title: DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1.
abstract: Sensing and responding to nutritional status is a major challenge for microbial life. In Escherichia coli, the global response to amino acid starvation is orchestrated by guanosine-3',5'-bisdiphosphate and the transcription factor DksA. DksA alters transcription by binding to RNA polymerase and allosterically modulating its activity. Using genetic analysis, photo-cross-linking, and structural modeling, we show that DksA binds and acts upon RNA polymerase through prominent features of both the nucleotide-access secondary channel and the active-site region. This work is, to our knowledge, the first demonstration of a molecular function for Sequence Insertion 1 in the β subunit of RNA polymerase and significantly advances our understanding of how DksA binds to RNA polymerase and alters transcription.
authors.affiliation: Department of Cell Biology, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489; Graduate School of Biomedical Studies, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489;
authors.forename: Andrey
authors.initials: A
authors.lastname: Parshin
authors.affiliation: Graduate Group in Biophysics, University of California, San Francisco, CA 94158;
authors.forename: Anthony L
authors.initials: AL
authors.lastname: Shiver
authors.affiliation: Department of Cell Biology, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489;
authors.forename: Jookyung
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Cell Biology, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489;
authors.forename: Maria
authors.initials: M
authors.lastname: Ozerova
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.affiliation: Department of Microbiology & Immunology, University of California, San Francisco, CA 94143-001; Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143-001; California Institute of Quantitative Biology, University of California, San Francisco, CA 94143-001 borukhse@rowan.edu cgrossucsf@gmail.com.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Gross
authors.affiliation: Department of Cell Biology, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489; borukhse@rowan.edu cgrossucsf@gmail.com.
authors.forename: Sergei
authors.initials: S
authors.lastname: Borukhov
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D008958:Models, Molecular; D011485:Protein Binding; D014158:Transcription, Genetic; D015032:Zinc / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; C090751:dksA protein, E coli; D012321:DNA-Directed RNA Polymerases; D015032:Zinc
keywords: lineage-specific insertions; molecular modeling; protein cross-linking; stringent response; transcription regulation