David C Grainger

Summary

Affiliation: University of Birmingham
Country: UK

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. pmc Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria
    Remus T Dame
    Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, Leiden, The Netherlands
    PLoS Genet 7:e1002123. 2011
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications22

  1. 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...
  2. 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...
  3. 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...
  4. 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. ..
  5. pmc Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria
    Remus T Dame
    Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, Leiden, The Netherlands
    PLoS Genet 7:e1002123. 2011
    ..We discuss the roles of the proteins identified to date as well as strategies that may be employed to discover new factors...
  6. 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
    ....
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. pmc The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein
    Kaneyoshi Yamamoto
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 193:1477-80. 2011
    ..coli chromosome in vivo, and we report that MntR binds to only four targets, adjacent to the mntH, mntR, yebN, and dps genes. Unexpectedly, we found that dps expression is directly repressed by Mn(2+)-MntR...
  17. 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...
  18. ncbi request reprint Widespread suppression of intragenic transcription initiation by H-NS
    Shivani S Singh
    Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    Genes Dev 28:214-9. 2014
    ..Thus, a major overlooked function of H-NS is to prevent transcription of spurious RNA. Our data provide a molecular description for the toxicity of horizontally acquired DNA and explain how this is counteracted by H-NS. ..
  19. 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...
  20. doi request reprint Multidisciplinary perspectives on bacterial genome organization and dynamics
    Remus T Dame
    Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, Leiden, The Netherlands
    Mol Microbiol 86:1023-30. 2012
    ....
  21. 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...
  22. 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...