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MBE Advance Access published online on March 13, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj125
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted March 6, 2006

Research Article

Enterobacterial Repetitive Intergenic Consensus (ERIC) Sequences in Escherichia coli: Evolution and Implications for ERIC-PCR

Lindsay A. Wilson 1 and Paul M. Sharp 2 *

1 Institute of Genetics, University of Nottingham, Nottingham, UK; Present address: Department of Zoology, University of British Columbia, Vancouver, Canada
2 Institute of Genetics, University of Nottingham, Nottingham, UK

* To whom correspondence should be addressed.
Paul M. Sharp, E-mail: paul{at}evol.nott.ac.uk


  Abstract

Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences are 127bp imperfect palindromes that occur in multiple copies in the genomes of enteric bacteria and vibrios. Here we investigate the distribution of these elements in the complete genome sequences of nine Escherichia coli (including Shigella species) strains. There is a significant tendency for copies to be adjacent to more highly expressed genes. There is considerable variation among strains with respect to the presence of an element in any particular intergenic region, but some copies appear to have been conserved since before the divergence of E. coli and Salmonella enterica. In comparisons of orthologous copies between these species, ERIC sequences are surprisingly conserved, implying that they have acquired some function, perhaps related to mRNA stability. The relationships among copies within E. coli is consistent with a master copy mode of generation. Insertion of new copies seems to occur at, and involve duplication of, the dinucleotide TA. Two classes of inserts of about 70bp each occur at different specific sites within ERIC sequences; these inserts evolve independently of the ERIC sequences. The small number of ERIC sequences in E. coli genomes indicates that a widely used bacterial fingerprinting method using primers based on ERIC sequences (ERIC-PCR) does not rely on the presence of ERIC sequences.

Keywords: ERIC sequences; Escherichia coli; repetitive sequences; master copy model; REP-PCR.
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