1
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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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2
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Young JW, Wason IS, Zhao Z, Kim S, Aoki H, Phanse S, Rattray DG, Foster LJ, Babu M, Duong van Hoa F. Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly. J Proteome Res 2022; 21:1748-1758. [PMID: 35616533 DOI: 10.1021/acs.jproteome.2c00129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The peptidisc membrane mimetic enables global reconstitution of the bacterial membrane proteome into water-soluble detergent-free particles, termed peptidisc libraries. We present here a method that combines peptidisc libraries and chromosomal-level gene tagging technology with affinity purification and mass spectrometry (AP/MS) to stabilize and identify fragile membrane protein complexes that exist at native expression levels. This method circumvents common artifacts caused by bait protein overproduction and protein complex dissociation due to lengthy exposure to detergents during protein isolation. Using the Escherichia coli Sec system as a case study, we identify an expanded version of the translocon, termed the HMD complex, consisting of nine different integral membrane subunits. This complex is stable in peptidiscs but dissociates in detergents. Guided by this native-level proteomic information, we design and validate a procedure that enables purification of the HMD complex with minimal protein dissociation. These results highlight the utility of peptidiscs and AP/MS to discover and stabilize fragile membrane protein assemblies. Data are available via ProteomeXchange with identifier PXD032315.
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Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Sunyoung Kim
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - David G Rattray
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohan Babu
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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3
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Zhang XX, Young JW, Foster LJ, Duong F. Nanodisc-Based Proteomics Identify Caj1 as an Hsp40 with Affinity for Phosphatidic Acid Lipids. J Proteome Res 2021; 20:4831-4839. [PMID: 34519218 DOI: 10.1021/acs.jproteome.1c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many soluble proteins interact with membranes to perform important biological functions, including signal transduction, regulation, transport, trafficking, and biogenesis. Despite their importance, these protein-membrane interactions are difficult to characterize due to their often-transient nature as well as phospholipids' poor solubility in aqueous solution. Here, we employ nanodiscs-small, water-soluble patches of a lipid bilayer encircled with amphipathic scaffold proteins-along with quantitative proteomics to identify lipid-binding proteins in Saccharomyces cerevisiae. Using nanodiscs reconstituted with yeast total lipid extracts or only phosphatidylethanolamine (PE-nanodiscs), we capture several known membrane-interacting proteins, including the Rab GTPases Sec4 and Ypt1, which play key roles in vesicle trafficking. Utilizing PE-nanodiscs enriched with phosphatidic acid (PEPA-nanodiscs), we specifically capture a member of the Hsp40/J-protein family, Caj1, whose function has recently been linked to membrane protein quality control. We show that the Caj1 interaction with liposomes containing PA is modulated by pH and PE lipids and depends on two patches of positively charged residues near the C-terminus of the protein. The protein Caj1 is the first example of an Hsp40/J-domain protein with affinity for membranes and phosphatidic acid lipid specificity. These findings highlight the utility of combining proteomics with lipid nanodiscs to identify and characterize protein-lipid interactions that may not be evident using other methods. Data are available via ProteomeXchange with the identifier PXD027992.
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Affiliation(s)
- Xiao X Zhang
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratory, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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4
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Koch S, Seinen AB, Kamel M, Kuckla D, Monzel C, Kedrov A, Driessen AJM. Single-molecule analysis of dynamics and interactions of the SecYEG translocon. FEBS J 2020; 288:2203-2221. [PMID: 33058437 DOI: 10.1111/febs.15596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/11/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Abstract
Protein translocation and insertion into the bacterial cytoplasmic membrane are the essential processes mediated by the Sec machinery. The core machinery is composed of the membrane-embedded translocon SecYEG that interacts with the secretion-dedicated ATPase SecA and translating ribosomes. Despite the simplicity and the available structural insights on the system, diverse molecular mechanisms and functional dynamics have been proposed. Here, we employ total internal reflection fluorescence microscopy to study the oligomeric state and diffusion of SecYEG translocons in supported lipid bilayers at the single-molecule level. Silane-based coating ensured the mobility of lipids and reconstituted translocons within the bilayer. Brightness analysis suggested that approx. 70% of the translocons were monomeric. The translocons remained in a monomeric form upon ribosome binding, but partial oligomerization occurred in the presence of nucleotide-free SecA. Individual trajectories of SecYEG in the lipid bilayer revealed dynamic heterogeneity of diffusion, as translocons commonly switched between slow and fast mobility modes with corresponding diffusion coefficients of 0.03 and 0.7 µm2 ·s-1 . Interactions with SecA ATPase had a minor effect on the lateral mobility, while bound ribosome:nascent chain complexes substantially hindered the diffusion of single translocons. Notably, the mobility of the translocon:ribosome complexes was not affected by the solvent viscosity or macromolecular crowding modulated by Ficoll PM 70, so it was largely determined by interactions within the lipid bilayer and at the interface. We suggest that the complex mobility of SecYEG arises from the conformational dynamics of the translocon and protein:lipid interactions.
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Affiliation(s)
- Sabrina Koch
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Anne-Bart Seinen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Biophysics, AMOLF, Amsterdam, The Netherlands
| | - Michael Kamel
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Daniel Kuckla
- Experimental Medical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Germany
| | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
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5
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Young JW, Wason IS, Zhao Z, Rattray DG, Foster LJ, Duong Van Hoa F. His-Tagged Peptidiscs Enable Affinity Purification of the Membrane Proteome for Downstream Mass Spectrometry Analysis. J Proteome Res 2020; 19:2553-2562. [PMID: 32364744 DOI: 10.1021/acs.jproteome.0c00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Characterization of the integral membrane proteome by mass spectrometry (MS) remains challenging due its high complexity and inherent insolubility. In a typical experiment, the cellular membranes are isolated, the proteins are solubilized and fractionated, and the detergent micelles are removed before MS analysis. Detergents are not compatible with mass spectrometry, however, and their removal from biological samples often results in reduced protein identification. As an alternative to detergents, we recently developed the peptidisc membrane mimetic, which allows entrapment of the cell envelope proteome into water-soluble particles, termed a "peptidisc library". Here, we employ a His-tagged version of the peptidisc peptide scaffold to enrich the reconstituted membrane proteome by affinity chromatography. This purification step reduces the sample complexity by depleting ribosomal and soluble proteins that often cosediment with cellular membranes. As a result, the peptidisc library is enriched in low-abundance membrane proteins. We apply this method to survey changes in the membrane proteome upon depletion of the SecDFyajC complex, the ancillary subunit of the Sec translocon. In the depleted strain, we detect increased membrane localization of the motor ATPase SecA, along with increased levels of an unannotated inner membrane protein, YibN. Together, these results demonstrate the utility of the peptidisc for global purification of membrane proteins and for monitoring change in the membrane proteome.
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Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David G Rattray
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Franck Duong Van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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6
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Cardiolipin is required in vivo for the stability of bacterial translocon and optimal membrane protein translocation and insertion. Sci Rep 2020; 10:6296. [PMID: 32286407 PMCID: PMC7156725 DOI: 10.1038/s41598-020-63280-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023] Open
Abstract
Translocation of preproteins across the Escherichia coli inner membrane requires anionic lipids by virtue of their negative head-group charge either in vivo or in situ. However, available results do not differentiate between the roles of monoanionic phosphatidylglycerol and dianionic cardiolipin (CL) in this essential membrane-related process. To define in vivo the molecular steps affected by the absence of CL in protein translocation and insertion, we analyzed translocon activity, SecYEG stability and its interaction with SecA in an E. coli mutant devoid of CL. Although no growth defects were observed, co- and post-translational translocation of α-helical proteins across inner membrane and the assembly of outer membrane β-barrel precursors were severely compromised in CL-lacking cells. Components of proton-motive force which could impair protein insertion into and translocation across the inner membrane, were unaffected. However, stability of the dimeric SecYEG complex and oligomerization properties of SecA were strongly compromised while the levels of individual SecYEG translocon components, SecA and insertase YidC were largely unaffected. These results demonstrate that CL is required in vivo for the stability of the bacterial translocon and its efficient function in co-translational insertion into and translocation across the inner membrane of E. coli.
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7
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Abstract
More than a third of all bacterial polypeptides, comprising the 'exportome', are transported to extracytoplasmic locations. Most of the exportome is targeted and inserts into ('membranome') or crosses ('secretome') the plasma membrane. The membranome and secretome use distinct targeting signals and factors, and driving forces, but both use the ubiquitous and essential Sec translocase and its SecYEG protein-conducting channel. Membranome export is co-translational and uses highly hydrophobic N-terminal signal anchor sequences recognized by the signal recognition particle on the ribosome, that also targets C-tail anchor sequences. Translating ribosomes drive movement of these polypeptides through the lateral gate of SecY into the inner membrane. On the other hand, secretome export is post-translational and carries two types of targeting signals: cleavable N-terminal signal peptides and multiple short hydrophobic targeting signals in their mature domains. Secretome proteins remain translocation competent due to occupying loosely folded to completely non-folded states during targeting. This is accomplished mainly by the intrinsic properties of mature domains and assisted by signal peptides and/or chaperones. Secretome proteins bind to the dimeric SecA subunit of the translocase. SecA converts from a dimeric preprotein receptor to a monomeric ATPase motor and drives vectorial crossing of chains through SecY aided by the proton motive force. Signal peptides are removed by signal peptidases and translocated chains fold or follow subsequent trafficking.
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8
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Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. Protein J 2020; 38:249-261. [PMID: 30972527 DOI: 10.1007/s10930-019-09830-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein translocation and membrane integration are fundamental, conserved processes. After or during ribosomal protein synthesis, precursor proteins containing an N-terminal signal sequence are directed to a conserved membrane protein complex called the Sec translocon (also known as the Sec translocase) in the endoplasmic reticulum membrane in eukaryotic cells, or the cytoplasmic membrane in bacteria. The Sec translocon comprises the Sec61 complex in eukaryotic cells, or the SecY complex in bacteria, and mediates translocation of substrate proteins across/into the membrane. Several membrane proteins are associated with the Sec translocon. In Escherichia coli, the membrane protein YidC functions not only as a chaperone for membrane protein biogenesis along with the Sec translocon, but also as an independent membrane protein insertase. To understand the molecular mechanism underlying these dynamic processes at the membrane, high-resolution structural models of these proteins are needed. This review focuses on X-ray crystallographic analyses of the Sec translocon and YidC and discusses the structural basis for protein translocation and integration.
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Affiliation(s)
- Tomoya Tsukazaki
- Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
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9
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Carlson ML, Stacey RG, Young JW, Wason IS, Zhao Z, Rattray DG, Scott N, Kerr CH, Babu M, Foster LJ, Duong Van Hoa F. Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. eLife 2019; 8:46615. [PMID: 31364989 PMCID: PMC6697469 DOI: 10.7554/elife.46615] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a ‘one-size fits all’ membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions. For example, we discover a trans-periplasmic supercomplex comprising subunits of the Bam and Sec machineries, including membrane-bound chaperones YfgM and PpiD. We identify RcsF and OmpA as bone fide interactors of BamA, and we show that MetQ association with the ABC transporter MetNI depends on its N-terminal lipid anchor. We also discover NlpA as a novel interactor of MetNI complex. Most of these interactions are largely undetected by standard detergent-based purification. Together, the peptidisc workflow applied to the proteomic field is emerging as a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation.
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Affiliation(s)
- Michael Luke Carlson
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - R Greg Stacey
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - John William Young
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Irvinder Singh Wason
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Zhiyu Zhao
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - David G Rattray
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Nichollas Scott
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Craig H Kerr
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mohan Babu
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Canada
| | - Leonard J Foster
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Franck Duong Van Hoa
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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10
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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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11
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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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12
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Carlson ML, Young JW, Zhao Z, Fabre L, Jun D, Li J, Li J, Dhupar HS, Wason I, Mills AT, Beatty JT, Klassen JS, Rouiller I, Duong F. The Peptidisc, a simple method for stabilizing membrane proteins in detergent-free solution. eLife 2018; 7:34085. [PMID: 30109849 PMCID: PMC6093710 DOI: 10.7554/elife.34085] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/05/2018] [Indexed: 12/15/2022] Open
Abstract
Membrane proteins are difficult to work with due to their insolubility in aqueous solution and quite often their poor stability in detergent micelles. Here, we present the peptidisc for their facile capture into water-soluble particles. Unlike the nanodisc, which requires scaffold proteins of different lengths and precise amounts of matching lipids, reconstitution of detergent solubilized proteins in peptidisc only requires a short amphipathic bi-helical peptide (NSPr) and no extra lipids. Multiple copies of the peptide wrap around to shield the membrane-exposed part of the target protein. We demonstrate the effectiveness of this ‘one size fits all’ method using five different membrane protein assemblies (MalFGK2, FhuA, SecYEG, OmpF, BRC) during ‘on-column’, ‘in-gel’, and ‘on-bead’ reconstitution embedded within the membrane protein purification protocol. The peptidisc method is rapid and cost-effective, and it may emerge as a universal tool for high-throughput stabilization of membrane proteins to advance modern biological studies. Surrounding every living cell is a biological membrane that is largely impermeable to water-soluble molecules. This hydrophobic (or “water-hating”) barrier preserves the contents of the cell and also regulates how the cell interacts with its environment. This latter function is critical and relies on a class of proteins that are embedded within the membrane and are also hydrophobic. The hydrophobic nature of membrane proteins is however inconvenient for biochemical studies which usually take place in water-based solutions. Therefore, membrane proteins are under-represented in biological research compared to the water-soluble ones, even though roughly one quarter of a cell’s proteins are membrane proteins. Researchers have developed a few tricks to keep membrane proteins soluble after they have been extracted from the membrane. An old but popular technique makes use of detergents, which are chemicals with opposing hydrophobic and hydrophilic properties (hydrophilic literally means “water-loving”). However, even mild detergents can damage membrane proteins and will sometimes lead to experimental artifacts. More recent tricks to stabilize membrane proteins without detergents have been described but remain laborious, costly or difficult to perform. To overcome these limitations, Carlson et al. developed a simple method to stabilize membrane proteins without detergent. Called the “peptidisc”, the method uses multiple copies of a unique peptide – a short sequence of the building blocks of protein – that had been redesigned to have optimal hydrophobic and hydrophilic properties. The idea was that the peptides would wrap around the hydrophobic parts of the membrane protein, and shield them from the watery solution. Indeed, when Carlson et al. mixed this peptide with five different membrane proteins from bacteria, all were perfectly soluble and functional without detergent. The ideal ratio of peptide needed to form a peptidisc around each membrane protein was reached automatically, without having to test many different conditions. This indicates that the peptidisc acts like a “one size fits all” scaffold. The peptidisc is a new tool that will allow more researchers, including those who are not expert biochemists, to study membrane proteins. This will yield a better understanding of the structure of a cell’s membrane and how it interacts with the environment. Since the approach is both simple and easy to apply, more membrane proteins can now also be included in high-throughput searches for potential new drugs for various medical conditions.
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Affiliation(s)
- Michael Luke Carlson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Lucien Fabre
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Daniel Jun
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Jianing Li
- Glycomics Centre and Department of Chemistry, University of Alberta, Alberta, Canada
| | - Jun Li
- Glycomics Centre and Department of Chemistry, University of Alberta, Alberta, Canada
| | - Harveer Singh Dhupar
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Irvin Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Allan T Mills
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - John S Klassen
- Glycomics Centre and Department of Chemistry, University of Alberta, Alberta, Canada
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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13
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McLean MA, Gregory MC, Sligar SG. Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins. Annu Rev Biophys 2018; 47:107-124. [PMID: 29494254 DOI: 10.1146/annurev-biophys-070816-033620] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The study of membrane proteins and receptors presents many challenges to researchers wishing to perform biophysical measurements to determine the structure, function, and mechanism of action of such components. In most cases, to be fully functional, proteins and receptors require the presence of a native phospholipid bilayer. In addition, many complex multiprotein assemblies involved in cellular communication require an integral membrane protein as well as a membrane surface for assembly and information transfer to soluble partners in a signaling cascade. Incorporation of membrane proteins into Nanodiscs renders the target soluble and provides a native bilayer environment with precisely controlled composition of lipids, cholesterol, and other components. Likewise, Nanodiscs provide a surface of defined area useful in revealing lipid specificity and affinities for the assembly of signaling complexes. In this review, we highlight several biophysical techniques made possible through the use of Nanodiscs.
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Affiliation(s)
- Mark A McLean
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; , ,
| | - Michael C Gregory
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; , ,
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; , ,
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14
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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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15
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Sugano Y, Furukawa A, Nureki O, Tanaka Y, Tsukazaki T. SecY-SecA fusion protein retains the ability to mediate protein transport. PLoS One 2017; 12:e0183434. [PMID: 28820900 PMCID: PMC5562318 DOI: 10.1371/journal.pone.0183434] [Citation(s) in RCA: 7] [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: 05/25/2017] [Accepted: 07/28/2017] [Indexed: 01/05/2023] Open
Abstract
In bacteria, the membrane protein complex SecY/E/G and SecA ATPase are essential for protein translocation. About 30% of newly synthesized proteins in the cytosol are targeted to and translocated across the cytoplasmic membrane by the Sec factors. Although a number of single-molecule analyses and structural studies, including the crystal structure of SecYEG complexed with SecA, have been published, the underlying molecular mechanisms and the functional oligomer states remain elusive. In this study, we constructed a fusion protein SecY-SecA, which induces the formation of the SecY-A/SecE/SecG complex (SecYAEG), to enable investigation of the molecular mechanisms by advanced single-molecule analyses. SecYAEG-reconstituted liposomes were found to possess protein translocation activity in vitro and form stable intermediates capable of the translocation using a mutant substrate protein. We additionally found that one unit of SecYAEG complex embedded into a nanodisc, using membrane scaffold proteins, interacts strongly with the substrate. The isolated SecYAEG-reconstituted nanodisc is a promising tool for investigation of the molecular mechanisms by which a single unit of Sec machinery mediates protein translocation.
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Affiliation(s)
- Yasunori Sugano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Arata Furukawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoshiki Tanaka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tomoya Tsukazaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- * E-mail:
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16
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Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM. A statistical framework for analyzing deep mutational scanning data. Genome Biol 2017; 18:150. [PMID: 28784151 PMCID: PMC5547491 DOI: 10.1186/s13059-017-1272-5] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022] Open
Abstract
Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error estimates for each measurement, capturing both sampling error and consistency between replicates. We apply our model to one novel and five published datasets comprising 243,732 variants and demonstrate its superiority in removing noisy variants and conducting hypothesis testing. Simulations show our model applies to scans based on cell growth or binding and handles common experimental errors. We implemented our model in Enrich2, software that can empower researchers analyzing deep mutational scanning data.
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Affiliation(s)
- Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannah Gelman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Nathan Lucas
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Sandra M Bajjalieh
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Terence P Speed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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17
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18
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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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19
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Raschle T, Lin C, Jungmann R, Shih WM, Wagner G. Controlled Co-reconstitution of Multiple Membrane Proteins in Lipid Bilayer Nanodiscs Using DNA as a Scaffold. ACS Chem Biol 2015; 10:2448-54. [PMID: 26356202 DOI: 10.1021/acschembio.5b00627] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nanodiscs constitute a tool for the solubilization of membrane proteins in a lipid bilayer, thus offering a near-native membrane environment. Many membrane proteins interact with other membrane proteins; however, the co-reconstitution of multiple membrane proteins in a single nanodisc is a random process that is adversely affected by several factors, including protein aggregation. Here, we present an approach for the controlled co-reconstitution of multiple membrane proteins in a single nanodisc. The temporary attachment of designated oligonucleotides to individual membrane proteins enables the formation of stable, detergent-solubilized membrane protein complexes by base-pairing of complementary oligonucleotide sequences, thus facilitating the insertion of the membrane protein complex into nanodiscs with defined stoichiometry and composition. As a proof of principle, nanodiscs containing a heterodimeric and heterotrimeric membrane protein complex were reconstituted using a fluorescently labeled voltage-gated anion channel (VDAC) as a model system.
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Affiliation(s)
- Thomas Raschle
- Department of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chenxiang Lin
- Department of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Ralf Jungmann
- Department of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - William M. Shih
- Department of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Gerhard Wagner
- Department of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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20
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Cléon F, Habersetzer J, Alcock F, Kneuper H, Stansfeld PJ, Basit H, Wallace MI, Berks BC, Palmer T. The TatC component of the twin-arginine protein translocase functions as an obligate oligomer. Mol Microbiol 2015; 98:111-29. [PMID: 26112072 PMCID: PMC5102672 DOI: 10.1111/mmi.13106] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 12/24/2022]
Abstract
The Tat protein export system translocates folded proteins across the bacterial cytoplasmic membrane and the plant thylakoid membrane. The Tat system in Escherichia coli is composed of TatA, TatB and TatC proteins. TatB and TatC form an oligomeric, multivalent receptor complex that binds Tat substrates, while multiple protomers of TatA assemble at substrate‐bound TatBC receptors to facilitate substrate transport. We have addressed whether oligomerisation of TatC is an absolute requirement for operation of the Tat pathway by screening for dominant negative alleles of tatC that inactivate Tat function in the presence of wild‐type tatC. Single substitutions that confer dominant negative TatC activity were localised to the periplasmic cap region. The variant TatC proteins retained the ability to interact with TatB and with a Tat substrate but were unable to support the in vivo assembly of TatA complexes. Blue‐native PAGE analysis showed that the variant TatC proteins produced smaller TatBC complexes than the wild‐type TatC protein. The substitutions did not alter disulphide crosslinking to neighbouring TatC molecules from positions in the periplasmic cap but abolished a substrate‐induced disulphide crosslink in transmembrane helix 5 of TatC. Our findings show that TatC functions as an obligate oligomer.
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Affiliation(s)
- François Cléon
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Johann Habersetzer
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Holger Kneuper
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Hajra Basit
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Mark I Wallace
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tracy Palmer
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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21
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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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22
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Abstract
An interesting concept in the organization of cellular membranes is the proposed existence of lipid rafts. Membranes of eukaryotic cells organize signal transduction proteins into membrane rafts or lipid rafts that are enriched in particular lipids such as cholesterol and are important for the correct functionality of diverse cellular processes. The assembly of lipid rafts in eukaryotes has been considered a fundamental step during the evolution of cellular complexity, suggesting that bacteria and archaea were organisms too simple to require such a sophisticated organization of their cellular membranes. However, it was recently discovered that bacteria organize many signal transduction, protein secretion, and transport processes in functional membrane microdomains, which are equivalent to the lipid rafts of eukaryotic cells. This review contains the most significant advances during the last 4 years in understanding the structural and biological role of lipid rafts in bacteria. Furthermore, this review shows a detailed description of a number of molecular and genetic approaches related to the discovery of bacterial lipid rafts as well as an overview of the group of tentative lipid-protein and protein-protein interactions that give consistency to these sophisticated signaling platforms. Additional data suggesting that lipid rafts are widely distributed in bacteria are presented in this review. Therefore, we discuss the available techniques and optimized protocols for the purification and analysis of raft-associated proteins in various bacterial species to aid in the study of bacterial lipid rafts in other laboratories that could be interested in this topic. Overall, the discovery of lipid rafts in bacteria reveals a new level of sophistication in signal transduction and membrane organization that was unexpected for bacteria and shows that bacteria are more complex than previously appreciated.
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Affiliation(s)
- Marc Bramkamp
- Department of Biology I, University of Munich (LMU), Planegg/Martinsried, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
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23
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Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG-SecDF-YajC-YidC. Proc Natl Acad Sci U S A 2014; 111:4844-9. [PMID: 24550475 DOI: 10.1073/pnas.1315901111] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The SecY/61 complex forms the protein-channel component of the ubiquitous protein secretion and membrane protein insertion apparatus. The bacterial version SecYEG interacts with the highly conserved YidC and SecDF-YajC subcomplex, which facilitates translocation into and across the membrane. Together, they form the holo-translocon (HTL), which we have successfully overexpressed and purified. In contrast to the homo-dimeric SecYEG, the HTL is a hetero-dimer composed of single copies of SecYEG and SecDF-YajC-YidC. The activities of the HTL differ from the archetypal SecYEG complex. It is more effective in cotranslational insertion of membrane proteins and the posttranslational secretion of a β-barreled outer-membrane protein driven by SecA and ATP becomes much more dependent on the proton-motive force. The activity of the translocating copy of SecYEG may therefore be modulated by association with different accessory subcomplexes: SecYEG (forming SecYEG dimers) or SecDF-YajC-YidC (forming the HTL). This versatility may provide a means to refine the secretion and insertion capabilities according to the substrate. A similar modularity may also be exploited for the translocation or insertion of a wide range of substrates across and into the endoplasmic reticular and mitochondrial membranes of eukaryotes.
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24
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Co-translational targeting and translocation of proteins to the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2392-402. [DOI: 10.1016/j.bbamcr.2013.02.021] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/16/2022]
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25
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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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26
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Kedrov A, Kusters I, Driessen AJM. Single-Molecule Studies of Bacterial Protein Translocation. Biochemistry 2013; 52:6740-54. [DOI: 10.1021/bi400913x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alexej Kedrov
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Ilja Kusters
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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27
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Karasawa A, Swier LJYM, Stuart MCA, Brouwers J, Helms B, Poolman B. Physicochemical factors controlling the activity and energy coupling of an ionic strength-gated ATP-binding cassette (ABC) transporter. J Biol Chem 2013; 288:29862-71. [PMID: 23979139 DOI: 10.1074/jbc.m113.499327] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cells control their volume through the accumulation of compatible solutes. The bacterial ATP-binding cassette transporter OpuA couples compatible solute uptake to ATP hydrolysis. Here, we study the gating mechanism and energy coupling of OpuA reconstituted in lipid nanodiscs. We show that anionic lipids are essential both for the gating and the energy coupling. The tight coupling between substrate binding on extracellular domains and ATP hydrolysis by cytoplasmic nucleotide-binding domains allows the study of transmembrane signaling in nanodiscs. From the tight coupling between processes at opposite sides of the membrane, we infer that the ATPase activity of OpuA in nanodiscs reflects solute translocation. Intriguingly, the substrate-dependent, ionic strength-gated ATPase activity of OpuA in nanodiscs is at least an order of magnitude higher than in lipid vesicles (i.e. with identical membrane lipid composition, ionic strength, and nucleotide and substrate concentrations). Even with the chemical components the same, the lateral pressure (profile) of the nanodiscs will differ from that of the vesicles. We thus propose that membrane tension limits translocation in vesicular systems. Increased macromolecular crowding does not activate OpuA but acts synergistically with ionic strength, presumably by favoring gating interactions of like-charged surfaces via excluded volume effects.
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Affiliation(s)
- Akira Karasawa
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre
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28
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Stoichiometry of SecYEG in the active translocase of Escherichia coli varies with precursor species. Proc Natl Acad Sci U S A 2013; 110:11815-20. [PMID: 23818593 DOI: 10.1073/pnas.1303289110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have established a reconstitution system for the translocon SecYEG in proteoliposomes in which 55% of the accessible translocons are active. This level corresponds to the fraction of translocons that are active in vitro when assessed in their native environment of cytoplasmic membrane vesicles. Assays using these robust reconstituted proteoliposomes and cytoplasmic membrane vesicles have revealed that the number of SecYEG units involved in an active translocase depends on the precursor undergoing transfer. The active translocase for the precursor of periplasmic galactose-binding protein contains twice the number of heterotrimeric units of SecYEG as does that for the precursor of outer membrane protein A.
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29
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Sanganna Gari RR, Frey NC, Mao C, Randall LL, King GM. Dynamic structure of the translocon SecYEG in membrane: direct single molecule observations. J Biol Chem 2013; 288:16848-16854. [PMID: 23609442 PMCID: PMC3675617 DOI: 10.1074/jbc.m113.471870] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/19/2013] [Indexed: 11/06/2022] Open
Abstract
Purified SecYEG was reconstituted into liposomes and studied in near-native conditions using atomic force microscopy. These SecYEG proteoliposomes were active in translocation assays. Changes in the structure of SecYEG as a function of time were directly visualized. The dynamics observed were significant in magnitude (∼1-10 Å) and were attributed to the two large loops of SecY linking transmembrane helices 6-7 and 8-9. In addition, we identified a distribution between monomers and dimers of SecYEG as well as a smaller population of higher order oligomers. This work provides a new vista of the flexible and dynamic structure of SecYEG, an intricate and vital membrane protein.
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Affiliation(s)
| | - Nathan C Frey
- Departments of Physics and Astronomy, Columbia, Missouri 65211
| | - Chunfeng Mao
- Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Linda L Randall
- Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Gavin M King
- Departments of Physics and Astronomy, Columbia, Missouri 65211; Biochemistry, University of Missouri, Columbia, Missouri 65211.
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30
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Glycolipozyme MPIase is essential for topology inversion of SecG during preprotein translocation. Proc Natl Acad Sci U S A 2013; 110:9734-9. [PMID: 23716687 DOI: 10.1073/pnas.1303160110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Presecretory proteins are translocated across biological membranes through protein-conducting channels such as Sec61 (eukaryotes) and SecYEG (bacteria). SecA, a translocation ATPase, pushes preproteins out with dynamic structural changes through SecYEG. SecG, a subunit of the SecYEG channel possessing two transmembrane stretches (TMs), undergoes topology inversion coupled with SecA-dependent translocation. Recently, we characterized membrane protein integrase (MPIase), a glycolipozyme involved in not only protein integration into membranes but also preprotein translocation. We report here that SecG inversion occurs only when MPIase associates with SecYEG. We also found that MPIase modulates the dimer orientation of SecYEG. Cysteine-scanning mutagenesis mapped SecG TM 2 to a relatively hydrophilic environment. The dimer formation of SecG, crosslinked at TM 2, was not observed on SecG inversion, indicating that SecYEG undergoes a dynamic structural change during preprotein translocation.
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Sachelaru I, Petriman NA, Kudva R, Kuhn P, Welte T, Knapp B, Drepper F, Warscheid B, Koch HG. YidC occupies the lateral gate of the SecYEG translocon and is sequentially displaced by a nascent membrane protein. J Biol Chem 2013; 288:16295-16307. [PMID: 23609445 DOI: 10.1074/jbc.m112.446583] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most membrane proteins are co-translationally inserted into the lipid bilayer via the universally conserved SecY complex and they access the lipid phase presumably via a lateral gate in SecY. In bacteria, the lipid transfer of membrane proteins from the SecY channel is assisted by the SecY-associated protein YidC, but details on the SecY-YidC interaction are unknown. By employing an in vivo and in vitro site-directed cross-linking approach, we have mapped the SecY-YidC interface and found YidC in contact with all four transmembrane domains of the lateral gate. This interaction did not require the SecDFYajC complex and was not influenced by SecA binding to SecY. In contrast, ribosomes dissociated the YidC contacts to lateral gate helices 2b and 8. The major contact between YidC and the lateral gate was lost in the presence of ribosome nascent chains and new SecY-YidC contacts appeared. These data demonstrate that the SecY-YidC interaction is influenced by nascent-membrane-induced lateral gate movements.
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Affiliation(s)
- Ilie Sachelaru
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany
| | - Narcis Adrian Petriman
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany
| | - Renuka Kudva
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany
| | - Patrick Kuhn
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany
| | - Thomas Welte
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany
| | | | - Friedel Drepper
- Fakultät für Biologie, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Zentrum für Biologische Signalstudien, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Fakultät für Biologie, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Zentrum für Biologische Signalstudien, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany.
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Akopian D, Dalal K, Shen K, Duong F, Shan SO. SecYEG activates GTPases to drive the completion of cotranslational protein targeting. ACTA ACUST UNITED AC 2013; 200:397-405. [PMID: 23401005 PMCID: PMC3575545 DOI: 10.1083/jcb.201208045] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
SecYEG drives conformational changes in the cotranslational targeting complex to activate it for GTP hydrolysis and the handover of the translating ribosome. Signal recognition particle (SRP) and its receptor (SR) comprise a highly conserved cellular machine that cotranslationally targets proteins to a protein-conducting channel, the bacterial SecYEG or eukaryotic Sec61p complex, at the target membrane. Whether SecYEG is a passive recipient of the translating ribosome or actively regulates this targeting machinery remains unclear. Here we show that SecYEG drives conformational changes in the cargo-loaded SRP–SR targeting complex that activate it for GTP hydrolysis and for handover of the translating ribosome. These results provide the first evidence that SecYEG actively drives the efficient delivery and unloading of translating ribosomes at the target membrane.
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Affiliation(s)
- David Akopian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Shen HH, Lithgow T, Martin LL. Reconstitution of membrane proteins into model membranes: seeking better ways to retain protein activities. Int J Mol Sci 2013; 14:1589-607. [PMID: 23344058 PMCID: PMC3565336 DOI: 10.3390/ijms14011589] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 02/01/2023] Open
Abstract
The function of any given biological membrane is determined largely by the specific set of integral membrane proteins embedded in it, and the peripheral membrane proteins attached to the membrane surface. The activity of these proteins, in turn, can be modulated by the phospholipid composition of the membrane. The reconstitution of membrane proteins into a model membrane allows investigation of individual features and activities of a given cell membrane component. However, the activity of membrane proteins is often difficult to sustain following reconstitution, since the composition of the model phospholipid bilayer differs from that of the native cell membrane. This review will discuss the reconstitution of membrane protein activities in four different types of model membrane - monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. Variation in the surrounding model environments for these four different types of membrane layer can affect the three-dimensional structure of reconstituted proteins and may possibly lead to loss of the proteins activity. We also discuss examples where the same membrane proteins have been successfully reconstituted into two or more model membrane systems with comparison of the observed activity in each system. Understanding of the behavioral changes for proteins in model membrane systems after membrane reconstitution is often a prerequisite to protein research. It is essential to find better solutions for retaining membrane protein activities for measurement and characterization in vitro.
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Affiliation(s)
- Hsin-Hui Shen
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne 3800, Australia; E-Mail:
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-3-9545-8159
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne 3800, Australia; E-Mail:
| | - Lisandra L. Martin
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia; E-Mail:
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Whitehouse S, Gold VAM, Robson A, Allen WJ, Sessions RB, Collinson I. Mobility of the SecA 2-helix-finger is not essential for polypeptide translocation via the SecYEG complex. ACTA ACUST UNITED AC 2012; 199:919-29. [PMID: 23209305 PMCID: PMC3518217 DOI: 10.1083/jcb.201205191] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Polypeptide translocation in bacteria, once underway, requires only one copy each of SecA and SecYEG and does not require the mobility of the SecA 2-helix-finger. The bacterial ATPase SecA and protein channel complex SecYEG form the core of an essential protein translocation machinery. The nature of the conformational changes induced by each stage of the hydrolytic cycle of ATP and how they are coupled to protein translocation are not well understood. The structure of the SecA–SecYEG complex revealed a 2-helix-finger (2HF) of SecA in an ideal position to contact the substrate protein and push it through the membrane. Surprisingly, immobilization of this finger at the edge of the protein channel had no effect on translocation, whereas its imposition inside the channel blocked transport. This analysis resolves the stoichiometry of the active complex, demonstrating that after the initiation process translocation requires only one copy each of SecA and SecYEG. The results also have important implications on the mechanism of energy transduction and the power stroke driving transport. Evidently, the 2HF is not a highly mobile transducing element of polypeptide translocation.
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Affiliation(s)
- Sarah Whitehouse
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
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Park E, Rapoport TA. Bacterial protein translocation requires only one copy of the SecY complex in vivo. ACTA ACUST UNITED AC 2012; 198:881-93. [PMID: 22927464 PMCID: PMC3432775 DOI: 10.1083/jcb.201205140] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In vivo probing of the oligomeric state of SecY during co- and post-translational translocation reveals that oligomerization is not required for this process. The transport of proteins across the plasma membrane in bacteria requires a channel formed from the SecY complex, which cooperates with either a translating ribosome in cotranslational translocation or the SecA ATPase in post-translational translocation. Whether translocation requires oligomers of the SecY complex is an important but controversial issue: it determines channel size, how the permeation of small molecules is prevented, and how the channel interacts with the ribosome and SecA. Here, we probe in vivo the oligomeric state of SecY by cross-linking, using defined co- and post-translational translocation intermediates in intact Escherichia coli cells. We show that nontranslocating SecY associated transiently through different interaction surfaces with other SecY molecules inside the membrane. These interactions were significantly reduced when a translocating polypeptide inserted into the SecY channel co- or post-translationally. Mutations that abolish the interaction between SecY molecules still supported viability of E. coli. These results show that a single SecY molecule is sufficient for protein translocation.
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Affiliation(s)
- Eunyong Park
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
Prokaryotes are characterized by an extreme flexibility of their respiratory systems allowing them to cope with various extreme environments. To date, supramolecular organization of respiratory systems appears as a conserved evolutionary feature as supercomplexes have been isolated in bacteria, archaea, and eukaryotes. Most of the yet identified supercomplexes in prokaryotes are involved in aerobic respiration and share similarities with those reported in mitochondria. Supercomplexes likely reflect a snapshot of the cellular respiration in a given cell population. While the exact nature of the determinants for supramolecular organization in prokaryotes is not understood, lipids, proteins, and subcellular localization can be seen as key players. Owing to the well-reported supramolecular organization of the mitochondrial respiratory chain in eukaryotes, several hypotheses have been formulated to explain the consequences of such arrangement and can be tested in the context of prokaryotes. Considering the inherent metabolic flexibility of a number of prokaryotes, cellular distribution and composition of the supramolecular assemblies should be studied in regards to environmental signals. This would pave the way to new concepts in cellular respiration.
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