Abstract
The abundance of all tetra- and pentanucleotide sequences is calculated for a set of DNA sequence data comprising 767,393 nucleotides of the E. coli K-12 genome. Observed frequencies are compared to those expected from a Markov chain prediction algorithm. Systematic and extreme non-random representations are found for special sets of sequences. These are interpreted as arising from incorporation of a 2'-deoxyguanosine residue opposite thymidine during replication which, in special sequence contexts, leads to a T/G mismatch that is simultaneously substrate for two competing DNA mismatch repair systems: the mutHLS and the VSP pathway. Processing by the former leads to error correction, by the latter to mutation fixation. The significance of the latter process, as demonstrated here, makes it unlikely that VSP repair has evolved mainly as a mutation avoidance mechanism. It is proposed that in E. coli K-12, VSP repair, together with DNA cytosine methylation, constitutes a mutagenesis/recombination system capable of promoting gene-conversion-like unidirectional transfer of short stretches of DNA sequence.
Full text
PDF





Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Boyer H. W., Chow L. T., Dugaiczyk A., Hedgpeth J., Goodman H. M. DNA substrate site for the EcoRII restriction endonuclease and modification methylase. Nat New Biol. 1973 Jul 11;244(132):40–43. doi: 10.1038/newbio244040a0. [DOI] [PubMed] [Google Scholar]
- Burks C., Cassidy M., Cinkosky M. J., Cumella K. E., Gilna P., Hayden J. E., Keen G. M., Kelley T. A., Kelly M., Kristofferson D. GenBank. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2221–2225. doi: 10.1093/nar/19.suppl.2221. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Coulondre C., Miller J. H., Farabaugh P. J., Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature. 1978 Aug 24;274(5673):775–780. doi: 10.1038/274775a0. [DOI] [PubMed] [Google Scholar]
- Dreiseikelmann B., Wackernagel W. Absence in Bacillus subtilis and Staphylococcus aureus of the sequence-specific deoxyribonucleic acid methylation that is conferred in Escherichia coli K-12 by the dam and dcm enzymes. J Bacteriol. 1981 Jul;147(1):259–261. doi: 10.1128/jb.147.1.259-261.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Duncan B. K., Miller J. H. Mutagenic deamination of cytosine residues in DNA. Nature. 1980 Oct 9;287(5782):560–561. doi: 10.1038/287560a0. [DOI] [PubMed] [Google Scholar]
- Dzidic S., Radman M. Genetic requirements for hyper-recombination by very short patch mismatch repair: involvement of Escherichia coli DNA polymerase I. Mol Gen Genet. 1989 Jun;217(2-3):254–256. doi: 10.1007/BF02464889. [DOI] [PubMed] [Google Scholar]
- Hennecke F., Kolmar H., Bründl K., Fritz H. J. The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease. Nature. 1991 Oct 24;353(6346):776–778. doi: 10.1038/353776a0. [DOI] [PubMed] [Google Scholar]
- Jones M., Wagner R., Radman M. Mismatch repair of deaminated 5-methyl-cytosine. J Mol Biol. 1987 Mar 5;194(1):155–159. doi: 10.1016/0022-2836(87)90724-8. [DOI] [PubMed] [Google Scholar]
- Kramer B., Kramer W., Fritz H. J. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell. 1984 Oct;38(3):879–887. doi: 10.1016/0092-8674(84)90283-6. [DOI] [PubMed] [Google Scholar]
- Kröger M., Wahl R., Rice P. Compilation of DNA sequences of Escherichia coli (update 1991). Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2023–2043. doi: 10.1093/nar/19.suppl.2023. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lieb M., Allen E., Read D. Very short patch mismatch repair in phage lambda: repair sites and length of repair tracts. Genetics. 1986 Dec;114(4):1041–1060. doi: 10.1093/genetics/114.4.1041. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lieb M. Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair. Genetics. 1991 May;128(1):23–27. doi: 10.1093/genetics/128.1.23. [DOI] [PMC free article] [PubMed] [Google Scholar]
- May M. S., Hattaman S. Deoxyribonucleic acid-cytosine methylation by host- and plasmid-controlled enzymes. J Bacteriol. 1975 Apr;122(1):129–138. doi: 10.1128/jb.122.1.129-138.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McClelland M., Jones R., Patel Y., Nelson M. Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Res. 1987 Aug 11;15(15):5985–6005. doi: 10.1093/nar/15.15.5985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Phillips G. J., Arnold J., Ivarie R. Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis. Nucleic Acids Res. 1987 Mar 25;15(6):2611–2626. doi: 10.1093/nar/15.6.2611. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Phillips G. J., Arnold J., Ivarie R. The effect of codon usage on the oligonucleotide composition of the E. coli genome and identification of over- and underrepresented sequences by Markov chain analysis. Nucleic Acids Res. 1987 Mar 25;15(6):2627–2638. doi: 10.1093/nar/15.6.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reynaud C. A., Anquez V., Grimal H., Weill J. C. A hyperconversion mechanism generates the chicken light chain preimmune repertoire. Cell. 1987 Feb 13;48(3):379–388. doi: 10.1016/0092-8674(87)90189-9. [DOI] [PubMed] [Google Scholar]
- Schlagman S., Hattman S., May M. S., Berger L. In vivo methylation by Escherichia coli K-12 mec+ deoxyribonucleic acid-cytosine methylase protects against in vitro cleavage by the RII restriction endonuclease (R. Eco RII). J Bacteriol. 1976 May;126(2):990–996. doi: 10.1128/jb.126.2.990-996.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zell R., Fritz H. J. DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues. EMBO J. 1987 Jun;6(6):1809–1815. doi: 10.1002/j.1460-2075.1987.tb02435.x. [DOI] [PMC free article] [PubMed] [Google Scholar]