1
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Orfanoudaki G, Markaki M, Chatzi K, Tsamardinos I, Economou A. MatureP: prediction of secreted proteins with exclusive information from their mature regions. Sci Rep 2017; 7:3263. [PMID: 28607462 PMCID: PMC5468347 DOI: 10.1038/s41598-017-03557-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
More than a third of the cellular proteome is non-cytoplasmic. Most secretory proteins use the Sec system for export and are targeted to membranes using signal peptides and mature domains. To specifically analyze bacterial mature domain features, we developed MatureP, a classifier that predicts secretory sequences through features exclusively computed from their mature domains. MatureP was trained using Just Add Data Bio, an automated machine learning tool. Mature domains are predicted efficiently with ~92% success, as measured by the Area Under the Receiver Operating Characteristic Curve (AUC). Predictions were validated using experimental datasets of mutated secretory proteins. The features selected by MatureP reveal prominent differences in amino acid content between secreted and cytoplasmic proteins. Amino-terminal mature domain sequences have enhanced disorder, more hydroxyl and polar residues and less hydrophobics. Cytoplasmic proteins have prominent amino-terminal hydrophobic stretches and charged regions downstream. Presumably, secretory mature domains comprise a distinct protein class. They balance properties that promote the necessary flexibility required for the maintenance of non-folded states during targeting and secretion with the ability of post-secretion folding. These findings provide novel insight in protein trafficking, sorting and folding mechanisms and may benefit protein secretion biotechnology.
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Affiliation(s)
- Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology-University of Crete, PO Box 1385, Heraklion, Crete, Greece
| | - Maria Markaki
- Computer Science Department, University of Crete, Heraklion, Greece
| | - Katerina Chatzi
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Ioannis Tsamardinos
- Computer Science Department, University of Crete, Heraklion, Greece.,Gnosis Data Analysis PC, Heraklion, Greece
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology-University of Crete, PO Box 1385, Heraklion, Crete, Greece. .,KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium.
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2
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Abstract
There is a consensus in the medical profession of the pressing need for novel antimicrobial agents due to issues related to drug resistance. In practice, solutions to this problem to a large degree lie with the identification of new and vital targets in bacteria and subsequently designing their inhibitors. We consider SecA a very promising antimicrobial target. In this review, we compile and analyze information available on SecA to show that inhibition of SecA has a multitude of consequences. Furthermore, we discuss issues critical to the design and evaluation of SecA inhibitors.
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3
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Zhang Q, Li Y, Olson R, Mukerji I, Oliver D. Conserved SecA Signal Peptide-Binding Site Revealed by Engineered Protein Chimeras and Förster Resonance Energy Transfer. Biochemistry 2016; 55:1291-300. [PMID: 26854513 DOI: 10.1021/acs.biochem.5b01115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Signal peptides are critical for the initiation of protein transport in bacteria by virtue of their recognition by the SecA ATPase motor protein followed by their transfer to the lateral gate region of the SecYEG protein-conducting channel complex. In this study, we have constructed and validated the use of signal peptide-attached SecA chimeras for conducting structural and functional studies on the initial step of SecA signal peptide interaction. We utilized this system to map the location and orientation of the bound alkaline phosphatase and KRRLamB signal peptides to a peptide-binding groove adjacent to the two-helix finger subdomain of SecA. These results support the existence of a single conserved SecA signal peptide-binding site that positions the signal peptide parallel to the two-helix finger subdomain of SecA, and they are also consistent with the proposed role of this subdomain in the transfer of the bound signal peptide from SecA into the protein-conducting channel of SecYEG protein. In addition, our work highlights the utility of this system to conveniently engineer and study the interaction of SecA with any signal peptide of interest as well as its potential use for X-ray crystallographic studies given issues with exogenous signal peptide solubility.
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Affiliation(s)
- Qi Zhang
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Yan Li
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Donald Oliver
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
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4
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Gouridis G, Karamanou S, Sardis MF, Schärer MA, Capitani G, Economou A. Quaternary dynamics of the SecA motor drive translocase catalysis. Mol Cell 2014; 52:655-66. [PMID: 24332176 DOI: 10.1016/j.molcel.2013.10.036] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/15/2013] [Accepted: 10/30/2013] [Indexed: 11/19/2022]
Abstract
Most secretory preproteins exit bacterial cells through the protein translocase, comprising the SecYEG channel and the dimeric peripheral ATPase motor SecA. Energetic coupling to work remains elusive. We now demonstrate that translocation is driven by unusually dynamic quaternary changes in SecA. The dimer occupies several successive states with distinct protomer arrangements. SecA docks on SecYEG as a dimer and becomes functionally asymmetric. Docking occurs via only one protomer. The second protomer allosterically regulates downstream steps. Binding of one preprotein signal peptide to the SecYEG-docked SecA protomer elongates the SecA dimer and triggers the translocase holoenzyme to obtain a lower activation energy conformation. ATP hydrolysis monomerizes the triggered SecA dimer, causing mature chain trapping and processive translocation. This is a unique example of one protein exploiting quaternary dynamics to become a substrate receptor, a "loading clamp," and a "processive motor." This mechanism has widespread implications on protein translocases, chaperones, and motors.
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Affiliation(s)
- Giorgos Gouridis
- Institute of Molecular Biology and Biotechnology (FORTH), University of Crete, P.O. Box 1385, Iraklio, Crete 71110, Greece
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology (FORTH), University of Crete, P.O. Box 1385, Iraklio, Crete 71110, Greece; Rega Institute, Department of Microbiology and Immunology, KU Leuven, 3000 Leuven, Belgium
| | - Marios Frantzeskos Sardis
- Institute of Molecular Biology and Biotechnology (FORTH), University of Crete, P.O. Box 1385, Iraklio, Crete 71110, Greece; Department of Biology, University of Crete, P.O. Box 1385, Iraklio, Crete 71110, Greece
| | | | - Guido Capitani
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology (FORTH), University of Crete, P.O. Box 1385, Iraklio, Crete 71110, Greece; Department of Biology, University of Crete, P.O. Box 1385, Iraklio, Crete 71110, Greece; Rega Institute, Department of Microbiology and Immunology, KU Leuven, 3000 Leuven, Belgium.
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5
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Auclair SM, Oliver DB, Mukerji I. Defining the solution state dimer structure of Escherichia coli SecA using Förster resonance energy transfer. Biochemistry 2013; 52:2388-401. [PMID: 23484952 DOI: 10.1021/bi301217t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Sec machinery constitutes the major pathway for protein translocation in bacteria. SecA is thought to act as a molecular motor driving translocation of the preprotein across the membrane by repeated ATP-driven cycles of insertion and retraction at the translocon channel. SecA is predominately a dimer under physiological conditions; however, its oligomeric state during active protein translocation is still unresolved. Five SecA crystal structures have been determined, each displaying a different dimer interface, suggesting that SecA may adopt different dimer configurations. In this study, a Förster resonance energy transfer approach was utilized with nine functional monocysteine SecA mutants labeled with appropriate dyes to determine the predominant solution state dimer. Three different dye pairs allowed interprotomer distances ranging from 20 to 140 Å to be investigated. Comparison of 15 experimentally determined distances with those predicted from X-ray structures showed the greatest agreement with the Bacillus subtilis SecA antiparallel dimer structure [Hunt, J., Weinkauf, S., Henry, L., Fak, J. J., McNicholas, P., Oliver, D. B., and Deisenhfer, J. (2002) Science 297, 2018-2026]. The binding of two signal peptides to SecA was also examined to determine their effect on SecA dimer structure. We found that the SecA dimer is maintained upon peptide binding; however, the preprotein cross-linking domain (PPXD) and helical wing domain regions experience significant conformational changes, and the PPXD movement is greatly enhanced by binding of an extended signal peptide containing 19 additional residues. Modeling of an "open" antiparallel dimer structure suggests that binding of preprotein to SecA induces an activated open conformation suitable for binding to SecYEG.
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Affiliation(s)
- Sarah M Auclair
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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6
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Abstract
SecA signal peptide interaction is critical for initiating protein translocation in the bacterial Sec-dependent pathway. Here, we have utilized the recent nuclear magnetic resonance (NMR) and Förster resonance energy transfer studies that mapped the location of the SecA signal peptide-binding site to design and isolate signal peptide-binding-defective secA mutants. Biochemical characterization of the mutant SecA proteins showed that Ser226, Val310, Ile789, Glu806, and Phe808 are important for signal peptide binding. A genetic system utilizing alkaline phosphatase secretion driven by different signal peptides was employed to demonstrate that both the PhoA and LamB signal peptides appear to recognize a common set of residues at the SecA signal peptide-binding site. A similar system containing either SecA-dependent or signal recognition particle (SRP)-dependent signal peptides along with the prlA suppressor mutation that is defective in signal peptide proofreading activity were employed to distinguish between SecA residues that are utilized more exclusively for signal peptide recognition or those that also participate in the proofreading and translocation functions of SecA. Collectively, our data allowed us to propose a model for the location of the SecA signal peptide-binding site that is more consistent with recent structural insights into this protein translocation system.
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7
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Traffic jam at the bacterial sec translocase: targeting the SecA nanomotor by small-molecule inhibitors. ACTA ACUST UNITED AC 2011; 18:685-98. [PMID: 21700205 DOI: 10.1016/j.chembiol.2011.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/27/2011] [Accepted: 04/28/2011] [Indexed: 11/20/2022]
Abstract
The rapid rise of drug-resistant bacteria is one of the most serious unmet medical needs facing the world. Despite this increasing problem of antibiotic resistance, the number of different antibiotics available for the treatment of serious infections is dwindling. Therefore, there is an urgent need for new antibacterial drugs, preferably with novel modes of action to potentially avoid cross-resistance with existing antibacterial agents. In recent years, increasing attention has been paid to bacterial protein secretion as a potential antibacterial target. Among the different protein secretion pathways that are present in bacterial pathogens, the general protein secretory (Sec) pathway is widely considered as an attractive target for antibacterial therapy. One of the key components of the Sec pathway is the peripheral membrane ATPase SecA, which provides the energy for the translocation of preproteins across the bacterial cytoplasmic membrane. In this review, we will provide an overview of research efforts on the discovery and development of small-molecule SecA inhibitors. Furthermore, recent advances on the structure and function of SecA and their potential impact on antibacterial drug discovery will be discussed.
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8
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Segers K, Klaassen H, Economou A, Chaltin P, Anné J. Development of a high-throughput screening assay for the discovery of small-molecule SecA inhibitors. Anal Biochem 2011; 413:90-6. [PMID: 21338570 DOI: 10.1016/j.ab.2011.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 02/08/2011] [Accepted: 02/08/2011] [Indexed: 10/18/2022]
Abstract
A major pathway for bacterial preprotein translocation is provided by the Sec-dependent preprotein translocation pathway. Proteins destined for Sec-dependent translocation are synthesized as preproteins with an N-terminal signal peptide, which targets them to the SecYEG translocase channel. The driving force for the translocation reaction is provided by the peripheral membrane ATPase SecA, which couples the hydrolysis of ATP to the stepwise transport of unfolded preproteins across the bacterial membrane. Since SecA is essential, highly conserved among bacterial species, and has no close human homologues, it represents a promising target for antibacterial chemotherapy. However, high-throughput screening (HTS) campaigns to identify SecA inhibitors are hampered by the low intrinsic ATPase activity of SecA and the requirement of hydrophobic membranes for measuring the membrane or translocation ATPase activity of SecA. To address this issue, we have developed a colorimetric high-throughput screening assay in a 384-well format, employing an Escherichia coli (E. coli) SecA mutant with elevated intrinsic ATPase activity. The assay was applied for screening of a chemical library consisting of ~27,000 compounds and proved to be highly reliable (average Z' factor of 0.89). In conclusion, a robust HTS assay has been established that will facilitate the search for novel SecA inhibitors.
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Affiliation(s)
- Kenneth Segers
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroederstraat 10, 3000 Leuven, Belgium.
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Tang Y, Pan X, Chen Y, Tai PC, Sui SF. Dimeric SecA couples the preprotein translocation in an asymmetric manner. PLoS One 2011; 6:e16498. [PMID: 21304597 PMCID: PMC3029384 DOI: 10.1371/journal.pone.0016498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 12/20/2010] [Indexed: 12/01/2022] Open
Abstract
The Sec translocase mediates the post-translational translocation of a number of preproteins through the inner membrane in bacteria. In the initiatory translocation step, SecB targets the preprotein to the translocase by specific interaction with its receptor SecA. The latter is the ATPase of Sec translocase which mediates the post-translational translocation of preprotein through the protein-conducting channel SecYEG in the bacterial inner membrane. We examined the structures of Escherichia coli Sec intermediates in solution as visualized by negatively stained electron microscopy in order to probe the oligomeric states of SecA during this process. The symmetric interaction pattern between the SecA dimer and SecB becomes asymmetric in the presence of proOmpA, and one of the SecA protomers predominantly binds to SecB/proOmpA. Our results suggest that during preprotein translocation, the two SecA protomers are different in structure and may play different roles.
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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, China
| | - Xijiang Pan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yong Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Phang C. 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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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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11
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Auclair SM, Moses JP, Musial-Siwek M, Kendall DA, Oliver DB, Mukerji I. Mapping of the signal peptide-binding domain of Escherichia coli SecA using Förster resonance energy transfer. Biochemistry 2010; 49:782-92. [PMID: 20025247 DOI: 10.1021/bi901446r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of the signal peptide-binding domain within SecA ATPase is an important goal for understanding the molecular basis of SecA preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. In this study, Forster resonance energy transfer methodology was employed to map the location of the SecA signal peptide-binding domain using a collection of functional monocysteine SecA mutants and alkaline phosphatase signal peptides labeled with appropriate donor-acceptor fluorophores. Fluorescence anisotropy measurements yielded an equilibrium binding constant of 1.4 or 10.7 muM for the alkaline phosphatase signal peptide labeled at residue 22 or 2, respectively, with SecA, and a binding stoichiometry of one signal peptide bound per SecA monomer. Binding affinity measurements performed with a monomer-biased mutant indicate that the signal peptide binds equally well to SecA monomer or dimer. Distance measurements determined for 13 SecA mutants show that the SecA signal peptide-binding domain encompasses a portion of the preprotein cross-linking domain but also includes regions of nucleotide-binding domain 1 and particularly the helical scaffold domain. The identified region lies at a multidomain interface within the heart of SecA, surrounded by and potentially responsive to domains important for binding nucleotide, mature portions of the preprotein, and the SecYEG channel. Our FRET-mapped binding domain, in contrast to the domain identified by NMR spectroscopy, includes the two-helix finger that has been shown to interact with the preprotein during translocation and lies at the entrance to the protein-conducting channel in the recently determined SecA-SecYEG structure.
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Affiliation(s)
- Sarah M Auclair
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
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Tang Y, Pan X, Tai PC, Sui SF. The structure of SecB/OmpA as visualized by electron microscopy: The mature region of the precursor protein binds asymmetrically to SecB. Biochem Biophys Res Commun 2010; 393:698-702. [PMID: 20170640 DOI: 10.1016/j.bbrc.2010.02.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
SecB, a molecular chaperone in Escherichia coli, binds a subset of precursor proteins that are exported across the plasma membrane via the Sec pathway. Previous studies showed that SecB bound directly to the mature region rather than to the signal sequence of the precursor protein. To determine the binding pattern of SecB and the mature region of the preprotein, here, we visualized the structure of the SecB/OmpA complex by electron microscopy. This complex is composed by two parts: the main density represents one SecB tetramer and the unfolded part of OmpA wrapping round it; the elongated smaller density represents the rest of OmpA. Each SecB protomer makes a different contribution to the binding of SecB with OmpA. The binding pattern between SecB tetramer and OmpA is asymmetric.
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Affiliation(s)
- Ying Tang
- State-Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Science, Tsinghua University, Beijing 100084, China
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Clérico EM, Maki JL, Gierasch LM. Use of synthetic signal sequences to explore the protein export machinery. Biopolymers 2008; 90:307-19. [PMID: 17918185 DOI: 10.1002/bip.20856] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The information for correct localization of newly synthesized proteins in both prokaryotes and eukaryotes resides in self-contained, often transportable targeting sequences. Of these, signal sequences specify that a protein should be secreted from a cell or incorporated into the cytoplasmic membrane. A central puzzle is presented by the lack of primary structural homology among signal sequences, although they share common features in their sequences. Synthetic signal peptides have enabled a wide range of studies of how these "zipcodes" for protein secretion are decoded and used to target proteins to the protein machinery that facilitates their translocation across and integration into membranes. We review research on how the information in signal sequences enables their passenger proteins to be correctly and efficiently localized. Synthetic signal peptides have made possible binding and crosslinking studies to explore how selectivity is achieved in recognition by the signal sequence-binding receptors, signal recognition particle, or SRP, which functions in all organisms, and SecA, which functions in prokaryotes and some organelles of prokaryotic origins. While progress has been made, the absence of atomic resolution structures for complexes of signal peptides and their receptors has definitely left many questions to be answered in the future.
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Affiliation(s)
- Eugenia M Clérico
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
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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: 340] [Impact Index Per Article: 20.0] [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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Abstract
Understanding the transport of hydrophilic proteins across biological membranes continues to be an important undertaking. The general secretory (Sec) pathway in Escherichia coli transports the majority of E. coli proteins from their point of synthesis in the cytoplasm to their sites of final localization, associating sequentially with a number of protein components of the transport machinery. The targeting signals for these substrates must be discriminated from those of proteins transported via other pathways. While targeting signals for each route have common overall characteristics, individual signal peptides vary greatly in their amino acid sequences. How do these diverse signals interact specifically with the proteins that comprise the appropriate transport machinery and, at the same time, avoid targeting to an alternate route? The recent publication of the crystal structures of components of the Sec transport machinery now allows a more thorough consideration of the interactions of signal sequences with these components.
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Affiliation(s)
| | - Debra A. Kendall
- To whom correspondence should be addressed. Mailing address: Department of Molecular and Cell Biology, 91 North Eagleville Road, The University of Connecticut, Storrs, CT 06269-3125. Phone: (860) 486-1891. Fax: (860) 486-4331. E-mail:
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Karamanou S, Gouridis G, Papanikou E, Sianidis G, Gelis I, Keramisanou D, Vrontou E, Kalodimos CG, Economou A. Preprotein-controlled catalysis in the helicase motor of SecA. EMBO J 2007; 26:2904-14. [PMID: 17525736 PMCID: PMC1894763 DOI: 10.1038/sj.emboj.7601721] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 04/17/2007] [Indexed: 11/08/2022] Open
Abstract
The cornerstone of the functionality of almost all motor proteins is the regulation of their activity by binding interactions with their respective substrates. In most cases, the underlying mechanism of this regulation remains unknown. Here, we reveal a novel mechanism used by secretory preproteins to control the catalytic cycle of the helicase 'DEAD' motor of SecA, the preprotein translocase ATPase. The central feature of this mechanism is a highly conserved salt-bridge, Gate1, that controls the opening/closure of the nucleotide cleft. Gate1 regulates the propagation of binding signal generated at the Preprotein Binding Domain to the nucleotide cleft, thus allowing the physical coupling of preprotein binding and release to the ATPase cycle. This relay mechanism is at play only after SecA has been previously 'primed' by binding to SecYEG, the transmembrane protein-conducting channel. The Gate1-controlled relay mechanism is essential for protein translocase catalysis and may be common in helicase motors.
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Affiliation(s)
- Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
| | - Giorgos Gouridis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
- Department of Biology, University of Crete, Crete, Greece
| | - Efrosyni Papanikou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
| | - Giorgos Sianidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
| | - Ioannis Gelis
- Department of Chemistry, Rutgers University, Newark, NJ, USA
| | | | - Eleftheria Vrontou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
- Department of Biology, University of Crete, Crete, Greece
| | | | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
- Department of Biology, University of Crete, Crete, Greece
- Institute of Molecular Biology and Biotechnology, University of Crete, PO Box 1385, 71110 Iraklio, Crete, Greece. Tel.: +30 2810 391166/391167; Fax: +30 2810 391166; E-mail:
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18
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Mitra K, Frank J, Driessen A. Co- and post-translational translocation through the protein-conducting channel: analogous mechanisms at work? Nat Struct Mol Biol 2007; 13:957-64. [PMID: 17082791 DOI: 10.1038/nsmb1166] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many proteins are translocated across, or integrated into, membranes. Both functions are fulfilled by the 'translocon/translocase', which contains a membrane-embedded protein-conducting channel (PCC) and associated soluble factors that drive translocation and insertion reactions using nucleotide triphosphates as fuel. This perspective focuses on reinterpreting existing experimental data in light of a recently proposed PCC model comprising a front-to-front dimer of SecY or Sec61 heterotrimeric complexes. In this new framework, we propose (i) a revised model for SRP-SR-mediated docking of the ribosome-nascent polypeptide to the PCC; (ii) that the dynamic interplay between protein substrate, soluble factors and PCC controls the opening and closing of a transmembrane channel across, and/or a lateral gate into, the membrane; and (iii) that co- and post-translational translocation, involving the ribosome and SecA, respectively, not only converge at the PCC but also use analogous mechanisms for coordinating protein translocation.
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Papanikolau Y, Papadovasilaki M, Ravelli RBG, McCarthy AA, Cusack S, Economou A, Petratos K. Structure of dimeric SecA, the Escherichia coli preprotein translocase motor. J Mol Biol 2006; 366:1545-57. [PMID: 17229438 DOI: 10.1016/j.jmb.2006.12.049] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 12/12/2006] [Accepted: 12/17/2006] [Indexed: 01/31/2023]
Abstract
SecA is the preprotein translocase ATPase subunit and a superfamily 2 (SF2) RNA helicase. Here we present the 2 A crystal structures of the Escherichia coli SecA homodimer in the apo form and in complex with ATP, ADP and adenosine 5'-[beta,gamma-imido]triphosphate (AMP-PNP). Each monomer contains the SF2 ATPase core (DEAD motor) built of two domains (nucleotide binding domain, NBD and intramolecular regulator of ATPase 2, IRA2), the preprotein binding domain (PBD), which is inserted in NBD and a carboxy-terminal domain (C-domain) linked to IRA2. The structures of the nucleotide complexes of SecA identify an interfacial nucleotide-binding cleft located between the two DEAD motor domains and residues critical for ATP catalysis. The dimer comprises two virtually identical protomers associating in an antiparallel fashion. Dimerization is mediated solely through extensive contacts of the DEAD motor domains leaving the C-domain facing outwards from the dimerization core. This dimerization mode explains the effect of functionally important mutations and is completely different from the dimerization models proposed for other SecA structures. The repercussion of these findings on translocase assembly and catalysis is discussed.
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Affiliation(s)
- Yannis Papanikolau
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, PO Box 1385, 71110 Heraklion, Greece
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20
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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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21
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Musial-Siwek M, Rusch SL, Kendall DA. Selective photoaffinity labeling identifies the signal peptide binding domain on SecA. J Mol Biol 2006; 365:637-48. [PMID: 17084862 PMCID: PMC1851904 DOI: 10.1016/j.jmb.2006.10.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 10/02/2006] [Accepted: 10/08/2006] [Indexed: 11/26/2022]
Abstract
SecA, an ATPase crucial to the Sec-dependent translocation machinery in Escherichia coli, recognizes and directly binds the N-terminal signal peptide of an exported preprotein. This interaction plays a central role in the targeting and transport of preproteins via the SecYEG channel. Here we identify the signal peptide binding groove (SPBG) on SecA addressing a key issue regarding the SecA-preprotein interaction. We employ a synthetic signal peptide containing the photoreactive benzoylphenylalanine to efficiently and specifically label SecA containing a unique Factor Xa site. Comparison of the photolabeled fragment from the subsequent proteolysis of several SecAs, which vary only in the location of the Factor Xa site, reveals one 53 residue segment in common with the entire series. The covalently modified SecA segment produced is the same in aqueous solution and in lipid vesicles. This spans amino acid residues 269 to 322 of the E. coli protein, which is distinct from a previously proposed signal peptide binding site, and contributes to a hydrophobic peptide binding groove evident in molecular models of SecA.
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Affiliation(s)
| | | | - Debra A. Kendall
- *Corresponding author. Department of Molecular and Cell Biology, 91 North Eagleville Road, University of Connecticut, Storrs, Connecticut 06269-3125, USA; Tel.: (860) 486-1891; Fax: (860) 486-4331; E-mail: ()
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22
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Crane JM, Suo Y, Lilly AA, Mao C, Hubbell WL, Randall LL. Sites of interaction of a precursor polypeptide on the export chaperone SecB mapped by site-directed spin labeling. J Mol Biol 2006; 363:63-74. [PMID: 16962134 PMCID: PMC2925277 DOI: 10.1016/j.jmb.2006.07.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/10/2006] [Accepted: 07/11/2006] [Indexed: 11/29/2022]
Abstract
Export of protein into the periplasm of Escherichia coli via the general secretory system requires that the transported polypeptides be devoid of stably folded tertiary structure. Capture of the precursor polypeptides before they fold is achieved by the promiscuous binding to the chaperone SecB. SecB delivers its ligand to export sites through its specific binding to SecA, a peripheral component of the membrane translocon. At the translocon the ligand is passed from SecB to SecA and subsequently through the SecYEG channel. We have previously used site-directed spin labeling and electron paramagnetic resonance spectroscopy to establish a docking model between SecB and SecA. Here we report use of the same strategy to map the pathway of a physiologic ligand, the unfolded form of precursor galactose-binding protein, on SecB. Our set of SecB variants each containing a single cysteine, which was used in the previous study, has been expanded to 48 residues, which cover 49% of the surface of SecB. The residues on SecB involved in contacts were identified as those that, upon addition of the unfolded polypeptide ligand, showed changes in spectral line shape consistent with restricted motion of the nitroxide. We conclude that the bound precursor makes contact with a large portion of the surface of the small chaperone. The sites on SecB that interact with the ligand are compared with the previously identified sites that interact with SecA and a model for transfer of the ligand is discussed.
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Affiliation(s)
- Jennine M Crane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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23
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Patel CN, Smith VF, Randall LL. Characterization of three areas of interactions stabilizing complexes between SecA and SecB, two proteins involved in protein export. Protein Sci 2006; 15:1379-86. [PMID: 16731972 PMCID: PMC2265093 DOI: 10.1110/ps.062141006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The general secretory, Sec, system translocates precursor polypeptides from the cytosol across the cytoplasmic membrane in Escherichia coli. SecB, a small cytosolic chaperone, captures the precursor polypeptides before they fold and delivers them to the membrane translocon through interactions with SecA. Both SecB and SecA display twofold symmetry and yet the complex between the two is stabilized by contacts that are distributed asymmetrically. Two distinct regions of interaction have been defined previously and here we identify a third. Calorimetric studies of complexes stabilized by different subsets of these interactions were carried out to determine the binding affinities and the thermodynamic parameters that underlie them. We show here that there is no change in affinity when either one of two contact areas out of the three is lacking. This fact and the asymmetry of the binding contacts may be important to the function of the complex in protein export.
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Affiliation(s)
- Chetan N Patel
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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24
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Keramisanou D, Biris N, Gelis I, Sianidis G, Karamanou S, Economou A, Kalodimos CG. Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat Struct Mol Biol 2006; 13:594-602. [PMID: 16783375 DOI: 10.1038/nsmb1108] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 05/12/2006] [Indexed: 01/01/2023]
Abstract
SecA is a helicase-like motor that couples ATP hydrolysis with the translocation of extracytoplasmic protein substrates. As in most helicases, this process is thought to occur through nucleotide-regulated rigid-body movement of the motor domains. NMR, thermodynamic and biochemical data show that SecA uses a novel mechanism wherein conserved regions lining the nucleotide cleft undergo cycles of disorder-order transitions while switching among functional catalytic states. The transitions are regulated by interdomain interactions mediated by crucial 'arginine finger' residues located on helicase motifs. Furthermore, we show that the nucleotide cleft allosterically communicates with the preprotein substrate-binding domain and the regulatory, membrane-inserting C domain, thereby allowing for the coupling of the ATPase cycle to the translocation activity. The intrinsic plasticity and functional disorder-order folding transitions coupled to ligand binding seem to provide a precise control of the catalytic activation process and simple regulation of allosteric mechanisms.
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25
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Musial-Siwek M, Rusch SL, Kendall DA. Probing the affinity of SecA for signal peptide in different environments. Biochemistry 2006; 44:13987-96. [PMID: 16229488 PMCID: PMC3094106 DOI: 10.1021/bi050882k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SecA, the peripheral subunit of the Escherichia coli preprotein translocase, interacts with a number of ligands during export, including signal peptides, membrane phospholipids, and nucleotides. Using fluorescence resonance energy transfer (FRET), we studied the interactions of wild-type (WT) and mutant SecAs with IAEDANS-labeled signal peptide, and how these interactions are modified in the presence of other transport ligands. We find that residues on the third alpha-helix in the preprotein cross-linking domain (PPXD) are important for the interaction of SecA and signal peptide. For SecA in aqueous solution, saturation binding data using FRET analysis fit a single-site binding model and yielded a Kd of 2.4 microM. FRET is inhibited for SecA in lipid vesicles relative to that in aqueous solution at a low signal peptide concentration. The sigmoidal nature of the binding curve suggests that SecA in lipids has two conformational states; our results do not support different oligomeric states of SecA. Using native gel electrophoresis, we establish signal peptide-induced SecA monomerization in both aqueous solution and lipid vesicles. Whereas the affinity of SecA for signal peptide in an aqueous environment is unaffected by temperature or the presence of nucleotides, in lipids the affinity decreases in the presence of ADP or AMP-PCP but increases at higher temperature. The latter finding is consistent with SecA existing in an elongated form while inserting the signal peptide into membranes.
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Affiliation(s)
| | | | - Debra A. Kendall
- To whom correspondence should be addressed: Department of Molecular and Cell Biology, 91 N. Eagleville Rd., University of Connecticut, Storrs, CT 06269-3125. Phone: (860) 486-1891. Fax: (860) 486-4331.
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26
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Papanikou E, Karamanou S, Baud C, Frank M, Sianidis G, Keramisanou D, Kalodimos CG, Kuhn A, Economou A. Identification of the Preprotein Binding Domain of SecA. J Biol Chem 2005; 280:43209-17. [PMID: 16243836 DOI: 10.1074/jbc.m509990200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA, the preprotein translocase ATPase, has a helicase DEAD motor. To catalyze protein translocation, SecA possesses two additional flexible domains absent from other helicases. Here we demonstrate that one of these "specificity domains" is a preprotein binding domain (PBD). PBD is essential for viability and protein translocation. PBD mutations do not abrogate the basal enzymatic properties of SecA (nucleotide binding and hydrolysis), nor do they prevent SecA binding to the SecYEG protein conducting channel. However, SecA PBD mutants fail to load preproteins onto SecYEG, and their translocation ATPase activity does not become stimulated by preproteins. Bulb and Stem, the two sterically proximal PBD substructures, are physically separable and have distinct roles. Stem binds signal peptides, whereas the Bulb binds mature preprotein regions as short as 25 amino acids. Binding of signal or mature region peptides or full-length preproteins causes distinct conformational changes to PBD and to the DEAD motor. We propose that (a) PBD is a preprotein receptor and a physical bridge connecting bound preproteins to the DEAD motor, and (b) preproteins control the ATPase cycle via PBD.
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Affiliation(s)
- Efrosyni Papanikou
- Institute of Molecular Biology and Biotechnology, F.O.R.T.H., University of Crete, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
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27
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Zhou J, Xu Z. The structural view of bacterial translocation-specific chaperone SecB: implications for function. Mol Microbiol 2005; 58:349-57. [PMID: 16194224 DOI: 10.1111/j.1365-2958.2005.04842.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
SecB is a molecular chaperone that functions in bacterial post-translational protein translocation pathway. It maintains newly synthesized precursor polypeptide chains in a translocation-competent state and guides them to the translocon via its high-affinity binding to the ligand as well as to the membrane-embedded ATPase SecA. Recent advances in elucidating the structures of SecB have enabled the examination of protein function in the structural context. Structures of SecB from both Haemophilus influenzae and Escherichia coli support the early two-subsite polypeptide-binding model. In addition, the detailed molecular interaction between SecB and SecA was revealed by a structure of SecB in complex with the C-terminal zinc-containing domain of SecA. These observations explain the dual role of SecB plays in the translocation pathway, as a molecular chaperone and a specific targeting factor. A model of SecB-SecA complex suggests that the binding of SecA to SecB changes the conformation of the polypeptide binding sites in the chaperone, enabling transfer of precursor polypeptides from SecB to SecA. Recent studies also show the presence of a second zinc-independent SecB binding site in SecA and the new interaction might contribute to the function of SecB.
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Affiliation(s)
- Jiahai Zhou
- Department of Biological Chemistry, Medical School and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
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28
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Chou YT, Gierasch LM. The Conformation of a Signal Peptide Bound by Escherichia coli Preprotein Translocase SecA. J Biol Chem 2005; 280:32753-60. [PMID: 16046390 DOI: 10.1074/jbc.m507532200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To understand the structural nature of signal sequence recognition by the preprotein translocase SecA, we have characterized the interactions of a signal peptide corresponding to a LamB signal sequence (modified to enhance aqueous solubility) with SecA by NMR methods. One-dimensional NMR studies showed that the signal peptide binds SecA with a moderately fast exchange rate (Kd approximately 10(-5) m). The line-broadening effects observed from one-dimensional and two-dimensional NMR spectra indicated that the binding mode does not equally immobilize all segments of this peptide. The positively charged arginine residues of the n-region and the hydrophobic residues of the h-region had less mobility than the polar residues of the c-region in the SecA-bound state, suggesting that this peptide has both electrostatic and hydrophobic interactions with the binding pocket of SecA. Transferred nuclear Overhauser experiments revealed that the h-region and part of the c-region of the signal peptide form an alpha-helical conformation upon binding to SecA. One side of the hydrophobic core of the helical h-region appeared to be more strongly bound in the binding pocket, whereas the extreme C terminus of the peptide was not intimately involved. These results argue that the positive charges at the n-region and the hydrophobic helical h-region are the selective features for recognition of signal sequences by SecA and that the signal peptide-binding site on SecA is not fully buried within its structure.
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Affiliation(s)
- Yi-Te Chou
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003-04510, USA
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29
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Zelazny AM, Calhoun LB, Li L, Shea YR, Fischer SH. Identification of Mycobacterium species by secA1 sequences. J Clin Microbiol 2005; 43:1051-8. [PMID: 15750059 PMCID: PMC1081289 DOI: 10.1128/jcm.43.3.1051-1058.2005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a novel molecular method for the differentiation and identification of 29 mycobacterial species. The target is the secA1 gene that codes for the essential protein SecA1, a key component of the major pathway of protein secretion across the cytoplasmic membrane. A 700-bp region of the secA1 gene was amplified and sequenced from 47 American Type Culture Collection strains of 29 Mycobacterium species as well as from 59 clinical isolates. Sequence variability in the amplified segment of the secA1 gene allowed the differentiation of all species except for the members of the Mycobacterium tuberculosis (MTB) complex, which had identical sequences. A range of 83.3 to 100% interspecies similarity was observed. All species could also be differentiated by their amino acid sequences as deduced from the sequenced region of the secA1 gene, with the exception of the MTB complex. Partial sequences of secA1 from clinical isolates belonging to nine frequently isolated species of mycobacteria revealed a very high intraspecies similarity at the DNA level (typically >99%; range, 96.0 to 100%); all clinical isolates were correctly identified. Comparison of the deduced 233-amino-acid sequences among clinical isolates of the same species showed between 99.6 and 100% similarity. To our knowledge, this is the first time a secretion-related gene has been used for the identification of the species within a bacterial genus.
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Affiliation(s)
- Adrian M Zelazny
- Microbiology Service, Departmant of Laboratory Medicine, Magnuson Clinical Center, National Institutes of Health, 10 Center Drive, MSC 1508, Bethesda, MD 20892-1508, USA
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30
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Baud C, Papanikou E, Karamanou S, Sianidis G, Kuhn A, Economou A. Purification of a functional mature region from a SecA-dependent preprotein. Protein Expr Purif 2005; 40:336-9. [PMID: 15766875 DOI: 10.1016/j.pep.2004.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 12/08/2004] [Indexed: 10/26/2022]
Abstract
Most of the bacterial proteins that are active in extracytoplasmic locations are translocated through the inner membrane by the Sec translocase. Translocase comprises a membrane "pore" and the peripheral ATPase SecA. Where preproteins bind to SecA and how they activate translocation ATPase remains elusive. To address this central question we have purified to homogeneity the mature and preprotein parts of an exported protein (pCH5EE). pCH5EE satisfies a minimal size required for protein translocation and its membrane insertion is SecA-dependent. Purified pCH5EE and CH5EE can form physical complexes with SecA and can functionally suppress the elevated ATPase of a constitutively activated mutant. These properties render pCH5EE and CH5EE unique tools for the biochemical mapping of the preprotein binding site on SecA.
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Affiliation(s)
- Catherine Baud
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
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31
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Vrontou E, Economou A. Structure and function of SecA, the preprotein translocase nanomotor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1694:67-80. [PMID: 15546658 DOI: 10.1016/j.bbamcr.2004.06.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 06/03/2004] [Accepted: 06/17/2004] [Indexed: 11/22/2022]
Abstract
Most secretory proteins that are destined for the periplasm or the outer membrane are exported through the bacterial plasma membrane by the Sec translocase. Translocase is a complex nanomachine that moves processively along its aminoacyl polymeric substrates effectively pumping them to the periplasmic space. The salient features of this process are: (a) a membrane-embedded "clamp" formed by the trimeric SecYEG protein, (b) a "motor" provided by the dimeric SecA ATPase, (c) regulatory subunits that optimize catalysis and (d) both chemical and electrochemical metabolic energy. Significant recent strides have allowed structural, biochemical and biophysical dissection of the export reaction. A model incorporating stepwise strokes of the translocase nanomachine at work is discussed.
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Affiliation(s)
- Eleftheria Vrontou
- Laboratory Unicellular, Organisms Group, Institute of Molecular Biology and Biotechnology, FO.R.T.H. and Department of Biology, University of Crete, Vassilika Vouton, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
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32
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Karamanou S, Sianidis G, Gouridis G, Pozidis C, Papanikolau Y, Papanikou E, Economou A. Escherichia coli SecA truncated at its termini is functional and dimeric. FEBS Lett 2005; 579:1267-71. [PMID: 15710424 DOI: 10.1016/j.febslet.2005.01.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 12/17/2004] [Accepted: 01/04/2005] [Indexed: 11/26/2022]
Abstract
Terminal residues in SecA, the dimeric ATPase motor of bacterial preprotein translocase, were proposed to be required for function and dimerization. To test this, we generated truncation mutants of the 901aa long SecA of Escherichia coli. We now show that deletions of carboxy-terminal domain (CTD), the extreme CTD of 70 residues, or of the N-terminal nonapeptide or of both, do not compromise protein translocation or viability. Deletion of additional C-terminal residues upstream of CTD compromised function. Functional truncation mutants like SecA9-861 are dimeric, conformationally similar to SecA, fully competent for nucleotide and SecYEG binding and for ATP catalysis. Our data demonstrate that extreme terminal SecA residues are not essential for SecA catalysis and dimerization.
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Affiliation(s)
- Spyridoula Karamanou
- Department of Biology, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas and University of Crete, Iraklio, Crete, Greece
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33
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Dalbey RE, Chen M. Sec-translocase mediated membrane protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1694:37-53. [DOI: 10.1016/j.bbamcr.2004.03.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 03/08/2004] [Accepted: 03/09/2004] [Indexed: 10/26/2022]
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34
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Facey SJ, Kuhn A. Membrane integration of E. coli model membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1694:55-66. [PMID: 15546657 DOI: 10.1016/j.bbamcr.2004.03.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 02/18/2004] [Accepted: 03/01/2004] [Indexed: 11/30/2022]
Abstract
The molecular events of membrane translocation and insertion have been investigated using a number of different model proteins. Each of these proteins has specific features that allow interaction with the membrane components which ensure that the proteins reach their specific local destination and final conformation. This review will give an overview on the best-characterized proteins studied in the bacterial system and emphasize the distinct aspects of the pathways.
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Affiliation(s)
- Sandra J Facey
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
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35
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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36
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Papanikou E, Karamanou S, Baud C, Sianidis G, Frank M, Economou A. Helicase Motif III in SecA is essential for coupling preprotein binding to translocation ATPase. EMBO Rep 2004; 5:807-11. [PMID: 15272299 PMCID: PMC1299117 DOI: 10.1038/sj.embor.7400206] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 06/22/2004] [Accepted: 06/22/2004] [Indexed: 11/09/2022] Open
Abstract
The SecA ATPase is a protein translocase motor and a superfamily 2 (SF2) RNA helicase. The ATPase catalytic core ('DEAD motor') contains the seven conserved SF2 motifs. Here, we demonstrate that Motif III is essential for SecA-mediated protein translocation and viability. SecA Motif III mutants can bind ligands (nucleotide, the SecYEG translocase 'channel', signal and mature preprotein domains), can catalyse basal and SecYEG-stimulated ATP hydrolysis and can be activated for catalysis. However, Motif III mutation specifically blocks the preprotein-stimulated 'translocation ATPase' at a step of the reaction pathway that lies downstream of ligand binding. A functional Motif III is required for optimal ligand-driven conformational changes and kinetic parameters that underlie optimal preprotein-modulated nucleotide cycling at the SecA DEAD motor. We propose that helicase Motif III couples preprotein binding to the SecA translocation ATPase and that catalytic activation of SF2 enzymes through Motif-III-mediated action is essential for both polypeptide and nucleic-acid substrates.
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Affiliation(s)
- Efrosyni Papanikou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas and Department of Biology, University of Crete, PO Box 1527, GR711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas and Department of Biology, University of Crete, PO Box 1527, GR711 10 Iraklio, Crete, Greece
| | - Catherine Baud
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas and Department of Biology, University of Crete, PO Box 1527, GR711 10 Iraklio, Crete, Greece
| | - Giorgos Sianidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas and Department of Biology, University of Crete, PO Box 1527, GR711 10 Iraklio, Crete, Greece
| | - Miriam Frank
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas and Department of Biology, University of Crete, PO Box 1527, GR711 10 Iraklio, Crete, Greece
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas and Department of Biology, University of Crete, PO Box 1527, GR711 10 Iraklio, Crete, Greece
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37
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Randall LL, Crane JM, Liu G, Hardy SJS. Sites of interaction between SecA and the chaperone SecB, two proteins involved in export. Protein Sci 2004; 13:1124-33. [PMID: 15010547 PMCID: PMC2280050 DOI: 10.1110/ps.03410104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
SecB, a small tetrameric cytosolic chaperone in Escherichia coli, facilitates the export of precursor poly-peptides by maintaining them in a nonnative conformation and passing them to SecA, which is a peripheral member of the membrane-bound translocation apparatus. It has been proposed by several laboratories that as SecA interacts with various components along the export pathway, it undergoes conformational changes that are crucial to its function. Here we report details of molecular interactions between SecA and SecB, which may serve as conformational switches. One site of interaction involves the final C-terminal 21 amino acids of SecA, which are positively charged and contain zinc. The C terminus of each subunit of the SecA dimer makes contact with the flat beta-sheet that is formed by each dimer of the SecB tetramer. Here we demonstrate that a second interaction exists between the extreme C-terminal alpha-helix of SecB and a site on SecA, as yet undefined but different from the C terminus of SecA. We investigated the energetics of the interactions by titration calorimetry and characterized the hydrodynamic properties of complexes stabilized by both interactions or each interaction singly using sedimentation velocity centrifugation.
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Affiliation(s)
- Linda L Randall
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Columbia, MO 65211, USA.
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38
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Vrontou E, Karamanou S, Baud C, Sianidis G, Economou A. Global co-ordination of protein translocation by the SecA IRA1 switch. J Biol Chem 2004; 279:22490-7. [PMID: 15007058 DOI: 10.1074/jbc.m401008200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA, the dimeric ATPase subunit of protein translocase, contains a DEAD helicase catalytic core that binds to a regulatory C-terminal domain. We now demonstrate that IRA1, a conserved helix-loop-helix structure in the C-domain, controls C-domain conformation through direct interdomain contacts. C-domain conformational changes are transmitted to the DEAD motor and alter its conformation. These interactions establish DEAD motor/C-domain conformational cross-talk that requires a functional IRA1. IRA1-controlled binding/release cycles of the C-domain to the DEAD motor couple this cross-talk to protein translocation chemistries, i.e. DEAD motor affinities for ligands (nucleotides, preprotein signal peptides, and SecYEG, the integral membrane component of translocase) and ATP turnover. IRA1-mediated global co-ordination of SecA catalysis is essential for protein translocation.
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Affiliation(s)
- Eleftheria Vrontou
- Department of Biology, University of Crete, PO Box 1527, GR-71110 Iraklio, Crete, Greece
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39
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Eser M, Ehrmann M. SecA-dependent quality control of intracellular protein localization. Proc Natl Acad Sci U S A 2003; 100:13231-4. [PMID: 14597695 PMCID: PMC263763 DOI: 10.1073/pnas.2234410100] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Complex secretion machineries mediate protein translocation across cellular membranes. These machines typically recognize their substrates via signal sequences, which are required for proper targeting to the translocon. We report that during posttranslational secretion the widely conserved targeting factor SecA performs a quality-control function that is based on a general chaperone activity. This quality-control mechanism involves assisted folding of signal sequenceless proteins, thereby excluding them from the secretion process. These results suggest that SecA channels proteins into one of two key pathways, posttranslational secretion or folding in the cytoplasm. Implications of this finding for intracellular protein localization are discussed.
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Affiliation(s)
- Markus Eser
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3US, United Kingdom
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40
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Zito CR, Oliver D. Two-stage binding of SecA to the bacterial translocon regulates ribosome-translocon interaction. J Biol Chem 2003; 278:40640-6. [PMID: 12907673 DOI: 10.1074/jbc.m308025200] [Citation(s) in RCA: 25] [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 bacterial translocon interacts with both SecA-bound preproteins and nascent chain-ribosome complexes during Sec and signal recognition particle-dependent protein translocation, respectively. In their inactive state, translocons are saturated with ribosomes and SecA protein, reflecting the inherent affinity of these components for one another. We found that SecA and ribosomes are bound simultaneously and noncompetitively to a common set of inactive translocons. Furthermore, we demonstrate that at a later stage in binding, SecA possesses a ribosome-translocon dissociation activity that is coupled to its ATP-dependent membrane insertion and retraction cycle that drives protein translocation. This novel activity is presumably important in the commitment of the translocon to the Sec-dependent pathway. These results also provide a rationale for the compatibility and regulation of multiple protein translocation pathways that each makes distinct demands on a common translocon core.
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Affiliation(s)
- Christopher R Zito
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459, USA
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41
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Abstract
The targeting of proteins into and across biological membranes to their correct cellular locations is mediated by a variety of transport pathways. These systems must couple the thermodynamically unfavorable processes of substrate translocation and integration with the expenditure of metabolic energy, using the free energy of ATP and GTP hydrolysis and/or a transmembrane protonmotive force. Several recent advances in our knowledge of the structure and function of these transport systems have provided insights into the mechanisms of energy transduction, force generation and energy use by different protein transport pathways.
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Affiliation(s)
- Nathan N Alder
- Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, TX 77843, USA
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42
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Sharma V, Arockiasamy A, Ronning DR, Savva CG, Holzenburg A, Braunstein M, Jacobs WR, Sacchettini JC. Crystal structure of Mycobacterium tuberculosis SecA, a preprotein translocating ATPase. Proc Natl Acad Sci U S A 2003; 100:2243-8. [PMID: 12606717 PMCID: PMC151325 DOI: 10.1073/pnas.0538077100] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2002] [Accepted: 12/12/2002] [Indexed: 11/18/2022] Open
Abstract
In bacteria, the majority of exported proteins are translocated by the Sec system, which recognizes the signal sequence of a preprotein and uses ATP and the proton motive force to mediate protein translocation across the cytoplasmic membrane. SecA is an essential protein component of this system, containing the molecular motor that facilitates translocation. Here we report the three-dimensional structure of the SecA protein of Mycobacterium tuberculosis. Each subunit of the homodimer contains a "motor" domain and a translocation domain. The structure predicts that SecA can interact with the SecYEG pore and function as a molecular ratchet that uses ATP hydrolysis for physical movement of the preprotein. Knowledge of this structure provides a framework for further elucidation of the translocation process.
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Affiliation(s)
- Vivek Sharma
- Center for Structural Biology, Institute of Biosciences and Technology, Houston, TX 77030, USA
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43
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Chou YT, Swain JF, Gierasch LM. Functionally significant mobile regions of Escherichia coli SecA ATPase identified by NMR. J Biol Chem 2002; 277:50985-90. [PMID: 12397065 DOI: 10.1074/jbc.m209237200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA, a 204-kDa homodimeric protein, is a major component of the cellular machinery that mediates the translocation of proteins across the Escherichia coli plasma membrane. SecA promotes translocation by nucleotide-modulated insertion and deinsertion into the cytoplasmic membrane once bound to both the signal sequence and portions of the mature domain of the preprotein. SecA is proposed to undergo major conformational changes during translocation. These conformational changes are accompanied by major rearrangements of SecA structural domains. To understand the interdomain rearrangements, we have examined SecA by NMR and identified regions that display narrow resonances indicating high mobility. The mobile regions of SecA have been assigned to a sequence from the second of two domains with nucleotide-binding folds (NBF-II; residues 564-579) and to the extreme C-terminal segment of SecA (residues 864-901), both of which are essential for preprotein translocation activity. Interactions with ligands suggest that the mobile regions are involved in functionally critical regulatory steps in SecA.
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Affiliation(s)
- Yi-Te Chou
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003-4510, USA
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Cleverley RM, Gierasch LM. Mapping the signal sequence-binding site on SRP reveals a significant role for the NG domain. J Biol Chem 2002; 277:46763-8. [PMID: 12244111 DOI: 10.1074/jbc.m207427200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present evidence that the signal recognition particle (SRP) recognizes signal sequences via the NG domain on the SRP54 protein subunit. Using a recently developed cross-linking method (Fancy, D. A., and Kodadek, T. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 6020-6024; Correction (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 1317), we find that signal peptides cross-link to the Escherichia coli SRP protein Ffh (the homologue of the mammalian SRP54 subunit) via the NG domain. Within the NG domain, the cross-linking site maps to the ras-like C-terminal subdomain termed the G domain. This result stands in contrast to previous studies, which concluded based on nascent chain cross-linking that the signal sequence bound to the adjacent M domain. As independent evidence of a direct binding interaction between the NG domain and the signal sequence, we find that the NG domain of Ffh binds signal peptides as an isolated entity. Our results suggest that the NG domain forms a substantial part of the binding site for the signal sequence.
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Affiliation(s)
- Robert M Cleverley
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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