title: Characteristics of σ-dependent pausing by RNA polymerases from Escherichia coli and Thermus aquaticus.
abstract: The σ(70) subunit of RNA polymerase (RNAP) is the major transcription initiation factor in Escherichia coli. During transcription initiation, conserved region 2 of the σ(70) subunit interacts with the -10 promoter element and plays a key role in DNA melting around the starting point of transcription. During transcription elongation, the σ(70) subunit can induce pauses in RNA synthesis owing to interactions of region 2 with DNA regions similar to the -10 promoter element. We demonstrated that the major σ subunit from Thermus aquaticus (σ(A)) is also able to induce transcription pausing by T. aquaticus RNAP. However, hybrid RNAP containing the σ(A) subunit and E. coli core RNAP is unable to form pauses during elongation, while being able to recognize promoters and initiate transcription. Inability of the σ(A) subunit to induce pausing by E. coli RNAP is explained by the substitutions of non-conserved amino acids in region 2, in the subregions interacting with the RNAP core enzyme. Thus, changes in the structure of region 2 of the σ(70) subunit have stronger effects on transcription pausing than on promoter recognition, likely by weakening the interactions of the σ subunit with the core RNAP during transcription elongation.
authors.affiliation: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
authors.forename: E V
authors.initials: EV
authors.lastname: Zhilina
authors.forename: N A
authors.initials: NA
authors.lastname: Miropolskaya
authors.forename: I A
authors.initials: IA
authors.lastname: Bass
authors.forename: K L
authors.initials: KL
authors.lastname: Brodolin
authors.forename: A V
authors.initials: AV
authors.lastname: Kulbachinskiy
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology*; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012313:RNA / Q000096:biosynthesis* / Q000235:genetics; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics; D013824:Thermus / Q000201:enzymology*; D014158:Transcription, Genetic
chemical_list: D012808:Sigma Factor; D012313:RNA; D004247:DNA; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases