1
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Knyazev DG, Winter L, Vogt A, Posch S, Öztürk Y, Siligan C, Goessweiner-Mohr N, Hagleitner-Ertugrul N, Koch HG, Pohl P. YidC from Escherichia coli Forms an Ion-Conducting Pore upon Activation by Ribosomes. Biomolecules 2023; 13:1774. [PMID: 38136645 PMCID: PMC10741985 DOI: 10.3390/biom13121774] [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: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The universally conserved protein YidC aids in the insertion and folding of transmembrane polypeptides. Supposedly, a charged arginine faces its hydrophobic lipid core, facilitating polypeptide sliding along YidC's surface. How the membrane barrier to other molecules may be maintained is unclear. Here, we show that the purified and reconstituted E. coli YidC forms an ion-conducting transmembrane pore upon ribosome or ribosome-nascent chain complex (RNC) binding. In contrast to monomeric YidC structures, an AlphaFold parallel YidC dimer model harbors a pore. Experimental evidence for a dimeric assembly comes from our BN-PAGE analysis of native vesicles, fluorescence correlation spectroscopy studies, single-molecule fluorescence photobleaching observations, and crosslinking experiments. In the dimeric model, the conserved arginine and other residues interacting with nascent chains point into the putative pore. This result suggests the possibility of a YidC-assisted insertion mode alternative to the insertase mechanism.
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Affiliation(s)
- Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Lukas Winter
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Sandra Posch
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Yavuz Öztürk
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nikolaus Goessweiner-Mohr
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nora Hagleitner-Ertugrul
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
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2
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Blaimschein N, Parameswaran H, Nagler G, Manioglu S, Helenius J, Ardelean C, Kuhn A, Guan L, Müller DJ. The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini. Structure 2023; 31:1419-1430.e5. [PMID: 37708891 PMCID: PMC10840855 DOI: 10.1016/j.str.2023.08.012] [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: 06/05/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
The insertion and folding of proteins into membranes is crucial for cell viability. Yet, the detailed contributions of insertases remain elusive. Here, we monitor how the insertase YidC guides the folding of the polytopic melibiose permease MelB into membranes. In vivo experiments using conditionally depleted E. coli strains show that MelB can insert in the absence of SecYEG if YidC resides in the cytoplasmic membrane. In vitro single-molecule force spectroscopy reveals that the MelB substrate itself forms two folding cores from which structural segments insert stepwise into the membrane. However, misfolding dominates, particularly in structural regions that interface the pseudo-symmetric α-helical domains of MelB. Here, YidC takes an important role in accelerating and chaperoning the stepwise insertion and folding process of both MelB folding cores. Our findings reveal a great flexibility of the chaperoning and insertase activity of YidC in the multifaceted folding processes of complex polytopic membrane proteins.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Hariharan Parameswaran
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Gisela Nagler
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Jonne Helenius
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland.
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3
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Dalbey RE, Kaushik S, Kuhn A. YidC as a potential antibiotic target. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119403. [PMID: 36427551 DOI: 10.1016/j.bbamcr.2022.119403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022]
Abstract
The membrane insertase YidC, is an essential bacterial component and functions in the folding and insertion of many membrane proteins during their biogenesis. It is a multispanning protein in the inner (cytoplasmic) membrane of Escherichia coli that binds its substrates in the "greasy slide" through hydrophobic interaction. The hydrophilic part of the substrate transiently localizes in the groove of YidC before it is translocated into the periplasm. The groove, which is flanked by the greasy slide, is within the center of the membrane, and provides a promising target for inhibitors that would block the insertase function of YidC. In addition, since the greasy slide is available for the binding of various substrates, it could also provide a binding site for inhibitory molecules. In this review we discuss in detail the structure and the mechanism of how YidC interacts not only with its substrates, but also with its partner proteins, the SecYEG translocase and the SRP signal recognition particle. Insight into the substrate binding to the YidC catalytic groove is presented. We wind up the review with the idea that the hydrophilic groove would be a potential site for drug binding and the feasibility of YidC-targeted drug development.
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Affiliation(s)
- Ross E Dalbey
- Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America.
| | - Sharbani Kaushik
- Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America
| | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany.
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4
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Polasa A, Hettige J, Immadisetty K, Moradi M. An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations. Front Mol Biosci 2022; 9:954262. [PMID: 36046607 PMCID: PMC9421054 DOI: 10.3389/fmolb.2022.954262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
YidC is a membrane protein that facilitates the insertion of newly synthesized proteins into lipid membranes. Through YidC, proteins are inserted into the lipid bilayer via the SecYEG-dependent complex. Additionally, YidC functions as a chaperone in protein folding processes. Several studies have provided evidence of its independent insertion mechanism. However, the mechanistic details of the YidC SecY-independent protein insertion mechanism remain elusive at the molecular level. This study elucidates the insertion mechanism of YidC at an atomic level through a combination of equilibrium and non-equilibrium molecular dynamics (MD) simulations. Different docking models of YidC-Pf3 in the lipid bilayer were built in this study to better understand the insertion mechanism. To conduct a complete investigation of the conformational difference between the two docking models developed, we used classical molecular dynamics simulations supplemented with a non-equilibrium technique. Our findings indicate that the YidC transmembrane (TM) groove is essential for this high-affinity interaction and that the hydrophilic nature of the YidC groove plays an important role in protein transport across the cytoplasmic membrane bilayer to the periplasmic side. At different stages of the insertion process, conformational changes in YidC’s TM domain and membrane core have a mechanistic effect on the Pf3 coat protein. Furthermore, during the insertion phase, the hydration and dehydration of the YidC’s hydrophilic groove are critical. These results demonstrate that Pf3 coat protein interactions with the membrane and YidC vary in different conformational states during the insertion process. Finally, this extensive study directly confirms that YidC functions as an independent insertase.
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5
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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6
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Chen Y, Sotomayor M, Capponi S, Hariharan B, Sahu ID, Haase M, Lorigan GA, Kuhn A, White SH, Dalbey RE. A hydrophilic microenvironment in the substrate-translocating groove of the YidC membrane insertase is essential for enzyme function. J Biol Chem 2022; 298:101690. [PMID: 35148995 PMCID: PMC8920935 DOI: 10.1016/j.jbc.2022.101690] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/27/2022] Open
Abstract
The YidC family of proteins are membrane insertases that catalyze the translocation of the periplasmic domain of membrane proteins via a hydrophilic groove located within the inner leaflet of the membrane. All homologs have a strictly conserved, positively charged residue in the center of this groove. In Bacillus subtilis, the positively charged residue has been proposed to be essential for interacting with negatively charged residues of the substrate, supporting a hypothesis that YidC catalyzes insertion via an early-step electrostatic attraction mechanism. Here, we provide data suggesting that the positively charged residue is important not for its charge but for increasing the hydrophilicity of the groove. We found that the positively charged residue is dispensable for Escherichia coli YidC function when an adjacent residue at position 517 was hydrophilic or aromatic, but was essential when the adjacent residue was apolar. Additionally, solvent accessibility studies support the idea that the conserved positively charged residue functions to keep the top and middle of the groove sufficiently hydrated. Moreover, we demonstrate that both the E. coli and Streptococcus mutans YidC homologs are functional when the strictly conserved arginine is replaced with a negatively charged residue, provided proper stabilization from neighboring residues. These combined results show that the positively charged residue functions to maintain a hydrophilic microenvironment in the groove necessary for the insertase activity, rather than to form electrostatic interactions with the substrates.
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Affiliation(s)
- Yuanyuan Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sara Capponi
- Department of Industrial and Applied Genomics, IBM AI and Cognitive Software Organization, IBM Almaden Research Center, San Jose, California, USA; NSF Center for Cellular Construction, University of California in San Francisco, San Francisco, California, USA
| | | | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA; Natural Science Division, Campbellsville University, Campbellsville, Kentucky, USA
| | - Maximilian Haase
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Stephen H White
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.
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7
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Structural and molecular mechanisms for membrane protein biogenesis by the Oxa1 superfamily. Nat Struct Mol Biol 2021; 28:234-239. [PMID: 33664512 DOI: 10.1038/s41594-021-00567-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Members of the Oxa1 superfamily perform membrane protein insertion in bacteria, the eukaryotic endoplasmic reticulum (ER), and endosymbiotic organelles. Here, we review recent structures of the three ER-resident insertases and discuss the extent to which structure and function are conserved with their bacterial counterpart YidC.
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8
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Molecular communication of the membrane insertase YidC with translocase SecYEG affects client proteins. Sci Rep 2021; 11:3940. [PMID: 33594158 PMCID: PMC7886851 DOI: 10.1038/s41598-021-83224-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/25/2021] [Indexed: 11/18/2022] Open
Abstract
The membrane insertase YidC inserts newly synthesized proteins by its hydrophobic slide consisting of the two transmembrane (TM) segments TM3 and TM5. Mutations in this part of the protein affect the insertion of the client proteins. We show here that a quintuple mutation, termed YidC-5S, inhibits the insertion of the subunit a of the FoF1 ATP synthase but has no effect on the insertion of the Sec-independent M13 procoat protein and the C-tail protein SciP. Further investigations show that the interaction of YidC-5S with SecY is inhibited. The purified and fluorescently labeled YidC-5S did not approach SecYEG when both were co-reconstituted in proteoliposomes in contrast to the co-reconstituted YidC wild type. These results suggest that TM3 and TM5 are involved in the formation of a common YidC-SecYEG complex that is required for the insertion of Sec/YidC-dependent client proteins.
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9
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A Celecoxib Derivative Eradicates Antibiotic-Resistant Staphylococcus aureus and Biofilms by Targeting YidC2 Translocase. Int J Mol Sci 2020; 21:ijms21239312. [PMID: 33297331 PMCID: PMC7730571 DOI: 10.3390/ijms21239312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 12/02/2022] Open
Abstract
The treatment of Staphylococcus aureus infections is impeded by the prevalence of MRSA and the formation of persisters and biofilms. Previously, we identified two celecoxib derivatives, Cpd36 and Cpd46, to eradicate MRSA and other staphylococci. Through whole-genome resequencing, we obtained several lines of evidence that these compounds might act by targeting the membrane protein translocase YidC2. Our data showed that ectopic expression of YidC2 in S. aureus decreased the bacterial susceptibility to Cpd36 and Cpd46, and that the YidC2-mediated tolerance to environmental stresses was suppressed by both compounds. Moreover, the membrane translocation of ATP synthase subunit c, a substrate of YidC2, was blocked by Cpd46, leading to a reduction in bacterial ATP production. Furthermore, we found that the thermal stability of bacterial YidC2 was enhanced, and introducing point mutations into the substrate-interacting cavity of YidC2 had a dramatic effect on Cpd36 binding via surface plasmon resonance assays. Finally, we demonstrated that these YidC2 inhibitors could effectively eradicate MRSA persisters and biofilms. Our findings highlight the potential of impeding YidC2-mediated translocation of membrane proteins as a new strategy for the treatment of bacterial infections.
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10
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Hariharan B, Pross E, Soman R, Kaushik S, Kuhn A, Dalbey RE. Polarity/charge as a determinant of translocase requirements for membrane protein insertion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183502. [PMID: 33130098 DOI: 10.1016/j.bbamem.2020.183502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/12/2020] [Accepted: 10/21/2020] [Indexed: 11/17/2022]
Abstract
The YidC insertase of Escherichia coli inserts membrane proteins with small periplasmic loops (~20 residues). However, it has difficulty transporting loops that contain positively charged residues compared to negatively charged residues and, as a result, increasing the positive charge has an increased requirement for the Sec machinery as compared to negatively charged loops (Zhu et al., 2013; Soman et al., 2014). This suggested that the polarity and charge of the periplasmic regions of membrane proteins determine the YidC and Sec translocase requirements for insertion. Here we tested this polarity/charge hypothesis by showing that insertion of our model substrate protein procoat-Lep can become YidC/Sec dependent when the periplasmic loop was converted to highly polar even in the absence of any charged residues. Moreover, adding a number of hydrophobic amino acids to a highly polar loop can decrease the Sec-dependence of the otherwise strictly Sec-dependent membrane proteins. We also demonstrate that the length of the procoat-Lep loop is indeed a determinant for Sec-dependence by inserting alanine residues that do not markedly change the overall hydrophilicity of the periplasmic loop. Taken together, the results support the polarity/charge hypothesis as a determinant for the translocase requirement for procoat insertion.
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Affiliation(s)
- Balasubramani Hariharan
- Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America
| | - Eva Pross
- Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany
| | - Raunak Soman
- Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America
| | - Sharbani Kaushik
- Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America
| | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany
| | - Ross E Dalbey
- Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America.
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11
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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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12
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Abstract
To identify the translocation components in cells, and to understand how they function in protein transport and membrane insertion, a variety of techniques have been used such as genetics, biochemistry, structural biology and single molecule methods. In particular, site-directed crosslinking between the client proteins and components of the translocation machineries have contributed significantly in the past and will do so in the future. One advantage of this technology is that it can be applied in vivo as well as in vitro and a comparison of the two approaches can be made. Also, the in vivo techniques allow time-dependent protocols which are essential for studying cellular pathways. Protein purification and reconstitution into proteoliposomes are the gold standard for studying membrane-based transport and translocation systems. With these biochemically defined approaches the function of each component in protein transport can be addressed individually with a plethora of biophysical techniques. Recently, the use of nanodiscs for reconstitution has added another extension of this reductionistic approach. Fluorescence based studies, cryo-microscopy and NMR spectroscopy have significantly added to our understanding how proteins move into and across membranes and will do this also in future.
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Affiliation(s)
- Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599, Stuttgart, Germany.
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13
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Tracking the Stepwise Movement of a Membrane-inserting Protein In Vivo. J Mol Biol 2020; 432:484-496. [DOI: 10.1016/j.jmb.2019.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022]
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14
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Kiefer D, Kuhn A. YidC-mediated membrane insertion. FEMS Microbiol Lett 2018; 365:4980910. [DOI: 10.1093/femsle/fny106] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/19/2018] [Indexed: 01/06/2023] Open
Affiliation(s)
- Dorothee Kiefer
- Department of Microbiology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Andreas Kuhn
- Department of Microbiology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
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15
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Each protomer of a dimeric YidC functions as a single membrane insertase. Sci Rep 2018; 8:589. [PMID: 29330366 PMCID: PMC5766580 DOI: 10.1038/s41598-017-18830-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022] Open
Abstract
The membrane insertase YidC catalyzes the entrance of newly synthesized proteins into the lipid bilayer. As an integral membrane protein itself, YidC can be found as a monomer, a dimer or also as a member of the holotranslocase SecYEGDF-YajC-YidC. To investigate whether the dimeric YidC is functional and whether two copies cooperate to insert a single substrate, we constructed a fusion protein where two copies of YidC are connected by a short linker peptide. The 120 kDa protein is stable and functional as it supports the membrane insertion of the M13 procoat protein, the C-tailed protein SciP and the fusion protein Pf3-Lep. Mutations that inhibit either protomer do not inactivate the insertase and rather keep it functional. When both protomers are defective, the substrate proteins accumulate in the cytoplasm. This suggests that the dimeric YidC operates as two insertases. Consistent with this, we show that the dimeric YidC can bind two substrate proteins simultaneously, suggesting that YidC indeed functions as a monomer.
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16
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Petriman NA, Jauß B, Hufnagel A, Franz L, Sachelaru I, Drepper F, Warscheid B, Koch HG. The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY. Sci Rep 2018; 8:578. [PMID: 29330529 PMCID: PMC5766551 DOI: 10.1038/s41598-017-19019-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/20/2017] [Indexed: 12/26/2022] Open
Abstract
YidC/Oxa1/Alb3 are essential proteins that operate independently or cooperatively with the Sec machinery during membrane protein insertion in bacteria, archaea and eukaryotic organelles. Although the interaction between the bacterial SecYEG translocon and YidC has been observed in multiple studies, it is still unknown which domains of YidC are in contact with the SecYEG translocon. By in vivo and in vitro site-directed and para-formaldehyde cross-linking we identified the auxiliary transmembrane domain 1 of E. coli YidC as a major contact site for SecY and SecG. Additional SecY contacts were observed for the tightly packed globular domain and the C1 loop of YidC, which reveals that the hydrophilic cavity of YidC faces the lateral gate of SecY. Surprisingly, YidC-SecYEG contacts were only observed when YidC and SecYEG were present at about stoichiometric concentrations, suggesting that the YidC-SecYEG contact in vivo is either very transient or only observed for a very small SecYEG sub-population. This is different for the YidC-SRP and YidC-FtsY interaction, which involves the C1 loop of YidC and is efficiently observed even at sub-stoichiometric concentrations of SRP/FtsY. In summary, our data provide a first detailed view on how YidC interacts with the SecYEG translocon and the SRP-targeting machinery.
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Affiliation(s)
- Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Benjamin Jauß
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Antonia Hufnagel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Lisa Franz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Ilie Sachelaru
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Friedel Drepper
- Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
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17
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Xin Y, Zhao Y, Zheng J, Zhou H, Zhang XC, Tian C, Huang Y. Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion. FASEB J 2018; 32:2411-2421. [PMID: 29295859 DOI: 10.1096/fj.201700893rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The evolutionarily conserved YidC/Oxa1/Alb3 family of proteins represents a unique membrane protein family that facilitates the insertion, folding, and assembly of a cohort of α-helical membrane proteins in all kingdoms of life, yet its underlying mechanisms remain elusive. We report the crystal structures of the full-length Thermotoga maritima YidC (TmYidC) and the TmYidC periplasmic domain (TmPD) at a resolution of 3.8 and 2.5 Å, respectively. The crystal structure of TmPD reveals a β-supersandwich fold but with apparently shortened β strands and different connectivity, as compared to the Escherichia coli YidC (EcYidC) periplasmic domain (EcPD). TmYidC in a detergent-solubilized state also adopts a monomeric form and its conserved core domain, which consists of 2 loosely associated α-helical bundles, assemble a fold similar to that of the other YidC homologues, yet distinct from that of the archaeal YidC-like DUF106 protein. Functional analysis using in vivo photo-crosslinking experiments demonstrates that Pf3 coat protein, a Sec-independent YidC substrate, exits to the lipid bilayer laterally via one of the 2 α-helical bundle interfaces: TM3-TM5. Engineered intramolecular disulfide bonds in TmYidC, in combination with complementation assays, suggest that significant rearrangement of the 2 α-helical bundles at the top of the hydrophilic groove is critical for TmYidC function. These experiments provide a more detailed mechanical insight into YidC-mediated membrane protein biogenesis.-Xin, Y., Zhao, Y., Zheng, J., Zhou, H., Zhang, X. C., Tian, C., Huang, Y. Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion.
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Affiliation(s)
- Yanlong Xin
- National Laboratory for Physical Science at Microscale, School of Life Science, University of Science and Technology of China, Hefei, China.,National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhao
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiangge Zheng
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changlin Tian
- National Laboratory for Physical Science at Microscale, School of Life Science, University of Science and Technology of China, Hefei, China.,High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, China
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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18
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Kuhn A, Haase M, Leptihn S. Assisted and Unassisted Protein Insertion into Liposomes. Biophys J 2017; 113:1187-1193. [PMID: 28454841 PMCID: PMC5607036 DOI: 10.1016/j.bpj.2017.03.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/30/2017] [Accepted: 03/31/2017] [Indexed: 02/04/2023] Open
Abstract
The insertion of newly synthesized membrane proteins is a well-regulated and fascinating process occurring in every living cell. Several translocases and insertases have been found in prokaryotic and eukaryotic cells, the Sec61 complex and the Get complex in the endoplasmic reticulum and the SecYEG complex and YidC in bacteria and archaea. In mitochondria, TOM and TIM complexes transport nuclear-encoded proteins, whereas the Oxa1 is required for the insertion of mitochondria-encoded membrane proteins. Related to the bacterial YidC and the mitochondrial Oxa1 are the Alb3 and Alb4 proteins in chloroplasts. These membrane insertases are comparably simple and can be studied in vitro, after their biochemical purification and reconstitution in artificial lipid bilayers such as liposomes or nanodiscs. Here, we describe the recent progress to study the molecular mechanism of YidC-dependent and unassisted membrane insertion at the single molecule level.
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Affiliation(s)
- Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Maximilian Haase
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Sebastian Leptihn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany.
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19
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YidC Insertase of Escherichia coli: Water Accessibility and Membrane Shaping. Structure 2017; 25:1403-1414.e3. [PMID: 28844594 DOI: 10.1016/j.str.2017.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/31/2017] [Accepted: 07/21/2017] [Indexed: 12/21/2022]
Abstract
The YidC/Oxa1/Alb3 family of membrane proteins function to insert proteins into membranes in bacteria, mitochondria, and chloroplasts. Recent X-ray structures of YidC from Bacillus halodurans and Escherichia coli revealed a hydrophilic groove that is accessible from the lipid bilayer and the cytoplasm. Here, we explore the water accessibility within the conserved core region of the E. coli YidC using in vivo cysteine alkylation scanning and molecular dynamics (MD) simulations of YidC in POPE/POPG membranes. As expected from the structure, YidC possesses an aqueous membrane cavity localized to the membrane inner leaflet. Both the scanning data and the MD simulations show that the lipid-exposed transmembrane helices 3, 4, and 5 are short, leading to membrane thinning around YidC. Close examination of the MD data reveals previously unrecognized structural features that are likely important for protein stability and function.
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20
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Abstract
The insertion and assembly of proteins into the inner membrane of bacteria are crucial for many cellular processes, including cellular respiration, signal transduction, and ion and pH homeostasis. This process requires efficient membrane targeting and insertion of proteins into the lipid bilayer in their correct orientation and proper conformation. Playing center stage in these events are the targeting components, signal recognition particle (SRP) and the SRP receptor FtsY, as well as the insertion components, the Sec translocon and the YidC insertase. Here, we will discuss new insights provided from the recent high-resolution structures of these proteins. In addition, we will review the mechanism by which a variety of proteins with different topologies are inserted into the inner membrane of Gram-negative bacteria. Finally, we report on the energetics of this process and provide information on how membrane insertion occurs in Gram-positive bacteria and Archaea. It should be noted that most of what we know about membrane protein assembly in bacteria is based on studies conducted in Escherichia coli.
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Affiliation(s)
- Andreas Kuhn
- Institute for Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Ross E Dalbey
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
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21
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Kuhn A, Kiefer D. Membrane protein insertase YidC in bacteria and archaea. Mol Microbiol 2017; 103:590-594. [PMID: 27879020 DOI: 10.1111/mmi.13586] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2016] [Indexed: 12/01/2022]
Abstract
The insertion of proteins into the prokaryotic plasma membrane is catalyzed by translocases and insertases. On one hand, the Sec translocase operates as a transmembrane channel that can open laterally to first bind and then release the hydrophobic segments of a substrate protein into the lipid bilayer. On the other hand, YidC insertases interact with their substrates in a groove-like structure at an amphiphilic protein-lipid interface thus allowing the transmembrane segments of the substrate to slide into the lipid bilayer. The recently published high-resolution structures of YidC provide new mechanistic insights of how transmembrane proteins achieve the transition from an aqueous environment in the cytoplasm to the hydrophobic lipid bilayer environment of the membrane.
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Affiliation(s)
- Andreas Kuhn
- Institute of Microbiology, University of Hohenheim, Stuttgart, 70599, Germany
| | - Dorothee Kiefer
- Institute of Microbiology, University of Hohenheim, Stuttgart, 70599, Germany
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22
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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23
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Abstract
The YidC/Alb3/Oxa1 family functions in the insertion and folding of proteins in the bacterial cytoplasmic membrane, the chloroplast thylakoid membrane, and the mitochondrial inner membrane. All members share a conserved region composed of five transmembrane regions. These proteins mediate membrane insertion of an assorted group of proteins, ranging from respiratory subunits in the mitochondria and light-harvesting chlorophyll-binding proteins in chloroplasts to ATP synthase subunits in bacteria. This review discusses the YidC/Alb3/Oxa1 protein family as well as their function in membrane insertion and two new structures of the bacterial YidC, which suggest a mechanism for membrane insertion by this family of insertases.
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Affiliation(s)
- Seth W Hennon
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Raunak Soman
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Lu Zhu
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Ross E Dalbey
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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24
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Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase. Sci Rep 2014; 4:7299. [PMID: 25466392 PMCID: PMC4252904 DOI: 10.1038/srep07299] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/17/2014] [Indexed: 11/08/2022] Open
Abstract
Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for membrane proteins. In Gram-negative bacteria, the transmembrane and periplasmic regions of YidC interact with the Sec proteins, forming a multi-protein complex for Sec-dependent membrane protein integration. Here, we report the crystal structure of full-length Escherichia coli YidC. The structure reveals that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase, and provided structural insight into the multi-protein complex.
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25
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A conserved cysteine residue of Bacillus subtilis SpoIIIJ is important for endospore development. PLoS One 2014; 9:e99811. [PMID: 25133632 PMCID: PMC4136701 DOI: 10.1371/journal.pone.0099811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/19/2014] [Indexed: 11/20/2022] Open
Abstract
During sporulation in Bacillus subtilis, the onset of activity of the late forespore-specific sigma factor σG coincides with completion of forespore engulfment by the mother cell. At this stage, the forespore becomes a free protoplast, surrounded by the mother cell cytoplasm and separated from it by two membranes that derive from the asymmetric division septum. Continued gene expression in the forespore, isolated from the surrounding medium, relies on the SpoIIIA-SpoIIQ secretion system assembled from proteins synthesised both in the mother cell and in the forespore. The membrane protein insertase SpoIIIJ, of the YidC/Oxa1/Alb3 family, is involved in the assembly of the SpoIIIA-SpoIIQ complex. Here we show that SpoIIIJ exists as a mixture of monomers and dimers stabilised by a disulphide bond. We show that residue Cys134 within transmembrane segment 2 (TM2) of SpoIIIJ is important to stabilise the protein in the dimeric form. Labelling of Cys134 with a Cys-reactive reagent could only be achieved under stringent conditions, suggesting a tight association at least in part through TM2, between monomers in the membrane. Substitution of Cys134 by an Ala results in accumulation of the monomer, and reduces SpoIIIJ function in vivo. Therefore, SpoIIIJ activity in vivo appears to require dimer formation.
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26
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Wickles S, Singharoy A, Andreani J, Seemayer S, Bischoff L, Berninghausen O, Soeding J, Schulten K, van der Sluis EO, Beckmann R. A structural model of the active ribosome-bound membrane protein insertase YidC. eLife 2014; 3:e03035. [PMID: 25012291 PMCID: PMC4124156 DOI: 10.7554/elife.03035] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.
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Affiliation(s)
- Stephan Wickles
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Jessica Andreani
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Seemayer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lukas Bischoff
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Soeding
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Eli O van der Sluis
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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27
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Hennon SW, Dalbey RE. Cross-Linking-Based Flexibility and Proximity Relationships between the TM Segments of the Escherichia coli YidC. Biochemistry 2014; 53:3278-86. [DOI: 10.1021/bi500257u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seth W. Hennon
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross E. Dalbey
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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28
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Dalbey RE, Kuhn A. How YidC inserts and folds proteins across a membrane. Nat Struct Mol Biol 2014; 21:435-6. [DOI: 10.1038/nsmb.2823] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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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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30
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Dalbey RE, Kuhn A, Zhu L, Kiefer D. The membrane insertase YidC. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1489-96. [PMID: 24418623 DOI: 10.1016/j.bbamcr.2013.12.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/19/2013] [Accepted: 12/31/2013] [Indexed: 12/28/2022]
Abstract
The membrane insertases YidC-Oxa1-Alb3 provide a simple cellular system that catalyzes the transmembrane topology of newly synthesized membrane proteins. The insertases are composed of a single protein with 5 to 6 transmembrane (TM) helices that contact hydrophobic segments of the substrate proteins. Since YidC also cooperates with the Sec translocase it is widely involved in the assembly of many different membrane proteins including proteins that obtain complex membrane topologies. Homologues found in mitochondria (Oxa1) and thylakoids (Alb3) point to a common evolutionary origin and also demonstrate the general importance of this cellular process. 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)
- Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Garbenstr 30, 70599 Stuttgart, Germany.
| | - Lu Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Doro Kiefer
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Garbenstr 30, 70599 Stuttgart, Germany
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31
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Seitl I, Wickles S, Beckmann R, Kuhn A, Kiefer D. The C-terminal regions of YidC from Rhodopirellula baltica and Oceanicaulis alexandrii bind to ribosomes and partially substitute for SRP receptor function in Escherichia coli. Mol Microbiol 2013; 91:408-21. [PMID: 24261830 DOI: 10.1111/mmi.12465] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2013] [Indexed: 01/21/2023]
Abstract
The marine Gram-negative bacteria Rhodopirellula baltica and Oceanicaulis alexandrii have, in contrast to Escherichia coli, membrane insertases with extended positively charged C-terminal regions similar to the YidC homologues in mitochondria and Gram-positive bacteria. We have found that chimeric forms of E. coli YidC fused to the C-terminal YidC regions from the marine bacteria mediate binding of YidC to ribosomes and therefore may have a functional role for targeting a nascent protein to the membrane. Here, we show in E. coli that an extended C-terminal region of YidC can compensate for a loss of SRP-receptor function in vivo. Furthermore, the enhanced affinity of the ribosome to the chimeric YidC allows the isolation of a ribosome nascent chain complex together with the C-terminally elongated YidC chimera. This complex was visualized at 8.6 Å by cryo-electron microscopy and shows a close contact of the ribosome and a YidC monomer.
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Affiliation(s)
- Ines Seitl
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599, Stuttgart, Germany
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32
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Soman R, Yuan J, Kuhn A, Dalbey RE. Polarity and charge of the periplasmic loop determine the YidC and sec translocase requirement for the M13 procoat lep protein. J Biol Chem 2013; 289:1023-32. [PMID: 24275657 DOI: 10.1074/jbc.m113.522250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During membrane biogenesis, the M13 procoat protein is inserted into the lipid bilayer in a strictly YidC-dependent manner with both the hydrophobic signal sequence and the membrane anchor sequence promoting translocation of the periplasmic loop via a hairpin mechanism. Here, we find that the translocase requirements can be altered for PClep in a predictable manner by changing the polarity and charge of the peptide region that is translocated across the membrane. When the polarity of the translocated peptide region is lowered and the charged residues in this region are removed, translocation of this loop region occurs largely by a YidC- and Sec-independent mechanism. When the polarity is increased to that of the wild-type procoat protein, the YidC insertase is essential for translocation. Further increasing the polarity, by adding charged residues, switches the insertion pathway to a YidC/Sec mechanism. Conversely, we find that increasing the hydrophobicity of the transmembrane segments of PClep can decrease the translocase requirement for translocation of the peptide chain. This study provides a framework to understand why the YidC and Sec machineries exist in parallel and demonstrates that the YidC insertase has a limited capacity to translocate a peptide chain on its own.
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Affiliation(s)
- Raunak Soman
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 and
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Zhu L, Kaback HR, Dalbey RE. YidC protein, a molecular chaperone for LacY protein folding via the SecYEG protein machinery. J Biol Chem 2013; 288:28180-94. [PMID: 23928306 DOI: 10.1074/jbc.m113.491613] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To understand how YidC and SecYEG function together in membrane protein topogenesis, insertion and folding of the lactose permease of Escherichia coli (LacY), a 12-transmembrane helix protein LacY that catalyzes symport of a galactoside and an H(+), was studied. Although both the SecYEG machinery and signal recognition particle are required for insertion of LacY into the membrane, YidC is not required for translocation of the six periplasmic loops in LacY. Rather, YidC acts as a chaperone, facilitating LacY folding. Upon YidC depletion, the conformation of LacY is perturbed, as judged by monoclonal antibody binding studies and by in vivo cross-linking between introduced Cys pairs. Disulfide cross-linking also demonstrates that YidC interacts with multiple transmembrane segments of LacY during membrane biogenesis. Moreover, YidC is strictly required for insertion of M13 procoat protein fused into the middle cytoplasmic loop of LacY. In contrast, the loops preceding and following the inserted procoat domain are dependent on SecYEG for insertion. These studies demonstrate close cooperation between the two complexes in membrane biogenesis and that YidC functions primarily as a foldase for LacY.
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Affiliation(s)
- Lu Zhu
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 and
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Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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Winterfeld S, Ernst S, Börsch M, Gerken U, Kuhn A. Real time observation of single membrane protein insertion events by the Escherichia coli insertase YidC. PLoS One 2013; 8:e59023. [PMID: 23527078 PMCID: PMC3602594 DOI: 10.1371/journal.pone.0059023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 02/09/2013] [Indexed: 11/18/2022] Open
Abstract
Membrane protein translocation and insertion is a central issue in biology. Here we focus on a minimal system, the membrane insertase YidC of Escherichia coli that inserts small proteins into the cytoplasmic membrane. In a reconstituted system individual insertion processes were followed by single-pair fluorescence resonance energy transfer (FRET), with a pair of fluorophores on YidC and the substrate Pf3 coat protein. After addition of N-terminally labeled Pf3 coat protein a close contact to YidC at its cytoplasmic label was observed. This allowed to monitor the translocation of the N-terminal domain of Pf3 coat protein across the membrane in real time. Translocation occurred within milliseconds as the label on the N-terminal domain rapidly approached the fluorophore on the periplasmic domain of YidC at the trans side of the membrane. After the close contact, the two fluorophores separated, reflecting the release of the translocated Pf3 coat protein from YidC into the membrane bilayer. When the Pf3 coat protein was labeled C-terminally, no translocation of the label was observed although efficient binding to the cytoplasmic positions of YidC occurred.
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Affiliation(s)
- Sophie Winterfeld
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Stefan Ernst
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
- 3 Institute of Physics, University of Stuttgart, Stuttgart, Germany
| | - Michael Börsch
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
- 3 Institute of Physics, University of Stuttgart, Stuttgart, Germany
| | - Uwe Gerken
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
- * E-mail:
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Neugebauer SA, Baulig A, Kuhn A, Facey SJ. Membrane Protein Insertion of Variant MscL Proteins Occurs at YidC and SecYEG of Escherichia coli. J Mol Biol 2012; 417:375-86. [DOI: 10.1016/j.jmb.2012.01.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/23/2011] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
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