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  Within-genome evolution of REPINs: a new familiy of miniature mobile DNA in bacteria

Bertels, F., & Rainey, P. B. (2011). Within-genome evolution of REPINs: a new familiy of miniature mobile DNA in bacteria. PLoS Genetics, 7(6): e1002132. doi:10.1371/journal.pgen.1002132.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-EBCD-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-EBCE-8
Genre: Journal Article

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 Creators:
Bertels, Frederic, Author
Rainey, Paul B.1, Author              
Affiliations:
1External Scientific Member Group Experimental and Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445637              

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 Abstract: Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of Pseudomonas fluorescens SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII) of repetitive extragenic palindromic (REP) sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins) and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs), combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT–containing bacterial genomes, including Escherichia coli K-12 and Nostoc punctiforme, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA.

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Language(s): eng - English
 Dates: 2010-12-162011-05-022011-06-16
 Publication Status: Published online
 Pages: -
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 Identifiers: DOI: 10.1371/journal.pgen.1002132
Other: 2844/S 39187
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Title: PLoS Genetics
  Abbreviation : PLoS Genet.
Source Genre: Journal
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Publ. Info: San Francisco, CA : Public Library of Science
Pages: 13 p. Volume / Issue: 7 (6) Sequence Number: e1002132 Start / End Page: - Identifier: ISSN: 1553-7390 (print)
ISSN: 1553-7404 (online)
CoNE: /journals/resource/1000000000017180