1
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Mets T, Kurata T, Ernits K, Johansson MJO, Craig SZ, Evora GM, Buttress JA, Odai R, Wallant KC, Nakamoto JA, Shyrokova L, Egorov AA, Doering CR, Brodiazhenko T, Laub MT, Tenson T, Strahl H, Martens C, Harms A, Garcia-Pino A, Atkinson GC, Hauryliuk V. Mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems. Cell Host Microbe 2024; 32:1059-1073.e8. [PMID: 38821063 DOI: 10.1016/j.chom.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Toxin-antitoxins (TAs) are prokaryotic two-gene systems composed of a toxin neutralized by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilizes the antitoxin by recognizing its chaperone addiction (ChAD) element. TACs mediate antiphage defense, but the mechanisms of viral sensing and restriction are unexplored. We identify two Escherichia coli antiphage TAC systems containing host inhibition of growth (HigBA) and CmdTA TA modules, HigBAC and CmdTAC. HigBAC is triggered through recognition of the gpV major tail protein of phage λ. Chaperone HigC recognizes gpV and ChAD via analogous aromatic molecular patterns, with gpV outcompeting ChAD to trigger toxicity. For CmdTAC, the CmdT ADP-ribosyltransferase toxin modifies mRNA to halt protein synthesis and limit phage propagation. Finally, we establish the modularity of TACs by creating a hybrid broad-spectrum antiphage system combining the CmdTA TA warhead with a HigC chaperone phage sensor. Collectively, these findings reveal the potential of TAC systems in broad-spectrum antiphage defense.
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Affiliation(s)
- Toomas Mets
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Karin Ernits
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Marcus J O Johansson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Sophie Z Craig
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Gabriel Medina Evora
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Jessica A Buttress
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Roni Odai
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Kyo Coppieters't Wallant
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Jose A Nakamoto
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Lena Shyrokova
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | | | | | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Alexander Harms
- ETH Zurich, Institute of Food, Nutrition and Health, 8092 Zürich, Switzerland
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; Virus Centre, Lund University, Lund, Sweden.
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia; Virus Centre, Lund University, Lund, Sweden; Science for Life Laboratory, Lund, Sweden.
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2
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Crossley JA, Allen WJ, Watkins DW, Sabir T, Radford SE, Tuma R, Collinson I, Fessl T. Dynamic coupling of fast channel gating with slow ATP-turnover underpins protein transport through the Sec translocon. EMBO J 2024; 43:1-13. [PMID: 38177311 PMCID: PMC10883268 DOI: 10.1038/s44318-023-00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
The Sec translocon is a highly conserved membrane assembly for polypeptide transport across, or into, lipid bilayers. In bacteria, secretion through the core channel complex-SecYEG in the inner membrane-is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate the conformational state of SecYEG throughout the ATP hydrolysis cycle of SecA. We show that the SecYEG channel fluctuations between open and closed states are much faster (~20-fold during translocation) than ATP turnover, and that the nucleotide status of SecA modulates the rates of opening and closure. The SecY variant PrlA4, which exhibits faster transport but unaffected ATPase rates, increases the dwell time in the open state, facilitating pre-protein diffusion through the pore and thereby enhancing translocation efficiency. Thus, rapid SecYEG channel dynamics are allosterically coupled to SecA via modulation of the energy landscape, and play an integral part in protein transport. Loose coupling of ATP-turnover by SecA to the dynamic properties of SecYEG is compatible with a Brownian-rachet mechanism of translocation, rather than strict nucleotide-dependent interconversion between different static states of a power stroke.
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Affiliation(s)
- Joel A Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Tara Sabir
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK.
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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3
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Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
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Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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4
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Guest RL, Silhavy TJ. Cracking outer membrane biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119405. [PMID: 36455781 PMCID: PMC9878550 DOI: 10.1016/j.bbamcr.2022.119405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
Abstract
The outer membrane is a distinguishing feature of the Gram-negative envelope. It lies on the external face of the peptidoglycan sacculus and forms a robust permeability barrier that protects extracytoplasmic structures from environmental insults. Overcoming the barrier imposed by the outer membrane presents a significant hurdle towards developing novel antibiotics that are effective against Gram-negative bacteria. As the outer membrane is an essential component of the cell, proteins involved in its biogenesis are themselves promising antibiotic targets. Here, we summarize key findings that have built our understanding of the outer membrane. Foundational studies describing the discovery and composition of the outer membrane as well as the pathways involved in its construction are discussed.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, United States of America.
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5
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Itskanov S, Park E. Mechanism of Protein Translocation by the Sec61 Translocon Complex. Cold Spring Harb Perspect Biol 2023; 15:a041250. [PMID: 35940906 PMCID: PMC9808579 DOI: 10.1101/cshperspect.a041250] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The endoplasmic reticulum (ER) is a major site for protein synthesis, folding, and maturation in eukaryotic cells, responsible for production of secretory proteins and most integral membrane proteins. The universally conserved protein-conducting channel Sec61 complex mediates core steps in these processes by translocating hydrophilic polypeptide segments of client proteins across the ER membrane and integrating hydrophobic transmembrane segments into the membrane. The Sec61 complex associates with several other molecular machines and enzymes to enable substrate engagement with the channel and coordination of protein translocation with translation, protein folding, and/or post-translational modifications. Recent cryo-electron microscopy and functional studies of these translocon complexes have greatly advanced our mechanistic understanding of Sec61-dependent protein biogenesis at the ER. Here, we will review the current models for how the Sec61 channel performs its functions in coordination with partner complexes.
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Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program
- California Institute for Quantitative Biosciences
| | - Eunyong Park
- California Institute for Quantitative Biosciences
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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6
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Eismann L, Fijalkowski I, Galmozzi CV, Koubek J, Tippmann F, Van Damme P, Kramer G. Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis. Cell Rep 2022; 41:111776. [PMID: 36476862 DOI: 10.1016/j.celrep.2022.111776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
The chaperone SecB has been implicated in de novo protein folding and translocation across the membrane, but it remains unclear which nascent polypeptides SecB binds, when during translation SecB acts, how SecB function is coordinated with other chaperones and targeting factors, and how polypeptide engagement contributes to protein biogenesis. Using selective ribosome profiling, we show that SecB binds many nascent cytoplasmic and translocated proteins generally late during translation and controlled by the chaperone trigger factor. Revealing an uncharted role in co-translational translocation, inner membrane proteins (IMPs) are the most prominent nascent SecB interactors. Unlike other substrates, IMPs are bound early during translation, following the membrane targeting by the signal recognition particle. SecB remains bound until translation is terminated, and contributes to membrane insertion. Our study establishes a role of SecB in the co-translational maturation of proteins from all cellular compartments and functionally implicates cytosolic chaperones in membrane protein biogenesis.
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Affiliation(s)
- Lena Eismann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Carla Verónica Galmozzi
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, 41013 Seville, Spain
| | - Jiří Koubek
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Frank Tippmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
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7
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González-Magaña A, Altuna J, Queralt-Martín M, Largo E, Velázquez C, Montánchez I, Bernal P, Alcaraz A, Albesa-Jové D. The P. aeruginosa effector Tse5 forms membrane pores disrupting the membrane potential of intoxicated bacteria. Commun Biol 2022; 5:1189. [PMID: 36335275 PMCID: PMC9637101 DOI: 10.1038/s42003-022-04140-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 10/20/2022] [Indexed: 11/08/2022] Open
Abstract
The type VI secretion system (T6SS) of Pseudomonas aeruginosa injects effector proteins into neighbouring competitors and host cells, providing a fitness advantage that allows this opportunistic nosocomial pathogen to persist and prevail during the onset of infections. However, despite the high clinical relevance of P. aeruginosa, the identity and mode of action of most P. aeruginosa T6SS-dependent effectors remain to be discovered. Here, we report the molecular mechanism of Tse5-CT, the toxic auto-proteolytic product of the P. aeruginosa T6SS exported effector Tse5. Our results demonstrate that Tse5-CT is a pore-forming toxin that can transport ions across the membrane, causing membrane depolarisation and bacterial death. The membrane potential regulates a wide range of essential cellular functions; therefore, membrane depolarisation is an efficient strategy to compete with other microorganisms in polymicrobial environments. The Pseudomonas aeruginosa Type 6 secretion effector Tse5 forms pores in the cytoplasmic membrane when ectopically produced and hence has a bacteriolytic effect by depolarising the inner membrane potential.
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Affiliation(s)
- Amaia González-Magaña
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Jon Altuna
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - Eneko Largo
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain.,Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940, Leioa, Spain
| | - Carmen Velázquez
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Itxaso Montánchez
- Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940, Leioa, Spain
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012, Sevilla, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - David Albesa-Jové
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain. .,Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain.
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8
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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9
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Zhu Z, Wang S, Shan SO. Ribosome profiling reveals multiple roles of SecA in cotranslational protein export. Nat Commun 2022; 13:3393. [PMID: 35697696 PMCID: PMC9192764 DOI: 10.1038/s41467-022-31061-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
SecA, an ATPase known to posttranslationally translocate secretory proteins across the bacterial plasma membrane, also binds ribosomes, but the role of SecA’s ribosome interaction has been unclear. Here, we used a combination of ribosome profiling methods to investigate the cotranslational actions of SecA. Our data reveal the widespread accumulation of large periplasmic loops of inner membrane proteins in the cytoplasm during their cotranslational translocation, which are specifically recognized and resolved by SecA in coordination with the proton motive force (PMF). Furthermore, SecA associates with 25% of secretory proteins with highly hydrophobic signal sequences at an early stage of translation and mediates their cotranslational transport. In contrast, the chaperone trigger factor (TF) delays SecA engagement on secretory proteins with weakly hydrophobic signal sequences, thus enforcing a posttranslational mode of their translocation. Our results elucidate the principles of SecA-driven cotranslational protein translocation and reveal a hierarchical network of protein export pathways in bacteria. Using a combination of ribosome profiling methods, Zhu et al. investigate the principles governing the cotranslational interaction of SecA with nascent proteins and reveal a hierarchical organization of protein export pathways in bacteria.
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Affiliation(s)
- Zikun Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shuai Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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10
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Ford HC, Allen WJ, Pereira GC, Liu X, Dillingham MS, Collinson I. Towards a molecular mechanism underlying mitochondrial protein import through the TOM and TIM23 complexes. eLife 2022; 11:75426. [PMID: 35674314 PMCID: PMC9255969 DOI: 10.7554/elife.75426] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/07/2022] [Indexed: 12/27/2022] Open
Abstract
Nearly all mitochondrial proteins need to be targeted for import from the cytosol. For the majority, the first port of call is the translocase of the outer membrane (TOM complex), followed by a procession of alternative molecular machines, conducting transport to their final destination. The pre-sequence translocase of the inner membrane (TIM23-complex) imports proteins with cleavable pre-sequences. Progress in understanding these transport mechanisms has been hampered by the poor sensitivity and time resolution of import assays. However, with the development of an assay based on split NanoLuc luciferase, we can now explore this process in greater detail. Here, we apply this new methodology to understand how ∆ψ and ATP hydrolysis, the two main driving forces for import into the matrix, contribute to the transport of pre-sequence-containing precursors (PCPs) with varying properties. Notably, we found that two major rate-limiting steps define PCP import time: passage of PCP across the outer membrane and initiation of inner membrane transport by the pre-sequence - the rates of which are influenced by PCP size and net charge. The apparent distinction between transport through the two membranes (passage through TOM is substantially complete before PCP-TIM engagement) is in contrast with the current view that import occurs through TOM and TIM in a single continuous step. Our results also indicate that PCPs spend very little time in the TIM23 channel - presumably rapid success or failure of import is critical for maintenance of mitochondrial fitness.
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Affiliation(s)
- Holly C Ford
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Gonçalo C Pereira
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Xia Liu
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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11
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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12
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Allen WJ, Corey RA, Watkins DW, Oliveira ASF, Hards K, Cook GM, Collinson I. Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion. eLife 2022; 11:e77586. [PMID: 35486093 PMCID: PMC9110029 DOI: 10.7554/elife.77586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain - notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism through which the PMF can aid transport by enabling a 'proton ratchet', wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction.
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Affiliation(s)
- William J Allen
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Robin A Corey
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - A Sofia F Oliveira
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
- School of Chemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Kiel Hards
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
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13
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Yang CI, Kim J, Shan SO. Ribosome-nascent chain interaction regulates N-terminal protein modification. J Mol Biol 2022; 434:167535. [PMID: 35278477 PMCID: PMC9126151 DOI: 10.1016/j.jmb.2022.167535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 01/02/2023]
Abstract
Numerous proteins initiate their folding, localization, and modifications early during translation, and emerging data show that the ribosome actively participates in diverse protein biogenesis pathways. Here we show that the ribosome imposes an additional layer of substrate selection during N-terminal methionine excision (NME), an essential protein modification in bacteria. Biochemical analyses show that cotranslational NME is exquisitely sensitive to a hydrophobic signal sequence or transmembrane domain near the N terminus of the nascent polypeptide. The ability of the nascent chain to access the active site of NME enzymes dictates NME efficiency, which is inhibited by confinement of the nascent chain on the ribosome surface and exacerbated by signal recognition particle. In vivo measurements corroborate the inhibition of NME by an N-terminal hydrophobic sequence, suggesting the retention of formylmethionine on a substantial fraction of the secretory and membrane proteome. Our work demonstrates how molecular features of a protein regulate its cotranslational modification and highlights the active participation of the ribosome in protein biogenesis pathways via interactions of the ribosome surface with the nascent protein.
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14
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Krishnamurthy S, Sardis MF, Eleftheriadis N, Chatzi KE, Smit JH, Karathanou K, Gouridis G, Portaliou AG, Bondar AN, Karamanou S, Economou A. Preproteins couple the intrinsic dynamics of SecA to its ATPase cycle to translocate via a catch and release mechanism. Cell Rep 2022; 38:110346. [PMID: 35139375 DOI: 10.1016/j.celrep.2022.110346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/22/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Protein machines undergo conformational motions to interact with and manipulate polymeric substrates. The Sec translocase promiscuously recognizes, becomes activated, and secretes >500 non-folded preprotein clients across bacterial cytoplasmic membranes. Here, we reveal that the intrinsic dynamics of the translocase ATPase, SecA, and of preproteins combine to achieve translocation. SecA possesses an intrinsically dynamic preprotein clamp attached to an equally dynamic ATPase motor. Alternating motor conformations are finely controlled by the γ-phosphate of ATP, while ADP causes motor stalling, independently of clamp motions. Functional preproteins physically bridge these independent dynamics. Their signal peptides promote clamp closing; their mature domain overcomes the rate-limiting ADP release. While repeated ATP cycles shift the motor between unique states, multiple conformationally frustrated prongs in the clamp repeatedly "catch and release" trapped preprotein segments until translocation completion. This universal mechanism allows any preprotein to promiscuously recognize the translocase, usurp its intrinsic dynamics, and become secreted.
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Affiliation(s)
- Srinath Krishnamurthy
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Marios-Frantzeskos Sardis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Nikolaos Eleftheriadis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Katerina E Chatzi
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Jochem H Smit
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany
| | - Giorgos Gouridis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands; Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Nikolaou Plastira 100, Heraklion, Crete, Greece
| | - Athina G Portaliou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, 077125 Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
| | - Spyridoula Karamanou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium.
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15
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Dadashi M, Chen L, Nasimian A, Ghavami S, Duan K. Putative RNA Ligase RtcB Affects the Switch between T6SS and T3SS in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:12561. [PMID: 34830443 PMCID: PMC8619066 DOI: 10.3390/ijms222212561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 01/22/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is a significant cause of infection in immunocompromised individuals, cystic fibrosis patients, and burn victims. To benefit its survival, the bacterium adapt to either a motile or sessile lifestyle when infecting the host. The motile bacterium has an often activated type III secretion system (T3SS), which is virulent to the host, whereas the sessile bacterium harbors an active T6SS and lives in biofilms. Regulatory pathways involving Gac-Rsm or secondary messengers such as c-di-GMP determine which lifestyle is favorable for P. aeruginosa. Here, we introduce the RNA binding protein RtcB as a modulator of the switch between motile and sessile bacterial lifestyles. Using the wild-type P. aeruginosa PAO1, and a retS mutant PAO1(∆retS) in which T3SS is repressed and T6SS active, we show that deleting rtcB led to simultaneous expression of T3SS and T6SS in both PAO1(∆rtcB) and PAO1(∆rtcB∆retS). The deletion of rtcB also increased biofilm formation in PAO1(∆rtcB) and restored the motility of PAO1(∆rtcB∆retS). RNA-sequencing data suggested RtcB as a global modulator affecting multiple virulence factors, including bacterial secretion systems. Competitive killing and infection assays showed that the three T6SS systems (H1, H2, and H3) in PAO1(∆rtcB) were activated into a functional syringe, and could compete with Escherichia coli and effectively infect lettuce. Western blotting and RT-PCR results showed that RtcB probably exerted its function through RsmA in PAO1(∆rtcB∆retS). Quantification of c-di-GMP showed an elevated intracellular levels in PAO1(∆rtcB), which likely drove the switch between T6SS and T3SS, and contributed to the altered phenotypes and characteristics observed. Our data demonstrate a pivotal role of RtcB in the virulence of P. aeruginosa by controlling multiple virulence determinants, such as biofilm formation, motility, pyocyanin production, T3SS, and T6SS secretion systems towards eukaryotic and prokaryotic cells. These findings suggest RtcB as a potential target for controlling P. aeruginosa colonization, establishment, and pathogenicity.
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Affiliation(s)
- Maryam Dadashi
- Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, MB R3E 0W2, Canada;
| | - Lin Chen
- College of Life Sciences, Northwest University, Xi’an 710069, China;
| | - Ahmad Nasimian
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0W2, Canada; (A.N.); (S.G.)
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0W2, Canada; (A.N.); (S.G.)
| | - Kangmin Duan
- Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, MB R3E 0W2, Canada;
- Department of Medical Microbiology and Infectious Disease, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
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16
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Sučec I, Bersch B, Schanda P. How do Chaperones Bind (Partly) Unfolded Client Proteins? Front Mol Biosci 2021; 8:762005. [PMID: 34760928 PMCID: PMC8573040 DOI: 10.3389/fmolb.2021.762005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/06/2021] [Indexed: 01/03/2023] Open
Abstract
Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.
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Affiliation(s)
- Iva Sučec
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Beate Bersch
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Paul Schanda
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria
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17
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Potteth US, Upadhyay T, Saini S, Saraogi I. Novel Antibacterial Targets in Protein Biogenesis Pathways. Chembiochem 2021; 23:e202100459. [PMID: 34643994 DOI: 10.1002/cbic.202100459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance has emerged as a global threat due to the ability of bacteria to quickly evolve in response to the selection pressure induced by anti-infective drugs. Thus, there is an urgent need to develop new antibiotics against resistant bacteria. In this review, we discuss pathways involving bacterial protein biogenesis as attractive antibacterial targets since many of them are essential for bacterial survival and virulence. We discuss the structural understanding of various components associated with bacterial protein biogenesis, which in turn can be utilized for rational antibiotic design. We highlight efforts made towards developing inhibitors of these pathways with insights into future possibilities and challenges. We also briefly discuss other potential targets related to protein biogenesis.
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Affiliation(s)
- Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India.,Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal - 462066, Madhya Pradesh, India
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18
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Balaji S. The transferred translocases: An old wine in a new bottle. Biotechnol Appl Biochem 2021; 69:1587-1610. [PMID: 34324237 DOI: 10.1002/bab.2230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 11/12/2022]
Abstract
The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.
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Affiliation(s)
- S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
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19
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Macošek J, Mas G, Hiller S. Redefining Molecular Chaperones as Chaotropes. Front Mol Biosci 2021; 8:683132. [PMID: 34195228 PMCID: PMC8237284 DOI: 10.3389/fmolb.2021.683132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular chaperones are the key instruments of bacterial protein homeostasis. Chaperones not only facilitate folding of client proteins, but also transport them, prevent their aggregation, dissolve aggregates and resolve misfolded states. Despite this seemingly large variety, single chaperones can perform several of these functions even on multiple different clients, thus suggesting a single biophysical mechanism underlying. Numerous recently elucidated structures of bacterial chaperone–client complexes show that dynamic interactions between chaperones and their client proteins stabilize conformationally flexible non-native client states, which results in client protein denaturation. Based on these findings, we propose chaotropicity as a suitable biophysical concept to rationalize the generic activity of chaperones. We discuss the consequences of applying this concept in the context of ATP-dependent and -independent chaperones and their functional regulation.
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20
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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: 30] [Impact Index Per Article: 10.0] [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.
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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
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21
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Jiang C, Wynne M, Huber D. How Quality Control Systems AID Sec-Dependent Protein Translocation. Front Mol Biosci 2021; 8:669376. [PMID: 33928127 PMCID: PMC8076867 DOI: 10.3389/fmolb.2021.669376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The evolutionarily conserved Sec machinery is responsible for transporting proteins across the cytoplasmic membrane. Protein substrates of the Sec machinery must be in an unfolded conformation in order to be translocated across (or inserted into) the cytoplasmic membrane. In bacteria, the requirement for unfolded proteins is strict: substrate proteins that fold (or misfold) prematurely in the cytoplasm prior to translocation become irreversibly trapped in the cytoplasm. Partially folded Sec substrate proteins and stalled ribosomes containing nascent Sec substrates can also inhibit translocation by blocking (i.e., “jamming”) the membrane-embedded Sec machinery. To avoid these issues, bacteria have evolved a complex network of quality control systems to ensure that Sec substrate proteins do not fold in the cytoplasm. This quality control network can be broken into three branches, for which we have defined the acronym “AID”: (i) avoidance of cytoplasmic intermediates through cotranslationally channeling newly synthesized Sec substrates to the Sec machinery; (ii) inhibition of folding Sec substrate proteins that transiently reside in the cytoplasm by molecular chaperones and the requirement for posttranslational modifications; (iii) destruction of products that could potentially inhibit translocation. In addition, several stress response pathways help to restore protein-folding homeostasis when environmental conditions that inhibit translocation overcome the AID quality control systems.
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Affiliation(s)
- Chen Jiang
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Damon Huber
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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22
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Molecular mechanism of networking among DegP, Skp and SurA in periplasm for biogenesis of outer membrane proteins. Biochem J 2021; 477:2949-2965. [PMID: 32729902 DOI: 10.1042/bcj20200483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
The biogenesis of outer membrane proteins (OMPs) is an extremely challenging process. In the periplasm of Escherichia coli, a group of quality control factors work together to exercise the safe-guard and quality control of OMPs. DegP, Skp and SurA are the three most prominent ones. Although extensive investigations have been carried out, the molecular mechanism regarding the networking among these proteins remains mostly mysterious. Our group has previously studied the molecular interactions of OMPs with SurA and Skp, using single-molecule detection (SMD). In this work, again using SMD, we studied how OmpC, a representative of OMPs, interacts with DegP, Skp and SurA collectively. Several important discoveries were made. The self-oligomerization of DegP to form hexamer occurs over hundred micromolars. When OmpC is in a monomer state at a low concentration, the OmpC·DegP6 and OmpC·DegP24 complexes form when the DegP concentration is around sub-micromolars and a hundred micromolars, respectively. High OmpC concentration promotes the binding affinity of DegP to OmpC by ∼100 folds. Skp and SurA behave differently when they interact synergistically with DegP in the presence of substrate. DegP can degrade SurA-protected OmpC, but Skp-protected OmpC forms the ternary complex OmpC·(Skp3)n·DegP6 (n = 1,2) to resist the DegP-mediated degradation. Combined with previous results, we were able to depict a comprehensive picture regarding the molecular mechanism of the networking among DegP, Skp and SurA in the periplasm for the OMPs biogenesis under physiological and stressed conditions.
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23
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Elfageih R, Karyolaimos A, Kemp G, de Gier J, von Heijne G, Kudva R. Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli. Protein Sci 2020; 29:2028-2037. [PMID: 32790204 PMCID: PMC7513700 DOI: 10.1002/pro.3927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 01/10/2023]
Abstract
Cotranslational protein folding studies using Force Profile Analysis, a method where the SecM translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide, have so far been limited mainly to small domains of cytosolic proteins that fold in close proximity to the translating ribosome. In this study, we investigate the cotranslational folding of the periplasmic, disulfide bond-containing Escherichia coli protein alkaline phosphatase (PhoA) in a wild-type strain background and a strain background devoid of the periplasmic thiol: disulfide interchange protein DsbA. We find that folding-induced forces can be transmitted via the nascent chain from the periplasm to the polypeptide transferase center in the ribosome, a distance of ~160 Å, and that PhoA appears to fold cotranslationally via at least two disulfide-stabilized folding intermediates. Thus, Force Profile Analysis can be used to study cotranslational folding of proteins in an extra-cytosolic compartment, like the periplasm.
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Affiliation(s)
- Rageia Elfageih
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | | | - Grant Kemp
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Jan‐Willem de Gier
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Gunnar von Heijne
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Science for Life Laboratory Stockholm UniversitySolnaSweden
| | - Renuka Kudva
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
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24
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Cai G, Scofield SR. Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes. PLoS One 2020; 15:e0231296. [PMID: 32407378 PMCID: PMC7224479 DOI: 10.1371/journal.pone.0231296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Phytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3' truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.
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Affiliation(s)
- Guohong Cai
- Crop Production and Pest Control Research Unit, Agricultural Research Service, USDA, and College of Agriculture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Steven R. Scofield
- Crop Production and Pest Control Research Unit, Agricultural Research Service, USDA, and College of Agriculture, Purdue University, West Lafayette, Indiana, United States of America
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25
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Del Val C, Bondar AN. Diversity and sequence motifs of the bacterial SecA protein motor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183319. [PMID: 32335021 DOI: 10.1016/j.bbamem.2020.183319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/17/2020] [Accepted: 04/19/2020] [Indexed: 12/24/2022]
Abstract
SecA is an essential component of the Sec protein secretion pathway in bacteria. Secretory proteins targeted to the Sec pathway by their N-terminal signal peptide bind to SecA, which couples binding and hydrolysis of adenosine triphosphate with movement of the secretory protein across the membrane-embedded SecYEG protein translocon. The phylogenetic diversity of bacteria raises the important question as to whether the region of SecA where the pre-protein binds has conserved sequence features that might impact the reaction mechanism of SecA. To address this question we established a large data set of SecA protein sequences and implemented a protocol to cluster and analyze these sequences according to features of two of the SecA functional domains, the protein binding domain and the nucleotide-binding domain 1. We identify remarkable sequence diversity of the protein binding domain, but also conserved motifs with potential role in protein binding. The N-terminus of SecA has sequence motifs that could help anchor SecA to the membrane. The overall sequence length and net estimated charge of SecA sequences depend on the organism.
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Affiliation(s)
- Coral Del Val
- University of Granada, Departmrent of Computer Science and Artificial Intelligence, E-18071 Granada, Spain; University of Granada, Andalusian Research Institute in Data Science and Computational Intelligence, E-18071 Granada, Spain.
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, D-14195 Berlin, Germany.
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26
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De Geyter J, Portaliou AG, Srinivasu B, Krishnamurthy S, Economou A, Karamanou S. Trigger factor is a bona fide secretory pathway chaperone that interacts with SecB and the translocase. EMBO Rep 2020; 21:e49054. [PMID: 32307852 DOI: 10.15252/embr.201949054] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
Bacterial secretory preproteins are translocated across the inner membrane post-translationally by the SecYEG-SecA translocase. Mature domain features and signal peptides maintain preproteins in kinetically trapped, largely soluble, folding intermediates. Some aggregation-prone preproteins require chaperones, like trigger factor (TF) and SecB, for solubility and/or targeting. TF antagonizes the contribution of SecB to secretion by an unknown molecular mechanism. We reconstituted this interaction in vitro and studied targeting and secretion of the model preprotein pro-OmpA. TF and SecB display distinct, unsuspected roles in secretion. Tightly associating TF:pro-OmpA targets the translocase at SecA, but TF prevents pro-OmpA secretion. In solution, SecB binds TF:pro-OmpA with high affinity. At the membrane, when bound to the SecA C-tail, SecB increases TF and TF:pro-OmpA affinities for the translocase and allows pro-OmpA to resume translocation. Our data reveal that TF, a main cytoplasmic folding pathway chaperone, is also a bona fide post-translational secretory chaperone that directly interacts with both SecB and the translocase to mediate regulated protein secretion. Thus, TF links the cytoplasmic folding and secretion chaperone networks.
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Affiliation(s)
- Jozefien De Geyter
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Athina G Portaliou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Bindu Srinivasu
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
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27
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Rosen CB, Bayley H, Rodriguez-Larrea D. Free-energy landscapes of membrane co-translocational protein unfolding. Commun Biol 2020; 3:160. [PMID: 32246057 PMCID: PMC7125183 DOI: 10.1038/s42003-020-0841-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
Protein post-translational translocation is found at the plasma membrane of prokaryotes and protein import into organellae. Translocon structures are becoming available, however the dynamics of proteins during membrane translocation remain largely obscure. Here we study, at the single-molecule level, the folding landscape of a model protein while forced to translocate a transmembrane pore. We use a DNA tag to drive the protein into the α-hemolysin pore under a quantifiable force produced by an applied electric potential. Using a voltage-quench approach we find that the protein fluctuates between the native state and an intermediate in the translocation process at estimated forces as low as 1.9 pN. The fluctuation kinetics provide the free energy landscape as a function of force. We show that our stable, ≈15 kBT, substrate can be unfolded and translocated with physiological membrane potentials and that selective divalent cation binding may have a profound effect on the translocation kinetics.
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Affiliation(s)
- Christian Bech Rosen
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Novozymes A/S, Biologiens Vej 2, 2800, Kgs. Lyngby, Denmark
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - David Rodriguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology (UPV/EHU) Barrio Sarriena s/n, Leioa, 48940, Spain.
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28
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Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. Protein J 2020; 38:249-261. [PMID: 30972527 DOI: 10.1007/s10930-019-09830-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein translocation and membrane integration are fundamental, conserved processes. After or during ribosomal protein synthesis, precursor proteins containing an N-terminal signal sequence are directed to a conserved membrane protein complex called the Sec translocon (also known as the Sec translocase) in the endoplasmic reticulum membrane in eukaryotic cells, or the cytoplasmic membrane in bacteria. The Sec translocon comprises the Sec61 complex in eukaryotic cells, or the SecY complex in bacteria, and mediates translocation of substrate proteins across/into the membrane. Several membrane proteins are associated with the Sec translocon. In Escherichia coli, the membrane protein YidC functions not only as a chaperone for membrane protein biogenesis along with the Sec translocon, but also as an independent membrane protein insertase. To understand the molecular mechanism underlying these dynamic processes at the membrane, high-resolution structural models of these proteins are needed. This review focuses on X-ray crystallographic analyses of the Sec translocon and YidC and discusses the structural basis for protein translocation and integration.
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Affiliation(s)
- Tomoya Tsukazaki
- Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
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29
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Roussel G, White SH. Binding of SecA ATPase monomers and dimers to lipid vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183112. [PMID: 31676370 DOI: 10.1016/j.bbamem.2019.183112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 11/29/2022]
Abstract
The Escherichia coli SecA ATPase motor protein is essential for secretion of proteins through the SecYEG translocon into the periplasmic space. Its function relies upon interactions with the surrounding lipid bilayer as well as SecYEG translocon. That negatively charged lipids are required for bilayer binding has been known for >25 years, but little systematic quantitative data is available. We have carried out an extensive investigation of SecA partitioning into large unilamellar vesicles (LUV) using a wide range of lipid and electrolyte compositions, including the principal cytoplasmic salt of E. coli, potassium glutamate, which we have shown stabilizes SecA. The water-to-bilayer transfer free energy is about -7.5 kcal mol-1 for typical E. coli lipid compositions. Although it has been established that SecA is dimeric in the cytoplasm, we find that the most widely cited dimer form (PDB 1M6N) binds only weakly to LUVs formed from E. coli lipids.
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Affiliation(s)
- Guillaume Roussel
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697, United States of America
| | - Stephen H White
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697, United States of America.
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30
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Wang S, Jomaa A, Jaskolowski M, Yang CI, Ban N, Shan SO. The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA. Nat Struct Mol Biol 2019; 26:919-929. [PMID: 31570874 PMCID: PMC6858539 DOI: 10.1038/s41594-019-0297-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/12/2019] [Indexed: 11/16/2022]
Abstract
Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.
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Affiliation(s)
- Shuai Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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31
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Phan TH, Houben ENG. Bacterial secretion chaperones: the mycobacterial type VII case. FEMS Microbiol Lett 2019; 365:5067300. [PMID: 30085058 PMCID: PMC6109436 DOI: 10.1093/femsle/fny197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chaperones are central players in maintaining the proteostasis in all living cells. Besides highly conserved generic chaperones that assist protein folding and assembly in the cytosol, additional more specific chaperones have evolved to ensure the successful trafficking of proteins with extra-cytoplasmic locations. Associated with the distinctive secretion systems present in bacteria, different dedicated chaperones have been described that not only keep secretory proteins in a translocation competent state, but often are also involved in substrate targeting to the specific translocation channel. Recently, a new class of such chaperones has been identified that are involved in the specific recognition of substrates transported via the type VII secretion pathway in mycobacteria. In this minireview, we provide an overview of the different bacterial chaperones with a focus on their roles in protein secretion and will discuss in detail the roles of mycobacterial type VII secretion chaperones in substrate recognition and targeting.
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Affiliation(s)
- Trang H Phan
- Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit, Amsterdam, The Netherlands
| | - Edith N G Houben
- Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit, Amsterdam, The Netherlands
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32
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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.
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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
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33
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Koch S, Exterkate M, López CA, Patro M, Marrink SJ, Driessen AJM. Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183035. [PMID: 31394098 DOI: 10.1016/j.bbamem.2019.183035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022]
Abstract
Protein translocation across the bacterial cytoplasmic membrane is an essential process catalyzed by the Sec translocase, which in its minimal form consists of the protein-conducting channel SecYEG, and the motor ATPase SecA. SecA binds via its positively charged N-terminus to membranes containing anionic phospholipids, leading to a lipid-bound intermediate. This interaction induces a conformational change in SecA, resulting in a high-affinity association with SecYEG, which initiates protein translocation. Here, we examined the effect of anionic lipids on the SecA-SecYEG interaction in more detail, and discovered a second, yet unknown, anionic lipid-dependent event that stimulates protein translocation. Based on molecular dynamics simulations we identified an anionic lipid-enriched region in vicinity of the lateral gate of SecY. Here, the anionic lipid headgroup accesses the lateral gate, thereby stabilizing the pre-open state of the channel. The simulations suggest flip-flop movement of phospholipid along the lateral gate. Electrostatic contribution of the anionic phospholipids at the lateral gate may directly stabilize positively charged residues of the signal sequence of an incoming preprotein. Such a mechanism allows for the correct positioning of the entrant peptide, thereby providing a long-sought explanation for the role of anionic lipids in signal sequence folding during protein translocation.
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Affiliation(s)
- Sabrina Koch
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Marten Exterkate
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Cesar A López
- Department of Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM, USA.
| | - Megha Patro
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Siewert J Marrink
- Department of Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
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34
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Ahdash Z, Pyle E, Allen WJ, Corey RA, Collinson I, Politis A. HDX-MS reveals nucleotide-dependent, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon. eLife 2019; 8:47402. [PMID: 31290743 PMCID: PMC6639072 DOI: 10.7554/elife.47402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/09/2019] [Indexed: 01/28/2023] Open
Abstract
The bacterial Sec translocon is a multi-protein complex responsible for translocating diverse proteins across the plasma membrane. For post-translational protein translocation, the Sec-channel – SecYEG – associates with the motor protein SecA to mediate the ATP-dependent transport of pre-proteins across the membrane. Previously, a diffusional-based Brownian ratchet mechanism for protein secretion has been proposed; the structural dynamics required to facilitate this mechanism remain unknown. Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal striking nucleotide-dependent conformational changes in the Sec protein-channel from Escherichia coli. In addition to the ATP-dependent opening of SecY, reported previously, we observe a counteracting, and ATP-dependent, constriction of SecA around the pre-protein. ATP binding causes SecY to open and SecA to close; while, ADP produced by hydrolysis, has the opposite effect. This alternating behaviour could help impose the directionality of the Brownian ratchet for protein transport through the Sec machinery.
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Affiliation(s)
- Zainab Ahdash
- Department of Chemistry, King's College London, London, United Kingdom
| | - Euan Pyle
- Department of Chemistry, King's College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom
| | | | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, London, United Kingdom
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35
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van Winden VJC, Houben ENG, Braunstein M. Protein Export into and across the Atypical Diderm Cell Envelope of Mycobacteria. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0043-2018. [PMID: 31400094 PMCID: PMC10957183 DOI: 10.1128/microbiolspec.gpp3-0043-2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 02/07/2023] Open
Abstract
Mycobacteria, including the infamous pathogen Mycobacterium tuberculosis, are high-GC Gram-positive bacteria with a distinctive cell envelope. Although there is a typical inner membrane, the mycobacterial cell envelope is unusual in having its peptidoglycan layer connected to a polymer of arabinogalactan, which in turn is covalently attached to long-chain mycolic acids that help form a highly impermeable mycobacterial outer membrane. This complex double-membrane, or diderm, cell envelope imparts mycobacteria with unique requirements for protein export into and across the cell envelope for secretion into the extracellular environment. In this article, we review the four protein export pathways known to exist in mycobacteria: two conserved systems that exist in all types of bacteria (the Sec and Tat pathways) and two specialized systems that exist in mycobacteria, corynebacteria, and a subset of low-GC Gram-positive bacteria (the SecA2 and type VII secretion pathways). We describe the progress made over the past 15 years in understanding each of these mycobacterial export pathways, and we highlight the need for research to understand the specific steps of protein export across the mycobacterial outer membrane.
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Affiliation(s)
- Vincent J C van Winden
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Edith N G Houben
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines, and Systems, Vrije Universiteit, Amsterdam, The Netherlands
| | - Miriam Braunstein
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599
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36
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Collinson I. The Dynamic ATP-Driven Mechanism of Bacterial Protein Translocation and the Critical Role of Phospholipids. Front Microbiol 2019; 10:1217. [PMID: 31275252 PMCID: PMC6594350 DOI: 10.3389/fmicb.2019.01217] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022] Open
Abstract
Protein secretion from the cell cytoplasm to the outside is essential for life. Bacteria do so for a range of membrane associated and extracellular activities, including envelope biogenesis, surface adherence, pathogenicity, and degradation of noxious chemicals such as antibiotics. The major route for this process is via the ubiquitous Sec system, residing in the plasma membrane. Translocation across (secretion) or into (insertion) the membrane is driven through the translocon by the action of associated energy-transducing factors or translating ribosomes. This review seeks to summarize the recent advances in the dynamic mechanisms of protein transport and the critical role played by lipids in this process. The article will include an exploration of how lipids are actively involved in protein translocation and the consequences of these interactions for energy transduction from ATP hydrolysis and the trans-membrane proton-motive-force (PMF).
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Affiliation(s)
- Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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37
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Posttranslational Targeting of a Recombinant Protein Promotes Its Efficient Secretion into the Escherichia coli Periplasm. Appl Environ Microbiol 2019; 85:AEM.00671-19. [PMID: 31003980 PMCID: PMC6581171 DOI: 10.1128/aem.00671-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Many recombinant proteins that are produced in Escherichia coli have to be targeted to the periplasm to be functional. N-terminal signal peptides can be used to direct recombinant proteins to the membrane-embedded Sec translocon, a multiprotein complex that translocates proteins across the membrane into the periplasm. We have recently shown that the cotranslational targeting of the single-chain variable antibody fragment BL1 saturates the capacity of the Sec translocon leading to impaired translocation of secretory proteins and protein misfolding/aggregation in the cytoplasm. In turn, protein production yields and biomass formation were low. Here, we study the consequences of targeting BL1 posttranslationally to the Sec translocon. Notably, the posttranslational targeting of BL1 does not saturate the Sec translocon capacity, and both biomass formation and protein production yields are increased. Analyzing the proteome of cells producing the posttranslationally targeted BL1 indicates that the decreased synthesis of endogenous secretory and membrane proteins prevents a saturation of the Sec translocon capacity. Furthermore, in these cells, highly abundant chaperones and proteases can clear misfolded/aggregated proteins from the cytoplasm, thereby improving the fitness of these cells. Thus, the posttranslational targeting of BL1 enables its efficient production in the periplasm due to a favorable adaptation of the E. coli proteome. We envisage that our observations can be used to engineer E. coli for the improved production of recombinant secretory proteins.IMPORTANCE The bacterium Escherichia coli is widely used to produce recombinant proteins. To fold properly, many recombinant proteins have to be targeted to the E. coli periplasm, but so far the impact of the targeting pathway of a recombinant protein to the periplasm has not been extensively investigated. Here, we show that the targeting pathway of a recombinant antibody fragment has a tremendous impact on cell physiology, ultimately affecting protein production yields in the periplasm and biomass formation. This indicates that studying the targeting and secretion of proteins into the periplasm could be used to design strategies to improve recombinant protein production yields.
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Abstract
Membranes surrounding the biological cell and its internal compartments host proteins that catalyze chemical reactions essential for the functioning of the cell. Rather than being a passive structural matrix that holds membrane-embedded proteins in place, the membrane can largely shape the conformational energy landscape of membrane proteins and impact the energetics of their chemical reaction. Here, we highlight the challenges in understanding how lipids impact the conformational energy landscape of macromolecular membrane complexes whose functioning involves chemical reactions including proton transfer. We review here advances in our understanding of how chemical reactions occur at membrane interfaces gleaned with both theoretical and experimental advances using simple protein systems as guides. Our perspective is that of bridging experiments with theory to understand general physicochemical principles of membrane reactions, with a long term goal of furthering our understanding of the role of the lipids on the functioning of complex macromolecular assemblies at the membrane interface.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| | - M Joanne Lemieux
- University of Alberta , Department of Biochemistry, Membrane Protein Disease Research Group , Edmonton , Alberta T6G 2H7 , Canada
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39
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Corey RA, Ahdash Z, Shah A, Pyle E, Allen WJ, Fessl T, Lovett JE, Politis A, Collinson I. ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery. eLife 2019; 8:41803. [PMID: 30601115 PMCID: PMC6335059 DOI: 10.7554/elife.41803] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/01/2019] [Indexed: 11/13/2022] Open
Abstract
Transport of proteins across membranes is a fundamental process, achieved in every cell by the 'Sec' translocon. In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. Previously, we proposed a Brownian ratchet model for transport, whereby the free energy of ATP-turnover favours the directional diffusion of the polypeptide (Allen et al., 2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. A combination of molecular simulation with hydrogendeuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP-induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria.
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Affiliation(s)
- Robin A Corey
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Zainab Ahdash
- Department of Chemistry, King's College London, London, United Kingdom
| | - Anokhi Shah
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, Scotland, United Kingdom
| | - Euan Pyle
- Department of Chemistry, King's College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Tomas Fessl
- University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, Scotland, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, London, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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40
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Substrate Proteins Take Shape at an Improved Bacterial Translocon. J Bacteriol 2018; 201:JB.00618-18. [PMID: 30322856 DOI: 10.1128/jb.00618-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022] Open
Abstract
Characterization of Sec-dependent bacterial protein transport has often relied on an in vitro protein translocation system comprised in part of Escherichia coli inverted inner membrane vesicles or, more recently, purified SecYEG translocons reconstituted into liposomes using mostly a single substrate (proOmpA). A paper published in this issue (P. Bariya and L. Randall, J Bacteriol 201:e00493-18, 2019, https://doi.org/10.1128/JB.00493-18) finds that inclusion of SecA protein during SecYEG proteoliposome reconstitution dramatically improves the number of active translocons. This experimentally useful and intriguing result that may arise from SecA membrane integration properties is discussed here. Furthermore, determination of the rate-limiting transport step for nine different substrates implicates the mature region distal to the signal peptide in the observed rate constant differences, indicating that more nuanced transport models that respond to differences in protein sequence and structure are needed.
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Petrů M, Wideman J, Moore K, Alcock F, Palmer T, Doležal P. Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria. BMC Biol 2018; 16:141. [PMID: 30466434 PMCID: PMC6251230 DOI: 10.1186/s12915-018-0607-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases but have lost others. While BamA and YidC were integrated into general mitochondrial protein transport pathways (as Sam50 and Oxa1), the inner membrane TAT translocase, which uniquely transports folded proteins across the membrane, was retained sporadically across the eukaryote tree. RESULTS We have identified mitochondrial TAT machinery in diverse eukaryotic lineages and define three different types of eukaryote-encoded TatABC-derived machineries (TatAC, TatBC and TatC-only). Here, we investigate TatAC and TatC-only machineries, which have not been studied previously. We show that mitochondria-encoded TatAC of the jakobid Andalucia godoyi represent the minimal functional pathway capable of substituting for the Escherichia coli TatABC complex and can transport at least one substrate. However, selected TatC-only machineries, from multiple eukaryotic lineages, were not capable of supporting the translocation of this substrate across the bacterial membrane. Despite the multiple losses of the TatC gene from the mitochondrial genome, the gene was never transferred to the cell nucleus. Although the major constraint preventing nuclear transfer of mitochondrial TatC is likely its high hydrophobicity, we show that in chloroplasts, such transfer of TatC was made possible due to modifications of the first transmembrane domain. CONCLUSIONS At its origin, mitochondria inherited three inner membrane translocases Sec, TAT and Oxa1 (YidC) from its bacterial ancestor. Our work shows for the first time that mitochondrial TAT has likely retained its unique function of transporting folded proteins at least in those few eukaryotes with TatA and TatC subunits encoded in the mitochondrial genome. However, mitochondria, in contrast to chloroplasts, abandoned the machinery multiple times in evolution. The overall lower hydrophobicity of the Oxa1 protein was likely the main reason why this translocase was nearly universally retained in mitochondrial biogenesis pathways.
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Affiliation(s)
- Markéta Petrů
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jeremy Wideman
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany
- Department of Biochemistry and Molecular Biology, Dalhousie University, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Kristoffer Moore
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Průmyslová 595, 252 50, Vestec, Czech Republic.
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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.
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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
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43
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Knyazev DG, Kuttner R, Zimmermann M, Sobakinskaya E, Pohl P. Driving Forces of Translocation Through Bacterial Translocon SecYEG. J Membr Biol 2018; 251:329-343. [PMID: 29330604 PMCID: PMC6028853 DOI: 10.1007/s00232-017-0012-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022]
Abstract
This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage. Second we will discuss the power stroke and Brownian ratcheting models of substrate translocation and the role that the two models assign to the putative driving forces: (i) ATP (SecA) and GTP (ribosome) hydrolysis, (ii) interaction with accessory proteins, (iii) membrane partitioning and folding, (iv) proton motive force (PMF), and (v) entropic contributions. Our analysis underlines how important energized membranes are for unravelling the translocation mechanism in future experiments.
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Affiliation(s)
- Denis G Knyazev
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria.
| | - Roland Kuttner
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | - Mirjam Zimmermann
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | | | - Peter Pohl
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
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44
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Hiller S, Burmann BM. Chaperone-client complexes: A dynamic liaison. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 289:142-155. [PMID: 29544626 DOI: 10.1016/j.jmr.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/08/2023]
Abstract
Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University for Gothenburg, 405 30 Göteborg, Sweden.
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45
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Findik BT, Smith VF, Randall LL. Penetration into membrane of amino-terminal region of SecA when associated with SecYEG in active complexes. Protein Sci 2018; 27:681-691. [PMID: 29247569 DOI: 10.1002/pro.3362] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 11/12/2022]
Abstract
The general secretory (Sec) system of Escherichia coli translocates both periplasmic and outer membrane proteins through the cytoplasmic membrane. The pathway through the membrane is provided by a highly conserved translocon, which in E. coli comprises two heterotrimeric integral membrane complexes, SecY, SecE, and SecG (SecYEG), and SecD, SecF, and YajC (SecDF/YajC). SecA is an associated ATPase that is essential to the function of the Sec system. SecA plays two roles, it targets precursors to the translocon with the help of SecB and it provides energy via hydrolysis of ATP. SecA exists both free in the cytoplasm and integrally membrane associated. Here we describe details of association of the amino-terminal region of SecA with membrane. We use site-directed spin labelling and electron paramagnetic resonance spectroscopy to show that when SecA is co-assembled into lipids with SecYEG to yield highly active translocons, the N-terminal region of SecA penetrates the membrane and lies at the interface between the polar and the hydrophobic regions, parallel to the plane of the membrane at a depth of approximately 5 Å. When SecA is bound to SecYEG, preassembled into proteoliposomes, or nonspecifically bound to lipids in the absence of SecYEG, the N-terminal region penetrates more deeply (8 Å). Implications of partitioning of the SecA N-terminal region into lipids on the complex between SecB carrying a precursor and SecA are discussed.
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Affiliation(s)
- Bahar T Findik
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Virginia F Smith
- Chemistry Department, U.S. Naval Academy, Annapolis, Maryland, 21402
| | - Linda L Randall
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
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46
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Motions of the SecA protein motor bound to signal peptide: Insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:416-427. [DOI: 10.1016/j.bbamem.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/31/2022]
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47
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Crane JM, Randall LL. The Sec System: Protein Export in Escherichia coli. EcoSal Plus 2017; 7:10.1128/ecosalplus.ESP-0002-2017. [PMID: 29165233 PMCID: PMC5807066 DOI: 10.1128/ecosalplus.esp-0002-2017] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, proteins found in the periplasm or the outer membrane are exported from the cytoplasm by the general secretory, Sec, system before they acquire stably folded structure. This dynamic process involves intricate interactions among cytoplasmic and membrane proteins, both peripheral and integral, as well as lipids. In vivo, both ATP hydrolysis and proton motive force are required. Here, we review the Sec system from the inception of the field through early 2016, including biochemical, genetic, and structural data.
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Affiliation(s)
- Jennine M. Crane
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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48
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Anti-Salmonella Activity Modulation of Mastoparan V1-A Wasp Venom Toxin-Using Protease Inhibitors, and Its Efficient Production via an Escherichia coli Secretion System. Toxins (Basel) 2017; 9:toxins9100321. [PMID: 29027924 PMCID: PMC5666368 DOI: 10.3390/toxins9100321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 12/27/2022] Open
Abstract
A previous study highlighted that mastoparan V1 (MP-V1), a mastoparan from the venom of the social wasp Vespula vulgaris, is a potent antimicrobial peptide against Salmonella infection, which causes enteric diseases. However, there exist some limits for its practical application due to the loss of its activity in an increased bacterial density and the difficulty of its efficient production. In this study, we first modulated successfully the antimicrobial activity of synthetic MP-V1 against an increased Salmonella population using protease inhibitors, and developed an Escherichia coli secretion system efficiently producing active MP-V1. The protease inhibitors used, except pepstatin A, significantly increased the antimicrobial activity of the synthetic MP-V1 at minimum inhibitory concentrations (determined against 10⁶ cfu/mL of population) against an increased population (10⁸ cfu/mL) of three different Salmonella serotypes, Gallinarum, Typhimurium and Enteritidis. Meanwhile, the E. coli strain harboring OmpA SS::MP-V1 was identified to successfully secrete active MP-V1 into cell-free supernatant, whose antimicrobial activity disappeared in the increased population (10⁸ cfu/mL) of Salmonella Typhimurium recovered by adding a protease inhibitor cocktail. Therefore, it has been concluded that our challenge using the E. coli secretion system with the protease inhibitors is an attractive strategy for practical application of peptide toxins, such as MP-V1.
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49
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Banerjee T, Zheng Z, Abolafia J, Harper S, Oliver D. The SecA protein deeply penetrates into the SecYEG channel during insertion, contacting most channel transmembrane helices and periplasmic regions. J Biol Chem 2017; 292:19693-19707. [PMID: 28986446 DOI: 10.1074/jbc.ra117.000130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 11/06/2022] Open
Abstract
The bacterial Sec-dependent system is the major protein-biogenic pathway for protein secretion across the cytoplasmic membrane or insertion of integral membrane proteins into the phospholipid bilayer. The mechanism of SecA-driven protein transport across the SecYEG channel complex has remained controversial with conflicting claims from biochemical and structural studies regarding the depth and extent of SecA insertion into SecYEG during ongoing protein transport. Here we utilized site-specific in vivo photo-crosslinking to thoroughly map SecY regions that are in contact with SecA during its insertion cycle. An arabinose-inducible, rapidly folding OmpA-GFP chimera was utilized to jam the SecYEG channels with an arrested substrate protein to "freeze" them in their SecA-inserted state. Examination of 117 sites distributed throughout SecY indicated that SecA not only interacts extensively with the cytosolic regions of SecY as shown previously, but it also interacts with most of the transmembrane helices and periplasmic regions of SecY, with a clustering of interaction sights around the lateral gate and pore ring regions. Our observations support previous reports of SecA membrane insertion during in vitro protein transport as well as those documenting the membrane penetration properties of this protein. They suggest that one or more SecA regions transiently integrate into the heart of the SecY channel complex to span the membrane to promote the protein transport cycle. These findings indicate that high-resolution structural information about the membrane-inserted state of SecA is still lacking and will be critical for elucidating the bacterial protein transport mechanism.
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Affiliation(s)
- Tithi Banerjee
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Zeliang Zheng
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Jane Abolafia
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Shelby Harper
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Donald Oliver
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
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50
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Wang S, Yang CI, Shan SO. SecA mediates cotranslational targeting and translocation of an inner membrane protein. J Cell Biol 2017; 216:3639-3653. [PMID: 28928132 PMCID: PMC5674894 DOI: 10.1083/jcb.201704036] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/17/2017] [Accepted: 08/02/2017] [Indexed: 12/02/2022] Open
Abstract
Proteins are thought to be delivered to the bacterial plasma membrane cotranslationally by signal recognition particle or posttranslationally by SecA. Wang et al. identify a new membrane protein–targeting pathway in bacteria in which SecA cotranslationally recognizes and targets the inner membrane protein RodZ, which harbors an internal transmembrane domain. Protein targeting to the bacterial plasma membrane was generally thought to occur via two major pathways: cotranslational targeting by signal recognition particle (SRP) and posttranslational targeting by SecA and SecB. Recently, SecA was found to also bind ribosomes near the nascent polypeptide exit tunnel, but the function of this SecA–ribosome contact remains unclear. In this study, we show that SecA cotranslationally recognizes the nascent chain of an inner membrane protein, RodZ, with high affinity and specificity. In vitro reconstitution and in vivo targeting assays show that SecA is necessary and sufficient to direct the targeting and translocation of RodZ to the bacterial plasma membrane in an obligatorily cotranslational mechanism. Sequence elements upstream and downstream of the RodZ transmembrane domain dictate nascent polypeptide selection by SecA instead of the SRP machinery. These findings identify a new route for the targeting of inner membrane proteins in bacteria and highlight the diversity of targeting pathways that enables an organism to accommodate diverse nascent proteins.
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Affiliation(s)
- Shuai Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
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