Nucleic Acids Research, 1992, Vol. 20, No. 7 1657-1662
© 1992
CHEMISTRY |
Statistical evaluation and biological interpretation of non-random abundance in the E.coli K-12 genome of tetra-and pentanucleotide sequences related to VSP DNA mismatch repair
Institut fur Molekulare Genetik, Georg-August-Universitat Göttingen GrisebachstraBe 8, W-3400 Göttingen 1Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität GieBen Frankfurter StraBe 107, W-6300 GieBen 2EMBL, Postfach 10.2209, MeyerhofstraBe 1 W-6900 Heidelberg, Germany
*To whom correspondence should be addressed
Received December 16, 1991. Revised February 26, 1992. Accepted February 26, 1992.
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';-deoxy-guanosine 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.
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