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Sharma A, Leach RN, Gell C, Zhang N, Burrows PC, Shepherd DA, Wigneshweraraj S, Smith DA, Zhang X, Buck M, Stockley PG, Tuma R. Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies. Nucleic Acids Res 2014; 42:5177-90. [PMID: 24553251 PMCID: PMC4005640 DOI: 10.1093/nar/gku146] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recognition of bacterial promoters is regulated by two distinct classes of sequence-specific sigma factors, σ70 or σ54, that differ both in their primary sequence and in the requirement of the latter for activation via enhancer-bound upstream activators. The σ54 version controls gene expression in response to stress, often mediating pathogenicity. Its activator proteins are members of the AAA+ superfamily and use adenosine triphosphate (ATP) hydrolysis to remodel initially auto-inhibited holoenzyme promoter complexes. We have mapped this remodeling using single-molecule fluorescence spectroscopy. Initial remodeling is nucleotide-independent and driven by binding both ssDNA during promoter melting and activator. However, DNA loading into the RNA polymerase active site depends on co-operative ATP hydrolysis by the activator. Although the coupled promoter recognition and melting steps may be conserved between σ70 and σ54, the domain movements of the latter have evolved to require an activator ATPase.
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Affiliation(s)
- Amit Sharma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Robert N. Leach
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Christopher Gell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Nan Zhang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Patricia C. Burrows
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Dale A. Shepherd
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Sivaramesh Wigneshweraraj
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - David Alastair Smith
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Xiaodong Zhang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Martin Buck
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- *To whom correspondence should be addressed. Tel: +44 1133 433092; Fax: +44 1133 437897;
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- Correspondence may also be addressed to Roman Tuma. Tel: +44 1133 433080; Fax: +44 1133 437897;
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2
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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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3
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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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4
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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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5
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Zhang N, Buck M. Formation of MgF3 (-)-dependent complexes between an AAA(+) ATPase and σ(54.). FEBS Open Bio 2012; 2:89-92. [PMID: 23650585 PMCID: PMC3642117 DOI: 10.1016/j.fob.2012.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 03/29/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022] Open
Abstract
The widely distributed bacterial σ(54)-dependent transcription regulates pathogenicity and numerous adaptive responses in diverse bacteria. Formation of the σ(54)-dependent open promoter complex is a multi-step process driven by AAA(+) ATPases. Non-hydrolysable nucleotide analogues are particularly suitable for studying such complexity by capturing various intermediate states along the energy coupling pathway. Here we report a novel ATP analogue, ADP-MgF3 (-), which traps an AAA(+) ATPase with its target σ(54). The MgF3 (-)-dependent complex is highly homogeneous and functional assays suggest it may represent an early transcription intermediate state valuable for structural studies.
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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
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6
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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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7
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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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8
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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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9
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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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10
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Visualizing the organization and reorganization of transcription complexes for gene expression. Biochem Soc Trans 2008; 36:776-9. [PMID: 18631157 DOI: 10.1042/bst0360776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regulated gene expression requires control of the transcription machinery, frequently through the establishment of different functional states of the transcribing enzyme RNA polymerase and its attendant activator proteins. In bacteria, major adaptive responses use an enhancer-dependent RNA polymerase, activated for transcription by a class of ATPases that remodel initial promoter complexes to form transcriptionally proficient open promoter complexes. In the present article, we summarize the integrated use of site-specific protein cleavage and DNA cross-linking methods, as well as FRET (fluorescence resonance energy transfer) in combination with X-ray crystallography and cryo-electron microscopy to gain insight into the organization of the enhancer-dependent sigma 54-RNA polymerase and the ATPase-driven activation mechanism.
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11
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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: 106] [Impact Index Per Article: 6.6] [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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12
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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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13
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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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14
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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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15
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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: 75] [Impact Index Per Article: 4.2] [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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