1
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Needs HI, Glover E, Pereira GC, Witt A, Hübner W, Dodding MP, Henley JM, Collinson I. Rescue of mitochondrial import failure by intercellular organellar transfer. Nat Commun 2024; 15:988. [PMID: 38307874 PMCID: PMC10837123 DOI: 10.1038/s41467-024-45283-2] [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: 02/01/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells, composed mostly of nuclear-encoded proteins imported from the cytosol. Thus, problems with the import machinery will disrupt their regenerative capacity and the cell's energy supplies - particularly troublesome for energy-demanding cells of nervous tissue and muscle. Unsurprisingly then, import breakdown is implicated in disease. Here, we explore the consequences of import failure in mammalian cells; wherein, blocking the import machinery impacts mitochondrial ultra-structure and dynamics, but, surprisingly, does not affect import. Our data are consistent with a response involving intercellular mitochondrial transport via tunnelling nanotubes to import healthy mitochondria and jettison those with blocked import sites. These observations support the existence of a widespread mechanism for the rescue of mitochondrial dysfunction.
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Affiliation(s)
- Hope I Needs
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Emily Glover
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Gonçalo C Pereira
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
- Nanna Therapeutics, Merrifield Centre, Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Alina Witt
- Fakultät für Physik, Universität Bielefeld, Bielefeld, Postfach 100131 D-33501, Germany
| | - Wolfgang Hübner
- Fakultät für Physik, Universität Bielefeld, Bielefeld, Postfach 100131 D-33501, Germany
| | - Mark P Dodding
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jeremy M Henley
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
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2
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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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Garrett SR, Mietrach N, Deme J, Bitzer A, Yang Y, Ulhuq FR, Kretschmer D, Heilbronner S, Smith TK, Lea SM, Palmer T. A type VII-secreted lipase toxin with reverse domain arrangement. Nat Commun 2023; 14:8438. [PMID: 38114483 PMCID: PMC10730906 DOI: 10.1038/s41467-023-44221-y] [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: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.
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Affiliation(s)
- Stephen R Garrett
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Nicole Mietrach
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Justin Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Alina Bitzer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Yaping Yang
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Fatima R Ulhuq
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Terry K Smith
- School of Biology, Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, United Kingdom
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Tracy Palmer
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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4
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Zhou W, Hao B, Bricker TM, Theg SM. A real-time analysis of protein transport via the twin arginine translocation pathway in response to different components of the protonmotive force. J Biol Chem 2023; 299:105286. [PMID: 37742925 PMCID: PMC10641609 DOI: 10.1016/j.jbc.2023.105286] [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: 07/17/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
The twin arginine translocation (Tat) pathway transports folded protein across the cytoplasmic membrane in bacteria, archaea, and across the thylakoid membrane in plants as well as the inner membrane in some mitochondria. In plant chloroplasts, the Tat pathway utilizes the protonmotive force (PMF) to drive protein translocation. However, in bacteria, it has been shown that Tat transport depends only on the transmembrane electrical potential (Δψ) component of PMF in vitro. To investigate the comprehensive PMF requirement in Escherichia coli, we have developed the first real-time assay to monitor Tat transport utilizing the NanoLuc Binary Technology in E. coli spheroplasts. This luminescence assay allows for continuous monitoring of Tat transport with high-resolution, making it possible to observe subtle changes in transport in response to different treatments. By applying the NanoLuc assay, we report that, under acidic conditions (pH = 6.3), ΔpH, in addition to Δψ, contributes energetically to Tat transport in vivo in E. coli spheroplasts. These results provide novel insight into the mechanism of energy utilization by the Tat pathway.
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Affiliation(s)
- Wenjie Zhou
- Department of Plant Biology, University of California, Davis, California, USA
| | - Binhan Hao
- Department of Plant Biology, University of California, Davis, California, USA
| | - Terry M Bricker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Steven M Theg
- Department of Plant Biology, University of California, Davis, California, USA.
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5
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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6
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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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7
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I Needs H, Lorriman JS, Pereira GC, Henley JM, Collinson I. The MitoLuc Assay System for Accurate Real-Time Monitoring of Mitochondrial Protein Import within Mammalian Cells. J Mol Biol 2023; 435:168129. [PMID: 37105499 DOI: 10.1016/j.jmb.2023.168129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023]
Abstract
Mitochondrial protein import is critical for organelle biogenesis, bioenergetic function and health. The mechanism of which is poorly understood, particularly of the mammalian system. To address this problem we have established an assay to quantitatively monitor mitochondrial import inside mammalian cells. The reporting is based on a split luciferase, whereby the large fragment is segregated in the mitochondrial matrix and the small complementary fragment is fused to the C-terminus of a purified recombinant precursor protein destined for import. Following import the complementary fragments combine to form an active luciferase-providing a sensitive, accurate and continuous measure of protein import. This advance allows detailed mechanistic examination of the transport process in live cells, including the analysis of import breakdown associated with disease, and high-throughput drug screening. Furthermore, the set-up has the potential to be adapted for the analysis of alternative transport systems within different cell types, and multicellular model organisms.
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Affiliation(s)
- Hope I Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - James S Lorriman
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Jeremy M Henley
- 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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8
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Abstract
Secretory proteins are cotranslationally or posttranslationally translocated across lipid membranes via a protein-conducting channel named SecY in prokaryotes and Sec61 in eukaryotes. The vast majority of secretory proteins in bacteria are driven through the channel posttranslationally by SecA, a highly conserved ATPase. How a polypeptide chain is moved by SecA through the SecY channel is poorly understood. Here, we report electron cryomicroscopy structures of the active SecA-SecY translocon with a polypeptide substrate. The substrate is captured in different translocation states when clamped by SecA with different nucleotides. Upon binding of an ATP analog, SecA undergoes global conformational changes to push the polypeptide substrate toward the channel in a way similar to how the RecA-like helicases translocate their nucleic acid substrates. The movements of the polypeptide substrates in the SecA-SecY translocon share a similar structural basis to those in the ribosome-SecY complex during cotranslational translocation.
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9
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Watkins DW, Williams SL, Collinson I. A bacterial secretosome for regulated envelope biogenesis and quality control? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36260397 DOI: 10.1099/mic.0.001255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Gram-negative bacterial envelope is the first line of defence against environmental stress and antibiotics. Therefore, its biogenesis is of considerable fundamental interest, as well as a challenge to address the growing problem of antimicrobial resistance. All bacterial proteins are synthesised in the cytosol, so inner- and outer-membrane proteins, and periplasmic residents have to be transported to their final destinations via specialised protein machinery. The Sec translocon, a ubiquitous integral inner-membrane (IM) complex, is key to this process as the major gateway for protein transit from the cytosol to the cell envelope; this can be achieved during their translation, or afterwards. Proteins need to be directed into the inner-membrane (usually co-translational), otherwise SecA utilises ATP and the proton-motive-force (PMF) to drive proteins across the membrane post-translationally. These proteins are then picked up by chaperones for folding in the periplasm, or delivered to the β-barrel assembly machinery (BAM) for incorporation into the outer-membrane. The core hetero-trimeric SecYEG-complex forms the hub for an extensive network of interactions that regulate protein delivery and quality control. Here, we conduct a biochemical exploration of this 'secretosome' -a very large, versatile and inter-changeable assembly with the Sec-translocon at its core; featuring interactions that facilitate secretion (SecDF), inner- and outer-membrane protein insertion (respectively, YidC and BAM), protein folding and quality control (e.g. PpiD, YfgM and FtsH). We propose the dynamic interplay amongst these, and other factors, act to ensure efficient envelope biogenesis, regulated to accommodate the requirements of cell elongation and division. We believe this organisation is critical for cell wall biogenesis and remodelling and thus its perturbation could be a means for the development of anti-microbials.
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Affiliation(s)
- Daniel W Watkins
- School of Biochemistry, University of Bristol, BS8 1TD, UK.,Present address: CytoSeek, Science Creates Old Market, Midland Road, Bristol, BS20JZ, UK
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, BS8 1TD, UK
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10
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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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11
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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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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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Recent Advancements in Tracking Bacterial Effector Protein Translocation. Microorganisms 2022; 10:microorganisms10020260. [PMID: 35208715 PMCID: PMC8876096 DOI: 10.3390/microorganisms10020260] [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: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria-host interactions are characterized by the delivery of bacterial virulence factors, i.e., effectors, into host cells where they counteract host immunity and exploit host responses allowing bacterial survival and spreading. These effectors are translocated into host cells by means of dedicated secretion systems such as the type 3 secretion system (T3SS). A comprehensive understanding of effector translocation in a spatio-temporal manner is of critical importance to gain insights into an effector’s mode of action. Various approaches have been developed to understand timing and order of effector translocation, quantities of translocated effectors and their subcellular localization upon translocation into host cells. Recently, the existing toolset has been expanded by newly developed state-of-the art methods to monitor bacterial effector translocation and dynamics. In this review, we elaborate on reported methods and discuss recent advances and shortcomings in this area of tracking bacterial effector translocation.
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14
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Cover TL. Tracking bacterial effector protein delivery into host cells. Mol Microbiol 2021; 116:724-728. [PMID: 34250669 DOI: 10.1111/mmi.14784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Bacterial Type IV secretion systems (T4SSs) are a functionally heterogeneous group of nanomachines that can deliver substrates into a wide range of target cells. The Helicobacter pylori Cag T4SS has an important role in the pathogenesis of gastric cancer. CagA, the only effector protein known to be secreted by the H. pylori Cag T4SS, enters human gastric cells and causes alterations in intracellular signaling that are linked to cancer pathogenesis. Understanding the molecular mechanisms by which CagA is delivered into gastric cells has been hindered by the lack of robust methods for monitoring this process. A publication in this issue of Molecular Microbiology describes a split luciferase assay for monitoring T4SS-mediated translocation of CagA into host cells. The use of this translocation reporter allowed the quantification of CagA translocation in real-time assays, thereby facilitating the analysis of the kinetics of CagA delivery. This system also allowed the tracking of several types of CagA fusion proteins and confirmed that protein unfolding is important for secretion by the Cag T4SS. This commentary discusses T4SS-dependent delivery of H. pylori CagA into host cells and the use of the split luciferase system for monitoring bacterial protein secretion and delivery into target cells.
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Affiliation(s)
- Timothy L Cover
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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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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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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