Mapping sigma 54-RNA polymerase interactions at the -24 consensus promoter element.
The sigma 54 promoter specificity factor is distinct from sigma 70-type factors. The sigma 54-RNA polymerase binds to promoters with conserved sequence elements at -24 and -12 and utilizes specialized enhancer-binding activators to convert, through an ATP-dependent process, closed promoter complexes to open promoter complexes. The interface between sigma 54-RNA polymerase and promoter DNA is poorly characterized, contrasting with sigma 70. Here, sigma 54 was modified with strategically positioned cleavage reagents to provide physical evidence that the highly conserved RpoN box motif of sigma 54 is close to and may therefore interact with the consensus -24 promoter element. We show that the spatial relationship between the sigma 54-RNA polymerase and the -24 promoter element remains unchanged during closed to open complex conversion and transcription initiation but changes during the early elongation phase. In contrast, the spatial relationship between sigma 54-RNA polymerase and the consensus -12 promoter element changes upon conversion of the closed promoter complex to an open one. We provide evidence that some -12 promoter region-sigma 54 interactions are dependent upon either the core RNA polymerase or a fork junction DNA structure at the -12-position, indicating that DNA fork junctions can substitute for core RNAP. We also show the beta-subunit flap domain contributes to different sets of sigma-promoter DNA interactions at sigma 54- and sigma 70-dependent promoters.
Burrows
Patricia C
PC
Department of Biological Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
Severinov
Konstantin
K
Ishihama
Akira
A
Buck
Martin
M
Wigneshweraraj
Siva R
SR
D000595:Amino Acid Sequence; D003545:Cysteine / Q000737:chemistry; D004247:DNA / Q000378:metabolism; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000378:metabolism; D004492:Edetic Acid / Q000031:analogs & derivatives*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins; D007711:Klebsiella pneumoniae / Q000235:genetics; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D051877:RNA Polymerase Sigma 54; D017386:Sequence Homology, Amino Acid; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016962:Sinorhizobium meliloti / Q000235:genetics; D014158:Transcription, Genetic
D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D012808:Sigma Factor; C497751:rpoN protein, E coli; C042007:1-(4-bromoacetamidobenzyl)EDTA; D004247:DNA; D004492:Edetic Acid; D010088:Oxidoreductases; C029130:nitrogenase reductase; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54; D003850:Deoxyribonuclease I; D003545:Cysteine