The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing.
Regulation of RNA polymerase during initiation, elongation, and termination of transcription is mediated in part by interactions with intrinsic regulatory signals encoded in the RNA and DNA that contact the enzyme. These interactions include contacts to an 8-9-bp RNA:DNA hybrid within the active-site cleft of the enzyme, contacts to the melted nontemplate DNA strand in the vicinity of the hybrid, contacts to exiting RNA upstream of the hybrid, and contacts to approximately 20 bp of duplex DNA downstream of the active site. Based on characterization of an amino acid substitution (G1161R) and a deletion (Delta1149-1190) in the jaw domain of the bacterial RNA polymerase largest subunit (beta'), we report here that contacts of the jaw domain to downstream DNA at the leading edge of the transcription complex contribute to regulation during all three phases of transcription. The results provide insight into the role of the jaw domain-downstream DNA contact in transcriptional initiation and pausing and suggest possible explanations for the previously reported isolation of the jaw mutants based on reduced ColEI plasmid replication.
Ederth
Josefine
J
Department of Microbiology, Stockholm University, S-10691 Stockholm, Sweden.
Artsimovitch
Irina
I
Isaksson
Leif A
LA
Landick
Robert
R
D000595:Amino Acid Sequence; D001419:Bacteria / Q000201:enzymology*; D001483:Base Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D007700:Kinetics; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
D017931:DNA Primers; D004269:DNA, Bacterial; D011994:Recombinant Proteins; D012321:DNA-Directed RNA Polymerases