Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins
10.1128/jb.177.3.660-666.1995
Crossref journal-article
American Society for Microbiology
Journal of Bacteriology (235)
Abstract

In Escherichia coli, T:G mismatches in specific contexts are corrected by a very short patch (VSP) repair system. Previous studies have shown that the product of gene vsr mediates correction of T:G to C:G in the 5'CTAGG/3'GGTCC context and in some related contexts. Amber mutations that arose in CAG sequences in gene cI of bacteriophage lambda were used to determine the effect of flanking bases on the repair of T:G mispairs arising during phage recombination. The experimental findings were combined with published data on mismatch repair of mutations in lambda gene P and E. coli gene lacI. While VSP repair was most efficient in the context 5'CTAGG, there was very significant correction when either the 5'C or the 3' G was replaced by another base. Some mismatch repair of TAG to CAG occurred in all contexts tested. Reduction in VSP repair caused by the lack of MutL or MutS was fully complemented by the addition of vsr+ plasmids when the T:G mispair was in the 5'CTAGG/3'GGTCC context. VSP repair was decreased in bacteria containing mutS+ on a multicopy plasmid. It is suggested that VSP repair maintains sequences such as the repetitive extragenic palindromic (REP) and Chi sequences, which have important roles in E. coli and closely related bacteria.

Bibliography

Lieb, M., & Rehmat, S. (1995). Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins. Journal of Bacteriology, 177(3), 660–666.

Authors 2
  1. M Lieb (first)
  2. S Rehmat (additional)
References 52 Referenced 30
  1. Au , K. G. , M. Cabrera , J. H. Miller , and P. Modrich . 1988 . Escherichia coli mutY gene product is required for specific A-G to CG mismatch correction . Proc. Natl. Acad. Sci. USA 86 : 9163 - 9166 . / Proc. Natl. Acad. Sci. USA / Escherichia coli mutY gene product is required for specific A-G to CG mismatch correction by Au K. G. (1988)
  2. Bachmann , B. J. 1972 . Pedigrees of some mutant strains of Escherichia coli K-12 . Bacteriol. Rev. 36 : 525 - 557 . (10.1128/br.36.4.525-557.1972) / Bacteriol. Rev. / Pedigrees of some mutant strains of Escherichia coli K-12 by Bachmann B. J. (1972)
  3. Bale , A. , M. d' Alarao , and M. G. Marinus . 1979 . Characterization of DNA adenine methylation mutants of Escherichia coli K12 . Mutat. Res. 59 : 157 - 165 . (10.1016/0027-5107(79)90153-2) / Mutat. Res. / Characterization of DNA adenine methylation mutants of Escherichia coli K12 by Bale A. (1979)
  4. Bhagwat , A. S. , and M. McClelland . 1992 . DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome . Nucleic Acids Res. 20 : 1663 - 1668 . (10.1093/nar/20.7.1663) / Nucleic Acids Res. / DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome by Bhagwat A. S. (1992)
  5. Blaisdell , B. E. , K. E. Rudd , A. Matin , and S. Karlin . 1993 . Significant dispersed recurrent DNA sequences in the Escherichia coli genome . J. Mol. Biol. 229 : 833 - 848 . (10.1006/jmbi.1993.1090) / J. Mol. Biol. / Significant dispersed recurrent DNA sequences in the Escherichia coli genome by Blaisdell B. E. (1993)
  6. Bonhoffer , F. 1966 . DNA transfer and DNA biosynthesis during bacterial conjugation . Z. Vererbungsl. 98 : 141 - 149 . / Z. Vererbungsl. / DNA transfer and DNA biosynthesis during bacterial conjugation by Bonhoffer F. (1966)
  7. Burge , C. , A. M. Campbell , and S. Karlin . 1992 . Over- and under-representation of short oligonucleotides in DNA sequences . Proc. Natl. Acad. Sci. USA 89 : 1358 - 1362 . (10.1073/pnas.89.4.1358) / Proc. Natl. Acad. Sci. USA / Over- and under-representation of short oligonucleotides in DNA sequences by Burge C. (1992)
  8. Burland , V. , G. Plunkett III , D. L. Daniels , and F. R. Blattner . 1993 . DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around origin of replication . Genomics 16 : 551 - 561 . (10.1006/geno.1993.1230) / Genomics / DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around origin of replication by Burland V. (1993)
  9. Cheng , K. C. , and G. R. Smith . 1984 . Recombinational hotspot activity of Chi-like sequences . J. Mol. Biol. 180 : 371 - 377 . (10.1016/S0022-2836(84)80009-1) / J. Mol. Biol. / Recombinational hotspot activity of Chi-like sequences by Cheng K. C. (1984)
  10. Coulondre , C. , and J. H. Miller . 1977 . Genetic studies of the lac repressor. III. Additional correlation of mutational sites with specific amino acid residues . J. Mol. Biol. 117 : 525 - 575 . / J. Mol. Biol. / Genetic studies of the lac repressor. III. Additional correlation of mutational sites with specific amino acid residues by Coulondre C. (1977)
  11. Coulondre , C. , J. H. Miller , P. J. Farabaugh , and W. Gilbert . 1978 . Molecular basis of base substitution hotspots in Escherichia coli . Nature (London) 274 : 775 - 780 . (10.1038/274775a0) / Nature (London) / Molecular basis of base substitution hotspots in Escherichia coli by Coulondre C. (1978)
  12. Daniels , D. L. , G. Plunkett , V. Burland , and F. R. Blattner . 1992 . Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes . Science 257 : 771 - 778 . (10.1126/science.1379743) / Science / Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes by Daniels D. L. (1992)
  13. Dimri , G. P. , K. E. Rudd , M. K. Morgan , H. Bayat , and G. F. -L. Ames . 1992 . Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria . J. Bacteriol. 174 : 4583 - 4593 . (10.1128/JB.174.14.4583-4593.1992) / J. Bacteriol. / Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria by Dimri G. P. (1992)
  14. Dzidic , S. , and M. Radman . 1989 . Genetic requirements for hyper-recombination by very short patch mismatch repair: involvement of Escherichia coli DNA polymerase I . Mol. Gen. Genet. 217 : 254 - 256 . (10.1007/BF02464889) / Mol. Gen. Genet. / Genetic requirements for hyper-recombination by very short patch mismatch repair: involvement of Escherichia coli DNA polymerase I by Dzidic S. (1989)
  15. Fisher , C. , R. J. Parks , M. L. Lauzon , and D. H. Evans . 1991 . Heteroduplex DNA formation is associated with replication and recombination in poxvirus-infected cells . Genetics 129 : 7 - 18 . (10.1093/genetics/129.1.7) / Genetics / Heteroduplex DNA formation is associated with replication and recombination in poxvirus-infected cells by Fisher C. (1991)
  16. Gabbara , S. , M. Wyszynski , and A. S. Bhagwat . 1994 . A DNA repair process in Escherichia coli corrects U:G and T:G mismatches at sites of cytosine methylation to C:G . Mol. Gen. Genet. 243 : 244 - 248 . (10.1007/BF00280322) / Mol. Gen. Genet. / A DNA repair process in Escherichia coli corrects U:G and T:G mismatches at sites of cytosine methylation to C:G by Gabbara S. (1994)
  17. Garcia , P. , A. -M. Gase , X. Kyriakidis , D. Baty , and M. Sicard . 1988 . DNA sequences required to induce localized conversion in Streptococcus pneumoniae transformation . Mol. Gen. Genet. 214 : 509 - 513 . (10.1007/BF00330488) / Mol. Gen. Genet. / DNA sequences required to induce localized conversion in Streptococcus pneumoniae transformation by Garcia P. (1988)
  18. Georgopoulos C. and I. Herskowitz. 1971. Escherichia coli mutants blocked inDNA synthesis p. 553-554. In A. D. Hershey (ed.) The bacteriophage lambda. Cold Spring Harbor Laboratory Cold Spring Harbor N.Y.
  19. Gläsner W. F. Hennecke and H.-J. Fritz. 1992. Enzymatic properties and biological functions of Vsr mismatch endonuclease p. 165-173. In D. M. J. Lilley H. Heumann and D. Suck (ed.) Structural tools for the analysis of protein-nucleic acid complexes. Berkhauser Verlag Basel.
  20. Grilley , M. , K. M. Welsh , S. -S. Su , and P. Modrich . 1989 . Isolation and identification of the Escherichia coli mutL gene product . J. Biol. Chem. 264 : 1000 - 1004 . (10.1016/S0021-9258(19)85043-3) / J. Biol. Chem. / Isolation and identification of the Escherichia coli mutL gene product by Grilley M. (1989)
  21. Hennecke , F. , H. Kolman , K. Brundl , and H. -J. Fritz . 1991 . The Vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease . Nature (London) 353 : 776 - 778 . (10.1038/353776a0) / Nature (London) / The Vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease by Hennecke F. (1991)
  22. Jones , M. , R. Wagner , and M. Radman . 1987 . Mismatch repair of deaminated 5-methyl-cytosine . J. Mol. Biol. 193 : 155 - 159 . (10.1016/0022-2836(87)90724-8) / J. Mol. Biol. / Mismatch repair of deaminated 5-methyl-cytosine by Jones M. (1987)
  23. Jones , M. , R. Wagner , and M. Radman . 1987 . Mismatch repair and recombination in E. coli . Cell 50 : 621 - 626 . (10.1016/0092-8674(87)90035-3) / Cell / Mismatch repair and recombination in E. coli by Jones M. (1987)
  24. Jones , M. , R. Wagner , and M. Radman . 1987 . Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence . Genetics 115 : 605 - 610 . (10.1093/genetics/115.4.605) / Genetics / Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence by Jones M. (1987)
  25. Lefevre , J. C. , A. M. Gase , A. C. Burger , P. Mostachfi , and A. M. Sicard . 1984 . Hyperrecombination at a specific DNA sequence in pneumococcal transformation . Proc. Natl. Acad. Sci. USA 81 : 5184 - 5188 . (10.1073/pnas.81.16.5184) / Proc. Natl. Acad. Sci. USA / Hyperrecombination at a specific DNA sequence in pneumococcal transformation by Lefevre J. C. (1984)
  26. Lieb , M. 1976 . Mapping missense and nonsense mutations in gene cI of bacteriophage lambda: marker effects . Mol. Gen. Genet. 146 : 285 - 290 . (10.1007/BF00701252) / Mol. Gen. Genet. / Mapping missense and nonsense mutations in gene cI of bacteriophage lambda: marker effects by Lieb M. (1976)
  27. Lieb , M. 1983 . Specific mismatch correction in bacteriophagecrosses by very short patch repair . Mol. Gen. Genet. 191 : 118 - 125 . (10.1007/BF00330898) / Mol. Gen. Genet. / Specific mismatch correction in bacteriophagecrosses by very short patch repair by Lieb M. (1983)
  28. Lieb , M. 1985 . Recombination in therepressor gene: evidence that very short patch (VSP) mismatch correction restores a specific sequence . Mol. Gen. Genet. 199 : 465 - 470 . (10.1007/BF00330759) / Mol. Gen. Genet. / Recombination in therepressor gene: evidence that very short patch (VSP) mismatch correction restores a specific sequence by Lieb M. (1985)
  29. Lieb , M. 1987 . Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites . J. Bacteriol. 169 : 5241 - 5246 . (10.1128/JB.169.11.5241-5246.1987) / J. Bacteriol. / Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites by Lieb M. (1987)
  30. Lieb , M. 1991 . Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair . Genetics 128 : 23 - 27 . (10.1093/genetics/128.1.23) / Genetics / Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair by Lieb M. (1991)
  31. Lieb M. Unpublished data.
  32. Lieb , M. , E. Allen , and D. Read . 1986 . Very short patch mismatch repair in phage ~: repair sites and lengths of repair tracts . Genetics 114 : 1041 - 1060 . (10.1093/genetics/114.4.1041) / Genetics / Very short patch mismatch repair in phage ~: repair sites and lengths of repair tracts by Lieb M. (1986)
  33. Lu , A. L. , and D. Y. Chang . 1988 . Repair of single base-pair transversion mismatches of Escherichia coli in vitro: correction of certain A/G mismatches is independent of dam methylation and host mut HLS gene functions . Genetics 118 : 593 - 600 . (10.1093/genetics/118.4.593) / Genetics / Repair of single base-pair transversion mismatches of Escherichia coli in vitro: correction of certain A/G mismatches is independent of dam methylation and host mut HLS gene functions by Lu A. L. (1988)
  34. Marinus , M. G. 1973 . Location of DNA methylation genes on the Escherichia coli K12 genetic map . Mol. Gen. Genet. 127 : 47 - 55 . (10.1007/BF00267782) / Mol. Gen. Genet. / Location of DNA methylation genes on the Escherichia coli K12 genetic map by Marinus M. G. (1973)
  35. Marinus M. G. 1973. Personal communication.
  36. May , M. S. , and S. Hattman . 1975 . Deoxyribonucleotide acid-cytosine methylation by host- and plasmid-controlled enzymes . J. Bacteriol. 122 : 129 - 138 . (10.1128/JB.122.1.129-138.1975) / J. Bacteriol. / Deoxyribonucleotide acid-cytosine methylation by host- and plasmid-controlled enzymes by May M. S. (1975)
  37. Merkl , R. , M. Kröger , P. Rice , and H. -J. Fritz . 1992 . Statistical evaluation and biological interpretation of non-random abundance in the E. coli K12 genome of tetra- and penta-nucleotide sequences related to VSP DNA mismatch repair . Nucleic Acids Res. 20 : 1657 - 1662 . (10.1093/nar/20.7.1657) / Nucleic Acids Res. / Statistical evaluation and biological interpretation of non-random abundance in the E. coli K12 genome of tetra- and penta-nucleotide sequences related to VSP DNA mismatch repair by Merkl R. (1992)
  38. Meselson M. 1988. Methyl-directed repair of DNA mismatches p. 91-113. In K. B. Low (ed.) The recombination of genetic materials. Academic Press New York. (10.1016/B978-0-12-456270-7.50009-6)
  39. Modrich , P. 1991 . Mechanisms and biological effects of mismatch repair. Annu . Rev. Genet. 25 : 229 - 253 . (10.1146/annurev.ge.25.120191.001305) / Rev. Genet. / Mechanisms and biological effects of mismatch repair. Annu by Modrich P. (1991)
  40. Radicella , J. B. , E. A. Clark , and M. S. Fox . 1988 . Some mismatch repair activities in Escherichia coli . Proc. Natl. Acad. Sci. USA 85 : 9674 - 9678 . (10.1073/pnas.85.24.9674) / Proc. Natl. Acad. Sci. USA / Some mismatch repair activities in Escherichia coli by Radicella J. B. (1988)
  41. Raposa , S. , and M. S. Fox . 1987 . Some features of base pair mismatch and heterology repair in Escherichia coli . Genetics 117 : 381 - 390 . (10.1093/genetics/117.3.381) / Genetics / Some features of base pair mismatch and heterology repair in Escherichia coli by Raposa S. (1987)
  42. Schultz , D. W. , and G. R. Smith . 1986 . Conservation of Chi cutting activity in terrestrial and murine enteric bacteria . J. Mol. Biol. 189 : 585 - 595 . (10.1016/0022-2836(86)90489-4) / J. Mol. Biol. / Conservation of Chi cutting activity in terrestrial and murine enteric bacteria by Schultz D. W. (1986)
  43. Shcherbakov , V. P. , and L. A. Plugina . 1991 . Marker-dependent recombination in T4 bacteriophage. III. Structural prerequisites for marker discrimination . Genetics 128 : 673 - 685 . (10.1093/genetics/128.4.673) / Genetics / Marker-dependent recombination in T4 bacteriophage. III. Structural prerequisites for marker discrimination by Shcherbakov V. P. (1991)
  44. Smith , G. R. 1988 . Homologous recombination in procaryotes . Microbiol. Rev. 52 : 1 - 28 . (10.1128/MR.52.1.1-28.1988) / Microbiol. Rev. / Homologous recombination in procaryotes by Smith G. R. (1988)
  45. Sohail , A. , M. Lieb , M. Dar , and A. S. Bhagwat . 1990 . A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene . J. Bacteriol. 172 : 4214 - 4221 . (10.1128/JB.172.8.4214-4221.1990) / J. Bacteriol. / A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene by Sohail A. (1990)
  46. Stahl , F. W. 1979 . Special sites in generalized recombination. Annu . Rev. Genet. 13 : 7 - 24 . (10.1146/annurev.ge.13.120179.000255) / Rev. Genet. / Special sites in generalized recombination. Annu by Stahl F. W. (1979)
  47. Stern , M. J. , G. F. -L. Ames , N. H. Smith , E. C. Robinson , and C. F. Higgins . 1984 . Repetitive extragenic palindromic sequences: a major component of the bacterial genome . Cell 37 : 1015 - 1026 . (10.1016/0092-8674(84)90436-7) / Cell / Repetitive extragenic palindromic sequences: a major component of the bacterial genome by Stern M. J. (1984)
  48. Su , S. - S. , and P. Modrich . 1986 . Escherichia coli MutS-encoded protein binds to mismatched DNA base pairs . Proc. Natl. Acad. Sci. USA 83 : 5057 - 5061 . (10.1073/pnas.83.14.5057) / Proc. Natl. Acad. Sci. USA / Escherichia coli MutS-encoded protein binds to mismatched DNA base pairs by Su S. (1986)
  49. Taylor A. (Fred Hutchinson Cancer Institute Seattle Wash.). 1993. Personal communication.
  50. Yang , Y. , and G. F. -L. Ames . 1988 . DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences . Proc. Natl. Acad. Sci. USA 85 : 8850 - 8854 . (10.1073/pnas.85.23.8850) / Proc. Natl. Acad. Sci. USA / DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences by Yang Y. (1988)
  51. Yura , T. , H. Mori , H. Nagari , T. Nagata , A. Ishihama , N. Fujita , K. Isono , K. Mizobuchi , and H. Nakata . 1992 . Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 minute region . Nucleic Acids Res. 20 : 3305 - 3308 . (10.1093/nar/20.13.3305) / Nucleic Acids Res. / Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 minute region by Yura T. (1992)
  52. Zell , R. , and H. Fritz . 1987 . DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues . EMBO J. 6 : 1809 - 1815 . (10.1002/j.1460-2075.1987.tb02435.x) / EMBO J. / DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues by Zell R. (1987)
Dates
Type When
Created 8 years, 9 months ago (Nov. 9, 2016, 11:33 a.m.)
Deposited 4 years, 1 month ago (July 29, 2021, 1:53 p.m.)
Indexed 1 year, 5 months ago (March 8, 2024, 12:21 a.m.)
Issued 30 years, 7 months ago (Feb. 1, 1995)
Published 30 years, 7 months ago (Feb. 1, 1995)
Published Print 30 years, 7 months ago (Feb. 1, 1995)
Funders 0

None

@article{Lieb_1995, title={Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins}, volume={177}, ISSN={1098-5530}, url={http://dx.doi.org/10.1128/jb.177.3.660-666.1995}, DOI={10.1128/jb.177.3.660-666.1995}, number={3}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Lieb, M and Rehmat, S}, year={1995}, month=feb, pages={660–666} }