title: Activity map of the Escherichia coli RNA polymerase bridge helix.
abstract: Transcription, the synthesis of RNA from a DNA template, is performed by multisubunit RNA polymerases (RNAPs) in all cellular organisms. The bridge helix (BH) is a distinct feature of all multisubunit RNAPs and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and RNA and DNA binding. Because the BH has been captured in both kinked and straight conformations in different crystals structures of RNAP, recently supported by molecular dynamics studies, it has been proposed that cycling between these conformations is an integral part of the nucleotide addition cycle. To further evaluate the role of the BH, we conducted systematic alanine scanning mutagenesis of the Escherichia coli RNAP BH to determine its contributions to activities required for transcription. Combining our data with an atomic model of E. coli RNAP, we suggest that alterations in the interactions between the BH and (i) the trigger loop, (ii) fork loop 2, and (iii) switch 2 can help explain the observed changes in RNAP functionality associated with some of the BH variants. Additionally, we show that extensive defects in E. coli RNAP functionality depend upon a single previously not studied lysine residue (Lys-781) that is strictly conserved in all bacteria. It appears that direct interactions made by the BH with other conserved features of RNAP are lost in some of the E. coli alanine substitution variants, which we infer results in conformational changes in RNAP that modify RNAP functionality.
authors.affiliation: Division of Biology, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kindgom.
authors.forename: Milija
authors.initials: M
authors.lastname: Jovanovic
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Burrows
authors.forename: Daniel
authors.initials: D
authors.lastname: Bose
authors.forename: Beatriz
authors.initials: B
authors.lastname: Cámara
authors.forename: Simone
authors.initials: S
authors.lastname: Wiesler
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhang
authors.forename: Sivaramesh
authors.initials: S
authors.lastname: Wigneshweraraj
authors.forename: Robert O J
authors.initials: RO
authors.lastname: Weinzierl
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
mesh_terms: D000409:Alanine / Q000737:chemistry; D000595:Amino Acid Sequence; D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D005816:Genetic Complementation Test; D008239:Lysine / Q000737:chemistry; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D016962:Sinorhizobium meliloti / Q000235:genetics
chemical_list: D012321:DNA-Directed RNA Polymerases; D008239:Lysine; D000409:Alanine