1
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Kang S, Jang BR, Lee KH. Characterization of the transcriptionally active form of dephosphorylated DctD complexed with dephospho-IIA Glc. mBio 2024; 15:e0033024. [PMID: 38564689 PMCID: PMC11077940 DOI: 10.1128/mbio.00330-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Bacterial enhancer-binding proteins (bEBPs) acquire a transcriptionally active state via phosphorylation. However, transcriptional activation by the dephosphorylated form of bEBP has been observed in DctD, which belongs to Group I bEBP. The formation of a complex between dephosphorylated DctD (d-DctD) and dephosphorylated IIAGlc (d-IIAGlc) is a prerequisite for the transcriptional activity of d-DctD. In the present study, characteristics of the transcriptionally active complex composed of d-IIAGlc and phosphorylation-deficient DctD (DctDD57Q) of Vibrio vulnificus were investigated in its multimeric conformation and DNA-binding ability. DctDD57Q formed a homodimer that could not bind to the DNA. In contrast, when DctDD57Q formed a complex with d-IIAGlc in a 1:1 molar ratio, it produced two conformations: dimer and dodecamer of the complex. Only the dodecameric complex exhibited ATP-hydrolyzing activity and DNA-binding affinity. For successful DNA-binding and transcriptional activation by the dodecameric d-IIAGlc/DctDD57Q complex, extended upstream activator sequences were required, which encompass the nucleotide sequences homologous to the known DctD-binding site and additional nucleotides downstream. This is the first report to demonstrate the molecular characteristics of a dephosphorylated bEBP complexed with another protein to form a transcriptionally active dodecameric complex, which has an affinity for a specific DNA-binding sequence.IMPORTANCEResponse regulators belonging to the bacterial two-component regulatory system activate the transcription initiation of their regulons when they are phosphorylated by cognate sensor kinases and oligomerized to the appropriate multimeric states. Recently, it has been shown that a dephosphorylated response regulator, DctD, could activate transcription in a phosphorylation-independent manner in Vibrio vulnificus. The dephosphorylated DctD activated transcription as efficiently as phosphorylated DctD when it formed a complex with dephosphorylated form of IIAGlc, a component of the glucose-phosphotransferase system. Functional mimicry of this complex with the typical form of transcriptionally active phosphorylated DctD led us to study the molecular characteristics of this heterodimeric complex. Through systematic analyses, it was surprisingly determined that a multimer constituted with 12 complexes gained the ability to hydrolyze ATP and recognize specific upstream activator sequences containing a typical inverted-repeat sequence flanked by distinct nucleotides.
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Affiliation(s)
- Sebin Kang
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Bo-Ram Jang
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kyu-Ho Lee
- Department of Life Science, Sogang University, Seoul, South Korea
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2
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Zhao H, Huang L, Liu W, Dong Q, Bai Q, Yuan J, Jiang Z, Chen M, Liu D, Wang J, Li Y, Wang P. Segmented Template-Directed Self-Assembly of Giant Truncated Triangular Supramolecules. Inorg Chem 2024; 63:4152-4159. [PMID: 38372260 DOI: 10.1021/acs.inorgchem.3c03899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The template-directed strategy has been extensively employed for the construction of supramolecular architectures. However, with the increase in the size and complexity of these structures, the synthesis difficulty of the templates escalates exponentially, thereby impeding the widespread application of this strategy. In this study, two truncated triangles T1 and T2 were successfully self-assembled through a novel segmented template strategy by segmenting the core triangular template into portions. Two metallo-organic ligands L2 and L3 were designed and synthesized by dividing the central stable triangle into three separate parts and incorporating them into the precursor ligands, which served as templates to guide the self-assembly process with ligands L1 and L4, respectively. The assembled structures were unambiguously characterized by multidimensional and multinuclear NMR (1H, COSY, NOESY), multidimensional mass spectrometry analysis (ESI-MS and TWIM-MS), and transmission electron microscopy (TEM). Moreover, we observed the formation of fiberlike nanotubes from single-molecule triangles by hierarchical self-assembly.
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Affiliation(s)
- He Zhao
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Linlin Huang
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Wenping Liu
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Qiangqiang Dong
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Qixia Bai
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Jie Yuan
- School of Chemistry and Chemical Engineering, Henan Normal University Xinxiang, Xinxiang 453007, Henan, China
| | - Zhilong Jiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Die Liu
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Jun Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Yiming Li
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Pingshan Wang
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
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3
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Banerjee B, Yuan X, Yang CH. Dissecting the molecular dance: c-di-GMP, cAMP-CRP, and VfmH collaboration in pectate lyase regulation for Dickeya dadantii-unveiling the soft rot pathogen's strategy. Microbiol Spectr 2023; 11:e0153723. [PMID: 37811940 PMCID: PMC10714721 DOI: 10.1128/spectrum.01537-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Bacteria respond to environmental changes and adapt to host systems. The response regulator VfmH of the Vfm quorum sensing system regulates a crucial virulence factor, pectate lyase (Pel), in Dickeya dadantii. At high c-di-GMP concentrations, VfmH binds c-di-GMP, resulting in the loss of its activation property in the Pel and virulence regulation in D. dadantii. VfmH binds to c-di-GMP via three conserved arginine residues, and mutations of these residues eliminate the c-di-GMP-related phenotypes of VfmH in Pel synthesis. Our data also show that VfmH interacts with CRP to regulate pelD transcription, thus integrating cyclic AMP and c-di-GMP signaling pathways to control virulence in D. dadantii. We propose that VfmH is an important intermediate factor incorporating quorum sensing and nucleotide signaling pathways for the collective regulation of D. dadantii pathogenesis.
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Affiliation(s)
- Biswarup Banerjee
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Xiaochen Yuan
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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4
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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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5
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Ye F, Gao F, Liu X, Buck M, Zhang X. Mechanisms of DNA opening revealed in AAA+ transcription complex structures. SCIENCE ADVANCES 2022; 8:eadd3479. [PMID: 36542713 PMCID: PMC9770992 DOI: 10.1126/sciadv.add3479] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ54), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ54 amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ54 inhibition while helping to open up DNA, using σ54 amino-terminal peptide as a pry bar.
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Affiliation(s)
- Fuzhou Ye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
| | - Forson Gao
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
| | - Xiaojiao Liu
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
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6
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Kotta-Loizou I, Giuliano MG, Jovanovic M, Schaefer J, Ye F, Zhang N, Irakleidi DA, Liu X, Zhang X, Buck M, Engl C. The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain. iScience 2022; 25:105425. [PMID: 36388977 PMCID: PMC9650030 DOI: 10.1016/j.isci.2022.105425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/21/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
CRISPR-associated Rossmann fold (CARF) domain signaling underpins modulation of CRISPR-Cas nucleases; however, the RtcR CARF domain controls expression of two conserved RNA repair enzymes, cyclase RtcA and ligase RtcB. Here, we demonstrate that RtcAB are required for RtcR-dependent transcription activation and directly bind to RtcR CARF. RtcAB catalytic activity is not required for complex formation with CARF, but is essential yet not sufficient for RtcRAB-dependent transcription activation, implying the need for an additional RNA repair-dependent activating signal. This signal differs from oligoadenylates, a known ligand of CARF domains, and instead appears to originate from the translation apparatus: RtcB repairs a tmRNA that rescues stalled ribosomes and increases translation elongation speed. Taken together, our data provide evidence for an expanded range for CARF domain signaling, including the first evidence of its control via in trans protein-protein interactions, and a feed-forward mechanism to regulate RNA repair required for a functioning translation apparatus.
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Affiliation(s)
- Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Maria Grazia Giuliano
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Milija Jovanovic
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Jorrit Schaefer
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Fuzhou Ye
- Section of Structural Biology, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Nan Zhang
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Danai Athina Irakleidi
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Xiaojiao Liu
- Section of Structural Biology, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Xiaodong Zhang
- Section of Structural Biology, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Christoph Engl
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
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7
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Kumar R, Roy C, Datta S. Delineating specific regions of N- terminal domain of T3SS ATPase YsaN of Yersinia enterocolitica governing its different oligomerization states. Front Mol Biosci 2022; 9:967974. [PMID: 36158578 PMCID: PMC9493007 DOI: 10.3389/fmolb.2022.967974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Oligomerization of YsaN, a putative T3SS-ATPase is a necessary and crucial event for T3SS functioning in Y. enterocolitica. Different oligomeric states have been proposed for similar ATPases, yet, the true nature of its activation and formation of different oligomers is still poorly understood. In-vitro studies of YsaN reveal that its activation and oligomerization depend on its N-terminal region and occur as a result of active catalysis of ATP in an ATP concentration-dependent manner following two-step cooperative kinetics. Also, the N-terminal 83 amino acid residues of YsaN are crucial for higher-order oligomer formation while YsaN∆83 is capable of hexamer formation upon oligomerization. Enzyme kinetics study shows reduced ATPase activity of YsaN∆83 (3.19 ± 0.09 μmol/min/mg) in comparison to YsaN (9.076 ± 0.72 μmol/min/mg). Negative-TEM study of YsaN and YsaN∆83 oligomer suggests that the formation of higher-order oligomer (probably dodecamer) occurs by stacking of two hexamers through their N-terminal faces involving N-terminal 83 amino acid residues which have been further supported by the docking of two hexamers during the in-silico study. These results suggest that YsaN is an oligomerization-activated T3SS ATPase, where distinct regions of its N-terminal domain regulate its different oligomeric nature and is essential for its activation.
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8
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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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9
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Yan XF, Yang C, Wang M, Yong Y, Deng Y, Gao YG. Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum-sensing system in Burkholderia cenocepacia. FEBS Lett 2021; 596:71-80. [PMID: 34837384 DOI: 10.1002/1873-3468.14244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 11/11/2022]
Abstract
Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum-sensing signaling molecule cis-2-dodecenoic acid (BDSF). As a bacterial enhancer-binding protein (bEBP), GtrR is composed of an N-terminal receiver domain, a central ATPases associated with diverse cellular activities (AAA+) ATPase σ54 -interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. In this work, we solved its AAA+ ATPase domain in both apo and GTP-bound forms. The structure revealed how GtrR specifically recognizes GTP. In addition, we also revealed that GtrR has moderate GTPase activity in vitro in the absence of its activation signal. Finally, we found the residues K170, D236, R311, and R357 in GtrR that are crucial to its biological function, any single mutation leading to completely abolishing GtrR activity.
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Affiliation(s)
- Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chunxi Yang
- Jiangxi provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yonlada Yong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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10
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Flores-Bautista E, Hernandez-Guerrero R, Huerta-Saquero A, Tenorio-Salgado S, Rivera-Gomez N, Romero A, Ibarra JA, Perez-Rueda E. Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms. PLoS One 2020; 15:e0237135. [PMID: 32822422 PMCID: PMC7446807 DOI: 10.1371/journal.pone.0237135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/20/2020] [Indexed: 11/18/2022] Open
Abstract
DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.
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Affiliation(s)
- Emanuel Flores-Bautista
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Rafael Hernandez-Guerrero
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Alejandro Huerta-Saquero
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, México
| | - Silvia Tenorio-Salgado
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Mérida, Yucatán, México
| | | | - Alba Romero
- Microbiota Host Interactions and Clostridia Research Group, Universidad Nacional Andrés Bello, Santiago de Chile, Chile
| | - Jose Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- * E-mail:
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11
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Bylino OV, Ibragimov AN, Shidlovskii YV. Evolution of Regulated Transcription. Cells 2020; 9:E1675. [PMID: 32664620 PMCID: PMC7408454 DOI: 10.3390/cells9071675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.
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Affiliation(s)
- Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
| | - Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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12
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Park KH, Kim S, Lee SJ, Cho JE, Patil VV, Dumbrepatil AB, Song HN, Ahn WC, Joo C, Lee SG, Shingler V, Woo EJ. Tetrameric architecture of an active phenol-bound form of the AAA + transcriptional regulator DmpR. Nat Commun 2020; 11:2728. [PMID: 32483114 PMCID: PMC7264223 DOI: 10.1038/s41467-020-16562-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/11/2020] [Indexed: 01/07/2023] Open
Abstract
The Pseudomonas putida phenol-responsive regulator DmpR is a bacterial enhancer binding protein (bEBP) from the AAA+ ATPase family. Even though it was discovered more than two decades ago and has been widely used for aromatic hydrocarbon sensing, the activation mechanism of DmpR has remained elusive. Here, we show that phenol-bound DmpR forms a tetramer composed of two head-to-head dimers in a head-to-tail arrangement. The DmpR-phenol complex exhibits altered conformations within the C-termini of the sensory domains and shows an asymmetric orientation and angle in its coiled-coil linkers. The structural changes within the phenol binding sites and the downstream ATPase domains suggest that the effector binding signal is propagated through the coiled-coil helixes. The tetrameric DmpR-phenol complex interacts with the σ54 subunit of RNA polymerase in presence of an ATP analogue, indicating that DmpR-like bEBPs tetramers utilize a mechanistic mode distinct from that of hexameric AAA+ ATPases to activate σ54-dependent transcription.
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Affiliation(s)
- Kwang-Hyun Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Sungchul Kim
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Su-Jin Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, 305-333, Republic of Korea
| | - Jee-Eun Cho
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Vinod Vikas Patil
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, 305-333, Republic of Korea
| | - Arti Baban Dumbrepatil
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Hyung-Nam Song
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Woo-Chan Ahn
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands.
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Victoria Shingler
- Department of Molecular Biology, Umeå University, 90187, Umeå, SE, Sweden
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea. .,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, 305-333, Republic of Korea.
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13
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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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14
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15
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Zhang Z, Li Y, Song B, Zhang Y, Jiang X, Wang M, Tumbleson R, Liu C, Wang P, Hao XQ, Rojas T, Ngo AT, Sessler JL, Newkome GR, Hla SW, Li X. Intra- and intermolecular self-assembly of a 20-nm-wide supramolecular hexagonal grid. Nat Chem 2020; 12:468-474. [PMID: 32284575 PMCID: PMC7375338 DOI: 10.1038/s41557-020-0454-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 03/03/2020] [Indexed: 11/09/2022]
Abstract
For the past three decades, the coordination-driven self-assembly of three-dimensional structures has undergone rapid progress; however, parallel efforts to create large discrete two-dimensional architectures-as opposed to polymers-have met with limited success. The synthesis of metallo-supramolecular systems with well-defined shapes and sizes in the range of 10-100 nm remains challenging. Here we report the construction of a series of giant supramolecular hexagonal grids, with diameters on the order of 20 nm and molecular weights greater than 65 kDa, through a combination of intra- and intermolecular metal-mediated self-assembly steps. The hexagonal intermediates and the resulting self-assembled grid architectures were imaged at submolecular resolution by scanning tunnelling microscopy. Characterization (including by scanning tunnelling spectroscopy) enabled the unambiguous atomic-scale determination of fourteen hexagonal grid isomers.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Environmental Research at Great Bay, Guangzhou University, Guangzhou, China
- Department of Chemistry, University of South Florida, Tampa, FL, USA
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, School of Chemistry, Central China Normal University, Wuhan, China
| | - Yiming Li
- Department of Chemistry, University of South Florida, Tampa, FL, USA.
| | - Bo Song
- Department of Chemistry, University of South Florida, Tampa, FL, USA
| | - Yuan Zhang
- Nanoscience and Technology Division, Argonne National Laboratory, Lemont, IL, USA.
- Department of Physics, Old Dominion University, Norfolk, VA, USA.
| | - Xin Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, China
| | - Ryan Tumbleson
- Nanoscience and Technology Division, Argonne National Laboratory, Lemont, IL, USA
- Nanoscale and Quantum Phenomena Institute and the Department of Physics and Astronomy, Ohio University, Athens, OH, USA
| | - Changlin Liu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, School of Chemistry, Central China Normal University, Wuhan, China
| | - Pingshan Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Environmental Research at Great Bay, Guangzhou University, Guangzhou, China
| | - Xin-Qi Hao
- College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Tomas Rojas
- Nanoscale and Quantum Phenomena Institute and the Department of Physics and Astronomy, Ohio University, Athens, OH, USA
- Materials Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anh T Ngo
- Materials Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Jonathan L Sessler
- Center for Supramolecular Chemistry and Catalysis, Shanghai University, Shanghai, China.
| | - George R Newkome
- Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Saw Wai Hla
- Nanoscience and Technology Division, Argonne National Laboratory, Lemont, IL, USA.
- Nanoscale and Quantum Phenomena Institute and the Department of Physics and Astronomy, Ohio University, Athens, OH, USA.
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, Tampa, FL, USA.
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16
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Danson AE, Jovanovic M, Buck M, Zhang X. Mechanisms of σ 54-Dependent Transcription Initiation and Regulation. J Mol Biol 2019; 431:3960-3974. [PMID: 31029702 PMCID: PMC7057263 DOI: 10.1016/j.jmb.2019.04.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 02/02/2023]
Abstract
Cellular RNA polymerase is a multi-subunit macromolecular assembly responsible for gene transcription, a highly regulated process conserved from bacteria to humans. In bacteria, sigma factors are employed to mediate gene-specific expression in response to a variety of environmental conditions. The major variant σ factor, σ54, has a specific role in stress responses. Unlike σ70-dependent transcription, which often can spontaneously proceed to initiation, σ54-dependent transcription requires an additional ATPase protein for activation. As a result, structures of a number of distinct functional states during the dynamic process of transcription initiation have been captured using the σ54 system with both x-ray crystallography and cryo electron microscopy, furthering our understanding of σ54-dependent transcription initiation and DNA opening. Comparisons with σ70 and eukaryotic polymerases reveal unique and common features during transcription initiation.
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Affiliation(s)
- Amy E Danson
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Milija Jovanovic
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
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17
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Nie X, Dong W, Yang C. Genomic reconstruction of σ 54 regulons in Clostridiales. BMC Genomics 2019; 20:565. [PMID: 31288763 PMCID: PMC6615313 DOI: 10.1186/s12864-019-5918-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background The σ54 factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ54 is present in many Clostridiales species that have great importance in human health and biotechnological applications, the cellular processes controlled by σ54 remain unknown. Results For systematic analysis of the regulatory functions of σ54, we performed comparative genomic reconstruction of transcriptional regulons of σ54 in 57 species from the Clostridiales order. The EBP-binding DNA motifs and regulated genes were identified for 263 EBPs that constitute 39 distinct groups. The reconstructed σ54 regulons contain the genes involved in fermentation and amino acid catabolism. The predicted σ54 binding sites in the genomes of Clostridiales spp. were verified by in vitro binding assays. To our knowledge, this is the first report about direct regulation of the Stickland reactions and butyrate and alcohols synthesis by σ54 and the respective EBPs. Considerable variations were demonstrated in the sizes and gene contents of reconstructed σ54 regulons between different Clostridiales species. It is proposed that σ54 controls butyrate and alcohols synthesis in solvent-producing species, regulates autotrophic metabolism in acetogenic species, and affects the toxin production in pathogenic species. Conclusions This study reveals previously unrecognized functions of σ54 and provides novel insights into the regulation of fermentation and amino acid metabolism in Clostridiales species, which could have potential applications in guiding the treatment and efficient utilization of these species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5918-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoqun Nie
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenyue Dong
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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18
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Noise in bacterial gene expression. Biochem Soc Trans 2018; 47:209-217. [PMID: 30578346 DOI: 10.1042/bst20180500] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/25/2022]
Abstract
The expression level of a gene can fluctuate significantly between individuals within a population of genetically identical cells. The resultant phenotypic heterogeneity could be exploited by bacteria to adapt to changing environmental conditions. Noise is hence a genome-wide phenomenon that arises from the stochastic nature of the biochemical reactions that take place during gene expression and the relatively low abundance of the molecules involved. The production of mRNA and proteins therefore occurs in bursts, with alternating episodes of high and low activity during transcription and translation. Single-cell and single-molecule studies demonstrated that noise within gene expression is influenced by a combination of both intrinsic and extrinsic factors. However, our mechanistic understanding of this process at the molecular level is still rather limited. Further investigation is necessary that takes into account the detailed knowledge of gene regulation gained from biochemical studies.
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19
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Wu GY, Chen LJ, Xu L, Zhao XL, Yang HB. Construction of supramolecular hexagonal metallacycles via coordination-driven self-assembly: Structure, properties and application. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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20
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Abstract
σN (also σ54) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σN is encoded as the first gene of a five-gene operon including rpoN (σN), ptsN, hpf, rapZ, and npr that has been genetically retained among species of Escherichia, Shigella, and Salmonella. In an increasing number of bacteria, σN has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors. For most pathogens how this is achieved is unknown. In enterohemorrhagic Escherichia coli (EHEC) O157, Salmonella enterica, and Borrelia burgdorferi, regulation of virulence by σN requires another alternative sigma factor, σS, yet the model by which σN-σS virulence regulation is predicted to occur is varied in each of these pathogens. In this review, the importance of σN to bacterial pathogenesis is introduced, and common features of σN-dependent virulence regulation discussed. Emphasis is placed on the molecular mechanisms underlying σN virulence regulation in E. coli O157. This includes a review of the structure and function of regulatory pathways connecting σN to virulence expression, predicted input signals for pathway stimulation, and the role for cognate σN activators in initiation of gene systems determining pathogenic behavior.
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21
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Gu H, Yang Y, Wang M, Chen S, Wang H, Li S, Ma Y, Wang J. Novel Cysteine Desulfidase CdsB Involved in Releasing Cysteine Repression of Toxin Synthesis in Clostridium difficile. Front Cell Infect Microbiol 2018; 7:531. [PMID: 29376034 PMCID: PMC5767170 DOI: 10.3389/fcimb.2017.00531] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/18/2017] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile, a major cause of nosocomial diarrhea and pseudomembranous colitis, still poses serious health-care challenges. The expression of its two main virulence factors, TcdA and TcdB, is reportedly repressed by cysteine, but molecular mechanism remains unclear. The cysteine desulfidase CdsB affects the virulence and infection progresses of some bacteria. The C. difficile strain 630 genome encodes a homolog of CdsB, and in the present study, we analyzed its role in C. difficile 630Δerm by constructing an isogenic ClosTron-based cdsB mutant. When C. difficile was cultured in TY broth supplemented with cysteine, the cdsB gene was rapidly induced during the exponential growth phase. The inactivation of cdsB not only affected the resistance of C. difficile to cysteine, but also altered the expression levels of intracellular cysteine-degrading enzymes and the production of hydrogen sulfide. This suggests that C. difficile CdsB is a major inducible cysteine-degrading enzyme. The inactivation of the cdsB gene in C. difficile also removed the cysteine-dependent repression of toxin production, but failed to remove the Na2S-dependent repression, which supports that the cysteine-dependent repression of toxin production is probably attributable to the accumulation of cysteine by-products. We also mapped a δ54 (SigL)-dependent promoter upstream from the cdsB gene, and cdsB expression was not induced in response to cysteine in the cdsR::ermB or sigL::ermB strain. Using a reporter gene fusion analysis, we identified the necessary promoter sequence for cysteine-dependent cdsB expression. Taken together, these results indicate that CdsB is a key inducible cysteine desulfidase in C. difficile which is regulated by δ54 and CdsR in response to cysteine and that cysteine-dependent regulation of toxin production is closely associated with cysteine degradation.
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Affiliation(s)
- Huawei Gu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yingyin Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Meng Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuyi Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Haiying Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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22
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Cryo-EM structures of the human INO80 chromatin-remodeling complex. Nat Struct Mol Biol 2017; 25:37-44. [PMID: 29323271 PMCID: PMC5777635 DOI: 10.1038/s41594-017-0003-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/01/2017] [Indexed: 11/08/2022]
Abstract
Access to chromatin for processes such as transcription and DNA repair requires the sliding of nucleosomes along DNA. This process is aided by chromatin-remodeling complexes, such as the multisubunit INO80 chromatin-remodeling complex. Here we present cryo-EM structures of the active core complex of human INO80 at 9.6 Å, with portions at 4.1-Å resolution, and reconstructions of combinations of subunits. Together, these structures reveal the architecture of the INO80 complex, including Ino80 and actin-related proteins, which is assembled around a single RUVBL1 (Tip49a) and RUVBL2 (Tip49b) AAA+ heterohexamer. An unusual spoked-wheel structural domain of the Ino80 subunit is engulfed by this heterohexamer; both, in combination, form the core of the complex. We also identify a cleft in RUVBL1 and RUVBL2, which forms a major interaction site for partner proteins and probably communicates these interactions to its nucleotide-binding sites.
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Abstract
Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes. The remodelling of sigma54 occurs through an ATP-binding and hydrolysis reaction carried out by the bEBPs. The regulation of bEBP self-assembly into typically homomeric hexamers allows regulated gene expression since the self-assembly is required for bEBP ATPase activity and its direct engagement with the sigma54 factor during the remodelling reaction. Crystallographic studies have now established that in the closed promoter complex, the sigma54 factor occupies the bacterial RNA polymerase in ways that will physically impede promoter DNA opening and the loading of melted out promoter DNA into the DNA-binding clefts of the RNA polymerase. Large-scale structural re-organizations of sigma54 require contact of the bEBP with an amino-terminal glutamine and leucine-rich sequence of sigma54, and lead to domain movements within the core RNA polymerase necessary for making open promoter complexes and synthesizing the nascent RNA transcript.
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Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol Cell 2017; 67:106-116.e4. [PMID: 28579332 PMCID: PMC5505868 DOI: 10.1016/j.molcel.2017.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/05/2017] [Indexed: 01/25/2023]
Abstract
Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. RNA polymerase closed complex (RPc) structure reveals DNA distortions by σ Intermediate complex (RPi) structure reveals the roles of AAA activator DNA distortion and opening are initiated in RPc and RPi before entering the RNAP RNAP conformation in RPi is significantly different from closed or open complex
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25
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Sysoeva TA. Assessing heterogeneity in oligomeric AAA+ machines. Cell Mol Life Sci 2017; 74:1001-1018. [PMID: 27669691 PMCID: PMC11107579 DOI: 10.1007/s00018-016-2374-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.
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Affiliation(s)
- Tatyana A Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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26
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Joly N, Martino L, Gigant E, Dumont J, Pintard L. Microtubule-severing activity of the AAA+ ATPase Katanin is essential for female meiotic spindle assembly. Development 2016; 143:3604-3614. [PMID: 27578779 DOI: 10.1242/dev.140830] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/12/2016] [Indexed: 02/03/2023]
Abstract
In most animals, female meiotic spindles are assembled in the absence of centrosomes. How microtubules (MTs) are organized into acentrosomal meiotic spindles is poorly understood. In Caenorhabditis elegans, assembly of female meiotic spindles requires MEI-1 and MEI-2, which constitute the microtubule-severing AAA+ ATPase Katanin. However, the role of MEI-2 is not known and whether MT severing is required for meiotic spindle assembly is unclear. Here, we show that the essential role of MEI-2 is to confer MT binding to Katanin, which in turn stimulates the ATPase activity of MEI-1, leading to MT severing. To test directly the contribution of MT severing to meiotic spindle assembly, we engineered Katanin variants that retained MT binding and MT bundling activities but that were inactive for MT severing. In vivo analysis of these variants showed disorganized microtubules that lacked focused spindle poles reminiscent of the Katanin loss-of-function phenotype, demonstrating that the MT-severing activity is essential for meiotic spindle assembly in C. elegans Overall, our results reveal the essential role of MEI-2 and provide the first direct evidence supporting an essential role of MT severing in meiotic spindle assembly in C. elegans.
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Affiliation(s)
- Nicolas Joly
- Institut Jacques Monod, Cell Cycle and Development Team, Centre National de la Recherche Scientifique and University of Paris Diderot and Sorbonne Paris Cité UMR7592, Paris 75013, France
| | - Lisa Martino
- Institut Jacques Monod, Cell Cycle and Development Team, Centre National de la Recherche Scientifique and University of Paris Diderot and Sorbonne Paris Cité UMR7592, Paris 75013, France
| | - Emmanuelle Gigant
- Institut Jacques Monod, Cell Division and Reproduction Team, Centre National de la Recherche Scientifique and University of Paris Diderot and Sorbonne Paris Cité UMR7592, Paris 75013, France
| | - Julien Dumont
- Institut Jacques Monod, Cell Division and Reproduction Team, Centre National de la Recherche Scientifique and University of Paris Diderot and Sorbonne Paris Cité UMR7592, Paris 75013, France
| | - Lionel Pintard
- Institut Jacques Monod, Cell Cycle and Development Team, Centre National de la Recherche Scientifique and University of Paris Diderot and Sorbonne Paris Cité UMR7592, Paris 75013, France
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27
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Nie X, Yang B, Zhang L, Gu Y, Yang S, Jiang W, Yang C. PTS regulation domain-containing transcriptional activator CelR and sigma factor σ54control cellobiose utilization inClostridium acetobutylicum. Mol Microbiol 2016; 100:289-302. [DOI: 10.1111/mmi.13316] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Xiaoqun Nie
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Bin Yang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Lei Zhang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Yang Gu
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Chen Yang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
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28
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Zhang N, Jovanovic G, McDonald C, Ces O, Zhang X, Buck M. Transcription Regulation and Membrane Stress Management in Enterobacterial Pathogens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:207-30. [DOI: 10.1007/978-3-319-32189-9_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Mechanistic insights into c-di-GMP-dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2015; 113:E209-18. [PMID: 26712005 DOI: 10.1073/pnas.1523148113] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. In many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-GMP. A main effector for c-di-GMP signaling in the opportunistic pathogen Pseudomonas aeruginosa is the transcription regulator FleQ. FleQ is a bacterial enhancer-binding protein (bEBP) with a central AAA+ ATPase σ(54)-interaction domain, flanked by a C-terminal helix-turn-helix DNA-binding motif and a divergent N-terminal receiver domain. Together with a second ATPase, FleN, FleQ regulates the expression of flagellar and exopolysaccharide biosynthesis genes in response to cellular c-di-GMP. Here we report structural and functional data that reveal an unexpected mode of c-di-GMP recognition that is associated with major conformational rearrangements in FleQ. Crystal structures of FleQ's AAA+ ATPase domain in its apo-state or bound to ADP or ATP-γ-S show conformations reminiscent of the activated ring-shaped assemblies of other bEBPs. As revealed by the structure of c-di-GMP-complexed FleQ, the second messenger interacts with the AAA+ ATPase domain at a site distinct from the ATP binding pocket. c-di-GMP interaction leads to active site obstruction, hexameric ring destabilization, and discrete quaternary structure transitions. Solution and cell-based studies confirm coupling of the ATPase active site and c-di-GMP binding, as well as the functional significance of crystallographic interprotomer interfaces. Taken together, our data offer unprecedented insight into conserved regulatory mechanisms of gene expression under direct c-di-GMP control via FleQ and FleQ-like bEBPs.
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30
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Osadnik H, Schöpfel M, Heidrich E, Mehner D, Lilie H, Parthier C, Risselada HJ, Grubmüller H, Stubbs MT, Brüser T. PspF-binding domain PspA1-144and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins. Mol Microbiol 2015; 98:743-59. [DOI: 10.1111/mmi.13154] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Hendrik Osadnik
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
| | - Michael Schöpfel
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - Eyleen Heidrich
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
| | - Denise Mehner
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - Christoph Parthier
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - H. Jelger Risselada
- Max Planck Institute for Biophysical Chemistry; Am Fassberg 11 Göttingen 37077 Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry; Am Fassberg 11 Göttingen 37077 Germany
| | - Milton T. Stubbs
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - Thomas Brüser
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
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31
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Dey S, Biswas M, Sen U, Dasgupta J. Unique ATPase site architecture triggers cis-mediated synchronized ATP binding in heptameric AAA+-ATPase domain of flagellar regulatory protein FlrC. J Biol Chem 2015; 290:8734-47. [PMID: 25688103 DOI: 10.1074/jbc.m114.611434] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 11/06/2022] Open
Abstract
Bacterial enhancer-binding proteins (bEBPs) oligomerize through AAA(+) domains and use ATP hydrolysis-driven energy to isomerize the RNA polymerase-σ(54) complex during transcriptional initiation. Here, we describe the first structure of the central AAA(+) domain of the flagellar regulatory protein FlrC (FlrC(C)), a bEBP that controls flagellar synthesis in Vibrio cholerae. Our results showed that FlrC(C) forms heptamer both in nucleotide (Nt)-free and -bound states without ATP-dependent subunit remodeling. Unlike the bEBPs such as NtrC1 or PspF, a novel cis-mediated "all or none" ATP binding occurs in the heptameric FlrC(C), because constriction at the ATPase site, caused by loop L3 and helix α7, restricts the proximity of the trans-protomer required for Nt binding. A unique "closed to open" movement of Walker A, assisted by trans-acting "Glu switch" Glu-286, facilitates ATP binding and hydrolysis. Fluorescence quenching and ATPase assays on FlrC(C) and mutants revealed that although Arg-349 of sensor II, positioned by trans-acting Glu-286 and Tyr-290, acts as a key residue to bind and hydrolyze ATP, Arg-319 of α7 anchors ribose and controls the rate of ATP hydrolysis by retarding the expulsion of ADP. Heptameric state of FlrC(C) is restored in solution even with the transition state mimicking ADP·AlF3. Structural results and pulldown assays indicated that L3 renders an in-built geometry to L1 and L2 causing σ(54)-FlrC(C) interaction independent of Nt binding. Collectively, our results underscore a novel mechanism of ATP binding and σ(54) interaction that strives to understand the transcriptional mechanism of the bEBPs, which probably interact directly with the RNA polymerase-σ(54) complex without DNA looping.
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Affiliation(s)
- Sanjay Dey
- From the Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016 and
| | - Maitree Biswas
- From the Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016 and
| | - Udayaditya Sen
- the Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - Jhimli Dasgupta
- From the Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016 and
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32
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Buck M, Engl C, Joly N, Jovanovic G, Jovanovic M, Lawton E, McDonald C, Schumacher J, Waite C, Zhang N. In vitro and in vivo methodologies for studying the Sigma 54-dependent transcription. Methods Mol Biol 2015; 1276:53-79. [PMID: 25665558 DOI: 10.1007/978-1-4939-2392-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Here we describe approaches and methods to assaying in vitro the major variant bacterial sigma factor, Sigma 54 (σ(54)), in a purified system. We include the complete transcription system, binding interactions between σ54 and its activators, as well as the self-assembly and the critical ATPase activity of the cognate activators which serve to remodel the closed promoter complexes. We also present in vivo methodologies that are used to study the impact of physiological processes, metabolic states, global signalling networks, and cellular architecture on the control of σ(54)-dependent gene expression.
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Affiliation(s)
- Martin Buck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK,
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33
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Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang X. The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR. Mol Microbiol 2015; 95:17-30. [PMID: 25354037 DOI: 10.1111/mmi.12844] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2014] [Indexed: 11/28/2022]
Abstract
σ(54)-dependent transcription controls a wide range of stress-related genes in bacteria and is tightly regulated. In contrast to σ(70), the σ(54)-RNA polymerase holoenzyme forms a stable closed complex at the promoter site that rarely isomerises into transcriptionally competent open complexes. The conversion into open complexes requires the ATPase activity of activator proteins that bind remotely upstream of the transcriptional start site. These activators belong to the large AAA protein family and the majority of them consist of an N-terminal regulatory domain, a central AAA domain and a C-terminal DNA binding domain. Here we use a functional variant of the NorR activator, a dedicated NO sensor, to provide the first structural and functional characterisation of a full length AAA activator in complex with its enhancer DNA. Our data suggest an inter-dependent and synergistic relationship of all three functional domains and provide an explanation for the dependence of NorR on enhancer DNA. Our results show that NorR readily assembles into higher order oligomers upon enhancer binding, independent of activating signals. Upon inducing signals, the N-terminal regulatory domain relocates to the periphery of the AAA ring. Together our data provide an assembly and activation mechanism for NorR.
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Affiliation(s)
- Matt Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
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34
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Zhou Y, Asahara H, Schneider N, Dranchak P, Inglese J, Chong S. Engineering bacterial transcription regulation to create a synthetic in vitro two-hybrid system for protein interaction assays. J Am Chem Soc 2014; 136:14031-8. [PMID: 25188838 PMCID: PMC4195380 DOI: 10.1021/ja502512g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcriptional activation of σ(54)-RNA polymerase holoenzyme (σ(54)-RNAP) in bacteria is dependent on a cis-acting DNA element (bacterial enhancer), which recruits the bacterial enhancer-binding protein to contact the holoenzyme via DNA looping. Using a constructive synthetic biology approach, we recapitulated such process of transcriptional activation by recruitment in a reconstituted cell-free system, assembled entirely from a defined number of purified components. We further engineered the bacterial enhancer-binding protein PspF to create an in vitro two-hybrid system (IVT2H), capable of carrying out gene regulation in response to expressed protein interactions. Compared with genetic systems and other in vitro methods, IVT2H not only allows detection of different types of protein interactions in just a few hours without involving cells but also provides a general correlation of the relative binding strength of the protein interaction with the IVT2H signal. Due to its reconstituted nature, IVT2H provides a biochemical assay platform with a clean and defined background. We demonstrated the proof-of-concept of using IVT2H as an alternative assay for high throughput screening of small-molecule inhibitors of protein-protein interaction.
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Affiliation(s)
- Ying Zhou
- New England Biolabs, Inc. 240 County Road, Ipswich, Massachusetts 01938, United States
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35
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Lu X, Li X, Guo K, Wang J, Huang M, Wang JL, Xie TZ, Moorefield CN, Cheng SZD, Wesdemiotis C, Newkome GR. One ligand in dual roles: self-assembly of a bis-rhomboidal-shaped, three-dimensional molecular wheel. Chemistry 2014; 20:13094-8. [PMID: 25155653 DOI: 10.1002/chem.201404358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 12/22/2022]
Abstract
A facile high yield, self-assembly process that leads to a terpyridine-based, three-dimensional, bis-rhomboidal-shaped, molecular wheel is reported. The desired coordination-driven supramolecular wheel involves eight structurally distorted tristerpyridine (tpy) ligands possessing a 60° angle between the adjacent tpy units and twelve Zn(2+) ions. The tpy ligand plays dual roles in the self-assembly process: two are staggered at 180° to create the internal hub, while six produce the external rim. The wheel can be readily generated by mixing the tpy ligand and Zn(2+) in a stoichiometric ratio of 2:3; full characterization is provided by ESI-MS, NMR spectroscopy, and TEM imaging.
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Affiliation(s)
- Xiaocun Lu
- Department of Polymer Science, Department of Chemistry, The University of Akron, 302 Buchtel Common, Akron, OH 44325 (USA) http://www.dendrimers.com
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36
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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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37
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Jovanovic M, Lawton E, Schumacher J, Buck M. Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the type III secretion system. FEMS Microbiol Lett 2014; 356:201-11. [PMID: 24863420 PMCID: PMC4145663 DOI: 10.1111/1574-6968.12476] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022] Open
Abstract
Pseudomonas syringae pv. tomato DC3000, a plant pathogenic gram-negative bacterium, employs the type III secretion system (T3SS) to cause disease in tomato and Arabidopsis and to induce the hypersensitive response in nonhost plants. The expression of T3SS is regulated by the HrpL extracytoplasmic sigma factor. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS and negative regulator HrpV. In this study, we analysed the organization of HrpRS and HrpV regulatory proteins and interplay between them. We identified one key residue I26 in HrpS required for repression by HrpV. Substitution of I26 in HrpS abolishes its interaction with HrpV and impairs interactions between HrpS and HrpR and the self-association of HrpS. We show that HrpS self-associates and can associate simultaneously with HrpR and HrpV. We now propose that HrpS has a central role in the assembly of the regulatory HrpRSV complex. Deletion analysis of HrpR and HrpS proteins showed that C-terminal parts of HrpR and HrpS confer determinants indispensable for their self-assembly.
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Affiliation(s)
- Milija Jovanovic
- Department of Life Sciences, Imperial College London, London, UK
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38
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Wang M, Wang C, Hao XQ, Liu J, Li X, Xu C, Lopez A, Sun L, Song MP, Yang HB, Li X. Hexagon Wreaths: Self-Assembly of Discrete Supramolecular Fractal Architectures Using Multitopic Terpyridine Ligands. J Am Chem Soc 2014; 136:6664-71. [DOI: 10.1021/ja501417g] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ming Wang
- Department
of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Chao Wang
- Department
of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Xin-Qi Hao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Jingjing Liu
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xiaohong Li
- College
of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Chenglong Xu
- College
of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Alberto Lopez
- Department
of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Luyi Sun
- Department of Chemical & Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Mao-Ping Song
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Hai-Bo Yang
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, Department
of Chemistry, East China Normal University, Shanghai 200062, P. R. China
| | - Xiaopeng Li
- Department
of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
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39
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Sysoeva TA, Chowdhury S, Nixon BT. Breaking symmetry in multimeric ATPase motors. Cell Cycle 2014; 13:1509-10. [PMID: 24755939 PMCID: PMC4050149 DOI: 10.4161/cc.28957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Tatyana A Sysoeva
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park, PA USA
| | - Saikat Chowdhury
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park, PA USA
| | - B Tracy Nixon
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park, PA USA
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40
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Abstract
Bacterial cells continuously sense and respond to their environment using their inherent signalling and gene regulatory networks. Cells are equipped with parallel signalling pathways, which can specifically cope with individual input signals, while interconnectivities between pathways lead to an enhanced complexity of regulatory responses that enable sophisticated adaptation. In principle, any cell signalling pathway may be rewired to respond to non-cognate signals by exchanging and recombining their underlying cognate signalling components. In the present article, we review the engineering strategies and use of chimaeric regulatory proteins in cell signalling pathways, especially the TCS (two-component signalling) system in bacteria, to achieve novel customized signalling or regulatory functions. We envisage that engineered chimaeric regulatory proteins can play an important role to aid both forward and reverse engineering of biological systems for many desired applications.
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41
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Afanasyeva A, Hirtreiter A, Schreiber A, Grohmann D, Pobegalov G, McKay AR, Tsaneva I, Petukhov M, Käs E, Grigoriev M, Werner F. Lytic water dynamics reveal evolutionarily conserved mechanisms of ATP hydrolysis by TIP49 AAA+ ATPases. Structure 2014; 22:549-59. [PMID: 24613487 PMCID: PMC3991330 DOI: 10.1016/j.str.2014.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/29/2014] [Accepted: 02/01/2014] [Indexed: 11/24/2022]
Abstract
Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis. We have studied the single TIP49 ortholog (mkTIP49) from the archaeon M. kandleri We propose a model for assembly of the pre-transition state for ATP hydrolysis Trans-aspartates downregulate ATP hydrolysis by mkTIP49 hexamers Mutational analysis confirms a highly conserved mechanism for lytic water activation
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Affiliation(s)
- Arina Afanasyeva
- Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia
| | - Angela Hirtreiter
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Anne Schreiber
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Georgii Pobegalov
- Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia
| | - Adam R McKay
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Irina Tsaneva
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Michael Petukhov
- Department of Biophysics, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia
| | - Emmanuel Käs
- UMR 5099, CNRS, Toulouse F-31000, France; Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse F-31000, France.
| | - Mikhail Grigoriev
- UMR 5099, CNRS, Toulouse F-31000, France; Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse F-31000, France.
| | - Finn Werner
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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42
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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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43
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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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44
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Sysoeva TA, Chowdhury S, Guo L, Nixon BT. Nucleotide-induced asymmetry within ATPase activator ring drives σ54-RNAP interaction and ATP hydrolysis. Genes Dev 2014; 27:2500-11. [PMID: 24240239 PMCID: PMC3841738 DOI: 10.1101/gad.229385.113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, crystallography, and electron microscopy (EM) reconstructions revealed that partial ATP occupancy caused the heptameric closed ring of the bacterial enhancer-binding protein (bEBP) NtrC1 to rearrange into a hexameric split ring of striking asymmetry. The highly conserved and functionally crucial GAFTGA loops responsible for interacting with σ54-RNA polymerase formed a spiral staircase. We propose that splitting of the ensemble directs ATP hydrolysis within the oligomer, and the ring's asymmetry guides interaction between ATPase and the complex of σ54 and promoter DNA. Similarity between the structure of the transcriptional activator NtrC1 and those of distantly related helicases Rho and E1 reveals a general mechanism in homomeric ATPases whereby complex allostery within the ring geometry forms asymmetric functional states that allow these biological motors to exert directional forces on their target macromolecules.
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Affiliation(s)
- Tatyana A Sysoeva
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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45
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Wang C, Hao XQ, Wang M, Guo C, Xu B, Tan EN, Zhang YY, Yu Y, Li ZY, Yang HB, Song MP, Li X. Self-assembly of giant supramolecular cubes with terpyridine ligands as vertices and metals on edges. Chem Sci 2014. [DOI: 10.1039/c3sc52965g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Giant metallo-supramolecular cubes were assembled by using tritopic terpyridine ligands as corners and metal ions as edges.
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Affiliation(s)
- Chao Wang
- Department of Chemistry and Biochemistry
- Texas State University
- San Marcos, USA
| | - Xin-Qi Hao
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450052, P. R. China
| | - Ming Wang
- Department of Chemistry and Biochemistry
- Texas State University
- San Marcos, USA
| | - Cunlan Guo
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Bingqian Xu
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Eric N. Tan
- Department of Chemistry and Biochemistry
- Texas State University
- San Marcos, USA
| | - Yan-Yan Zhang
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- East China Normal University
- Shanghai 200062, P. R. China
| | - Yihua Yu
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- East China Normal University
- Shanghai 200062, P. R. China
| | - Zhong-Yu Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes
- Department of Chemistry
- East China Normal University
- Shanghai 200062, P. R. China
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes
- Department of Chemistry
- East China Normal University
- Shanghai 200062, P. R. China
| | - Mao-Ping Song
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450052, P. R. China
| | - Xiaopeng Li
- Department of Chemistry and Biochemistry
- Texas State University
- San Marcos, USA
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46
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Mehta P, Jovanovic G, Lenn T, Bruckbauer A, Engl C, Ying L, Buck M. Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells. Nat Commun 2013; 4:1997. [PMID: 23764692 PMCID: PMC3709507 DOI: 10.1038/ncomms2997] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/09/2013] [Indexed: 12/02/2022] Open
Abstract
Bacterial enhancer-dependent transcription systems support major adaptive responses and offer a singular paradigm in gene control analogous to complex eukaryotic systems. Here we report new mechanistic insights into the control of one-membrane stress-responsive bacterial enhancer-dependent system. Using millisecond single-molecule fluorescence microscopy of live cells we determine the localizations, two-dimensional diffusion dynamics and stoichiometries of complexes of the bacterial enhancer-binding ATPase PspF during its action at promoters as regulated by inner membrane interacting negative controller PspA. We establish that a stable repressive PspF–PspA complex is located in the nucleoid, transiently communicating with the inner membrane via PspA. The PspF as a hexamer stably binds only one of the two psp promoters at a time, suggesting that psp promoters will fire asynchronously and cooperative interactions of PspF with the basal transcription complex influence dynamics of the PspF hexamer–DNA complex and regulation of the psp promoters. Cellular adaptive responses require temporal and spatial control of key regulatory protein complexes. Mehta et al. describe the dynamic interaction of a transcriptional activator mediating membrane stress response in E. coli with its negative regulator, the cell membrane and the transcription machinery.
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Affiliation(s)
- Parul Mehta
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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47
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Sysoeva TA, Yennawar N, Allaire M, Nixon BT. Crystallization and preliminary X-ray analysis of the ATPase domain of the σ(54)-dependent transcription activator NtrC1 from Aquifex aeolicus bound to the ATP analog ADP-BeFx. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1384-8. [PMID: 24316836 PMCID: PMC3855726 DOI: 10.1107/s174430911302976x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 10/30/2013] [Indexed: 11/10/2022]
Abstract
One way that bacteria regulate the transcription of specific genes to adapt to environmental challenges is to use different σ factors that direct the RNA polymerase holoenzyme to distinct promoters. Unlike σ(70) RNA polymerase (RNAP), σ(54) RNAP is unable to initiate transcription without an activator: enhancer-binding protein (EBP). All EBPs contain one ATPase domain that belongs to the family of ATPases associated with various cellular activities (AAA+ ATPases). AAA+ ATPases use the energy of ATP hydrolysis to remodel different target macromolecules to perform distinct functions. These mechanochemical enzymes are known to form ring-shaped oligomers whose conformations strongly depend upon nucleotide status. Here, the crystallization of the AAA+ ATPase domain of an EBP from Aquifex aeolicus, NtrC1, in the presence of the non-hydrolyzable ATP analog ADP-BeFx is reported. X-ray diffraction data were collected from two crystals from two different protein fractions of the NtrC1 ATPase domain. Previously, this domain was co-crystallized with ADP and ATP, but the latter crystals were grown from the Walker B substitution variant E239A. Therefore, the new data sets are the first for a wild-type EBP ATPase domain co-crystallized with an ATP analog and they reveal a new crystal form. The resulting structure(s) will shed light on the mechanism of EBP-type transcription activators.
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Affiliation(s)
- Tatyana A. Sysoeva
- Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Marc Allaire
- NLSL, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - B. Tracy Nixon
- Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
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48
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Vidangos N, Maris AE, Young A, Hong E, Pelton JG, Batchelor JD, Wemmer DE. Structure, function, and tethering of DNA-binding domains in σ⁵⁴ transcriptional activators. Biopolymers 2013; 99:1082-96. [PMID: 23818155 PMCID: PMC3932985 DOI: 10.1002/bip.22333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 06/18/2013] [Indexed: 11/07/2022]
Abstract
We compare the structure, activity, and linkage of DNA-binding domains (DBDs) from σ(54) transcriptional activators and discuss how the properties of the DBDs and the linker to the neighboring domain are affected by the overall properties and requirements of the full proteins. These transcriptional activators bind upstream of specific promoters that utilize σ(54)-polymerase. Upon receiving a signal the activators assemble into hexamers, which then, through adenosine triphosphate (ATP) hydrolysis, drive a conformational change in polymerase that enables transcription initiation. We present structures of the DBDs of activators nitrogen regulatory protein C 1 (NtrC1) and Nif-like homolog 2 (Nlh2) from the thermophile Aquifex aeolicus. The structures of these domains and their relationship to other parts of the activators are discussed. These structures are compared with previously determined structures of the DBDs of NtrC4, NtrC, ZraR, and factor for inversion stimulation. The N-terminal linkers that connect the DBDs to the central domains in NtrC1 and Nlh2 were studied and found to be unstructured. Additionally, a crystal structure of full-length NtrC1 was solved, but density of the DBDs was extremely weak, further indicating that the linker between ATPase and DBDs functions as a flexible tether. Flexible linking of ATPase and DBDs is likely necessary to allow assembly of the active hexameric ATPase ring. The comparison of this set of activators also shows clearly that strong dimerization of the DBD only occurs when other domains do not dimerize strongly.
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Affiliation(s)
- Natasha Vidangos
- Department of Chemistry and QB3 Institute, University of California, Berkeley, CA, 94720-1460
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49
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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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50
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MuB is an AAA+ ATPase that forms helical filaments to control target selection for DNA transposition. Proc Natl Acad Sci U S A 2013; 110:E2441-50. [PMID: 23776210 DOI: 10.1073/pnas.1309499110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MuB is an ATP-dependent nonspecific DNA-binding protein that regulates the activity of the MuA transposase and captures target DNA for transposition. Mechanistic understanding of MuB function has previously been hindered by MuB's poor solubility. Here we combine bioinformatic, mutagenic, biochemical, and electron microscopic analyses to unmask the structure and function of MuB. We demonstrate that MuB is an ATPase associated with diverse cellular activities (AAA+ ATPase) and forms ATP-dependent filaments with or without DNA. We also identify critical residues for MuB's ATPase, DNA binding, protein polymerization, and MuA interaction activities. Using single-particle electron microscopy, we show that MuB assembles into a helical filament, which binds the DNA in the axial channel. The helical parameters of the MuB filament do not match those of the coated DNA. Despite this protein-DNA symmetry mismatch, MuB does not deform the DNA duplex. These findings, together with the influence of MuB filament size on strand-transfer efficiency, lead to a model in which MuB-imposed symmetry transiently deforms the DNA at the boundary of the MuB filament and results in a bent DNA favored by MuA for transposition.
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