David C Grainger

Summary

Affiliation: University of Birmingham
Country: UK

Publications

  1. doi request reprint Methods for studying global patterns of DNA binding by bacterial transcription factors and RNA polymerase
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
    Biochem Soc Trans 36:754-7. 2008
  2. pmc Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    J Bacteriol 186:6938-43. 2004
  3. pmc Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    Proc Natl Acad Sci U S A 102:17693-8. 2005
  4. doi request reprint Selective repression by Fis and H-NS at the Escherichia coli dps promoter
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
    Mol Microbiol 68:1366-77. 2008
  5. pmc Transcription factor distribution in Escherichia coli: studies with FNR protein
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nucleic Acids Res 35:269-78. 2007
  6. pmc Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nucleic Acids Res 34:4642-52. 2006
  7. ncbi request reprint Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with the C-terminal domain of the RNA polymerase alpha subunit
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 51:1311-20. 2004
  8. ncbi request reprint Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with its DNA target site and with domain 4 of the RNA polymerase sigma subunit
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 51:1297-309. 2004
  9. ncbi request reprint Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression
    Douglas F Browning
    School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
    Mol Microbiol 57:496-510. 2005
  10. ncbi request reprint Binding of the Escherichia coli MelR protein to the melAB promoter: orientation of MelR subunits and investigation of MelR-DNA contacts
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 48:335-48. 2003

Collaborators

Detail Information

Publications18

  1. doi request reprint Methods for studying global patterns of DNA binding by bacterial transcription factors and RNA polymerase
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
    Biochem Soc Trans 36:754-7. 2008
    ..Here, we discuss the benefits of this approach and the application of this technique to bacterial systems...
  2. pmc Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    J Bacteriol 186:6938-43. 2004
    ..coli for MelR. This was confirmed by a transcriptomics experiment to analyze RNA in cells either with or without melR...
  3. pmc Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    Proc Natl Acad Sci U S A 102:17693-8. 2005
    ....
  4. doi request reprint Selective repression by Fis and H-NS at the Escherichia coli dps promoter
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
    Mol Microbiol 68:1366-77. 2008
    ..Our data suggest a simple model to explain how the Dps-dependent super-compaction of the folded chromosome is triggered as cell growth ceases...
  5. pmc Transcription factor distribution in Escherichia coli: studies with FNR protein
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nucleic Acids Res 35:269-78. 2007
    ..Control experiments showed that, like FNR, the distribution of the nucleoid-associated protein, IHF, is little altered when cells enter stationary phase, whilst RNA polymerase undergoes a complete redistribution...
  6. pmc Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
    David C Grainger
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nucleic Acids Res 34:4642-52. 2006
    ..Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase...
  7. ncbi request reprint Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with the C-terminal domain of the RNA polymerase alpha subunit
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 51:1311-20. 2004
    ..Finally, we used alanine scanning to identify determinants in the C-terminal domain of the RNA polymerase alpha subunit that are important for MelR-dependent activation of the melAB promoter...
  8. ncbi request reprint Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with its DNA target site and with domain 4 of the RNA polymerase sigma subunit
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 51:1297-309. 2004
    ..5 was improved. We show that this is detrimental to MelR-dependent transcription activation because bound MelR is mispositioned so that it is unable to make 'correct' interactions with sigma...
  9. ncbi request reprint Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression
    Douglas F Browning
    School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
    Mol Microbiol 57:496-510. 2005
    ..Hence, Fis protein is a major factor responsible for catabolite repression at the nrf promoter, and Fis can override activation by FNR and NarL or NarP...
  10. ncbi request reprint Binding of the Escherichia coli MelR protein to the melAB promoter: orientation of MelR subunits and investigation of MelR-DNA contacts
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 48:335-48. 2003
    ..Epistasis experiments provided evidence that supports the proposed orientation of binding of MelR at its target site...
  11. pmc Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR
    Shivanthi Samarasinghe
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nucleic Acids Res 36:2667-76. 2008
    ..We show that repression requires a complex involving four DNA-bound MelR molecules, and that the global CRP regulator plays little or no role...
  12. pmc E. coli Fis protein insulates the cbpA gene from uncontrolled transcription
    Kiran Chintakayala
    Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
    PLoS Genet 9:e1003152. 2013
    ..Disruption of the cbpA gene prompts dramatic changes in DNA topology. Thus, our work identifies a novel role for Fis and incorporates CbpA into the growing network of factors that mediate bacterial chromosome structure...
  13. doi request reprint Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression
    Douglas F Browning
    School of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, UK
    Curr Opin Microbiol 13:773-80. 2010
    ..Some specific examples, involving the E. coli IHF and Fis proteins, that illustrate new principles, are described in detail...
  14. pmc H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions
    Shivani S Singh
    Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, USA
    PLoS Genet 9:e1003589. 2013
    ..This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. Our work provides mechanistic insight into nucleoprotein structure and its effect on protein-DNA interactions in prokaryotic cells. ..
  15. doi request reprint A conserved acidic amino acid mediates the interaction between modulators and co-chaperones in enterobacteria
    Kiran Chintakayala
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    J Mol Biol 411:313-20. 2011
    ..Here, we have used a combination of genetics and biochemistry to identify the co-chaperone contact determinant of CbpM. We show that the nature of the interaction is conserved in enterobacteria...
  16. pmc The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
    Nucleic Acids Res 36:3950-5. 2008
    ..We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness...
  17. ncbi request reprint Extensive functional overlap between sigma factors in Escherichia coli
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 13:806-14. 2006
    ..SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon...
  18. ncbi request reprint Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, MA 02115, USA
    Mol Microbiol 65:21-6. 2007
    ..Here we review recent applications of ChIP-chip to the study of bacteria, which provide important and unexpected insights into transcription and chromosome organization...