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Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
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Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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2
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Young JW, Wason IS, Zhao Z, Kim S, Aoki H, Phanse S, Rattray DG, Foster LJ, Babu M, Duong van Hoa F. Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly. J Proteome Res 2022; 21:1748-1758. [PMID: 35616533 DOI: 10.1021/acs.jproteome.2c00129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The peptidisc membrane mimetic enables global reconstitution of the bacterial membrane proteome into water-soluble detergent-free particles, termed peptidisc libraries. We present here a method that combines peptidisc libraries and chromosomal-level gene tagging technology with affinity purification and mass spectrometry (AP/MS) to stabilize and identify fragile membrane protein complexes that exist at native expression levels. This method circumvents common artifacts caused by bait protein overproduction and protein complex dissociation due to lengthy exposure to detergents during protein isolation. Using the Escherichia coli Sec system as a case study, we identify an expanded version of the translocon, termed the HMD complex, consisting of nine different integral membrane subunits. This complex is stable in peptidiscs but dissociates in detergents. Guided by this native-level proteomic information, we design and validate a procedure that enables purification of the HMD complex with minimal protein dissociation. These results highlight the utility of peptidiscs and AP/MS to discover and stabilize fragile membrane protein assemblies. Data are available via ProteomeXchange with identifier PXD032315.
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Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Sunyoung Kim
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - David G Rattray
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohan Babu
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Ozma MA, Khodadadi E, Rezaee MA, Asgharzadeh M, Aghazadeh M, Zeinalzadeh E, Ganbarov K, Kafil H. Bacterial proteomics and its application for pathogenesis studies. Curr Pharm Biotechnol 2021; 23:1245-1256. [PMID: 34503411 DOI: 10.2174/1389201022666210908153234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 01/09/2023]
Abstract
Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which leads to preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, to study bacterial proteins, macromolecules are involved in the bacteria's structures and functions. These protein-based methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions such as biofilm formation, antibiotic resistance, and adaptation to the environment, which are helpful in promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis that causes rapid, easy, and accurate diagnosis of the infections.
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Affiliation(s)
- Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsaneh Khodadadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Aghazadeh
- Microbiome and Health Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Hossein Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614711. Iran
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Refined measurement of SecA-driven protein secretion reveals that translocation is indirectly coupled to ATP turnover. Proc Natl Acad Sci U S A 2020; 117:31808-31816. [PMID: 33257538 DOI: 10.1073/pnas.2010906117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The universally conserved Sec system is the primary method cells utilize to transport proteins across membranes. Until recently, measuring the activity-a prerequisite for understanding how biological systems work-has been limited to discontinuous protein transport assays with poor time resolution or reported by large, nonnatural tags that perturb the process. The development of an assay based on a split superbright luciferase (NanoLuc) changed this. Here, we exploit this technology to unpick the steps that constitute posttranslational protein transport in bacteria. Under the conditions deployed, the transport of a model preprotein substrate (proSpy) occurs at 200 amino acids (aa) per minute, with SecA able to dissociate and rebind during transport. Prior to that, there is no evidence for a distinct, rate-limiting initiation event. Kinetic modeling suggests that SecA-driven transport activity is best described by a series of large (∼30 aa) steps, each coupled to hundreds of ATP hydrolysis events. The features we describe are consistent with a nondeterministic motor mechanism, such as a Brownian ratchet.
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5
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Cardiolipin is required in vivo for the stability of bacterial translocon and optimal membrane protein translocation and insertion. Sci Rep 2020; 10:6296. [PMID: 32286407 PMCID: PMC7156725 DOI: 10.1038/s41598-020-63280-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023] Open
Abstract
Translocation of preproteins across the Escherichia coli inner membrane requires anionic lipids by virtue of their negative head-group charge either in vivo or in situ. However, available results do not differentiate between the roles of monoanionic phosphatidylglycerol and dianionic cardiolipin (CL) in this essential membrane-related process. To define in vivo the molecular steps affected by the absence of CL in protein translocation and insertion, we analyzed translocon activity, SecYEG stability and its interaction with SecA in an E. coli mutant devoid of CL. Although no growth defects were observed, co- and post-translational translocation of α-helical proteins across inner membrane and the assembly of outer membrane β-barrel precursors were severely compromised in CL-lacking cells. Components of proton-motive force which could impair protein insertion into and translocation across the inner membrane, were unaffected. However, stability of the dimeric SecYEG complex and oligomerization properties of SecA were strongly compromised while the levels of individual SecYEG translocon components, SecA and insertase YidC were largely unaffected. These results demonstrate that CL is required in vivo for the stability of the bacterial translocon and its efficient function in co-translational insertion into and translocation across the inner membrane of E. coli.
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Carlson ML, Stacey RG, Young JW, Wason IS, Zhao Z, Rattray DG, Scott N, Kerr CH, Babu M, Foster LJ, Duong Van Hoa F. Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. eLife 2019; 8:46615. [PMID: 31364989 PMCID: PMC6697469 DOI: 10.7554/elife.46615] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a ‘one-size fits all’ membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions. For example, we discover a trans-periplasmic supercomplex comprising subunits of the Bam and Sec machineries, including membrane-bound chaperones YfgM and PpiD. We identify RcsF and OmpA as bone fide interactors of BamA, and we show that MetQ association with the ABC transporter MetNI depends on its N-terminal lipid anchor. We also discover NlpA as a novel interactor of MetNI complex. Most of these interactions are largely undetected by standard detergent-based purification. Together, the peptidisc workflow applied to the proteomic field is emerging as a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation.
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Affiliation(s)
- Michael Luke Carlson
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - R Greg Stacey
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - John William Young
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Irvinder Singh Wason
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Zhiyu Zhao
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - David G Rattray
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Nichollas Scott
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Craig H Kerr
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mohan Babu
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Canada
| | - Leonard J Foster
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Franck Duong Van Hoa
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Komarudin AG, Driessen AJM. SecA-Mediated Protein Translocation through the SecYEG Channel. Microbiol Spectr 2019; 7:10.1128/microbiolspec.psib-0028-2019. [PMID: 31373268 PMCID: PMC10957188 DOI: 10.1128/microbiolspec.psib-0028-2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 01/02/2023] Open
Abstract
In bacteria, the Sec translocase mediates the translocation of proteins into and across the cytoplasmic membrane. It consists of a protein conducting channel SecYEG, the ATP-dependent motor SecA, and the accessory SecDF complex. Here we discuss the function and structure of the Sec translocase.
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Affiliation(s)
- Amalina Ghaisani Komarudin
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and the Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and the Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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Sanganna Gari RR, Chattrakun K, Marsh BP, Mao C, Chada N, Randall LL, King GM. Direct visualization of the E. coli Sec translocase engaging precursor proteins in lipid bilayers. SCIENCE ADVANCES 2019; 5:eaav9404. [PMID: 31206019 PMCID: PMC6561738 DOI: 10.1126/sciadv.aav9404] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Escherichia coli exports proteins via a translocase comprising SecA and the translocon, SecYEG. Structural changes of active translocases underlie general secretory system function, yet directly visualizing dynamics has been challenging. We imaged active translocases in lipid bilayers as a function of precursor protein species, nucleotide species, and stage of translocation using atomic force microscopy (AFM). Starting from nearly identical initial states, SecA more readily dissociated from SecYEG when engaged with the precursor of outer membrane protein A as compared to the precursor of galactose-binding protein. For the SecA that remained bound to the translocon, the quaternary structure varied with nucleotide, populating SecA2 primarily with adenosine diphosphate (ADP) and adenosine triphosphate, and the SecA monomer with the transition state analog ADP-AlF3. Conformations of translocases exhibited precursor-dependent differences on the AFM imaging time scale. The data, acquired under near-native conditions, suggest that the translocation process varies with precursor species.
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Affiliation(s)
| | - Kanokporn Chattrakun
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Brendan P. Marsh
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Chunfeng Mao
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Gavin M. King
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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