1
|
Sobakinskaya E, Müh F. Physical mechanisms of the Sec machinery operation. Phys Chem Chem Phys 2024. [PMID: 39435495 PMCID: PMC11494458 DOI: 10.1039/d4cp03201b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 10/08/2024] [Indexed: 10/23/2024]
Abstract
The Sec complex, composed of a motor protein SecA and a channel SecYEG, is an ATP-driven molecular machine for the transport of proteins across the plasma membrane in bacteria. Today, there is a consensus about a general "rough" model of the complex activation and operation, which, however, lacks understanding of the physical mechanisms behind it. Molecular dynamics simulations were employed to address a way of allosteric activation, conformational transition of SecYEG from the closed to the open state, and driving forces of protein transport. We found that binding of SecA (in the ATP-bound state) and the protein signal sequence leads to a transmembrane helix rearrangment that weakens contacts inside the hydrophobic core of SecYEG and provides a driving force for plug opening. The conformational transitions are enabled by a delicate interplay between hydrophobic forces on one side and PEES (proton motive force, external - due to binding with the translocation partners - entropic, and solvent-induced) on the other side. In the open state, SecYEG still provides a barrier for bulky residues that contributes to the driving forces of transport. Other important contributions come from SecA and the membrane potential acting in different stages of protein transport to guarantee a nearly constant driving force. Given that the different forces act on different types of residues, the suggested mechanisms taken together provide a directional motion for any substrate, thereby maximizing the efficiency of the Sec machinery.
Collapse
Affiliation(s)
- Ekaterina Sobakinskaya
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Strasse 69, A-4040 Linz, Austria.
| | - Frank Müh
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Strasse 69, A-4040 Linz, Austria.
| |
Collapse
|
2
|
Sarfatis A, Wang Y, Twumasi-Ankrah N, Moffitt JR. Highly Multiplexed Spatial Transcriptomics in Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601034. [PMID: 38979245 PMCID: PMC11230453 DOI: 10.1101/2024.06.27.601034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensal B. thetaiotaomicron to micron-scale niches in the mammalian colon. We envision bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments.
Collapse
Affiliation(s)
- Ari Sarfatis
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Yuanyou Wang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Nana Twumasi-Ankrah
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Jeffrey R. Moffitt
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| |
Collapse
|
3
|
Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
Collapse
Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| |
Collapse
|
4
|
Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021; 8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal coordination of protein transport is an essential cornerstone of the bacterial adaptation to different environmental conditions. By adjusting the protein composition of extra-cytosolic compartments, like the inner and outer membranes or the periplasmic space, protein transport mechanisms help shaping protein homeostasis in response to various metabolic cues. The universally conserved SecYEG translocon acts at the center of bacterial protein transport and mediates the translocation of newly synthesized proteins into and across the cytoplasmic membrane. The ability of the SecYEG translocon to transport an enormous variety of different substrates is in part determined by its ability to interact with multiple targeting factors, chaperones and accessory proteins. These interactions are crucial for the assisted passage of newly synthesized proteins from the cytosol into the different bacterial compartments. In this review, we summarize the current knowledge about SecYEG-mediated protein transport, primarily in the model organism Escherichia coli, and describe the dynamic interaction of the SecYEG translocon with its multiple partner proteins. We furthermore highlight how protein transport is regulated and explore recent developments in using the SecYEG translocon as an antimicrobial target.
Collapse
Affiliation(s)
- Julia Oswald
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Robert Njenga
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| |
Collapse
|
5
|
Dynamics of Membrane Proteins Monitored by Single-Molecule Fluorescence Across Multiple Timescales. Methods Mol Biol 2021. [PMID: 33582997 DOI: 10.1007/978-1-0716-0724-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Single-molecule techniques provide insights into the heterogeneity and dynamics of ensembles and enable the extraction of mechanistic information that is complementary to high-resolution structural techniques. Here, we describe the application of single-molecule Förster resonance energy transfer to study the dynamics of integral membrane protein complexes on timescales spanning sub-milliseconds to minutes (10-9-102 s).
Collapse
|
6
|
Genetic Evidence for SecY Translocon-Mediated Import of Two Contact-Dependent Growth Inhibition (CDI) Toxins. mBio 2021; 12:mBio.03367-20. [PMID: 33531386 PMCID: PMC7858069 DOI: 10.1128/mbio.03367-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Many bacterial species interact via direct cell-to-cell contact using CDI systems, which provide a mechanism to inject toxins that inhibit bacterial growth into one another. Here, we find that two CDI toxins, one that depolarizes membranes and another that degrades RNA, exploit the universally conserved SecY translocon machinery used to export proteins for target cell entry. The C-terminal (CT) toxin domains of contact-dependent growth inhibition (CDI) CdiA proteins target Gram-negative bacteria and must breach both the outer and inner membranes of target cells to exert growth inhibitory activity. Here, we examine two CdiA-CT toxins that exploit the bacterial general protein secretion machinery after delivery into the periplasm. A Ser281Phe amino acid substitution in transmembrane segment 7 of SecY, the universally conserved channel-forming subunit of the Sec translocon, decreases the cytotoxicity of the membrane depolarizing orphan10 toxin from enterohemorrhagic Escherichia coli EC869. Target cells expressing secYS281F and lacking either PpiD or YfgM, two SecY auxiliary factors, are fully protected from CDI-mediated inhibition either by CdiA-CTo10EC869 or by CdiA-CTGN05224, the latter being an EndoU RNase CdiA toxin from Klebsiella aerogenes GN05224 that has a related cytoplasm entry domain. RNase activity of CdiA-CTGN05224 was reduced in secYS281F target cells and absent in secYS281F ΔppiD or secYS281F ΔyfgM target cells during competition co-cultures. Importantly, an allele-specific mutation in secY (secYG313W) renders ΔppiD or ΔyfgM target cells specifically resistant to CdiA-CTGN05224 but not to CdiA-CTo10EC869, further suggesting a direct interaction between SecY and the CDI toxins. Our results provide genetic evidence of a unique confluence between the primary cellular export route for unfolded polypeptides and the import pathways of two CDI toxins.
Collapse
|
7
|
Itskanov S, Kuo KM, Gumbart JC, Park E. Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Nat Struct Mol Biol 2021; 28:162-172. [PMID: 33398175 PMCID: PMC8236211 DOI: 10.1038/s41594-020-00541-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022]
Abstract
Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. Here, we determined cryo-EM structures of several variants of Sec61–Sec62–Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and lumenal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation.
Collapse
Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
| |
Collapse
|
8
|
Refined measurement of SecA-driven protein secretion reveals that translocation is indirectly coupled to ATP turnover. Proc Natl Acad Sci U S A 2020; 117:31808-31816. [PMID: 33257538 DOI: 10.1073/pnas.2010906117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The universally conserved Sec system is the primary method cells utilize to transport proteins across membranes. Until recently, measuring the activity-a prerequisite for understanding how biological systems work-has been limited to discontinuous protein transport assays with poor time resolution or reported by large, nonnatural tags that perturb the process. The development of an assay based on a split superbright luciferase (NanoLuc) changed this. Here, we exploit this technology to unpick the steps that constitute posttranslational protein transport in bacteria. Under the conditions deployed, the transport of a model preprotein substrate (proSpy) occurs at 200 amino acids (aa) per minute, with SecA able to dissociate and rebind during transport. Prior to that, there is no evidence for a distinct, rate-limiting initiation event. Kinetic modeling suggests that SecA-driven transport activity is best described by a series of large (∼30 aa) steps, each coupled to hundreds of ATP hydrolysis events. The features we describe are consistent with a nondeterministic motor mechanism, such as a Brownian ratchet.
Collapse
|
9
|
Palmer T, Finney AJ, Saha CK, Atkinson GC, Sargent F. A holin/peptidoglycan hydrolase-dependent protein secretion system. Mol Microbiol 2020; 115:345-355. [PMID: 32885520 DOI: 10.1111/mmi.14599] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022]
Abstract
Gram-negative bacteria have evolved numerous pathways to secrete proteins across their complex cell envelopes. Here, we describe a protein secretion system that uses a holin membrane protein in tandem with a cell wall-editing enzyme to mediate the secretion of substrate proteins from the periplasm to the cell exterior. The identity of the cell wall-editing enzymes involved was found to vary across biological systems. For instance, the chitinase secretion pathway of Serratia marcescens uses an endopeptidase to facilitate secretion, whereas the secretion of Typhoid toxin in Salmonella enterica serovar Typhi relies on a muramidase. Various families of holins are also predicted to be involved. Genomic analysis indicates that this pathway is conserved and implicated in the secretion of hydrolytic enzymes and toxins for a range of bacteria. The pairing of holins from different families with various types of peptidoglycan hydrolases suggests that this secretion pathway evolved multiple times. We suggest that the complementary bodies of evidence presented is sufficient to propose that the pathway be named the Type 10 Secretion System (TXSS).
Collapse
Affiliation(s)
- Tracy Palmer
- Microbes in Health & Disease, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Alexander J Finney
- Plant & Microbial Biology, School of Natural and Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne, UK
| | - Chayan Kumar Saha
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Gemma C Atkinson
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Frank Sargent
- Plant & Microbial Biology, School of Natural and Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne, UK
| |
Collapse
|
10
|
Cranford-Smith T, Jamshad M, Jeeves M, Chandler RA, Yule J, Robinson A, Alam F, Dunne KA, Aponte Angarita EH, Alanazi M, Carter C, Henderson IR, Lovett JE, Winn P, Knowles T, Huber D. Iron is a ligand of SecA-like metal-binding domains in vivo. J Biol Chem 2020; 295:7516-7528. [PMID: 32241912 PMCID: PMC7247292 DOI: 10.1074/jbc.ra120.012611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/26/2020] [Indexed: 12/12/2022] Open
Abstract
The ATPase SecA is an essential component of the bacterial Sec machinery, which transports proteins across the cytoplasmic membrane. Most SecA proteins contain a long C-terminal tail (CTT). In Escherichia coli, the CTT contains a structurally flexible linker domain and a small metal-binding domain (MBD). The MBD coordinates zinc via a conserved cysteine-containing motif and binds to SecB and ribosomes. In this study, we screened a high-density transposon library for mutants that affect the susceptibility of E. coli to sodium azide, which inhibits SecA-mediated translocation. Results from sequencing this library suggested that mutations removing the CTT make E. coli less susceptible to sodium azide at subinhibitory concentrations. Copurification experiments suggested that the MBD binds to iron and that azide disrupts iron binding. Azide also disrupted binding of SecA to membranes. Two other E. coli proteins that contain SecA-like MBDs, YecA and YchJ, also copurified with iron, and NMR spectroscopy experiments indicated that YecA binds iron via its MBD. Competition experiments and equilibrium binding measurements indicated that the SecA MBD binds preferentially to iron and that a conserved serine is required for this specificity. Finally, structural modeling suggested a plausible model for the octahedral coordination of iron. Taken together, our results suggest that SecA-like MBDs likely bind to iron in vivo.
Collapse
Affiliation(s)
- Tamar Cranford-Smith
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mohammed Jamshad
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Rachael A Chandler
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jack Yule
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ashley Robinson
- Institute for Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Farhana Alam
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Karl A Dunne
- Institute for Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Edwin H Aponte Angarita
- Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mashael Alanazi
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Department of Biology, College of Science, Jouf University, Saudi Arabia
| | - Cailean Carter
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ian R Henderson
- Institute for Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Janet E Lovett
- SUPA, School of Physics and Astronomy and BSRC, University of St. Andrews, St. Andrews KY16 9SS, United Kingdom
| | - Peter Winn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Timothy Knowles
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Damon Huber
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
| |
Collapse
|
11
|
Ferric Citrate Regulator FecR Is Translocated across the Bacterial Inner Membrane via a Unique Twin-Arginine Transport-Dependent Mechanism. J Bacteriol 2020; 202:JB.00541-19. [PMID: 32015149 PMCID: PMC7148137 DOI: 10.1128/jb.00541-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023] Open
Abstract
In Escherichia coli, citrate-mediated iron transport is a key nonheme pathway for the acquisition of iron. Binding of ferric citrate to the outer membrane protein FecA induces a signal cascade that ultimately activates the cytoplasmic sigma factor FecI, resulting in transcription of the fecABCDE ferric citrate transport genes. Central to this process is signal transduction mediated by the inner membrane protein FecR. FecR spans the inner membrane through a single transmembrane helix, which is flanked by cytoplasm- and periplasm-orientated moieties at the N and C termini. The transmembrane helix of FecR resembles a twin-arginine signal sequence, and the substitution of the paired arginine residues of the consensus motif decouples the FecR-FecI signal cascade, rendering the cells unable to activate transcription of the fec operon when grown on ferric citrate. Furthermore, the fusion of beta-lactamase C-terminal to the FecR transmembrane helix results in translocation of the C-terminal domain that is dependent on the twin-arginine translocation (Tat) system. Our findings demonstrate that FecR belongs to a select group of bitopic inner membrane proteins that contain an internal twin-arginine signal sequence.IMPORTANCE Iron is essential for nearly all living organisms due to its role in metabolic processes and as a cofactor for many enzymes. The FecRI signal transduction pathway regulates citrate-mediated iron import in many Gram-negative bacteria, including Escherichia coli The interactions of FecR with the outer membrane protein FecA and cytoplasmic anti-sigma factor FecI have been extensively studied. However, the mechanism by which FecR inserts into the membrane has not previously been reported. In this study, we demonstrate that the targeting of FecR to the cytoplasmic membrane is dependent on the Tat system. As such, FecR represents a new class of bitopic Tat-dependent membrane proteins with an internal twin-arginine signal sequence.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles. Microorganisms 2019; 8:microorganisms8010059. [PMID: 31905784 PMCID: PMC7023208 DOI: 10.3390/microorganisms8010059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
Collapse
|
14
|
Jauss B, Petriman NA, Drepper F, Franz L, Sachelaru I, Welte T, Steinberg R, Warscheid B, Koch HG. Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli. J Biol Chem 2019; 294:19167-19183. [PMID: 31699901 DOI: 10.1074/jbc.ra119.010686] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The SecYEG translocon constitutes the major protein transport channel in bacteria and transfers an enormous variety of different secretory and inner-membrane proteins. The minimal core of the SecYEG translocon consists of three inner-membrane proteins, SecY, SecE, and SecG, which, together with appropriate targeting factors, are sufficient for protein transport in vitro However, in vivo the SecYEG translocon has been shown to associate with multiple partner proteins, likely allowing the SecYEG translocon to process its diverse substrates. To obtain a global view on SecYEG plasticity in Escherichia coli, here we performed a quantitative interaction proteomic analysis, which identified several known SecYEG-interacting proteins, verified the interaction of SecYEG with quality-control proteins, and revealed several previously unknown putative SecYEG-interacting proteins. Surprisingly, we found that the chaperone complex PpiD/YfgM is the most prominent interaction partner of SecYEG. Detailed analyses of the PpiD-SecY interaction by site-directed cross-linking revealed that PpiD and the established SecY partner protein YidC use almost completely-overlapping binding sites on SecY. Both PpiD and YidC contacted the lateral gate, the plug domain, and the periplasmic cavity of SecY. However, quantitative MS and cross-linking analyses revealed that despite having almost identical binding sites, their binding to SecY is noncompetitive. This observation suggests that the SecYEG translocon forms different substrate-independent subassemblies in which SecYEG either associates with YidC or with the PpiD/YfgM complex. In summary, the results of this study indicate that the PpiD/YfgM chaperone complex is a primary interaction partner of the SecYEG translocon.
Collapse
Affiliation(s)
- Benjamin Jauss
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lisa Franz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ilie Sachelaru
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Thomas Welte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
15
|
Cranford-Smith T, Huber D. The way is the goal: how SecA transports proteins across the cytoplasmic membrane in bacteria. FEMS Microbiol Lett 2019; 365:4969678. [PMID: 29790985 PMCID: PMC5963308 DOI: 10.1093/femsle/fny093] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/10/2018] [Indexed: 02/06/2023] Open
Abstract
In bacteria, translocation of most soluble secreted proteins (and outer membrane proteins in Gram-negative bacteria) across the cytoplasmic membrane by the Sec machinery is mediated by the essential ATPase SecA. At its core, this machinery consists of SecA and the integral membrane proteins SecYEG, which form a protein conducting channel in the membrane. Proteins are recognised by the Sec machinery by virtue of an internally encoded targeting signal, which usually takes the form of an N-terminal signal sequence. In addition, substrate proteins must be maintained in an unfolded conformation in the cytoplasm, prior to translocation, in order to be competent for translocation through SecYEG. Recognition of substrate proteins occurs via SecA—either through direct recognition by SecA or through secondary recognition by a molecular chaperone that delivers proteins to SecA. Substrate proteins are then screened for the presence of a functional signal sequence by SecYEG. Proteins with functional signal sequences are translocated across the membrane in an ATP-dependent fashion. The current research investigating each of these steps is reviewed here.
Collapse
Affiliation(s)
- Tamar Cranford-Smith
- Institute for Microbiology and Infection School of Biosciences University of Birmingham Edgbaston Birmingham B15 2TT, UK
| | - Damon Huber
- Institute for Microbiology and Infection School of Biosciences University of Birmingham Edgbaston Birmingham B15 2TT, UK
| |
Collapse
|
16
|
Ma C, Wu X, Sun D, Park E, Catipovic MA, Rapoport TA, Gao N, Li L. Structure of the substrate-engaged SecA-SecY protein translocation machine. Nat Commun 2019; 10:2872. [PMID: 31253804 PMCID: PMC6599042 DOI: 10.1038/s41467-019-10918-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/10/2019] [Indexed: 11/28/2022] Open
Abstract
The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecA’s two-helix finger is close to the polypeptide, while SecA’s clamp interacts with the polypeptide in a sequence-independent manner by inducing a short β-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel. Proteins are translocated across membranes through the Sec61/SecY channel. Here, the authors present the structure of a translocating peptide chain trapped inside the SecA-SecY complex which suggests how peptides are actively moved through the channel.
Collapse
Affiliation(s)
- Chengying Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Xiaofei Wu
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Dongjie Sun
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Eunyong Park
- University of California-Berkeley, Stanley Hall, Berkeley, CA, 94720, USA
| | - Marco A Catipovic
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Tom A Rapoport
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| | - Long Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
17
|
Jamshad M, Knowles TJ, White SA, Ward DG, Mohammed F, Rahman KF, Wynne M, Hughes GW, Kramer G, Bukau B, Huber D. The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity. eLife 2019; 8:48385. [PMID: 31246174 PMCID: PMC6620043 DOI: 10.7554/elife.48385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022] Open
Abstract
In bacteria, the translocation of proteins across the cytoplasmic membrane by the Sec machinery requires the ATPase SecA. SecA binds ribosomes and recognises nascent substrate proteins, but the molecular mechanism of nascent substrate recognition is unknown. We investigated the role of the C-terminal tail (CTT) of SecA in nascent polypeptide recognition. The CTT consists of a flexible linker (FLD) and a small metal-binding domain (MBD). Phylogenetic analysis and ribosome binding experiments indicated that the MBD interacts with 70S ribosomes. Disruption of the MBD only or the entire CTT had opposing effects on ribosome binding, substrate-protein binding, ATPase activity and in vivo function, suggesting that the CTT influences the conformation of SecA. Site-specific crosslinking indicated that F399 in SecA contacts ribosomal protein uL29, and binding to nascent chains disrupts this interaction. Structural studies provided insight into the CTT-mediated conformational changes in SecA. Our results suggest a mechanism for nascent substrate protein recognition.
Collapse
Affiliation(s)
- Mohammed Jamshad
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J Knowles
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Scott A White
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Kazi Fahmida Rahman
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gareth W Hughes
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, Heidelberg, Germany
| | - Damon Huber
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
18
|
Young J, Duong F. Investigating the stability of the SecA-SecYEG complex during protein translocation across the bacterial membrane. J Biol Chem 2019; 294:3577-3587. [PMID: 30602566 DOI: 10.1074/jbc.ra118.006447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/21/2018] [Indexed: 11/06/2022] Open
Abstract
During posttranslational translocation in Escherichia coli, polypeptide substrates are driven across the membrane through the SecYEG protein-conducting channel using the ATPase SecA, which binds to SecYEG and couples nucleotide hydrolysis to polypeptide movement. Recent studies suggest that SecA is a highly dynamic enzyme, able to repeatedly bind and dissociate from SecYEG during substrate translocation, but other studies indicate that these dynamics, here referred to as "SecA processivity," are not a requirement for transport. We employ a SecA mutant (PrlD23) that associates more tightly to membranes than WT SecA, in addition to a SecA-SecYEG cross-linked complex, to demonstrate that SecA-SecYEG binding and dissociation events are important for efficient transport of the periplasmic protein proPhoA. Strikingly however, we find that transport of the precursor of the outer membrane protein proOmpA does not depend on SecA processivity. By exchanging signal sequence and protein domains of similar size between PhoA and OmpA, we find that SecA processivity is not influenced by the sequence of the protein substrate. In contrast, using an extended proOmpA variant and a truncated derivative of proPhoA, we show that SecA processivity is affected by substrate length. These findings underscore the importance of the dynamic nature of SecA-SecYEG interactions as a function of the preprotein substrate, features that have not yet been reported using other biophysical or in vivo methods.
Collapse
Affiliation(s)
- John Young
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
19
|
Far-reaching cellular consequences of tat deletion in Escherichia coli revealed by comprehensive proteome analyses. Microbiol Res 2019; 218:97-107. [DOI: 10.1016/j.micres.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/21/2018] [Accepted: 10/27/2018] [Indexed: 11/22/2022]
|
20
|
Barros-Barbosa A, Rodrigues TA, Ferreira MJ, Pedrosa AG, Teixeira NR, Francisco T, Azevedo JE. The intrinsically disordered nature of the peroxisomal protein translocation machinery. FEBS J 2018; 286:24-38. [PMID: 30443986 DOI: 10.1111/febs.14704] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Despite having a membrane that is impermeable to all but the smallest of metabolites, peroxisomes acquire their newly synthesized (cytosolic) matrix proteins in an already folded conformation. In some cases, even oligomeric proteins have been reported to translocate the organelle membrane. The protein sorting machinery that accomplishes this feat must be rather flexible and, unsurprisingly, several of its key components have large intrinsically disordered domains. Here, we provide an overview on these domains and their interactions trying to infer their functional roles in this protein sorting pathway.
Collapse
Affiliation(s)
- Aurora Barros-Barbosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Nélson R Teixeira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| |
Collapse
|
21
|
Fernandez DE. Two paths diverged in the stroma: targeting to dual SEC translocase systems in chloroplasts. PHOTOSYNTHESIS RESEARCH 2018; 138:277-287. [PMID: 29951837 DOI: 10.1007/s11120-018-0541-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
Chloroplasts inherited systems and strategies for protein targeting, translocation, and integration from their cyanobacterial ancestor. Unlike cyanobacteria however, chloroplasts in green algae and plants contain two distinct SEC translocase/integrase systems: the SEC1 system in the thylakoid membrane and the SEC2 system in the inner envelope membrane. This review summarizes the mode of action of SEC translocases, identification of components of the SEC2 system, evolutionary history of SCY and SECA genes, and previous work on the co- and post-translational targeting of lumenal and thylakoid membrane proteins to the SEC1 system. Recent work identifying substrates for the SEC2 system and potential features that may contribute to inner envelope targeting are also discussed.
Collapse
Affiliation(s)
- Donna E Fernandez
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
|
24
|
Specific cardiolipin-SecY interactions are required for proton-motive force stimulation of protein secretion. Proc Natl Acad Sci U S A 2018; 115:7967-7972. [PMID: 30012626 DOI: 10.1073/pnas.1721536115] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transport of proteins across or into membranes is a vital biological process, achieved in every cell by the conserved Sec machinery. In bacteria, SecYEG combines with the SecA motor protein for secretion of preproteins across the plasma membrane, powered by ATP hydrolysis and the transmembrane proton-motive force (PMF). The activities of SecYEG and SecA are modulated by membrane lipids, particularly cardiolipin (CL), a specialized phospholipid known to associate with a range of energy-transducing machines. Here, we identify two specific CL binding sites on the Thermotoga maritima SecA-SecYEG complex, through application of coarse-grained molecular dynamics simulations. We validate the computational data and demonstrate the conserved nature of the binding sites using in vitro mutagenesis, native mass spectrometry, biochemical analysis, and fluorescence spectroscopy of Escherichia coli SecYEG. The results show that the two sites account for the preponderance of functional CL binding to SecYEG, and mediate its roles in ATPase and protein transport activity. In addition, we demonstrate an important role for CL in the conferral of PMF stimulation of protein transport. The apparent transient nature of the CL interaction might facilitate proton exchange with the Sec machinery, and thereby stimulate protein transport, by a hitherto unexplored mechanism. This study demonstrates the power of coupling the high predictive ability of coarse-grained simulation with experimental analyses, toward investigation of both the nature and functional implications of protein-lipid interactions.
Collapse
|
25
|
Valverde JR, Gullón S, Mellado RP. Modelling the metabolism of protein secretion through the Tat route in Streptomyces lividans. BMC Microbiol 2018; 18:59. [PMID: 29898665 PMCID: PMC6000921 DOI: 10.1186/s12866-018-1199-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/30/2018] [Indexed: 01/03/2023] Open
Abstract
Background Streptomyces lividans has demonstrated its value as an efficient host for protein production due to its ability to secrete functional proteins directly to the media. Secretory proteins that use the major Sec route need to be properly folded outside the cell, whereas secretory proteins using the Tat route appear outside the cell correctly folded. This feature makes the Tat system very attractive for the production of natural or engineered Tat secretory proteins. S. lividans cells are known to respond differently to overproduction and secretion of Tat versus Sec proteins. Increased understanding of the impact of protein secretion through the Tat route can be obtained by a deeper analysis of the metabolic impact associated with protein production, and its dependence on protein origin, composition, secretion mechanisms, growth phases and nutrients. Flux Balance Analysis of Genome-Scale Metabolic Network models provides a theoretical framework to investigate cell metabolism under different constraints. Results We have built new models for various S. lividans strains to better understand the mechanisms associated with overproduction of proteins secreted through the Tat route. We compare models of an S. lividans Tat-dependent agarase overproducing strain with those of the S. lividans wild-type, an S. lividans strain carrying the multi-copy plasmid vector and an α-amylase Sec-dependent overproducing strain. Using updated genomic, transcriptomic and experimental data we could extend existing S. lividans models and produce a new model which produces improved results largely extending the coverage of S. lividans strains, the number of genes and reactions being considered, the predictive behaviour and the dependence on specification of exchange constraints. Comparison of the optimized solutions obtained highlights numerous changes between Tat- and Sec-dependent protein secreting strains affecting the metabolism of carbon, amino acids, nucleotides, lipids and cofactors, and variability analysis predicts a large potential for protein overproduction. Conclusions This work provides a detailed look to metabolic changes associated to Tat-dependent protein secretion reproducing experimental observations and identifying changes that are specific to each secretory route, presenting a novel, improved, more accurate and strain-independent model of S. lividans, thus opening the way for enhanced metabolic engineering of protein overproduction in S. lividans. Electronic supplementary material The online version of this article (10.1186/s12866-018-1199-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- José R Valverde
- Scientific Computing Service. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Sonia Gullón
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Rafael P Mellado
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| |
Collapse
|
26
|
Fessl T, Watkins D, Oatley P, Allen WJ, Corey RA, Horne J, Baldwin SA, Radford SE, Collinson I, Tuma R. Dynamic action of the Sec machinery during initiation, protein translocation and termination. eLife 2018; 7:35112. [PMID: 29877797 PMCID: PMC6021171 DOI: 10.7554/elife.35112] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/05/2018] [Indexed: 11/13/2022] Open
Abstract
Protein translocation across cell membranes is a ubiquitous process required for protein secretion and membrane protein insertion. In bacteria, this is mostly mediated by the conserved SecYEG complex, driven through rounds of ATP hydrolysis by the cytoplasmic SecA, and the trans-membrane proton motive force. We have used single molecule techniques to explore SecY pore dynamics on multiple timescales in order to dissect the complex reaction pathway. The results show that SecA, both the signal sequence and mature components of the pre-protein, and ATP hydrolysis each have important and specific roles in channel unlocking, opening and priming for transport. After channel opening, translocation proceeds in two phases: a slow phase independent of substrate length, and a length-dependent transport phase with an intrinsic translocation rate of ~40 amino acids per second for the proOmpA substrate. Broad translocation rate distributions reflect the stochastic nature of polypeptide transport.
Collapse
Affiliation(s)
- Tomas Fessl
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Daniel Watkins
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Peter Oatley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Robin Adam Corey
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Jim Horne
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Steve A Baldwin
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| |
Collapse
|
27
|
Kleiner-Grote GRM, Risse JM, Friehs K. Secretion of recombinant proteins from E. coli. Eng Life Sci 2018; 18:532-550. [PMID: 32624934 DOI: 10.1002/elsc.201700200] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 11/10/2022] Open
Abstract
The microorganism Escherichia coli is commonly used for recombinant protein production. Despite several advantageous characteristics like fast growth and high protein yields, its inability to easily secrete recombinant proteins into the extracellular medium remains a drawback for industrial production processes. To overcome this limitation, a multitude of approaches to enhance the extracellular yield and the secretion efficiency of recombinant proteins have been developed in recent years. Here, a comprehensive overview of secretion mechanisms for recombinant proteins from E. coli is given and divided into three main sections. First, the structure of the E. coli cell envelope and the known natural secretion systems are described. Second, the use and optimization of different one- or two-step secretion systems for recombinant protein production, as well as further permeabilization methods are discussed. Finally, the often-overlooked role of cell lysis in secretion studies and its analysis are addressed. So far, effective approaches for increasing the extracellular protein concentration to more than 10 g/L and almost 100% secretion efficiency exist, however, the large range of optimization methods and their combinations suggests that the potential for secretory protein production from E. coli has not yet been fully realized.
Collapse
Affiliation(s)
| | - Joe M Risse
- Fermentation Engineering Bielefeld University Bielefeld Germany.,Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Karl Friehs
- Fermentation Engineering Bielefeld University Bielefeld Germany.,Center for Biotechnology Bielefeld University Bielefeld Germany
| |
Collapse
|
28
|
Yazdi AK, Vezina GC, Shilton BH. An alternate mode of oligomerization for E. coli SecA. Sci Rep 2017; 7:11747. [PMID: 28924213 PMCID: PMC5603524 DOI: 10.1038/s41598-017-11648-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/29/2017] [Indexed: 11/08/2022] Open
Abstract
SecA is the ATPase of preprotein translocase. SecA is a dimer in solution and changes in its oligomeric state may function in preprotein translocation. The SecA-N68 construct, in which the C-terminal helical domains of SecA are deleted, was used to investigate the mechanism of SecA oligomerization. SecA-N68 is in equilibrium between monomers, dimers, and tetramers. Subunit interactions in the SecA-N68 tetramer are mediated entirely by unstructured regions at its N- and C-termini: when the termini are deleted to yield SecA-N68∆NC, the construct is completely monomeric. This monomeric construct yielded crystals diffracting to 2.6 Å that were used to solve the structure of SecA-N68, including the "preprotein crosslinking domain" (PPXD) that was missing from previous E. coli SecA structures. The SecA-N68 structure was combined with small angle X-ray scattering (SAXS) data to construct a model of the SecA-N68 tetramer that is consistent with the essential roles of the extreme N- and C-termini in oligomerization. This mode of oligomerization, which depends on binding of the extreme N-terminus to the DEAD motor domains, NBD1 and NBD2, was used to model a novel parallel and flexible SecA solution dimer that agrees well with SAXS data.
Collapse
Affiliation(s)
- Aliakbar Khalili Yazdi
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Grant C Vezina
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Brian H Shilton
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| |
Collapse
|
29
|
Abstract
We came together in Leeds to commemorate and celebrate the life and achievements of Prof. Stephen Baldwin. For many years we, together with Sheena Radford and Roman Tuma (colleagues also of the University of Leeds), have worked together on the problem of protein translocation through the essential and ubiquitous Sec system. Inspired and helped by Steve we may finally be making progress. My seminar described our latest hypothesis for the molecular mechanism of protein translocation, supported by results collected in Bristol and Leeds on the tractable bacterial secretion process–commonly known as the Sec system; work that will be published elsewhere. Below is a description of the alternative and contested models for protein translocation that we all have been contemplating for many years. This review will consider their pros and cons.
Collapse
|
30
|
Abstract
Many proteins are translocated across the endoplasmic reticulum (ER) membrane in eukaryotes or the plasma membrane in prokaryotes. These proteins use hydrophobic signal sequences or transmembrane (TM) segments to trigger their translocation through the protein-conducting Sec61/SecY channel. Substrates are first directed to the channel by cytosolic targeting factors, which use hydrophobic pockets to bind diverse signal and TM sequences. Subsequently, these hydrophobic sequences insert into the channel, docking into a groove on the outside of the lateral gate of the channel, where they also interact with lipids. Structural data and biochemical experiments have elucidated how channel partners, the ribosome in cotranslational translocation, and the eukaryotic ER chaperone BiP or the prokaryotic cytosolic SecA ATPase in posttranslational translocation move polypeptides unidirectionally across the membrane. Structures of auxiliary components of the bacterial translocon, YidC and SecD/F, provide additional insight. Taken together, these recent advances result in mechanistic models of protein translocation.
Collapse
Affiliation(s)
- Tom A Rapoport
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Long Li
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Eunyong Park
- The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065;
| |
Collapse
|
31
|
Tooke FJ, Babot M, Chandra G, Buchanan G, Palmer T. A unifying mechanism for the biogenesis of membrane proteins co-operatively integrated by the Sec and Tat pathways. eLife 2017; 6. [PMID: 28513434 PMCID: PMC5449189 DOI: 10.7554/elife.26577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
The majority of multi-spanning membrane proteins are co-translationally inserted into the bilayer by the Sec pathway. An important subset of membrane proteins have globular, cofactor-containing extracytoplasmic domains requiring the dual action of the co-translational Sec and post-translational Tat pathways for integration. Here, we identify further unexplored families of membrane proteins that are dual Sec-Tat-targeted. We establish that a predicted heme-molybdenum cofactor-containing protein, and a complex polyferredoxin, each require the concerted action of two translocases for their assembly. We determine that the mechanism of handover from Sec to Tat pathway requires the relatively low hydrophobicity of the Tat-dependent transmembrane domain. This, coupled with the presence of C-terminal positive charges, results in abortive insertion of this transmembrane domain by the Sec pathway and its subsequent release at the cytoplasmic side of the membrane. Together, our data points to a simple unifying mechanism governing the assembly of dual targeted membrane proteins.
Collapse
Affiliation(s)
- Fiona J Tooke
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marion Babot
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Grant Buchanan
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| |
Collapse
|
32
|
Bradley PH, Pollard KS. Proteobacteria explain significant functional variability in the human gut microbiome. MICROBIOME 2017; 5:36. [PMID: 28330508 PMCID: PMC5363007 DOI: 10.1186/s40168-017-0244-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/13/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance between individuals. RESULTS To account for these biases, we developed a powerful test of gene variability called CCoDA, which is applicable to shotgun metagenomes from any environment and can integrate data from multiple studies. Our analysis of healthy human fecal metagenomes from three separate cohorts revealed thousands of genes whose abundance differs significantly and consistently between people, including glycolytic enzymes, lipopolysaccharide biosynthetic genes, and secretion systems. Even housekeeping pathways contain a mix of variable and invariable genes, though most highly conserved genes are significantly invariable. Variable genes tend to be associated with Proteobacteria, as opposed to taxa used to define enterotypes or the dominant phyla Bacteroidetes and Firmicutes. CONCLUSIONS These results establish limits on functional redundancy and predict specific genes and taxa that may explain physiological differences between gut microbiomes.
Collapse
Affiliation(s)
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA USA
- Division of Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, CA USA
| |
Collapse
|
33
|
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.
Collapse
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;
| |
Collapse
|
34
|
SecA Cotranslationally Interacts with Nascent Substrate Proteins In Vivo. J Bacteriol 2016; 199:JB.00622-16. [PMID: 27795329 PMCID: PMC5198489 DOI: 10.1128/jb.00622-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/03/2016] [Indexed: 12/22/2022] Open
Abstract
SecA is an essential component of the Sec machinery in bacteria, which is responsible for transporting proteins across the cytoplasmic membrane. Recent work from our laboratory indicates that SecA binds to ribosomes. Here, we used two different approaches to demonstrate that SecA also interacts with nascent polypeptides in vivo and that these polypeptides are Sec substrates. First, we photo-cross-linked SecA to ribosomes in vivo and identified mRNAs that copurify with SecA. Microarray analysis of the copurifying mRNAs indicated a strong enrichment for proteins containing Sec-targeting sequences. Second, we used a 2-dimensional (2-D) gel approach to analyze radioactively labeled nascent polypeptides that copurify with SecA, including maltose binding protein, a well-characterized SecA substrate. The interaction of SecA with nascent chains was not strongly affected in cells lacking SecB or trigger factor, both of which also interact with nascent Sec substrates. Indeed, the ability of SecB to interact with nascent chains was disrupted in strains in which the interaction between SecA and the ribosome was defective. Analysis of the interaction of SecA with purified ribosomes containing arrested nascent chains in vitro indicates that SecA can begin to interact with a variety of nascent chains when they reach a length of ∼110 amino acids, which is considerably shorter than the length required for interaction with SecB. Our results suggest that SecA cotranslationally recognizes nascent Sec substrates and that this recognition could be required for the efficient delivery of these proteins to the membrane-embedded Sec machinery. IMPORTANCE SecA is an ATPase that provides the energy for the translocation of proteins across the cytoplasmic membrane by the Sec machinery in bacteria. The translocation of most of these proteins is uncoupled from protein synthesis and is frequently described as “posttranslational.” Here, we show that SecA interacts with nascent Sec substrates. This interaction is not dependent on SecB or trigger factor, which also interact with nascent Sec substrates. Moreover, the interaction of SecB with nascent polypeptides is dependent on the interaction of SecA with the ribosome, suggesting that interaction of the nascent chain with SecA precedes interaction with SecB. Our results suggest that SecA could recognize substrate proteins cotranslationally in order to efficiently target them for uncoupled protein translocation.
Collapse
|
35
|
Manganas P, MacPherson L, Tokatlidis K. Oxidative protein biogenesis and redox regulation in the mitochondrial intermembrane space. Cell Tissue Res 2016; 367:43-57. [PMID: 27632163 PMCID: PMC5203823 DOI: 10.1007/s00441-016-2488-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
Abstract
Mitochondria are organelles that play a central role in cellular metabolism, as they are responsible for processes such as iron/sulfur cluster biogenesis, respiration and apoptosis. Here, we describe briefly the various protein import pathways for sorting of mitochondrial proteins into the different subcompartments, with an emphasis on the targeting to the intermembrane space. The discovery of a dedicated redox-controlled pathway in the intermembrane space that links protein import to oxidative protein folding raises important questions on the redox regulation of this process. We discuss the salient features of redox regulation in the intermembrane space and how such mechanisms may be linked to the more general redox homeostasis balance that is crucial not only for normal cell physiology but also for cellular dysfunction.
Collapse
Affiliation(s)
- Phanee Manganas
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Lisa MacPherson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Kostas Tokatlidis
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
36
|
Szewczyk J, Collet JF. The Journey of Lipoproteins Through the Cell: One Birthplace, Multiple Destinations. Adv Microb Physiol 2016; 69:1-50. [PMID: 27720009 DOI: 10.1016/bs.ampbs.2016.07.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial lipoproteins are a very diverse group of proteins characterized by the presence of an N-terminal lipid moiety that serves as a membrane anchor. Lipoproteins have a wide variety of crucial functions, ranging from envelope biogenesis to stress response. In Gram-negative bacteria, lipoproteins can be targeted to various destinations in the cell, including the periplasmic side of the cytoplasmic or outer membrane, the cell surface or the external milieu. The sorting mechanisms have been studied in detail in Escherichia coli, but exceptions to the rules established in this model bacterium exist in other bacteria. In this chapter, we will present the current knowledge on lipoprotein sorting in the cell. Our particular focus will be on the surface-exposed lipoproteins that appear to be much more common than previously assumed. We will discuss the different targeting strategies, provide numerous examples of surface-exposed lipoproteins and discuss the techniques used to assess their surface exposure.
Collapse
Affiliation(s)
- J Szewczyk
- WELBIO, Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - J-F Collet
- WELBIO, Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
| |
Collapse
|
37
|
Bandara M, Corey RA, Martin R, Skehel JM, Blocker AJ, Jenkinson HF, Collinson I. Composition and Activity of the Non-canonical Gram-positive SecY2 Complex. J Biol Chem 2016; 291:21474-21484. [PMID: 27551046 PMCID: PMC5076819 DOI: 10.1074/jbc.m116.729806] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/14/2016] [Indexed: 11/24/2022] Open
Abstract
The accessory Sec system in Streptococcus gordonii DL1 is a specialized export system that transports a large serine-rich repeat protein, Hsa, to the bacterial surface. The system is composed of core proteins SecA2 and SecY2 and accessory Sec proteins Asp1–Asp5. Similar to canonical SecYEG, SecY2 forms a channel for translocation of the Hsa adhesin across the cytoplasmic membrane. Accessory Sec proteins Asp4 and Asp5 have been suggested to work alongside SecY2 to form the translocon, similar to the associated SecY, SecE, and SecG of the canonical system (SecYEG). To test this theory, S. gordonii secY2, asp4, and asp5 were co-expressed in Escherichia coli. The resultant complex was subsequently purified, and its composition was confirmed by mass spectrometry to be SecY2-Asp4-Asp5. Like SecYEG, the non-canonical complex activates the ATPase activity of the SecA motor (SecA2). This study also shows that Asp4 and Asp5 are necessary for optimal adhesion of S. gordonii to glycoproteins gp340 and fibronectin, known Hsa binding partners, as well as for early stage biofilm formation. This work opens new avenues for understanding the structure and function of the accessory Sec system.
Collapse
Affiliation(s)
- Mikaila Bandara
- From the School of Oral and Dental Sciences, Lower Maudlin Street, Bristol BS1 2LY.,the School of Biochemistry and.,School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, and
| | | | | | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Ariel J Blocker
- the School of Biochemistry and.,School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, and
| | - Howard F Jenkinson
- From the School of Oral and Dental Sciences, Lower Maudlin Street, Bristol BS1 2LY
| | | |
Collapse
|
38
|
Membrane protein insertion and assembly by the bacterial holo-translocon SecYEG-SecDF-YajC-YidC. Biochem J 2016; 473:3341-54. [PMID: 27435098 PMCID: PMC5095914 DOI: 10.1042/bcj20160545] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/19/2016] [Indexed: 02/03/2023]
Abstract
Protein secretion and membrane insertion occur through the ubiquitous Sec machinery. In this system, insertion involves the targeting of translating ribosomes via the signal recognition particle and its cognate receptor to the SecY (bacteria and archaea)/Sec61 (eukaryotes) translocon. A common mechanism then guides nascent transmembrane helices (TMHs) through the Sec complex, mediated by associated membrane insertion factors. In bacteria, the membrane protein 'insertase' YidC ushers TMHs through a lateral gate of SecY to the bilayer. YidC is also thought to incorporate proteins into the membrane independently of SecYEG. Here, we show the bacterial holo-translocon (HTL) - a supercomplex of SecYEG-SecDF-YajC-YidC - is a bona fide resident of the Escherichia coli inner membrane. Moreover, when compared with SecYEG and YidC alone, the HTL is more effective at the insertion and assembly of a wide range of membrane protein substrates, including those hitherto thought to require only YidC.
Collapse
|
39
|
Kleanthous C, Armitage JP. The bacterial cell envelope. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0019. [PMID: 26370932 DOI: 10.1098/rstb.2015.0019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Judith P Armitage
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| |
Collapse
|
40
|
Baldridge RD, Rapoport TA. Autoubiquitination of the Hrd1 Ligase Triggers Protein Retrotranslocation in ERAD. Cell 2016; 166:394-407. [PMID: 27321670 DOI: 10.1016/j.cell.2016.05.048] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/19/2016] [Accepted: 05/13/2016] [Indexed: 12/16/2022]
Abstract
Misfolded proteins of the ER are retrotranslocated to the cytosol, where they are polyubiquitinated, extracted from the membrane, and degraded by the proteasome. To investigate how the ER-associated Degradation (ERAD) machinery can accomplish retrotranslocation of a misfolded luminal protein domain across a lipid bilayer, we have reconstituted retrotranslocation with purified S. cerevisiae proteins, using proteoliposomes containing the multi-spanning ubiquitin ligase Hrd1. Retrotranslocation of the luminal domain of a membrane-spanning substrate is triggered by autoubiquitination of Hrd1. Substrate ubiquitination is a subsequent event, and the Cdc48 ATPase that completes substrate extraction from the membrane is not required for retrotranslocation. Ubiquitination of lysines in Hrd1's RING-finger domain is required for substrate retrotranslocation in vitro and for ERAD in vivo. Our results suggest that Hrd1 forms a ubiquitin-gated protein-conducting channel.
Collapse
Affiliation(s)
- Ryan D Baldridge
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
41
|
Allen WJ, Corey RA, Oatley P, Sessions RB, Baldwin SA, Radford SE, Tuma R, Collinson I. Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation. eLife 2016; 5. [PMID: 27183269 PMCID: PMC4907695 DOI: 10.7554/elife.15598] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/14/2016] [Indexed: 01/25/2023] Open
Abstract
The essential process of protein secretion is achieved by the ubiquitous Sec machinery. In prokaryotes, the drive for translocation comes from ATP hydrolysis by the cytosolic motor-protein SecA, in concert with the proton motive force (PMF). However, the mechanism through which ATP hydrolysis by SecA is coupled to directional movement through SecYEG is unclear. Here, we combine all-atom molecular dynamics (MD) simulations with single molecule FRET and biochemical assays. We show that ATP binding by SecA causes opening of the SecY-channel at long range, while substrates at the SecY-channel entrance feed back to regulate nucleotide exchange by SecA. This two-way communication suggests a new, unifying 'Brownian ratchet' mechanism, whereby ATP binding and hydrolysis bias the direction of polypeptide diffusion. The model represents a solution to the problem of transporting inherently variable substrates such as polypeptides, and may underlie mechanisms of other motors that translocate proteins and nucleic acids.
Collapse
Affiliation(s)
| | - Robin Adam Corey
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Peter Oatley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Steve A Baldwin
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
42
|
Corey RA, Allen WJ, Komar J, Masiulis S, Menzies S, Robson A, Collinson I. Unlocking the Bacterial SecY Translocon. Structure 2016; 24:518-527. [PMID: 26973090 PMCID: PMC4826270 DOI: 10.1016/j.str.2016.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 11/25/2022]
Abstract
The Sec translocon performs protein secretion and membrane protein insertion at the plasma membrane of bacteria and archaea (SecYEG/β), and the endoplasmic reticular membrane of eukaryotes (Sec61). Despite numerous structures of the complex, the mechanism underlying translocation of pre-proteins, driven by the ATPase SecA in bacteria, remains unresolved. Here we present a series of biochemical and computational analyses exploring the consequences of signal sequence binding to SecYEG. The data demonstrate that a signal sequence-induced movement of transmembrane helix 7 unlocks the translocon and that this conformational change is communicated to the cytoplasmic faces of SecY and SecE, involved in SecA binding. Our findings progress the current understanding of the dynamic action of the translocon during the translocation initiation process. The results suggest that the converging effects of the signal sequence and SecA at the cytoplasmic face of SecYEG are decisive for the intercalation and translocation of pre-protein through the SecY channel. Validation of previously observed signal sequence-induced “unlocking” of SecYEG Conformational changes upon SecYEG unlocking are relayed to SecA binding site Unlocking the translocon perturbs the interaction between SecY and SecE Conformational changes distinct between secretion and membrane protein insertion
Collapse
Affiliation(s)
- Robin A Corey
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Joanna Komar
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Simonas Masiulis
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Sam Menzies
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Alice Robson
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.
| |
Collapse
|