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Pr is a member of a restricted class of σ70-dependent promoters that lack a recognizable -10 element
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). (Shingler)
Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). (Shingler)
Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
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2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no 22, 11308-11320 p.Article in journal (Refereed) Published
Abstract [en]

The Pr promoter is the first verified member of a class of bacterial σ(70)-promoters that only possess a single match to consensus within its -10 element. In its native context, the activity of this promoter determines the ability of Pseudomonas putida CF600 to degrade phenolic compounds, which provides proof-of-principle for the significance of such promoters. Lack of identity within the -10 element leads to non-detection of Pr-like promoters by current search engines, because of their bias for detection of the -10 motif. Here, we report a mutagenesis analysis of Pr that reveals strict sequence requirements for its activity that includes an essential -15 element and preservation of non-consensus bases within its -35 and -10 elements. We found that highly similar promoters control plasmid- and chromosomally- encoded phenol degradative systems in various Pseudomonads. However, using a purpose-designed promoter-search algorithm and activity analysis of potential candidate promoters, no bona fide Pr-like promoter could be found in the entire genome of P. putida KT2440. Hence, Pr-like σ(70)-promoters, which have the potential to be a widely distributed class of previously unrecognized promoters, are in fact highly restricted and remain in a class of their own.

Place, publisher, year, edition, pages
2012. Vol. 40, no 22, 11308-11320 p.
National Category
Natural Sciences
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URN: urn:nbn:se:umu:diva-61252DOI: 10.1093/nar/gks934PubMedID: 23066105OAI: oai:DiVA.org:umu-61252DiVA: diva2:565321
Available from: 2012-11-07 Created: 2012-11-07 Last updated: 2017-12-07Bibliographically approved

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Del Peso-Santos, TeresaLandfors, MattiasSkärfstad, EleonoreRyden, PatrikShingler, Victoria
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