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

URN to cite this document:

urn:nbn:de:bvb:355-epub-109267 Copy

DOI to cite this document:

10.5283/epub.10926 Copy

Merkl, Rainer ; Kröger, Manfred ; Rice, Peter ; Fritz, Hans Joachim

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Date of publication of this fulltext: 16 Nov 2009 15:26

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Details

Item type:	Article
Journal or Publication Title:	Nucleic Acids Research
Publisher:	Oxford University Press
Volume:	20
Number of Issue or Book Chapter:	7
Page Range:	pp. 1657-1662
Date:	1992
Institutions:	Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Rainer Merkl
Identification Number:	Value Type 1579456 PubMed ID
Classification:	Notation Type Algorithms MESH Bacillus subtilis/genetics MESH Base Composition MESH DNA Repair/genetics* MESH DNA Replication/genetics MESH DNA, Bacterial/chemistry MESH DNA, Bacterial/genetics* MESH Escherichia coli/genetics* MESH Genome, Bacterial MESH Markov Chains MESH Mutation/genetics MESH Repetitive Sequences, Nucleic Acid/genetics* MESH Site-Specific DNA Methyltransferase (Cytosine-Specific)/genetics MESH
Keywords:	Algorithms Bacillus subtilis/genetics Base Composition DNA Repair/*genetics DNA Replication/genetics DNA, Bacterial/chemistry/*genetics Escherichia coli/*genetics Genome, Bacterial Markov Chains Mutation/genetics Repetitive Sequences, Nucleic Acid/*genetics Site-Specific DNA Methyltransferase (Cytosine-Specific)/genetics Support, Non-U.S. Gov't
Dewey Decimal Classification:	500 Science > 570 Life sciences
Status:	Published
Refereed:	Yes, this version has been refereed
Created at the University of Regensburg:	No
Item ID:	10926

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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 ...

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.

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