Pr is a member of a restricted class of σ70-dependent promoters that lack a recognizable -10 element.
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.
Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden.
Teresa
T
Del Peso-Santos
Mattias
M
Landfors
Eleonore
E
Skärfstad
Patrik
P
Ryden
Victoria
V
Shingler
D004269:DNA, Bacterial / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D016296:Mutagenesis; D059372:Nucleotide Motifs; D010636:Phenols / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011549:Pseudomonas / Q000235:genetics / Q000378:metabolism; D012808:Sigma Factor / Q000378:metabolism*
D004269:DNA, Bacterial; D010636:Phenols; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases