72 results found
Duchi D, Gryte K, Robb NC, et al., 2017, Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes., Nucleic Acids Res
Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP-DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.
Pader V, Hakim S, Painter KL, et al., 2017, Staphylococcus aureus inactivates daptomycin by releasing membrane phospholipids, NATURE MICROBIOLOGY, Vol: 2, ISSN: 2058-5276
Sarkar P, Switzer A, Peters C, et al., 2017, Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli, NUCLEIC ACIDS RESEARCH, Vol: 45, Pages: 11131-11143, ISSN: 0305-1048
Tabib-Salazar A, Liu B, Shadrin A, et al., 2017, Full shut-off of Escherichia coli RNA-polymerase by T7 phage requires a small phage-encoded DNA-binding protein, NUCLEIC ACIDS RESEARCH, Vol: 45, Pages: 7697-7707, ISSN: 0305-1048
du Plessis J, Cloete R, Burchell L, et al., 2017, Exploring the potential of T7 bacteriophage protein Gp2 as a novel inhibitor of mycobacterial RNA polymerase, TUBERCULOSIS, Vol: 106, Pages: 82-90, ISSN: 1472-9792
Brown DR, Sheppard CM, Burchell L, et al., 2016, The Xp10 Bacteriophage Protein P7 Inhibits Transcription by the Major and Major Variant Forms of the Host RNA Polymerase via a Common Mechanism, JOURNAL OF MOLECULAR BIOLOGY, Vol: 428, Pages: 3911-3919, ISSN: 0022-2836
Figueira R, Brown DR, Ferreira D, et al., 2015, Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase YeaG, SCIENTIFIC REPORTS, Vol: 5, ISSN: 2045-2322
Thompson CC, Griffiths C, Nicod SS, et al., 2015, The Rsb Phosphoregulatory Network Controls Availability of the Primary Sigma Factor in Chlamydia trachomatis and Influences the Kinetics of Growth and Development, PLOS PATHOGENS, Vol: 11, ISSN: 1553-7366
Brown DR, Barton G, Pan Z, et al., 2014, Nitrogen stress response and stringent response are coupled in Escherichia coli, NATURE COMMUNICATIONS, Vol: 5, ISSN: 2041-1723
Brown DR, Barton G, Pan Z, et al., 2014, Combinatorial stress responses: direct coupling of two major stress responses in Escherichia coli., Microb Cell, Vol: 1, Pages: 315-317, ISSN: 2311-2638
Nitrogen is an essential element for all life, and this is no different for the bacterial cell. Numerous cellular macromolecules contain nitrogen, including proteins, nucleic acids and cell wall components. In Escherichia coli and related bacteria, the nitrogen stress (Ntr) response allows cells to rapidly sense and adapt to nitrogen limitation by scavenging for alternative nitrogen sources through the transcriptional activation of transport systems and catabolic and biosynthetic operons by the global transcriptional regulator NtrC. Nitrogen-starved bacterial cells also synthesize the (p)ppGpp effector molecules of a second global bacterial stress response - the stringent response. Recently, we showed that the transcription of relA, the gene which encodes the major (p)ppGpp synthetase in E. coli, is activated by NtrC during nitrogen starvation. Our results revealed that in E. coli and related bacteria, NtrC functions in combinatorial stress and serves to couple two major stress responses, the Ntr response and stringent response.
Liu B, Shadrin A, Sheppard C, et al., 2014, A bacteriophage transcription regulator inhibits bacterial transcription initiation by Sigma-factor displacement, NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 4294-4305, ISSN: 0305-1048
Liu B, Shadrin A, Sheppard C, et al., 2014, The sabotage of the bacterial transcription machinery by a small bacteriophage protein., Bacteriophage, Vol: 4, ISSN: 2159-7073
Many bacteriophages produce small proteins that specifically interfere with the bacterial host transcription machinery and thus contribute to the acquisition of the bacterial cell by the bacteriophage. We recently described how a small protein, called P7, produced by the Xp10 bacteriophage inhibits bacterial transcription initiation by causing the dissociation of the promoter specificity sigma factor subunit from the host RNA polymerase holoenzyme. In this addendum to the original publication, we present the highlights of that research.
Nicod SS, Weinzierl RO, Burchell L, et al., 2014, Systematic mutational analysis of the LytTR DNA binding domain of Staphylococcus aureus virulence gene transcription factor AgrA., Nucleic Acids Research, Vol: 42, Pages: 12523-12536, ISSN: 1362-4962
Most DNA-binding bacterial transcription factors contact DNA through a recognition α-helix in their DNA-binding domains. An emerging class of DNA-binding transcription factors, predominantly found in pathogenic bacteria interact with the DNA via a relatively novel type of DNA-binding domain, called the LytTR domain, which mainly comprises β strands. Even though the crystal structure of the LytTR domain of the virulence gene transcription factor AgrA from Staphylococcus aureus bound to its cognate DNA sequence is available, the contribution of specific amino acid residues in the LytTR domain of AgrA to transcription activation remains elusive. Here, for the first time, we have systematically investigated the role of amino acid residues in transcription activation in a LytTR domain-containing transcription factor. Our analysis, which involves in vivo and in vitro analyses and molecular dynamics simulations of S. aureus AgrA identifies a highly conserved tyrosine residue, Y229, as a major amino acid determinant for maximal activation of transcription by AgrA and provides novel insights into structure-function relationships in S. aureus AgrA.
Pader V, James EH, Painter KL, et al., 2014, The Agr Quorum-Sensing System Regulates Fibronectin Binding but Not Hemolysis in the Absence of a Functional Electron Transport Chain, INFECTION AND IMMUNITY, Vol: 82, Pages: 4337-4347, ISSN: 0019-9567
Painter KL, Krishna A, Wigneshweraraj S, et al., 2014, What role does the quorum-sensing accessory gene regulator system play during Staphylococcus aureus bacteremia?, TRENDS IN MICROBIOLOGY, Vol: 22, Pages: 676-685, ISSN: 0966-842X
Sharma A, Leach RN, Gell C, et al., 2014, Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies, NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 5177-5190, ISSN: 0305-1048
Thomas MS, Wigneshweraraj S, 2014, Regulation of virulence gene expression, VIRULENCE, Vol: 5, Pages: 832-834, ISSN: 2150-5594
Bae B, Davis E, Brown D, et al., 2013, Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of sigma(70) domain 1.1, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 19772-19777, ISSN: 0027-8424
James EH, Edwards AM, Wigneshweraraj S, 2013, Transcriptional downregulation of agr expression in Staphylococcus aureus during growth in human serum can be overcome by constitutively active mutant forms of the sensor kinase AgrC, FEMS MICROBIOLOGY LETTERS, Vol: 349, Pages: 153-162, ISSN: 0378-1097
Schumacher J, Behrends V, Pan Z, et al., 2013, Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC In Vivo, MBIO, Vol: 4, ISSN: 2150-7511
Shadrin A, Sheppard C, Savalia D, et al., 2013, Overexpression of Escherichia coli udk mimics the absence of T7 Gp2 function and thereby abrogates successful infection by T7 phage, MICROBIOLOGY-SGM, Vol: 159, Pages: 269-274, ISSN: 1350-0872
Sheppard C, James E, Barton G, et al., 2013, A non-bacterial transcription factor inhibits bacterial transcription by a multipronged mechanism, RNA BIOLOGY, Vol: 10, Pages: 495-501, ISSN: 1547-6286
Chakraborty A, Wang D, Ebright YW, et al., 2012, Opening and Closing of the Bacterial RNA Polymerase Clamp, SCIENCE, Vol: 337, Pages: 591-595, ISSN: 0036-8075
Drennan A, Kraemer M, Capp M, et al., 2012, Key Roles of the Downstream Mobile Jaw of Escherichia coli RNA Polymerase in Transcription Initiation, BIOCHEMISTRY, Vol: 51, Pages: 9447-9459, ISSN: 0006-2960
Drennan A, Saecker R, Heitkamp S, et al., 2012, E. Coli RNA Polymerase: A Molecular DNA Opening Machine, BIOPHYSICAL JOURNAL, Vol: 102, Pages: 286A-286A, ISSN: 0006-3495
James E, Liu M, Sheppard C, et al., 2012, Structural and Mechanistic Basis for the Inhibition of Escherichia coli RNA Polymerase by T7 Gp2, MOLECULAR CELL, Vol: 47, Pages: 755-766, ISSN: 1097-2765
Shadrin A, Sheppard C, Severinov K, et al., 2012, Substitutions in the Escherichia coli RNA polymerase inhibitor T7 Gp2 that allow inhibition of transcription when the primary interaction interface between Gp2 and RNA polymerase becomes compromised, MICROBIOLOGY-SGM, Vol: 158, Pages: 2753-2764, ISSN: 1350-0872
Jovanovic M, Burrows PC, Bose D, et al., 2011, Activity Map of the Escherichia coli RNA Polymerase Bridge Helix, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 286, Pages: 14469-14479, ISSN: 0021-9258
Mekler V, Minakhin L, Sheppard C, et al., 2011, Molecular Mechanism of Transcription Inhibition by Phage T7 gp2 Protein, JOURNAL OF MOLECULAR BIOLOGY, Vol: 413, Pages: 1016-1027, ISSN: 0022-2836
Reynolds J, Wigneshweraraj S, 2011, Molecular Insights into the Control of Transcription Initiation at the Staphylococcus aureus agr operon, JOURNAL OF MOLECULAR BIOLOGY, Vol: 412, Pages: 862-881, ISSN: 0022-2836
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