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Crane JM, Randall LL. The Sec System: Protein Export in Escherichia coli. EcoSal Plus 2017; 7:10.1128/ecosalplus.ESP-0002-2017. [PMID: 29165233 PMCID: PMC5807066 DOI: 10.1128/ecosalplus.esp-0002-2017] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, proteins found in the periplasm or the outer membrane are exported from the cytoplasm by the general secretory, Sec, system before they acquire stably folded structure. This dynamic process involves intricate interactions among cytoplasmic and membrane proteins, both peripheral and integral, as well as lipids. In vivo, both ATP hydrolysis and proton motive force are required. Here, we review the Sec system from the inception of the field through early 2016, including biochemical, genetic, and structural data.
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Affiliation(s)
- Jennine M. Crane
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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Yan S, Wu G. Large-scale evolutionary analyses on SecB subunits of bacterial sec system. PLoS One 2015; 10:e0120417. [PMID: 25775430 PMCID: PMC4361572 DOI: 10.1371/journal.pone.0120417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/21/2015] [Indexed: 01/10/2023] Open
Abstract
Protein secretion systems are extremely important in bacteria because they are involved in many fundamental cellular processes. Of the various secretion systems, the Sec system is composed of seven different subunits in bacteria, and subunit SecB brings secreted preproteins to subunit SecA, which with SecYEG and SecDF forms a complex for the translocation of secreted preproteins through the inner membrane. Because of the wide existence of Sec system across bacteria, eukaryota, and archaea, each subunit of the Sec system has a complicated evolutionary relationship. Until very recently, 5,162 SecB sequences have been documented in UniProtKB, however no phylogenetic study has been conducted on a large sampling of SecBs from bacterial Sec secretion system, and no statistical study has been conducted on such size of SecBs in order to exhaustively investigate their variances of pairwise p-distance along taxonomic lineage from kingdom to phylum, to class, to order, to family, to genus and to organism. To fill in these knowledge gaps, 3,813 bacterial SecB sequences with full taxonomic lineage from kingdom to organism covering 4 phyla, 11 classes, 41 orders, 82 families, 269 genera, and 3,744 organisms were studied. Phylogenetic analysis revealed how the SecBs evolved without compromising their function with examples of 3-D structure comparison of two SecBs from Proteobacteria, and possible factors that affected the SecB evolution were considered. The average pairwise p-distances showed that the variance varied greatly in each taxonomic group. Finally, the variance was further partitioned into inter- and intra-clan variances, which could correspond to vertical and horizontal gene transfers, with relevance for Achromobacter, Brevundimonas, Ochrobactrum, and Pseudoxanthomonas.
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Affiliation(s)
- Shaomin Yan
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Guang Wu
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- * E-mail:
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Suo Y, Hardy SJS, Randall LL. The basis of asymmetry in the SecA:SecB complex. J Mol Biol 2014; 427:887-900. [PMID: 25534082 DOI: 10.1016/j.jmb.2014.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022]
Abstract
During export in Escherichia coli, SecB, a homotetramer structurally organized as a dimer of dimers, forms a complex with two protomers of SecA, which is the ATPase that provides energy to transfer a precursor polypeptide through the membrane via the SecYEG translocon. There are two areas of contact on SecB that stabilize the SecA:SecB complex: the flat sides of the SecB tetramer and the C-terminal 13 residues of SecB. These contacts within the complex are distributed asymmetrically. Breaking contact between SecA and the sides of SecB results in release of only one protomer of SecA yielding a complex of stoichiometry SecA1:SecB4. This complex mediates export; however, the coupling of ATP hydrolysis to movements of the precursor through the translocon is much less efficient than the coupling by the SecA2:SecB4 complex. Here we used heterotetrameric species of SecB to understand the source of the asymmetry in the contacts and its role in the functioning of the complex. The model of interactions presented suggests a way that binding between SecA and SecB might decrease the affinity of precursor polypeptides for SecB and facilitate the transfer to SecA.
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Affiliation(s)
- Yuying Suo
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Simon J S Hardy
- Department of Biology, University of York, York YO10 5DD, UK
| | - Linda L Randall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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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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Biotechnological advances on penicillin G acylase: pharmaceutical implications, unique expression mechanism and production strategies. Biotechnol Adv 2013; 31:1319-32. [PMID: 23721991 DOI: 10.1016/j.biotechadv.2013.05.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 05/06/2013] [Accepted: 05/19/2013] [Indexed: 01/20/2023]
Abstract
In light of unrestricted use of first-generation penicillins, these antibiotics are now superseded by their semisynthetic counterparts for augmented antibiosis. Traditional penicillin chemistry involves the use of hazardous chemicals and harsh reaction conditions for the production of semisynthetic derivatives and, therefore, is being displaced by the biosynthetic platform using enzymatic transformations. Penicillin G acylase (PGA) is one of the most relevant and widely used biocatalysts for the industrial production of β-lactam semisynthetic antibiotics. Accordingly, considerable genetic and biochemical engineering strategies have been devoted towards PGA applications. This article provides a state-of-the-art review in recent biotechnological advances associated with PGA, particularly in the production technologies with an emphasis on using the Escherichia coli expression platform.
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Bechtluft P, Kedrov A, Slotboom DJ, Nouwen N, Tans SJ, Driessen AJM. Tight hydrophobic contacts with the SecB chaperone prevent folding of substrate proteins. Biochemistry 2010; 49:2380-8. [PMID: 20146530 DOI: 10.1021/bi902051e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular chaperone SecB binds to hydrophobic sections of unfolded secretory proteins and thereby prevents their premature folding prior to secretion by the translocase of Escherichia coli. Here, we have investigated the effect of the single-residue mutation of leucine 42 to arginine (L42R) centrally positioned in the polypeptide binding pocket of SecB on its chaperonin function. The mutant retains its tetrameric structure and SecA targeting function but is defective in its holdase activity. Isothermal titration calorimetry and single-molecule optical tweezer studies suggest that the SecB(L42R) mutant exhibits a reduced polypeptide binding affinity allowing for partial folding of the bound polypeptide chain rendering it translocation-incompetent.
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Affiliation(s)
- Philipp Bechtluft
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Bechtluft P, Nouwen N, Tans SJ, Driessen AJM. SecB--a chaperone dedicated to protein translocation. MOLECULAR BIOSYSTEMS 2009; 6:620-7. [PMID: 20237639 DOI: 10.1039/b915435c] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SecB is a molecular chaperone in Gram-negative bacteria dedicated to the post-translational translocation of proteins across the cytoplasmic membrane. The entire surface of this chaperone is used for both of its native functions in protein targeting and unfolding. Single molecule studies revealed how SecB affects the folding pathway of proteins and how it prevents the tertiary structure formation and aggregation to support protein translocation.
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Affiliation(s)
- Philipp Bechtluft
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.
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Gatsos X, Perry AJ, Anwari K, Dolezal P, Wolynec PP, Likić VA, Purcell AW, Buchanan SK, Lithgow T. Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev 2008; 32:995-1009. [PMID: 18759741 PMCID: PMC2635482 DOI: 10.1111/j.1574-6976.2008.00130.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/18/2008] [Indexed: 11/17/2022] Open
Abstract
The assembly of beta-barrel proteins into membranes is a fundamental process that is essential in Gram-negative bacteria, mitochondria and plastids. Our understanding of the mechanism of beta-barrel assembly is progressing from studies carried out in Escherichia coli and Neisseria meningitidis. Comparative sequence analysis suggests that while many components mediating beta-barrel protein assembly are conserved in all groups of bacteria with outer membranes, some components are notably absent. The Alphaproteobacteria in particular seem prone to gene loss and show the presence or absence of specific components mediating the assembly of beta-barrels: some components of the pathway appear to be missing from whole groups of bacteria (e.g. Skp, YfgL and NlpB), other proteins are conserved but are missing characteristic domains (e.g. SurA). This comparative analysis is also revealing important structural signatures that are vague unless multiple members from a protein family are considered as a group (e.g. tetratricopeptide repeat (TPR) motifs in YfiO, beta-propeller signatures in YfgL). Given that the process of the beta-barrel assembly is conserved, analysis of outer membrane biogenesis in Alphaproteobacteria, the bacterial group that gave rise to mitochondria, also promises insight into the assembly of beta-barrel proteins in eukaryotes.
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Affiliation(s)
- Xenia Gatsos
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Andrew J Perry
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Khatira Anwari
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Pavel Dolezal
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - P Peter Wolynec
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Vladimir A Likić
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
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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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Ponstingl H, Kabir T, Gorse D, Thornton JM. Morphological aspects of oligomeric protein structures. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2005; 89:9-35. [PMID: 15895504 DOI: 10.1016/j.pbiomolbio.2004.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Features of multimeric proteins are reviewed to shed light on the formation of protein assemblies from a structural perspective. The features comprise biochemical and geometric properties. They are compiled on new low-redundancy sets of crystal structures of homomeric proteins with different symmetry and subunit multiplicity, as well as on a set of heteromeric proteins. Crystal structures of likely monomers provide a control group.
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Affiliation(s)
- Hannes Ponstingl
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Abstract
The chaperone SecB from Escherichia coli is primarily involved in passing precursor proteins into the Sec system via specific interactions with SecA. The crystal structure of SecB from E. coli has been solved to 2.35 A resolution. The structure shows flexibility in the crossover loop and the helix-connecting loop, regions that have been implicated to be part of the SecB substrate-binding site. Moreover conformational variability of Trp36 is observed as well as different loop conformations for the different monomers. Based on this, we speculate that SecB can regulate the access or extent of its hydrophobic substrate-binding site, by modulating the conformation of the crossover loop and the helix-connecting loop. The structure also clearly explains why the tetrameric equilibrium is shifted towards the dimeric state in the mutant SecBCys76Tyr. The buried cysteine residue is crucial for tight packing, and mutations are likely to disrupt the tetramer formation but not the dimer formation.
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Affiliation(s)
- Carien Dekker
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, England, NW7 1AA, UK.
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Van Montfort R, Slingsby C, Vierling E. Structure and function of the small heat shock protein/alpha-crystallin family of molecular chaperones. ADVANCES IN PROTEIN CHEMISTRY 2002; 59:105-56. [PMID: 11868270 DOI: 10.1016/s0065-3233(01)59004-x] [Citation(s) in RCA: 300] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- R Van Montfort
- Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Panse VG, Beena K, Philipp R, Trommer WE, Vogel PD, Varadarajan R. Electron spin resonance and fluorescence studies of the bound-state conformation of a model protein substrate to the chaperone SecB. J Biol Chem 2001; 276:33681-8. [PMID: 11435433 DOI: 10.1074/jbc.m104466200] [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] [Indexed: 11/06/2022] Open
Abstract
SecB is a homotetrameric, cytosolic chaperone that forms part of the protein translocation machinery in Escherichia coli. We have investigated the bound-state conformation of a model protein substrate of SecB, bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin-labeling and pyrene fluorescence methods. BPTI is a 58-residue protein and contains three disulfide groups between residues 5 and 55, 14 and 38, as well as 30 and 51. Mutants of BPTI that contained only a single disulfide were reduced, and the free cysteines were labeled with either thiol-specific spin labels or pyrene maleimide. The relative proximity of the labeled residues was studied using either electron spin resonance spectroscopy or fluorescence spectroscopy. The data suggest that SecB binds a collapsed coil of reduced unfolded BPTI, which then undergoes a structural rearrangement to a more extended state upon binding to SecB. Binding occurs at multiple sites on the substrate, and the binding site on each SecB monomer accommodates less than 21 substrate residues. In addition, we have labeled four solvent-accessible cysteine residues in the SecB tetramer and have investigated their relative spatial arrangement in the presence and absence of the substrate protein. The electron spin resonance data suggest that these cysteine residues are in close proximity (15 A) when no substrate protein is bound but move away to a distance of greater than 20 A when SecB binds substrate. This is the first direct evidence of a conformational change in SecB upon binding of a substrate protein.
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Affiliation(s)
- V G Panse
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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