1
|
Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
Collapse
Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| |
Collapse
|
2
|
Northrop J, Oliver DB, Mukerji I. Förster Resonance Energy Transfer Mapping: A New Methodology to Elucidate Global Structural Features. J Vis Exp 2022:10.3791/63433. [PMID: 35377367 PMCID: PMC10639101 DOI: 10.3791/63433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2023] Open
Abstract
Förster resonance energy transfer (FRET) is an established fluorescence-based method used to successfully measure distances in and between biomolecules in vitro as well as within cells. In FRET, the efficiency of energy transfer, measured by changes in fluorescence intensity or lifetime, relates to the distance between two fluorescent molecules or labels. Determination of dynamics and conformational changes from the distances are just some examples of applications of this method to biological systems. Under certain conditions, this methodology can add to and enhance existing X-ray crystal structures by providing information regarding dynamics, flexibility, and adaptation to binding surfaces. We describe the use of FRET and associated distance determinations to elucidate structural properties, through the identification of a binding site or the orientations of dimer subunits. Through judicious choice of labeling sites, and often employment of multiple labeling strategies, we have successfully applied these mapping methods to determine global structural properties in a protein-DNA complex and the SecA-SecYEG protein translocation system. In the SecA-SecYEG system, we have used FRET mapping methods to identify the preprotein-binding site and determine the local conformation of the bound signal sequence region. This study outlines the steps for performing FRET mapping studies, including identification of appropriate labeling sites, discussion of possible labels including non-native amino acid residues, labeling procedures, how to perform measurements, and interpreting the data.
Collapse
Affiliation(s)
- Jack Northrop
- Molecular Biology and Biochemistry Department, Wesleyan University
| | - Donald B Oliver
- Molecular Biology and Biochemistry Department, Wesleyan University; Molecular Biophysics Program, Wesleyan University
| | - Ishita Mukerji
- Molecular Biology and Biochemistry Department, Wesleyan University; Molecular Biophysics Program, Wesleyan University;
| |
Collapse
|
3
|
Komarudin AG, Driessen AJM. SecA-Mediated Protein Translocation through the SecYEG Channel. Microbiol Spectr 2019; 7:10.1128/microbiolspec.psib-0028-2019. [PMID: 31373268 PMCID: PMC10957188 DOI: 10.1128/microbiolspec.psib-0028-2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 01/02/2023] Open
Abstract
In bacteria, the Sec translocase mediates the translocation of proteins into and across the cytoplasmic membrane. It consists of a protein conducting channel SecYEG, the ATP-dependent motor SecA, and the accessory SecDF complex. Here we discuss the function and structure of the Sec translocase.
Collapse
Affiliation(s)
- Amalina Ghaisani Komarudin
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and the Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and the Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Lahiri S, Li Y, Hingorani MM, Mukerji I. MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination. Biophys J 2018; 115:2087-2101. [PMID: 30467025 DOI: 10.1016/j.bpj.2018.10.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023] Open
Abstract
In many organisms, MutSγ plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3' overhangs, single-stranded (ss) forks, and the displacement loop with nanomolar affinity. The weakest binding affinities are detected for an intact duplex and open-junction construct. Similar to the human protein, Sc Msh4-Msh5 exhibits the highest affinity for the HJ with a Kd < 0.4 nM in solution. Energy-transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing an ss end. Upon binding, Sc Msh4-Msh5 displaces the ss away from the duplex in most of the ss-containing intermediates, potentially enabling the binding of RPA and other proteins. In the case of the junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding, Msh4-Msh5 stacks an open-junction construct to the same extent as the standard junction. Stabilization of the junction in the stacked conformation is generally refractory to branch migration, which is consistent with a potential role for MutSγ to stabilize HJs and prevent branch migration until resolution by MutLγ. The different binding modalities observed suggest that Msh4-Msh5 not only binds to and stabilizes stacked junctions but also participates in meiotic recombination before junction formation through the stabilization of single-end invasion intermediates.
Collapse
Affiliation(s)
- Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Yan Li
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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]
|