1
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Germany EM, Thewasano N, Imai K, Maruno Y, Bamert RS, Stubenrauch CJ, Dunstan RA, Ding Y, Nakajima Y, Lai X, Webb CT, Hidaka K, Tan KS, Shen H, Lithgow T, Shiota T. Dual recognition of multiple signals in bacterial outer membrane proteins enhances assembly and maintains membrane integrity. eLife 2024; 12:RP90274. [PMID: 38226797 PMCID: PMC10945584 DOI: 10.7554/elife.90274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Outer membrane proteins (OMPs) are essential components of the outer membrane of Gram-negative bacteria. In terms of protein targeting and assembly, the current dogma holds that a 'β-signal' imprinted in the final β-strand of the OMP engages the β-barrel assembly machinery (BAM) complex to initiate membrane insertion and assembly of the OMP into the outer membrane. Here, we revealed an additional rule that signals equivalent to the β-signal are repeated in other, internal β-strands within bacterial OMPs, by peptidomimetic and mutational analysis. The internal signal is needed to promote the efficiency of the assembly reaction of these OMPs. BamD, an essential subunit of the BAM complex, recognizes the internal signal and the β-signal, arranging several β-strands and partial folding for rapid OMP assembly. The internal signal-BamD ordering system is not essential for bacterial viability but is necessary to retain the integrity of the outer membrane against antibiotics and other environmental insults.
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Affiliation(s)
- Edward M Germany
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Nakajohn Thewasano
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Yuki Maruno
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Rebecca S Bamert
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Christopher J Stubenrauch
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Rhys A Dunstan
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Yue Ding
- Department of Materials Science and Engineering, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash UniversityClaytonAustralia
| | - Yukari Nakajima
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - XiangFeng Lai
- Department of Materials Science and Engineering, Monash UniversityClaytonAustralia
| | - Chaille T Webb
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Kentaro Hidaka
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
| | - Kher Shing Tan
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Hsinhui Shen
- Department of Materials Science and Engineering, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash UniversityClaytonAustralia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash UniversityClaytonAustralia
- Infection Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash UniversityClaytonAustralia
| | - Takuya Shiota
- Frontier Science Research Center, University of MiyazakiMiyazakiJapan
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazakiJapan
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2
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Shen C, Chang S, Luo Q, Chan KC, Zhang Z, Luo B, Xie T, Lu G, Zhu X, Wei X, Dong C, Zhou R, Zhang X, Tang X, Dong H. Structural basis of BAM-mediated outer membrane β-barrel protein assembly. Nature 2023; 617:185-193. [PMID: 37100902 DOI: 10.1038/s41586-023-05988-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of materials1-3. All known OMPs share the antiparallel β-strand topology4, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial β-barrel assembly machinery (BAM) to initiate OMP folding5,6; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.
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Affiliation(s)
- Chongrong Shen
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shenghai Chang
- Department of Biophysics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinghua Luo
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Kevin Chun Chan
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
| | - Zhibo Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Bingnan Luo
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Teng Xie
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guangwen Lu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xiaofeng Zhu
- College of Life Science, Sichuan University, Chengdu, China
| | - Xiawei Wei
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Changjiang Dong
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Xing Zhang
- Department of Biophysics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaodi Tang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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3
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The conformations and basal conformational dynamics of translocation factor SecDF vary with translocon SecYEG interaction. J Biol Chem 2022; 298:102412. [PMID: 36007614 PMCID: PMC9508474 DOI: 10.1016/j.jbc.2022.102412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
The general secretory, or Sec, system is a primary protein export pathway from the cytosol of Escherichia coli and all eubacteria. Integral membrane protein complex SecDF is a translocation factor that enhances polypeptide secretion, which is driven by the Sec translocase, consisting of translocon SecYEG and ATPase SecA. SecDF is thought to utilize a proton gradient to effectively pull precursor proteins from the cytoplasm into the periplasm. Working models have been developed to describe the structure and function of SecDF, but important mechanistic questions remain unanswered. Atomic force microscopy (AFM) is a powerful technique for studying the dynamics of single-molecule systems including membrane proteins in near-native conditions. The sharp tip of the AFM provides direct access to membrane-external protein conformations. Here, we acquired AFM images and kymographs (∼100 ms resolution) to visualize SecDF protrusions in near-native supported lipid bilayers and compared the experimental data to simulated AFM images based on static structures. When studied in isolation, SecDF exhibited a stable and compact conformation close to the lipid bilayer surface, indicative of a resting state. Interestingly, upon SecYEG introduction, we observed changes in both SecDF conformation and conformational dynamics. The population of periplasmic protrusions corresponding to an intermediate form of SecDF, which is thought to be active in precursor protein handling, increased >9-fold. In conjunction, our dynamics measurements revealed an enhancement in the transition rate between distinct SecDF conformations when the translocon was present. Together, this work provides a novel vista of basal-level SecDF conformational dynamics in near-native conditions.
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4
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Zheng Z, Blum A, Banerjee T, Wang Q, Dantis V, Oliver D. Determination of the Oligomeric State of SecYEG Protein Secretion Channel Complex Using in Vivo Photo- and Disulfide Cross-linking. J Biol Chem 2016; 291:5997-6010. [PMID: 26747607 DOI: 10.1074/jbc.m115.694844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Indexed: 11/06/2022] Open
Abstract
SecYEG protein of bacteria or Sec61αβγ of eukaryotes is a universally conserved heterotrimeric protein channel complex that accommodates the partitioning of membrane proteins into the lipid bilayer as well as the secretion of proteins to the trans side of the plasma or endoplasmic reticular membrane, respectively. SecYEG function is facilitated by cytosolic partners, mainly a nascent chain-ribosome complex or the SecA ATPase motor protein. Extensive efforts utilizing both biochemical and biophysical approaches have been made to determine whether SecYEG functions as a monomer or a dimer, but such approaches have often generated conflicting results. Here we have employed site-specific in vivo photo-cross-linking or cysteine cross-linking, along with co-immunoprecipitation or SecA footprinting techniques to readdress this issue. Our findings show that the SecY dimer to monomer ratio is relatively constant regardless of whether translocons are actively engaged with protein substrate or not. Under the former conditions the SecY dimer can be captured associated with a translocon-jammed substrate, indicative of SecY dimer function. Furthermore, SecA ATPase can be cross-linked to two copies of SecY when the complex contains a translocation intermediate. Collectively, our results suggest that SecYEG dimers are functional units of the translocon.
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Affiliation(s)
- Zeliang Zheng
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Amy Blum
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Tithi Banerjee
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Qianyu Wang
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Virginia Dantis
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Donald Oliver
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459.
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5
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Cléon F, Habersetzer J, Alcock F, Kneuper H, Stansfeld PJ, Basit H, Wallace MI, Berks BC, Palmer T. The TatC component of the twin-arginine protein translocase functions as an obligate oligomer. Mol Microbiol 2015; 98:111-29. [PMID: 26112072 PMCID: PMC5102672 DOI: 10.1111/mmi.13106] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 12/24/2022]
Abstract
The Tat protein export system translocates folded proteins across the bacterial cytoplasmic membrane and the plant thylakoid membrane. The Tat system in Escherichia coli is composed of TatA, TatB and TatC proteins. TatB and TatC form an oligomeric, multivalent receptor complex that binds Tat substrates, while multiple protomers of TatA assemble at substrate‐bound TatBC receptors to facilitate substrate transport. We have addressed whether oligomerisation of TatC is an absolute requirement for operation of the Tat pathway by screening for dominant negative alleles of tatC that inactivate Tat function in the presence of wild‐type tatC. Single substitutions that confer dominant negative TatC activity were localised to the periplasmic cap region. The variant TatC proteins retained the ability to interact with TatB and with a Tat substrate but were unable to support the in vivo assembly of TatA complexes. Blue‐native PAGE analysis showed that the variant TatC proteins produced smaller TatBC complexes than the wild‐type TatC protein. The substitutions did not alter disulphide crosslinking to neighbouring TatC molecules from positions in the periplasmic cap but abolished a substrate‐induced disulphide crosslink in transmembrane helix 5 of TatC. Our findings show that TatC functions as an obligate oligomer.
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Affiliation(s)
- François Cléon
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Johann Habersetzer
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Holger Kneuper
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Hajra Basit
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Mark I Wallace
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tracy Palmer
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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6
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Hsieh YH, Zou J, Jin JS, Yang H, Chen Y, Jiang C, Yang J, Tai PC. Monitoring channel activities of proteoliposomes with SecA and Cx26 gap junction in single oocytes. Anal Biochem 2015; 480:58-66. [PMID: 25862083 DOI: 10.1016/j.ab.2015.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
Establishing recordable channels in membranes of oocytes formed by expressing exogenous complementary DNA (cDNA) or messenger RNA (mRNA) has contributed greatly to understanding the molecular mechanisms of channel functions. Here, we report the extension of this semi-physiological system for monitoring the channel activity of preassembled membrane proteins in single cell oocytes by injecting reconstituted proteoliposomes along with substrates or regulatory molecules. We build on the observation that SecA from various bacteria forms active protein-conducting channels with injection of proteoliposomes, protein precursors, and ATP-Mg(2+). Such activity was enhanced by reconstituted SecYEG-SecDF•YajC liposome complexes that could be monitored easily and efficiently, providing correlation of in vitro and intact cell functionality. In addition, inserting reconstituted gap junction Cx26 liposomes into the oocytes allowed the demonstration of intracellular/extracellular Ca(2+)-regulated hemi-channel activities. The channel activities can be detected rapidly after injection, can be monitored for various effectors, and are dependent on specific exogenous lipid compositions. This simple and effective functional system with low endogenous channel activity should have broad applications for monitoring the specific channel activities of complex interactions of purified membrane proteins with their effectors and regulatory molecules.
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Affiliation(s)
- Ying-Hsin Hsieh
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Juan Zou
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Jin-Shan Jin
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Hsiuchin Yang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Yanyi Chen
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Chun Jiang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny Yang
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Phang C Tai
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
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7
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Hsieh YH, Huang YJ, Jin JS, Yu L, Yang H, Jiang C, Wang B, Tai PC. Mechanisms of Rose Bengal inhibition on SecA ATPase and ion channel activities. Biochem Biophys Res Commun 2014; 454:308-12. [PMID: 25450394 DOI: 10.1016/j.bbrc.2014.10.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
SecA is an essential protein possessing ATPase activity in bacterial protein translocation for which Rose Bengal (RB) is the first reported sub-micromolar inhibitor in ATPase activity and protein translocation. Here, we examined the mechanisms of inhibition on various forms of SecA ATPase by conventional enzymatic assays, and by monitoring the SecA-dependent channel activity in the semi-physiological system in cells. We build on the previous observation that SecA with liposomes form active protein-conducting channels in the oocytes. Such ion channel activity is enhanced by purified Escherichia coli SecYEG-SecDF·YajC liposome complexes. Inhibition by RB could be monitored, providing correlation of in vitro activity and intact cell functionality. In this work, we found the intrinsic SecA ATPase is inhibited by RB competitively at low ATP concentration, and non-competitively at high ATP concentrations while the translocation ATPase with precursors and SecYEG is inhibited non-competitively by RB. The Inhibition by RB on SecA channel activity in the oocytes with exogenous ATP-Mg(2+), mimicking translocation ATPase activity, is also non-competitive. The non-competitive inhibition on channel activity has also been observed with SecA from other bacteria which otherwise would be difficult to examine without the cognate precursors and membranes.
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Affiliation(s)
- Ying-Hsin Hsieh
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Ying-Ju Huang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Jin-Shan Jin
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Liyan Yu
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Hsiuchin Yang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Chun Jiang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Binghe Wang
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Phang C Tai
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States.
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8
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Kedrov A, Kusters I, Driessen AJM. Single-Molecule Studies of Bacterial Protein Translocation. Biochemistry 2013; 52:6740-54. [DOI: 10.1021/bi400913x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alexej Kedrov
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Ilja Kusters
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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9
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Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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10
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Sanganna Gari RR, Frey NC, Mao C, Randall LL, King GM. Dynamic structure of the translocon SecYEG in membrane: direct single molecule observations. J Biol Chem 2013; 288:16848-16854. [PMID: 23609442 PMCID: PMC3675617 DOI: 10.1074/jbc.m113.471870] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/19/2013] [Indexed: 11/06/2022] Open
Abstract
Purified SecYEG was reconstituted into liposomes and studied in near-native conditions using atomic force microscopy. These SecYEG proteoliposomes were active in translocation assays. Changes in the structure of SecYEG as a function of time were directly visualized. The dynamics observed were significant in magnitude (∼1-10 Å) and were attributed to the two large loops of SecY linking transmembrane helices 6-7 and 8-9. In addition, we identified a distribution between monomers and dimers of SecYEG as well as a smaller population of higher order oligomers. This work provides a new vista of the flexible and dynamic structure of SecYEG, an intricate and vital membrane protein.
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Affiliation(s)
| | - Nathan C Frey
- Departments of Physics and Astronomy, Columbia, Missouri 65211
| | - Chunfeng Mao
- Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Linda L Randall
- Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Gavin M King
- Departments of Physics and Astronomy, Columbia, Missouri 65211; Biochemistry, University of Missouri, Columbia, Missouri 65211.
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11
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Glycolipozyme MPIase is essential for topology inversion of SecG during preprotein translocation. Proc Natl Acad Sci U S A 2013; 110:9734-9. [PMID: 23716687 DOI: 10.1073/pnas.1303160110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Presecretory proteins are translocated across biological membranes through protein-conducting channels such as Sec61 (eukaryotes) and SecYEG (bacteria). SecA, a translocation ATPase, pushes preproteins out with dynamic structural changes through SecYEG. SecG, a subunit of the SecYEG channel possessing two transmembrane stretches (TMs), undergoes topology inversion coupled with SecA-dependent translocation. Recently, we characterized membrane protein integrase (MPIase), a glycolipozyme involved in not only protein integration into membranes but also preprotein translocation. We report here that SecG inversion occurs only when MPIase associates with SecYEG. We also found that MPIase modulates the dimer orientation of SecYEG. Cysteine-scanning mutagenesis mapped SecG TM 2 to a relatively hydrophilic environment. The dimer formation of SecG, crosslinked at TM 2, was not observed on SecG inversion, indicating that SecYEG undergoes a dynamic structural change during preprotein translocation.
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12
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Solov'eva TF, Novikova OD, Portnyagina OY. Biogenesis of β-barrel integral proteins of bacterial outer membrane. BIOCHEMISTRY (MOSCOW) 2013; 77:1221-36. [PMID: 23240560 DOI: 10.1134/s0006297912110016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gram-negative bacteria are enveloped by two membranes, the inner (cytoplasmic) (CM) and the outer (OM). The majority of integral outer membrane proteins are arranged in β-barrels of cylindrical shape composed of amphipathic antiparallel β-strands. In bacteria, β-barrel proteins function as water-filled pores, active transporters, enzymes, receptors, and structural proteins. Proteins of bacterial OM are synthesized in the cytoplasm as unfolded polypeptides with an N-terminal sequence that marks them for transport across the CM. Precursors of membrane proteins move through the aqueous medium of the cytosol and periplasm under the protection of chaperones (SecB, Skp, SurA, and DegP), then cross the CM via the Sec system composed of a polypeptide-conducting channel (SecYEG) and ATPase (SecA), the latter providing the energy for the translocation of the pre-protein. Pre-protein folding and incorporation in the OM require the participation of the Bam-complex, probably without the use of energy. This review summarizes current data on the biogenesis of the β-barrel proteins of bacterial OM. Data on the structure of the proteins included in the multicomponent system for delivery of the OM proteins to their destination in the cell and on their complexes with partners, including pre-proteins, are presented. Molecular models constructed on the basis of structural, genetic, and biochemical studies that describe the mechanisms of β-barrel protein assembly by this molecular transport machinery are also considered.
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Affiliation(s)
- T F Solov'eva
- Elyakov Pacific Institute of Bioorganic Chemistry, Russian Academy of Sciences, Vladivostok, 690022, Russia.
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13
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Zhou Q, Sun S, Tai P, Sui SF. Structural characterization of the complex of SecB and metallothionein-labeled proOmpA by cryo-electron microscopy. PLoS One 2012; 7:e47015. [PMID: 23056562 PMCID: PMC3464278 DOI: 10.1371/journal.pone.0047015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022] Open
Abstract
ProOmpA is a preprotein that is translocated across the plasma membrane by the general secretory pathway in Escherichia coli. The molecular chaperon SecB in Sec pathway can recognize and bind proOmpA for its translocation. However, the structure of the SecB/proOmpA complex remains unknown. Here, we constructed an uncleavable proOmpA fused with metallothionein at its C-terminus and labeled it with metals in vitro for the study of cryo-electron microscopy. Using single particle cryo-electron microscopy, we reconstructed 3D structure of the stable SecB/proOmpA complex. The structure shows that the major portion of preprotein locates on one side of SecB tetramer, resulting in an asymmetric binding pattern. This work also provides a possible approach to the structure determination of small protein complexes by cryo-electron microscopy.
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Affiliation(s)
- Qiang Zhou
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Phang Tai
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Sen-Fang Sui
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
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14
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Bonardi F, Nouwen N, Feringa BL, Driessen AJM. Protein conducting channels—mechanisms, structures and applications. MOLECULAR BIOSYSTEMS 2012; 8:709-19. [DOI: 10.1039/c2mb05433g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Luirink J, Yu Z, Wagner S, de Gier JW. Biogenesis of inner membrane proteins in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:965-76. [PMID: 22201544 DOI: 10.1016/j.bbabio.2011.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/05/2011] [Accepted: 12/12/2011] [Indexed: 11/26/2022]
Abstract
The inner membrane proteome of the model organism Escherichia coli is composed of inner membrane proteins, lipoproteins and peripherally attached soluble proteins. Our knowledge of the biogenesis of inner membrane proteins is rapidly increasing. This is in particular true for the early steps of biogenesis - protein targeting to and insertion into the membrane. However, our knowledge of inner membrane protein folding and quality control is still fragmentary. Furthering our knowledge in these areas will bring us closer to understand the biogenesis of individual inner membrane proteins in the context of the biogenesis of the inner membrane proteome of Escherichia coli as a whole. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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Affiliation(s)
- Joen Luirink
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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16
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A single copy of SecYEG is sufficient for preprotein translocation. EMBO J 2011; 30:4387-97. [PMID: 21897368 DOI: 10.1038/emboj.2011.314] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 07/15/2011] [Indexed: 11/08/2022] Open
Abstract
The heterotrimeric SecYEG complex comprises a protein-conducting channel in the bacterial cytoplasmic membrane. SecYEG functions together with the motor protein SecA in preprotein translocation. Here, we have addressed the functional oligomeric state of SecYEG when actively engaged in preprotein translocation. We reconstituted functional SecYEG complexes labelled with fluorescent markers into giant unilamellar vesicles at a natively low density. Förster's resonance energy transfer and fluorescence (cross-) correlation spectroscopy with single-molecule sensitivity allowed for independent observations of the SecYEG and preprotein dynamics, as well as complex formation. In the presence of ATP and SecA up to 80% of the SecYEG complexes were loaded with a preprotein translocation intermediate. Neither the interaction with SecA nor preprotein translocation resulted in the formation of SecYEG oligomers, whereas such oligomers can be detected when enforced by crosslinking. These data imply that the SecYEG monomer is sufficient to form a functional translocon in the lipid membrane.
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17
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Dalal K, Duong F. The SecY complex: conducting the orchestra of protein translocation. Trends Cell Biol 2011; 21:506-14. [DOI: 10.1016/j.tcb.2011.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 04/11/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022]
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18
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Affiliation(s)
- Christine L. Hagan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; ,
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19
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Quaternary structure of SecA in solution and bound to SecYEG probed at the single molecule level. Structure 2011; 19:430-9. [PMID: 21397193 DOI: 10.1016/j.str.2010.12.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/17/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022]
Abstract
Dual-color fluorescence-burst analysis (DCFBA) was applied to measure the quaternary structure and high-affinity binding of the bacterial motor protein SecA to the protein-conducting channel SecYEG reconstituted into lipid vesicles. DCFBA is an equilibrium technique that enables the direct observation and quantification of protein-protein interactions at the single molecule level. SecA binds to SecYEG as a dimer with a nucleotide- and preprotein-dependent dissociation constant. One of the SecA protomers binds SecYEG in a salt-resistant manner, whereas binding of the second protomer is salt sensitive. Because protein translocation is salt sensitive, we conclude that the dimeric state of SecA is required for protein translocation. A structural model for the dimeric assembly of SecA while bound to SecYEG is proposed based on the crystal structures of the Thermotoga maritima SecA-SecYEG and the Escherichia coli SecA dimer.
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20
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SecA, a remarkable nanomachine. Cell Mol Life Sci 2011; 68:2053-66. [PMID: 21479870 PMCID: PMC3101351 DOI: 10.1007/s00018-011-0681-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 03/22/2011] [Accepted: 03/28/2011] [Indexed: 01/03/2023]
Abstract
Biological cells harbor a variety of molecular machines that carry out mechanical work at the nanoscale. One of these nanomachines is the bacterial motor protein SecA which translocates secretory proteins through the protein-conducting membrane channel SecYEG. SecA converts chemically stored energy in the form of ATP into a mechanical force to drive polypeptide transport through SecYEG and across the cytoplasmic membrane. In order to accommodate a translocating polypeptide chain and to release transmembrane segments of membrane proteins into the lipid bilayer, SecYEG needs to open its central channel and the lateral gate. Recent crystal structures provide a detailed insight into the rearrangements required for channel opening. Here, we review our current understanding of the mode of operation of the SecA motor protein in concert with the dynamic SecYEG channel. We conclude with a new model for SecA-mediated protein translocation that unifies previous conflicting data.
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21
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Tang Y, Pan X, Tai PC, Sui S. Electron microscopic visualization of asymmetric precursor translocation intermediates: SecA functions as a dimer. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1049-56. [PMID: 21104364 DOI: 10.1007/s11427-010-4061-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 07/22/2010] [Indexed: 11/27/2022]
Abstract
SecA, the ATPase of Sec translocase, mediates the post-translational translocation of preprotein through the protein-conducting channel SecYEG in the bacterial inner membrane. Here we report the structures of Escherichia coli Sec intermediates during preprotein translocation as visualized by electron microscopy to probe the oligomeric states of SecA during this process. We found that the translocase holoenzyme is symmetrically assembled by SecA and SecYEG on proteoliposomes, whereas the translocation intermediate 31 (I(31)) becomes asymmetric because of the presence of preprotein. Moreover, SecA is a dimer in these two translocation complexes. This work also shows surface topological changes in the components of translocation intermediates by immunogold labeling. The channel entry for preprotein translocation was found at the center of the I(31) structures. Our results indicate that the presence of preprotein introduces asymmetry into translocation intermediates, while SecA remains dimeric during the translocation process.
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Affiliation(s)
- Ying Tang
- State-Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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22
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du Plessis DJF, Nouwen N, Driessen AJM. The Sec translocase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:851-65. [PMID: 20801097 DOI: 10.1016/j.bbamem.2010.08.016] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/19/2010] [Accepted: 08/20/2010] [Indexed: 11/18/2022]
Abstract
The vast majority of proteins trafficking across or into the bacterial cytoplasmic membrane occur via the translocon. The translocon consists of the SecYEG complex that forms an evolutionarily conserved heterotrimeric protein-conducting membrane channel that functions in conjunction with a variety of ancillary proteins. For posttranslational protein translocation, the translocon interacts with the cytosolic motor protein SecA that drives the ATP-dependent stepwise translocation of unfolded polypeptides across the membrane. For the cotranslational integration of membrane proteins, the translocon interacts with ribosome-nascent chain complexes and membrane insertion is coupled to polypeptide chain elongation at the ribosome. These processes are assisted by the YidC and SecDF(yajC) complex that transiently interacts with the translocon. This review summarizes our current understanding of the structure-function relationship of the translocon and its interactions with ancillary components during protein translocation and membrane protein insertion. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- David J F du Plessis
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751NN Haren, The Netherlands
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23
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Facey SJ, Kuhn A. Biogenesis of bacterial inner-membrane proteins. Cell Mol Life Sci 2010; 67:2343-62. [PMID: 20204450 PMCID: PMC11115511 DOI: 10.1007/s00018-010-0303-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 02/01/2010] [Accepted: 02/03/2010] [Indexed: 11/26/2022]
Abstract
All cells must traffic proteins into and across their membranes. In bacteria, several pathways have evolved to enable protein transfer across the inner membrane, the periplasm, and the outer membrane. The major route of protein translocation in and across the cytoplasmic membrane is the general secretion pathway (Sec-pathway). The biogenesis of membrane proteins not only requires protein translocation but also coordinated targeting to the membrane beforehand and folding and assembly into their protein complexes afterwards to function properly in the cell. All these processes are responsible for the biogenesis of membrane proteins that mediate essential functions of the cell such as selective transport, energy conversion, cell division, extracellular signal sensing, and motility. This review will highlight the most recent developments on the structure and function of bacterial membrane proteins, focusing on the journey that integral membrane proteins take to find their final destination in the inner membrane.
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Affiliation(s)
- Sandra J. Facey
- Institute of Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Andreas Kuhn
- Institute of Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
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24
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25
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Price CE, Driessen AJM. Biogenesis of membrane bound respiratory complexes in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:748-66. [PMID: 20138092 DOI: 10.1016/j.bbamcr.2010.01.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/21/2010] [Accepted: 01/27/2010] [Indexed: 11/19/2022]
Abstract
Escherichia coli is one of the preferred bacteria for studies on the energetics and regulation of respiration. Respiratory chains consist of primary dehydrogenases and terminal reductases or oxidases linked by quinones. In order to assemble this complex arrangement of protein complexes, synthesis of the subunits occurs in the cytoplasm followed by assembly in the cytoplasm and/or membrane, the incorporation of metal or organic cofactors and the anchoring of the complex to the membrane. In the case of exported metalloproteins, synthesis, assembly and incorporation of metal cofactors must be completed before translocation across the cytoplasmic membrane. Coordination data on these processes is, however, scarce. In this review, we discuss the various processes that respiratory proteins must undergo for correct assembly and functional coupling to the electron transport chain in E. coli. Targeting to and translocation across the membrane together with cofactor synthesis and insertion are discussed in a general manner followed by a review of the coordinated biogenesis of individual respiratory enzyme complexes. Lastly, we address the supramolecular organization of respiratory enzymes into supercomplexes and their localization to specialized domains in the membrane.
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Affiliation(s)
- Claire E Price
- Department of Molecular Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
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26
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Stephenson K. Sec-dependent protein translocation across biological membranes: evolutionary conservation of an essential protein transport pathway (Review). Mol Membr Biol 2009; 22:17-28. [PMID: 16092521 DOI: 10.1080/09687860500063308] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
All living organisms, no matter how simple or complex, possess the ability to translocate proteins across biological membranes and into different cellular compartments. Although a range of membrane transport processes exist, the major pathway used to translocate proteins across the bacterial cytoplasmic membrane or the eukaryotic endoplasmic reticulum membrane is conserved and is known as the Sec or Sec61 pathway, respectively. Over the past two decades the Sec and Sec61 pathways have been studied extensively and are well characterised at the genetic and biochemical levels. However, it is only now with the recent structural determination of a number of the key elements of the pathways that the translocation complex is beginning to give up its secrets in exquisite molecular detail. This article will focus on the routes of Sec- and Sec61-dependent membrane targeting and the nature of the translocation channel in bacteria and eukaryotes.
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Affiliation(s)
- Keith Stephenson
- School of Biochemistry and Microbiology, Leeds University, Leeds, UK.
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27
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Boy D, Koch HG. Visualization of distinct entities of the SecYEG translocon during translocation and integration of bacterial proteins. Mol Biol Cell 2009; 20:1804-15. [PMID: 19158385 DOI: 10.1091/mbc.e08-08-0886] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The universally conserved SecYEG/Sec61 translocon constitutes the major protein-conducting channel in the cytoplasmic membrane of bacteria and the endoplasmic reticulum membrane of eukaryotes. It is engaged in both translocating secretory proteins across the membrane as well as in integrating membrane proteins into the lipid phase of the membrane. In the current study we have detected distinct SecYEG translocon complexes in native Escherichia coli membranes. Blue-Native-PAGE revealed the presence of a 200-kDa SecYEG complex in resting membranes. When the SecA-dependent secretory protein pOmpA was trapped inside the SecYEG channel, a smaller SecY-containing complex of approximately 140-kDa was observed, which probably corresponds to a monomeric SecYEG-substrate complex. Trapping the SRP-dependent polytopic membrane protein mannitol permease in the SecYEG translocon, resulted in two complexes of 250 and 600 kDa, each containing both SecY and the translocon-associated membrane protein YidC. The appearance of both complexes was correlated with the number of transmembrane domains that were exposed during targeting of mannitol permease to the membrane. These results suggest that the assembly or the stability of the bacterial SecYEG translocon is influenced by the substrate that needs to be transported.
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Affiliation(s)
- Diana Boy
- Institut für Biochemie und Molekularbiologie, ZBMZ, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
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28
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Chen S, Fan Y, Shen X, Sun P, Jiang G, Shen Y, Xue W, Li Y, Chen X. A molecular modeling study of the interaction between SRP-receptor complex and peptide translocon. Biochem Biophys Res Commun 2008; 377:346-350. [DOI: 10.1016/j.bbrc.2008.09.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 09/24/2008] [Indexed: 10/21/2022]
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A single Sec61-complex functions as a protein-conducting channel. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2375-83. [DOI: 10.1016/j.bbamcr.2008.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 08/06/2008] [Accepted: 08/06/2008] [Indexed: 12/30/2022]
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30
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Ménétret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW. Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure 2008; 16:1126-37. [PMID: 18611385 DOI: 10.1016/j.str.2008.05.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 05/12/2008] [Accepted: 05/12/2008] [Indexed: 12/20/2022]
Abstract
During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures.
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Affiliation(s)
- Jean-François Ménétret
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA
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31
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Karamanou S, Bariami V, Papanikou E, Kalodimos CG, Economou A. Assembly of the translocase motor onto the preprotein-conducting channel. Mol Microbiol 2008; 70:311-22. [PMID: 18761620 DOI: 10.1111/j.1365-2958.2008.06402.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacterial protein secretion is catalysed by the SecYEG protein-conducting channel complexed with the SecA ATPase motor. To gain insight into the SecA-SecYEG interaction we used peptide arrays, thermodynamic quantification, mutagenesis and functional assays. Our data reveal that: (i) SecA binds with low affinity on several, peripheral, exposed SecYEG sites. This largely electrostatic association is modulated by temperature and nucleotides. (ii) Binding sites cluster in five major binding 'regions': three that are exclusively cytoplasmic and two that reach the periplasm. (iii) Both the N-terminal and c-terminal regions of SecA participate in binding interactions and share some sites. (iv) Several of these sites are essential for translocase catalysis. Our data provide residue-level dissection of the SecYEG-SecA interaction. Two models of assembly of SecA on dimeric SecYEG are discussed.
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Affiliation(s)
- Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology-FoRTH, PO Box 1385, Iraklio, Crete, Greece
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32
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Abstract
Export of secretory proteins across and insertion of membrane proteins into the cytoplasmic membrane of Escherichia coli and other bacteria is mediated by the enzyme complex translocase. The last decade has seen a major advance in the understanding of the mechanism of these processes. A large part of this progress can be attributed to the development of general and powerful methods to study the translocase activity in vitro. Here we describe a transcription-translation method used to analyze the insertion of membrane proteins into E. coli inner membrane vesicles and a rapid and quantitative fluorescent method to analyze the translocation of secretory proteins.
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33
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Structure of the oligosaccharyl transferase complex at 12 A resolution. Structure 2008; 16:432-40. [PMID: 18334218 DOI: 10.1016/j.str.2007.12.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 11/30/2007] [Accepted: 12/12/2007] [Indexed: 11/23/2022]
Abstract
Oligosaccharyl transferase (OT) catalyzes the transfer of a lipid-linked oligosaccharide to the nascent polypeptide emerging from the translocon. Currently, there is no structural information on the membrane-embedded OT complex, which consists of eight different polypeptide chains. We report a 12 A resolution cryo-electron microscopy structure of OT from yeast. We mapped the locations of four essential OT subunits through a maltose-binding protein fusion strategy. OT was found to have a large domain in the lumenal side of endoplasmic reticulum where the catalysis occurs. The lumenal domain mainly comprises the catalytic Stt3p, the donor substrate-recognizing Wbp1p, and the acceptor substrate-recognizing Ost1p. A prominent groove was observed between these subunits, and we propose that the nascent polypeptide from the translocon threads through this groove while being scanned by the Ost1p subunit for the presence of the glycosylation sequon.
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Affiliation(s)
- Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
| | - Nico Nouwen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
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Antonoaea R, Fürst M, Nishiyama KI, Müller M. The periplasmic chaperone PpiD interacts with secretory proteins exiting from the SecYEG translocon. Biochemistry 2008; 47:5649-56. [PMID: 18439025 DOI: 10.1021/bi800233w] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Sec translocon of Escherichia coli mediates the export of numerous secretory and membrane proteins. To dissect the passage of an exported protein across the Sec translocon into consecutive steps, we generated in vitro translocation intermediates of a polypeptide chain, which by its N-terminus is anchored in the membrane and by its C-terminus tethered to the ribosome. We find that in this situation, the motor protein SecA propagates translocation of a peptide loop across SecYEG prior to the removal of ribosomes. Upon SecA-driven exit from the translocon, this loop is brought into the immediate vicinity of the membrane-anchored, periplasmic chaperone PpiD. Consistent with a coupling between translocation across the SecYEG translocon and folding by periplasmic chaperones, a lack of PpiD retards the release of a translocating outer membrane protein into the periplasm.
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Affiliation(s)
- Raluca Antonoaea
- Institut für Biochemie and Molekularbiologie and Zentrum für Biochemie and Molekulare Zellforschung, Universität Freiburg, Hermann-Herder-Strasse 7, D-79104 Freiburg, Germany
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Kida Y, Morimoto F, Sakaguchi M. Two translocating hydrophilic segments of a nascent chain span the ER membrane during multispanning protein topogenesis. ACTA ACUST UNITED AC 2008; 179:1441-52. [PMID: 18166653 PMCID: PMC2373506 DOI: 10.1083/jcb.200707050] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During protein integration into the endoplasmic reticulum, the N-terminal domain preceding the type I signal-anchor sequence is translocated through a translocon. By fusing a streptavidin-binding peptide tag to the N terminus, we created integration intermediates of multispanning membrane proteins. In a cell-free system, N-terminal domain (N-domain) translocation was arrested by streptavidin and resumed by biotin. Even when N-domain translocation was arrested, the second hydrophobic segment mediated translocation of the downstream hydrophilic segment. In one of the defined intermediates, two hydrophilic segments and two hydrophobic segments formed a transmembrane disposition in a productive state. Both of the translocating hydrophilic segments were crosslinked with a translocon subunit, Sec61α. We conclude that two translocating hydrophilic segment in a single membrane protein can span the membrane during multispanning topogenesis flanking the translocon. Furthermore, even after six successive hydrophobic segments entered the translocon, N-domain translocation could be induced to restart from an arrested state. These observations indicate the remarkably flexible nature of the translocon.
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Affiliation(s)
- Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
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37
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Hu P, Bian Z, Fan M, Huang M, Zhang P. Sec translocase and sortase A are colocalised in a locus in the cytoplasmic membrane of Streptococcus mutans. Arch Oral Biol 2008; 53:150-4. [DOI: 10.1016/j.archoralbio.2007.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 08/18/2007] [Accepted: 08/21/2007] [Indexed: 11/30/2022]
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38
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Salgado-Pabón W, Jain S, Turner N, van der Does C, Dillard JP. A novel relaxase homologue is involved in chromosomal DNA processing for type IV secretion in Neisseria gonorrhoeae. Mol Microbiol 2007; 66:930-47. [PMID: 17927698 PMCID: PMC2586181 DOI: 10.1111/j.1365-2958.2007.05966.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Neisseria gonorrhoeae type IV secretion system secretes chromosomal DNA that acts in natural transformation. To examine the mechanism of DNA processing for secretion, we made mutations in the putative relaxase gene traI and used nucleases to characterize the secreted DNA. The nuclease experiments demonstrated that the secreted DNA is single-stranded and blocked at the 5' end. Mutation of traI identified Tyr93 as required for DNA secretion, while substitution of Tyr201 resulted in intermediate levels of DNA secretion. TraI exhibits features of relaxases, but also has features that are absent in previously characterized relaxases, including an HD phosphohydrolase domain and an N-terminal hydrophobic region. The HD domain residue Asp120 was required for wild-type levels of DNA secretion. Subcellular localization studies demonstrated that the TraI N-terminal region promotes membrane interaction. We propose that Tyr93 initiates DNA processing and Tyr201 is required for termination or acts in DNA binding. Disruption of an inverted-repeat sequence eliminated DNA secretion, suggesting that this sequence may serve as the origin of transfer for chromosomal DNA secretion. The TraI domain architecture, although not previously described, is present in 53 uncharacterized proteins, suggesting that the mechanism of TraI function is a widespread process for DNA donation.
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Affiliation(s)
- Wilmara Salgado-Pabón
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Bol R, de Wit JG, Driessen AJM. The Active Protein-conducting Channel of Escherichia coli Contains an Apolar Patch. J Biol Chem 2007; 282:29785-93. [PMID: 17699162 DOI: 10.1074/jbc.m702140200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein translocation across the cytoplasmic membrane of Escherichia coli is mediated by translocase, a complex of a protein-conducting channel, SecYEG, and a peripheral motor domain, SecA. SecYEG has been proposed to constitute an aqueous path for proteins to pass the membrane in an unfolded state. To probe the solvation state of the active channel, the polarity sensitive fluorophore N-((2-(iodoacetoxy)ethyl)-N-methyl) amino-7-nitrobenz-2-oxa-1,3-diazole was introduced at specific positions in the C-terminal region of the secretory protein proOmpA. Fluorescence measurements with defined proOmpA-DHFR translocation intermediates indicate mostly a water-exposed environment with a hydrophobic region in the center of the channel.
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Affiliation(s)
- Redmar Bol
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, The Netherlands
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Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:1735-56. [PMID: 17935691 DOI: 10.1016/j.bbamem.2007.07.015] [Citation(s) in RCA: 343] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/23/2007] [Accepted: 07/24/2007] [Indexed: 11/20/2022]
Abstract
In bacteria, two major pathways exist to secrete proteins across the cytoplasmic membrane. The general Secretion route, termed Sec-pathway, catalyzes the transmembrane translocation of proteins in their unfolded conformation, whereupon they fold into their native structure at the trans-side of the membrane. The Twin-arginine translocation pathway, termed Tat-pathway, catalyses the translocation of secretory proteins in their folded state. Although the targeting signals that direct secretory proteins to these pathways show a high degree of similarity, the translocation mechanisms and translocases involved are vastly different.
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Lin BR, Gierasch LM, Jiang C, Tai PC. Electrophysiological studies in Xenopus oocytes for the opening of Escherichia coli SecA-dependent protein-conducting channels. J Membr Biol 2007; 214:103-13. [PMID: 17530158 PMCID: PMC2896742 DOI: 10.1007/s00232-006-0079-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 11/16/2006] [Indexed: 11/25/2022]
Abstract
Protein translocation in Escherichia coli requires protein-conducting channels in cytoplasmic membranes to allow precursor peptides to pass through with adenosine triphosphate (ATP) hydrolysis. Here, we report a novel, sensitive method that detects the opening of the SecA-dependent protein-conducting channels at the nanogram level. E. coli inverted membrane vesicles were injected into Xenopus oocytes, and ionic currents were recorded using the two-electrode voltage clamp. Currents were observed only in the presence of E. coli SecA in conjunction with E. coli membranes. Observed currents showed outward rectification in the presence of KCl as permeable ions and were significantly enhanced by coinjection with the precursor protein proOmpA or active LamB signal peptide. Channel activity was blockable with sodium azide or adenylyl 5'-(beta,gamma-methylene)-diphosphonate, a nonhydrolyzable ATP analogue, both of which are known to inhibit SecA protein activity. Endogenous oocyte precursor proteins also stimulated ion current activity and can be inhibited by puromycin. In the presence of puromycin, exogenous proOmpA or LamB signal peptides continued to enhance ionic currents. Thus, the requirement of signal peptides and ATP hydrolysis for the SecA-dependent currents resembles biochemical protein translocation assay with E. coli membrane vesicles, indicating that the Xenopus oocyte system provides a sensitive assay to study the role of Sec and precursor proteins in the formation of protein-conducting channels using electrophysiological methods.
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Affiliation(s)
- Bor-Ruei Lin
- Department of Biology, Georgia State University, 24 Peachtree Center Avenue, Atlanta, GA 30303, USA
| | - Lila M. Gierasch
- Departments of Biochemistry and Molecular Biology and of Chemistry, University of Massachusetts, 710 N. Pleasant Street, Amherst, MA 01003, USA
| | - Chun Jiang
- Department of Biology, Georgia State University, 24 Peachtree Center Avenue, Atlanta, GA 30303, USA
| | - Phang C. Tai
- Department of Biology, Georgia State University, 24 Peachtree Center Avenue, Atlanta, GA 30303, USA
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Alami M, Dalal K, Lelj-Garolla B, Sligar SG, Duong F. Nanodiscs unravel the interaction between the SecYEG channel and its cytosolic partner SecA. EMBO J 2007; 26:1995-2004. [PMID: 17396152 PMCID: PMC1852787 DOI: 10.1038/sj.emboj.7601661] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Accepted: 03/02/2007] [Indexed: 11/08/2022] Open
Abstract
The translocon is a membrane-embedded protein assembly that catalyzes protein movement across membranes. The core translocon, the SecYEG complex, forms oligomers, but the protein-conducting channel is at the center of the monomer. Defining the properties of the SecYEG protomer is thus crucial to understand the underlying function of oligomerization. We report here the reconstitution of a single SecYEG complex into nano-scale lipid bilayers, termed Nanodiscs. These water-soluble particles allow one to probe the interactions of the SecYEG complex with its cytosolic partner, the SecA dimer, in a membrane-like environment. The results show that the SecYEG complex triggers dissociation of the SecA dimer, associates only with the SecA monomer and suffices to (pre)-activate the SecA ATPase. Acidic lipids surrounding the SecYEG complex also contribute to the binding affinity and activation of SecA, whereas mutations in the largest cytosolic loop of the SecY subunit, known to abolish the translocation reaction, disrupt both the binding and activation of SecA. Altogether, the results define the fundamental contribution of the SecYEG protomer in the translocation subreactions and illustrate the power of nanoscale lipid bilayers in analyzing the dynamics occurring at the membrane.
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Affiliation(s)
- Meriem Alami
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Kush Dalal
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Barbara Lelj-Garolla
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3. Tel.: +1 604 822 5975; Fax: +1 604 822 5227; E-mail:
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Robson A, Collinson I. The structure of the Sec complex and the problem of protein translocation. EMBO Rep 2007; 7:1099-103. [PMID: 17077865 PMCID: PMC1679778 DOI: 10.1038/sj.embor.7400832] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 09/13/2006] [Indexed: 11/09/2022] Open
Abstract
Proteins synthesized in the cytosol either remain there or are localized to a specific membrane and subsequently translocated to another cellular compartment. These extracytosolic proteins have to cross, or be inserted into, a phospholipid bilayer-a process governed by membrane-bound protein transporters designed to recognize and receive appropriate polypeptides and thread them through the membrane. One such translocation complex, SecY/Sec61, is found in every cell, in either the plasma membrane of bacteria and archaea or the endoplasmic reticulum membrane of eukaryotes. Recent structural findings, combined with previous genetic and biochemical studies, have helped to describe how the passage of proteins through the membrane might occur, but several points of uncertainty remain.
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Affiliation(s)
- Alice Robson
- Department of Biochemistry, School of Medical Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- Department of Biochemistry, School of Medical Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
- Tel: +44 117 928 9786; Fax: + 44 117 928 8274
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Economou A, Christie PJ, Fernandez RC, Palmer T, Plano GV, Pugsley AP. Secretion by numbers: Protein traffic in prokaryotes. Mol Microbiol 2007; 62:308-19. [PMID: 17020575 PMCID: PMC3873778 DOI: 10.1111/j.1365-2958.2006.05377.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Almost all aspects of protein traffic in bacteria were covered at the ASM-FEMS meeting on the topic in Iraklio, Crete in May 2006. The studies presented ranged from mechanistic analysis of specific events leading proteins to their final destinations to the physiological roles of the targeted proteins. Among the highlights from the meeting that are reviewed here are the molecular dynamics of SecA protein, membrane protein insertion, type III secretion needles and chaperones, type IV secretion, the two partner and autosecretion systems, the 'secretion competent state', and the recently discovered type VI secretion system.
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Affiliation(s)
- Anastasias Economou
- Institute of Molecular Biology and Biotechnology, F.O.R.T.H and University of Crete, PO Box 1527, GR-711 10 Iraklio, Crete, Greece
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, University of Texas-Houston, Medical School, Houston, TX 77030, USA
| | - Rachel C. Fernandez
- Department of Microbiology and Immunology, University of British Columbia, 2559-2350 Health Sciences Mall, 300-6174 University Blvd., Vancouver, BC, V6T 1Z3, Canada
| | - Tracy Palmer
- Department of Molecular Microbiology, John Innes Centre, Conley Lane, Norwich, NR4 7UH, UK
| | - Greg V. Plano
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, PO Box 016960 (R-138), Miami, FL 33101, USA
| | - Anthony P. Pugsley
- Molecular Genetics Unit and CNRS URA2172, Institut Pasteur, 25, rue du Dr Roux, 75724 Paris CEDEX 15, France
- For correspondence. ; Tel. (+33) 145688494; Fax (+33) 145688960
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Jilaveanu LB, Oliver DB. In vivo membrane topology of Escherichia coli SecA ATPase reveals extensive periplasmic exposure of multiple functionally important domains clustering on one face of SecA. J Biol Chem 2006; 282:4661-4668. [PMID: 17166834 DOI: 10.1074/jbc.m610828200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Sec-dependent protein translocation pathway promotes the transport of proteins into or across the bacterial plasma membrane. SecA ATPase has been shown to be a nanomotor that associates with its protein cargo as well as the SecYEG channel complex and to undergo ATP-driven cycles of membrane insertion and retraction that promote stepwise protein translocation. Previous studies have shown that both the 65-kDa N-domain and 30-kDa C-domain of SecA appear to undergo such membrane cycling. In the present study we performed in vivo sulfhydryl labeling of an extensive collection of monocysteine secA mutants under topologically specific conditions to identify regions of SecA that are accessible to the trans side of the membrane in its membrane-integrated state. Our results show that distinct regions of five of six SecA domains were labeled under these conditions, and such labeling clusters to a single face of the SecA structure. Our results demarcate an extensive face of SecA that interacts with SecYEG and is in fluid contact with the protein-conducting channel. The observed domain-specific labeling patterns should also provide important constraints on model building efforts in this dynamic system.
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Affiliation(s)
- Lucia B Jilaveanu
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Donald B Oliver
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459.
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Mori H, Ito K. The Long α-Helix of SecA Is Important for the ATPase Coupling of Translocation. J Biol Chem 2006; 281:36249-56. [PMID: 17005557 DOI: 10.1074/jbc.m606906200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA contains two ATPase folds (NBF1 and NBF2) and other interaction/regulatory domains, all of which are connected by a long helical scaffold domain (HSD) running along the molecule. Here we identified a functionally important and spatially adjacent pair of SecA residues, Arg-642 on HSD and Glu-400 on NBF1. A charge-reversing substitution at either position as well as disulfide tethering of these positions inactivated the translocation activity. Interestingly, however, the translocation-inactive SecA variants fully retained the ability to up-regulate the ATPase in response to a preprotein and the SecYEG translocon. The translocation defect was suppressible by second site alterations at the hinge-forming boundary of NBF2 and HSD. Based on these results, we propose that the motor function of SecA is realized by ligand-activated ATPase engine and its HSD-mediated conversion into the mechanical work of preprotein translocation.
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Affiliation(s)
- Hiroyuki Mori
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
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Mori H, Ito K. Different modes of SecY-SecA interactions revealed by site-directed in vivo photo-cross-linking. Proc Natl Acad Sci U S A 2006; 103:16159-64. [PMID: 17060619 PMCID: PMC1621050 DOI: 10.1073/pnas.0606390103] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While the SecA ATPase drives protein translocation across the bacterial cytoplasmic membrane by interacting with the SecYEG translocon, molecular details of SecA-SecY interaction remain poorly understood. Here, we studied SecY-SecA interaction by using an in vivo site-directed cross-linking technique developed by Schultz and coworkers [Chin, J. W., Martin, A. B., King, D. S., Wang, L., Schultz, P. G. (2002) Proc. Natl. Acad. Sci. USA 99:11020-11024 and Chin, J. W., Schultz, P. G. (2002) ChemBioChem 3:1135-1137]. Benzoyl-phenylalanine introduced into specific SecY positions at the second, fourth, fifth, and sixth cytoplasmic domains allowed UV cross-linking with SecA. Cross-linked products exhibited two distinct electrophoretic mobilities. SecA cross-linking at the most C-terminal cytoplasmic region (C6) was specifically enhanced in the presence of NaN(3), which arrests the ATPase cycle, and this enhancement was canceled by cis placement of some secY mutations that affect SecY-SecA cooperation. In vitro experiments showed directly that SecA approaches C6 when it is engaging in ATP-dependent preprotein translocation. On the basis of these findings, we propose that the C6 tail of SecY interacts with the working form of SecA, whereas C4-C5 loops may offer constitutive SecA-binding sites.
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Affiliation(s)
- Hiroyuki Mori
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Koreaki Ito
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
- *To whom correspondence should be addressed. E-mail:
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49
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Vassylyev DG, Mori H, Vassylyeva MN, Tsukazaki T, Kimura Y, Tahirov TH, Ito K. Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer. J Mol Biol 2006; 364:248-58. [PMID: 17059823 DOI: 10.1016/j.jmb.2006.09.061] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 09/19/2006] [Accepted: 09/24/2006] [Indexed: 11/16/2022]
Abstract
The mechanism of pre-protein export through the bacterial cytoplasmic membrane, in which the SecA ATPase plays a crucial role as an "energy supplier", is poorly understood. In particular, biochemical and structural studies provide contradictory data as to the oligomeric state of SecA when it is integrated into the active trans-membrane translocase. Here, we report the 2.8 A resolution crystal structure of the Thermus thermophilus SecA protein (TtSecA). Whereas the structure of the TtSecA monomer closely resembles that from other bacteria, the oligomeric state of TtSecA is strikingly distinct. In contrast to the antiparallel (head-to-tail) dimerization reported previously for the other bacterial systems, TtSecA forms parallel (head-to-head) dimers that are reminiscent of open scissors. The dimer interface is abundant in bulky Arg and Lys side-chains from both subunits, which stack on one another to form an unusual "basic zipper" that is highly conserved, as revealed by homology modeling and sequence analysis. The basic zipper is sealed on both ends by two pairs of the salt bridges formed between the basic side-chains from the zipper and two invariant acidic residues. The organization of the dimers, in which the two pre-protein binding domains are located proximal to each other at the tip of the "scissors", might allow a concerted mode of substrate recognition while the opening/closing of the scissors might facilitate translocation.
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Affiliation(s)
- Dmitry G Vassylyev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 434 Kaul Genetics Building, 720 20(th) Street South, Birmingham, AL 35294, USA.
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50
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van der Sluis EO, Nouwen N, Koch J, de Keyzer J, van der Does C, Tampé R, Driessen AJM. Identification of Two Interaction Sites in SecY that Are Important for the Functional Interaction with SecA. J Mol Biol 2006; 361:839-49. [PMID: 16890955 DOI: 10.1016/j.jmb.2006.07.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 07/03/2006] [Accepted: 07/12/2006] [Indexed: 11/24/2022]
Abstract
The motor protein SecA drives the translocation of (pre-)proteins across the SecYEG channel in the bacterial cytoplasmic membrane by nucleotide-dependent cycles of conformational changes often referred to as membrane insertion/de-insertion. Despite structural data on SecA and an archaeal homolog of SecYEG, the identity of the sites of interaction between SecA and SecYEG are unknown. Here, we show that SecA can be cross-linked to several residues in cytoplasmic loop 5 (C5) of SecY, and that SecA directly interacts with a part of transmembrane segment 4 (TMS4) of SecY that is buried in the membrane region of SecYEG. Mutagenesis of either the conserved Arg357 in C5 or Glu176 in TMS4 interferes with the catalytic activity of SecA but not with binding of SecA to SecYEG. Our data explain how conformational changes in SecA could be directly coupled to the previously proposed opening mechanism of the SecYEG channel.
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Affiliation(s)
- Eli O van der Sluis
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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