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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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Lindič N, Loboda J, Usenik A, Vidmar R, Turk D. The Structure of Clostridioides difficile SecA2 ATPase Exposes Regions Responsible for Differential Target Recognition of the SecA1 and SecA2-Dependent Systems. Int J Mol Sci 2020; 21:ijms21176153. [PMID: 32858965 PMCID: PMC7503281 DOI: 10.3390/ijms21176153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 11/17/2022] Open
Abstract
SecA protein is a major component of the general bacterial secretory system. It is an ATPase that couples nucleotide hydrolysis to protein translocation. In some Gram-positive pathogens, a second paralogue, SecA2, exports a different set of substrates, usually virulence factors. To identify SecA2 features different from SecA(1)s, we determined the crystal structure of SecA2 from Clostridioides difficile, an important nosocomial pathogen, in apo and ATP-γ-S-bound form. The structure reveals a closed monomer lacking the C-terminal tail (CTT) with an otherwise similar multidomain organization to its SecA(1) homologues and conserved binding of ATP-γ-S. The average in vitro ATPase activity rate of C. difficile SecA2 was 2.6 ± 0.1 µmolPi/min/µmol. Template-based modeling combined with evolutionary conservation analysis supports a model where C. difficile SecA2 in open conformation binds the target protein, ensures its movement through the SecY channel, and enables dimerization through PPXD/HWD cross-interaction of monomers during the process. Both approaches exposed regions with differences between SecA(1) and SecA2 homologues, which are in agreement with the unique adaptation of SecA2 proteins for a specific type of substrate, a role that can be addressed in further studies.
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Affiliation(s)
- Nataša Lindič
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia; (N.L.); (J.L.); (A.U.); (R.V.)
| | - Jure Loboda
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia; (N.L.); (J.L.); (A.U.); (R.V.)
| | - Aleksandra Usenik
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia; (N.L.); (J.L.); (A.U.); (R.V.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia; (N.L.); (J.L.); (A.U.); (R.V.)
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia; (N.L.); (J.L.); (A.U.); (R.V.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova Cesta 39, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-477-3857
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Abstract
To identify the translocation components in cells, and to understand how they function in protein transport and membrane insertion, a variety of techniques have been used such as genetics, biochemistry, structural biology and single molecule methods. In particular, site-directed crosslinking between the client proteins and components of the translocation machineries have contributed significantly in the past and will do so in the future. One advantage of this technology is that it can be applied in vivo as well as in vitro and a comparison of the two approaches can be made. Also, the in vivo techniques allow time-dependent protocols which are essential for studying cellular pathways. Protein purification and reconstitution into proteoliposomes are the gold standard for studying membrane-based transport and translocation systems. With these biochemically defined approaches the function of each component in protein transport can be addressed individually with a plethora of biophysical techniques. Recently, the use of nanodiscs for reconstitution has added another extension of this reductionistic approach. Fluorescence based studies, cryo-microscopy and NMR spectroscopy have significantly added to our understanding how proteins move into and across membranes and will do this also in future.
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Affiliation(s)
- Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599, Stuttgart, Germany.
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Motions of the SecA protein motor bound to signal peptide: Insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:416-427. [DOI: 10.1016/j.bbamem.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/31/2022]
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Khalili Yazdi A, Namjoshi S, Hackett J, Ghonaim N, Shilton BH. Characterization of a polypeptide-binding site in the DEAD Motor of the SecA ATPase. FEBS Lett 2017; 591:3378-3390. [DOI: 10.1002/1873-3468.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 11/07/2022]
Affiliation(s)
| | - Sarita Namjoshi
- Department of Biochemistry; University of Western Ontario; London Canada
| | - Jesse Hackett
- Department of Biochemistry; University of Western Ontario; London Canada
| | - Nour Ghonaim
- Department of Biochemistry; University of Western Ontario; London Canada
| | - Brian H. Shilton
- Department of Biochemistry; University of Western Ontario; London Canada
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Abstract
All bacteria utilize pathways to export proteins from the cytoplasm to the bacterial cell envelope or extracellular space. Many exported proteins function in essential physiological processes or in virulence. Consequently, the responsible protein export pathways are commonly essential and/or are important for pathogenesis. The general Sec protein export pathway is conserved and essential in all bacteria, and it is responsible for most protein export. The energy for Sec export is provided by the SecA ATPase. Mycobacteria and some Gram-positive bacteria have two SecA paralogs: SecA1 and SecA2. SecA1 is essential and works with the canonical Sec pathway to perform the bulk of protein export. The nonessential SecA2 exports a smaller subset of proteins and is required for the virulence of pathogens such as Mycobacterium tuberculosis. In this article, we review our current understanding of the mechanism of the SecA1 and SecA2 export pathways and discuss some of their better-studied exported substrates. We focus on proteins with established functions in M. tuberculosis pathogenesis and proteins that suggest potential roles for SecA1 and SecA2 in M. tuberculosis dormancy.
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Date SS, Chen CYC, Chen Y, Jansen M. Experimentally optimized threading structures of the proton-coupled folate transporter. FEBS Open Bio 2016; 6:216-30. [PMID: 27047750 PMCID: PMC4794783 DOI: 10.1002/2211-5463.12041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/13/2016] [Accepted: 01/29/2016] [Indexed: 12/18/2022] Open
Abstract
The proton‐coupled folate transporter (PCFT, SLC46A1) transports folic acid across the plasma membrane, together with an excess of protons such that the net charge translocation is positive. We developed 3D structural models of PCFT threaded onto the X‐ray structures of major facilitator superfamily (MFS) members that were identified as close structural homologues. The model of PCFT threaded onto the glycerol‐3‐phosphate transporter (GlpT) structure is consistent with detailed accessibility studies in the absence of extracellular substrate and at pH 7.4 presented here, and additionally with a multitude of other mutagenesis and functional studies. Characteristic MFS structural features are preserved in this PCFT model, such as 12 transmembrane helices divided into two pseudosymmetric bundles, and a high density of positive charges on the periphery of the cytoplasmic site that allow interactions with negatively charged lipid head‐groups. Under the experimental conditions, PCFT predominantly samples the resting state, which in this case is inward‐open. Several positions lining the substrate cavity have been identified. Motif A, a helix‐turn‐helix motif that is a hallmark of MFS transporters between transmembrane segments II and III is oriented appropriately to interact with residues from transmembrane segments IV as well as XI upon conformational transition to the outward‐open state. A charge‐relay system between three charged residues as well as apposing glycines in two α‐helices, both contributed to by motif A, become engaged when PCFT is modeled on the outward‐open state of a putative proton‐driven transporter (YajR).
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Affiliation(s)
- Swapneeta S Date
- Department of Cell Physiology and Molecular Biophysics School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
| | - Cheng-Yen Charles Chen
- Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Medical Student Summer Research Program School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
| | - Yidong Chen
- Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Medical Student Summer Research Program School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
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Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2. J Bacteriol 2015; 198:720-30. [PMID: 26668263 DOI: 10.1128/jb.00696-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/01/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 (MtbSecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how MtbSecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG. IMPORTANCE SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG.
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Wowor AJ, Yan Y, Auclair SM, Yu D, Zhang J, May ER, Gross ML, Kendall DA, Cole JL. Analysis of SecA dimerization in solution. Biochemistry 2014; 53:3248-60. [PMID: 24786965 PMCID: PMC4030788 DOI: 10.1021/bi500348p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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The Sec pathway mediates translocation
of protein across the inner
membrane of bacteria. SecA is a motor protein that drives translocation
of preprotein through the SecYEG channel. SecA reversibly dimerizes
under physiological conditions, but different dimer interfaces have
been observed in SecA crystal structures. Here, we have used biophysical
approaches to address the nature of the SecA dimer that exists in
solution. We have taken advantage of the extreme salt sensitivity
of SecA dimerization to compare the rates of hydrogen–deuterium
exchange of the monomer and dimer and have analyzed the effects of
single-alanine substitutions on dimerization affinity. Our results
support the antiparallel dimer arrangement observed in one of the
crystal structures of Bacillus subtilis SecA. Additional
residues lying within the preprotein binding domain and the C-terminus
are also protected from exchange upon dimerization, indicating linkage
to a conformational transition of the preprotein binding domain from
an open to a closed state. In agreement with this interpretation,
normal mode analysis demonstrates that the SecA dimer interface influences
the global dynamics of SecA such that dimerization stabilizes the
closed conformation.
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Affiliation(s)
- Andy J Wowor
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, Connecticut 06269, United States
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Rao C V S, De Waelheyns E, Economou A, Anné J. Antibiotic targeting of the bacterial secretory pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1762-83. [PMID: 24534745 DOI: 10.1016/j.bbamcr.2014.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 02/06/2023]
Abstract
Finding new, effective antibiotics is a challenging research area driven by novel approaches required to tackle unconventional targets. In this review we focus on the bacterial protein secretion pathway as a target for eliminating or disarming pathogens. We discuss the latest developments in targeting the Sec-pathway for novel antibiotics focusing on two key components: SecA, the ATP-driven motor protein responsible for driving preproteins across the cytoplasmic membrane and the Type I signal peptidase that is responsible for the removal of the signal peptide allowing the release of the mature protein from the membrane. We take a bird's-eye view of other potential targets in the Sec-pathway as well as other Sec-dependent or Sec-independent protein secretion pathways as targets for the development of novel antibiotics. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Smitha Rao C V
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Evelien De Waelheyns
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium; Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, P.O. Box 1385, GR-711 10 Iraklio, Crete, Greece; Department of Biology, University of Crete, P.O. Box 1385, GR-71110 Iraklio, Crete, Greece.
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
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