1
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Sharma P, Vaiwala R, Gopinath AK, Chockalingam R, Ayappa KG. Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7791-7811. [PMID: 38451026 DOI: 10.1021/acs.langmuir.3c03474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.
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Affiliation(s)
- Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Amar Krishna Gopinath
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rajalakshmi Chockalingam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
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2
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Palmer T, Berks BC. The twin-arginine translocation (Tat) system. Curr Biol 2024; 34:R267-R268. [PMID: 38593766 DOI: 10.1016/j.cub.2024.02.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
In this Quick guide, Palmer and Berks introduce the twin-arginine translocation (Tat) systems. Tats are found in a variety of microbes and microbe-derived organelles, and are known to translocate folded substrate proteins across biological membranes.
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Affiliation(s)
- Tracy Palmer
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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3
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Hickman SJ, Miller HL, Bukys A, Kapanidis AN, Berks BC. Aberrant Topologies of Bacterial Membrane Proteins Revealed by High Sensitivity Fluorescence Labelling. J Mol Biol 2024; 436:168368. [PMID: 37977298 DOI: 10.1016/j.jmb.2023.168368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
The cytoplasmic membrane compartmentalises the bacterial cell into cytoplasm and periplasm. Proteins located in this membrane have a defined topology that is established during their biogenesis. However, the accuracy of this fundamental biosynthetic process is unknown. We developed compartment-specific fluorescence labelling methods with up to single-molecule sensitivity. Application of these methods to the single and multi-spanning membrane proteins of the Tat protein transport system revealed rare topogenesis errors. This methodology also detected low level soluble protein mislocalization from the cytoplasm to the periplasm. This study shows that it is possible to uncover rare errors in protein localization by leveraging the high sensitivity of fluorescence methods.
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Affiliation(s)
- Samuel J Hickman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
| | - Alfredas Bukys
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom; Kavli Institute for Nanoscience Discovery, University of Oxford, Sherrington Road, Oxford OX1 3QU, United Kingdom.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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4
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Diepold A. Defining Assembly Pathways by Fluorescence Microscopy. Methods Mol Biol 2024; 2715:383-394. [PMID: 37930541 DOI: 10.1007/978-1-0716-3445-5_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems are among the largest protein complexes in prokaryotes and display remarkably complex architectures. Their assembly often follows clearly defined pathways. Deciphering these pathways not only reveals how bacteria accomplish to build these large functional complexes but can provide crucial information on the interactions and subcomplexes within secretion systems, their distribution within the bacterium, and even functional insights. Fluorescence microscopy provides a powerful tool for biological imaging, which presents an interesting method to accurately define the biogenesis of macromolecular complexes using fluorescently labeled components. Here, I describe the use of this method to decipher the assembly pathway of bacterial secretion systems.
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Affiliation(s)
- Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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5
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Stockwald ER, Steger LME, Vollmer S, Gottselig C, Grage SL, Bürck J, Afonin S, Fröbel J, Blümmel AS, Setzler J, Wenzel W, Walther TH, Ulrich AS. Length matters: Functional flip of the short TatA transmembrane helix. Biophys J 2023; 122:2125-2146. [PMID: 36523158 PMCID: PMC10257086 DOI: 10.1016/j.bpj.2022.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The twin arginine translocase (Tat) exports folded proteins across bacterial membranes. The putative pore-forming or membrane-weakening component (TatAd in B. subtilis) is anchored to the lipid bilayer via an unusually short transmembrane α-helix (TMH), with less than 16 residues. Its tilt angle in different membranes was analyzed under hydrophobic mismatch conditions, using synchrotron radiation circular dichroism and solid-state NMR. Positive mismatch (introduced either by reconstitution in short-chain lipids or by extending the hydrophobic TMH length) increased the helix tilt of the TMH as expected. Negative mismatch (introduced either by reconstitution in long-chain lipids or by shortening the TMH), on the other hand, led to protein aggregation. These data suggest that the TMH of TatA is just about long enough for stable membrane insertion. At the same time, its short length is a crucial factor for successful translocation, as demonstrated here in native membrane vesicles using an in vitro translocation assay. Furthermore, when reconstituted in model membranes with negative spontaneous curvature, the TMH was found to be aligned parallel to the membrane surface. This intrinsic ability of TatA to flip out of the membrane core thus seems to play a key role in its membrane-destabilizing effect during Tat-dependent translocation.
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Affiliation(s)
- Eva R Stockwald
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany
| | - Lena M E Steger
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Stefanie Vollmer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany
| | - Christina Gottselig
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany
| | - Stephan L Grage
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Julia Fröbel
- University of Freiburg, Institute of Biochemistry and Molecular Biology, Freiburg, Germany
| | - Anne-Sophie Blümmel
- University of Freiburg, Institute of Biochemistry and Molecular Biology, Freiburg, Germany
| | - Julia Setzler
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Karlsruhe, Germany
| | - Wolfgang Wenzel
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Karlsruhe, Germany
| | - Torsten H Walther
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany.
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6
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Hao B, Zhou W, Theg SM. The polar amino acid in the TatA transmembrane helix is not strictly necessary for protein function. J Biol Chem 2023; 299:102998. [PMID: 36764519 PMCID: PMC10124905 DOI: 10.1016/j.jbc.2023.102998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
The twin-arginine translocation (Tat) pathway utilizes the proton-motive force (pmf) to transport folded proteins across cytoplasmic membranes in bacteria and archaea, as well as across the thylakoid membrane in plants and the inner membrane in mitochondria. In most species, the minimal components required for Tat activity consist of three subunits, TatA, TatB, and TatC. Previous studies have shown that a polar amino acid is present at the N-terminus of the TatA transmembrane helix (TMH) across many different species. In order to systematically assess the functional importance of this polar amino acid in the TatA TMH in Escherichia coli, we examined a complete set of 19-amino-acid substitutions. Unexpectedly, although being preferred overall, our experiments suggest that the polar amino acid is not necessary for a functional TatA. Hydrophilicity and helix-stabilizing properties of this polar amino acid were found to be highly correlated with the Tat activity. Specifically, change in charge status of the amino acid side chain due to pH resulted in a shift in hydrophilicity, which was demonstrated to impact the Tat transport activity. Furthermore, we identified a four-residue motif at the N-terminus of the TatA TMH by sequence alignment. Using a biochemical approach, we found that the N-terminal motif was functionally significant, with evidence indicating a potential role in the preference for utilizing different pmf components. Taken together, these findings yield new insights into the functionality of TatA and its potential role in the Tat transport mechanism.
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Affiliation(s)
- Binhan Hao
- Plant Biology Department, University of California, Davis, California, USA
| | - Wenjie Zhou
- Plant Biology Department, University of California, Davis, California, USA
| | - Steven M Theg
- Plant Biology Department, University of California, Davis, California, USA.
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7
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Severi E, Bunoro Batista M, Lannoy A, Stansfeld PJ, Palmer T. Characterization of a TatA/TatB binding site on the TatC component of the Escherichia coli twin arginine translocase. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001298. [PMID: 36790402 PMCID: PMC10197872 DOI: 10.1099/mic.0.001298] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 02/16/2023]
Abstract
The twin arginine transport (Tat) pathway exports folded proteins across the cytoplasmic membranes of prokaryotes and the thylakoid membranes of chloroplasts. In Escherichia coli and other Gram-negative bacteria, the Tat machinery comprises TatA, TatB and TatC components. A Tat receptor complex, formed from all three proteins, binds Tat substrates, which triggers receptor organization and recruitment of further TatA molecules to form the active Tat translocon. The polytopic membrane protein TatC forms the core of the Tat receptor and harbours two binding sites for the sequence-related TatA and TatB proteins. A 'polar' cluster binding site, formed by TatC transmembrane helices (TMH) 5 and 6 is occupied by TatB in the resting receptor and exchanges for TatA during receptor activation. The second binding site, lying further along TMH6, is occupied by TatA in the resting state, but its functional relevance is unclear. Here we have probed the role of this second binding site through a programme of random and targeted mutagenesis. Characterization of three stably produced TatC variants, P221R, M222R and L225P, each of which is inactive for protein transport, demonstrated that the substitutions did not affect assembly of the Tat receptor. Moreover, the substitutions that we analysed did not abolish TatA or TatB binding to either binding site. Using targeted mutagenesis we introduced bulky substitutions into the TatA binding site. Molecular dynamics simulations and crosslinking analysis indicated that TatA binding at this site was substantially reduced by these amino acid changes, but TatC retained function. While it is not clear whether TatA binding at the TMH6 site is essential for Tat activity, the isolation of inactivating substitutions indicates that this region of the protein has a critical function.
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Affiliation(s)
- Emmanuele Severi
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Mariana Bunoro Batista
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Adelie Lannoy
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Phillip J. Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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8
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Alcock F, Berks BC. New insights into the Tat protein transport cycle from characterizing the assembled Tat translocon. Mol Microbiol 2022; 118:637-651. [PMID: 36151601 PMCID: PMC10092561 DOI: 10.1111/mmi.14984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Abstract
The twin-arginine protein translocation (Tat) system transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane of chloroplasts. The Tat translocation site is transiently assembled by the recruitment of multiple TatA proteins to a substrate-activated TatBC receptor complex in a process requiring the protonmotive force. The ephemeral nature of the Tat translocation site has so far precluded its isolation. We now report that detergent solubilization of membranes during active transport allows the recovery of receptor complexes that are associated with elevated levels of TatA. We apply this biochemical analysis in combination with live cell fluorescence imaging to Tat systems trapped in the assembled state. We resolve sub-steps in the Tat translocation cycle and infer that TatA assembly precedes the functional interaction of TatA with a polar cluster site on TatC. We observe that dissipation of the protonmotive force releases TatA oligomers from the assembled translocation site demonstrating that the stability of the TatA oligomer does not depend on binding to the receptor complex and implying that the TatA oligomer is assembled at the periphery of the receptor complex. This work provides new insight into the Tat transport cycle and advances efforts to isolate the active Tat translocon.
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Affiliation(s)
- Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK.,Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
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9
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Brüser T, Mehner-Breitfeld D. Occurrence and potential mechanism of holin-mediated non-lytic protein translocation in bacteria. MICROBIAL CELL (GRAZ, AUSTRIA) 2022; 9:159-173. [PMID: 36262927 PMCID: PMC9527704 DOI: 10.15698/mic2022.10.785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022]
Abstract
Holins are generally believed to generate large membrane lesions that permit the passage of endolysins across the cytoplasmic membrane of prokaryotes, ultimately resulting in cell wall degradation and cell lysis. However, there are more and more examples known for non-lytic holin-dependent secretion of proteins by bacteria, indicating that holins somehow can transport proteins without causing large membrane lesions. Phage-derived holins can be used for a non-lytic endolysin translocation to permeabilize the cell wall for the passage of secreted proteins. In addition, clostridia, which do not possess the Tat pathway for transport of folded proteins, most likely employ non-lytic holin-mediated transport also for secretion of toxins and bacteriocins that are incompatible with the general Sec pathway. The mechanism for non-lytic holin-mediated transport is unknown, but the recent finding that the small holin TpeE mediates a non-lytic toxin secretion in Clostridium perfringens opened new perspectives. TpeE contains only one short transmembrane helix that is followed by an amphipathic helix, which is reminiscent of TatA, the membrane-permeabilizing component of the Tat translocon for folded proteins. Here we review the known cases of non-lytic holin-mediated transport and then focus on the structural and functional comparison of TatA and TpeE, resulting in a mechanistic model for holin-mediated transport. This model is strongly supported by a so far not recognized naturally occurring holin-endolysin fusion protein.
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Affiliation(s)
- Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
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10
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Sharma A, Chowdhury R, Musser SM. Oligomerization state of the functional bacterial twin-arginine translocation (Tat) receptor complex. Commun Biol 2022; 5:988. [PMID: 36123532 PMCID: PMC9485244 DOI: 10.1038/s42003-022-03952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 09/06/2022] [Indexed: 11/09/2022] Open
Abstract
The twin-arginine translocation (Tat) system transports folded proteins across bacterial and plastid energy transducing membranes. Ion leaks are generally considered to be mitigated by the creation and destruction of the translocation conduit in a cargo-dependent manner, a mechanism that enables tight sealing around a wide range of cargo shapes and sizes. In contrast to the variable stoichiometry of the active translocon, the oligomerization state of the receptor complex is considered more consistently stable but has proved stubbornly difficult to establish. Here, using a single molecule photobleaching analysis of individual inverted membrane vesicles, we demonstrate that Tat receptor complexes are tetrameric in native membranes with respect to both TatB and TatC. This establishes a maximal diameter for a resting state closed pore. A large percentage of Tat-deficient vesicles explains the typically low transport efficiencies observed. This individual reaction chamber approach will facilitate examination of the effects of stochastically distributed molecules.
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Affiliation(s)
- Ankith Sharma
- Department of Molecular and Cellular Medicine, Texas A&M University, School of Medicine, 1114 TAMU, College Station, TX, 77843, USA
| | - Rajdeep Chowdhury
- Department of Molecular and Cellular Medicine, Texas A&M University, School of Medicine, 1114 TAMU, College Station, TX, 77843, USA
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, Texas A&M University, School of Medicine, 1114 TAMU, College Station, TX, 77843, USA.
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11
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Jackson V, Hermann J, Tynan CJ, Rolfe DJ, Corey RA, Duncan AL, Noriega M, Chu A, Kalli AC, Jones EY, Sansom MSP, Martin-Fernandez ML, Seiradake E, Chavent M. The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X 3-small transmembrane motifs. Structure 2022; 30:1354-1365.e5. [PMID: 35700726 DOI: 10.1016/j.str.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/03/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Fibronectin Leucine-rich Repeat Transmembrane (FLRT 1-3) proteins are a family of broadly expressed single-spanning transmembrane receptors that play key roles in development. Their extracellular domains mediate homotypic cell-cell adhesion and heterotypic protein interactions with other receptors to regulate cell adhesion and guidance. These in trans FLRT interactions determine the formation of signaling complexes of varying complexity and function. Whether FLRTs also interact at the surface of the same cell, in cis, remains unknown. Here, molecular dynamics simulations reveal two dimerization motifs in the FLRT2 transmembrane helix. Single particle tracking experiments show that these Small-X3-Small motifs synergize with a third dimerization motif encoded in the extracellular domain to permit the cis association and co-diffusion patterns of FLRT2 receptors on cells. These results may point to a competitive switching mechanism between in cis and in trans interactions, which suggests that homotypic FLRT interaction mirrors the functionalities of classic adhesion molecules.
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Affiliation(s)
- Verity Jackson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Julia Hermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Christopher J Tynan
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Daniel J Rolfe
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Maxime Noriega
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Amy Chu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, LS2 9NL, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK.
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France.
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12
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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13
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Mehner-Breitfeld D, Ringel MT, Tichy DA, Endter LJ, Stroh KS, Lünsdorf H, Risselada HJ, Brüser T. TatA and TatB generate a hydrophobic mismatch important for the function and assembly of the Tat translocon in Escherichia coli. J Biol Chem 2022; 298:102236. [PMID: 35809643 PMCID: PMC9424591 DOI: 10.1016/j.jbc.2022.102236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
The twin-arginine translocation (Tat) system serves to translocate folded proteins across energy-transducing membranes in bacteria, archaea, plastids, and some mitochondria. In Escherichia coli, TatA, TatB, and TatC constitute functional translocons. TatA and TatB both possess an N-terminal transmembrane helix (TMH) followed by an amphipathic helix. The TMHs of TatA and TatB generate a hydrophobic mismatch with the membrane, as the helices comprise only 12 consecutive hydrophobic residues; however, the purpose of this mismatch is unclear. Here, we shortened or extended this stretch of hydrophobic residues in either TatA, TatB, or both and analyzed effects on translocon function and assembly. We found the WT length helices functioned best, but some variation was clearly tolerated. Defects in function were exacerbated by simultaneous mutations in TatA and TatB, indicating partial compensation of mutations in each by the other. Furthermore, length variation in TatB destabilized TatBC-containing complexes, revealing that the 12-residue-length is important but not essential for this interaction and translocon assembly. To also address potential effects of helix length on TatA interactions, we characterized these interactions by molecular dynamics simulations, after having characterized the TatA assemblies by metal-tagging transmission electron microscopy. In these simulations, we found that interacting short TMHs of larger TatA assemblies were thinning the membrane and—together with laterally-aligned tilted amphipathic helices—generated a deep V-shaped membrane groove. We propose the 12 consecutive hydrophobic residues may thus serve to destabilize the membrane during Tat transport, and their conservation could represent a delicate compromise between functionality and minimization of proton leakage.
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Affiliation(s)
| | - Michael T Ringel
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Daniel Alexander Tichy
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany; Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Laura J Endter
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Kai Steffen Stroh
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | | | - Herre Jelger Risselada
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany.
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14
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Hao B, Zhou W, Theg SM. Hydrophobic mismatch is a key factor in protein transport across lipid bilayer membranes via the Tat pathway. J Biol Chem 2022; 298:101991. [PMID: 35490783 PMCID: PMC9207671 DOI: 10.1016/j.jbc.2022.101991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway transports folded proteins across membranes in bacteria, thylakoids, plant mitochondria, and archaea. In most species, the active Tat machinery consists of three independent subunits: TatA, TatB, and TatC. TatA and TatB possess short transmembrane alpha helices (TMHs), both of which are only 15 residues long in Escherichia coli. Such short TMHs cause a hydrophobic mismatch between Tat subunits and the membrane bilayer, although the functional significance of this mismatch is unclear. Here, we sought to address the functional importance of the hydrophobic mismatch in the Tat transport mechanism in E. coli. We conducted three different assays to evaluate the effect of TMH length mutants on Tat activity and observed that the TMHs of TatA and TatB appear to be evolutionarily tuned to 15 amino acids, with activity dropping off following any modification of this length. Surprisingly, TatA and TatB with as few as 11 residues in their TMHs can still insert into the membrane bilayer, albeit with a decline in membrane integrity. These findings support a model of Tat transport utilizing localized toroidal pores that form when the membrane bilayer is thinned to a critical threshold. In this context, we conclude that the 15-residue length of the TatA and TatB TMHs can be seen as a compromise between the need for some hydrophobic mismatch to allow the membrane to reversibly reach the threshold thinness required for toroidal pore formation and the permanently destabilizing effect of placing even shorter helices into these energy-transducing membranes.
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Affiliation(s)
- Binhan Hao
- Plant Biology Department, University of California, Davis, CA 95616
| | - Wenjie Zhou
- Plant Biology Department, University of California, Davis, CA 95616
| | - Steven M Theg
- Plant Biology Department, University of California, Davis, CA 95616.
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15
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Khalid S, Schroeder C, Bond PJ, Duncan AL. What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35294337 PMCID: PMC9558347 DOI: 10.1099/mic.0.001165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cell envelopes are compositionally complex and crowded and while highly dynamic in some areas, their molecular motion is very limited, to the point of being almost static in others. Therefore, it is no real surprise that studying them at high resolution across a range of temporal and spatial scales requires a number of different techniques. Details at atomistic to molecular scales for up to tens of microseconds are now within range for molecular dynamics simulations. Here we review how such simulations have contributed to our current understanding of the cell envelopes of Gram-negative bacteria.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Cyril Schroeder
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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16
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Petrů M, Dohnálek V, Füssy Z, Doležal P. Fates of Sec, Tat, and YidC Translocases in Mitochondria and Other Eukaryotic Compartments. Mol Biol Evol 2021; 38:5241-5254. [PMID: 34436602 PMCID: PMC8662606 DOI: 10.1093/molbev/msab253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Formation of mitochondria by the conversion of a bacterial endosymbiont was a key moment in the evolution of eukaryotes. It was made possible by outsourcing the endosymbiont's genetic control to the host nucleus, while developing the import machinery for proteins synthesized on cytosolic ribosomes. The original protein export machines of the nascent organelle remained to be repurposed or were completely abandoned. This review follows the evolutionary fates of three prokaryotic inner membrane translocases Sec, Tat, and YidC. Homologs of all three translocases can still be found in current mitochondria, but with different importance for mitochondrial function. Although the mitochondrial YidC homolog, Oxa1, became an omnipresent independent insertase, the other two remained only sporadically present in mitochondria. Only a single substrate is known for the mitochondrial Tat and no function has yet been assigned for the mitochondrial Sec. Finally, this review compares these ancestral mitochondrial proteins with their paralogs operating in the plastids and the endomembrane system.
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Affiliation(s)
- Markéta Petrů
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vít Dohnálek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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17
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Taw MN, Li M, Kim D, Rocco MA, Waraho-Zhmayev D, DeLisa MP. Engineering a Supersecreting Strain of Escherichia coli by Directed Coevolution of the Multiprotein Tat Translocation Machinery. ACS Synth Biol 2021; 10:2947-2958. [PMID: 34757717 DOI: 10.1021/acssynbio.1c00183] [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] [Indexed: 11/30/2022]
Abstract
Escherichia coli remains one of the preferred hosts for biotechnological protein production due to its robust growth in culture and ease of genetic manipulation. It is often desirable to export recombinant proteins into the periplasmic space for reasons related to proper disulfide bond formation, prevention of aggregation and proteolytic degradation, and ease of purification. One such system for expressing heterologous secreted proteins is the twin-arginine translocation (Tat) pathway, which has the unique advantage of delivering correctly folded proteins into the periplasm. However, transit times for proteins through the Tat translocase, comprised of the TatABC proteins, are much longer than for passage through the SecYEG pore, the translocase associated with the more widely utilized Sec pathway. To date, a high protein flux through the Tat pathway has yet to be demonstrated. To address this shortcoming, we employed a directed coevolution strategy to isolate mutant Tat translocases for their ability to deliver higher quantities of heterologous proteins into the periplasm. Three supersecreting translocases were selected that each exported a panel of recombinant proteins at levels that were significantly greater than those observed for wild-type TatABC or SecYEG translocases. Interestingly, all three of the evolved Tat translocases exhibited quality control suppression, suggesting that increased translocation flux was gained by relaxation of substrate proofreading. Overall, our discovery of more efficient translocase variants paves the way for the use of the Tat system as a powerful complement to the Sec pathway for secreted production of both commodity and high value-added proteins.
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Affiliation(s)
- May N. Taw
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Daniel Kim
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Mark A. Rocco
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Dujduan Waraho-Zhmayev
- Biological Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Matthew P. DeLisa
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Cornell Institute of Biotechnology, Cornell University, 130 Biotechnology Building, Ithaca, New York 14853, United States
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18
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Bageshwar UK, DattaGupta A, Musser SM. Influence of the TorD signal peptide chaperone on Tat-dependent protein translocation. PLoS One 2021; 16:e0256715. [PMID: 34499687 PMCID: PMC8428690 DOI: 10.1371/journal.pone.0256715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway transports folded proteins across energetic membranes. Numerous Tat substrates contain co-factors that are inserted before transport with the assistance of redox enzyme maturation proteins (REMPs), which bind to the signal peptide of precursor proteins. How signal peptides are transferred from a REMP to a binding site on the Tat receptor complex remains unknown. Since the signal peptide mediates both interactions, possibilities include: i) a coordinated hand-off mechanism; or ii) a diffusional search after REMP dissociation. We investigated the binding interaction between substrates containing the TorA signal peptide (spTorA) and its cognate REMP, TorD, and the effect of TorD on the in vitro transport of such substrates. We found that Escherichia coli TorD is predominantly a monomer at low micromolar concentrations (dimerization KD > 50 μM), and this monomer binds reversibly to spTorA (KD ≈ 1 μM). While TorD binds to membranes (KD ≈ 100 nM), it has no apparent affinity for Tat translocons and it inhibits binding of a precursor substrate to the membrane. TorD has a minimal effect on substrate transport by the Tat system, being mildly inhibitory at high concentrations. These data are consistent with a model in which the REMP-bound signal peptide is shielded from recognition by the Tat translocon, and spontaneous dissociation of the REMP allows the substrate to engage the Tat machinery. Thus, the REMP does not assist with targeting to the Tat translocon, but rather temporarily shields the signal peptide.
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Affiliation(s)
- Umesh K. Bageshwar
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, TX, United States of America
| | - Antara DattaGupta
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, TX, United States of America
| | - Siegfried M. Musser
- Department of Molecular and Cellular Medicine, Texas A&M University, College of Medicine, The Texas A&M Health Science Center, TX, United States of America
- * E-mail:
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19
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Liu J, Yin F, Liu T, Li S, Tan C, Li L, Zhou R, Huang Q. The Tat system and its dependent cell division proteins are critical for virulence of extra-intestinal pathogenic Escherichia coli. Virulence 2020; 11:1279-1292. [PMID: 32962530 PMCID: PMC7549933 DOI: 10.1080/21505594.2020.1817709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/23/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022] Open
Abstract
The twin-arginine translocation (Tat) system is involved in a variety of important bacterial physiological processes. Conserved among bacteria and crucial for virulence, the Tat system is deemed as a promising anti-microbial drug target. However, the mechanism of how the Tat system functions in bacterial pathogenesis has not been fully understood. In this study, we showed that the Tat system was critical for the virulence of an extra-intestinal pathogenic E. coli (ExPEC) strain PCN033. A total of 20 Tat-related mutant strains were constructed, and competitive infection assays were performed to evaluate the relative virulence of these mutants. The results demonstrated that several Tat substrate mutants, including the ΔsufI, ΔamiAΔamiC double mutant as well as each single mutant, ΔyahJ, ΔcueO, and ΔnapG, were significantly outcompeted by the WT strain, among which the ΔsufI and ΔamiAΔamiC strains showed the lowest competitive index (CI) value. Results of individual mouse infection assay, in vitro cell adhesion assay, whole blood bactericidal assay, and serum bactericidal assay further confirmed the virulence attenuation phenotype of the ΔsufI and ΔamiAΔamiC strains. Moreover, the two mutants displayed chained morphology in the log phase resembling the Δtat and were defective in stress response. Our results suggest that the Tat system and its dependent cell division proteins SufI, AmiA, and AmiC play critical roles during ExPEC pathogenesis.
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Affiliation(s)
- Jinjin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Fan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Te Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
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20
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Bernal-Cabas M, Miethke M, Antelo-Varela M, Aguilar Suárez R, Neef J, Schön L, Gabarrini G, Otto A, Becher D, Wolf D, van Dijl JM. Functional association of the stress-responsive LiaH protein and the minimal TatAyCy protein translocase in Bacillus subtilis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118719. [DOI: 10.1016/j.bbamcr.2020.118719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 01/07/2023]
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21
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Abstract
Gram-negative bacteria are protected by a multicompartmental molecular architecture known as the cell envelope that contains two membranes and a thin cell wall. As the cell envelope controls influx and efflux of molecular species, in recent years both experimental and computational studies of such architectures have seen a resurgence due to the implications for antibiotic development. In this article we review recent progress in molecular simulations of bacterial membranes. We show that enormous progress has been made in terms of the lipidic and protein compositions of bacterial systems. The simulations have moved away from the traditional setup of one protein surrounded by a large patch of the same lipid type toward a more bio-logically representative viewpoint. Simulations with multiple cell envelope components are also emerging. We review some of the key method developments that have facilitated recent progress, discuss some current limitations, and offer a perspective on future directions.
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Affiliation(s)
- Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton S017 1BJ, United Kingdom
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22
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Palmer T, Stansfeld PJ. Targeting of proteins to the twin-arginine translocation pathway. Mol Microbiol 2020; 113:861-871. [PMID: 31971282 PMCID: PMC7317946 DOI: 10.1111/mmi.14461] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/12/2020] [Accepted: 01/12/2020] [Indexed: 02/06/2023]
Abstract
The twin-arginine protein transport (Tat pathway) is found in prokaryotes and plant organelles and transports folded proteins across membranes. Targeting of substrates to the Tat system is mediated by the presence of an N-terminal signal sequence containing a highly conserved twin-arginine motif. The Tat machinery comprises membrane proteins from the TatA and TatC families. Assembly of the Tat translocon is dynamic and is triggered by the interaction of a Tat substrate with the Tat receptor complex. This review will summarise recent advances in our understanding of Tat transport, focusing in particular on the roles played by Tat signal peptides in protein targeting and translocation.
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Affiliation(s)
- Tracy Palmer
- Faculty of Medical Sciences, Centre for Bacterial Cell Biology, Biosciences Institute, Molecular and Cellular Microbiology Theme, Newcastle University, Newcastle upon Tyne, England
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
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23
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Abstract
The Tat pathway for protein translocation across bacterial membranes stands out for its selective handling of fully folded cargo proteins. In this review, we provide a comprehensive summary of our current understanding of the different known Tat components, their assembly into different complexes, and their specific roles in the protein translocation process. In particular, this overview focuses on the Gram-negative bacterium Escherichia coli and the Gram-positive bacterium Bacillus subtilis. Using these organisms as examples, we discuss structural features of Tat complexes alongside mechanistic models that allow for the Tat pathway's unique protein proofreading and transport capabilities. Finally, we highlight recent advances in exploiting the Tat pathway for biotechnological benefit, the production of high-value pharmaceutical proteins.
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24
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Zinecker S, Jakob M, Klösgen RB. Functional reconstitution of TatB into the thylakoidal Tat translocase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118606. [PMID: 31733260 DOI: 10.1016/j.bbamcr.2019.118606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
We have established an experimental system for the functional analysis of thylakoidal TatB, a component of the membrane-integral TatBC receptor complex of the thylakoidal Twin-arginine protein transport (Tat) machinery. For this purpose, the intrinsic TatB activity of isolated pea thylakoids was inhibited by affinity-purified antibodies and substituted by supplementing the assays with TatB protein either obtained by in vitro translation or purified after heterologous expression in E. coli. Tat transport activity of such reconstituted thylakoids, which was analysed with the authentic Tat substrate pOEC16, reached routinely 20-25% of the activity of mock-treated thylakoid vesicles analysed in parallel. In contrast, supplementation of the assays with the purified antigen comprising all but the N-terminal transmembrane helix of thylakoidal TatB did not result in Tat transport reconstitution which confirms that transport relies strictly on the activity of the TatB protein added and is not due to restoration of the intrinsic TatB activity by antibody release. Unexpectedly, even a mutated TatB protein (TatB,E10C) assumed to be incapable of assembling into the TatBC receptor complex showed low but considerable transport reconstitution underlining the sensitivity of the approach and its suitability for further functional analyses of protein variants. Finally, quantification of TatB demand suggests that TatA and TatB are required in approximately equimolar amounts to achieve Tat-dependent thylakoid transport.
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Affiliation(s)
- Sarah Zinecker
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany
| | - Mario Jakob
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany
| | - Ralf Bernd Klösgen
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
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25
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Fröbel J, Blümmel AS, Drepper F, Warscheid B, Müller M. Surface-exposed domains of TatB involved in the structural and functional assembly of the Tat translocase in Escherichia coli. J Biol Chem 2019; 294:13902-13914. [PMID: 31341014 DOI: 10.1074/jbc.ra119.009298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/10/2019] [Indexed: 11/06/2022] Open
Abstract
Twin-arginine-dependent translocases transport folded proteins across bacterial, archaeal, and chloroplast membranes. Upon substrate binding, they assemble from hexahelical TatC and single-spanning TatA and TatB membrane proteins. Although structural and functional details of individual Tat subunits have been reported previously, the sequence and dynamics of Tat translocase assembly remain to be determined. Employing the zero-space cross-linker N,N'-dicyclohexylcarbodiimide (DCCD) in combination with LC-MS/MS, we identified as yet unknown intra- and intermolecular contact sites of TatB and TatC. In addition to their established intramembrane binding sites, both proteins were thus found to contact each other through the soluble N terminus of TatC and the interhelical linker region around the conserved glutamyl residue Glu49 of TatB from Escherichia coli Functional analyses suggested that by interacting with the TatC N terminus, TatB improves the formation of a proficient substrate recognition site of TatC. The Glu49 region of TatB was found also to contact distinct downstream sites of a neighboring TatB molecule and to thereby mediate oligomerization of TatB within the TatBC receptor complex. Finally, we show that global DCCD-mediated cross-linking of TatB and TatC in membrane vesicles or, alternatively, creating covalently linked TatC oligomers prevents TatA from occupying a position close to the TatBC-bound substrate. Collectively, our results are consistent with a circular arrangement of the TatB and TatC units within the TatBC receptor complex and with TatA entering the interior TatBC-binding cavity through lateral gates between TatBC protomers.
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Affiliation(s)
- Julia Fröbel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Anne-Sophie Blümmel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Institute of Biology II, Biochemistry-Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry-Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias Müller
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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26
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Hamsanathan S, Musser SM. The Tat protein transport system: intriguing questions and conundrums. FEMS Microbiol Lett 2019; 365:5000164. [PMID: 29897510 DOI: 10.1093/femsle/fny123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/11/2018] [Indexed: 12/21/2022] Open
Abstract
The Tat machinery catalyzes the transport of folded proteins across the cytoplasmic membrane in bacteria and the thylakoid membrane in plants. Transport occurs only in the presence of an electric field (Δψ) and/or a pH (ΔpH) gradient, and thus, Tat transport is considered to be dependent on the proton motive force (pmf). This presents a fundamental and major challenge, namely, that the Tat system catalyzes the movement of large folded protein cargos across a membrane without collapse of ion gradients. Current models argue that the active translocon assembles de novo for each cargo transported, thus providing an effective gating mechanism to minimize ion leakage. A limited structural understanding of the intermediates occurring during transport and the role of the pmf in stabilizing and/or driving this process have hindered the development of more detailed models. A fundamental question that remains unanswered is whether the pmf is actually 'consumed', providing an energetic driving force for transport, or alternatively, whether its presence is instead necessary to provide the appropriate environment for the translocon components to become active. Including addressing this issue in greater detail, we explore a series of additional questions that challenge current models, and, hopefully, motivate future work.
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Affiliation(s)
- Shruthi Hamsanathan
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, 1114 TAMU, College Station, TX 77843, USA
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, 1114 TAMU, College Station, TX 77843, USA
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27
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Abstract
The twin-arginine protein translocation (Tat) system has been characterized in bacteria, archaea and the chloroplast thylakoidal membrane. This system is distinct from other protein transport systems with respect to two key features. Firstly, it accepts cargo proteins with an N-terminal signal peptide that carries the canonical twin-arginine motif, which is essential for transport. Second, the Tat system only accepts and translocates fully folded cargo proteins across the respective membrane. Here, we review the core essential features of folded protein transport via the bacterial Tat system, using the three-component TatABC system of Escherichia coli and the two-component TatAC systems of Bacillus subtilis as the main examples. In particular, we address features of twin-arginine signal peptides, the essential Tat components and how they assemble into different complexes, mechanistic features and energetics of Tat-dependent protein translocation, cytoplasmic chaperoning of Tat cargo proteins, and the remarkable proofreading capabilities of the Tat system. In doing so, we present the current state of our understanding of Tat-dependent protein translocation across biological membranes, which may serve as a lead for future investigations.
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Affiliation(s)
- Kelly M. Frain
- The School of Biosciences, University of Kent, Canterbury, CT2 7NZ UK
| | - Colin Robinson
- The School of Biosciences, University of Kent, Canterbury, CT2 7NZ UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen (UMCG), Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, The Netherlands
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28
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Geise H, Heidrich ES, Nikolin CS, Mehner-Breitfeld D, Brüser T. A Potential Late Stage Intermediate of Twin-Arginine Dependent Protein Translocation in Escherichia coli. Front Microbiol 2019; 10:1482. [PMID: 31354642 PMCID: PMC6637791 DOI: 10.3389/fmicb.2019.01482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/14/2019] [Indexed: 02/01/2023] Open
Abstract
The twin-arginine translocation (Tat) system transports folded proteins across membranes of prokaryotes, plant plastids, and some mitochondria. According to blue-native polyacrylamide gel electrophoresis after solubilization with digitonin, distinct interactions between the components TatA, TatB, and TatC result in two major TatBC-containing complexes in Escherichia coli that can bind protein substrates. We now report the first detection of a TatABC complex that likely represents the state at which transport occurs. This complex was initially found when the photo cross-linking amino acid p-benzoyl-l-phenylalanine (Bpa) was introduced at position I50 on the periplasmic side of the first trans-membrane domain of TatC. Cross-linking of TatCI50Bpa resulted in TatC-TatC-cross-links, indicating a close proximity to neighboring TatC in the complex. However, the new complex was not caused by cross-links but rather by non-covalent side chain interactions, as it was also detectable without UV-cross-linking or with an I50Y exchange. The new complex did not contain any detectable substrate. It was slightly upshifted relative to previously reported substrate-containing TatABC complexes. In the absence of TatA, an inactive TatBCI50Bpa complex was formed of the size of wild-type substrate-containing TatABC complexes, suggesting that TatB occupies TatA-binding sites at TatCI50Bpa. When substrate binding was abolished by point mutations, this TatBCI50Bpa complex shifted analogously to active TatABCI50Bpa complexes, indicating that a defect substrate-binding site further enhances TatB association to TatA-binding sites. Only TatA could shift the complex with an intact substrate-binding site, which explains the TatA requirement for substrate transport by TatABC systems.
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Affiliation(s)
- Hendrik Geise
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | | | | | - Thomas Brüser
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
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Ghosh D, Boral D, Vankudoth KR, Ramasamy S. Analysis of haloarchaeal twin-arginine translocase pathway reveals the diversity of the machineries. Heliyon 2019; 5:e01587. [PMID: 31193317 PMCID: PMC6525301 DOI: 10.1016/j.heliyon.2019.e01587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/23/2019] [Accepted: 04/24/2019] [Indexed: 01/10/2023] Open
Abstract
The twin-arginine translocase (Tat) pathway transports folded proteins across the plasma membrane and plays a critical role in protein transport in haloarchaea. Computational analysis and previous experimental evidence suggested that the Tat pathway transports almost the entire secretome in haloarchaea. The TatC, receptor component of this pathway shows greater variation in membrane topology in haloarchaea than in other organisms. The presence of a unique fourteen-transmembrane TatC homolog (TatCt) in haloarchaea, over and above the expected TatC topological variants, indicates a strong correlation between the additional homologs and the large number of substrates transported via the haloarchaeal Tat pathway. Various combinations of TatC homologs with different topologies—TatCo, TatCt, TatCn, and TatCx have been observed in haloarchaea. In this report, on the basis of these combinations we have segregated all haloarchaeal Tat substrates into two groups. The first group consists of substrates that are transported by TatCt alone, whereas the second group consists of substrates that are transported by the other TatC homologs (TatCo, TatCn, and TatCx). The various haloarchaea TatA components also shows the possible segregation towards the substrates. We have also identified the possible homologs for Tat substrate chaperones, which act as a quality-control mechanism for proper protein folding. Further sequence analysis implies that the two TatC domains of TatCt complement each other's functionally. Substrate analysis also revealed subtle differences between the substrates being transported by various homologs: further experimental analysis is therefore required for better understanding of the complexities of the haloarchaeal Tat pathway.
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Affiliation(s)
- Deepanjan Ghosh
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Debjyoti Boral
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Koteswara Rao Vankudoth
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- Corresponding author.
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Abstract
The inner membrane of Gram-negative bacteria is a ~6 nm thick phospholipid bilayer. It forms a semi-permeable barrier between the cytoplasm and periplasm allowing only regulated export and import of ions, sugar polymers, DNA and proteins. Inner membrane proteins, embedded via hydrophobic transmembrane α-helices, play an essential role in this regulated trafficking: they mediate insertion into the membrane (insertases) or complete crossing of the membrane (translocases) or both. The Gram-negative inner membrane is equipped with a variety of different insertases and translocases. Many of them are specialized, taking care of the export of only a few protein substrates, while others have more general roles. Here, we focus on the three general export/insertion pathways, the secretory (Sec) pathway, YidC and the twin-arginine translocation (TAT) pathway, focusing closely on the Escherichia coli (E. coli) paradigm. We only briefly mention dedicated export pathways found in different Gram-negative bacteria. The Sec system deals with the majority of exported proteins and functions both as a translocase for secretory proteins and an insertase for membrane proteins. The insertase YidC assists the Sec system or operates independently on membrane protein clients. Sec and YidC, in common with most export pathways, require their protein clients to be in soluble non-folded states to fit through the translocation channels and grooves. The TAT pathway is an exception, as it translocates folded proteins, some loaded with prosthetic groups.
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Affiliation(s)
- Jozefien De Geyter
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Dries Smets
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.
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New CP, Ma Q, Dabney-Smith C. Routing of thylakoid lumen proteins by the chloroplast twin arginine transport pathway. PHOTOSYNTHESIS RESEARCH 2018; 138:289-301. [PMID: 30101370 DOI: 10.1007/s11120-018-0567-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Thylakoids are complex sub-organellar membrane systems whose role in photosynthesis makes them critical to life. Thylakoids require the coordinated expression of both nuclear- and plastid-encoded proteins to allow rapid response to changing environmental conditions. Transport of cytoplasmically synthesized proteins to thylakoids or the thylakoid lumen is complex; the process involves transport across up to three membrane systems with routing through three aqueous compartments. Protein transport in thylakoids is accomplished by conserved ancestral prokaryotic plasma membrane translocases containing novel adaptations for the sub-organellar location. This review focuses on the evolutionarily conserved chloroplast twin arginine transport (cpTat) pathway. An overview is provided of known aspects of the cpTat components, energy requirements, and mechanisms with a focus on recent discoveries. Some of the most exciting new studies have been in determining the structural architecture of the membrane complex involved in forming the point of passage for the precursor and binding features of the translocase components. The cpTat system is of particular interest because it transports folded protein domains using only the proton motive force for energy. The implications for mechanism of translocation by recent studies focusing on interactions between membrane Tat components and with the translocating precursor will be discussed.
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Affiliation(s)
- Christopher Paul New
- Cellular, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH, 45056, USA
| | - Qianqian Ma
- Cellular, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH, 45056, USA
| | - Carole Dabney-Smith
- Cellular, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH, 45056, USA.
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
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Petrů M, Wideman J, Moore K, Alcock F, Palmer T, Doležal P. Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria. BMC Biol 2018; 16:141. [PMID: 30466434 PMCID: PMC6251230 DOI: 10.1186/s12915-018-0607-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases but have lost others. While BamA and YidC were integrated into general mitochondrial protein transport pathways (as Sam50 and Oxa1), the inner membrane TAT translocase, which uniquely transports folded proteins across the membrane, was retained sporadically across the eukaryote tree. RESULTS We have identified mitochondrial TAT machinery in diverse eukaryotic lineages and define three different types of eukaryote-encoded TatABC-derived machineries (TatAC, TatBC and TatC-only). Here, we investigate TatAC and TatC-only machineries, which have not been studied previously. We show that mitochondria-encoded TatAC of the jakobid Andalucia godoyi represent the minimal functional pathway capable of substituting for the Escherichia coli TatABC complex and can transport at least one substrate. However, selected TatC-only machineries, from multiple eukaryotic lineages, were not capable of supporting the translocation of this substrate across the bacterial membrane. Despite the multiple losses of the TatC gene from the mitochondrial genome, the gene was never transferred to the cell nucleus. Although the major constraint preventing nuclear transfer of mitochondrial TatC is likely its high hydrophobicity, we show that in chloroplasts, such transfer of TatC was made possible due to modifications of the first transmembrane domain. CONCLUSIONS At its origin, mitochondria inherited three inner membrane translocases Sec, TAT and Oxa1 (YidC) from its bacterial ancestor. Our work shows for the first time that mitochondrial TAT has likely retained its unique function of transporting folded proteins at least in those few eukaryotes with TatA and TatC subunits encoded in the mitochondrial genome. However, mitochondria, in contrast to chloroplasts, abandoned the machinery multiple times in evolution. The overall lower hydrophobicity of the Oxa1 protein was likely the main reason why this translocase was nearly universally retained in mitochondrial biogenesis pathways.
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Affiliation(s)
- Markéta Petrů
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jeremy Wideman
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany
- Department of Biochemistry and Molecular Biology, Dalhousie University, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Kristoffer Moore
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Průmyslová 595, 252 50, Vestec, Czech Republic.
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Mychack A, Amrutha RN, Chung C, Cardenas Arevalo K, Reddy M, Janakiraman A. A synergistic role for two predicted inner membrane proteins of Escherichia coli in cell envelope integrity. Mol Microbiol 2018; 111:317-337. [PMID: 30368949 DOI: 10.1111/mmi.14157] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2018] [Indexed: 01/21/2023]
Abstract
The bacterial cytoplasmic membrane is a principal site of protein translocation, lipid and peptidoglycan biogenesis, signal transduction, transporters and energy generating components of the respiratory chain. Although 25-30% of bacterial proteomes consist of membrane proteins, a comprehensive understanding of their influence on fundamental cellular processes is incomplete. Here, we show that YciB and DcrB, two small cytoplasmic membrane proteins of previously unknown functions, play an essential synergistic role in maintaining cell envelope integrity of Escherichia coli. Lack of both YciB and DcrB results in pleiotropic cell defects including increased levels of lipopolysaccharide, membrane vesiculation, dynamic shrinking and extension of the cytoplasmic membrane accompanied by lysis and cell death. The stalling of an abundant outer membrane lipoprotein, Lpp, at the periplasmic face of the inner membrane leads to lethal inner membrane-peptidoglycan linkages. Additionally, the periplasmic chaperone Skp contributes to yciB dcrB mutant cell death by possibly mistargeting stalled porins into the inner membrane. Consistent with the idea of a compromised envelope in the yciB dcrB mutant, multiple envelope stress response systems are induced, with Cpx signal transduction being required for growth. Taken together, our results suggest a fundamental role for YciB and DcrB in cell envelope biogenesis.
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Affiliation(s)
- Aaron Mychack
- Department of Biology, The City College of CUNY, New York, NY, 10031, USA.,Program in Biology, The Graduate Center, CUNY, Fifth Avenue, New York, NY, 10016, USA
| | - R N Amrutha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Charlie Chung
- Department of Biology, The City College of CUNY, New York, NY, 10031, USA
| | | | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Anuradha Janakiraman
- Department of Biology, The City College of CUNY, New York, NY, 10031, USA.,Program in Biology, The Graduate Center, CUNY, Fifth Avenue, New York, NY, 10016, USA
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Ma Q, Fite K, New CP, Dabney‐Smith C. Thylakoid-integrated recombinant Hcf106 participates in the chloroplast twin arginine transport system. PLANT DIRECT 2018; 2:e00090. [PMID: 31245690 PMCID: PMC6508782 DOI: 10.1002/pld3.90] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 06/09/2023]
Abstract
The chloroplast twin arginine transport (cpTat) system distinguishes itself as a protein transport pathway by translocating fully folded proteins, using the proton-motive force (PMF) as the sole source of energy. The cpTat pathway is evolutionarily conserved with the Tat pathway found in the plasma membrane of many prokaryotes. The cpTat (Escherichia coli) system uses three proteins, Tha4 (TatA), Hcf106 (TatB), and cpTatC (TatC), to form a transient translocase allowing the passage of precursor proteins. Briefly, cpTatC and Hcf106, with Tha4, form the initial receptor complex responsible for precursor protein recognition and binding in an energy-independent manner, while a separate pool of Tha4 assembles with the precursor-bound receptor complex in the presence the PMF. Analysis by blue-native polyacrylamide gel electrophoresis (BN-PAGE) shows that the receptor complex, in the absence of precursor, migrates near 700 kDa and contains cpTatC and Hcf106 with little Tha4 remaining after detergent solubilization. To investigate the role that Hcf106 may play in receptor complex oligomerization and/or stability, systematic cysteine substitutions were made in positions from the N-terminal transmembrane domain to the end of the predicted amphipathic helix of the protein. BN-PAGE analysis allowed us to identify the locations of amino acids in Hcf106 that were critical for interacting with cpTatC. Oxidative cross-linking allowed us to map interactions of the transmembrane domain and amphipathic helix region of Hcf106. In addition, we showed that in vitro expressed, integrated Hcf106 can interact with the precursor signal peptide domain and imported cpTatC, strongly suggesting that a subpopulation of the integrated Hcf106 is participating in competent cpTat complexes.
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Affiliation(s)
- Qianqian Ma
- Graduate Program in Cell, Molecular, and Structural BiologyMiami UniversityOxfordOhio
- Present address:
Johns Hopkins University School of MedicineBaltimoreMaryland
| | - Kristen Fite
- Department of Chemistry and BiochemistryMiami UniversityOxfordOhio
- Present address:
Boonshoft School of MedicineWright State UniversityDaytonOhio
| | - Christopher Paul New
- Graduate Program in Cell, Molecular, and Structural BiologyMiami UniversityOxfordOhio
| | - Carole Dabney‐Smith
- Graduate Program in Cell, Molecular, and Structural BiologyMiami UniversityOxfordOhio
- Department of Chemistry and BiochemistryMiami UniversityOxfordOhio
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35
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Habersetzer J, Moore K, Cherry J, Buchanan G, Stansfeld PJ, Palmer T. Substrate-triggered position switching of TatA and TatB during Tat transport in Escherichia coli. Open Biol 2018; 7:rsob.170091. [PMID: 28814647 PMCID: PMC5577447 DOI: 10.1098/rsob.170091] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 07/19/2017] [Indexed: 01/29/2023] Open
Abstract
The twin-arginine protein transport (Tat) machinery mediates the translocation of folded proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. The Escherichia coli Tat system comprises TatC and two additional sequence-related proteins, TatA and TatB. The active translocase is assembled on demand, with substrate-binding at a TatABC receptor complex triggering recruitment and assembly of multiple additional copies of TatA; however, the molecular interactions mediating translocase assembly are poorly understood. A ‘polar cluster’ site on TatC transmembrane (TM) helix 5 was previously identified as binding to TatB. Here, we use disulfide cross-linking and molecular modelling to identify a new binding site on TatC TM helix 6, adjacent to the polar cluster site. We demonstrate that TatA and TatB each have the capacity to bind at both TatC sites, however in vivo this is regulated according to the activation state of the complex. In the resting-state system, TatB binds the polar cluster site, with TatA occupying the TM helix 6 site. However when the system is activated by overproduction of a substrate, TatA and TatB switch binding sites. We propose that this substrate-triggered positional exchange is a key step in the assembly of an active Tat translocase.
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Affiliation(s)
- Johann Habersetzer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kristoffer Moore
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jon Cherry
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Grant Buchanan
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Checchetto V, Szabo I. Novel Channels of the Outer Membrane of Mitochondria: Recent Discoveries Change Our View. Bioessays 2018; 40:e1700232. [PMID: 29682771 DOI: 10.1002/bies.201700232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/09/2018] [Indexed: 01/12/2023]
Abstract
Ion channels mediate ion flux across biological membranes and regulate important organellar and cellular tasks. A recent study revealed the presence of four new proteins, the MIM complex (composed by Mim1 and Mim2), Ayr1, OMC7, and OMC8, that are able to form ion-conducting channels in the outer mitochondria membrane (OMM). These findings strongly indicate that the OMM is endowed with many solute-specific channels, in addition to porins and known channels mediating protein import into mitochondria. These solute-specific channels provide essential pathways for the controlled transport of ions and metabolites and may thus add a further layer of specificity to the regulation of mitochondrial function at the organelle-cytosol and/or inter-organellar interface. Future studies will be required to fully understand the way(s) of regulation of these new channels and to integrate them into signaling pathways within the cells.
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Affiliation(s)
| | - Ildiko Szabo
- Department of Biology, University of Padova, Padua 35121, Italy
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37
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Nicoludis JM, Gaudet R. Applications of sequence coevolution in membrane protein biochemistry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:895-908. [PMID: 28993150 PMCID: PMC5807202 DOI: 10.1016/j.bbamem.2017.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
Abstract
Recently, protein sequence coevolution analysis has matured into a predictive powerhouse for protein structure and function. Direct methods, which use global statistical models of sequence coevolution, have enabled the prediction of membrane and disordered protein structures, protein complex architectures, and the functional effects of mutations in proteins. The field of membrane protein biochemistry and structural biology has embraced these computational techniques, which provide functional and structural information in an otherwise experimentally-challenging field. Here we review recent applications of protein sequence coevolution analysis to membrane protein structure and function and highlight the promising directions and future obstacles in these fields. We provide insights and guidelines for membrane protein biochemists who wish to apply sequence coevolution analysis to a given experimental system.
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Affiliation(s)
- John M Nicoludis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, United States.
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38
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Ulfig A, Freudl R. The early mature part of bacterial twin-arginine translocation (Tat) precursor proteins contributes to TatBC receptor binding. J Biol Chem 2018; 293:7281-7299. [PMID: 29593092 DOI: 10.1074/jbc.ra118.002576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/22/2018] [Indexed: 11/06/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway transports folded proteins across bacterial membranes. Tat precursor proteins possess a conserved twin-arginine (RR) motif in their signal peptides that is involved in the binding of the proteins to the membrane-associated TatBC receptor complex. In addition, the hydrophobic region in the Tat signal peptides also contributes to TatBC binding, but whether regions beyond the signal-peptide cleavage site are involved in this process is unknown. Here, we analyzed the contribution of the early mature protein part of the Escherichia coli trimethylamine N-oxide reductase (TorA) to productive TatBC receptor binding. We identified substitutions in the 30 amino acids immediately following the TorA signal peptide (30aa-region) that restored export of a transport-defective TorA[KQ]-30aa-MalE precursor, in which the RR residues had been replaced by a lysine-glutamine pair. Some of these substitutions increased the hydrophobicity of the N-terminal part of the 30aa-region and thereby likely enhanced hydrophobic substrate-receptor interactions within the hydrophobic TatBC substrate-binding cavity. Another class of substitutions increased the positive net charge of the region's C-terminal part, presumably leading to strengthened electrostatic interactions between the mature substrate part and the cytoplasmic TatBC regions. Furthermore, we identified substitutions in the C-terminal domains of TatB following the transmembrane segment that restored transport of various transport-defective TorA-MalE derivatives. Some of these substitutions most likely affected the orientation or conformation of the flexible, carboxy-proximal helices of TatB. Therefore, we propose that a tight accommodation of the folded mature region by TatB contributes to productive binding of Tat substrates to TatBC.
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Affiliation(s)
- Agnes Ulfig
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, D-52425 Jülich, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, D-52425 Jülich, Germany.
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39
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Wojnowska M, Gault J, Yong SC, Robinson CV, Berks BC. Precursor-Receptor Interactions in the Twin Arginine Protein Transport Pathway Probed with a New Receptor Complex Preparation. Biochemistry 2018; 57:1663-1671. [PMID: 29460615 PMCID: PMC5852461 DOI: 10.1021/acs.biochem.8b00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The twin arginine translocation (Tat) system moves folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plant chloroplasts. Signal peptide-bearing substrates of the Tat pathway (precursor proteins) are recognized at the membrane by the TatBC receptor complex. The only established preparation of the TatBC complex uses the detergent digitonin, rendering it unsuitable for biophysical analysis. Here we show that the detergent glyco-diosgenin (GDN) can be used in place of digitonin to isolate homogeneous TatBC complexes that bind precursor proteins with physiological specificity. We use this new preparation to quantitatively characterize TatBC-precursor interactions in a fully defined system. Additionally, we show that the GDN-solubilized TatBC complex co-purifies with substantial quantities of phospholipids.
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Affiliation(s)
- Marta Wojnowska
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Shee Chien Yong
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Ben C Berks
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
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40
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Cherak SJ, Turner RJ. Assembly pathway of a bacterial complex iron sulfur molybdoenzyme. Biomol Concepts 2018; 8:155-167. [PMID: 28688222 DOI: 10.1515/bmc-2017-0011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/10/2017] [Indexed: 11/15/2022] Open
Abstract
Protein folding and assembly into macromolecule complexes within the living cell are complex processes requiring intimate coordination. The biogenesis of complex iron sulfur molybdoenzymes (CISM) requires use of a system specific chaperone - a redox enzyme maturation protein (REMP) - to help mediate final folding and assembly. The CISM dimethyl sulfoxide (DMSO) reductase is a bacterial oxidoreductase that utilizes DMSO as a final electron acceptor for anaerobic respiration. The REMP DmsD strongly interacts with DMSO reductase to facilitate folding, cofactor-insertion, subunit assembly and targeting of the multi-subunit enzyme prior to membrane translocation and final assembly and maturation into a bioenergetic catalytic unit. In this article, we discuss the biogenesis of DMSO reductase as an example of the participant network for bacterial CISM maturation pathways.
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41
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Unanticipated functional diversity among the TatA-type components of the Tat protein translocase. Sci Rep 2018; 8:1326. [PMID: 29358647 PMCID: PMC5777986 DOI: 10.1038/s41598-018-19640-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/29/2017] [Indexed: 11/08/2022] Open
Abstract
Twin-arginine translocation (Tat) systems transport folded proteins that harbor a conserved arginine pair in their signal peptides. They assemble from hexahelical TatC-type and single-spanning TatA-type proteins. Many Tat systems comprise two functionally diverse, TatA-type proteins, denominated TatA and TatB. Some bacteria in addition express TatE, which thus far has been characterized as a functional surrogate of TatA. For the Tat system of Escherichia coli we demonstrate here that different from TatA but rather like TatB, TatE contacts a Tat signal peptide independently of the proton-motive force and restricts the premature processing of a Tat signal peptide. Furthermore, TatE embarks at the transmembrane helix five of TatC where it becomes so closely spaced to TatB that both proteins can be covalently linked by a zero-space cross-linker. Our results suggest that in addition to TatB and TatC, TatE is a further component of the Tat substrate receptor complex. Consistent with TatE being an autonomous TatAB-type protein, a bioinformatics analysis revealed a relatively broad distribution of the tatE gene in bacterial phyla and highlighted unique protein sequence features of TatE orthologs.
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Hamsanathan S, Anthonymuthu TS, Bageshwar UK, Musser SM. A Hinged Signal Peptide Hairpin Enables Tat-Dependent Protein Translocation. Biophys J 2018; 113:2650-2668. [PMID: 29262359 DOI: 10.1016/j.bpj.2017.09.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/23/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
The Tat machinery catalyzes the transport of folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane in plants. Using fluorescence quenching and cross-linking approaches, we demonstrate that the Escherichia coli TatBC complex catalyzes insertion of a pre-SufI signal peptide hairpin that penetrates about halfway across the membrane bilayer. Analysis of 512 bacterial Tat signal peptides using secondary structure prediction and docking algorithms suggest that this hairpin interaction mode is generally conserved. An internal cross-link in the signal peptide that blocks transport but does not affect binding indicates that a signal peptide conformational change is required during translocation. These results suggest, to our knowledge, a novel hairpin-hinge model in which the signal peptide hairpin unhinges during movement of the mature domain across the membrane. Thus, in addition to enabling the necessary recognition, the interaction of Tat signal peptides with the receptor complex plays a critical role in the transport process itself.
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Affiliation(s)
- Shruthi Hamsanathan
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, College Station, Texas
| | - Tamil S Anthonymuthu
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Umesh K Bageshwar
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, College Station, Texas
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, Texas A&M University, College Station, Texas.
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Blümmel AS, Drepper F, Knapp B, Eimer E, Warscheid B, Müller M, Fröbel J. Structural features of the TatC membrane protein that determine docking and insertion of a twin-arginine signal peptide. J Biol Chem 2017; 292:21320-21329. [PMID: 29089385 DOI: 10.1074/jbc.m117.812560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/26/2017] [Indexed: 11/06/2022] Open
Abstract
Twin-arginine translocation (Tat) systems transport folded proteins across cellular membranes with the concerted action of mostly three membrane proteins: TatA, TatB, and TatC. Hetero-oligomers of TatB and TatC form circular substrate-receptor complexes with a central binding cavity for twin-arginine-containing signal peptides. After binding of the substrate, energy from an electro-chemical proton gradient is transduced into the recruitment of TatA oligomers and into the actual translocation event. We previously reported that Tat-dependent protein translocation into membrane vesicles of Escherichia coli is blocked by the compound N,N'-dicyclohexylcarbodiimide (DCCD, DCC). We have now identified a highly conserved glutamate residue in the transmembrane region of E. coli TatC, which when modified by DCCD interferes with the deep insertion of a Tat signal peptide into the TatBC receptor complex. Our findings are consistent with a hydrophobic binding cavity formed by TatB and TatC inside the lipid bilayer. Moreover, we found that DCCD mediates discrete intramolecular cross-links of E. coli TatC involving both its N- and C-tails. These results confirm the close proximity of two distant sequence sections of TatC proposed to concertedly function as the primary docking site for twin-arginine signal peptides.
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Affiliation(s)
- Anne-Sophie Blümmel
- From the Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine.,the Spemann Graduate School of Biology and Medicine (SGBM).,the Faculty of Biology
| | - Friedel Drepper
- the Institute of Biology II, Biochemistry: Functional Proteomics, Faculty of Biology, and.,the BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Knapp
- the Institute of Biology II, Biochemistry: Functional Proteomics, Faculty of Biology, and
| | - Ekaterina Eimer
- From the Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine.,the Faculty of Biology
| | - Bettina Warscheid
- the Institute of Biology II, Biochemistry: Functional Proteomics, Faculty of Biology, and.,the BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias Müller
- From the Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine,
| | - Julia Fröbel
- From the Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine
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Alcock F, Damen MP, Levring J, Berks BC. In vivo experiments do not support the charge zipper model for Tat translocase assembly. eLife 2017; 6:30127. [PMID: 28857741 PMCID: PMC5601993 DOI: 10.7554/elife.30127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/30/2017] [Indexed: 12/29/2022] Open
Abstract
The twin-arginine translocase (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the plant thylakoid membrane. The Tat translocation site is formed by substrate-triggered oligomerization of the protein TatA. Walther and co-workers have proposed a structural model for the TatA oligomer in which TatA monomers self-assemble using electrostatic 'charge zippers' (Cell (2013) 132: 15945). This model was supported by in vitro analysis of the oligomeric state of TatA variants containing charge-inverting substitutions. Here we have used live cell assays of TatA assembly and function in Escherichia coli to re-assess the roles of the charged residues of TatA. Our results do not support the charge zipper model. Instead, we observe that substitutions of charged residues located in the TatA amphipathic helix lock TatA in an assembled state, suggesting that these charged residues play a critical role in the protein translocation step that follows TatA assembly.
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Affiliation(s)
- Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Merel Pm Damen
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jesper Levring
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Computational studies of membrane proteins: from sequence to structure to simulation. Curr Opin Struct Biol 2017; 45:133-141. [DOI: 10.1016/j.sbi.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/19/2022]
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Abstract
The general secretory pathway (Sec) and twin-arginine translocase (Tat) operate in parallel to export proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. Substrates are targeted to their respective machineries by N-terminal signal peptides that share a tripartite organization; however, Tat signal peptides harbor a conserved and almost invariant arginine pair that is critical for efficient targeting to the Tat machinery. Tat signal peptides interact with a membrane-bound receptor complex comprised of TatB and TatC components, with TatC containing the twin-arginine recognition site. Here, we isolated suppressors in the signal peptide of the Tat substrate, SufI, that restored Tat transport in the presence of inactivating substitutions in the TatC twin-arginine binding site. These suppressors increased signal peptide hydrophobicity, and copurification experiments indicated that they restored binding to the variant TatBC complex. The hydrophobic suppressors could also act in cis to suppress substitutions at the signal peptide twin-arginine motif that normally prevent targeting to the Tat pathway. Highly hydrophobic variants of the SufI signal peptide containing four leucine substitutions retained the ability to interact with the Tat system. The hydrophobic signal peptides of two Sec substrates, DsbA and OmpA, containing twin lysine residues, were shown to mediate export by the Tat pathway and to copurify with TatBC. These findings indicate that there is unprecedented overlap between Sec and Tat signal peptides and that neither the signal peptide twin-arginine motif nor the TatC twin-arginine recognition site is an essential mechanistic feature for operation of the Tat pathway.IMPORTANCE Protein export is an essential process in all prokaryotes. The Sec and Tat export pathways operate in parallel, with the Sec machinery transporting unstructured precursors and the Tat pathway transporting folded proteins. Proteins are targeted to the Tat pathway by N-terminal signal peptides that contain an almost invariant twin-arginine motif. Here, we make the surprising discovery that the twin arginines are not essential for recognition of substrates by the Tat machinery and that this requirement can be bypassed by increasing the signal peptide hydrophobicity. We further show that signal peptides of bona fide Sec substrates can also mediate transport by the Tat pathway. Our findings suggest that key features of the Tat targeting mechanism have evolved to prevent mistargeting of substrates to the Sec pathway rather than being a critical requirement for function of the Tat pathway.
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Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. J Phys Chem Lett 2017; 8:2513-2518. [PMID: 28467715 DOI: 10.1021/acs.jpclett.7b00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology: multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.
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Affiliation(s)
- Alister Boags
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street, 138671 Singapore
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, 117543 Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
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Ulfig A, Fröbel J, Lausberg F, Blümmel AS, Heide AK, Müller M, Freudl R. The h-region of twin-arginine signal peptides supports productive binding of bacterial Tat precursor proteins to the TatBC receptor complex. J Biol Chem 2017; 292:10865-10882. [PMID: 28515319 DOI: 10.1074/jbc.m117.788950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/12/2017] [Indexed: 11/06/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway transports folded proteins across bacterial membranes. Tat precursor proteins possess a conserved twin-arginine (RR) motif in their signal peptides that is involved in their binding to the Tat translocase, but some facets of this interaction remain unclear. Here, we investigated the role of the hydrophobic (h-) region of the Escherichia coli trimethylamine N-oxide reductase (TorA) signal peptide in TatBC receptor binding in vivo and in vitro We show that besides the RR motif, a minimal, functional h-region in the signal peptide is required for Tat-dependent export in Escherichia coli Furthermore, we identified mutations in the h-region that synergistically suppressed the export defect of a TorA[KQ]-30aa-MalE Tat reporter protein in which the RR motif was replaced with a lysine-glutamine pair. Strikingly, all suppressor mutations increased the hydrophobicity of the h-region. By systematically replacing a neutral residue in the h-region with various amino acids, we detected a positive correlation between the hydrophobicity of the h-region and the translocation efficiency of the resulting reporter variants. In vitro cross-linking of residues located in the periplasmically-oriented part of the TatBC receptor to TorA[KQ]-30aa-MalE reporter variants harboring a more hydrophobic h-region in their signal peptides confirmed that unlike in TorA[KQ]-30aa-MalE with an unaltered h-region, the mutated reporters moved deep into the TatBC-binding cavity. Our results clearly indicate that, besides the Tat motif, the h-region of the Tat signal peptides is another important binding determinant that significantly contributes to the productive interaction of Tat precursor proteins with the TatBC receptor complex.
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Affiliation(s)
- Agnes Ulfig
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, D-52425 Jülich, Germany and
| | - Julia Fröbel
- the Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
| | - Frank Lausberg
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, D-52425 Jülich, Germany and
| | - Anne-Sophie Blümmel
- the Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
| | - Anna Katharina Heide
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, D-52425 Jülich, Germany and
| | - Matthias Müller
- the Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Strasse 17, D-79104 Freiburg, Germany
| | - Roland Freudl
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, D-52425 Jülich, Germany and
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Huang Q, Alcock F, Kneuper H, Deme JC, Rollauer SE, Lea SM, Berks BC, Palmer T. A signal sequence suppressor mutant that stabilizes an assembled state of the twin arginine translocase. Proc Natl Acad Sci U S A 2017; 114:E1958-E1967. [PMID: 28223511 PMCID: PMC5347605 DOI: 10.1073/pnas.1615056114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The twin-arginine protein translocation (Tat) system mediates transport of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of chloroplasts. The Tat system of Escherichia coli is made up of TatA, TatB, and TatC components. TatBC comprise the substrate receptor complex, and active Tat translocases are formed by the substrate-induced association of TatA oligomers with this receptor. Proteins are targeted to TatBC by signal peptides containing an essential pair of arginine residues. We isolated substitutions, locating to the transmembrane helix of TatB that restored transport activity to Tat signal peptides with inactivating twin arginine substitutions. A subset of these variants also suppressed inactivating substitutions in the signal peptide binding site on TatC. The suppressors did not function by restoring detectable signal peptide binding to the TatBC complex. Instead, site-specific cross-linking experiments indicate that the suppressor substitutions induce conformational change in the complex and movement of the TatB subunit. The TatB F13Y substitution was associated with the strongest suppressing activity, even allowing transport of a Tat substrate lacking a signal peptide. In vivo analysis using a TatA-YFP fusion showed that the TatB F13Y substitution resulted in signal peptide-independent assembly of the Tat translocase. We conclude that Tat signal peptides play roles in substrate targeting and in triggering assembly of the active translocase.
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Affiliation(s)
- Qi Huang
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Holger Kneuper
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Justin C Deme
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Sarah E Rollauer
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom;
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