Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1997 Mar;145(3):563–572. doi: 10.1093/genetics/145.3.563

Deletion Formation between the Two Salmonella Typhimurium Flagellin Genes Encoded on the Mini F Plasmid: Escherichia Coli Ssb Alleles Enhance Deletion Rates and Change Hot-Spot Preference for Deletion Endpoints

T Mukaihara 1, M Enomoto 1
PMCID: PMC1207842  PMID: 9055067

Abstract

Deletion formation between the 5'-mostly homologous sequences and between the 3'-homeologous sequences of the two Salmonella typhimurium flagellin genes was examined using plasmid-based deletion-detection systems in various Escherichia coli genetic backgrounds. Deletions in plasmid pLC103 occur between the 5' sequences, but not between the 3' sequences, in both RecA-independent and RecA-dependent ways. Because the former is predominant, deletion formation in a recA background depends on the length of homologous sequences between the two genes. Deletion rates were enhanced 30- to 50-fold by the mismatch repair defects, mutS, mutL and uvrD, and 250-fold by the ssb-3 allele, but the effect of the mismatch defects was canceled by the ΔrecA allele. Rates of the deletion between the 3' sequences in plasmid pLC107 were enhanced 17- to 130-fold by ssb alleles, but not by other alleles. For deletions in pLC107, 96% of the endpoints in the recA(+) background and 88% in ΔrecA were in the two hot spots of the 60- and 33-nucleotide (nt) homologous sequences, whereas in the ssb-3 background >50% of the endpoints were in four- to 14-nt direct repeats dispersed in the entire 3' sequences. The deletion formation between the homeologous sequences is RecA-independent but depends on the length of consecutive homologies. The mutant ssb allele lowers this dependency and results in the increase in deletion rates. Roles of mutant SSB are discussed with relation to misalignment in replication slippage.

Full Text

The Full Text of this article is available as a PDF (3.1 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Albertini A. M., Hofer M., Calos M. P., Miller J. H. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell. 1982 Jun;29(2):319–328. doi: 10.1016/0092-8674(82)90148-9. [DOI] [PubMed] [Google Scholar]
  2. Arthur H. M., Lloyd R. G. Hyper-recombination in uvrD mutants of Escherichia coli K-12. Mol Gen Genet. 1980;180(1):185–191. doi: 10.1007/BF00267368. [DOI] [PubMed] [Google Scholar]
  3. Bi X., Liu L. F. recA-independent and recA-dependent intramolecular plasmid recombination. Differential homology requirement and distance effect. J Mol Biol. 1994 Jan 14;235(2):414–423. doi: 10.1006/jmbi.1994.1002. [DOI] [PubMed] [Google Scholar]
  4. Bi X., Lyu Y. L., Liu L. F. Specific stimulation of recA-independent plasmid recombination by a DNA sequence at a distance. J Mol Biol. 1995 Apr 14;247(5):890–902. doi: 10.1006/jmbi.1995.0188. [DOI] [PubMed] [Google Scholar]
  5. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  7. Chédin F., Dervyn E., Dervyn R., Ehrlich S. D., Noirot P. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol Microbiol. 1994 May;12(4):561–569. doi: 10.1111/j.1365-2958.1994.tb01042.x. [DOI] [PubMed] [Google Scholar]
  8. DasGupta U., Weston-Hafer K., Berg D. E. Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322. Genetics. 1987 Jan;115(1):41–49. doi: 10.1093/genetics/115.1.41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. DiGate R. J., Marians K. J. Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III. J Biol Chem. 1989 Oct 25;264(30):17924–17930. [PubMed] [Google Scholar]
  10. Dianov G. L., Kuzminov A. V., Mazin A. V., Salganik R. I. Molecular mechanisms of deletion formation in Escherichia coli plasmids. I. Deletion formation mediated by long direct repeats. Mol Gen Genet. 1991 Aug;228(1-2):153–159. doi: 10.1007/BF00282460. [DOI] [PubMed] [Google Scholar]
  11. Egner C., Berg D. E. Excision of transposon Tn5 is dependent on the inverted repeats but not on the transposase function of Tn5. Proc Natl Acad Sci U S A. 1981 Jan;78(1):459–463. doi: 10.1073/pnas.78.1.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Enomoto M., Stocker B. A. Transduction by phage P1kc in Salmonella typhimurium. Virology. 1974 Aug;60(2):503–514. doi: 10.1016/0042-6822(74)90344-4. [DOI] [PubMed] [Google Scholar]
  13. Feinstein S. I., Low K. B. Hyper-recombining recipient strains in bacterial conjugation. Genetics. 1986 May;113(1):13–33. doi: 10.1093/genetics/113.1.13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Homma M., Fujita H., Yamaguchi S., Iino T. Regions of Salmonella typhimurium flagellin essential for its polymerization and excretion. J Bacteriol. 1987 Jan;169(1):291–296. doi: 10.1128/jb.169.1.291-296.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hulton C. S., Seirafi A., Hinton J. C., Sidebotham J. M., Waddell L., Pavitt G. D., Owen-Hughes T., Spassky A., Buc H., Higgins C. F. Histone-like protein H1 (H-NS), DNA supercoiling, and gene expression in bacteria. Cell. 1990 Nov 2;63(3):631–642. doi: 10.1016/0092-8674(90)90458-q. [DOI] [PubMed] [Google Scholar]
  16. Iino T. Genetics of structure and function of bacterial flagella. Annu Rev Genet. 1977;11:161–182. doi: 10.1146/annurev.ge.11.120177.001113. [DOI] [PubMed] [Google Scholar]
  17. Joys T. M. The covalent structure of the phase-1 flagellar filament protein of Salmonella typhimurium and its comparison with other flagellins. J Biol Chem. 1985 Dec 15;260(29):15758–15761. [PubMed] [Google Scholar]
  18. Kelman Z., O'Donnell M. DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu Rev Biochem. 1995;64:171–200. doi: 10.1146/annurev.bi.64.070195.001131. [DOI] [PubMed] [Google Scholar]
  19. Kushner S. R., Nagaishi H., Templin A., Clark A. J. Genetic recombination in Escherichia coli: the role of exonuclease I. Proc Natl Acad Sci U S A. 1971 Apr;68(4):824–827. doi: 10.1073/pnas.68.4.824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lederberg E M, Lederberg J. Genetic Studies of Lysogenicity in Escherichia Coli. Genetics. 1953 Jan;38(1):51–64. doi: 10.1093/genetics/38.1.51. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lejeune P., Danchin A. Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1990 Jan;87(1):360–363. doi: 10.1073/pnas.87.1.360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lloyd R. G. lexA dependent recombination in uvrD strains of Escherichia coli. Mol Gen Genet. 1983;189(1):157–161. doi: 10.1007/BF00326069. [DOI] [PubMed] [Google Scholar]
  23. Lovett S. T., Feschenko V. V. Stabilization of diverged tandem repeats by mismatch repair: evidence for deletion formation via a misaligned replication intermediate. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7120–7124. doi: 10.1073/pnas.93.14.7120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lovett S. T., Gluckman T. J., Simon P. J., Sutera V. A., Jr, Drapkin P. T. Recombination between repeats in Escherichia coli by a recA-independent, proximity-sensitive mechanism. Mol Gen Genet. 1994 Nov 1;245(3):294–300. doi: 10.1007/BF00290109. [DOI] [PubMed] [Google Scholar]
  25. Luisi-DeLuca C., Lovett S. T., Kolodner R. D. Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12 mutants. Genetics. 1989 Jun;122(2):269–278. doi: 10.1093/genetics/122.2.269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Lundblad V., Kleckner N. Mismatch repair mutations of Escherichia coli K12 enhance transposon excision. Genetics. 1985 Jan;109(1):3–19. doi: 10.1093/genetics/109.1.3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Maloy S. R., Nunn W. D. Selection for loss of tetracycline resistance by Escherichia coli. J Bacteriol. 1981 Feb;145(2):1110–1111. doi: 10.1128/jb.145.2.1110-1111.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Mazin A. V., Kuzminov A. V., Dianov G. L., Salganik R. I. Mechanisms of deletion formation in Escherichia coli plasmids. II. Deletions mediated by short direct repeats. Mol Gen Genet. 1991 Aug;228(1-2):209–214. doi: 10.1007/BF00282467. [DOI] [PubMed] [Google Scholar]
  29. Newton S. M., Wasley R. D., Wilson A., Rosenberg L. T., Miller J. F., Stocker B. A. Segment IV of a Salmonella flagellin gene specifies flagellar antigen epitopes. Mol Microbiol. 1991 Feb;5(2):419–425. doi: 10.1111/j.1365-2958.1991.tb02124.x. [DOI] [PubMed] [Google Scholar]
  30. Pang P. P., Lundberg A. S., Walker G. C. Identification and characterization of the mutL and mutS gene products of Salmonella typhimurium LT2. J Bacteriol. 1985 Sep;163(3):1007–1015. doi: 10.1128/jb.163.3.1007-1015.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Rayssiguier C., Thaler D. S., Radman M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature. 1989 Nov 23;342(6248):396–401. doi: 10.1038/342396a0. [DOI] [PubMed] [Google Scholar]
  32. Schmellik-Sandage C. S., Tessman E. S. Signal strains that can detect certain DNA replication and membrane mutants of Escherichia coli: isolation of a new ssb allele, ssb-3. J Bacteriol. 1990 Aug;172(8):4378–4385. doi: 10.1128/jb.172.8.4378-4385.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Schofield M. A., Agbunag R., Michaels M. L., Miller J. H. Cloning and sequencing of Escherichia coli mutR shows its identity to topB, encoding topoisomerase III. J Bacteriol. 1992 Aug;174(15):5168–5170. doi: 10.1128/jb.174.15.5168-5170.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Shapira S. K., Chou J., Richaud F. V., Casadaban M. J. New versatile plasmid vectors for expression of hybrid proteins coded by a cloned gene fused to lacZ gene sequences encoding an enzymatically active carboxy-terminal portion of beta-galactosidase. Gene. 1983 Nov;25(1):71–82. doi: 10.1016/0378-1119(83)90169-5. [DOI] [PubMed] [Google Scholar]
  35. Tominaga A., Ikemizu S., Enomoto M. Site-specific recombinase genes in three Shigella subgroups and nucleotide sequences of a pinB gene and an invertible B segment from Shigella boydii. J Bacteriol. 1991 Jul;173(13):4079–4087. doi: 10.1128/jb.173.13.4079-4087.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Trinh T. Q., Sinden R. R. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature. 1991 Aug 8;352(6335):544–547. doi: 10.1038/352544a0. [DOI] [PubMed] [Google Scholar]
  37. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]
  38. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  39. Wei L. N., Joys T. M. Covalent structure of three phase-1 flagellar filament proteins of Salmonella. J Mol Biol. 1985 Dec 20;186(4):791–803. doi: 10.1016/0022-2836(85)90397-3. [DOI] [PubMed] [Google Scholar]
  40. Whoriskey S. K., Schofield M. A., Miller J. H. Isolation and characterization of Escherichia coli mutants with altered rates of deletion formation. Genetics. 1991 Jan;127(1):21–30. doi: 10.1093/genetics/127.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Williams K. R., Murphy J. B., Chase J. W. Characterization of the structural and functional defect in the Escherichia coli single-stranded DNA binding protein encoded by the ssb-1 mutant gene. Expression of the ssb-1 gene under lambda pL regulation. J Biol Chem. 1984 Oct 10;259(19):11804–11811. [PubMed] [Google Scholar]
  42. Worth L., Jr, Clark S., Radman M., Modrich P. Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3238–3241. doi: 10.1073/pnas.91.8.3238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Yi T. M., Stearns D., Demple B. Illegitimate recombination in an Escherichia coli plasmid: modulation by DNA damage and a new bacterial gene. J Bacteriol. 1988 Jul;170(7):2898–2903. doi: 10.1128/jb.170.7.2898-2903.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES