.,, and D. E. Berg. 1994. Ordered cosmid library and high-resolution physical-genetic map of Helicobacter pylori strain NCTC11638. Mol. Microbiol. 11:509523.
7. Burucoa, C. Personal communication.
8. Campbell, E. A.,, S. Y. Choi,, and H. R. Masure. 1998. A competence regulon in Streptococcus pneumoniae revealed by genomic analysis. Mol. Microbiol. 27:929939.
9. Cox, M. M.,, M. F. Goodman,, K. N. Kreuzer,, D. J. Sherratt,, S. J. Sandler,, and K. J. Marians. 2000. The importance of repairing stalled replication forks. Nature 404:3741.
10. Dang, T. A.,, X. R. Zhou,, B. Graf,, and P. J. Christie. 1999. Dimerization of the Agrobacterium tumefaciens VirB4 ATPase and the effect of ATP-binding cassette mutations on the assembly and function of the T-DNA transporter. Mol. Microbiol. 32:12391253.
11. 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: 311318.
12. De Ungria, M. C.,, T. Kolesnikow,, P. T. Cox,, and A. Lee. 1999. Molecular characterization and interstrain variability of pHPSl, a plasmid isolated from the Sydney strain (SS1) of Helicobacter pylori. Plasmid 41:97109.
12a.. Donahue, J. P.,, D. A. Israel,, R. M. Peek, Jr.,, M. J. Blaser,, and G. G. Miller. 2000. Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori. Mol. Microbiol. 37:10661074.
13. Dorocicz, I. R.,, P. M. Williams,, and R. J. Redfield. 1993. The Haemophilus influenzae adenylate cyclase gene: cloning, sequence, and essential role in competence. J. Bacteriol. 175: 71427149.
14. Dubnau, D. 1999. DNA uptake in bacteria. Annu. Rev. Microbiol. 53:217244.
15. Eisen, J. A. 1998. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 26:42914300.
16. Fernandez, S.,, S. Ayora,, and J. C. Alonso. 2000. Bacillus subtilis homologous recombination: genes and products. Res. Microbiol. 151:481486.
17. Fischer, W.,, and R. Haas. Unpublished data.
18. Goodman, S. D.,, and J. J. Scocca. 1988. Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. Proc. Natl. Acad. Sci. USA 85:69826986.
19. Grilley, M.,, J. Griffith,, and P. Modrich. 1993. Bidirectional excision in methyl-directed mismatch repair. J. Biol. Chem. 268:1183011837.
20. Haas, R.,, T. F. Meyer,, and J. P. van Putten. 1993. Aflagellated mutants of Helicobacter pylori generated by genetic transformation of naturally competent strains using transposon shuttle mutagenesis. Mol. Microbiol. 8:753760.
21. Heintschel von Heinegg, E.,, H. P. Nalik,, and E. N. Schmid. 1993. Characterisation of a Helicobacter pylori phage (HP1). J. Med. Microbiol. 38:245249.
22. Heuermann, D.,, and R. Haas. 1998. A stable shuttle vector system for efficient genetic complementation of Helicobacter pylori strains by transformation and conjugation. Mol. Gen. Genet. 257:519528.
23. Hofreuter, D.,, and R. Haas. Unpublished data.
24. Hofreuter, D.,, S. Odenbreit,, G. Henke,, and R. Haas. 1998. Natural competence for DNA transformation in Helicobacter pylori: identification and genetic characterization of the comB locus. Mol. Microbiol. 28:10271038.
25. Hofreuter, D.,, S. Odenbreit,, J. Püls,, D. Schwan,, and R. Haas. 2000. Genetic competence in Helicobacter pylori: mechanisms and biological implications. Res. Microbiol. 151:487491.
26. Horst, J. P.,, T. H. Wu,, and M. G. Marinus. 1999. Escherichia coli mutator genes. Trends Microbiol. 7:2936.
27. Israel, D. A.,, A. S. Lou,, and M. J. Blaser. 2000. Characteristics of Helicobacter pylori natural transformation. FEMS Microbiol. Lett. 186:275280.
28. Jiang, Q.,, K. Hiratsuka,, and D. E. Taylor. 1996. Variability of gene order in different Helicobacter pylori strains contributes to genome diversity. Mol. Microbiol. 20:833842.
29. Karudapuram, S.,, and G. J. Barcak. 1997. The Haemophilus influenzae dprABC genes constitute a competence-inducible operon that requires the product of the tfoX (sxyj gene for transcriptional activation. J. Bacteriol. 179:48154820.
30. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25:156165.
31. Kuipers, E. J.,, D. A. Israel,, J. G. Kusters,, and M. J. Blaser. 1998. Evidence for a conjugation-like mechanism of DNA transfer in Helicobacter pylori. ]. Bacteriol. 180:29012905.
32. Lorenz, M. G.,, and W. Wackernagel. 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:563602.
33. Lovett, S. T.,, and R. D. Kolodner. 1989. Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 86:26272631.
34. Majewski, S. I. H.,, and C. S. Goodwin. 1988. Restriction endonuclease analysis of the genome of Campylobacter pylori with a rapid extraction method: evidence for considerable genomic variation. J. Infect. Dis. 157:465471.
35. Mark, I.,, C. Rayssiguier,, and M. Radman. 1995. Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Cell 80:507515.
36. McGowan, C. C.,, A. Necheva,, S. A. Thompson,, T. L. Cover,, and M. J. Blaser. 1998. Acid-induced expression of an LPS-associated gene in Helicobacter pylori. Mol. Microbiol. 30: 1931.
37. Mendonca, V. M.,, H. D. Klepin,, and S. W. Matson. 1995. DNA helicases in recombination and repair: construction of a ΔuvrD ΔhelD ΔrecQ mutant deficient in recombination and repair. J. Bacteriol. 177:13261335.
38. Minnis, J. A.,, T. E. Taylor,, J. E. Knesek,, W. L. Peterson,, and S. A. Mclntire. 1995. Characterization of a 3.5-kbp plasmid from Helicobacter pylori. Plasmid 34:2236.
39. Nedenskov-Sorensen, P.,, G. Bukholm,, and K. Bovre. 1990. Natural competence for genetic transformation in Campylobacter pylori. J. Infect. Dis. 161:365366.
40. Odenbreit, S.,, M. Till,, and R. Haas. 1996. Optimized BlaM-transposon shuttle mutagenesis of Helicobacter pylori allows the identification of novel genetic loci involved in bacterial virulence. Mol. Microbiol. 20:361373.
41. Palmen, R.,, B. Vosman,, P. Buijsman,, C. K. Breek,, and K. J. Hellingwerf. 1993. Physiological characterization of natural transformation in Acinetobacter calcoaceticus.J. Gen. Microbiol. 139:295305.
42. Parkhill, J.,, B. W. Wren,, K. Mungall,, J. M. Ketley,, C. Churcher,, D. Basham,, T. Chillingworth,, R. M. Davies,, T. Felt-well,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Moule,, M. J. Pallen,, C. W. Penn,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, A. H. van Vliet,, S. Whitehead,, and B. G. Barrell. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665668.
43. Prowedi, R.,, and D. Dubnau. 1999. ComEA is a DNA receptor for transformation of competent Bacillus subtilis. Mol. Microbiol. 31:271280.
44. Radman, M. 1976. An endonuclease from Escherichia coli that introduces single polynucleotide chain scissions in ultraviolet-irradiated DNA. J. Biol. Chem. 251:14381445.
45. Rebeck, G. W.,, and L. Samson. 1991. Increased spontaneous mutation and alkylation sensitivity of Escherichia coli strains lacking the ogt 06-methylguanine DNA repair methyltransfer-ase. J. Bacteriol. 173:20682076.
46. Recchia, G. D.,, and D. J. Sherratt. 1999. Conservation of xer site-specific recombination genes in bacteria. Mol. Microbiol. 34:11461148.
47. Sancar, A. 1994. Mechanisms of DNA excision repair. Science 266:19541956.
48. Sandler, S. J.,, and K. J. Marians. 2000. Role of PriA in replication fork reactivation in Escherichia coli. J. Bacteriol. 182: 913.
49. Saunders, N. J.,, J. F. Peden,, and E. R. Moxon. 1999. Absence in Helicobacter pylori of an uptake sequence for enhancing uptake of homospecific DNA during transformation. Microbiology 145:35233528.
50. Schmitt, W.,, S. Odenbreit,, D. Heuermann,, and R. Haas. 1995. Cloning of the Helicobacter pylori recA gene and functional characterization of its product. Mol. Gen. Genet. 248: 563572.
51. Simor, A. E.,, B. Shames,, B. Drumm,, P. Sherman,, D. E. Low,, and J. L. Penner. 1990. Typing of Campylobacter pylori by bacterial DNA restriction endonuclease analysis and determination of plasmid profile. J. Clin. Microbiol. 28:8386.
52. Sjolund, M. Personal communication.
53. Smeets, L. C.,, J. J. Bijlsma,, S. Y. Boomkens,, C. M. Vanden-broucke-Grauls,, and J. G. Kusters. 2000. comH, a novel gene essential for natural transformation of Helicobacter pylori. J. Bacteriol. 182:39483954.
54. Smeets, L. C.,, J. J. Bijlsma,, E. J. Kuipers,, C. M. Vanden-broucke-Grauls,, and J. G. Kusters. 2000. The dprA gene is required for natural transformation of Helicobacter pylori. FEMS Immunol. Med. Microbiol. 27:99102.
55. Smith, G. R. 1989. Homologous recombination in E. coli: multiple pathways for multiple reasons. Cell 58:807809.
56. Solomon, J. M.,, and A. D. Grossman. 1996. Who's competent and when: regulation of natural genetic competence in bacteria. Trends Genet. 12:150155.
57. Song, Y.,, and N. J. Sargentini. 1996. Escherichia coli DNA repair genes radA and sms are the same gene. J. Bacteriol. 178: 50455048.
58. Stern, A.,, and T. F. Meyer. 1987. Common mechanism controlling phase and antigenic variation in pathogenic Neisseriae. Mol. Microbiol. 1:512.
59. Suerbaum, S.,, J. M. Smith,, K. Bapumia,, G. Morelli,, N. H. Smith,, E. Kunstmann,, I. Dyrek,, and M. Achtman. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95:1261912624.
60. Thompson, S. A.,, and M. J. Blaser. 1995. Isolation of the Helicobacter pylori recA gene and involvement of the recA region in resistance to low pH. Infect. Immun. 63:21852193.
61. Thompson, S. A.,, R. L. Latch,, and J. M. Blaser. 1998. Molecular characterization of the Helicobacter pylori uvrB gene. Gene 209:113122.
62. Tomb, J.-F.,, O. White,, A. R. Kerlavage,, R. A. Clayton,, G. G. Sutton,, R. D. Fleischmann,, K. A. Ketchum,, H. P. Klenk,, S. Gill,, B. A. Dougherty,, K. Nelson,, J. Quakenbush,, L. Zhou,, E. F. Kirkness,, S. Peterson,, B. Loftus,, D. Richardson,, R. Dodson,, H. G. Khalak,, A. Glodek,, K. McKenney,, L. M. Fitzegerald,, N. Lee,, M. D. Adams,, E. K. Hickey,, D. E. Berg,, J. D. Gocayne,, T. R. Utterback,, J. D. Peterson,, J. M. Kelley,, M. D. Cotton,, J. M. Weidman,, C. Fujii,, C. Bowman,, L. Watthey,, E. Wallin,, W. S. Hayes,, M. Borodovsky,, P. D. Karp,, H. O. Smith,, C. M. Fraser,, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539547.
63. Tsai-Wu, J. J.,, H. F. Liu,, and A. L. Lu. 1992. Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidi-nic endonuclease activities on A:C and A:G mispairs. Proc. Natl. Acad. Sci. USA 89:87798783.
64. Umezu, K.,, N. W. Chi, andR. D. 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 90:38753879.
65. Wang, G.,, M. Z. Humayun,, and D. E. Taylor. 1999. Mutation as an origin of genetic variability in Helicobacter pylori. Trends Microbiol. 7:488493.
66. Wang, Y.,, K. P. Roos,, and D. E. Taylor. 1993. Transformation of Helicobacter pylori by chromosomal metronidazole resistance and by a plasmid with a selectable chloramphenicol resistance marker. J. Gen. Microbiol. 139:24852493.
67. Wang, Y.,, and D. E. Taylor. 1990. Natural transformation in Campylobacter species. J. Bacteriol. 172:949955.
68. West, S. C. 1996. The RuvABC proteins and Holliday junction processing in Escherichia coli. J. Bacteriol. 178:12371241.
69. Whitby, M. C.,, L. Ryder,, and R. G. Lloyd. 1993. Reverse branch migration of Holliday junctions by RecG protein: a new mechanism for resolution of intermediates in recombination and DNA repair. Cell 75:341350.


Generic image for table
Table 1

genes that may be involved in homologous recombination and recombinational repair

Citation: Fischer W, Hofreuter D, Haas R. 2001. Natural Transformation, Recombination, and Repair, p 249-257. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch22

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error