title: Open complex formation in vitro by sigma38 (rpoS) RNA polymerase: roles for region 2 amino acids.
abstract: Non-functional mutants of sigma(38)(sigma(S)) were studied in vitro to identify the nature of their defects. Mutations in four amino acids led to severe defects in DNA binding and enzyme isomerization with promoter fork junction probes containing single-stranded non-template DNA. The same properties were previously seen with DNA mutations at the fork junction, implying that sigma:DNA interactions at the fork junction are used both for DNA binding and enzyme isomerization. An overlapping set of four mutants had defects that appear to be associated with DNA melting to create the fork junction. When mapped onto the sigma(70) structure, these groups of mutants suggest motifs used by sigma factors to melt DNA and isomerize RNA polymerase to form functional open promoter complexes.
authors.affiliation: Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California-Los Angeles, 405 Hilgard Avenue, Room 440, P.O. Box 951569, Los Angeles, CA 90024-1569, USA.
authors.forename: Shun Jin
authors.initials: SJ
authors.lastname: Lee
authors.forename: Jay D
authors.initials: JD
authors.lastname: Gralla
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D015342:DNA Probes / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D004926:Escherichia coli / Q000201:enzymology; D007536:Isomerism; D009154:Mutation; D010957:Plasmids / Q000235:genetics; D011196:Potassium Permanganate / Q000737:chemistry; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013696:Temperature; D024363:Transcription Initiation Site
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D015342:DNA Probes; D004277:DNA, Single-Stranded; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D011196:Potassium Permanganate; D004247:DNA