1
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Myronidi I, Ring A, Wu F, Ljungdahl PO. ER-localized Shr3 is a selective co-translational folding chaperone necessary for amino acid permease biogenesis. J Cell Biol 2023; 222:e202208060. [PMID: 37477900 PMCID: PMC10359922 DOI: 10.1083/jcb.202208060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 04/16/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023] Open
Abstract
Proteins with multiple membrane-spanning segments (MS) co-translationally insert into the endoplasmic reticulum (ER) membrane of eukaryotic cells. Shr3, an ER membrane-localized chaperone in Saccharomyces cerevisiae, is required for the functional expression of a family of 18 amino acid permeases (AAP) comprised of 12 MS. We have used comprehensive scanning mutagenesis and deletion analysis of Shr3 combined with a modified split-ubiquitin approach to probe chaperone-substrate interactions in vivo. Shr3 selectively interacts with nested C-terminal AAP truncations in marked contrast to similar truncations of non-Shr3 substrate sugar transporters. Shr3-AAP interactions initiate with the first four MS of AAP and successively strengthen but weaken abruptly when all 12 MS are present. Shr3-AAP interactions are based on structural rather than sequence-specific interactions involving membrane and luminal domains of Shr3. The data align with Shr3 engaging nascent N-terminal chains of AAP, functioning as a scaffold to facilitate folding as translation completes.
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Affiliation(s)
- Ioanna Myronidi
- Department of Molecular Biosciences, The Wenner-Gren Institute, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Andreas Ring
- Department of Molecular Biosciences, The Wenner-Gren Institute, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Fei Wu
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Per O. Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, SciLifeLab, Stockholm University, Stockholm, Sweden
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2
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Whitley P, Grau B, Gumbart JC, Martínez-Gil L, Mingarro I. Folding and Insertion of Transmembrane Helices at the ER. Int J Mol Sci 2021; 22:ijms222312778. [PMID: 34884581 PMCID: PMC8657811 DOI: 10.3390/ijms222312778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023] Open
Abstract
In eukaryotic cells, the endoplasmic reticulum (ER) is the entry point for newly synthesized proteins that are subsequently distributed to organelles of the endomembrane system. Some of these proteins are completely translocated into the lumen of the ER while others integrate stretches of amino acids into the greasy 30 Å wide interior of the ER membrane bilayer. It is generally accepted that to exist in this non-aqueous environment the majority of membrane integrated amino acids are primarily non-polar/hydrophobic and adopt an α-helical conformation. These stretches are typically around 20 amino acids long and are known as transmembrane (TM) helices. In this review, we will consider how transmembrane helices achieve membrane integration. We will address questions such as: Where do the stretches of amino acids fold into a helical conformation? What is/are the route/routes that these stretches take from synthesis at the ribosome to integration through the ER translocon? How do these stretches ‘know’ to integrate and in which orientation? How do marginally hydrophobic stretches of amino acids integrate and survive as transmembrane helices?
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Affiliation(s)
- Paul Whitley
- Department of Biology and Biochemistry, Centre for Regenerative Medicine, University of Bath, Bath BA2 7AY, UK;
| | - Brayan Grau
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - James C. Gumbart
- School of Physics, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Luis Martínez-Gil
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
- Correspondence: ; Tel.: +34-963543796
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3
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Shishido H, Yoon JS, Yang Z, Skach WR. CFTR trafficking mutations disrupt cotranslational protein folding by targeting biosynthetic intermediates. Nat Commun 2020; 11:4258. [PMID: 32848127 PMCID: PMC7450043 DOI: 10.1038/s41467-020-18101-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/04/2020] [Indexed: 02/03/2023] Open
Abstract
Protein misfolding causes a wide spectrum of human disease, and therapies that target misfolding are transforming the clinical care of cystic fibrosis. Despite this success, however, very little is known about how disease-causing mutations affect the de novo folding landscape. Here we show that inherited, disease-causing mutations located within the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) have distinct effects on nascent polypeptides. Two of these mutations (A455E and L558S) delay compaction of the nascent NBD1 during a critical window of synthesis. The observed folding defect is highly dependent on nascent chain length as well as its attachment to the ribosome. Moreover, restoration of the NBD1 cotranslational folding defect by second site suppressor mutations also partially restores folding of full-length CFTR. These findings demonstrate that nascent folding intermediates can play an important role in disease pathogenesis and thus provide potential targets for pharmacological correction.
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Affiliation(s)
- Hideki Shishido
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Jae Seok Yoon
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Zhongying Yang
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - William R Skach
- Cystic Fibrosis Foundation, 4550 Montgomery Ave., Suite 1100N, Bethesda, MD, 20814, USA.
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4
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Snapp EL, McCaul N, Quandte M, Cabartova Z, Bontjer I, Källgren C, Nilsson I, Land A, von Heijne G, Sanders RW, Braakman I. Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide. eLife 2017; 6:26067. [PMID: 28753126 PMCID: PMC5577925 DOI: 10.7554/elife.26067] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/26/2017] [Indexed: 12/29/2022] Open
Abstract
Like all other secretory proteins, the HIV-1 envelope glycoprotein gp160 is targeted to the endoplasmic reticulum (ER) by its signal peptide during synthesis. Proper gp160 folding in the ER requires core glycosylation, disulfide-bond formation and proline isomerization. Signal-peptide cleavage occurs only late after gp160 chain termination and is dependent on folding of the soluble subunit gp120 to a near-native conformation. We here detail the mechanism by which co-translational signal-peptide cleavage is prevented. Conserved residues from the signal peptide and residues downstream of the canonical cleavage site form an extended alpha-helix in the ER membrane, which covers the cleavage site, thus preventing cleavage. A point mutation in the signal peptide breaks the alpha helix allowing co-translational cleavage. We demonstrate that postponed cleavage of gp160 enhances functional folding of the molecule. The change to early cleavage results in decreased viral fitness compared to wild-type HIV.
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Affiliation(s)
- Erik Lee Snapp
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nicholas McCaul
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matthias Quandte
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Zuzana Cabartova
- National Institute of Public Health, National Reference Laboratory for Viral Hepatitis, Prague, Czech Republic
| | - Ilja Bontjer
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam, Academic Medical Center, Amsterdam, Netherlands
| | - Carolina Källgren
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Aafke Land
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rogier W Sanders
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam, Academic Medical Center, Amsterdam, Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
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5
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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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6
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7
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Quality control of nonstop membrane proteins at the ER membrane and in the cytosol. Sci Rep 2016; 6:30795. [PMID: 27481473 PMCID: PMC4969602 DOI: 10.1038/srep30795] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/11/2016] [Indexed: 11/08/2022] Open
Abstract
Since messenger RNAs without a stop codon (nonstop mRNAs) for organelle-targeted proteins and their translation products (nonstop proteins) generate clogged translocon channels as well as stalled ribosomes, cells have mechanisms to degrade nonstop mRNAs and nonstop proteins and to clear the translocons (e.g. the Sec61 complex) by release of nonstop proteins into the organellar lumen. Here we followed the fate of nonstop endoplasmic reticulum (ER) membrane proteins with different membrane topologies in yeast to evaluate the importance of the Ltn1-dependent cytosolic degradation and the Dom34-dependent release of the nonstop membrane proteins. Ltn1-dependent degradation differed for membrane proteins with different topologies and its failure did not affect ER protein import or cell growth. On the other hand, failure in the Dom34-dependent release of the nascent polypeptide from the ribosome led to the block of the Sec61 channel and resultant inhibition of other protein import into the ER caused cell growth defects. Therefore, the nascent chain release from the translation apparatus is more instrumental in clearance of the clogged ER translocon channel and thus maintenance of normal cellular functions.
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8
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Ellgaard L, McCaul N, Chatsisvili A, Braakman I. Co- and Post-Translational Protein Folding in the ER. Traffic 2016; 17:615-38. [PMID: 26947578 DOI: 10.1111/tra.12392] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/26/2016] [Accepted: 03/03/2016] [Indexed: 12/19/2022]
Abstract
The biophysical rules that govern folding of small, single-domain proteins in dilute solutions are now quite well understood. The mechanisms underlying co-translational folding of multidomain and membrane-spanning proteins in complex cellular environments are often less clear. The endoplasmic reticulum (ER) produces a plethora of membrane and secretory proteins, which must fold and assemble correctly before ER exit - if these processes fail, misfolded species accumulate in the ER or are degraded. The ER differs from other cellular organelles in terms of the physicochemical environment and the variety of ER-specific protein modifications. Here, we review chaperone-assisted co- and post-translational folding and assembly in the ER and underline the influence of protein modifications on these processes. We emphasize how method development has helped advance the field by allowing researchers to monitor the progression of folding as it occurs inside living cells, while at the same time probing the intricate relationship between protein modifications during folding.
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Affiliation(s)
- Lars Ellgaard
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas McCaul
- Cellular Protein Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Anna Chatsisvili
- Cellular Protein Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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9
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Patterson MA, Bandyopadhyay A, Devaraneni PK, Woodward J, Rooney L, Yang Z, Skach WR. The Ribosome-Sec61 Translocon Complex Forms a Cytosolically Restricted Environment for Early Polytopic Membrane Protein Folding. J Biol Chem 2015; 290:28944-52. [PMID: 26254469 DOI: 10.1074/jbc.m115.672261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022] Open
Abstract
Transmembrane topology of polytopic membrane proteins (PMPs) is established in the endoplasmic reticulum (ER) by the ribosome Sec61-translocon complex (RTC) through iterative cycles of translocation initiation and termination. It remains unknown, however, whether tertiary folding of transmembrane domains begins after the nascent polypeptide integrates into the lipid bilayer or within a proteinaceous environment proximal to translocon components. To address this question, we used cysteine scanning mutagenesis to monitor aqueous accessibility of stalled translation intermediates to determine when, during biogenesis, hydrophilic peptide loops of the aquaporin-4 (AQP4) water channel are delivered to cytosolic and lumenal compartments. Results showed that following ribosome docking on the ER membrane, the nascent polypeptide was shielded from the cytosol as it emerged from the ribosome exit tunnel. Extracellular loops followed a well defined path through the ribosome, the ribosome translocon junction, the Sec61-translocon pore, and into the ER lumen coincident with chain elongation. In contrast, intracellular loops (ICLs) and C-terminalresidues exited the ribosome into a cytosolically shielded environment and remained inaccessible to both cytosolic and lumenal compartments until translation was terminated. Shielding of ICL1 and ICL2, but not the C terminus, became resistant to maneuvers that disrupt electrostatic ribosome interactions. Thus, the early folding landscape of polytopic proteins is shaped by a spatially restricted environment localized within the assembled ribosome translocon complex.
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Affiliation(s)
- Melissa A Patterson
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Anannya Bandyopadhyay
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Prasanna K Devaraneni
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Josha Woodward
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - LeeAnn Rooney
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Zhongying Yang
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - William R Skach
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and the Cystic Fibrosis Foundation Therapeutics (CFFT), Cystic Fibrosis Foundation, Bethesda, Maryland 20814
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10
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Taubert J, Brüser T. Twin-arginine translocation-arresting protein regions contact TatA and TatB. Biol Chem 2015; 395:827-36. [PMID: 25003386 DOI: 10.1515/hsz-2014-0170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/10/2014] [Indexed: 11/15/2022]
Abstract
Tat systems translocate folded proteins across biological membranes of prokaryotes and plant plastids. TatBC complexes recognize N-terminal Tat signal peptides that contain a sequence motif with two conserved arginines (RR-motif), and transport takes place after a recruitment of TatA. Unfolded Tat substrate domains lower translocation efficiency and too long linkers lead to translocation arrest. To identify the components that interact with transported proteins during their passage through the translocon, we used a Tat substrate that arrests translocation at a long unfolded linker region, and we chose in vivo site-directed photo cross-linking to specifically detect the interactions of this linker region. For comparison, we included the interactions of the signal peptide and of the folded domain at the C-terminus of this construct. The data show that the linker contacts only two, structurally similar Tat components, namely TatA and TatB. These contacts depend on the recognition of the Tat-specific signal peptide. Only when membrane translocation of the globular domain was allowed--i.e., in the absence of the linker--we observed the same TatAB-contacts also to the globular domain. The data thus suggest that mature protein domains are translocated through a TatAB environment.
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11
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Stone TA, Schiller N, von Heijne G, Deber CM. Hydrophobic blocks facilitate lipid compatibility and translocon recognition of transmembrane protein sequences. Biochemistry 2015; 54:1465-73. [PMID: 25635746 PMCID: PMC4341838 DOI: 10.1021/bi5014886] [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] [Indexed: 02/08/2023]
Abstract
![]()
Biophysical hydrophobicity scales
suggest that partitioning of
a protein segment from an aqueous phase into a membrane is governed
by its perceived segmental hydrophobicity but do not establish specifically
(i) how the segment is identified in vivo for translocon-mediated
insertion or (ii) whether the destination lipid bilayer is biochemically
receptive to the inserted sequence. To examine the congruence between
these dual requirements, we designed and synthesized a library of
Lys-tagged peptides of a core length sufficient to span a bilayer
but with varying patterns of sequence, each composed of nine Leu residues,
nine Ser residues, and one (central) Trp residue. We found that peptides
containing contiguous Leu residues (Leu-block peptides, e.g., LLLLLLLLLWSSSSSSSSS),
in comparison to those containing discontinuous stretches of Leu residues
(non-Leu-block peptides, e.g., SLSLLSLSSWSLLSLSLLS),
displayed greater helicity (circular dichroism spectroscopy), traveled
slower during sodium dodecyl sulfate–polyacrylamide gel electrophoresis,
had longer reverse phase high-performance liquid chromatography retention
times on a C-18 column, and were helical when reconstituted into 1-palmitoyl-2-oleoylglycero-3-phosphocholine
liposomes, each observation indicating superior lipid compatibility
when a Leu-block is present. These parameters were largely paralleled
in a biological membrane insertion assay using microsomal membranes
from dog pancreas endoplasmic reticulum, where we found only the Leu-block
sequences successfully inserted; intriguingly, an amphipathic peptide
(SLLSSLLSSWLLSSLLSSL;
Leu face, Ser face) with biophysical properties similar to those of
Leu-block peptides failed to insert. Our overall results identify
local sequence lipid compatibility rather than average hydrophobicity
as a principal determinant of transmembrane segment potential, while
demonstrating that further subtleties of hydrophobic and helical patterning,
such as circumferential hydrophobicity in Leu-block segments, promote
translocon-mediated insertion.
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Affiliation(s)
- Tracy A Stone
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children , Toronto M5G 0A4, Ontario, Canada
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12
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Mgr2 functions as lateral gatekeeper for preprotein sorting in the mitochondrial inner membrane. Mol Cell 2014; 56:641-52. [PMID: 25454944 DOI: 10.1016/j.molcel.2014.10.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/14/2014] [Accepted: 10/09/2014] [Indexed: 11/21/2022]
Abstract
The majority of preproteins destined for mitochondria carry N-terminal presequences. The presequence translocase of the inner mitochondrial membrane (TIM23 complex) plays a central role in protein sorting. Preproteins are either translocated through the TIM23 complex into the matrix or are laterally released into the inner membrane. We report that the small hydrophobic protein Mgr2 controls the lateral release of preproteins. Mgr2 interacts with preproteins in transit through the TIM23 complex. Overexpression of Mgr2 delays preprotein release, whereas a lack of Mgr2 promotes preprotein sorting into the inner membrane. Preproteins with a defective inner membrane sorting signal are translocated into the matrix in wild-type mitochondria but are released into the inner membrane in Mgr2-deficient mitochondria. We conclude that Mgr2 functions as a lateral gatekeeper of the mitochondrial presequence translocase, providing quality control for the membrane sorting of preproteins.
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Wunderley L, Leznicki P, Payapilly A, High S. SGTA regulates the cytosolic quality control of hydrophobic substrates. J Cell Sci 2014; 127:4728-39. [PMID: 25179605 PMCID: PMC4215715 DOI: 10.1242/jcs.155648] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hydrophobic amino acids are normally shielded from the cytosol and their exposure is often used as an indicator of protein misfolding to enable the chaperone-mediated recognition and quality control of aberrant polypeptides. Mislocalised membrane proteins (MLPs) represent a particular challenge to cellular quality control, and, in this study, membrane protein fragments have been exploited to study a specialised pathway that underlies the efficient detection and proteasomal degradation of MLPs. Our data show that the BAG6 complex and SGTA compete for cytosolic MLPs by recognition of their exposed hydrophobicity, and the data suggest that SGTA acts to maintain these substrates in a non-ubiquitylated state. Hence, SGTA might counter the actions of BAG6 to delay the ubiquitylation of specific precursors and thereby increase their opportunity for successful post-translational delivery to the endoplasmic reticulum. However, when SGTA is overexpressed, the normally efficient removal of aberrant MLPs is delayed, increasing their steady-state level and promoting aggregation. Our data suggest that SGTA regulates the cellular fate of a range of hydrophobic polypeptides should they become exposed to the cytosol.
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Affiliation(s)
- Lydia Wunderley
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Pawel Leznicki
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Aishwarya Payapilly
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Stephen High
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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14
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Reithinger JH, Yim C, Kim S, Lee H, Kim H. Structural and functional profiling of the lateral gate of the Sec61 translocon. J Biol Chem 2014; 289:15845-55. [PMID: 24753257 PMCID: PMC4140938 DOI: 10.1074/jbc.m113.533794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/17/2014] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily conserved Sec61 translocon mediates the translocation and membrane insertion of proteins. For the integration of proteins into the membrane, the Sec61 translocon opens laterally to the lipid bilayer. Previous studies suggest that the lateral opening of the channel is mediated by the helices TM2b and TM7 of a pore-forming subunit of the Sec61 translocon. To map key residues in TM2b and TM7 in yeast Sec61 that modulate lateral gating activity, we performed alanine scanning and in vivo site-directed photocross-linking experiments. Alanine scanning identified two groups of critical residues in the lateral gate, one group that leads to defects in the translocation and membrane insertion of proteins and the other group that causes faster translocation and facilitates membrane insertion. Photocross-linking data show that the former group of residues is located at the interface of the lateral gate. Furthermore, different degrees of defects for the membrane insertion of single- and double-spanning membrane proteins were observed depending on whether the mutations were located in TM2b or TM7. These results demonstrate subtle differences in the molecular mechanism of the signal sequence binding/opening of the lateral gate and membrane insertion of a succeeding transmembrane segment in a polytopic membrane protein.
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Affiliation(s)
- Johannes H Reithinger
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Chewon Yim
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| | - Sungmin Kim
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| | - Hunsang Lee
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| | - Hyun Kim
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
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15
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Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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16
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17
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Gogala M, Becker T, Beatrix B, Armache JP, Barrio-Garcia C, Berninghausen O, Beckmann R. Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Nature 2014; 506:107-10. [DOI: 10.1038/nature12950] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 12/10/2013] [Indexed: 12/18/2022]
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18
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Mackinnon AL, Paavilainen VO, Sharma A, Hegde RS, Taunton J. An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate. eLife 2014; 3:e01483. [PMID: 24497544 PMCID: PMC3913039 DOI: 10.7554/elife.01483] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Membrane protein biogenesis requires the coordinated movement of hydrophobic transmembrane domains (TMD) from the cytosolic vestibule of the Sec61 channel into the lipid bilayer. Molecular insight into TMD integration has been hampered by the difficulty of characterizing intermediates during this intrinsically dynamic process. In this study, we show that cotransin, a substrate-selective Sec61 inhibitor, traps nascent TMDs in the cytosolic vestibule, permitting detailed interrogation of an early pre-integration intermediate. Site-specific crosslinking revealed the pre-integrated TMD docked to Sec61 near the cytosolic tip of the lateral gate. Escape from cotransin-arrest depends not only on cotransin concentration, but also on the biophysical properties of the TMD. Genetic selection of cotransin-resistant cancer cells uncovered multiple mutations clustered near the lumenal plug of Sec61α, thus revealing cotransin’s likely site of action. Our results suggest that TMD/lateral gate interactions facilitate TMD transfer into the membrane, a process that is allosterically modulated by cotransin binding to the plug. DOI:http://dx.doi.org/10.7554/eLife.01483.001 Cells are surrounded by a plasma membrane that acts like a barrier around the cell—keeping the cell’s boundaries distinct from surrounding cells and helping to regulate the contents of the cell. This plasma membrane is made up mostly of two layers of fatty molecules, and is also studded with proteins. Some of these membrane proteins act as channels that allow nutrients and other chemicals to enter and leave the cell, while others allow the cell to communicate with other cells and the outside environment. Like all proteins, membrane proteins are chains of amino acids that are linked together by a molecular machine called a ribosome. The ribosomes that make membrane proteins are located on the outside of a membrane-enclosed compartment within the cell called the endoplasmic reticulum. To eventually become embedded within a membrane, a new protein must—at the same time as it is being built—enter a channel within the membrane of the endoplasmic reticulum. The newly synthesized protein chain enters this channel, called Sec61, via an entrance near the ribosome and then threads its way toward the inside of the endoplasmic reticulum. However, there is also a ‘side-gate’ in Sec61 that allows specific segments the new protein to escape the channel and become embedded within the membrane. From here, the membrane protein can be trafficked to other destinations within the cell, including the plasma membrane. However, how the newly forming protein chain passes through the side-gate of Sec61 is not well understood. Now MacKinnon, Paavilainen et al. have used a small molecule called cotransin—which is known to interfere with the passage of proteins through Sec61—to observe the interactions between the Sec61 channel and the new protein. Cotransin appears to trap the new protein chain within the Sec61 channel by essentially ‘locking’ the side-gate. MacKinnon, Paavilainen et al. observed that the trapped protein interacts with the inside of the channel at the end closest to the ribosome—which is the likely location of the side-gate. In contrast, cotransin likely binds at the other end of the channel, to a piece of Sec61 that serves to plug the exit into the endoplasmic reticulum; and this plug is directly connected to the side-gate. By preventing the plug from moving out of the way, cotransin can somehow stop the new protein from passing through the side-gate. However, MacKinnon, Paavilainen et al. did find that some membrane proteins with certain physical and chemical properties could get through the gate, despite the presence of cotransin. The next challenge is to resolve exactly how interactions between cotransin and the Sec61 plug can block the escape of new proteins into the membrane. DOI:http://dx.doi.org/10.7554/eLife.01483.002
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Affiliation(s)
- Andrew L Mackinnon
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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Reorientation of the first signal-anchor sequence during potassium channel biogenesis at the Sec61 complex. Biochem J 2014; 456:297-309. [PMID: 24015703 PMCID: PMC3898203 DOI: 10.1042/bj20130100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The majority of the polytopic proteins that are synthesized at the ER (endoplasmic reticulum) are integrated co-translationally via the Sec61 translocon, which provides lateral access for their hydrophobic TMs (transmembrane regions) to the phospholipid bilayer. A prolonged association between TMs of the potassium channel subunit, TASK-1 [TWIK (tandem-pore weak inwardly rectifying potassium channel)-related acid-sensitive potassium channel 1], and the Sec61 complex suggests that the ER translocon co-ordinates the folding/assembly of the TMs present in the nascent chain. The N-terminus of both TASK-1 and Kcv (potassium channel protein of chlorella virus), another potassium channel subunit of viral origin, has access to the N-glycosylation machinery located in the ER lumen, indicating that the Sec61 complex can accommodate multiple arrangements/orientations of TMs within the nascent chain, both in vitro and in vivo. Hence the ER translocon can provide the ribosome-bound nascent chain with a dynamic environment in which it can explore a range of different conformations en route to its correct transmembrane topology and final native structure. The Sec61 translocon provides an unexpectedly flexible and dynamic environment within which transmembrane regions of nascent polypeptides can be completely reoriented during the biosynthesis of multiple-spanning membrane proteins.
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20
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Abstract
The Sec61 translocon forms a pore to translocate polypeptide sequences across the membrane and offers a lateral gate for membrane integration of hydrophobic (H) segments. A central constriction of six apolar residues has been shown to form a seal, but also to determine the hydrophobicity threshold for membrane integration: Mutation of these residues in yeast Sec61p to glycines, serines, aspartates, or lysines lowered the hydrophobicity required for integration; mutation to alanines increased it. Whereas four leucines distributed in an oligo-alanine H segment were sufficient for 50% integration, we now find four leucines in the N-terminal half of the H segment to produce significantly more integration than in the C-terminal half, suggesting functional asymmetry within the translocon. Scanning a cluster of three leucines through an oligo-alanine H segment showed high integration levels, except around the position matching that of the hydrophobic constriction in the pore where integration was strongly reduced. Both asymmetry and the position effect of H-segment integration disappeared upon mutation of the constriction residues to glycines or serines, demonstrating that hydrophobicity at this position within the translocon is responsible for the phenomenon. Asymmetry was largely retained, however, when constriction residues were replaced by alanines. These results reflect on the integration mechanism of transmembrane domains and show that membrane insertion of H segments strongly depends not only on their intrinsic hydrophobicity but also on the local conditions in the translocon interior. Thus, the contribution of hydrophobic residues in the H segment is not simply additive and displays cooperativeness depending on their relative position.
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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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Transmembrane segments form tertiary hairpins in the folding vestibule of the ribosome. J Mol Biol 2013; 426:185-98. [PMID: 24055377 DOI: 10.1016/j.jmb.2013.09.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/30/2013] [Accepted: 09/11/2013] [Indexed: 11/21/2022]
Abstract
Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100Å of tunnel from the peptidyltransferase center to the exit port. Proximal to the exit port is a "folding vestibule" that permits the nascent peptide to compact and explore conformational space for potential tertiary folding partners. The latter occurs for cytosolic subdomains but has not yet been shown for transmembrane segments. We now demonstrate, using an accessibility assay and an improved intramolecular crosslinking assay, that the helical transmembrane S3b-S4 hairpin ("paddle") of a voltage-gated potassium (Kv) channel, a critical region of the Kv voltage sensor, forms in the vestibule. S3-S4 hairpin interactions are detected at an early stage of Kv biogenesis. Moreover, this vestibule hairpin is consistent with a closed-state conformation of the Kv channel in the plasma membrane.
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Onishi Y, Yamagishi M, Imai K, Fujita H, Kida Y, Sakaguchi M. Stop-and-Move of a Marginally Hydrophobic Segment Translocating across the Endoplasmic Reticulum Membrane. J Mol Biol 2013; 425:3205-16. [PMID: 23747484 DOI: 10.1016/j.jmb.2013.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 10/26/2022]
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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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Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J Am Chem Soc 2013; 135:2291-7. [PMID: 23298280 PMCID: PMC3573731 DOI: 10.1021/ja310777k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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For the vast majority of membrane proteins, insertion
into a membrane
is not direct, but rather is catalyzed by a protein-conducting channel,
the translocon. This channel provides a lateral exit into the bilayer
while simultaneously offering a pathway into the aqueous lumen. The
determinants of a nascent protein’s choice between these two
pathways are not comprehensively understood, although both energetic
and kinetic factors have been observed. To elucidate the specific
roles of some of these factors, we have carried out extensive all-atom
molecular dynamics simulations of different nascent transmembrane
segments embedded in a ribosome-bound bacterial translocon, SecY.
Simulations on the μs time scale reveal a spontaneous motion
of the substrate segment into the membrane or back into the channel,
depending on its hydrophobicity. Potential of mean force (PMF) calculations
confirm that the observed motion is the result of local free-energy
differences between channel and membrane. Based on these and other
PMFs, the time-dependent probability of membrane insertion is determined
and is shown to mimic a two-state partition scheme with an apparent
free energy that is compressed relative to the molecular-level PMFs.
It is concluded that insertion kinetics underlies the experimentally
observed thermodynamic partitioning process.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30363, USA
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Tail-extension following the termination codon is critical for release of the nascent chain from membrane-bound ribosomes in a reticulocyte lysate cell-free system. Biochem Biophys Res Commun 2013; 430:567-72. [DOI: 10.1016/j.bbrc.2012.11.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 11/27/2012] [Indexed: 11/20/2022]
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