title: Role of the RNA polymerase alpha subunits in CII-dependent activation of the bacteriophage lambda pE promoter: identification of important residues and positioning of the alpha C-terminal domains.
abstract: The bacteriophage lambda CII protein stimulates the activity of three phage promoters, p(E), p(I) and p(aQ), upon binding to a site overlapping the -35 element at each promoter. Here we used preparations of RNA polymerase carrying a DNA cleavage reagent attached to specific residues in the C-terminal domain of the RNA polymerase alpha subunit (alphaCTD) to demonstrate that one alphaCTD binds near position -41 at p(E), whilst the other alphaCTD binds further upstream. The alphaCTD bound near position -41 is oriented such that its 261 determinant is in close proximity to sigma(70). The location of alphaCTD in CII-dependent complexes at the p(E) promoter is very similar to that found at many activator-independent promoters, and represents an alternative configuration for alphaCTD at promoters where activators bind sites overlapping the -35 region. We also used an in vivo alanine scan analysis to show that the DNA-binding determinant of alphaCTD is involved in stimulation of the p(E) promoter by CII, and this was confirmed by in vitro transcription assays. We also show that whereas the K271E substitution in alphaCTD results in a drastic decrease in CII-dependent activation of p(E), the p(I) and p(aQ) promoters are less sensitive to this substitution, suggesting that the role of alphaCTD at the three lysogenic promoters may be different.
authors.affiliation: Division of Genomic Medicine, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK.
authors.forename: Barbara
authors.initials: B
authors.lastname: Kedzierska
authors.forename: David J
authors.initials: DJ
authors.lastname: Lee
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Wegrzyn
authors.forename: Stephen J W
authors.initials: SJ
authors.lastname: Busby
authors.forename: Mark S
authors.initials: MS
authors.lastname: Thomas
mesh_terms: D000409:Alanine / Q000235:genetics / Q000378:metabolism; D010582:Bacteriophage lambda / Q000201:enzymology* / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites; D018983:DNA Footprinting; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015967:Gene Expression Regulation, Viral; D017665:Hydroxyl Radical; D008242:Lysogeny / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000378:metabolism*; D015533:Transcriptional Activation; D014764:Viral Proteins
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D014764:Viral Proteins; C039000:cII protein, bacteriophage lambda; D017665:Hydroxyl Radical; D012321:DNA-Directed RNA Polymerases; C113275:RNA polymerase alpha subunit; D000409:Alanine