David J Lee

Summary

Affiliation: University of Birmingham
Country: UK

Publications

  1. 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
  2. pmc Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex
    David J Lee
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 190:1284-9. 2008
  3. doi request reprint Activating transcription in bacteria
    David J Lee
    School of Biosciences, University of Birmingham, United Kingdom
    Annu Rev Microbiol 66:125-52. 2012
  4. pmc Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains
    David J Lee
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
    BMC Microbiol 9:252. 2009
  5. 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
  6. pmc Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site
    Douglas F Browning
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 192:3824-8. 2010
  7. ncbi request reprint Location of the Escherichia coli RNA polymerase alpha subunit C-terminal domain at an FNR-dependent promoter: analysis using an artificial nuclease
    Anne M L Barnard
    School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
    FEBS Lett 558:13-8. 2004
  8. pmc Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization
    Kerry Hollands
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
    Mol Microbiol 75:1098-111. 2010
  9. pmc The Escherichia coli regulator of sigma 70 protein, Rsd, can up-regulate some stress-dependent promoters by sequestering sigma 70
    Jennie E Mitchell
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 189:3489-95. 2007
  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

Publications19

  1. 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...
  2. pmc Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex
    David J Lee
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 190:1284-9. 2008
    ..coli genome...
  3. doi request reprint Activating transcription in bacteria
    David J Lee
    School of Biosciences, University of Birmingham, United Kingdom
    Annu Rev Microbiol 66:125-52. 2012
    ..Alternatively, activation can be due to factors that interact with RNA polymerase and change its preferences for target promoters. We summarize the different mechanistic options for activation that are focused directly on RNA polymerase...
  4. pmc Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains
    David J Lee
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
    BMC Microbiol 9:252. 2009
    ..coli K-12 strains. However, we have had limited success with these lambda-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains...
  5. 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...
  6. pmc Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site
    Douglas F Browning
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 192:3824-8. 2010
    ..The NsrR target is inactivated by mutation at the Salmonella enterica serovar Typhimurium nrf promoter...
  7. ncbi request reprint Location of the Escherichia coli RNA polymerase alpha subunit C-terminal domain at an FNR-dependent promoter: analysis using an artificial nuclease
    Anne M L Barnard
    School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
    FEBS Lett 558:13-8. 2004
    ..coli transcription activator that is related to FNR. In complementary experiments, we show that the second alpha subunit C-terminal domain of RNA polymerase can be repositioned by upstream-bound CRP, but not by upstream-bound FNR...
  8. pmc Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization
    Kerry Hollands
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
    Mol Microbiol 75:1098-111. 2010
    ..The organization of the different promoter elements and the activator binding site at the trg promoter is the same as at the aer promoter, suggesting a common activation mechanism...
  9. pmc The Escherichia coli regulator of sigma 70 protein, Rsd, can up-regulate some stress-dependent promoters by sequestering sigma 70
    Jennie E Mitchell
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 189:3489-95. 2007
    ..Our experiments support a model in which the role of Rsd is primarily to sequester sigma(70), thereby increasing the levels of RNA polymerase containing the alternative sigma(38) factor...
  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. pmc DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes
    Matej Butala
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
    Nucleic Acids Res 37:e37. 2009
    ..We illustrate the method by investigating the proteins bound to the colicin K gene regulatory region, either before or after induction of the colicin K gene promoter...
  12. doi request reprint A global view of Escherichia coli Rsd protein and its interactions
    Sarah E Piper
    School of Biosciences, University of Birmingham, Birmingham, UK
    Mol Biosyst 5:1943-7. 2009
    ..Rsd expression is controlled by two promoters, P1 and P2. Experiments with lac fusions show that the P2 promoter is stronger than P1, that P2 is active in all phases of growth, and that this accounts for the high levels of Rsd...
  13. pmc Repression by cyclic AMP receptor protein at a distance
    David J Lee
    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    MBio 3:e00289-12. 2012
    ..Hence, disruption of this interaction can lead to either down- or upregulation, depending on its location...
  14. pmc The Escherichia coli K-12 NarL and NarP proteins insulate the nrf promoter from the effects of integration host factor
    Douglas F Browning
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
    J Bacteriol 188:7449-56. 2006
    ..The acs-nrf regulatory region is conserved in other pathogenic E. coli strains and related enteric bacteria but differs in Salmonella enterica serovar Typhimurium...
  15. ncbi request reprint Exploitation of a chemical nuclease to investigate the location and orientation of the Escherichia coli RNA polymerase alpha subunit C-terminal domains at simple promoters that are activated by cyclic AMP receptor protein
    David J Lee
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    J Biol Chem 278:52944-52. 2003
    ..Here we present data from experiments with simple Escherichia coli promoters that are activated by the cyclic AMP receptor protein...
  16. pmc Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains
    Lewis E H Bingle
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
    PLoS ONE 9:e80160. 2014
    ..Negative regulation by Ler of PerC, itself a positive regulator of the ler promoter, suggests a negative feedback loop involving these proteins. ..
  17. pmc Location and dynamics of an active promoter in Escherichia coli K-12
    María Antonia Sánchez-Romero
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U K
    Biochem J 441:481-5. 2012
    ..We conclude that transcription from the cloned promoter is driving the location of the plasmid and that specific locations in bacterial cells may favour gene expression...
  18. pmc The C-terminal domain of the Escherichia coli RNA polymerase alpha subunit plays a role in the CI-dependent activation of the bacteriophage lambda pM promoter
    Barbara Kedzierska
    Department of Molecular Biology, University of Gdansk, Kladki 24, Gdansk, Poland
    Nucleic Acids Res 35:2311-20. 2007
    ..These results suggest that contacts between CI and both alphaCTD and sigma are required for efficient CI-dependent activation of p(M)...
  19. pmc 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
    Barbara Kedzierska
    Division of Genomic Medicine, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK
    Nucleic Acids Res 32:834-41. 2004
    ....