Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.
We recently described a novel basal bacterial promoter element that is located downstream of the -10 consensus promoter element and is recognized by region 1.2 of the sigma subunit of RNA polymerase (RNAP). In the case of Thermus aquaticus RNAP, this element has a consensus sequence GGGA and allows transcription initiation in the absence of the -35 element. In contrast, the Escherichia coli RNAP is unable to initiate transcription from GGGA-containing promoters that lack the -35 element. In the present study, we demonstrate that sigma subunits from both E. coli and T. aquaticus specifically recognize the GGGA element and that the observed species specificity of recognition of GGGA-containing promoters is determined by the RNAP core enzyme. We further demonstrate that transcription initiation by T. aquaticus RNAP on GGGA-containing promoters in the absence of the -35 element requires sigma region 4 and C-terminal domains of the alpha subunits, which interact with upstream promoter DNA. When in the context of promoters containing the -35 element, the GGGA element is recognized by holoenzyme RNAPs from both E. coli and T. aquaticus and increases stability of promoter complexes formed on these promoters. Thus, GGGA is a bona fide basal promoter element that can function in various bacteria and, depending on the properties of the RNAP core enzyme and the presence of additional promoter elements, determine species-specific differences in promoter recognition.
Barinova
Nataliya
N
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
Kuznedelov
Konstantin
K
Severinov
Konstantin
K
Kulbachinskiy
Andrey
A
D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009843:Oligoribonucleotides / Q000737:chemistry; D011401:Promoter Regions, Genetic; D013379:Substrate Specificity; D013824:Thermus / Q000201:enzymology / Q000235:genetics*; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D012321:DNA-Directed RNA Polymerases