1
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Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
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2
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Cooperativity in ATP Hydrolysis by MopR Is Modulated by Its Signal Reception Domain and by Its Protein and Phenol Concentrations. J Bacteriol 2022; 204:e0017922. [PMID: 35862728 PMCID: PMC9380524 DOI: 10.1128/jb.00179-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The NtrC family of AAA+ proteins are bacterial transcriptional regulators that control σ54-dependent RNA polymerase transcription under certain stressful conditions. MopR, which is a member of this family, is responsive to phenol and stimulates its degradation. Biochemical studies to understand the role of ATP and phenol in oligomerization and allosteric regulation, which are described here, show that MopR undergoes concentration-dependent oligomerization in which dimers assemble into functional hexamers. The oligomerization occurs in a nucleation-dependent manner with a tetrameric intermediate. Additionally, phenol binding is shown to be responsible for shifting MopR's equilibrium from a repressed state (high affinity toward ATP) to a functionally active, derepressed state with low-affinity for ATP. Based on these findings, we propose a model for allosteric regulation of MopR. IMPORTANCE The NtrC family of bacterial transcriptional regulators are enzymes with a modular architecture that harbor a signal sensing domain followed by a AAA+ domain. MopR, a NtrC family member, responds to phenol and activates phenol adaptation pathways that are transcribed by σ54-dependent RNA polymerases. Our results show that for efficient ATP hydrolysis, MopR assembles as functional hexamers and that this activity of MopR is regulated by its effector (phenol), ATP, and protein concentration. Our findings, and the kinetic methods we employ, should be useful in dissecting the allosteric mechanisms of other AAA+ proteins, in general, and NtrC family members in particular.
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Chakrabortty T, Roy Chowdhury S, Ghosh B, Sen U. Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding. J Mol Biol 2021; 434:167354. [PMID: 34774564 DOI: 10.1016/j.jmb.2021.167354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/09/2023]
Abstract
VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for σ54-RNAP binding and REC domain phosphorylation. Moreover, transcription from PvpsL, a promoter of biofilm biosynthesis, has been documented in presence of σ70-RNAP/VpsR/c-di-GMP complex. It was proposed that c-di-GMP and VpsR together form an active transcription complex with σ70-RNAP. However, the impact of c-di-GMP imparted on VpsR that leads to transcription activation with σ70-RNAP remained elusive, largely due to the lack of the structure of VpsR and knowledge about c-di-GMP:VpsR interactions. In this direction we have solved the crystal structure of VpsRRA, containing REC and AAA+ domains, in apo, AMPPNP/GMPPNP and c-di-GMP bound states. Structures of VpsRRA unveiled distinctive REC domain orientation that leads to a novel dimeric association and noncanonical ATP/GTP binding. Moreover, we have demonstrated that at physiological pH VpsR remains as monomer having no ATPase activity but c-di-GMP imparted cooperativity to convert it to dimer with potent activity. Crystal structure of c-di-GMP:VpsRRA complex reveals that c-di-GMP binds near the C-terminal end of AAA+ domain. Trp quenching studies on VpsRR, VpsRA, VpsRRA, VpsRAD with c-di-GMP additionally demonstrated that c-di-GMP could potentially bind VpsRD. We propose that c-di-GMP mediated tethering of VpsRD with VpsRA could likely favor generating the specific protein-DNA architecture for transcription activation.
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Affiliation(s)
- Tulika Chakrabortty
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India. https://twitter.com/@TulikaC02382598
| | - Sanghati Roy Chowdhury
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India
| | - Biplab Ghosh
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India.
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4
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Hernández VM, Arteaga A, Dunn MF. Diversity, properties and functions of bacterial arginases. FEMS Microbiol Rev 2021; 45:6308370. [PMID: 34160574 DOI: 10.1093/femsre/fuab034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
The metalloenzyme arginase hydrolyzes L-arginine to produce L-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor L-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation, and biochemical features of arginases in a variety of bacterial species.
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Affiliation(s)
- Victor M Hernández
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Alejandra Arteaga
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
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5
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Engl C, Jovanovic G, Brackston RD, Kotta-Loizou I, Buck M. The route to transcription initiation determines the mode of transcriptional bursting in E. coli. Nat Commun 2020; 11:2422. [PMID: 32415118 PMCID: PMC7229158 DOI: 10.1038/s41467-020-16367-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ70 and σ54). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ70-controlled stress response is regulated via the burst size, while that of the σ54-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ54 differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems. Transcription noise in bacteria is often attributed to burstiness, but the mechanisms are unclear. Here, the authors show that the transition from low to high expression can be regulated via burst size or burst frequency, depending on the mode of transcription initiation determined by different sigma factors.
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Affiliation(s)
- Christoph Engl
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Goran Jovanovic
- Faculty of Medicine, Department of Medicine, Imperial College London, London, SW7 2AZ, UK.,Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.,Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Rowan D Brackston
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Ioly Kotta-Loizou
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Martin Buck
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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6
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Yu H, Chen Z, Wang N, Yu S, Yan Y, Huo YX. Engineering transcription factor BmoR for screening butanol overproducers. Metab Eng 2019; 56:28-38. [PMID: 31449878 DOI: 10.1016/j.ymben.2019.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/09/2019] [Accepted: 08/22/2019] [Indexed: 01/15/2023]
Abstract
The wild-type transcription factors are sensitive to their corresponding signal molecules. Using wild-type transcription factors as biosensors to screen industrial overproducers are generally impractical because of their narrow detection ranges. This study took transcription factor BmoR as an example and aimed to expand the detection range of BmoR for screening alcohols overproducers. Firstly, a BmoR mutation library was established, and the mutations distributed randomly in all predicted functional domains of BmoR. Structure of BmoR-isobutanol complex were modelled, and isobutanol binding sites were confirmed by site-directed mutagenesis. Subsequently, the effects of the mutations on the detection range or output were confirmed in the BmoR mutants. Four combinatorial mutants containing one increased-detection-range mutation and one enhanced-output mutation were constructed. Compared with wild-type BmoR, F276A/E627N BmoR and D333N/E627N BmoR have wider detection ranges (0-100 mM) and relatively high outputs to the isobutanol added quantitatively or produced intracellularly, demonstrating they have potential for screening isobutanol overproduction strains. This work presented an example of engineering the wild-type transcription factors with physiological significance for industrial utilization.
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Affiliation(s)
- Huan Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China; UCLA Institute for Technology Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, 30602, GA, USA
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China; UCLA Institute for Technology Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China.
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7
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Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK. Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. mBio 2018. [PMID: 30042196 DOI: 10.1128/mbio] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic Escherichia coli O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire sap operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene (sspA) was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens.IMPORTANCE Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using E. coli O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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Affiliation(s)
- Lauren A Cowley
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alison S Low
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Neil Perry
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - David L Gally
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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8
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Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK. Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. mBio 2018; 9:e00705-18. [PMID: 30042196 PMCID: PMC6058288 DOI: 10.1128/mbio.00705-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/27/2018] [Indexed: 01/01/2023] Open
Abstract
Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic Escherichia coli O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire sap operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene (sspA) was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens.IMPORTANCE Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using E. coli O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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Affiliation(s)
- Lauren A Cowley
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alison S Low
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Neil Perry
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - David L Gally
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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9
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Crystal structure of Aquifex aeolicus σ N bound to promoter DNA and the structure of σ N-holoenzyme. Proc Natl Acad Sci U S A 2017; 114:E1805-E1814. [PMID: 28223493 DOI: 10.1073/pnas.1619464114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σN fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σN The structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σN that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σN in blocking transcription activity and in maintaining the activator sensitivity of σN.
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10
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Li LF, Fu LJ, Lin JQ, Pang X, Liu XM, Wang R, Wang ZB, Lin JQ, Chen LX. The σ54-dependent two-component system regulating sulfur oxidization (Sox) system in Acidithiobacillus caldus and some chemolithotrophic bacteria. Appl Microbiol Biotechnol 2016; 101:2079-2092. [DOI: 10.1007/s00253-016-8026-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 11/30/2022]
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11
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Brown DR, Sheppard CM, Burchell L, Matthews S, Wigneshweraraj S. The Xp10 Bacteriophage Protein P7 Inhibits Transcription by the Major and Major Variant Forms of the Host RNA Polymerase via a Common Mechanism. J Mol Biol 2016; 428:3911-3919. [PMID: 27515396 PMCID: PMC5053324 DOI: 10.1016/j.jmb.2016.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/24/2023]
Abstract
The σ factor is a functionally obligatory subunit of the bacterial transcription machinery, the RNA polymerase. Bacteriophage-encoded small proteins that either modulate or inhibit the bacterial RNAP to allow the temporal regulation of bacteriophage gene expression often target the activity of the major bacterial σ factor, σ70. Previously, we showed that during Xanthomonas oryzae phage Xp10 infection, the phage protein P7 inhibits the host RNAP by preventing the productive engagement with the promoter and simultaneously displaces the σ70 factor from the RNAP. In this study, we demonstrate that P7 also inhibits the productive engagement of the bacterial RNAP containing the major variant bacterial σ factor, σ54, with its cognate promoter. The results suggest for the first time that the major variant form of the host RNAP can also be targeted by bacteriophage-encoded transcription regulatory proteins. Since the major and major variant σ factor interacting surfaces in the RNAP substantially overlap, but different regions of σ70 and σ54 are used for binding to the RNAP, our results further underscore the importance of the σ–RNAP interface in bacterial RNAP function and regulation and potentially for intervention by antibacterials. Xp10 phage transcription regulator P7 inhibits transcription by RNAP containing σ54. P7 prevents the productive engagement of the σ54–RNAP with the promoter DNA. • P7 disrupts preformed σ54–RNAP-promoter complexes.
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Affiliation(s)
- D R Brown
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK.
| | - C M Sheppard
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
| | - L Burchell
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
| | - S Matthews
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
| | - S Wigneshweraraj
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK.
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12
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Lee JH, Sundin GW, Zhao Y. Identification of the HrpS binding site in the hrpL promoter and effect of the RpoN binding site of HrpS on the regulation of the type III secretion system in Erwinia amylovora. MOLECULAR PLANT PATHOLOGY 2016; 17:691-702. [PMID: 26440313 PMCID: PMC6638409 DOI: 10.1111/mpp.12324] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The type III secretion system (T3SS) is a key pathogenicity factor in Erwinia amylovora. Previous studies have demonstrated that the T3SS in E. amylovora is transcriptionally regulated by an RpoN-HrpL sigma factor cascade, which is activated by the bacterial alarmone (p)ppGpp. In this study, the binding site of HrpS, an enhancer binding protein, was identified for the first time in plant-pathogenic bacteria. Complementation of the hrpL mutant with promoter deletion constructs of the hrpL gene and promoter activity analyses using various lengths of the hrpL promoter fused to a promoter-less green fluorescent protein (gfp) reporter gene delineated the upstream region for HrpS binding. Sequence analysis revealed a dyad symmetry sequence between -138 and -125 nucleotides (TGCAA-N4-TTGCA) as the potential HrpS binding site, which is conserved in the promoter of the hrpL gene among plant enterobacterial pathogens. Results of quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and electrophoresis mobility shift assay coupled with site-directed mutagenesis (SDM) analysis showed that the intact dyad symmetry sequence was essential for HrpS binding, full activation of T3SS gene expression and virulence. In addition, the role of the GAYTGA motif (RpoN binding site) of HrpS in the regulation of T3SS gene expression in E. amylovora was characterized by complementation of the hrpS mutant using mutant variants generated by SDM. Results showed that a Y100F substitution of HrpS complemented the hrpS mutant, whereas Y100A and Y101A substitutions did not. These results suggest that tyrosine (Y) and phenylalanine (F) function interchangeably in the conserved GAYTGA motif of HrpS in E. amylovora.
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Affiliation(s)
- Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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13
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Darbari VC, Lawton E, Lu D, Burrows PC, Wiesler S, Joly N, Zhang N, Zhang X, Buck M. Molecular basis of nucleotide-dependent substrate engagement and remodeling by an AAA+ activator. Nucleic Acids Res 2014; 42:9249-61. [PMID: 25063294 PMCID: PMC4132715 DOI: 10.1093/nar/gku588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Binding and hydrolysis of ATP is universally required by AAA+ proteins to underpin their mechano-chemical work. Here we explore the roles of the ATPase site in an AAA+ transcriptional activator protein, the phage shock protein F (PspF), by specifically altering the Walker B motif sequence required in catalyzing ATP hydrolysis. One such mutant, the E108Q variant, is defective in ATP hydrolysis but fully remodels target transcription complexes, the RNAP-σ54 holoenzyme, in an ATP dependent manner. Structural analysis of the E108Q variant reveals that unlike wild-type protein, which has distinct conformations for E108 residue in the ATP and ADP bound forms, E108Q adapts the same conformation irrespective of nucleotide bound. Our data show that the remodeling activities of E108Q are strongly favored on pre-melted DNA and engagement with RNAP-σ54 using ATP binding can be sufficient to convert the inactive holoenzyme to an active form, while hydrolysis per se is required for nucleic acid remodeling that leads to transcription bubble formation. Furthermore, using linked dimer constructs, we show that RNAP-σ54 engagement by adjacent subunits within a hexamer are required for this protein remodeling activity while DNA remodeling activity can tolerate defective ATP hydrolysis of alternating subunits.
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Affiliation(s)
- Vidya C Darbari
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Ed Lawton
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Duo Lu
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Patricia C Burrows
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Simone Wiesler
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Nicolas Joly
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Nan Zhang
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Xiaodong Zhang
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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14
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Determination of the self-association residues within a homomeric and a heteromeric AAA+ enhancer binding protein. J Mol Biol 2014; 426:1692-710. [PMID: 24434682 DOI: 10.1016/j.jmb.2014.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/17/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
The σ(54)-dependent transcription in bacteria requires specific activator proteins, bacterial enhancer binding protein (bEBP), members of the AAA+ (ATPases Associated with various cellular Activities) protein family. The bEBPs usually form oligomers in order to hydrolyze ATP and make open promoter complexes. The bEBP formed by HrpR and HrpS activates transcription from the σ(54)-dependent hrpL promoter responsible for triggering the Type Three Secretion System in Pseudomonas syringae pathovars. Unlike other bEBPs that usually act as homohexamers, HrpR and HrpS operate as a highly co-dependent heterohexameric complex. To understand the organization of the HrpRS complex and the HrpR and HrpS strict co-dependence, we have analyzed the interface between subunits using the random and directed mutagenesis and available crystal structures of several closely related bEBPs. We identified key residues required for the self-association of HrpR (D32, E202 and K235) with HrpS (D32, E200 and K233), showed that the HrpR D32 and HrpS K233 residues form interacting pairs directly involved in an HrpR-HrpS association and that the change in side-chain length at position 233 in HrpS affects self-association and interaction with the HrpR and demonstrated that the HrpS D32, E200 and K233 are not involved in negative regulation imposed by HrpV. We established that the equivalent residues K30, E200 and E234 in a homo-oligomeric bEBP, PspF, are required for the subunit communication and formation of an oligomeric lock that cooperates with the ATP γ-phosphate sensing PspF residue R227, providing insights into their roles in the heteromeric HrpRS co-complex.
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15
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Zhang N, Gordiyenko Y, Joly N, Lawton E, Robinson CV, Buck M. Subunit dynamics and nucleotide-dependent asymmetry of an AAA(+) transcription complex. J Mol Biol 2013; 426:71-83. [PMID: 24055699 DOI: 10.1016/j.jmb.2013.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/21/2013] [Accepted: 08/24/2013] [Indexed: 01/22/2023]
Abstract
Bacterial enhancer binding proteins (bEBPs) are transcription activators that belong to the AAA(+) protein family. They form higher-order self-assemblies to regulate transcription initiation at stress response and pathogenic promoters. The precise mechanism by which these ATPases utilize ATP binding and hydrolysis energy to remodel their substrates remains unclear. Here we employed mass spectrometry of intact complexes to investigate subunit dynamics and nucleotide occupancy of the AAA(+) domain of one well-studied bEBP in complex with its substrate, the σ(54) subunit of RNA polymerase. Our results demonstrate that the free AAA(+) domain undergoes significant changes in oligomeric states and nucleotide occupancy upon σ(54) binding. Such changes likely correlate with one transition state of ATP and are associated with an open spiral ring formation that is vital for asymmetric subunit function and interface communication. We confirmed that the asymmetric subunit functionality persists for open promoter complex formation using single-chain forms of bEBP lacking the full complement of intact ATP hydrolysis sites. Outcomes reconcile low- and high-resolution structures and yield a partial sequential ATP hydrolysis model for bEBPs.
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Affiliation(s)
- Nan Zhang
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
| | - Yuliya Gordiyenko
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Nicolas Joly
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Batiment Buffon, 15 rue Helene Brion, 75205 Paris Cedex 13, France
| | - Edward Lawton
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Martin Buck
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
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16
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A key hydrophobic patch identified in an AAA⁺ protein essential for its in trans inhibitory regulation. J Mol Biol 2013; 425:2656-69. [PMID: 23659791 PMCID: PMC3791423 DOI: 10.1016/j.jmb.2013.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/11/2013] [Accepted: 04/20/2013] [Indexed: 11/22/2022]
Abstract
Bacterial enhancer binding proteins (bEBPs) are a subclass of the AAA+ (ATPases Associated with various cellular Activities) protein family. They are responsible for σ54-dependent transcription activation during infection and function under many stressful growth conditions. The majority of bEBPs are regulated in their formation of ring-shaped hexameric self-assemblies via an amino-terminal domain through its phosphorylation or ligand binding. In contrast, the Escherichia coli phage shock protein F (PspF) is negatively regulated in trans by phage shock protein A (PspA). Up to six PspA subunits suppress PspF hexamer action. Here, we present biochemical evidence that PspA engages across the side of a PspF hexameric ring. We identify three key binding determinants located in a surface-exposed ‘W56 loop’ of PspF, which form a tightly packed hydrophobic cluster, the ‘YLW’ patch. We demonstrate the profound impact of the PspF W56 loop residues on ATP hydrolysis, the σ54 binding loop 1, and the self-association interface. We infer from single-chain studies that for complete PspF inhibition to occur, more than three PspA subunits need to bind a PspF hexamer with at least two binding to adjacent PspF subunits. By structural modelling, we propose that PspA binds to PspF via its first two helical domains. After PspF binding-induced conformational changes, PspA may then share structural similarities with a bEBP regulatory domain. What is the mechanism of in trans inhibition of oligomeric self-assemblies? Inhibitor initially docks on the AAA+ domain at a hydrophobic patch. Consequently, ATPase and self-association of the AAA+ domain are altered. Inhibitor’s structure mimics the evolutionarily divergent in cis regulatory domain. In trans inhibition of oligomeric AAA+ domains requires multiple contacts.
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17
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Sabbatini M, Vezzoli A, Milani M, Bertoni G. Evidence for self-association of the alternative sigma factor σ 54. FEBS J 2013; 280:1371-8. [DOI: 10.1111/febs.12129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 12/21/2012] [Accepted: 01/11/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Massimo Sabbatini
- Department of Life Sciences; Università degli Studi di Milano; Milan; Italy
| | - Alessandro Vezzoli
- Department of Life Sciences; Università degli Studi di Milano; Milan; Italy
| | | | - Giovanni Bertoni
- Department of Life Sciences; Università degli Studi di Milano; Milan; Italy
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18
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The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription. Microbiol Mol Biol Rev 2013; 76:497-529. [PMID: 22933558 DOI: 10.1128/mmbr.00006-12] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial enhancer binding proteins (bEBPs) are transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ(54). We present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. The review is structured by introducing each of the three domains in turn: the central catalytic domain, the N-terminal regulatory domain, and the C-terminal DNA binding domain. The role of the central catalytic domain is presented with particular reference to (i) oligomerization, (ii) ATP hydrolysis, and (iii) the key GAFTGA motif that contacts σ(54) for remodeling. Each of these functions forms a potential target of the signal-sensing N-terminal regulatory domain, which can act either positively or negatively to control the activation of σ(54)-dependent transcription. Finally, we focus on the DNA binding function of the C-terminal domain and the enhancer sites to which it binds. Particular attention is paid to the importance of σ(54) to the bacterial cell and its unique role in regulating transcription.
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19
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Zhang N, Joly N, Buck M. A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements. Nucleic Acids Res 2012; 40:9139-52. [PMID: 22772990 PMCID: PMC3467059 DOI: 10.1093/nar/gks661] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Initiation of σ(54)-dependent transcription requires assistance to melt DNA at the promoter site but is impeded by numerous protein-protein and nucleo-protein interactions. To alleviate these inhibitory interactions, hexameric bacterial enhancer binding proteins (bEBP), a subset of the ATPases associated with various cellular activities (AAA+) protein family, are required to remodel the transcription complex using energy derived from ATP hydrolysis. However, neither the process of energy conversion nor the internal architecture of the closed promoter complex is well understood. Escherichia coli Phage shock protein F (PspF), a well-studied bEBP, contains a surface-exposed loop 1 (L1). L1 is key to the energy coupling process by interacting with Region I of σ(54) (σ(54)(RI)) in a nucleotide dependent manner. Our analyses uncover new levels of complexity in the engagement of a multimeric bEBP with a basal transcription complex via several L1s. The mechanistic implications for these multivalent L1 interactions are elaborated in the light of available structures for the bEBP and its target complexes.
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Affiliation(s)
- Nan Zhang
- Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
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20
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Joly N, Zhang N, Buck M, Zhang X. Coupling AAA protein function to regulated gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:108-16. [PMID: 21906631 DOI: 10.1016/j.bbamcr.2011.08.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/19/2011] [Accepted: 08/22/2011] [Indexed: 10/17/2022]
Abstract
AAA proteins (ATPases Associated with various cellular Activities) are involved in almost all essential cellular processes ranging from DNA replication, transcription regulation to protein degradation. One class of AAA proteins has evolved to adapt to the specific task of coupling ATPase activity to activating transcription. These upstream promoter DNA bound AAA activator proteins contact their target substrate, the σ(54)-RNA polymerase holoenzyme, through DNA looping, reminiscent of the eukaryotic enhance binding proteins. These specialised macromolecular machines remodel their substrates through ATP hydrolysis that ultimately leads to transcriptional activation. We will discuss how AAA proteins are specialised for this specific task.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Imperial College London, London, SW7 2AZ, UK
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21
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Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification. Biochem Soc Trans 2011; 39:289-93. [PMID: 21265790 DOI: 10.1042/bst0390289] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A flavorubredoxin and its associated oxidoreductase (encoded by norV and norW respectively) detoxify NO (nitric oxide) to form N2O (nitrous oxide) under anaerobic conditions in Escherichia coli. Transcription of the norVW genes is activated in response to NO by the σ54-dependent regulator and dedicated NO sensor, NorR, a member of the bacterial enhancer-binding protein family. In the absence of NO, the catalytic activity of the central ATPase domain of NorR is repressed by the N-terminal regulatory domain that contains a non-haem iron centre. Binding of NO to this centre results in the formation of a mononitrosyl iron species, enabling the activation of ATPase activity. Our studies suggest that the highly conserved GAFTGA loop in the ATPase domain, which engages with the alternative σ factor σ54 to activate transcription, is a target for intramolecular repression by the regulatory domain. Binding of NorR to three conserved enhancer sites upstream of the norVW promoter is essential for transcriptional activation and promotes the formation of a stable higher-order NorR nucleoprotein complex. We propose that enhancer-driven assembly of this oligomeric complex, in which NorR apparently forms a DNA-bound hexamer in the absence of NO, provides a 'poised' system for transcriptional activation that can respond rapidly to nitrosative stress.
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22
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Bush M, Ghosh T, Tucker N, Zhang X, Dixon R. Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR. Mol Microbiol 2011; 77:1278-88. [PMID: 20624215 PMCID: PMC2941729 DOI: 10.1111/j.1365-2958.2010.07290.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacterial enhancer binding proteins (bEBPs) are specialized transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ54. Transcriptional activation by the NorR bEBP is controlled by a regulatory GAF domain that represses the ATPase activity of the central AAA+ domain in the absence of nitric oxide. Here, we investigate the mechanism of interdomain repression in NorR by characterizing substitutions in the AAA+ domain that bypass repression by the regulatory domain. Most of these substitutions are located in the vicinity of the surface-exposed loops that engage σ54 during the ATP hydrolysis cycle or in the highly conserved GAFTGA motif that directly contacts σ54. Biochemical studies suggest that the bypass mutations in the GAFTGA loop do not influence the DNA binding properties of NorR or the assembly of higher order oligomers in the presence of enhancer DNA, and as expected these variants retain the ability to activate open complex formation in vitro. We identify a crucial arginine residue in the GAF domain that is essential for interdomain repression and demonstrate that hydrophobic substitutions at this position suppress the bypass phenotype of the GAFTGA substitutions. These observations suggest a novel mechanism for negative regulation in bEBPs in which the GAF domain targets the σ54-interaction surface to prevent access of the AAA+ domain to the sigma factor.
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Affiliation(s)
- Matthew Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney NR4 7UH, UK
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23
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Joly N, Buck M. Single chain forms of the enhancer binding protein PspF provide insights into geometric requirements for gene activation. J Biol Chem 2011; 286:12734-42. [PMID: 21300807 DOI: 10.1074/jbc.m110.203554] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Genetic information in the DNA is accessed by the molecular machine RNA polymerase following a highly conserved process, invariably involving the transition between double-stranded and single-stranded DNA states. In the case of the bacterial enhancer-dependent RNA polymerase (which is essential for adaptive responses and bacterial pathogenesis), the DNA melting event depends on specialized hexameric AAA+ ATPase activators. Involvement of such factors in transcription was demonstrated 25 years ago, but why these activators need to be hexameric, whether all the subunits operate identically, what is the contribution of each of the six subunits within the hexamer (structural, functional, or both), and how many active subunits are required for transcription activation remain open questions. Using engineered single-chain polypeptides covalently linking two or three subunits of the activator (allowing the subunit distribution within a hexamer to be fixed), we now show that (i) individual subunits have differential contributions to the activities of the oligomer and (ii) only a fraction of the subunits within the hexameric ATPase is directly required for gene activation. We establish that nucleotide-dependent coordination across three subunits of the hexameric bacterial enhancer binding proteins (bEBPs) is necessary for engagement and remodeling of the closed complex (RPc). Outcomes revealed features of bEBP, distinguishing their mode of action from fully processive AAA+ proteins or from simple bimodal switches. We now propose that the hexamer functions with asymmetric organization, potentially involving a split planar (open ring) or spiral character.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
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24
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Jovanovic M, James EH, Burrows PC, Rego FGM, Buck M, Schumacher J. Regulation of the co-evolved HrpR and HrpS AAA+ proteins required for Pseudomonas syringae pathogenicity. Nat Commun 2011; 2:177. [PMID: 21285955 PMCID: PMC3105312 DOI: 10.1038/ncomms1177] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 01/05/2011] [Indexed: 11/26/2022] Open
Abstract
The bacterial AAA+ enhancer-binding proteins (EBPs) HrpR and HrpS (HrpRS) of Pseudomonas syringae (Ps) activate σ54-dependent transcription at the hrpL promoter; triggering type-three secretion system-mediated pathogenicity. In contrast with singly acting EBPs, the evolution of the strictly co-operative HrpRS pair raises questions of potential benefits and mechanistic differences this transcription control system offers. Here, we show distinct properties of HrpR and HrpS variants, indicating functional specialization of these non-redundant, tandemly arranged paralogues. Activities of HrpR, HrpS and their control proteins HrpV and HrpG from Ps pv. tomato DC3000 in vitro establish that HrpRS forms a transcriptionally active hetero-hexamer, that there is a direct negative regulatory role for HrpV through specific binding to HrpS and that HrpG suppresses HrpV. The distinct HrpR and HrpS functionalities suggest how partial paralogue degeneration has potentially led to a novel control mechanism for EBPs and indicate subunit-specific roles for EBPs in σ54-RNA polymerase activation. HrpR and HrpS enhancer-binding proteins of Pseudomonas syringae activate σ54-dependent transcription of the HrpL promoter and are required for type-three secretion pathogenicity. Here, the authors demonstrate that, despite being co-regulated, HrpR and HrpS each have distinct functions for activating σ54.
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Affiliation(s)
- Milija Jovanovic
- Division of Biology, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
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25
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Joly N, Engl C, Jovanovic G, Huvet M, Toni T, Sheng X, Stumpf MPH, Buck M. Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology. FEMS Microbiol Rev 2010; 34:797-827. [PMID: 20636484 DOI: 10.1111/j.1574-6976.2010.00240.x] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The bacterial phage shock protein (Psp) response functions to help cells manage the impacts of agents impairing cell membrane function. The system has relevance to biotechnology and to medicine. Originally discovered in Escherichia coli, Psp proteins and homologues are found in Gram-positive and Gram-negative bacteria, in archaea and in plants. Study of the E. coli and Yersinia enterocolitica Psp systems provides insights into how membrane-associated sensory Psp proteins might perceive membrane stress, signal to the transcription apparatus and use an ATP-hydrolysing transcription activator to produce effector proteins to overcome the stress. Progress in understanding the mechanism of signal transduction by the membrane-bound Psp proteins, regulation of the psp gene-specific transcription activator and the cell biology of the system is presented and discussed. Many features of the action of the Psp system appear to be dominated by states of self-association of the master effector, PspA, and the transcription activator, PspF, alongside a signalling pathway that displays strong conditionality in its requirement.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Imperial College London, South Kensington, London, UK
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26
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Abstract
Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP) enzymes and is highly regulated through the action of gene regulatory complexes. Important mechanistic insights have been gained from structural studies on multisubunit RNAP from bacteria, yeast and archaea, although the initiation process that involves the conversion of the inactive transcription complex to an active one has yet to be fully understood. RNAPs are unambiguously closely related in structure and function across all kingdoms of life and have conserved mechanisms. In bacteria, sigma (sigma) factors direct RNAP to specific promoter sites and the RNAP/sigma holoenzyme can either form a stable closed complex that is incompetent for transcription (as in the case of sigma(54)) or can spontaneously proceed to an open complex that is competent for transcription (as in the case of sigma(70)). The conversion of the RNAP/sigma(54) closed complex to an open complex requires ATP hydrolysis by enhancer-binding proteins, hence providing an ideal model system for studying the initiation process biochemically and structurally. In this review, we present recent structural studies of the two major bacterial RNAP holoenzymes and focus on mechanistic advances in the transcription initiation process via enhancer-binding proteins.
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Affiliation(s)
- Tamaswati Ghosh
- Department of Life Sciences, Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, London, UK
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27
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A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase. Proc Natl Acad Sci U S A 2010; 107:9376-81. [PMID: 20439713 DOI: 10.1073/pnas.1001188107] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP hydrolysis-dependent molecular machines and motors often drive regulated conformational transformations in cell signaling and gene regulation complexes. Conformational reorganization of a gene regulation complex containing the major variant form of bacterial RNA polymerase (RNAP), Esigma(54), requires engagement with its cognate ATP-hydrolyzing activator protein. Importantly, this activated RNAP is essential for a number of adaptive responses, including those required for bacterial pathogenesis. Here we characterize the initial encounter between the enhancer-dependent Esigma(54) and its cognate activator AAA+ ATPase protein, before ADP+P(i) formation, using a small primed RNA (spRNA) synthesis assay. The results show that in a prehydrolysis state, sufficient activator-dependent rearrangements in Esigma(54) have occurred to allow engagement of the RNAP active site with single-stranded promoter DNA to support spRNA synthesis, but not to melt the promoter DNA. This catalytically competent transcription intermediate has similarity with the open promoter complex, in that the RNAP dynamics required for DNA scrunching should be occurring. Significantly, this work highlights that prehydrolysis states of ATPases are functionally important in the molecular transformations they drive.
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28
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Joly N, Buck M. Engineered interfaces of an AAA+ ATPase reveal a new nucleotide-dependent coordination mechanism. J Biol Chem 2010; 285:15178-15186. [PMID: 20197281 DOI: 10.1074/jbc.m110.103150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homohexameric ring AAA(+) ATPases are found in all kingdoms of life and are involved in all cellular processes. To accommodate the large spectrum of substrates, the conserved AAA(+) core has become specialized through the insertion of specific substrate-binding motifs. Given their critical roles in cellular function, understanding the nucleotide-driven mechanisms of action is of wide importance. For one type of member AAA(+) protein (phage shock protein F, PspF), we identified and established the functional significance of strategically placed arginine and glutamate residues that form interacting pairs in response to nucleotide binding. We show that these interactions are critical for "cis" and "trans" subunit communication, which support coordination between subunits for nucleotide-dependent substrate remodeling. Using an allele-specific suppression approach for ATPase and substrate remodeling, we demonstrate that the targeted residues directly interact and are unlikely to make any other pairwise critical interactions. We then propose a mechanistic rationale by which the nucleotide-bound state of adjacent subunits can be sensed without direct involvement of R-finger residues. As the structural AAA(+) core is conserved, we propose that the functional networks established here could serve as a template to identify similar residue pairs in other AAA(+) proteins.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Martin Buck
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom.
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29
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Koechler S, Cleiss-Arnold J, Proux C, Sismeiro O, Dillies MA, Goulhen-Chollet F, Hommais F, Lièvremont D, Arsène-Ploetze F, Coppée JY, Bertin PN. Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans. BMC Microbiol 2010; 10:53. [PMID: 20167112 PMCID: PMC2848651 DOI: 10.1186/1471-2180-10-53] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism. RESULTS In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (sigma54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 sigma54-dependent promoter motif was identified upstream of aoxAB coding sequences. CONCLUSION These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.
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Affiliation(s)
- Sandrine Koechler
- UMR7156 Génétique Moléculaire, Génomique et Microbiologie, CNRS Université de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France
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30
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Zhang N, Joly N, Burrows PC, Jovanovic M, Wigneshweraraj SR, Buck M. The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins. Nucleic Acids Res 2009; 37:5981-92. [PMID: 19692583 PMCID: PMC2764435 DOI: 10.1093/nar/gkp658] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
σ54-dependent transcription requires activation by bacterial enhancer binding proteins (bEBPs). bEBPs are members of the AAA+ (ATPases associated with various cellular activities) protein family and typically form hexameric structures that are crucial for their ATPase activity. The precise mechanism by which the energy derived from ATP hydrolysis is coupled to biological output has several unknowns. Here we use Escherichia coli PspF, a model bEBP involved in the transcription of stress response genes (psp operon), to study determinants of its contact features with the closed promoter complex. We demonstrate that substitution of a highly conserved phenylalanine (F85) residue within the L1 loop GAFTGA motif affects (i) the ATP hydrolysis rate of PspF, demonstrating the link between L1 and the nucleotide binding pocket; (ii) the internal organization of the hexameric ring; and (iii) σ54 interactions. Importantly, we provide evidence for a close relationship between F85 and the −12 DNA fork junction structure, which may contribute to key interactions during the energy coupling step and the subsequent remodelling of the Eσ54 closed complex. The functionality of F85 is distinct from that of other GAFTGA residues, especially T86 where in contrast to F85 a clean uncoupling phenotype is observed.
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Affiliation(s)
- Nan Zhang
- Division of Biology, Sir Alexander Fleming Building, and Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College London, London SW7 2AZ, UK
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31
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Burrows PC, Joly N, Nixon BT, Buck M. Comparative analysis of activator-Esigma54 complexes formed with nucleotide-metal fluoride analogues. Nucleic Acids Res 2009; 37:5138-50. [PMID: 19553192 PMCID: PMC2731916 DOI: 10.1093/nar/gkp541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) containing the major variant σ54 factor forms open promoter complexes in a reaction in which specialized activator proteins hydrolyse ATP. Here we probe binding interactions between σ54-RNAP (Eσ54) and the ATPases associated with various cellular activities (AAA+) domain of the Escherichia coli activator protein, PspF, using nucleotide-metal fluoride (BeF and AlF) analogues representing ground and transition states of ATP, which allow complexes (that are otherwise too transient with ATP) to be captured. We show that the organization and functionality of the ADP–BeF- and ADP–AlF-dependent complexes greatly overlap. Our data support an activation pathway in which the initial ATP-dependent binding of the activator to the Eσ54 closed complex results in the re-organization of Eσ54 with respect to the transcription start-site. However, the nucleotide-dependent binding interactions between the activator and the Eσ54 closed complex are in themselves insufficient for forming open promoter complexes when linear double-stranded DNA is present in the initial closed complex.
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Affiliation(s)
- Patricia C Burrows
- Department of Life Sciences, Division of Biology, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
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32
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Xiao Y, Wigneshweraraj SR, Weinzierl R, Wang YP, Buck M. Construction and functional analyses of a comprehensive sigma54 site-directed mutant library using alanine-cysteine mutagenesis. Nucleic Acids Res 2009; 37:4482-97. [PMID: 19474350 PMCID: PMC2715252 DOI: 10.1093/nar/gkp419] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction and open complex formation. To systematically define sigma(54) residues that contribute to each of these functions and to generate a resource for site specific protein labeling, a complete mutant library of sigma(54) was constructed by alanine-cysteine scanning mutagenesis. Amino acid residues from 3 to 476 of Cys(-)sigma(54) were systematically mutated to alanine and cysteine in groups of two adjacent residues at a time. The influences of each substitution pair upon the functions of sigma(54) were analyzed in vivo and in vitro and the functions of many residues were revealed for the first time. Increased sigma(54) isomerization activity seldom corresponded with an increased transcription activity of the holoenzyme, suggesting the steps after sigma(54) isomerization, likely to be changes in core RNAP structure, are also strictly regulated or rate limiting to open complex formation. A linkage between core RNAP-binding activity and activator responsiveness indicates that the sigma(54)-core RNAP interface changes upon activation.
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Affiliation(s)
- Yan Xiao
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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33
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Burrows PC, Schumacher J, Amartey S, Ghosh T, Burgis TA, Zhang X, Nixon BT, Buck M. Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein. Mol Microbiol 2009; 73:519-33. [PMID: 19486295 PMCID: PMC2745333 DOI: 10.1111/j.1365-2958.2009.06744.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre-sensor I insertion (pre-SIi) AAA+ superclade. In the bacterial σ54-dependent enhancer binding protein phage shock protein F (PspF) the pre-SIi loop adopts different conformations depending on the nucleotide-bound state. Single amino acid substitutions within the dynamic pre-SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site-specific protein–DNA proximity assay to measure the contribution of the pre-SIi loop in σ54-dependent transcription and demonstrate that the pre-SIi loop is a major structural feature mediating nucleotide state-dependent differential engagement with Eσ54. We suggest that much, if not all, of the action of the pre-SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre-SIi variant and in accordance with the high covariance between some pre-SIi residues and distinct residues outside the pre-SIi sequence.
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Affiliation(s)
- Patricia C Burrows
- Department of Life Sciences, Division of Biology, Imperial College London, London, UK
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34
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Burrows PC, Joly N, Cannon WV, Cámara BP, Rappas M, Zhang X, Dawes K, Nixon BT, Wigneshweraraj SR, Buck M. Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting. J Mol Biol 2009; 387:306-19. [PMID: 19356588 DOI: 10.1016/j.jmb.2009.01.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 01/24/2009] [Accepted: 01/26/2009] [Indexed: 11/18/2022]
Abstract
ATP-driven remodelling of initial RNA polymerase (RNAP) promoter complexes occurs as a major post recruitment strategy used to control gene expression. Using a model-enhancer-dependent bacterial system (sigma54-RNAP, Esigma54) and a slowly hydrolysed ATP analogue (ATPgammaS), we provide evidence for a nucleotide-dependent temporal pathway leading to DNA melting involving a small set of sigma54-DNA conformational states. We demonstrate that the ATP hydrolysis-dependent remodelling of Esigma54 occurs in at least two distinct temporal steps. The first detected remodelling phase results in changes in the interactions between the promoter specificity sigma54 factor and the promoter DNA. The second detected remodelling phase causes changes in the relationship between the promoter DNA and the core RNAP catalytic beta/beta' subunits, correlating with the loading of template DNA into the catalytic cleft of RNAP. It would appear that, for Esigma54 promoters, loading of template DNA within the catalytic cleft of RNAP is dependent on fast ATP hydrolysis steps that trigger changes in the beta' jaw domain, thereby allowing acquisition of the open complex status.
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Affiliation(s)
- Patricia C Burrows
- Division of Biology, Department of Life Sciences, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
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35
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Organization of an activator-bound RNA polymerase holoenzyme. Mol Cell 2008; 32:337-46. [PMID: 18995832 PMCID: PMC2680985 DOI: 10.1016/j.molcel.2008.09.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 05/30/2008] [Accepted: 09/05/2008] [Indexed: 12/31/2022]
Abstract
Transcription initiation involves the conversion from closed promoter complexes, comprising RNA polymerase (RNAP) and double-stranded promoter DNA, to open complexes, in which the enzyme is able to access the DNA template in a single-stranded form. The complex between bacterial RNAP and its major variant sigma factor σ54 remains as a closed complex until ATP hydrolysis-dependent remodeling by activator proteins occurs. This remodeling facilitates DNA melting and allows the transition to the open complex. Here we present cryoelectron microscopy reconstructions of bacterial RNAP in complex with σ54 alone, and of RNAP-σ54 with an AAA+ activator. Together with photo-crosslinking data that establish the location of promoter DNA within the complexes, we explain why the RNAP-σ54 closed complex is unable to access the DNA template and propose how the structural changes induced by activator binding can initiate conformational changes that ultimately result in formation of the open complex.
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36
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Schumacher J, Joly N, Claeys-Bouuaert IL, Aziz SA, Rappas M, Zhang X, Buck M. Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA+ ring ATPase. J Mol Biol 2008; 381:1-12. [PMID: 18599077 DOI: 10.1016/j.jmb.2008.05.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 05/28/2008] [Accepted: 05/29/2008] [Indexed: 11/16/2022]
Abstract
AAA(+) proteins are ubiquitous mechanochemical ATPases that use energy from ATP hydrolysis to remodel their versatile substrates. The AAA(+) characteristic hexameric ring assemblies raise important questions about if and how six often identical subunits coordinate hydrolysis and associated motions. The PspF AAA(+) domain, PspF(1-275), remodels the bacterial sigma(54)-RNA polymerase to activate transcription. Analysis of ATP substrate inhibition kinetics on ATP hydrolysis in hexameric PspF(1-275) indicates negative homotropic effects between subunits. Functional determinants required for allosteric control identify: (i) an important link between the ATP bound ribose moiety and the SensorII motif that would allow nucleotide-dependent *-helical */beta subdomain dynamics; and (ii) establishes a novel regulatory role for the SensorII helix in PspF, which may apply to other AAA(+) proteins. Consistent with functional data, homotropic control appears to depend on nucleotide state-dependent subdomain angles imposing dynamic symmetry constraints in the AAA(+) ring. Homotropic coordination is functionally important to remodel the sigma(54) promoter. We propose a structural symmetry-based model for homotropic control in the AAA(+) characteristic ring architecture.
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Affiliation(s)
- Jörg Schumacher
- Division of Biology, Imperial College London, London SW7 2AZ, UK.
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37
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Joly N, Burrows PC, Buck M. An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation. J Biol Chem 2008; 283:13725-35. [PMID: 18326037 DOI: 10.1074/jbc.m800801200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AAA+ proteins (ATPases associated with various cellular activities) contribute to many cellular processes and typically function as higher order oligomers permitting the coordination of nucleotide hydrolysis for functional output, which leads to substrate remodeling. The precise mechanisms that enable the relay of nucleotide hydrolysis to their specific functional outputs are largely unknown. Here we use PspF, a specialized AAA+ protein required for enhancer-dependent transcription activation in Escherichia coli, as a model system to address this question. We demonstrate that a conserved asparagine is involved in internal organization of the oligomeric ring, regulation of ATPase activity by "trans" factors, and optimizing substrate remodeling. We provide evidence that the spatial relationship between the asparagine residue and the Walker B motif is one key element in the conformational signaling pathway that leads to substrate remodeling. Such functional organization most likely applies to other AAA+ proteins, including Ltag (simian virus 40), Rep40 (Adeno-associated virus-2), and p97 (Mus musculus) in which the asparagine to Walker B motif relationship is conserved.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
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38
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Wigneshweraraj S, Bose D, Burrows PC, Joly N, Schumacher J, Rappas M, Pape T, Zhang X, Stockley P, Severinov K, Buck M. Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor. Mol Microbiol 2008; 68:538-46. [PMID: 18331472 DOI: 10.1111/j.1365-2958.2008.06181.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial sigma (sigma) factors confer gene specificity upon the RNA polymerase, the central enzyme that catalyses gene transcription. The binding of the alternative sigma factor sigma(54) confers upon the RNA polymerase special functional and regulatory properties, making it suited for control of several major adaptive responses. Here, we summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery.
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Affiliation(s)
- Sivaramesh Wigneshweraraj
- Department of Microbiology, Division of Investigative Sciences, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK.
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39
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Abstract
bEBPs (bacterial enhancer-binding proteins) are AAA+ (ATPase associated with various cellular activities) transcription activators that activate gene transcription through a specific bacterial sigma factor, sigma(54). Sigma(54)-RNAP (RNA polymerase) binds to promoter DNA sites and forms a stable closed complex, unable to proceed to transcription. The closed complex must be remodelled using energy from ATP hydrolysis provided by bEBPs to melt DNA and initiate transcription. Recently, large amounts of structural and biochemical data have produced insights into how ATP hydrolysis within the active site of bEBPs is coupled to the re-modelling of the closed complex. In the present article, we review some of the key nucleotides, mutations and techniques used and how they have contributed towards our understanding of the function of bEBPs.
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40
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Jordan S, Rietkötter E, Strauch MA, Kalamorz F, Butcher BG, Helmann JD, Mascher T. LiaRS-dependent gene expression is embedded in transition state regulation in Bacillus subtilis. MICROBIOLOGY-SGM 2007; 153:2530-2540. [PMID: 17660417 DOI: 10.1099/mic.0.2007/006817-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Maintaining envelope integrity is crucial for the survival of any bacterial cell, especially those living in a complex and ever-changing habitat such as the soil ecosystem. The LiaRS two-component system is part of the regulatory network orchestrating the cell-envelope stress response in Bacillus subtilis. It responds to perturbations of the cell envelope, especially the presence of antibiotics that interfere with the lipid II cycle, such as bacitracin or vancomycin. LiaRS-dependent regulation is strictly repressed by the membrane protein LiaF in the absence of inducing conditions. Here, it is shown that the LiaR-dependent liaI promoter is induced at the onset of stationary phase without addition of exogenous stresses. Its activity is embedded in the complex regulatory cascade governing adaptation at the onset of stationary phase. The liaI promoter is directly repressed by the transition state regulator AbrB and responds indirectly to the activity of Spo0A, the master regulator of sporulation. The activity of the liaI promoter is therefore tightly regulated by at least five regulators to ensure an appropriate level of liaIH expression.
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Affiliation(s)
- Sina Jordan
- Department of General Microbiology, Georg-August-University, 37077 Göttingen, Germany
| | - Eva Rietkötter
- Department of General Microbiology, Georg-August-University, 37077 Göttingen, Germany
| | - Mark A Strauch
- Department of Biomedical Sciences, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Falk Kalamorz
- Department of General Microbiology, Georg-August-University, 37077 Göttingen, Germany
| | - Bronwyn G Butcher
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Thorsten Mascher
- Department of General Microbiology, Georg-August-University, 37077 Göttingen, Germany
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41
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Joly N, Rappas M, Buck M, Zhang X. Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride. J Mol Biol 2007; 375:1206-11. [PMID: 18082766 DOI: 10.1016/j.jmb.2007.11.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/14/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
Mechanochemical proteins rely on ATP hydrolysis to establish the different functional states required for their biological output. Studying the transient functional intermediate states these proteins adopt as they progress through the ATP hydrolysis cycle is key to understanding the molecular basis of their mechanism. Many of these intermediates have been successfully 'trapped' and functionally characterised using ATP analogues. Here, we present a new nucleotide analogue, AMP-AlF(x), which traps PspF, a bacterial enhancer binding protein, in a stable complex with the sigma(54)-RNA polymerase holoenzyme. The crystal structure of AMP-AlF(x)*PspF(1-275) provides new information on protein-nucleotide interactions and suggests that the beta and gamma phosphates are more important than the alpha phosphate in terms of sensing nucleotide bound states. In addition, functional data obtained with AMP-AlF(x) establish distinct roles for the conserved catalytic AAA(+) (ATPases associated with various cellular activities) residues, suggesting that AMP-AlF(x) is a powerful new tool to study AAA(+) protein family members and, more generally, Walker motif ATPases.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
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42
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Protein-DNA interactions that govern AAA+ activator-dependent bacterial transcription initiation. J Mol Biol 2007; 375:43-58. [PMID: 18005983 DOI: 10.1016/j.jmb.2007.10.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 10/04/2007] [Accepted: 10/04/2007] [Indexed: 11/24/2022]
Abstract
Transcriptional control at the promoter melting step is not yet well understood. In this study, a site-directed photo-cross-linking method was used to systematically analyse component protein-DNA interactions that govern promoter melting by the enhancer-dependent Escherichia coli RNA polymerase (RNAP) containing the sigma(54) promoter specificity factor (E sigma(54)) at a single base pair resolution in three functional states. The sigma(54)-factor imposes tight control upon the RNAP by creating a regulatory switch where promoter melting nucleates, approximately 12 bp upstream of the transcription start site. Promoter melting by E sigma(54) is only triggered upon remodelling of this regulatory switch by a specialised activator protein in an ATP-hydrolysing reaction. We demonstrate that prior to DNA melting, only the sigma(54)-factor directly interacts with the promoter in the regulatory switch within the initial closed E sigma(54)-promoter complex and one intermediate E sigma(54)-promoter complex. We establish that activator-induced conformational rearrangements in the regulatory switch are a prerequisite to allow the promoter to enter the catalytic cleft of the RNAP and hence establish the transcriptionally competent open complex, where full promoter melting occurs. These results significantly advance our current understanding of the structural transitions occurring at bacterial promoters, where regulation occurs at the DNA melting step.
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43
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Joly N, Rappas M, Wigneshweraraj SR, Zhang X, Buck M. Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein. Mol Microbiol 2007; 66:583-95. [PMID: 17883390 DOI: 10.1111/j.1365-2958.2007.05901.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial enhancer binding proteins (bEBP) are members of the AAA+ protein family and have a highly conserved 'DE' Walker B motif thought to be involved in the catalytic function of the protein with an active role in nucleotide hydrolysis. Based on detailed structural data, we analysed the functionality of the conserved 'DE' Walker B motif of a bEBP model, phage shock protein F (PspF), to investigate the role of these residues in the sigma(54)-dependent transcription activation process. We established their role in the regulation of PspF self-association and in the relay of the ATPase activity to the remodelling of an RNA polymerase.promoter complex (Esigma(54).DNA). Specific substitutions of the conserved glutamate (E) allowed the identification of new functional ATP.bEBP.Esigma(54) complexes which are stable and transcriptionally competent, providing a new tool to study the initial events of the sigma(54)-dependent transcription activation process. In addition, we show the importance of this glutamate residue in sigma(54).DNA conformation sensing, permitting the identification of new intermediate stages within the transcription activation pathway.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
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44
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Buck M, Bose D, Burrows P, Cannon W, Joly N, Pape T, Rappas M, Schumacher J, Wigneshweraraj S, Zhang X. A second paradigm for gene activation in bacteria. Biochem Soc Trans 2007; 34:1067-71. [PMID: 17073752 DOI: 10.1042/bst0341067] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Control of gene expression is key to development and adaptation. Using purified transcription components from bacteria, we employ structural and functional studies in an integrative manner to elaborate a detailed description of an obligatory step, the accessing of the DNA template, in gene expression. Our work focuses on a specialized molecular machinery that utilizes ATP hydrolysis to initiate DNA opening and permits a description of how the events triggered by ATP hydrolysis within a transcriptional activator can lead to DNA opening and transcription. The bacterial EBPs (enhancer binding proteins) that belong to the AAA(+) (ATPases associated with various cellular activities) protein family remodel the RNAP (RNA polymerase) holoenzyme containing the sigma(54) factor and convert the initial, transcriptionally silent promoter complex into a transcriptionally proficient open complex using transactions that reflect the use of ATP hydrolysis to establish different functional states of the EBP. A molecular switch within the model EBP we study [called PspF (phage shock protein F)] is evident, and functions to control the exposure of a solvent-accessible flexible loop that engages directly with the initial RNAP promoter complex. The sigma(54) factor then controls the conformational changes in the RNAP required to form the open promoter complex.
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Affiliation(s)
- M Buck
- Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.
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45
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Schumacher J, Joly N, Rappas M, Bradley D, Wigneshweraraj SR, Zhang X, Buck M. Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase. J Biol Chem 2007; 282:9825-9833. [PMID: 17242399 DOI: 10.1074/jbc.m611532200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcriptional initiation invariably involves the transition from a closed RNA polymerase (RNAP) promoter complex to a transcriptional competent open complex. Activators of the bacterial sigma(54)-RNAP are AAA+ proteins that couple ATP hydrolysis to restructure the sigma(54)-RNAP promoter complex. Structures of the sigma(54) activator PspF AAA+ domain (PspF(1-275)) bound to sigma(54) show two loop structures proximal to sigma(54) as follows: the sigma(54) contacting the GAFTGA loop 1 structure and loop 2 that classifies sigma(54) activators as pre-sensor 1 beta-hairpin AAA+ proteins. We report activities for PspF(1-275) mutated in the AAA+ conserved sensor I threonine/asparagine motif (PspF(1-275)(T148A), PspF(1-275)(N149A), and PspF(1-275)(N149S)) within the second region of homology. We show that sensor I asparagine plays a direct role in ATP hydrolysis. However, low hydrolysis rates are sufficient for functional output in vitro. In contrast, PspF(1-275)(T148A) has severe defects at the distinct step of sigma(54) promoter restructuring. This defect is not because of the failure of PspF(1-275)(T148A) to stably engage with the closed sigma(54) promoter, indicating (i) an important role in ATP hydrolysis-associated motions during energy coupling for remodeling and (ii) distinguishing PspF(1-275)(T148A) from PspF(1-275) variants involved in signaling to the GAFTGA loop 1, which fail to stably engage with the promoter. Activities of loop 2 PspF(1-275) variants are similar to those of PspF(1-275)(T148A) suggesting a functional signaling link between Thr(148) and loop 2. In PspF(1-275) this link relies on the conserved nucleotide state-dependent interaction between the Walker B residue Glu(108) and Thr(148). We propose that hydrolysis is relayed via Thr(148) to loop 2 creating motions that provide mechanical force to the GAFTGA loop 1 that contacts sigma(54).
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Affiliation(s)
- Jörg Schumacher
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Nicolas Joly
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mathieu Rappas
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Dominic Bradley
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Xiaodong Zhang
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin Buck
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom.
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46
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Sirijovski N, Olsson U, Lundqvist J, Al-Karadaghi S, Willows R, Hansson M. ATPase activity associated with the magnesium chelatase H-subunit of the chlorophyll biosynthetic pathway is an artefact. Biochem J 2006; 400:477-84. [PMID: 16928192 PMCID: PMC1698598 DOI: 10.1042/bj20061103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Magnesium chelatase inserts Mg2+ into protoporphyrin IX and is the first unique enzyme of the chlorophyll biosynthetic pathway. It is a heterotrimeric enzyme, composed of I- (40 kDa), D- (70 kDa) and H- (140 kDa) subunits. The I- and D-proteins belong to the family of AAA+ (ATPases associated with various cellular activities), but only I-subunit hydrolyses ATP to ADP. The D-subunits provide a platform for the assembly of the I-subunits, which results in a two-tiered hexameric ring complex. However, the D-subunits are unstable in the chloroplast unless ATPase active I-subunits are present. The H-subunit binds protoporphyrin and is suggested to be the catalytic subunit. Previous studies have indicated that the H-subunit also has ATPase activity, which is in accordance with an earlier suggested two-stage mechanism of the reaction. In the present study, we demonstrate that gel filtration chromatography of affinity-purified Rhodobacter capsulatus H-subunit produced in Escherichia coli generates a high- and a low-molecular-mass fraction. Both fractions were dominated by the H-subunit, but the ATPase activity was only found in the high-molecular-mass fraction and magnesium chelatase activity was only associated with the low-molecular-mass fraction. We demonstrated that light converted monomeric low-molecular-mass H-subunit into high-molecular-mass aggregates. We conclude that ATP utilization by magnesium chelatase is solely connected to the I-subunit and suggest that a contaminating E. coli protein, which binds to aggregates of the H-subunit, caused the previously reported ATPase activity of the H-subunit.
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Affiliation(s)
- Nick Sirijovski
- *Department of Biochemistry, Lund University, Box 124, SE-22100 Lund, Sweden
| | - Ulf Olsson
- *Department of Biochemistry, Lund University, Box 124, SE-22100 Lund, Sweden
| | - Joakim Lundqvist
- †Department of Molecular Biophysics, Lund University, Box 124, SE-22100 Lund, Sweden
| | - Salam Al-Karadaghi
- †Department of Molecular Biophysics, Lund University, Box 124, SE-22100 Lund, Sweden
| | - Robert D. Willows
- ‡Department of Biological Science, Macquarie University, Macquarie Drive, North Ryde 2109, Australia
| | - Mats Hansson
- *Department of Biochemistry, Lund University, Box 124, SE-22100 Lund, Sweden
- To whom correspondence should be addressed (email )
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47
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Rappas M, Bose D, Zhang X. Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. Curr Opin Struct Biol 2006; 17:110-6. [PMID: 17157497 DOI: 10.1016/j.sbi.2006.11.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 10/30/2006] [Accepted: 11/24/2006] [Indexed: 10/23/2022]
Abstract
Bacterial transcription relies on the binding of dissociable sigma (sigma) factors to RNA polymerase (RNAP) for promoter specificity. The major variant sigma factor (sigma54) forms a stable closed complex with RNAP bound to DNA that rarely spontaneously isomerises to an open complex. ATP hydrolysis by bacterial enhancer-binding proteins is used to remodel the RNAP-sigma54-DNA closed complex. Recently, a wealth of structural information on bacterial enhancer-binding proteins has enabled unprecedented insights into their mechanism. These data provide a structural basis for nucleotide binding and hydrolysis, oligomerisation and the conversion of ATPase activity into remodelling events within the RNAP-sigma54 closed complex, and represent advances towards a complete understanding of the sigma54-dependent transcription activation mechanism.
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Affiliation(s)
- Mathieu Rappas
- Centre for Structural Biology, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
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48
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Dago AE, Wigneshweraraj SR, Buck M, Morett E. A role for the conserved GAFTGA motif of AAA+ transcription activators in sensing promoter DNA conformation. J Biol Chem 2006; 282:1087-97. [PMID: 17090527 DOI: 10.1074/jbc.m608715200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription from sigma54-dependent bacterial promoters can be regarded as a second paradigm for bacterial gene transcription. The initial sigma54-RNA polymerase (RNAP).promoter complex, the closed complex, is transcriptionally silent. The transcriptionally proficient sigma54-RNAP.promoter complex, the open complex, is formed upon remodeling of the closed complex by actions of a specialized activator protein that belongs to the AAA (ATPases associated with various cellular activities) protein family in an ATP hydrolysis-dependent reaction. The integrity of a highly conserved signature motif in the AAA activator (known as the GAFTGA motif) is important for the remodeling activity of the AAA activator and for open complex formation. We now provide evidence that the invariant threo-nine residue of the GAFTGA motif plays a role in sensing the DNA downstream of the sigma54-RNAP-binding site and in coupling this information to sigma54-RNAP via the conserved regulatory Region I domain of sigma54 during open complex formation.
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Affiliation(s)
- Angel Ernesto Dago
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos 62210, México
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49
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Joly N, Schumacher J, Buck M. Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator. J Biol Chem 2006; 281:34997-5007. [PMID: 16973614 DOI: 10.1074/jbc.m606628200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic AAA+ domain (PspF1-275) of an enhancer-binding protein is necessary and sufficient to contact sigma54-RNA polymerase holoenzyme (Esigma54), remodel it, and in so doing catalyze open promoter complex formation. Whether ATP binding and hydrolysis is coordinated between subunits of PspF and the precise nature of the nucleotide(s) bound to the oligomeric forms responsible for substrate remodeling are unknown. We demonstrate that ADP stimulates the intrinsic ATPase activity of PspF1-275 and propose that this heterogeneous nucleotide occupancy in a PspF1-275 hexamer is functionally important for specific activity. Binding of ADP and ATP triggers the formation of functional PspF1-275 hexamers as shown by a gain of specific activity. Furthermore, ATP concentrations congruent with stoichiometric ATP binding to PspF1-275 inhibit ATP hydrolysis and Esigma54-promoter open complex formation. Demonstration of a heterogeneous nucleotide-bound state of a functional PspF1-275.Esigma54 complex provides clear biochemical evidence for heterogeneous nucleotide occupancy in this AAA+ protein. Based on our data, we propose a stochastic nucleotide binding and a coordinated hydrolysis mechanism in PspF1-275 hexamers.
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Affiliation(s)
- Nicolas Joly
- Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, United Kingdom
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50
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Leach RN, Gell C, Wigneshweraraj S, Buck M, Smith A, Stockley PG. Mapping ATP-dependent activation at a sigma54 promoter. J Biol Chem 2006; 281:33717-26. [PMID: 16926155 DOI: 10.1074/jbc.m605731200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sigma(54) promoter specificity factor is distinct from other bacterial RNA polymerase (RNAP) sigma factors in that it forms a transcriptionally silent closed complex upon promoter binding. Transcriptional activation occurs through a nucleotide-dependent isomerization of sigma(54), mediated via its interactions with an enhancer-binding activator protein that utilizes the energy released in ATP hydrolysis to effect structural changes in sigma(54) and core RNA polymerase. The organization of sigma(54)-promoter and sigma(54)-RNAP-promoter complexes was investigated by fluorescence resonance energy transfer assays using sigma(54) single cysteine-mutants labeled with an acceptor fluorophore and donor fluorophore-labeled DNA sequences containing mismatches that mimic nifH early- and late-melted promoters. The results show that sigma(54) undergoes spatial rearrangements of functionally important domains upon closed complex formation. sigma(54) and sigma(54)-RNAP promoter complexes reconstituted with the different mismatched DNA constructs were assayed by the addition of the activator phage shock protein F in the presence or absence of ATP and of non-hydrolysable analogues. Nucleotide-dependent alterations in fluorescence resonance energy transfer efficiencies identify different functional states of the activator-sigma(54)-RNAP-promoter complex that exist throughout the mechano-chemical transduction pathway of transcriptional activation, i.e. from closed to open promoter complexes. The results suggest that open complex formation only occurs efficiently on replacement of a repressive fork junction with down-stream melted DNA.
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Affiliation(s)
- Robert N Leach
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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