An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae

Most sequenced strains from Pasteurellaceae and Neisseriae contain hundreds to thousands of uptake sequence (US) motifs in their genome, which are associated with natural competence for DNA uptake. The mechanism of their recognition is still unclear, and I searched for intragenic location patterns of these motifs for clues about their distribution. In all cases, one orientation of the US has a higher occurrence in the reading frame, and in all Pasteurellaceae, the US and the reverse complement motifs are biased towards the gene termini. These findings could help design experimental set-ups to study preferential DNA uptake, thereby further unravelling the phenomenon of natural competence.ReviewersThis article was reviewed by Arcady Mushegian and I. King Jordan.

• Publication year

  2008

• Venue

  Biology Direct

• Publication date

  2008-03-27

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/1745-6150-3-12PMID 18371225PMCID 2346458
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2004influential reference
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