A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition.
In bacteria, promoter recognition depends on the RNA polymerase sigma subunit, which combines with the catalytically proficient RNA polymerase core to form the holoenzyme. The major class of bacterial promoters is defined by two conserved elements (the -10 and -35 elements, which are 10 and 35 nucleotides upstream of the initiation point, respectively) that are contacted by sigma in the holoenzyme. We show that recognition of promoters of this class depends on the "flexible flap" domain of the RNA polymerase beta subunit. The flap interacts with conserved region 4 of sigma and triggers a conformational change that moves region 4 into the correct position for interaction with the -35 element. Because the flexible flap is evolutionarily conserved, this domain may facilitate promoter recognition by specificity factors in eukaryotes as well.
Kuznedelov
Konstantin
K
Waksman Institute, Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA.
Minakhin
Leonid
L
Niedziela-Majka
Anita
A
Dove
Simon L
SL
Rogulja
Dragana
D
Nickels
Bryce E
BE
Hochschild
Ann
A
Heyduk
Tomasz
T
Severinov
Konstantin
K
D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004735:Energy Transfer; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D020035:Holoenzymes / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D012808:Sigma Factor / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D020798:Two-Hybrid System Techniques
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D020035:Holoenzymes; D011993:Recombinant Fusion Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases