Pr is a member of a restricted class of σ70-dependent promoters that lack a recognizable -10 element

Nucleic Acids Res. 2012 Dec;40(22):11308-20. doi: 10.1093/nar/gks934. Epub 2012 Oct 11.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial / chemistry*
  • DNA-Directed RNA Polymerases / metabolism*
  • Mutagenesis
  • Nucleotide Motifs
  • Phenols / metabolism
  • Promoter Regions, Genetic*
  • Pseudomonas / genetics
  • Pseudomonas / metabolism
  • Sigma Factor / metabolism*

Substances

  • DNA, Bacterial
  • Phenols
  • Sigma Factor
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases