1
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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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2
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Bogdanov M. Preparation of Uniformly Oriented Inverted Inner (Cytoplasmic) Membrane Vesicles from Gram-Negative Bacterial Cells. Methods Mol Biol 2024; 2715:159-180. [PMID: 37930527 PMCID: PMC10724710 DOI: 10.1007/978-1-0716-3445-5_10] [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] [Indexed: 11/07/2023]
Abstract
The complex double-membrane organization of the envelope in Gram-negative bacteria places unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on cytoplasm facing leaflet of cytoplasmic (inner) membrane (IM), across IM and between IM and outer membrane (OM). Uniformly oriented inside-out (ISO) vesicles became functional requisite for many biochemical reconstitution functional assays, vectorial proteomics, and vectorial lipidomics. Due to these demands, it is necessary to develop simple and reliable approaches for preparation of uniformly oriented IM membrane vesicles and validation of their sidedness. The uniformly ISO oriented membrane vesicles which have the cytoplasmic face of the membrane on the outside and the periplasmic side facing the sealed lumen can be obtained following intact cell disruption by a single passage through a French pressure cell (French press) at desired total pressure. Although high-pressure lysis leads to the formation of mostly inverted membrane vesicles (designated and abbreviated usually as ISO vesicles, everted or inverted membrane vesicles (IMVs)), inconclusive results are quite common. This uncertainty is due mainly by applying a different pressures, using either intact cells or spheroplasts and presence or absence of sucrose during rupture procedure. Many E. coli envelope fractionation techniques result in heterogeneity among isolated IM membrane vesicles. In part, this is due to difficulties in simple validation of sidedness of oriented membrane preparations of unknown sidedness. The sidedness of various preparations of membrane vesicles can be inferred from the orientation of residing uniformly oriented transmembrane protein. We outline the method in which the orientation of membrane vesicles can be verified by mapping of uniform or mixed topologies of essential protein E. coli protein leader peptidase (LepB) by advanced SCAM™. Although the protocol discussed in this chapter has been developed using Escherichia coli and Yersinia pseudotuberculosis, it can be directly adapted to other Gram-negative bacteria including pathogens.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry & Molecular Biology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA.
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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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Atomic Force Microscopy Reveals Complexity Underlying General Secretory System Activity. Int J Mol Sci 2022; 24:ijms24010055. [PMID: 36613499 PMCID: PMC9820662 DOI: 10.3390/ijms24010055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
The translocation of specific polypeptide chains across membranes is an essential activity for all life forms. The main components of the general secretory (Sec) system of E. coli include integral membrane translocon SecYEG, peripheral ATPase SecA, and SecDF, an ancillary complex that enhances polypeptide secretion by coupling translocation to proton motive force. Atomic force microscopy (AFM), a single-molecule imaging technique, is well suited to unmask complex, asynchronous molecular activities of membrane-associated proteins including those comprising the Sec apparatus. Using AFM, the dynamic structure of membrane-external protein topography of Sec system components can be directly visualized with high spatial-temporal precision. This mini-review is focused on AFM imaging of the Sec system in near-native fluid conditions where activity can be maintained and biochemically verified. Angstrom-scale conformational changes of SecYEG are reported on 100 ms timescales in fluid lipid bilayers. The association of SecA with SecYEG, forming membrane-bound SecYEG/SecA translocases, is directly visualized. Recent work showing topographical aspects of the translocation process that vary with precursor species is also discussed. The data suggests that the Sec system does not employ a single translocation mechanism. We posit that differences in the spatial frequency distribution of hydrophobic content within precursor sequences may be a determining factor in mechanism selection. Precise AFM investigations of active translocases are poised to advance our currently vague understanding of the complicated macromolecular movements underlying protein export across membranes.
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5
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The conformations and basal conformational dynamics of translocation factor SecDF vary with translocon SecYEG interaction. J Biol Chem 2022; 298:102412. [PMID: 36007614 PMCID: PMC9508474 DOI: 10.1016/j.jbc.2022.102412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
The general secretory, or Sec, system is a primary protein export pathway from the cytosol of Escherichia coli and all eubacteria. Integral membrane protein complex SecDF is a translocation factor that enhances polypeptide secretion, which is driven by the Sec translocase, consisting of translocon SecYEG and ATPase SecA. SecDF is thought to utilize a proton gradient to effectively pull precursor proteins from the cytoplasm into the periplasm. Working models have been developed to describe the structure and function of SecDF, but important mechanistic questions remain unanswered. Atomic force microscopy (AFM) is a powerful technique for studying the dynamics of single-molecule systems including membrane proteins in near-native conditions. The sharp tip of the AFM provides direct access to membrane-external protein conformations. Here, we acquired AFM images and kymographs (∼100 ms resolution) to visualize SecDF protrusions in near-native supported lipid bilayers and compared the experimental data to simulated AFM images based on static structures. When studied in isolation, SecDF exhibited a stable and compact conformation close to the lipid bilayer surface, indicative of a resting state. Interestingly, upon SecYEG introduction, we observed changes in both SecDF conformation and conformational dynamics. The population of periplasmic protrusions corresponding to an intermediate form of SecDF, which is thought to be active in precursor protein handling, increased >9-fold. In conjunction, our dynamics measurements revealed an enhancement in the transition rate between distinct SecDF conformations when the translocon was present. Together, this work provides a novel vista of basal-level SecDF conformational dynamics in near-native conditions.
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6
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Gupta R, Toptygin D, Kaiser CM. Synchronized Real-time Measurement of Sec-mediated Protein Translocation. Bio Protoc 2021; 11:e4129. [PMID: 34541047 DOI: 10.21769/bioprotoc.4129] [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: 12/22/2020] [Revised: 05/09/2021] [Accepted: 05/27/2021] [Indexed: 11/02/2022] Open
Abstract
The Sec translocon, consisting of a heterotrimeric transmembrane channel (SecYEG) and an associated ATPase (SecA), catalyzes the export of unfolded proteins from the cytosol in bacteria. Kinetically resolving protein translocation at high resolution yields mechanistic insight into the process. Translocation is typically followed by measuring the protection of proteins transported into lipid vesicles, which only allows visualization of translocation after it has already been completed and limits time resolution. Here, we describe the implementation of an assay for measuring translocation in real-time. By priming the reconstituted translocon with suitably engineered substrate proteins, the kinetics of the actual translocation process can be resolved at high resolution. To analyze translocation kinetics, we developed a detailed kinetic model of the process that includes on-pathway and off-pathway processes. Together, this experimental protocol and model permit detailed mechanistic analyses of Sec-dependent protein translocation. Graphic abstract: Synchronized real-time measurements, combined with a detailed kinetic model, enable a mechanistic analysis of protein transport.
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Affiliation(s)
- Riti Gupta
- CMDB Graduate Program, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA
| | - Dmitri Toptygin
- Department of Biology, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA
| | - Christian M Kaiser
- Department of Biology, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA.,Department of Biophysics, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA
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7
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Davis MM, Lamichhane R, Bruce BD. Elucidating Protein Translocon Dynamics with Single-Molecule Precision. Trends Cell Biol 2021; 31:569-583. [PMID: 33865650 DOI: 10.1016/j.tcb.2021.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/28/2023]
Abstract
Translocons are protein assemblies that facilitate the targeting and transport of proteins into and across biological membranes. Our understanding of these systems has been advanced using genetics, biochemistry, and structural biology. Despite these classic advances, until recently we have still largely lacked a detailed understanding of how translocons recognize and facilitate protein translocation. With the advent and improvements of cryogenic electron microscopy (cryo-EM) single-particle analysis and single-molecule fluorescence microscopy, the details of how translocons function are finally emerging. Here, we introduce these methods and evaluate their importance in understanding translocon structure, function, and dynamics.
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Affiliation(s)
- Madeline M Davis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Graduate Program in Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
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8
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Rauch J, Barton J, Kwiatkowski M, Wunderlich M, Steffen P, Moderzynski K, Papp S, Höhn K, Schwanke H, Witt S, Richardt U, Mehlhoop U, Schlüter H, Pianka V, Fleischer B, Tappe D, Osterloh A. GroEL is an immunodominant surface-exposed antigen of Rickettsia typhi. PLoS One 2021; 16:e0253084. [PMID: 34111210 PMCID: PMC8191997 DOI: 10.1371/journal.pone.0253084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/28/2021] [Indexed: 11/26/2022] Open
Abstract
Rickettsioses are neglected and emerging potentially fatal febrile diseases that are caused by obligate intracellular bacteria, rickettsiae. Rickettsia (R.) typhi and R. prowazekii constitute the typhus group (TG) of rickettsiae and are the causative agents of endemic and epidemic typhus, respectively. We recently generated a monoclonal antibody (BNI52) against R. typhi. Characterization of BNI52 revealed that it specifically recognizes TG rickettsiae but not the members of the spotted fever group (SFG) rickettsiae. We further show that BNI52 binds to protein fragments of ±30 kDa that are exposed on the bacterial surface and also present in the periplasmic space. These protein fragments apparently derive from the cytosolic GroEL protein of R. typhi and are also recognized by antibodies in the sera from patients and infected mice. Furthermore, BNI52 opsonizes the bacteria for the uptake by antigen presenting cells (APC), indicating a contribution of GroEL-specific antibodies to protective immunity. Finally, it is interesting that the GroEL protein belongs to 32 proteins that are differentially downregulated by R. typhi after passage through immunodeficient BALB/c CB17 SCID mice. This could be a hint that the rickettsia GroEL protein may have immunomodulatory properties as shown for the homologous protein from several other bacteria, too. Overall, the results of this study provide evidence that GroEL represents an immunodominant antigen of TG rickettsiae that is recognized by the humoral immune response against these pathogens and that may be interesting as a vaccine candidate. Apart from that, the BNI52 antibody represents a new tool for specific detection of TG rickettsiae in various diagnostic and experimental setups.
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Affiliation(s)
- Jessica Rauch
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Barton
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Malte Wunderlich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Pascal Steffen
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Stefanie Papp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Katharina Höhn
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hella Schwanke
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Susanne Witt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ulricke Richardt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ute Mehlhoop
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Verena Pianka
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Dennis Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anke Osterloh
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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9
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Chattrakun K, Schaefer KG, Chandler LS, Marsh BP, King GM. Atomic Force Microscopy Reveals Membrane Protein Activity at the Single Molecule Level. Methods Mol Biol 2021; 2302:81-99. [PMID: 33877624 DOI: 10.1007/978-1-0716-1394-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Atomic force microscopy has emerged as a valuable complementary technique in membrane structural biology. The apparatus is capable of probing individual membrane proteins in fluid lipid bilayers at room temperature with spatial resolution at the molecular length scale. Protein conformational dynamics are accessible over a range of biologically relevant timescales. This chapter presents methodology our group uses to achieve robust AFM image data of the General Secretory system, the primary pathway of protein export from the cytoplasm to the periplasm of E. coli. Emphasis is given to measuring and maintaining biochemical activity and to objective AFM image processing methods. For example, the biochemical assays can be used to determine chemomechanical coupling efficiency of surface adsorbed translocases. The Hessian blob algorithm and its extension to nonlocalized linear features, the line detection algorithm, provide automated feature delineations. Many of the methods discussed here can be applied to other membrane protein systems of interest.
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Affiliation(s)
- Kanokporn Chattrakun
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Katherine G Schaefer
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Lucas S Chandler
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Brendan P Marsh
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA. .,Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, USA.
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10
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Refined measurement of SecA-driven protein secretion reveals that translocation is indirectly coupled to ATP turnover. Proc Natl Acad Sci U S A 2020; 117:31808-31816. [PMID: 33257538 DOI: 10.1073/pnas.2010906117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The universally conserved Sec system is the primary method cells utilize to transport proteins across membranes. Until recently, measuring the activity-a prerequisite for understanding how biological systems work-has been limited to discontinuous protein transport assays with poor time resolution or reported by large, nonnatural tags that perturb the process. The development of an assay based on a split superbright luciferase (NanoLuc) changed this. Here, we exploit this technology to unpick the steps that constitute posttranslational protein transport in bacteria. Under the conditions deployed, the transport of a model preprotein substrate (proSpy) occurs at 200 amino acids (aa) per minute, with SecA able to dissociate and rebind during transport. Prior to that, there is no evidence for a distinct, rate-limiting initiation event. Kinetic modeling suggests that SecA-driven transport activity is best described by a series of large (∼30 aa) steps, each coupled to hundreds of ATP hydrolysis events. The features we describe are consistent with a nondeterministic motor mechanism, such as a Brownian ratchet.
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11
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Comparison of Single and Multiple Turnovers of SecYEG in Escherichia coli. J Bacteriol 2020; 202:JB.00462-20. [PMID: 32989086 DOI: 10.1128/jb.00462-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/18/2020] [Indexed: 01/01/2023] Open
Abstract
Precursor proteins are translocated across the cytoplasmic membrane in Escherichia coli by the general secretory, or Sec, pathway. The main components of the pathway are the integral membrane heterotrimeric SecYEG complex and the peripheral membrane ATPase, SecA. In this study, we have applied an in vitro assay using inverted cytoplasmic membrane vesicles to investigate the complex cycle that leads to translocation. We compared the apparent rate constants for nine precursors under two experimental conditions, single turnover and multiple turnovers. For each precursor, the rate constant for a single turnover was higher than for multiple turnovers, indicating that a different step limits the rate under the two conditions. We conclude that the rate-limiting step for a single turnover is an early step in the initial phase of transit through the channel, whereas the rate of multiple turnovers is limited by the resetting of the translocon. The presence of the chaperone SecB during multiple turnovers increased the maximal amplitude translocated for the three precursor species tested, pGBP, pPhoA, and proOmpA, and also increased the apparent rate constants for both pGBP and pPhoA. The rate constant for proOmpA was decreased by the presence of SecB.IMPORTANCE Vastly different experimental techniques and conditions have been used to study export in E. coli We demonstrated that altering experimental conditions can change the step that is observed during study. Investigators should consider specific experimental conditions when comparing data from different laboratories, as well as when comparing data from different experiments within a laboratory. We have shown that each precursor species has inherent properties that determine the translocation rate; thus generalizations from studies of a single species must be made with caution. A summary of advantages and disadvantages in use of nine precursors is presented.
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12
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King GM, Kosztin I. Towards a Quantitative Understanding of Protein-Lipid Bilayer Interactions at the Single Molecule Level: Opportunities and Challenges. J Membr Biol 2020; 254:17-28. [PMID: 33196888 DOI: 10.1007/s00232-020-00151-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
Protein-lipid interfaces are among the most fundamental in biology. Yet applying conventional techniques to study the biophysical attributes of these systems is challenging and has left many unknowns. For example, what is the kinetic pathway and energy landscape experienced by a polypeptide chain when in close proximity to a fluid lipid bilayer? Here we review the experimental and theoretical progress we have made in addressing this question from a single molecule perspective. Some remaining impediments are also discussed.
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Affiliation(s)
- Gavin M King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA.
| | - Ioan Kosztin
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA.
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13
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Roussel G, White SH. The SecA ATPase motor protein binds to Escherichia coli liposomes only as monomers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183358. [PMID: 32416191 DOI: 10.1016/j.bbamem.2020.183358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
Abstract
The essential SecA motor ATPase acts in concert with the SecYEG translocon to secrete proteins into the periplasmic space of Escherichia coli. In aqueous solutions, SecA exists largely as dimers, but the oligomeric state on membranes is less certain. Crystallographic studies have suggested several possible solution dimeric states, but its oligomeric state when bound to membranes directly or indirectly via the translocon is controversial. We have shown using disulfide crosslinking that the principal solution dimer, corresponding to a crystallographic dimer (PDB 1M6N), binds only weakly to large unilamellar vesicles (LUV) formed from E. coli lipids. We report here that other soluble crosslinked crystallographic dimers also bind weakly, if at all, to LUV. Furthermore, using a simple glutaraldehyde crosslinking scheme, we show that SecA is always monomeric when bound to LUV formed from E. coli lipids.
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Affiliation(s)
- Guillaume Roussel
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA 92697, United States of America
| | - Stephen H White
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA 92697, United States of America.
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14
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Chattrakun K, Hoogerheide DP, Mao C, Randall LL, King GM. Protein Translocation Activity in Surface-Supported Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:12246-12256. [PMID: 31448613 PMCID: PMC10906442 DOI: 10.1021/acs.langmuir.9b01928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Surface-supported lipid bilayers are used widely throughout the nanoscience community as cellular membrane mimics. For example, they are frequently employed in single-molecule atomic force microscopy (AFM) studies to shed light on membrane protein conformational dynamics and folding. However, in AFM as well as in other surface-sensing techniques, the close proximity of the supporting surface raises questions about preservation of the biochemical activity. Employing the model translocase from the general secretory (Sec) system of Escherichia coli, here we quantify the activity via two biochemical assays in surface-supported bilayers. The first assesses ATP hydrolysis and the second assesses polypeptide translocation across the membrane via protection from added protease. Hydrolysis assays revealed distinct levels of activation ranging from medium (translocase-activated) to high (translocation-associated) that were similar to traditional solution experiments and further identified an adenosine triphosphatase population exhibiting characteristics of conformational hysteresis. Translocation assays revealed turn over numbers that were comparable to solution but with a 10-fold reduction in apparent rate constant. Despite differences in kinetics, the chemomechanical coupling (ATP hydrolyzed per residue translocated) only varied twofold on glass compared to solution. The activity changed with the topographic complexity of the underlying surface. Rough glass coverslips were favored over atomically flat mica, likely due to differences in frictional coupling between the translocating polypeptide and surface. Neutron reflectometry and AFM corroborated the biochemical measurements and provided structural characterization of the submembrane space and upper surface of the bilayer. Overall, the translocation activity was maintained for the surface-adsorbed Sec system, albeit with a slower rate-limiting step. More generally, polypeptide translocation activity measurements yield valuable quantitative metrics to assess the local environment about surface-supported lipid bilayers.
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Affiliation(s)
- Kanokporn Chattrakun
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Chunfeng Mao
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Gavin M. King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
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15
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Ito K, Mori H, Chiba S. Monitoring substrate enables real-time regulation of a protein localization pathway. FEMS Microbiol Lett 2019; 365:4983124. [PMID: 29790986 DOI: 10.1093/femsle/fny109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein localization machinery supports cell survival and physiology, suggesting the potential importance of its expression regulation. Here, we summarize a remarkable scheme of regulation, which allows real-time feedback regulation of the machinery expression. A class of regulatory nascent polypeptides, called monitoring substrates, undergoes force-sensitive translation arrest. The resulting ribosome stalling on the mRNA then affects mRNA folding to expose the ribosome-binding site of the downstream target gene and upregulate its translation. The target gene encodes a component of the localization machinery, whose physical action against the monitoring substrate leads to arrest cancellation. Thus, this scheme of feedback loop allows the cell to adjust the amount of the machinery to correlate inversely with the effectiveness of the process at a given moment. The system appears to have emerged late in evolution, in which a narrow range of organisms selected a distinct monitoring substrate-machinery combination. Currently, regulatory systems of SecM-SecA, VemP-SecDF2 and MifM-YidC2 are known to occur in different bacterial species.
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Affiliation(s)
- Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
| | - Hiroyuki Mori
- Japan and Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
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16
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Sanganna Gari RR, Chattrakun K, Marsh BP, Mao C, Chada N, Randall LL, King GM. Direct visualization of the E. coli Sec translocase engaging precursor proteins in lipid bilayers. SCIENCE ADVANCES 2019; 5:eaav9404. [PMID: 31206019 PMCID: PMC6561738 DOI: 10.1126/sciadv.aav9404] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Escherichia coli exports proteins via a translocase comprising SecA and the translocon, SecYEG. Structural changes of active translocases underlie general secretory system function, yet directly visualizing dynamics has been challenging. We imaged active translocases in lipid bilayers as a function of precursor protein species, nucleotide species, and stage of translocation using atomic force microscopy (AFM). Starting from nearly identical initial states, SecA more readily dissociated from SecYEG when engaged with the precursor of outer membrane protein A as compared to the precursor of galactose-binding protein. For the SecA that remained bound to the translocon, the quaternary structure varied with nucleotide, populating SecA2 primarily with adenosine diphosphate (ADP) and adenosine triphosphate, and the SecA monomer with the transition state analog ADP-AlF3. Conformations of translocases exhibited precursor-dependent differences on the AFM imaging time scale. The data, acquired under near-native conditions, suggest that the translocation process varies with precursor species.
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Affiliation(s)
| | - Kanokporn Chattrakun
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Brendan P. Marsh
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Chunfeng Mao
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Gavin M. King
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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17
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Young J, Duong F. Investigating the stability of the SecA-SecYEG complex during protein translocation across the bacterial membrane. J Biol Chem 2019; 294:3577-3587. [PMID: 30602566 DOI: 10.1074/jbc.ra118.006447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/21/2018] [Indexed: 11/06/2022] Open
Abstract
During posttranslational translocation in Escherichia coli, polypeptide substrates are driven across the membrane through the SecYEG protein-conducting channel using the ATPase SecA, which binds to SecYEG and couples nucleotide hydrolysis to polypeptide movement. Recent studies suggest that SecA is a highly dynamic enzyme, able to repeatedly bind and dissociate from SecYEG during substrate translocation, but other studies indicate that these dynamics, here referred to as "SecA processivity," are not a requirement for transport. We employ a SecA mutant (PrlD23) that associates more tightly to membranes than WT SecA, in addition to a SecA-SecYEG cross-linked complex, to demonstrate that SecA-SecYEG binding and dissociation events are important for efficient transport of the periplasmic protein proPhoA. Strikingly however, we find that transport of the precursor of the outer membrane protein proOmpA does not depend on SecA processivity. By exchanging signal sequence and protein domains of similar size between PhoA and OmpA, we find that SecA processivity is not influenced by the sequence of the protein substrate. In contrast, using an extended proOmpA variant and a truncated derivative of proPhoA, we show that SecA processivity is affected by substrate length. These findings underscore the importance of the dynamic nature of SecA-SecYEG interactions as a function of the preprotein substrate, features that have not yet been reported using other biophysical or in vivo methods.
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Affiliation(s)
- John Young
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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18
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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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19
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Coassembly of SecYEG and SecA Fully Restores the Properties of the Native Translocon. J Bacteriol 2018; 201:JB.00493-18. [PMID: 30275279 DOI: 10.1128/jb.00493-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/21/2018] [Indexed: 01/06/2023] Open
Abstract
In all cells, a highly conserved channel transports proteins across membranes. In Escherichia coli, that channel is SecYEG. Many investigations of this protein complex have used purified SecYEG reconstituted into proteoliposomes. How faithfully do activities of reconstituted systems reflect the properties of SecYEG in the native membrane environment? We investigated by comparing three in vitro systems: the native membrane environment of inner membrane vesicles and two methods of reconstitution. One method was the widely used reconstitution of SecYEG alone into lipid bilayers. The other was our method of coassembly of SecYEG with SecA, the ATPase of the translocase. For nine different precursor species we assessed parameters that characterize translocation: maximal amplitude of competent precursor translocated, coupling of energy to transfer, and apparent rate constant. In addition, we investigated translocation in the presence and absence of chaperone SecB. For all nine precursors, SecYEG coassembled with SecA was as active as SecYEG in native membrane for each of the parameters studied. Effects of SecB on transport of precursors faithfully mimicked observations made in vivo From investigation of the nine different precursors, we conclude that the apparent rate constant, which reflects the step that limits the rate of translocation, is dependent on interactions with the translocon of portions of the precursors other than the leader. In addition, in some cases the rate-limiting step is altered by the presence of SecB. Candidates for the rate-limiting step that are consistent with our data are discussed.IMPORTANCE This work presents a comprehensive quantification of the parameters of transport by the Sec general secretory system in the three in vitro systems. The standard reconstitution used by most investigators can be enhanced to yield six times as many active translocons simply by adding SecA to SecYEG during reconstitution. This robust system faithfully reflects the properties of translocation in native membrane vesicles. We have expanded the number of precursors studied to nine. This has allowed us to conclude that the rate constant for translocation varies with precursor species.
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20
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Chada N, Chattrakun K, Marsh BP, Mao C, Bariya P, King GM. Single-molecule observation of nucleotide induced conformational changes in basal SecA-ATP hydrolysis. SCIENCE ADVANCES 2018; 4:eaat8797. [PMID: 30397644 PMCID: PMC6200364 DOI: 10.1126/sciadv.aat8797] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/13/2018] [Indexed: 05/06/2023]
Abstract
SecA is the critical adenosine triphosphatase that drives preprotein transport through the translocon, SecYEG, in Escherichia coli. This process is thought to be regulated by conformational changes of specific domains of SecA, but real-time, real-space measurement of these changes is lacking. We use single-molecule atomic force microscopy (AFM) to visualize nucleotide-dependent conformations and conformational dynamics of SecA. Distinct topographical populations were observed in the presence of specific nucleotides. AFM investigations during basal adenosine triphosphate (ATP) hydrolysis revealed rapid, reversible transitions between a compact and an extended state at the ~100-ms time scale. A SecA mutant lacking the precursor-binding domain (PBD) aided interpretation. Further, the biochemical activity of SecA prepared for AFM was confirmed by tracking inorganic phosphate release. We conclude that ATP-driven dynamics are largely due to PBD motion but that other segments of SecA contribute to this motion during the transition state of the ATP hydrolysis cycle.
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Affiliation(s)
- Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Kanokporn Chattrakun
- Department of Physics and Astronomy, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Brendan P. Marsh
- Department of Physics and Astronomy, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Chunfeng Mao
- Department of Biochemistry, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Priya Bariya
- Department of Biochemistry, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Gavin M. King
- Department of Physics and Astronomy, University of Missouri–Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri–Columbia, Columbia, MO 65211, USA
- Corresponding author.
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21
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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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22
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Marsh BP, Chada N, Sanganna Gari RR, Sigdel KP, King GM. The Hessian Blob Algorithm: Precise Particle Detection in Atomic Force Microscopy Imagery. Sci Rep 2018; 8:978. [PMID: 29343783 PMCID: PMC5772630 DOI: 10.1038/s41598-018-19379-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/29/2017] [Indexed: 11/09/2022] Open
Abstract
Imaging by atomic force microscopy (AFM) offers high-resolution descriptions of many biological systems; however, regardless of resolution, conclusions drawn from AFM images are only as robust as the analysis leading to those conclusions. Vital to the analysis of biomolecules in AFM imagery is the initial detection of individual particles from large-scale images. Threshold and watershed algorithms are conventional for automatic particle detection but demand manual image preprocessing and produce particle boundaries which deform as a function of user-defined parameters, producing imprecise results subject to bias. Here, we introduce the Hessian blob to address these shortcomings. Combining a scale-space framework with measures of local image curvature, the Hessian blob formally defines particle centers and their boundaries, both to subpixel precision. Resulting particle boundaries are independent of user defined parameters, with no image preprocessing required. We demonstrate through direct comparison that the Hessian blob algorithm more accurately detects biomolecules than conventional AFM particle detection techniques. Furthermore, the algorithm proves largely insensitive to common imaging artifacts and noise, delivering a stable framework for particle analysis in AFM.
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Affiliation(s)
- Brendan P Marsh
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America.,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 OWA, United Kingdom
| | - Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - Raghavendar Reddy Sanganna Gari
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America.,School of Medicine, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Krishna P Sigdel
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America. .,Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, United States of America.
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23
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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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24
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Abstract
We came together in Leeds to commemorate and celebrate the life and achievements of Prof. Stephen Baldwin. For many years we, together with Sheena Radford and Roman Tuma (colleagues also of the University of Leeds), have worked together on the problem of protein translocation through the essential and ubiquitous Sec system. Inspired and helped by Steve we may finally be making progress. My seminar described our latest hypothesis for the molecular mechanism of protein translocation, supported by results collected in Bristol and Leeds on the tractable bacterial secretion process–commonly known as the Sec system; work that will be published elsewhere. Below is a description of the alternative and contested models for protein translocation that we all have been contemplating for many years. This review will consider their pros and cons.
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25
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Hsieh YH, Huang YJ, Zhang H, Liu Q, Lu Y, Yang H, Houghton J, Jiang C, Sui SF, Tai PC. Dissecting structures and functions of SecA-only protein-conducting channels: ATPase, pore structure, ion channel activity, protein translocation, and interaction with SecYEG/SecDF•YajC. PLoS One 2017; 12:e0178307. [PMID: 28575061 PMCID: PMC5456053 DOI: 10.1371/journal.pone.0178307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/10/2017] [Indexed: 11/30/2022] Open
Abstract
SecA is an essential protein in the major bacterial Sec-dependent translocation pathways. E. coli SecA has 901 aminoacyl residues which form multi-functional domains that interact with various ligands to impart function. In this study, we constructed and purified tethered C-terminal deletion fragments of SecA to determine the requirements for N-terminal domains interacting with lipids to provide ATPase activity, pore structure, ion channel activity, protein translocation and interactions with SecYEG-SecDF•YajC. We found that the N-terminal fragment SecAN493 (SecA1-493) has low, intrinsic ATPase activity. Larger fragments have greater activity, becoming highest around N619-N632. Lipids greatly stimulated the ATPase activities of the fragments N608-N798, reaching maximal activities around N619. Three helices in amino-acyl residues SecA619-831, which includes the "Helical Scaffold" Domain (SecA619-668) are critical for pore formation, ion channel activity, and for function with SecYEG-SecDF•YajC. In the presence of liposomes, N-terminal domain fragments of SecA form pore-ring structures at fragment-size N640, ion channel activity around N798, and protein translocation capability around N831. SecA domain fragments ranging in size between N643-N669 are critical for functional interactions with SecYEG-SecDF•YajC. In the presence of liposomes, inactive C-terminal fragments complement smaller non-functional N-terminal fragments to form SecA-only pore structures with ion channel activity and protein translocation ability. Thus, SecA domain fragment interactions with liposomes defined critical structures and functional aspects of SecA-only channels. These data provide the mechanistic basis for SecA to form primitive, low-efficiency, SecA-only protein-conducting channels, as well as the minimal parameters for SecA to interact functionally with SecYEG-SecDF•YajC to form high-efficiency channels.
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Affiliation(s)
- Ying-hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Ying-ju Huang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Hao Zhang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Qian Liu
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Yang Lu
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Hsiuchin Yang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - John Houghton
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Chun Jiang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing China
| | - Phang C. Tai
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
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26
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Matin TR, Sigdel KP, Utjesanovic M, Marsh BP, Gallazzi F, Smith VF, Kosztin I, King GM. Single-Molecule Peptide-Lipid Affinity Assay Reveals Interplay between Solution Structure and Partitioning. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4057-4065. [PMID: 28343391 DOI: 10.1021/acs.langmuir.7b00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interactions between short protein segments and phospholipid bilayers dictate fundamental aspects of cellular activity and have important applications in biotechnology. Yet, the lack of a suitable methodology for directly probing these interactions has hindered the mechanistic understanding. We developed a precision atomic force microscopy-based single-molecule force spectroscopy assay and probed partitioning into lipid bilayers by measuring the mechanical force experienced by a peptide. Protein segments were constructed from the peripheral membrane protein SecA, a key ATPase in bacterial secretion. We focused on the first 10 amino-terminal residues of SecA (SecA2-11) that are lipophilic. In addition to the core SecA2-11 sequence, constructs with nearly identical chemical composition but with differing geometry were used: two copies of SecA2-11 linked in series and two copies SecA2-11 linked in parallel. Lipid bilayer partitioning interactions of peptides with differing structures were distinguished. To model the energetic landscape, a theory of diffusive barrier crossing was extended to incorporate a superposition of potential barriers with variable weights. Analysis revealed two dissociation pathways for the core SecA2-11 sequence with well-separated intrinsic dissociation rates. Molecular dynamics simulations showed that the three peptides had significant conformational differences in solution that correlated well with the measured variations in the propensity to partition into the bilayer. The methodology is generalizable and can be applied to other peptide and lipid species.
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Affiliation(s)
| | | | | | | | | | - Virginia F Smith
- Department of Chemistry, United States Naval Academy , Annapolis, Maryland 21402, United States
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27
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Allen WJ, Corey RA, Oatley P, Sessions RB, Baldwin SA, Radford SE, Tuma R, Collinson I. Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation. eLife 2016; 5. [PMID: 27183269 PMCID: PMC4907695 DOI: 10.7554/elife.15598] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/14/2016] [Indexed: 01/25/2023] Open
Abstract
The essential process of protein secretion is achieved by the ubiquitous Sec machinery. In prokaryotes, the drive for translocation comes from ATP hydrolysis by the cytosolic motor-protein SecA, in concert with the proton motive force (PMF). However, the mechanism through which ATP hydrolysis by SecA is coupled to directional movement through SecYEG is unclear. Here, we combine all-atom molecular dynamics (MD) simulations with single molecule FRET and biochemical assays. We show that ATP binding by SecA causes opening of the SecY-channel at long range, while substrates at the SecY-channel entrance feed back to regulate nucleotide exchange by SecA. This two-way communication suggests a new, unifying 'Brownian ratchet' mechanism, whereby ATP binding and hydrolysis bias the direction of polypeptide diffusion. The model represents a solution to the problem of transporting inherently variable substrates such as polypeptides, and may underlie mechanisms of other motors that translocate proteins and nucleic acids.
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Affiliation(s)
| | - Robin Adam Corey
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Peter Oatley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Steve A Baldwin
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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28
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Zheng Z, Blum A, Banerjee T, Wang Q, Dantis V, Oliver D. Determination of the Oligomeric State of SecYEG Protein Secretion Channel Complex Using in Vivo Photo- and Disulfide Cross-linking. J Biol Chem 2016; 291:5997-6010. [PMID: 26747607 DOI: 10.1074/jbc.m115.694844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Indexed: 11/06/2022] Open
Abstract
SecYEG protein of bacteria or Sec61αβγ of eukaryotes is a universally conserved heterotrimeric protein channel complex that accommodates the partitioning of membrane proteins into the lipid bilayer as well as the secretion of proteins to the trans side of the plasma or endoplasmic reticular membrane, respectively. SecYEG function is facilitated by cytosolic partners, mainly a nascent chain-ribosome complex or the SecA ATPase motor protein. Extensive efforts utilizing both biochemical and biophysical approaches have been made to determine whether SecYEG functions as a monomer or a dimer, but such approaches have often generated conflicting results. Here we have employed site-specific in vivo photo-cross-linking or cysteine cross-linking, along with co-immunoprecipitation or SecA footprinting techniques to readdress this issue. Our findings show that the SecY dimer to monomer ratio is relatively constant regardless of whether translocons are actively engaged with protein substrate or not. Under the former conditions the SecY dimer can be captured associated with a translocon-jammed substrate, indicative of SecY dimer function. Furthermore, SecA ATPase can be cross-linked to two copies of SecY when the complex contains a translocation intermediate. Collectively, our results suggest that SecYEG dimers are functional units of the translocon.
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Affiliation(s)
- Zeliang Zheng
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Amy Blum
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Tithi Banerjee
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Qianyu Wang
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Virginia Dantis
- 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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29
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Chada N, Sigdel KP, Gari RRS, Matin TR, Randall LL, King GM. Glass is a Viable Substrate for Precision Force Microscopy of Membrane Proteins. Sci Rep 2015; 5:12550. [PMID: 26228793 PMCID: PMC4521160 DOI: 10.1038/srep12550] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Though ubiquitous in optical microscopy, glass has long been overlooked as a specimen supporting surface for high resolution atomic force microscopy (AFM) investigations due to its roughness. Using bacteriorhodopsin from Halobacterium salinarum and the translocon SecYEG from Escherichia coli, we demonstrate that faithful images of 2D crystalline and non-crystalline membrane proteins in lipid bilayers can be obtained on microscope cover glass following a straight-forward cleaning procedure. Direct comparison between AFM data obtained on glass and on mica substrates show no major differences in image fidelity. Repeated association of the ATPase SecA with the cytoplasmic protrusion of SecYEG demonstrates that the translocon remains competent for binding after tens of minutes of continuous AFM imaging. This opens the door for precision long-timescale investigations of the active translocase in near-native conditions and, more generally, for integration of high resolution biological AFM with many powerful optical techniques that require non-birefringent substrates.
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Affiliation(s)
- Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | - Krishna P Sigdel
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | | | - Tina Rezaie Matin
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | - Linda L Randall
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | - Gavin M King
- 1] Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA [2] Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211 USA
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The pilus usher controls protein interactions via domain masking and is functional as an oligomer. Nat Struct Mol Biol 2015; 22:540-6. [PMID: 26052892 PMCID: PMC4496297 DOI: 10.1038/nsmb.3044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/12/2015] [Indexed: 12/21/2022]
Abstract
The chaperone-usher (CU) pathway assembles organelles termed pili or
fimbriae in Gram-negative bacteria. Type 1 pili expressed by uropathogenic
Escherichia coli are prototypical structures assembled by
the CU pathway. Biogenesis of pili by the CU pathway requires a periplasmic
chaperone and an outer membrane protein termed the usher (FimD). We show that
the FimD C-terminal domains provide the high-affinity substrate binding site,
but that these domains are masked in the resting usher. Domain masking requires
the FimD plug domain, which serves as a switch controlling usher activation. We
demonstrate that usher molecules can act in trans for pilus
biogenesis, providing conclusive evidence for a functional usher oligomer. These
results reveal mechanisms by which molecular machines such as the usher regulate
and harness protein-protein interactions, and suggest that ushers may interact
in a cooperative manner during pilus assembly in bacteria.
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Suo Y, Hardy SJS, Randall LL. The basis of asymmetry in the SecA:SecB complex. J Mol Biol 2014; 427:887-900. [PMID: 25534082 DOI: 10.1016/j.jmb.2014.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022]
Abstract
During export in Escherichia coli, SecB, a homotetramer structurally organized as a dimer of dimers, forms a complex with two protomers of SecA, which is the ATPase that provides energy to transfer a precursor polypeptide through the membrane via the SecYEG translocon. There are two areas of contact on SecB that stabilize the SecA:SecB complex: the flat sides of the SecB tetramer and the C-terminal 13 residues of SecB. These contacts within the complex are distributed asymmetrically. Breaking contact between SecA and the sides of SecB results in release of only one protomer of SecA yielding a complex of stoichiometry SecA1:SecB4. This complex mediates export; however, the coupling of ATP hydrolysis to movements of the precursor through the translocon is much less efficient than the coupling by the SecA2:SecB4 complex. Here we used heterotetrameric species of SecB to understand the source of the asymmetry in the contacts and its role in the functioning of the complex. The model of interactions presented suggests a way that binding between SecA and SecB might decrease the affinity of precursor polypeptides for SecB and facilitate the transfer to SecA.
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Affiliation(s)
- Yuying Suo
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Simon J S Hardy
- Department of Biology, University of York, York YO10 5DD, UK
| | - Linda L Randall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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Zhang L, Jiang W, Nan J, Almqvist J, Huang Y. The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1809-16. [DOI: 10.1016/j.bbamem.2014.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 12/27/2022]
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Castanié-Cornet MP, Bruel N, Genevaux P. Chaperone networking facilitates protein targeting to the bacterial cytoplasmic membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1442-56. [PMID: 24269840 DOI: 10.1016/j.bbamcr.2013.11.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/10/2013] [Accepted: 11/13/2013] [Indexed: 12/22/2022]
Abstract
Nascent polypeptides emerging from the ribosome are assisted by a pool of molecular chaperones and targeting factors, which enable them to efficiently partition as cytosolic, integral membrane or exported proteins. Extensive genetic and biochemical analyses have significantly expanded our knowledge of chaperone tasking throughout this process. In bacteria, it is known that the folding of newly-synthesized cytosolic proteins is mainly orchestrated by three highly conserved molecular chaperones, namely Trigger Factor (TF), DnaK (HSP70) and GroEL (HSP60). Yet, it has been reported that these major chaperones are strongly involved in protein translocation pathways as well. This review describes such essential molecular chaperone functions, with emphasis on both the biogenesis of inner membrane proteins and the post-translational targeting of presecretory proteins to the Sec and the twin-arginine translocation (Tat) pathways. Critical interplay between TF, DnaK, GroEL and other molecular chaperones and targeting factors, including SecB, SecA, the signal recognition particle (SRP) and the redox enzyme maturation proteins (REMPs) is also discussed. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Marie-Pierre Castanié-Cornet
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
| | - Nicolas Bruel
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France.
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Taufik I, Kedrov A, Exterkate M, Driessen AJ. Monitoring the Activity of Single Translocons. J Mol Biol 2013; 425:4145-53. [DOI: 10.1016/j.jmb.2013.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
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Membrane chaperone SecDF plays a role in the secretion of Listeria monocytogenes major virulence factors. J Bacteriol 2013; 195:5262-72. [PMID: 24056100 DOI: 10.1128/jb.00697-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive human intracellular pathogen that infects diverse mammalian cells. Upon invasion, L. monocytogenes secretes multiple virulence factors that target host cellular processes and promote infection. It has been presumed, but was not empirically established, that the Sec translocation system is the primary mediator of this secretion. Here, we validate an important role for SecDF, a component of the Sec system, in the secretion of several critical L. monocytogenes virulence factors. A ΔsecDF mutant is demonstrated to exhibit impaired membrane translocation of listeriolysin O (LLO), PlcA, PlcB, and ActA, factors that mediate L. monocytogenes phagosomal escape and spread from cell to cell. This impaired translocation was monitored by accumulation of the factors on the bacterial membrane and by reduced activity upon secretion. This defect in secretion is shown to be associated with a severe intracellular growth defect of the ΔsecDF mutant in macrophages and a less virulent phenotype in mice, despite normal growth in laboratory medium. We further show that SecDF is upregulated when the bacteria reside in macrophage phagosomes and that it is necessary for efficient phagosomal escape. Taken together, these data support the premise that SecDF plays a role as a chaperone that facilitates the translocation of L. monocytogenes virulence factors during infection.
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