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

Abstract

The Pr promoter is the first verified member of a class of bacterial σ70-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 σ70-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.