title: Determinants of RNA polymerase alpha subunit for interaction with beta, beta', and sigma subunits: hydroxyl-radical protein footprinting.
abstract: Escherichia coli RNA polymerase (RNAP) alpha subunit serves as the initiator for RNAP assembly, which proceeds according to the pathway 2 alpha-->alpha 2-->alpha 2 beta-->alpha 2 beta beta'-->alpha 2 beta beta' sigma. In this work, we have used hydroxyl-radical protein footprinting to define determinants of alpha for interaction with beta, beta', and sigma. Our results indicate that amino acids 30-75 of alpha are protected from hydroxyl-radical-mediated proteolysis upon interaction with beta (i.e., in alpha 2 beta, alpha 2 beta beta', and alpha 2 beta beta' sigma), and amino acids 175-210 of alpha are protected from hydroxyl-radical-mediated proteolysis upon interaction with beta' (i.e., in alpha 2 beta beta' and alpha 2 beta beta' sigma). The protected regions are conserved in the alpha homologs of prokaryotic, eukaryotic, archaeal, and chloroplast RNAPs and contain sites of substitutions that affect RNAP assembly. We conclude that the protected regions define determinants of alpha for direct functional interaction with beta and beta'. The observed maximal magnitude of protection upon interaction with beta and the observed maximal magnitude of protection upon interaction with beta' both correspond to the expected value for complete protection of one of the two alpha protomers of RNAP (i.e., 50% protection). We propose that only one of the two alpha protomers of RNAP interacts with beta and that only one of the two alpha protomers of RNAP interacts with beta'.
authors.affiliation: Department of Biochemistry and Molecular Biology, St. Louis University Medical School, MO 63104, USA.
authors.forename: T
authors.initials: T
authors.lastname: Heyduk
authors.forename: E
authors.initials: E
authors.lastname: Heyduk
authors.forename: K
authors.initials: K
authors.lastname: Severinov
authors.forename: H
authors.initials: H
authors.lastname: Tang
authors.forename: R H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology; D001665:Binding Sites; D002736:Chloroplasts / Q000201:enzymology; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D006639:Histidine; D006868:Hydrolysis; D017665:Hydroxyl Radical; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D055503:Protein Multimerization; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D017386:Sequence Homology, Amino Acid; D016324:Sequence Tagged Sites; D013045:Species Specificity
chemical_list: D046911:Macromolecular Substances; D011994:Recombinant Proteins; D017665:Hydroxyl Radical; D006639:Histidine; D012321:DNA-Directed RNA Polymerases