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Ye J, Kan CH, Yang X, Ma C. Inhibition of bacterial RNA polymerase function and protein-protein interactions: a promising approach for next-generation antibacterial therapeutics. RSC Med Chem 2024; 15:1471-1487. [PMID: 38784472 PMCID: PMC11110800 DOI: 10.1039/d3md00690e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/25/2024] [Indexed: 05/25/2024] Open
Abstract
The increasing prevalence of multidrug-resistant pathogens necessitates the urgent development of new antimicrobial agents with innovative modes of action for the next generation of antimicrobial therapy. Bacterial transcription has been identified and widely studied as a viable target for antimicrobial development. The main focus of these studies has been the discovery of inhibitors that bind directly to the core enzyme of RNA polymerase (RNAP). Over the past two decades, substantial advancements have been made in understanding the properties of protein-protein interactions (PPIs) and gaining structural insights into bacterial RNAP and its associated factors. This has led to the crucial role of computational methods in aiding the identification of new PPI inhibitors to affect the RNAP function. In this context, bacterial transcriptional PPIs present promising, albeit challenging, targets for the creation of new antimicrobials. This review will succinctly outline the structural foundation of bacterial transcription networks and provide a summary of the known small molecules that target transcription PPIs.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Kowloon Hong Kong SAR China
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University Hefei 230032 China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin Hong Kong SAR China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin Hong Kong SAR China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Kowloon Hong Kong SAR China
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2
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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3
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Wenholz DS, Miller M, Dawson C, Bhadbhade M, Black DS, Griffith R, Dinh H, Cain A, Lewis P, Kumar N. Inhibitors of bacterial RNA polymerase transcription complex. Bioorg Chem 2021; 118:105481. [PMID: 34801947 DOI: 10.1016/j.bioorg.2021.105481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 01/28/2023]
Abstract
A series of hybrid compounds that incorporated anthranilic acid with activated 1H-indoles through a glyoxylamide linker were designed to target bacterial RNA polymerase holoenzyme formation using computational docking. Synthesis, in vitro transcription inhibition assays, and biological testing of the hybrids identified a range of potent anti-transcription inhibitors with activity against a range of pathogenic bacteria with MICs as low as 3.1 μM. A structure activity relationship study identified the key structural components necessary for inhibition of both bacterial growth and transcription. Correlation of in vitro transcription inhibition activity with in vivo mechanism of action was established using fluorescence microscopy and resistance passaging using Gram-positive bacteria showed no resistance development over 30 days. Furthermore, no toxicity was observed from the compounds in a wax moth larvae model, establishing a platform for the development of a series of new antibacterial drugs with an established mode of action.
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Affiliation(s)
- Daniel S Wenholz
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Michael Miller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Catherine Dawson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Mohan Bhadbhade
- Mark Wainwright Analytical Centre, UNSW Sydney, NSW 2052, Australia
| | - David StC Black
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Renate Griffith
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Hue Dinh
- Department of Biological Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Amy Cain
- Department of Biological Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Peter Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia.
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4
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Ganapathy S, Wiegard JC, Hartmann RK. Rapid preparation of 6S RNA-free B. subtilis σ A-RNA polymerase and σ A. J Microbiol Methods 2021; 190:106324. [PMID: 34506811 DOI: 10.1016/j.mimet.2021.106324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 11/25/2022]
Abstract
The regulatory 6S-1 and 6S-2 RNAs of B. subtilis bind to the housekeeping RNA polymerase holoenzyme (σA-RNAP) with submicromolar affinity. We observed copurification of endogenous 6S RNAs from a published B. subtilis strain expressing a His-tagged RNAP. Such 6S RNA contaminations in σA-RNAP preparations reduce the fraction of enzymes that are accessible for binding to DNA promoters. In addition, this leads to background RNA synthesis by σA-RNAP utilizing copurified 6S RNA as template for the synthesis of short abortive transcripts termed product RNAs (pRNAs). To avoid this problem we constructed a B. subtilis strain expressing His-tagged RNAP but carrying deletions of the two 6S RNA genes. The His-tagged, 6S RNA-free σA-RNAP holoenzyme can be prepared with sufficient purity and activity by a single affinity step. We also report expression and separate purification of B. subtilis σA that can be added to the His-tagged RNAP to maximize the amount of holoenzyme and, by inference, in vitro transcription activity.
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Affiliation(s)
- Sweetha Ganapathy
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Jana Christin Wiegard
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany.
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5
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Abstract
The low G + C Gram-positive bacteria represent some of the most medically and industrially important microorganisms. They are relied on for the production of food and dietary supplements, enzymes and antibiotics, as well as being responsible for the majority of nosocomial infections and serving as a reservoir for antibiotic resistance. Control of gene expression in this group is more highly studied than in any bacteria other than the Gram-negative model Escherichia coli, yet until recently no structural information on RNA polymerase (RNAP) from this group was available. This review will summarize recent reports on the high-resolution structure of RNAP from the model low G + C representative Bacillus subtilis, including the role of auxiliary subunits δ and ε, and outline approaches for the development of antimicrobials to target RNAP from this group.
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Affiliation(s)
- Michael Miller
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Aaron J Oakley
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Peter J Lewis
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia.,School Of Chemistry And Molecular Bioscience, University Of Wollongong And Illawarra Health And Medical Research Institute, Wollongong, Nsw, Australia
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6
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Bange G, Bedrunka P. Physiology of guanosine-based second messenger signaling in Bacillus subtilis. Biol Chem 2021; 401:1307-1322. [PMID: 32881708 DOI: 10.1515/hsz-2020-0241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/22/2020] [Indexed: 12/19/2022]
Abstract
The guanosine-based second messengers (p)ppGpp and c-di-GMP are key players of the physiological regulation of the Gram-positive model organism Bacillus subtilis. Their regulatory spectrum ranges from key metabolic processes over motility to biofilm formation. Here we review our mechanistic knowledge on their synthesis and degradation in response to environmental and stress signals as well as what is known on their cellular effectors and targets. Moreover, we discuss open questions and our gaps in knowledge on these two important second messengers.
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Affiliation(s)
- Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, Marburg, D-35043,Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, Marburg, D-35043,Germany
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7
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de Dios R, Santero E, Reyes-Ramírez F. Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses. Int J Mol Sci 2021; 22:ijms22083900. [PMID: 33918849 PMCID: PMC8103513 DOI: 10.3390/ijms22083900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/03/2023] Open
Abstract
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.
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8
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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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9
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Newing TP, Oakley AJ, Miller M, Dawson CJ, Brown SHJ, Bouwer JC, Tolun G, Lewis PJ. Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD. Nat Commun 2020; 11:6420. [PMID: 33339820 PMCID: PMC7749167 DOI: 10.1038/s41467-020-20157-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria.
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Affiliation(s)
- Timothy P Newing
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Michael Miller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Catherine J Dawson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Simon H J Brown
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - James C Bouwer
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Gökhan Tolun
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.
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10
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Sartini S, Levati E, Maccesi M, Guerra M, Spadoni G, Bach S, Benincasa M, Scocchi M, Ottonello S, Rivara S, Montanini B. New Antimicrobials Targeting Bacterial RNA Polymerase Holoenzyme Assembly Identified with an in Vivo BRET-Based Discovery Platform. ACS Chem Biol 2019; 14:1727-1736. [PMID: 31310497 DOI: 10.1021/acschembio.9b00178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Bacterial resistance represents a major health threat worldwide, and the development of new therapeutics, including innovative antibiotics, is urgently needed. We describe a discovery platform, centered on in silico screening and in vivo bioluminescence resonance energy transfer in yeast cells, for the identification of new antimicrobials that, by targeting the protein-protein interaction between the β'-subunit and the initiation factor σ70 of bacterial RNA polymerase, inhibit holoenzyme assembly and promoter-specific transcription. Out of 34 000 candidate compounds, we identified seven hits capable of interfering with this interaction. Two derivatives of one of these hits proved to be effective in inhibiting transcription in vitro and growth of the Gram-positive pathogens Staphylococcus aureus and Listeria monocytogenes. Upon supplementation of a permeability adjuvant, one derivative also effectively inhibited Escherichia coli growth. On the basis of the chemical structures of these inhibitors, we generated a ligand-based pharmacophore model that will guide the rational discovery of increasingly effective antibacterial agents.
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Affiliation(s)
- Sara Sartini
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124 Parma, Italy
| | - Elisabetta Levati
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Martina Maccesi
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Matteo Guerra
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Gilberto Spadoni
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, 61029 Urbino, Italy
| | - Stéphane Bach
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Team Physiology and Cell Fate, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Monica Benincasa
- Department of Life Sciences, University of Trieste, 34128 Trieste, Italy
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34128 Trieste, Italy
| | - Simone Ottonello
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Silvia Rivara
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Barbara Montanini
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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11
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12
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Wenholz DS, Zeng M, Ma C, Mielczarek M, Yang X, Bhadbhade M, Black DSC, Lewis PJ, Griffith R, Kumar N. Small molecule inhibitors of bacterial transcription complex formation. Bioorg Med Chem Lett 2017; 27:4302-4308. [PMID: 28866270 DOI: 10.1016/j.bmcl.2017.08.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 11/26/2022]
Abstract
Knoevenagel condensation was employed to generate a set of molecules potentially capable of inhibiting the RNA polymerase-σ70/σA interaction in bacteria. Synthesis was achieved via reactions between a variety of indole-7-carbaldehydes and rhodanine, N-allylrhodanine, barbituric acid or thiobarbituric acid. A library of structurally diverse compounds was examined by enzyme-linked immunosorbent assay (ELISA) to assess the inhibition of the targeted protein-protein interaction. Inhibition of bacterial growth was also evaluated using Bacillus subtilis and Escherichia coli cultures. The structure-activity relationship studies demonstrated the significance of particular structural features of the synthesized molecules for RNA polymerase-σ70/σA interaction inhibition and antibacterial activity. Docking was investigated as an in silico method for the further development of the compounds.
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Affiliation(s)
- Daniel S Wenholz
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Ming Zeng
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | | | - Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | - Mohan Bhadbhade
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - David St C Black
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Renate Griffith
- School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia; Australian Centre for Nanomedicine, UNSW Sydney, Kensington, NSW 2052, Australia.
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13
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Xue X, Davis MC, Steeves T, Bishop A, Breen J, MacEacheron A, Kesthely CA, Hsu F, MacLellan SR. Characterization of a protein-protein interaction within the SigO-RsoA two-subunit σ factor: the σ70 region 2.3-like segment of RsoA mediates interaction with SigO. MICROBIOLOGY-SGM 2016; 162:1857-1869. [PMID: 27558998 DOI: 10.1099/mic.0.000358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
σ factors are single subunit general transcription factors that reversibly bind core RNA polymerase and mediate gene-specific transcription in bacteria. Previously, an atypical two-subunit σ factor was identified that activates transcription from a group of related promoters in Bacillus subtilis. Both of the subunits, named SigO and RsoA, share primary sequence similarity with the canonical σ70 family of σ factors and interact with each other and with RNA polymerase subunits. Here we show that the σ70 region 2.3-like segment of RsoA is unexpectedly sufficient for interaction with the amino-terminus of SigO and the β' subunit. A mutational analysis of RsoA identified aromatic residues conserved amongst all RsoA homologues, and often amongst canonical σ factors, that are particularly important for the SigO-RsoA interaction. In a canonical σ factor, region 2.3 amino acids bind non-template strand DNA, trapping the promoter in a single-stranded state required for initiation of transcription. Accordingly, we speculate that RsoA region 2.3 protein-binding activity likely arose from a motif that, at least in its ancestral protein, participated in DNA-binding interactions.
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Affiliation(s)
- Xiaowei Xue
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Thomas Steeves
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Adam Bishop
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Jillian Breen
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | | | | | - FoSheng Hsu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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14
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Thach O, Mielczarek M, Ma C, Kutty SK, Yang X, Black DS, Griffith R, Lewis PJ, Kumar N. From indole to pyrrole, furan, thiophene and pyridine: Search for novel small molecule inhibitors of bacterial transcription initiation complex formation. Bioorg Med Chem 2016; 24:1171-82. [DOI: 10.1016/j.bmc.2016.01.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
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15
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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16
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Ma C, Yang X, Lewis PJ. Bacterial Transcription Inhibitor of RNA Polymerase Holoenzyme Formation by Structure-Based Drug Design: From in Silico Screening to Validation. ACS Infect Dis 2016; 2:39-46. [PMID: 27622946 DOI: 10.1021/acsinfecdis.5b00058] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial transcription is a proven target for antibacterial research. However, most of the known inhibitors targeting transcription are from natural extracts or are hits from screens where the binding site remains unidentified. Using an RNA polymerase holoenzyme homology structure from the model Gram-positive organism Bacillus subtilis, we created a pharmacophore model and used it for in silico screening of a publicly available library for compounds able to inhibit holoenzyme formation. The hits demonstrated specific affinity to bacterial RNA polymerase and excellent activity using in vitro assays and showed no binding to the equivalent structure from human RNA polymerase II. The target specificity in live cells and antibacterial activity was demonstrated in microscopy and growth inhibition experiments. This is the first example of targeted inhibitor development for a bacterial RNA polymerase, outlining a complete discovery process from virtual screening to biochemical validation. This approach could serve as an appropriate platform for the future identification of inhibitors of bacterial transcription.
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Affiliation(s)
- Cong Ma
- School of Environmental and Life
Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Xiao Yang
- School of Environmental and Life
Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J. Lewis
- School of Environmental and Life
Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
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17
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Shaaban S, Roller A, Maulide N. Visible-Light, Metal-Free α-Amino C(sp3)-H Activation through 1,5-Hydrogen Migration: A Concise Method for the Preparation of Bis(indolyl)alkanes. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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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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19
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Synthesis and biological activity of novel mono-indole and mono-benzofuran inhibitors of bacterial transcription initiation complex formation. Bioorg Med Chem 2015; 23:1763-75. [DOI: 10.1016/j.bmc.2015.02.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/12/2015] [Accepted: 02/17/2015] [Indexed: 11/23/2022]
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20
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Ma C, Mobli M, Yang X, Keller AN, King GF, Lewis PJ. RNA polymerase-induced remodelling of NusA produces a pause enhancement complex. Nucleic Acids Res 2015; 43:2829-40. [PMID: 25690895 PMCID: PMC4357713 DOI: 10.1093/nar/gkv108] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Pausing during transcription elongation is a fundamental activity in all kingdoms of life. In bacteria, the essential protein NusA modulates transcriptional pausing, but its mechanism of action has remained enigmatic. By combining structural and functional studies we show that a helical rearrangement induced in NusA upon interaction with RNA polymerase is the key to its modulatory function. This conformational change leads to an allosteric re-positioning of conserved basic residues that could enable their interaction with an RNA pause hairpin that forms in the exit channel of the polymerase. This weak interaction would stabilize the paused complex and increases the duration of the transcriptional pause. Allosteric spatial re-positioning of regulatory elements may represent a general approach used across all taxa for modulation of transcription and protein–RNA interactions.
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Affiliation(s)
- Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew N Keller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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21
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A vector system that allows simple generation of mutant Escherichia coli RNA polymerase. Plasmid 2014; 75:37-41. [PMID: 24992039 DOI: 10.1016/j.plasmid.2014.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/22/2022]
Abstract
We describe a dual vector-based system for overproduction of recombinant Escherichia coli RNA polymerase (RNAP). A cleavable deca-histidine tag (His10) was incorporated into the C-terminus of the β' subunit to facilitate protein purification. Unique restriction sites were introduced into the genes encoding the β and β' subunits (rpoB and rpoC, respectively), facilitating mutation of functionally significant subunit fragments through insertion of modified PCR fragments into the appropriate vector. RNAP with an R275A substitution in the β' subunit, which is essential for interaction with transcription initiation factor σ, was generated and exhibited reduced activity compared to native recombinant RNAP.
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22
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Wiedermannová J, Sudzinová P, Kovaľ T, Rabatinová A, Šanderova H, Ramaniuk O, Rittich Š, Dohnálek J, Fu Z, Halada P, Lewis P, Krásny L. Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res 2014; 42:5151-63. [PMID: 24520113 PMCID: PMC4005671 DOI: 10.1093/nar/gku113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) is an essential multisubunit protein complex required for gene expression. Here, we characterize YvgS (HelD) from Bacillus subtilis, a novel binding partner of RNAP. We show that HelD interacts with RNAP-core between the secondary channel of RNAP and the alpha subunits. Importantly, we demonstrate that HelD stimulates transcription in an ATP-dependent manner by enhancing transcriptional cycling and elongation. We demonstrate that the stimulatory effect of HelD can be amplified by a small subunit of RNAP, delta. In vivo, HelD is not essential but it is required for timely adaptations of the cell to changing environment. In summary, this study establishes HelD as a valid component of the bacterial transcription machinery.
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Affiliation(s)
- Jana Wiedermannová
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 12843, Czech Republic, Department of Structure Analysis of Biomacromolecules, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Prague 16206, Czech Republic, Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia and Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
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23
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Mielczarek M, Devakaram RV, Ma C, Yang X, Kandemir H, Purwono B, Black DS, Griffith R, Lewis PJ, Kumar N. Synthesis and biological activity of novel bis-indole inhibitors of bacterial transcription initiation complex formation. Org Biomol Chem 2014; 12:2882-94. [DOI: 10.1039/c4ob00460d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of novel bis-indole amides and glyoxylamides as bacterial transcription complex formation inhibitors and their structure–activity relationships are discussed.
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Affiliation(s)
- Marcin Mielczarek
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Ruth V. Devakaram
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Cong Ma
- School of Environmental and Life Sciences
- University of Newcastle
- Callaghan, Australia
| | - Xiao Yang
- School of Environmental and Life Sciences
- University of Newcastle
- Callaghan, Australia
| | - Hakan Kandemir
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Bambang Purwono
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - David StC. Black
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Renate Griffith
- School of Medical Sciences
- Department of Pharmacology
- The University of New South Wales
- Sydney, Australia
| | - Peter J. Lewis
- School of Environmental and Life Sciences
- University of Newcastle
- Callaghan, Australia
| | - Naresh Kumar
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
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24
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Ma C, Yang X, Kandemir H, Mielczarek M, Johnston EB, Griffith R, Kumar N, Lewis PJ. Inhibitors of bacterial transcription initiation complex formation. ACS Chem Biol 2013; 8:1972-80. [PMID: 23751807 DOI: 10.1021/cb400231p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Antibiotic resistance is a growing global problem, with very few new compounds in development. Bacterial transcription is an underutilized target for antibiotics, which has been attributed to the similarity of the active site of RNA polymerases (RNAPs) across all domains of life and the ease with which resistance can arise through point mutation at multiple sites within this conserved region. In this study we have taken a rational approach to design a novel set of compounds that specifically target the formation of transcription initiation complexes by preventing the unique bacterial σ initiation factor from binding to RNAP. We have identified the region of RNAP to which these compounds bind and demonstrate that one compound, GKL003, has an inhibition constant in the low nanomolar range. This compound has activity against both Gram-positive and -negative organisms, including a community acquired methicillin-resistant strain of the major pathogen Staphylococcus aureus.
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Affiliation(s)
- Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | | | | | - Elecia B Johnston
- 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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25
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Yang X, Lewis PJ. The interaction between bacterial transcription factors and RNA polymerase during the transition from initiation to elongation. Transcription 2012; 1:66-9. [PMID: 21326893 DOI: 10.4161/trns.1.2.12791] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 06/24/2010] [Accepted: 06/25/2010] [Indexed: 11/19/2022] Open
Abstract
There are three stages of transcription: initiation, elongation and termination, and traditionally there has been a clear distinction between the stages. The specificity factor sigma is completely released from bacterial RNA polymerase after initiation, and then recycled for another round of transcription. Elongation factors then associate with the polymerase followed by termination factors (where necessary). These factors dissociate prior to initiation of a new round of transcription. However, there is growing evidence suggesting that sigma factors can be retained in the elongation complex. The structure of bacterial RNAP in complex with an essential elongation factor NusA has recently been published, which suggested rather than competing for the major σ binding site, NusA binds to a discrete region on RNAP. A model was proposed to help explain the way in which both factors could be associated with RNAP during the transition from transcription initiation to elongation.
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Affiliation(s)
- Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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26
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Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H. Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR. Nucleic Acids Res 2012; 40:4178-92. [PMID: 22238377 PMCID: PMC3351151 DOI: 10.1093/nar/gkr1316] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bacillus subtilis encodes redox-sensing MarR-type regulators of the OhrR and DUF24-families that sense organic hydroperoxides, diamide, quinones or aldehydes via thiol-based redox-switches. In this article, we characterize the novel redox-sensing MarR/DUF24-family regulator HypR (YybR) that is activated by disulphide stress caused by diamide and NaOCl in B. subtilis. HypR controls positively a flavin oxidoreductase HypO that confers protection against NaOCl stress. The conserved N-terminal Cys14 residue of HypR has a lower pK(a) of 6.36 and is essential for activation of hypO transcription by disulphide stress. HypR resembles a 2-Cys-type regulator that is activated by Cys14-Cys49' intersubunit disulphide formation. The crystal structures of reduced and oxidized HypR proteins were resolved revealing structural changes of HypR upon oxidation. In reduced HypR a hydrogen-bonding network stabilizes the reactive Cys14 thiolate that is 8-9 Å apart from Cys49'. HypR oxidation breaks these H-bonds, reorients the monomers and moves the major groove recognition α4 and α4' helices ∼4 Å towards each other. This is the first crystal structure of a redox-sensing MarR/DUF24 family protein in bacteria that is activated by NaOCl stress. Since hypochloric acid is released by activated macrophages, related HypR-like regulators could function to protect pathogens against the host immune defense.
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Affiliation(s)
- Gottfried J Palm
- Institute for Biochemistry, Ernst-Moritz-Arndt-University of Greifswald, D-17487 Greifswald, Germany
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27
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Sojka L, Kouba T, Barvík I, Sanderová H, Maderová Z, Jonák J, Krásny L. Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis. Nucleic Acids Res 2011; 39:4598-611. [PMID: 21303765 PMCID: PMC3113569 DOI: 10.1093/nar/gkr032] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In bacteria, rapid changes in gene expression can be achieved by affecting the activity of RNA polymerase with small molecule effectors during transcription initiation. An important small molecule effector is the initiating nucleoside triphosphate (iNTP). At some promoters, an increasing iNTP concentration stimulates promoter activity, while a decreasing concentration has the opposite effect. Ribosomal RNA (rRNA) promoters from Gram-positive Bacillus subtilis are regulated by the concentration of their iNTP. Yet, the sequences of these promoters do not emulate the sequence characteristics of [iNTP]-regulated rRNA promoters of Gram-negative Escherichia coli. Here, we identified the 3′-promoter region, corresponding to the transcription bubble, as key for B. subtilis rRNA promoter regulation via the concentration of the iNTP. Within this region, the conserved −5T (3 bp downstream from the −10 hexamer) is required for this regulation. Moreover, we identified a second class of [iNTP]-regulated promoters in B. subtilis where the sequence determinants are not limited to the transcription bubble region. Overall, it seems that various sequence combinations can result in promoter regulation by [iNTP] in B. subtilis. Finally, this study demonstrates how the same type of regulation can be achieved with strikingly different promoter sequences in phylogenetically distant species.
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Affiliation(s)
- Ludek Sojka
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic
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28
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Essential biological processes of an emerging pathogen: DNA replication, transcription, and cell division in Acinetobacter spp. Microbiol Mol Biol Rev 2010; 74:273-97. [PMID: 20508250 DOI: 10.1128/mmbr.00048-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within the last 15 years, members of the bacterial genus Acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. The driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. There is an urgent need for new antibacterial compounds to combat the threat imposed by Acinetobacter spp. and other intractable bacterial pathogens. The essential processes of chromosomal DNA replication, transcription, and cell division are attractive targets for the rational design of antimicrobial drugs. The goal of this review is to examine the wealth of genome sequence and gene knockout data now available for Acinetobacter spp., highlighting those aspects of essential systems that are most suitable as drug targets. Acinetobacter spp. show several key differences from other pathogenic gammaproteobacteria, particularly in global stress response pathways. The involvement of these pathways in short- and long-term antibiotic survival suggests that Acinetobacter spp. cope with antibiotic-induced stress differently from other microorganisms.
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29
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Bisicchia P, Lioliou E, Noone D, Salzberg LI, Botella E, Hübner S, Devine KM. Peptidoglycan metabolism is controlled by the WalRK (YycFG) and PhoPR two-component systems in phosphate-limited Bacillus subtilis cells. Mol Microbiol 2010; 75:972-89. [PMID: 20487291 DOI: 10.1111/j.1365-2958.2009.07036.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In Bacillus subtilis, the WalRK (YycFG) two-component system controls peptidoglycan metabolism in exponentially growing cells while PhoPR controls the response to phosphate limitation. Here we examine the roles of WalRK and PhoPR in peptidoglycan metabolism in phosphate-limited cells. We show that B. subtilis cells remain viable in a phosphate-limited state for an extended period and resume growth rapidly upon phosphate addition, even in the absence of a PhoPR-mediated response. Peptidoglycan synthesis occurs in phosphate-limited wild-type cells at approximately 27% the rate of exponentially growing cells, and at approximately 18% the rate of exponentially growing cells in the absence of PhoPR. In phosphate-limited cells, the WalRK regulon genes yocH, cwlO(yvcE), lytE and ydjM are expressed in a manner that is dependent on the WalR recognition sequence and deleting these genes individually reduces the rate of peptidoglycan synthesis. We show that ydjM expression can be activated by PhoP approximately P in vitro and that PhoP occupies its promoter in phosphate-limited cells. However, iseA(yoeB) expression cannot be repressed by PhoP approximately P in vitro, but can be repressed by non-phosphorylated WalR in vitro. Therefore, we conclude that peptidoglycan metabolism is controlled by both WalRK and PhoPR in phosphate-limited B. subtilis cells.
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Affiliation(s)
- Paola Bisicchia
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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30
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Camacho A, Salas M. DNA bending and looping in the transcriptional control of bacteriophage phi29. FEMS Microbiol Rev 2010; 34:828-41. [PMID: 20412311 DOI: 10.1111/j.1574-6976.2010.00219.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Recent studies on the regulation of phage phi29 gene expression reveal new ways to accomplish the processes required for the orderly gene expression in prokaryotic systems. These studies revealed a novel DNA-binding domain in the phage main transcriptional regulator and the nature and dynamics of the multimeric DNA-protein complex responsible for the switch from early to late gene expression. This review describes the features of the regulatory mechanism that leads to the simultaneous activation and repression of transcription, and discusses it in the context of the role of the topological modification of the DNA carried out by two phage-encoded proteins working synergistically with the DNA.
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Affiliation(s)
- Ana Camacho
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
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