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Zachrdla M, Padrta P, Rabatinová A, Šanderová H, Barvík I, Krásný L, Žídek L. Solution structure of domain 1.1 of the σ A factor from Bacillus subtilis is preformed for binding to the RNA polymerase core. J Biol Chem 2017; 292:11610-11617. [PMID: 28539362 DOI: 10.1074/jbc.m117.784074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/19/2017] [Indexed: 11/06/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) requires σ factors to recognize promoter sequences. Domain 1.1 of primary σ factors (σ1.1) prevents their binding to promoter DNA in the absence of RNAP, and when in complex with RNAP, it occupies the DNA-binding channel of RNAP. Currently, two 3D structures of σ1.1 are available: from Escherichia coli in complex with RNAP and from T. maritima solved free in solution. However, these two structures significantly differ, and it is unclear whether this difference is due to an altered conformation upon RNAP binding or to differences in intrinsic properties between the proteins from these two distantly related species. Here, we report the solution structure of σ1.1 from the Gram-positive bacterium Bacillus subtilis We found that B. subtilis σ1.1 is highly compact because of additional stabilization not present in σ1.1 from the other two species and that it is more similar to E. coli σ1.1. Moreover, modeling studies suggested that B. subtilis σ1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas T. maritima σ1.1 must be rearranged to fit therein. Thus, the mesophilic species B. subtilis and E. coli share the same σ1.1 fold, whereas the fold of σ1.1 from the thermophile T. maritima is distinctly different. Finally, we describe an intriguing similarity between σ1.1 and δ, an RNAP-associated protein in B. subtilis, bearing implications for the so-far unknown binding site of δ on RNAP. In conclusion, our results shed light on the conformational changes of σ1.1 required for its accommodation within bacterial RNAP.
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Affiliation(s)
- Milan Zachrdla
- Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Petr Padrta
- Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Alžbeta Rabatinová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, The Czech Academy of Sciences, CZ-14220 Prague 4, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, The Czech Academy of Sciences, CZ-14220 Prague 4, Czech Republic
| | - Ivan Barvík
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, CZ-12116 Prague 2, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, The Czech Academy of Sciences, CZ-14220 Prague 4, Czech Republic.
| | - Lukáš Žídek
- Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.
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Yang X, Ma C, Lewis PJ. Identification of inhibitors of bacterial RNA polymerase. Methods 2015; 86:45-50. [PMID: 25976836 DOI: 10.1016/j.ymeth.2015.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/28/2015] [Accepted: 05/05/2015] [Indexed: 01/09/2023] Open
Abstract
Very few clinically available antibiotics target bacterial RNA polymerase (RNAP) suggesting it is an underutilized target. The advent of detailed structural information of RNAP holoenzyme (HE) has allowed the design and in silico screening of novel transcription inhibitors. Here, we describe our approach for the design and testing of small molecule transcription inhibitors that work by preventing the interaction between the essential transcription initiation factor σ and RNAP. With the appropriate structural information this approach can be easily modified to other essential protein-protein interactions.
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Affiliation(s)
- Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia.
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Buncherd H, Nessen MA, Nouse N, Stelder SK, Roseboom W, Dekker HL, Arents JC, Smeenk LE, Wanner MJ, van Maarseveen JH, Yang X, Lewis PJ, de Koning LJ, de Koster CG, de Jong L. Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry. J Proteomics 2012; 75:2205-15. [DOI: 10.1016/j.jprot.2012.01.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/12/2012] [Accepted: 01/20/2012] [Indexed: 10/14/2022]
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Johnston EB, Lewis PJ, Griffith R. The interaction of Bacillus subtilis sigmaA with RNA polymerase. Protein Sci 2010; 18:2287-97. [PMID: 19735077 DOI: 10.1002/pro.239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
RNA polymerase (RNAP) is an essential and highly conserved enzyme in all organisms. The process of transcription initiation is fundamentally different between prokaryotes and eukaryotes. In prokaryotes, initiation is regulated by sigma factors, making the essential interaction between sigma factors and RNAP an attractive target for antimicrobial agents. Our objective was to achieve the first step in the process of developing novel antimicrobial agents, namely to prove experimentally that the interaction between a bacterial RNAP and an essential sigma factor can be disrupted by introducing carefully designed mutations into sigma(A) of Bacillus subtilis. This disruption was demonstrated qualitatively by Far-Western blotting. Design of mutant sigmas was achieved by computer-aided visualization of the RNAP-sigma interface of the B. subtilis holoenzyme (RNAP + sigma) constructed using a homology modeling approach with published crystal structures of bacterial RNAPs. Models of the holoenzyme and the core RNAP were rigorously built, evaluated, and validated. To allow a high-quality RNAP-sigma interface model to be constructed for the design of mutations, a crucial error in the B. subtilis sigma(A) sequence in published databases at amino acid 165 had to be corrected first. The new model was validated through determination of RNAP-sigma interactions using targeted mutations.
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Affiliation(s)
- Elecia B Johnston
- Discipline of Biological Sciences, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
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5
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Yang X, Doherty GP, Lewis PJ. Tandem affinity purification vectors for use in gram positive bacteria. Plasmid 2008; 59:54-62. [DOI: 10.1016/j.plasmid.2007.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/17/2007] [Accepted: 11/11/2007] [Indexed: 01/12/2023]
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6
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Barker JJ. Antibacterial drug discovery and structure-based design. Drug Discov Today 2006; 11:391-404. [PMID: 16635801 DOI: 10.1016/j.drudis.2006.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
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Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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Davies KM, Dedman AJ, van Horck S, Lewis PJ. The NusA:RNA polymerase ratio is increased at sites of rRNA synthesis inBacillus subtilis. Mol Microbiol 2005. [DOI: 10.1111/j.1365-2958.2005.04669.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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