1
|
DiGuilio A, Cheng B, Zhong F, Jha R, Wan Y, Anghel SA, Hu H, Shishkova E, Ji Z, Coon JJ, Keenan RJ. The prolyl isomerase FKBP11 is a secretory translocon accessory factor. Mol Biol Cell 2024; 35:ar135. [PMID: 39259761 DOI: 10.1091/mbc.e24-07-0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024] Open
Abstract
Eukaryotic cells encode thousands of secretory and membrane proteins, many of which are cotranslationally translocated into the endoplasmic reticulum (ER). Nascent polypeptides entering the ER encounter a network of molecular chaperones and enzymes that facilitate their folding. A rate-limiting step for some proteins is the trans-to-cis isomerization of the peptide bond between proline and the residue preceding it. The human ER contains six prolyl isomerases, but the function, organization, and substrate range of these proteins is not clear. Here we show that the metazoan-specific, prolyl isomerase FKBP11 binds to ribosome-translocon complexes (RTCs) in the ER membrane, dependent on its single transmembrane domain and a conserved, positively charged region at its cytosolic C-terminus. High-throughput mRNA sequencing shows selective engagement with ribosomes synthesizing secretory and membrane proteins with long translocated segments, and functional analysis shows reduced stability of two such proteins, EpCAM and PTTG1IP, in cells depleted of FKBP11. We propose that FKBP11 is a translocon accessory factor that acts on a broad range of soluble secretory and transmembrane proteins during their synthesis at the ER.
Collapse
Affiliation(s)
- Amanda DiGuilio
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Ben Cheng
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Frank Zhong
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637
| | - Roshan Jha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Yu Wan
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60628
| | - S Andrei Anghel
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637
| | - Hong Hu
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhe Ji
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60628
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Joshua J Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Morgridge Institute for Research, Madison, WI 53515
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53506
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| |
Collapse
|
2
|
Dos Santos TMA, Thomson BD, Marquez MD, Pan L, Monfared TH, Kahne DE. Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex. Proc Natl Acad Sci U S A 2024; 121:e2409672121. [PMID: 39378083 DOI: 10.1073/pnas.2409672121] [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: 05/14/2024] [Accepted: 08/29/2024] [Indexed: 10/10/2024] Open
Abstract
The assembly of β-barrel proteins into membranes is mediated by the evolutionarily conserved β-barrel assembly machine (BAM) complex. In Escherichia coli, BAM folds numerous substrates which vary considerably in size and shape. How BAM is able to efficiently fold such a diverse array of β-barrel substrates is not clear. Here, we develop a disulfide crosslinking method to trap native substrates in vivo as they fold on BAM. By placing a cysteine within the luminal wall of the BamA barrel as well as in the substrate β-strands, we can compare the residence time of each substrate strand within the BamA lumen. We validated this method using two defective, slow-folding substrates. We used this method to characterize stable intermediates which occur during folding of two structurally different native substrates. Strikingly, these intermediates occur during identical stages of folding for both substrates: soon after folding has begun and just before folding is completed. We suggest that these intermediates arise due to barriers to folding that are common between β-barrel substrates, and that the BAM catalyst is able to fold so many different substrates because it addresses these common challenges.
Collapse
Affiliation(s)
- Thiago M A Dos Santos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Benjamin D Thomson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Melissa D Marquez
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Lydia Pan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Tabasom H Monfared
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Daniel E Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| |
Collapse
|
3
|
Ma T, Li X, Montalbán-López M, Wu X, Zheng Z, Mu D. Effect of the Membrane Insertase YidC on the Capacity of Lactococcus lactis to Secret Recombinant Proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39382634 DOI: 10.1021/acs.jafc.4c04665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
Lactococcus lactis is a crucial food-grade cell factory for secreting valuable peptides and proteins primarily via the Sec-dependent pathway. YidC, a membrane insertase, facilitates protein insertion into the lipid membrane for the translocation. However, the mechanistic details of how YidC affects protein secretion in L. lactis remain elusive. This study investigates the effects of deleting yidC1/yidC2 on L. lactis phenotypes and protein secretion. Compared to the original strain, deleting yidC2 significantly decreased the relative biomass, electroporation efficiency, and F-ATP activity by 25%, 47%, and 33%, respectively, and weakened growth and stress resistance, whereas deleting yidC1 had a minimal impact. The absence of either yidC1 or yidC2 reduced target proteins secretion. Meanwhile, there is a considerable alteration in the transcription levels of genes involved in the secretion pathway, with secY transcription increasing over 135-fold. Our results provide a theoretical foundation for further improving target protein secretion and investigating the YidC function.
Collapse
Affiliation(s)
- Tiange Ma
- School of Food and Biological Engineering, Anhui Fermented Food Engineering Research Center, Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Xingjiang Li
- School of Food and Biological Engineering, Anhui Fermented Food Engineering Research Center, Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230601, China
- Gongda Biotech (Huangshan) Limited Company, Huangshan 245400, China
| | - Manuel Montalbán-López
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Xuefeng Wu
- School of Food and Biological Engineering, Anhui Fermented Food Engineering Research Center, Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Zhi Zheng
- School of Food and Biological Engineering, Anhui Fermented Food Engineering Research Center, Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Dongdong Mu
- School of Food and Biological Engineering, Anhui Fermented Food Engineering Research Center, Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230601, China
- Gongda Biotech (Huangshan) Limited Company, Huangshan 245400, China
| |
Collapse
|
4
|
Introini B, Cui W, Chu X, Zhang Y, Alves AC, Eckhardt-Strelau L, Golusik S, Tol M, Vogel H, Yuan S, Kudryashev M. Structure of tetrameric forms of the serotonin-gated 5-HT3 A receptor ion channel. EMBO J 2024; 43:4451-4471. [PMID: 39232129 PMCID: PMC11480441 DOI: 10.1038/s44318-024-00191-5] [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: 03/19/2024] [Revised: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 09/06/2024] Open
Abstract
Multimeric membrane proteins are produced in the endoplasmic reticulum and transported to their target membranes which, for ion channels, is typically the plasma membrane. Despite the availability of many fully assembled channel structures, our understanding of assembly intermediates, multimer assembly mechanisms, and potential functions of non-standard assemblies is limited. We demonstrate that the pentameric ligand-gated serotonin 5-HT3A receptor (5-HT3AR) can assemble to tetrameric forms and report the structures of the tetramers in plasma membranes of cell-derived microvesicles and in membrane memetics using cryo-electron microscopy and tomography. The tetrameric structures have near-symmetric transmembrane domains, and asymmetric extracellular domains, and can bind serotonin molecules. Computer simulations, based on our cryo-EM structures, were used to decipher the assembly pathway of pentameric 5-HT3R and suggest a potential functional role for the tetrameric receptors.
Collapse
Affiliation(s)
- Bianca Introini
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany
| | - Wenqiang Cui
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofeng Chu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Yingyi Zhang
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Sabrina Golusik
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Menno Tol
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Horst Vogel
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Faculty of Pharmaceutical Sciences, Shenzhen University of Advanced Technology (SUAT), Shenzhen, China.
| | - Shuguang Yuan
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- AlphaMol Science Ltd, Shenzhen, 518055, China.
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany.
| |
Collapse
|
5
|
Kinoshita T. Towards a thorough understanding of mammalian glycosylphosphatidylinositol-anchored protein biosynthesis. Glycobiology 2024; 34:cwae061. [PMID: 39129667 DOI: 10.1093/glycob/cwae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/01/2024] [Accepted: 08/10/2024] [Indexed: 08/13/2024] Open
Abstract
Glycosylphosphatidylinositols (GPIs) are glycolipids found ubiquitously in eukaryotes. They consist of a glycan and an inositol phospholipid, and act as membrane anchors of many cell-surface proteins by covalently linking to their C-termini. GPIs also exist as unlinked, free glycolipids on the cell surface. In human cells, at least 160 proteins with various functions are GPI-anchored proteins. Because the attachment of GPI is required for the cell-surface expression of GPI-anchored proteins, a thorough knowledge of the molecular basis of mammalian GPI-anchored protein biosynthesis is important for understanding the basic biochemistry and biology of GPI-anchored proteins and their medical significance. In this paper, I review our previous knowledge of the biosynthesis of mammalian GPI-anchored proteins and then examine new findings made since 2020.
Collapse
Affiliation(s)
- Taroh Kinoshita
- Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamada-oka, Suita, Osaka, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka, Japan
| |
Collapse
|
6
|
Ikeda Y, Miyazaki R, Tsukazaki T, Akiyama Y, Mori H. Translation arrest cancellation of VemP, a secretion monitor in Vibrio, is regulated by multiple cis and trans factors, including SecY. J Biol Chem 2024; 300:107735. [PMID: 39233231 PMCID: PMC11470409 DOI: 10.1016/j.jbc.2024.107735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
VemP is a secretory protein in the Vibrio species that monitors cellular protein-transport activity through its translation arrest, allowing expression of the downstream secD2-secF2 genes in the same operon, which encode components of the protein translocation machinery. When cellular protein-transport function is fully active, secD2/F2 expression remains repressed as VemP translation arrest is canceled immediately. The VemP arrest cancellation occurs on the SecY/E/G translocon in a late stage in the translocation process and requires both trans factors, SecD/F and PpiD/YfgM, and a cis element, Arg-85 in VemP; however, the detailed molecular mechanism remains elusive. This study aimed to elucidate how VemP passing through SecY specifically monitors SecD/F function. Genetic and biochemical studies showed that SecY is involved in the VemP arrest cancellation and that the arrested VemP is stably associated with a specific site in the protein-conducting pore of SecY. VemP-Bla reporter analyses revealed that a short hydrophobic segment adjacent to Arg-85 plays a critical role in the regulated arrest cancellation with its hydrophobicity correlating with the stability of the VemP arrest. We identified Gln-65 and Pro-67 in VemP as novel elements important for the regulation. We propose a model for the regulation of the VemP arrest cancellation by multiple cis elements and trans factors with different roles.
Collapse
Affiliation(s)
- Yuki Ikeda
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ryoji Miyazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Tomoya Tsukazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroyuki Mori
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| |
Collapse
|
7
|
Wenzell NA, Tuch BB, McMinn DL, Lyons MJ, Kirk CJ, Taunton J. Global signal peptide profiling reveals principles of selective Sec61 inhibition. Nat Chem Biol 2024; 20:1154-1163. [PMID: 38519575 DOI: 10.1038/s41589-024-01592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 02/26/2024] [Indexed: 03/25/2024]
Abstract
Cotransins target the Sec61 translocon and inhibit the biogenesis of an undefined subset of secretory and membrane proteins. Remarkably, cotransin inhibition depends on the unique signal peptide (SP) of each Sec61 client, which is required for cotranslational translocation into the endoplasmic reticulum. It remains unknown how an SP's amino acid sequence and biophysical properties confer sensitivity to structurally distinct cotransins. Here we describe a fluorescence-based, pooled-cell screening platform to interrogate nearly all human SPs in parallel. We profiled two cotransins with distinct effects on cancer cells and discovered a small subset of SPs, including the oncoprotein human epidermal growth factor receptor 3 (HER3), with increased sensitivity to the more selective cotransin, KZR-9873. By comparing divergent mouse and human orthologs, we unveiled a position-dependent effect of arginine on SP sensitivity. Our multiplexed profiling platform reveals how cotransins can exploit subtle sequence differences to achieve SP discrimination.
Collapse
Affiliation(s)
- Nicole A Wenzell
- Chemistry and Chemical Biology Program, University of California, San Francisco, San Francisco, CA, USA
| | - Brian B Tuch
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | - Matthew J Lyons
- Chemistry and Chemical Biology Program, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
8
|
Carilo I, Senju Y, Yokoyama T, Robinson RC. Intercompatibility of eukaryotic and Asgard archaea ribosome-translocon machineries. J Biol Chem 2024; 300:107673. [PMID: 39128722 PMCID: PMC11417166 DOI: 10.1016/j.jbc.2024.107673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 08/02/2024] [Indexed: 08/13/2024] Open
Abstract
In all domains of life, the ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. Phylogenetic analyses indicate the inheritance of eukaryotic Sec61/oligosaccharyltransferase/translocon-associated protein translocon subunits from an Asgard archaea ancestor. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show compatibility between the eukaryotic ribosome-translocon complex and Asgard signal peptides and transmembrane proteins. We find that Asgard translocon proteins from Candidatus Prometheoarchaeum syntrophicum strain Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Furthermore, we show that the cytoplasmic domain of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 oligosaccharyltransferase 1 (ribophorin I) can interact with eukaryotic ribosomes. Our data indicate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet-to-be-translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have contributed to propagating the new translocon location, leading to their loss from the cell membrane.
Collapse
Affiliation(s)
- Isaac Carilo
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan; School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
| |
Collapse
|
9
|
Hegde RS, Keenan RJ. A unifying model for membrane protein biogenesis. Nat Struct Mol Biol 2024; 31:1009-1017. [PMID: 38811793 PMCID: PMC7616256 DOI: 10.1038/s41594-024-01296-5] [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: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
α-Helical integral membrane proteins comprise approximately 25% of the proteome in all organisms. The membrane proteome is highly diverse, varying in the number, topology, spacing and properties of transmembrane domains. This diversity imposes different constraints on the insertion of different regions of a membrane protein into the lipid bilayer. Here, we present a cohesive framework to explain membrane protein biogenesis, in which different parts of a nascent substrate are triaged between Oxa1 and SecY family members for insertion. In this model, Oxa1 family proteins insert transmembrane domains flanked by short translocated segments, whereas the SecY channel is required for insertion of transmembrane domains flanked by long translocated segments. Our unifying model rationalizes evolutionary, genetic, biochemical and structural data across organisms and provides a foundation for future mechanistic studies of membrane protein biogenesis.
Collapse
Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
10
|
Sun Y, Tao X, Han Y, Lin X, Tian R, Wang H, Chang P, Sun Q, Ge L, Zhang M. A dual role of ERGIC-localized Rabs in TMED10-mediated unconventional protein secretion. Nat Cell Biol 2024; 26:1077-1092. [PMID: 38926505 DOI: 10.1038/s41556-024-01445-4] [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: 11/22/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Cargo translocation across membranes is a crucial aspect of secretion. In conventional secretion signal peptide-equipped proteins enter the endoplasmic reticulum (ER), whereas a subset of cargo lacking signal peptides translocate into the ER-Golgi intermediate compartment (ERGIC) in a process called unconventional protein secretion (UcPS). The regulatory events at the ERGIC in UcPS are unclear. Here we reveal the involvement of ERGIC-localized small GTPases, Rab1 (Rab1A and Rab1B) and Rab2A, in regulating UcPS cargo transport via TMED10 on the ERGIC. Rab1 enhances TMED10 translocator activity, promoting cargo translocation into the ERGIC, whereas Rab2A, in collaboration with KIF5B, regulates ERGIC compartmentalization, establishing a UcPS-specific compartment. This study highlights the pivotal role of ERGIC-localized Rabs in governing cargo translocation and specifying the ERGIC's function in UcPS.
Collapse
Affiliation(s)
- Yuxin Sun
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuan Tao
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yaping Han
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Rui Tian
- Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haodong Wang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pei Chang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qiming Sun
- Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Min Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| |
Collapse
|
11
|
Yeter-Alat H, Belgareh-Touzé N, Le Saux A, Huvelle E, Mokdadi M, Banroques J, Tanner NK. The RNA Helicase Ded1 from Yeast Is Associated with the Signal Recognition Particle and Is Regulated by SRP21. Molecules 2024; 29:2944. [PMID: 38931009 PMCID: PMC11206880 DOI: 10.3390/molecules29122944] [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: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The DEAD-box RNA helicase Ded1 is an essential yeast protein involved in translation initiation that belongs to the DDX3 subfamily. The purified Ded1 protein is an ATP-dependent RNA-binding protein and an RNA-dependent ATPase, but it was previously found to lack substrate specificity and enzymatic regulation. Here we demonstrate through yeast genetics, yeast extract pull-down experiments, in situ localization, and in vitro biochemical approaches that Ded1 is associated with, and regulated by, the signal recognition particle (SRP), which is a universally conserved ribonucleoprotein complex required for the co-translational translocation of polypeptides into the endoplasmic reticulum lumen and membrane. Ded1 is physically associated with SRP components in vivo and in vitro. Ded1 is genetically linked with SRP proteins. Finally, the enzymatic activity of Ded1 is inhibited by SRP21 in the presence of SCR1 RNA. We propose a model where Ded1 actively participates in the translocation of proteins during translation. Our results provide a new understanding of the role of Ded1 during translation.
Collapse
Affiliation(s)
- Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226 CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France;
| | - Agnès Le Saux
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology, LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis 1002, Tunisia
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, Tunis 1080, Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| |
Collapse
|
12
|
Lewis AJO, Zhong F, Keenan RJ, Hegde RS. Structural analysis of the dynamic ribosome-translocon complex. eLife 2024; 13:RP95814. [PMID: 38896445 PMCID: PMC11186639 DOI: 10.7554/elife.95814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
Collapse
Affiliation(s)
- Aaron JO Lewis
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Frank Zhong
- Department of Molecular Genetics and Cell Biology, The University of ChicagoChicagoUnited States
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | | |
Collapse
|
13
|
Mattos D, Neves WD, Kitamura T, Pradhan R, Wan X, da Hora CC, Tranter D, Kazemi S, Yu X, Tripathy N, Paavilainen VO, McPhail KL, Oishi S, Badr CE, Ishmael JE. Diastereomers of Coibamide A Show Altered Sec61 Client Selectivity and Ligand-Dependent Activity against Patient-Derived Glioma Stem-like Cells. ACS Pharmacol Transl Sci 2024; 7:1823-1838. [PMID: 38898945 PMCID: PMC11184607 DOI: 10.1021/acsptsci.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 06/21/2024]
Abstract
Coibamide A (CbA) is a cyanobacterial lariat depsipeptide that selectively inhibits multiple secreted and integral membrane proteins from entering the endoplasmic reticulum secretory pathway through binding the alpha subunit of the Sec61 translocon. As a complex peptide-based macrocycle with 13 stereogenic centers, CbA is presumed to adopt a conformationally restricted orientation in the ligand-bound state, resulting in potent antitumor and antiangiogenic bioactivity. A stereochemical structure-activity relationship for CbA was previously defined based on cytotoxicity against established cancer cell lines. However, the ability of synthetic isomers to inhibit the biosynthesis of specific Sec61 substrates was unknown. Here, we report that two less toxic diastereomers of CbA, [L-Hiv2]-CbA and [L-Hiv2, L-MeAla11]-CbA, are pharmacologically active Sec61 inhibitors. Both compounds inhibited the expression of a secreted reporter (Gaussia luciferase), VEGF-A, and a Type 1 membrane protein (VCAM1), while [L-Hiv2]-CbA also decreased the expression of ICAM1 and BiP/GRP78. Analysis of 43 different chemokines in the secretome of SF-268 glioblastoma cells revealed different inhibitory profiles for the two diastereomers. When the cytotoxic potential of CbA compounds was compared against a panel of patient-derived glioblastoma stem-like cells (GSCs), Sec61 inhibitors were remarkably toxic to five of the six GSCs tested. Each ligand showed a distinct cytotoxic potency and selectivity pattern for CbA-sensitive GSCs, with IC50 values ranging from subnanomolar to low micromolar concentrations. Together, these findings highlight the extreme sensitivity of GSCs to Sec61 modulation and the importance of ligand stereochemistry in determining the spectrum of inhibited Sec61 client proteins.
Collapse
Affiliation(s)
- Daphne
R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Willian das Neves
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Takashi Kitamura
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richa Pradhan
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Xuemei Wan
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Cintia Carla da Hora
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Dale Tranter
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Soheila Kazemi
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Xinhui Yu
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nirmalya Tripathy
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | | | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Christian E. Badr
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| |
Collapse
|
14
|
Kok M, Brodsky JL. The biogenesis of potassium transporters: implications of disease-associated mutations. Crit Rev Biochem Mol Biol 2024; 59:154-198. [PMID: 38946646 PMCID: PMC11444911 DOI: 10.1080/10409238.2024.2369986] [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: 03/29/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 07/02/2024]
Abstract
The concentration of intracellular and extracellular potassium is tightly regulated due to the action of various ion transporters, channels, and pumps, which reside primarily in the kidney. Yet, potassium transporters and cotransporters play vital roles in all organs and cell types. Perhaps not surprisingly, defects in the biogenesis, function, and/or regulation of these proteins are linked to range of catastrophic human diseases, but to date, few drugs have been approved to treat these maladies. In this review, we discuss the structure, function, and activity of a group of potassium-chloride cotransporters, the KCCs, as well as the related sodium-potassium-chloride cotransporters, the NKCCs. Diseases associated with each of the four KCCs and two NKCCs are also discussed. Particular emphasis is placed on how these complex membrane proteins fold and mature in the endoplasmic reticulum, how non-native forms of the cotransporters are destroyed in the cell, and which cellular factors oversee their maturation and transport to the cell surface. When known, we also outline how the levels and activities of each cotransporter are regulated. Open questions in the field and avenues for future investigations are further outlined.
Collapse
Affiliation(s)
- Morgan Kok
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
15
|
Vismpas D, Förster F. RAMPing up knowledge of the translocon. eLife 2024; 13:e98548. [PMID: 38787756 PMCID: PMC11126307 DOI: 10.7554/elife.98548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024] Open
Abstract
Advanced cryo-EM approaches reveal surprising insights into the molecular structure that allows nascent proteins to be inserted into the membrane of the endoplasmic reticulum.
Collapse
Affiliation(s)
- Dimitrios Vismpas
- Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtNetherlands
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtNetherlands
| |
Collapse
|
16
|
Hegde RS. Getting membrane proteins into shape. Mol Cell 2024; 84:1821-1823. [PMID: 38759622 DOI: 10.1016/j.molcel.2024.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
In this issue, Ji et al.1 show how a multipass membrane protein that initially inserts into the endoplasmic reticulum in a mostly inverted topology is post-translationally dislocated, re-inserted, and folded with the help of ATP13A1, a P-type ATPase.
Collapse
|
17
|
Ji J, Cui MK, Zou R, Wu MZ, Ge MX, Li J, Zhang ZR. An ATP13A1-assisted topogenesis pathway for folding multi-spanning membrane proteins. Mol Cell 2024; 84:1917-1931.e15. [PMID: 38723633 DOI: 10.1016/j.molcel.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Many multi-spanning membrane proteins contain poorly hydrophobic transmembrane domains (pTMDs) protected from phospholipid in mature structure. Nascent pTMDs are difficult for translocon to recognize and insert. How pTMDs are discerned and packed into mature, muti-spanning configuration remains unclear. Here, we report that pTMD elicits a post-translational topogenesis pathway for its recognition and integration. Using six-spanning protein adenosine triphosphate-binding cassette transporter G2 (ABCG2) and cultured human cells as models, we show that ABCG2's pTMD2 can pass through translocon into the endoplasmic reticulum (ER) lumen, yielding an intermediate with inserted yet mis-oriented downstream TMDs. After translation, the intermediate recruits P5A-ATPase ATP13A1, which facilitates TMD re-orientation, allowing further folding and the integration of the remaining lumen-exposed pTMD2. Depleting ATP13A1 or disrupting pTMD-characteristic residues arrests intermediates with mis-oriented and exposed TMDs. Our results explain how a "difficult" pTMD is co-translationally skipped for insertion and post-translationally buried into the final correct structure at the late folding stage to avoid excessive lipid exposure.
Collapse
Affiliation(s)
- Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Meng-Ke Cui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Rong Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Ming-Zhi Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China.
| |
Collapse
|
18
|
Kawanaka R, Jin H, Aoe T. Unraveling the Connection: Pain and Endoplasmic Reticulum Stress. Int J Mol Sci 2024; 25:4995. [PMID: 38732214 PMCID: PMC11084550 DOI: 10.3390/ijms25094995] [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: 04/03/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Pain is a complex and multifaceted experience. Recent research has increasingly focused on the role of endoplasmic reticulum (ER) stress in the induction and modulation of pain. The ER is an essential organelle for cells and plays a key role in protein folding and calcium dynamics. Various pathological conditions, such as ischemia, hypoxia, toxic substances, and increased protein production, may disturb protein folding, causing an increase in misfolding proteins in the ER. Such an overload of the folding process leads to ER stress and causes the unfolded protein response (UPR), which increases folding capacity in the ER. Uncompensated ER stress impairs intracellular signaling and cell function, resulting in various diseases, such as diabetes and degenerative neurological diseases. ER stress may be a critical universal mechanism underlying human diseases. Pain sensations involve the central as well as peripheral nervous systems. Several preclinical studies indicate that ER stress in the nervous system is enhanced in various painful states, especially in neuropathic pain conditions. The purpose of this narrative review is to uncover the intricate relationship between ER stress and pain, exploring molecular pathways, implications for various pain conditions, and potential therapeutic strategies.
Collapse
Affiliation(s)
- Ryoko Kawanaka
- Department of Anesthesiology, Chiba Medical Center, Teikyo University, Ichihara 299-0111, Japan
| | - Hisayo Jin
- Department of Anesthesiology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Tomohiko Aoe
- Pain Center, Chiba Medical Center, Teikyo University, Ichihara 299-0111, Japan
| |
Collapse
|
19
|
Skowyra ML, Feng P, Rapoport TA. Towards solving the mystery of peroxisomal matrix protein import. Trends Cell Biol 2024; 34:388-405. [PMID: 37743160 PMCID: PMC10957506 DOI: 10.1016/j.tcb.2023.08.005] [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: 06/12/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.
Collapse
Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
20
|
Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. Proc Natl Acad Sci U S A 2024; 121:e2319476121. [PMID: 38621120 PMCID: PMC11047089 DOI: 10.1073/pnas.2319476121] [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: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 04/17/2024] Open
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.
Collapse
Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Cristian Rocha-Roa
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
| | - Matthew A. Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Stefano Vanni
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
- Swiss National Center for Competence in Research Bio-Inspired Materials, University of Fribourg, FribourgCH-1700, Switzerland
| |
Collapse
|
21
|
Majchrzak M, Stojanović O, Ajjaji D, Ben M'barek K, Omrane M, Thiam AR, Klemm RW. Perilipin membrane integration determines lipid droplet heterogeneity in differentiating adipocytes. Cell Rep 2024; 43:114093. [PMID: 38602875 DOI: 10.1016/j.celrep.2024.114093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
The storage of fat within lipid droplets (LDs) of adipocytes is critical for whole-body health. Acute fatty acid (FA) uptake by differentiating adipocytes leads to the formation of at least two LD classes marked by distinct perilipins (PLINs). How this LD heterogeneity arises is an important yet unresolved cell biological problem. Here, we show that an unconventional integral membrane segment (iMS) targets the adipocyte specific LD surface factor PLIN1 to the endoplasmic reticulum (ER) and facilitates high-affinity binding to the first LD class. The other PLINs remain largely excluded from these LDs until FA influx recruits them to a second LD population. Preventing ER targeting turns PLIN1 into a soluble, cytoplasmic LD protein, reduces its LD affinity, and switches its LD class specificity. Conversely, moving the iMS to PLIN2 leads to ER insertion and formation of a separate LD class. Our results shed light on how differences in organelle targeting and disparities in lipid affinity of LD surface factors contribute to formation of LD heterogeneity.
Collapse
Affiliation(s)
- Mario Majchrzak
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ozren Stojanović
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Dalila Ajjaji
- Laboratoire de Physique de l'École Normale Supérieure (ENS), Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Kalthoum Ben M'barek
- Laboratoire de Physique de l'École Normale Supérieure (ENS), Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Mohyeddine Omrane
- Laboratoire de Physique de l'École Normale Supérieure (ENS), Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École Normale Supérieure (ENS), Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Robin W Klemm
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, UK; Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.
| |
Collapse
|
22
|
Krantz BA. Anthrax Toxin: Model System for Studying Protein Translocation. J Mol Biol 2024; 436:168521. [PMID: 38458604 DOI: 10.1016/j.jmb.2024.168521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/08/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Dedicated translocase channels are nanomachines that often, but not always, unfold and translocate proteins through narrow pores across the membrane. Generally, these molecular machines utilize external sources of free energy to drive these reactions, since folded proteins are thermodynamically stable, and once unfolded they contain immense diffusive configurational entropy. To catalyze unfolding and translocate the unfolded state at appreciable timescales, translocase channels often utilize analogous peptide-clamp active sites. Here we describe how anthrax toxin has been used as a biophysical model system to study protein translocation. The tripartite bacterial toxin is composed of an oligomeric translocase channel, protective antigen (PA), and two enzymes, edema factor (EF) and lethal factor (LF), which are translocated by PA into mammalian host cells. Unfolding and translocation are powered by the endosomal proton gradient and are catalyzed by three peptide-clamp sites in the PA channel: the α clamp, the ϕ clamp, and the charge clamp. These clamp sites interact nonspecifically with the chemically complex translocating chain, serve to minimize unfolded state configurational entropy, and work cooperatively to promote translocation. Two models of proton gradient driven translocation have been proposed: (i) an extended-chain Brownian ratchet mechanism and (ii) a proton-driven helix-compression mechanism. These models are not mutually exclusive; instead the extended-chain Brownian ratchet likely operates on β-sheet sequences and the helix-compression mechanism likely operates on α-helical sequences. Finally, we compare and contrast anthrax toxin with other related and unrelated translocase channels.
Collapse
Affiliation(s)
- Bryan A Krantz
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, 650 W. Baltimore Street, Baltimore, MD 21201, USA.
| |
Collapse
|
23
|
Fujiwara K, Tsuji N, Yoshida M, Takada H, Chiba S. Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery. Nat Commun 2024; 15:2711. [PMID: 38565864 PMCID: PMC10987492 DOI: 10.1038/s41467-024-46993-3] [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: 08/28/2023] [Accepted: 02/02/2024] [Indexed: 04/04/2024] Open
Abstract
Regulatory arrest peptides interact with specific residues on bacterial ribosomes and arrest their own translation. Here, we analyse over 30,000 bacterial genome sequences to identify additional Sec/YidC-related arrest peptides, followed by in vivo and in vitro analyses. We find that Sec/YidC-related arrest peptides show patchy, but widespread, phylogenetic distribution throughout the bacterial domain. Several of the identified peptides contain distinct conserved sequences near the C-termini, but are still able to efficiently stall bacterial ribosomes in vitro and in vivo. In addition, we identify many arrest peptides that share an R-A-P-P-like sequence, suggesting that this sequence might serve as a common evolutionary seed to overcome ribosomal structural differences across species.
Collapse
Affiliation(s)
- Keigo Fujiwara
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan.
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
| | - Naoko Tsuji
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Mayu Yoshida
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan.
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
| |
Collapse
|
24
|
Shin MK, Chang J, Park J, Lee HJ, Woo JS, Kim YK. Nonsense-mediated mRNA decay of mRNAs encoding a signal peptide occurs primarily after mRNA targeting to the endoplasmic reticulum. Mol Cells 2024; 47:100049. [PMID: 38513766 PMCID: PMC11016901 DOI: 10.1016/j.mocell.2024.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024] Open
Abstract
Translation of messenger ribonucleic acids (mRNAs) encoding integral membrane proteins or secreted proteins occurs on the surface of the endoplasmic reticulum (ER). When a nascent signal peptide is synthesized from the mRNAs, the ribosome-nascent chain complex (RNC) is recognized by the signal recognition particle (SRP) and then transported to the surface of the ER. The appropriate targeting of the RNC-SRP complex to the ER is monitored by a quality control pathway, a nuclear cap-binding complex (CBC)-ensured translational repression of RNC-SRP (CENTRE). In this study, using ribosome profiling of CBC-associated and eukaryotic translation initiation factor 4E-associated mRNAs, we reveal that, at the transcriptomic level, CENTRE is in charge of the translational repression of the CBC-RNC-SRP until the complex is specifically transported to the ER. We also find that CENTRE inhibits the nonsense-mediated mRNA decay (NMD) of mRNAs within the CBC-RNC-SRP. The NMD occurs only after the CBC-RNC-SRP is targeted to the ER and after eukaryotic translation initiation factor 4E replaces CBC. Our data indicate dual surveillance for properly targeting mRNAs encoding integral membrane or secretory proteins to the ER. CENTRE blocks gene expression at the translation level before the CBC-RNC-SRP delivery to the ER, and NMD monitors mRNA quality after its delivery to the ER.
Collapse
Affiliation(s)
- Min-Kyung Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joori Park
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyuk-Joon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| |
Collapse
|
25
|
Zhu Q, Zhu X, Zhang L. ER membrane complex (EMC): Structure, functions, and roles in diseases. FASEB J 2024; 38:e23539. [PMID: 38498340 DOI: 10.1096/fj.202302266r] [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: 11/02/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024]
Abstract
The endoplasmic reticulum (ER) is the largest membrane system in eukaryotic cells and is the primary site for the biosynthesis of lipids and carbohydrates, as well as for the folding, assembly, modification, and transport of secreted and integrated membrane proteins. The ER membrane complex (EMC) on the ER membrane is an ER multiprotein complex that affects the quality control of membrane proteins, which is abundant and widely preserved. Its disruption has been found to affect a wide range of processes, including protein and lipid synthesis, organelle communication, endoplasmic reticulum stress, and viral maturation, and may lead to neurodevelopmental disorders and cancer. Therefore, EMC has attracted the attention of many scholars and become a hot field. In this paper, we summarized the main contributions of the research of EMC in the past nearly 15 years, and reviewed the structure and function of EMC as well as its related diseases. We hope this review will promote further progress of research on EMC.
Collapse
Affiliation(s)
- Qi Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xianjun Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lin Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| |
Collapse
|
26
|
Muthukumar G, Stevens TA, Inglis AJ, Esantsi TK, Saunders RA, Schulte F, Voorhees RM, Guna A, Weissman JS. Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology. Mol Cell 2024; 84:1101-1119.e9. [PMID: 38428433 DOI: 10.1016/j.molcel.2024.01.028] [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: 07/31/2023] [Revised: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse proteins remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways that act on substrates based on their topology. NAC is required for the efficient targeting of polytopic proteins, whereas signal-anchored proteins require TTC1, a cytosolic chaperone that physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, the targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.
Collapse
Affiliation(s)
- Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alina Guna
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
27
|
Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN. RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nat Commun 2024; 15:2432. [PMID: 38503735 PMCID: PMC10951233 DOI: 10.1038/s41467-024-46761-3] [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: 08/30/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024] Open
Abstract
Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.
Collapse
Affiliation(s)
- Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Sara Gabrielli
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
| |
Collapse
|
28
|
Gersteuer F, Morici M, Gabrielli S, Fujiwara K, Safdari HA, Paternoga H, Bock LV, Chiba S, Wilson DN. The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nat Commun 2024; 15:2431. [PMID: 38503753 PMCID: PMC10951299 DOI: 10.1038/s41467-024-46762-2] [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: 10/30/2023] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Nascent polypeptide chains can induce translational stalling to regulate gene expression. This is exemplified by the E. coli secretion monitor (SecM) arrest peptide that induces translational stalling to regulate expression of the downstream encoded SecA, an ATPase that co-operates with the SecYEG translocon to facilitate insertion of proteins into or through the cytoplasmic membrane. Here we present the structure of a ribosome stalled during translation of the full-length E. coli SecM arrest peptide at 2.0 Å resolution. The structure reveals that SecM arrests translation by stabilizing the Pro-tRNA in the A-site, but in a manner that prevents peptide bond formation with the SecM-peptidyl-tRNA in the P-site. By employing molecular dynamic simulations, we also provide insight into how a pulling force on the SecM nascent chain can relieve the SecM-mediated translation arrest. Collectively, the mechanisms determined here for SecM arrest and relief are also likely to be applicable for a variety of other arrest peptides that regulate components of the protein localization machinery identified across a wide range of bacteria lineages.
Collapse
Affiliation(s)
- Felix Gersteuer
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Sara Gabrielli
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
| |
Collapse
|
29
|
Jung SJ, Sridhara S, Ott M. Early steps in the biogenesis of mitochondrially encoded oxidative phosphorylation subunits. IUBMB Life 2024; 76:125-139. [PMID: 37712772 DOI: 10.1002/iub.2784] [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: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
The complexes mediating oxidative phosphorylation (OXPHOS) in the inner mitochondrial membrane consist of proteins encoded in the nuclear or the mitochondrial DNA. The mitochondrially encoded membrane proteins (mito-MPs) represent the catalytic core of these complexes and follow complicated pathways for biogenesis. Owing to their overall hydrophobicity, mito-MPs are co-translationally inserted into the inner membrane by the Oxa1 insertase. After insertion, OXPHOS biogenesis factors mediate the assembly of mito-MPs into complexes and participate in the regulation of mitochondrial translation, while protein quality control factors recognize and degrade faulty or excess proteins. This review summarizes the current understanding of these early steps occurring during the assembly of mito-MPs by concentrating on results obtained in the model organism baker's yeast.
Collapse
Affiliation(s)
- Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Ott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| |
Collapse
|
30
|
Gamerdinger M, Deuerling E. Cotranslational sorting and processing of newly synthesized proteins in eukaryotes. Trends Biochem Sci 2024; 49:105-118. [PMID: 37919225 DOI: 10.1016/j.tibs.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Ribosomes interact with a variety of different protein biogenesis factors that guide newly synthesized proteins to their native 3D shapes and cellular localization. Depending on the type of translated substrate, a distinct set of cotranslational factors must interact with the ribosome in a timely and coordinated manner to ensure proper protein biogenesis. While cytonuclear proteins require cotranslational maturation and folding factors, secretory proteins must be maintained in an unfolded state and processed cotranslationally by transport and membrane translocation factors. Here we explore the specific cotranslational processing steps for cytonuclear, secretory, and membrane proteins in eukaryotes and then discuss how the nascent polypeptide-associated complex (NAC) cotranslationally sorts these proteins into the correct protein biogenesis pathway.
Collapse
Affiliation(s)
- Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.
| |
Collapse
|
31
|
Knauer JF, Schulz C, Zemella A, Wüstenhagen DA, Walter RM, Küpper JH, Kubick S. Synthesis of mono Cytochrome P450 in a modified CHO-CPR cell-free protein production platform. Sci Rep 2024; 14:1271. [PMID: 38218994 PMCID: PMC10787779 DOI: 10.1038/s41598-024-51781-6] [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: 05/05/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Cytochromes P450 (CYPs) are a group of monooxygenases that can be found in almost all kinds of organisms. For CYPs to receive electrons from co-substrate NADPH, the activity of NADPH-Cytochrome-P450-oxidoreductase (CPR) is required as well. In humans, CYPs are an integral part of liver-based phase-1 biotransformation, which is essential for the metabolization of multiple xenobiotics and drugs. Consequently, CYPs are important players during drug development and therefore these enzymes are implemented in diverse screening applications. For these applications it is usually advantageous to use mono CYP microsomes containing only the CYP of interest. The generation of mono-CYP containing mammalian cells and vesicles is difficult since endogenous CYPs are present in many cell types that contain the necessary co-factors. By obtaining translationally active lysates from a modified CHO-CPR cell line, it is now possible to generate mono CYPs in a cell-free protein synthesis process in a straightforward manner. As a proof of principle, the synthesis of active human CYPs from three different CYP450 gene families (CYP1A2, CYP2B6 and CYP3A4), which are of outstanding interest in industry and academia was demonstrated. Luciferase based activity assays confirm the activity of the produced CYPs and enable the individual adaptation of the synthesis process for efficient cell-free enzyme production. Furthermore, they allow for substrate and inhibitor screenings not only for wild-type CYPs but also for mutants and further CYP isoforms and variants. As an example, the turnover of selected CYP substrates by cell-free synthesized CYPs was demonstrated via an indirect luciferase assay-based screening setup.
Collapse
Affiliation(s)
- Jan Felix Knauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Berlin, Germany
| | - Christian Schulz
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Jan-Heiner Küpper
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| |
Collapse
|
32
|
He F, Gao YW, Ye ZX, Huang HJ, Tian CH, Zhang CX, Chen JP, Li JM, Lu JB. Comparative transcriptomic analysis of salivary glands between the zoophytophagous Cyrtorhinus lividipennis and the phytozoophagous Apolygus lucorum. BMC Genomics 2024; 25:53. [PMID: 38212677 PMCID: PMC10785411 DOI: 10.1186/s12864-023-09956-4] [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: 12/01/2023] [Accepted: 12/31/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Saliva plays a crucial role in shaping the feeding behavior of insects, involving processes such as food digestion and the regulation of interactions between insects and their hosts. Cyrtorhinus lividipennis serves as a predominant natural enemy of rice pests, while Apolygus lucorum, exhibiting phytozoophagous feeding behavior, is a destructive agricultural pest. In this study, a comparative transcriptome analysis, incorporating the published genomes of C.lividipennis and A.lucorum, was conducted to reveal the role of salivary secretion in host adaptation. RESULTS In contrast to A.lucorum, C.lividipennis is a zoophytophagous insect. A de novo genome analysis of C.lividipennis yielded 19,706 unigenes, including 16,217 annotated ones. On the other hand, A.lucorum had altogether 20,111 annotated genes, as obtained from the published official gene set (20,353 unigenes). Functional analysis of the top 1,000 salivary gland (SG)-abundant genes in both insects revealed that the SG was a dynamically active tissue engaged in protein synthesis and secretion. Predictions of other tissues and signal peptides were compared. As a result, 94 and 157 salivary proteins were identified in C.lividipennis and A.lucorum, respectively, and were categorized into 68 and 81 orthogroups. Among them, 26 orthogroups were shared, potentially playing common roles in digestion and detoxification, including several venom serine proteases. Furthermore, 42 and 55 orthogroups were exclusive in C.lividipennis and A.lucorum, respectively, which were exemplified by a hyaluronidase in C.lividipennis that was associated with predation, while polygalacturonases in A.lucorum were involved in mesophyll-feeding patterns. CONCLUSIONS Findings in this study provide a comprehensive insight into saliva secretions in C.lividipennis and A.lucorum via a transcriptome approach, reflecting the intricate connections between saliva secretions and feeding behaviors. It is found that conserved salivary secretions are involved in shaping the overlapping feeding patterns, while a plethora of unique salivary secretions may drive the evolution of specific feeding behaviors crucial for their survival. These results enhance our understanding of the feeding mechanisms in different insects from the perspective of saliva and contribute to future environmentally friendly pest control by utilizing predatory insects.
Collapse
Affiliation(s)
- Fang He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Yang-Wei Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Cai-Hong Tian
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
- Institute of Insect Science, Zhejiang University, 310058, Hangzhou, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China
| | - Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211, Ningbo, China.
| |
Collapse
|
33
|
Lao J, Sun H, Wang A, Wu M, Liu D, Zhang Y, Chen C, Xia Q, Ma S. Effect of eIF6 on the development of silk glands and silk protein synthesis of the silkworm, Bombyx mori. Int J Biol Macromol 2024; 256:128316. [PMID: 38000606 DOI: 10.1016/j.ijbiomac.2023.128316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
The silkworm is a lepidopteran domesticated from the wild silkworm, mostly valued for its efficient synthesis of silk protein. This species' ability to spin silk has supported the 5500-year-old silk industry and the globally known "Silk Road", making the transformation of mulberry leaves into silk of great concern. Therefore, research on the silk-related genes of silkworms and their regulatory mechanisms has attracted increasing attention. Previous studies have revealed that domestic silk gland cells are endoreduplication cells, and their high-copy genome and special chromatin conformation provide conditions for the high expression of silk proteins. In this study, we systematically investigate the expression pattern of eukaryotic initiation factors (eIFs) and identified the eIF6 as a eukaryotic translation initiation factor involved in the synthesis of silk proteins. We generated an eIF6 gene deletion mutant strain of silkworm using the CRISPR/Cas9 system and investigated the function of eIF6 in silk gland development and silk protein synthesis. The results showed that deletion of eIF6 inhibited the individual development of silkworm larvae, inhibited the development of silk glands, and significantly reduced the cocoon layer ratio. Therefore, we elucidated the function of eIF6 in the development of silk glands and the synthesis of silk proteins, which is important for further elucidation of the developmental process of silk glands and the mechanism underlying the ultra-high expression of silk proteins.
Collapse
Affiliation(s)
- Junjie Lao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Hao Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Aoming Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Mingke Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Dan Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Yan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Chaojie Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China.
| | - Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China.
| |
Collapse
|
34
|
Wu H, Smalinskaitė L, Hegde RS. EMC rectifies the topology of multipass membrane proteins. Nat Struct Mol Biol 2024; 31:32-41. [PMID: 37957425 PMCID: PMC10803268 DOI: 10.1038/s41594-023-01120-6] [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: 04/25/2023] [Accepted: 09/08/2023] [Indexed: 11/15/2023]
Abstract
Most eukaryotic multipass membrane proteins are inserted into the membrane of the endoplasmic reticulum. Their transmembrane domains (TMDs) are thought to be inserted co-translationally as they emerge from a membrane-bound ribosome. Here we find that TMDs near the carboxyl terminus of mammalian multipass proteins are inserted post-translationally by the endoplasmic reticulum membrane protein complex (EMC). Site-specific crosslinking shows that the EMC's cytosol-facing hydrophilic vestibule is adjacent to a pre-translocated C-terminal tail. EMC-mediated insertion is mostly agnostic to TMD hydrophobicity, favored for short uncharged C-tails and stimulated by a preceding unassembled TMD bundle. Thus, multipass membrane proteins can be released by the ribosome-translocon complex in an incompletely inserted state, requiring a separate EMC-mediated post-translational insertion step to rectify their topology, complete biogenesis and evade quality control. This sequential co-translational and post-translational mechanism may apply to ~250 diverse multipass proteins, including subunits of the pentameric ion channel family that are crucial for neurotransmission.
Collapse
Affiliation(s)
- Haoxi Wu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | |
Collapse
|
35
|
Duan Z, Chen K, Yang T, You R, Chen B, Li J, Liu L. Mechanisms of Endoplasmic Reticulum Protein Homeostasis in Plants. Int J Mol Sci 2023; 24:17599. [PMID: 38139432 PMCID: PMC10743519 DOI: 10.3390/ijms242417599] [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: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Maintenance of proteome integrity is essential for cell function and survival in changing cellular and environmental conditions. The endoplasmic reticulum (ER) is the major site for the synthesis of secretory and membrane proteins. However, the accumulation of unfolded or misfolded proteins can perturb ER protein homeostasis, leading to ER stress and compromising cellular function. Eukaryotic organisms have evolved sophisticated and conserved protein quality control systems to ensure protein folding fidelity via the unfolded protein response (UPR) and to eliminate potentially harmful proteins via ER-associated degradation (ERAD) and ER-phagy. In this review, we summarize recent advances in our understanding of the mechanisms of ER protein homeostasis in plants and discuss the crosstalk between different quality control systems. Finally, we will address unanswered questions in this field.
Collapse
Affiliation(s)
- Zhihao Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Kai Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Tao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Ronghui You
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Binzhao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
36
|
Daskivich GJ, Brodsky JL. The generation of detergent-insoluble clipped fragments from an ERAD substrate in mammalian cells. Sci Rep 2023; 13:21508. [PMID: 38057493 PMCID: PMC10700608 DOI: 10.1038/s41598-023-48769-z] [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: 07/28/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Proteostasis ensures the proper synthesis, folding, and trafficking of proteins and is required for cellular and organellar homeostasis. This network also oversees protein quality control within the cell and prevents accumulation of aberrant proteins, which can lead to cellular dysfunction and disease. For example, protein aggregates irreversibly disrupt proteostasis and can exert gain-of-function toxic effects. Although this process has been examined in detail for cytosolic proteins, how endoplasmic reticulum (ER)-tethered, aggregation-prone proteins are handled is ill-defined. To determine how a membrane protein with a cytoplasmic aggregation-prone domain is routed for ER-associated degradation (ERAD), we analyzed a new model substrate, TM-Ubc9ts. In yeast, we previously showed that TM-Ubc9ts ERAD requires Hsp104, which is absent in higher cells. In transient and stable HEK293 cells, we now report that TM-Ubc9ts degradation is largely proteasome-dependent, especially at elevated temperatures. In contrast to yeast, clipped TM-Ubc9ts polypeptides, which are stabilized upon proteasome inhibition, accumulate and are insoluble at elevated temperatures. TM-Ubc9ts cleavage is independent of the intramembrane protease RHBDL4, which clips other classes of ERAD substrates. These studies highlight an unappreciated mechanism underlying the degradation of aggregation-prone substrates in the ER and invite further work on other proteases that contribute to ERAD.
Collapse
Affiliation(s)
- Grant J Daskivich
- A320 Langley Hall, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jeffrey L Brodsky
- A320 Langley Hall, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| |
Collapse
|
37
|
Page KR, Nguyen VN, Pleiner T, Tomaleri GP, Wang ML, Guna A, Wang TY, Chou TF, Voorhees RM. Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569054. [PMID: 38076791 PMCID: PMC10705394 DOI: 10.1101/2023.11.28.569054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we systematically studied the biogenesis of a panel of membrane proteins, including several G-protein coupled receptors (GPCRs). We observed a central role for the insertase, the ER membrane protein complex (EMC), and developed a dual-guide approach to identify genetic modifiers of the EMC. We found that the back of sec61 (BOS) complex, a component of the 'multipass translocon', was a physical and genetic interactor of the EMC. Functional and structural analysis of the EMC•BOS holocomplex showed that characteristics of a GPCR's soluble domain determine its biogenesis pathway. In contrast to prevailing models, no single insertase handles all substrates. We instead propose a unifying model for coordination between the EMC, multipass translocon, and Sec61 for biogenesis of diverse membrane proteins in human cells.
Collapse
|
38
|
Pan Y, Zhan J, Jiang Y, Xia D, Scheuring S. A concerted ATPase cycle of the protein transporter AAA-ATPase Bcs1. Nat Commun 2023; 14:6369. [PMID: 37821516 PMCID: PMC10567702 DOI: 10.1038/s41467-023-41806-5] [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: 03/16/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023] Open
Abstract
Bcs1, a homo-heptameric transmembrane AAA-ATPase, facilitates folded Rieske iron-sulfur protein translocation across the inner mitochondrial membrane. Structures in different nucleotide states (ATPγS, ADP, apo) provided conformational snapshots, but the kinetics and structural transitions of the ATPase cycle remain elusive. Here, using high-speed atomic force microscopy (HS-AFM) and line scanning (HS-AFM-LS), we characterized single-molecule Bcs1 ATPase cycling. While the ATP conformation had ~5600 ms lifetime, independent of the ATP-concentration, the ADP/apo conformation lifetime was ATP-concentration dependent and reached ~320 ms at saturating ATP-concentration, giving a maximum turnover rate of 0.17 s-1. Importantly, Bcs1 ATPase cycle conformational changes occurred in concert. Furthermore, we propose that the transport mechanism involves opening the IMS gate through energetically costly straightening of the transmembrane helices, potentially driving rapid gate resealing. Overall, our results establish a concerted ATPase cycle mechanism in Bcs1, distinct from other AAA-ATPases that use a hand-over-hand mechanism.
Collapse
Affiliation(s)
- Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Jingyu Zhan
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yining Jiang
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, New York, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
39
|
Bramkamp M, Scheffers DJ. Bacterial membrane dynamics: Compartmentalization and repair. Mol Microbiol 2023; 120:490-501. [PMID: 37243899 DOI: 10.1111/mmi.15077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
In every bacterial cell, the plasma membrane plays a key role in viability as it forms a selective barrier between the inside of the cell and its environment. This barrier function depends on the physical state of the lipid bilayer and the proteins embedded or associated with the bilayer. Over the past decade or so, it has become apparent that many membrane-organizing proteins and principles, which were described in eukaryote systems, are ubiquitous and play important roles in bacterial cells. In this minireview, we focus on the enigmatic roles of bacterial flotillins in membrane compartmentalization and bacterial dynamins and ESCRT-like systems in membrane repair and remodeling.
Collapse
Affiliation(s)
- Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol 2023; 19:1054-1062. [PMID: 37169961 PMCID: PMC10449633 DOI: 10.1038/s41589-023-01326-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
Collapse
Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Dale Tranter
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Eric Lowe
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | | | - Vahid Abrishami
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicole A Wenzell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Ville O Paavilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
42
|
Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555937. [PMID: 37693532 PMCID: PMC10491306 DOI: 10.1101/2023.09.01.555937] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases". These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit-card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place, and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far overlooked role in membrane dynamics as scramblases.
Collapse
Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Matthew A. Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland
| |
Collapse
|
43
|
Muthukumar G, Stevens TA, Inglis AJ, Esantsi TK, Saunders RA, Schulte F, Voorhees RM, Guna A, Weissman JS. Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553624. [PMID: 37645817 PMCID: PMC10462106 DOI: 10.1101/2023.08.16.553624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mitochondrial outer membrane α-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse substrates remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse α-helical substrates reveals that these components are organized into distinct targeting pathways which act on substrates based on their topology. NAC is required for efficient targeting of polytopic proteins whereas signal-anchored proteins require TTC1, a novel cytosolic chaperone which physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.
Collapse
Affiliation(s)
- Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Taylor A. Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J. Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Theodore K. Esantsi
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Reuben A. Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rebecca M. Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alina Guna
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge 02142, MA
| |
Collapse
|
44
|
Pleiner T, Hazu M, Pinton Tomaleri G, Nguyen VN, Januszyk K, Voorhees RM. A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. J Cell Biol 2023; 222:e202212007. [PMID: 37199759 PMCID: PMC10200711 DOI: 10.1083/jcb.202212007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/31/2023] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Tail-anchored (TA) proteins play essential roles in mammalian cells, and their accurate localization is critical for proteostasis. Biophysical similarities lead to mistargeting of mitochondrial TA proteins to the ER, where they are delivered to the insertase, the ER membrane protein complex (EMC). Leveraging an improved structural model of the human EMC, we used mutagenesis and site-specific crosslinking to map the path of a TA protein from its cytosolic capture by methionine-rich loops to its membrane insertion through a hydrophilic vestibule. Positively charged residues at the entrance to the vestibule function as a selectivity filter that uses charge-repulsion to reject mitochondrial TA proteins. Similarly, this selectivity filter retains the positively charged soluble domains of multipass substrates in the cytosol, thereby ensuring they adopt the correct topology and enforcing the "positive-inside" rule. Substrate discrimination by the EMC provides a biochemical explanation for one role of charge in TA protein sorting and protects compartment integrity by limiting protein misinsertion.
Collapse
Affiliation(s)
- Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vy N. Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kurt Januszyk
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rebecca M. Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
45
|
Tipper DJ, Harley CA. Spf1 and Ste24: quality controllers of transmembrane protein topology in the eukaryotic cell. Front Cell Dev Biol 2023; 11:1220441. [PMID: 37635876 PMCID: PMC10456885 DOI: 10.3389/fcell.2023.1220441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
DNA replication, transcription, and translation in eukaryotic cells occur with decreasing but still high fidelity. In contrast, for the estimated 33% of the human proteome that is inserted as transmembrane (TM) proteins, insertion with a non-functional inverted topology is frequent. Correct topology is essential for function and trafficking to appropriate cellular compartments and is controlled principally by responses to charged residues within 15 residues of the inserted TM domain (TMD); the flank with the higher positive charge remains in the cytosol (inside), following the positive inside rule (PIR). Yeast (Saccharomyces cerevisiae) mutants that increase insertion contrary to the PIR were selected. Mutants with strong phenotypes were found only in SPF1 and STE24 (human cell orthologs are ATP13A1 and ZMPSte24) with, at the time, no known relevant functions. Spf1/Atp13A1 is now known to dislocate to the cytosol TM proteins inserted contrary to the PIR, allowing energy-conserving reinsertion. We hypothesize that Spf1 and Ste24 both recognize the short, positively charged ER luminal peptides of TM proteins inserted contrary to the PIR, accepting these peptides into their large membrane-spanning, water-filled cavities through interaction with their many interior surface negative charges. While entry was demonstrated for Spf1, no published evidence directly demonstrates substrate entry to the Ste24 cavity, internal access to its zinc metalloprotease (ZMP) site, or active withdrawal of fragments, which may be essential for function. Spf1 and Ste24 comprise a PIR quality control system that is conserved in all eukaryotes and presumably evolved in prokaryotic progenitors as they gained differentiated membrane functions. About 75% of the PIR is imposed by this quality control system, which joins the UPR, ERAD, and autophagy (ER-phagy) in coordinated, overlapping quality control of ER protein function.
Collapse
Affiliation(s)
- Donald J. Tipper
- University of Massachusetts Medical School, Worcester, MA, United States
| | - Carol A. Harley
- i3S-Instituto de Investigação e Inovação em Saude, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| |
Collapse
|
46
|
Abstract
Protein translocases, such as the bacterial SecY complex, the Sec61 complex of the endoplasmic reticulum (ER) and the mitochondrial translocases, facilitate the transport of proteins across membranes. In addition, they catalyze the insertion of integral membrane proteins into the lipid bilayer. Several membrane insertases cooperate with these translocases, thereby promoting the topogenesis, folding and assembly of membrane proteins. Oxa1 and BamA family members serve as core components in the two major classes of membrane insertases. They facilitate the integration of proteins with α-helical transmembrane domains and of β-barrel proteins into lipid bilayers, respectively. Members of the Oxa1 family were initially found in the internal membranes of bacteria, mitochondria and chloroplasts. Recent studies, however, also identified several Oxa1-type insertases in the ER, where they serve as catalytically active core subunits in the ER membrane protein complex (EMC), the guided entry of tail-anchored (GET) and the GET- and EMC-like (GEL) complex. The outer membrane of bacteria, mitochondria and chloroplasts contain β-barrel proteins, which are inserted by members of the BamA family. In this Cell Science at a Glance article and the accompanying poster, we provide an overview of these different types of membrane insertases and discuss their function.
Collapse
Affiliation(s)
- Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | | |
Collapse
|
47
|
Durmusoglu D, Al'Abri I, Li Z, Islam Williams T, Collins LB, Martínez JL, Crook N. Improving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach. Microb Cell Fact 2023; 22:109. [PMID: 37287064 PMCID: PMC10245609 DOI: 10.1186/s12934-023-02117-y] [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: 01/16/2023] [Accepted: 05/20/2023] [Indexed: 06/09/2023] Open
Abstract
The probiotic yeast Saccharomyces boulardii (Sb) is a promising chassis to deliver therapeutic proteins to the gut due to Sb's innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineer Sb strains with enhanced levels of protein secretion. In this work, we explored genetic modifications in both cis- (i.e. to the expression cassette of the secreted protein) and trans- (i.e. to the Sb genome) that enhance Sb's ability to secrete proteins, taking a Clostridioides difficile Toxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by sixfold (76-458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 and 463 mg/L. Then, guided by prior knowledge of S. cerevisiae's secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficient Sb strain that produces 5045 mg/L secretory NPA, an improvement of > tenfold over wild-type Sb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion in Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability of Sb to deliver therapeutics to the gut and other settings to which it is adapted.
Collapse
Affiliation(s)
- Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Ibrahim Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Taufika Islam Williams
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, USA
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Leonard B Collins
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, USA
| | - José L Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
48
|
Shiota N, Shimokawa-Chiba N, Fujiwara K, Chiba S. Identification of Bacillus subtilis YidC substrates using a MifM-instructed translation arrest-based reporter. J Mol Biol 2023:168172. [PMID: 37290739 DOI: 10.1016/j.jmb.2023.168172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023]
Abstract
YidC is a member of the YidC/Oxa1/Alb3 protein family that is crucial for membrane protein biogenesis in the bacterial plasma membrane. While YidC facilitates the folding and complex assembly of membrane proteins along with the Sec translocon, it also functions as a Sec-independent membrane protein insertase in the YidC-only pathway. However, little is known about how membrane proteins are recognized and sorted by these pathways, especially in Gram-positive bacteria, for which only a small number of YidC substrates have been identified to date. In this study, we aimed to identify Bacillus subtilis membrane proteins whose membrane insertion depends on SpoIIIJ, the primary YidC homolog in B. subtilis. We took advantage of the translation arrest sequence of MifM, which can monitor YidC-dependent membrane insertion. Our systematic screening identified eight membrane proteins as candidate SpoIIIJ substrates. Results of our genetic study also suggest that the conserved arginine in the hydrophilic groove of SpoIIIJ is crucial for the membrane insertion of the substrates identified here. However, in contrast to MifM, a previously identified YidC substrate, the importance of the negatively charged residue on the substrates for membrane insertion varied depending on the substrate. These results suggest that B. subtilis YidC uses substrate-specific interactions to facilitate membrane insertion.
Collapse
Affiliation(s)
- Narumi Shiota
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
| | - Naomi Shimokawa-Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Keigo Fujiwara
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Japan.
| |
Collapse
|
49
|
Xue X, Wu X, Liu L, Liu L, Zhu F. ERVW-1 Activates ATF6-Mediated Unfolded Protein Response by Decreasing GANAB in Recent-Onset Schizophrenia. Viruses 2023; 15:1298. [PMID: 37376599 PMCID: PMC10304270 DOI: 10.3390/v15061298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Schizophrenia, a mental disorder, afflicts 1% of the worldwide population. The dysregulation of homeostasis in the endoplasmic reticulum (ER) has been implicated in schizophrenia. Moreover, recent studies indicate that ER stress and the unfolded protein response (UPR) are linked to this mental disorder. Our previous research has verified that endogenous retrovirus group W member 1 envelope (ERVW-1), a risk factor for schizophrenia, is elevated in individuals with schizophrenia. Nevertheless, no literature is available regarding the underlying relationship between ER stress and ERVW-1 in schizophrenia. The aim of our research was to investigate the molecular mechanism connecting ER stress and ERVW-1 in schizophrenia. Here, we employed Gene Differential Expression Analysis to predict differentially expressed genes (DEGs) in the human prefrontal cortex of schizophrenic patients and identified aberrant expression of UPR-related genes. Subsequent research indicated that the UPR gene called XBP1 had a positive correlation with ATF6, BCL-2, and ERVW-1 in individuals with schizophrenia using Spearman correlation analysis. Furthermore, results from the enzyme-linked immunosorbent assay (ELISA) suggested increased serum protein levels of ATF6 and XBP1 in schizophrenic patients compared with healthy controls, exhibiting a strong correlation with ERVW-1 using median analysis and Mann-Whitney U analysis. However, serum GANAB levels were decreased in schizophrenic patients compared with controls and showed a significant negative correlation with ERVW-1, ATF6, and XBP1 in schizophrenic patients. Interestingly, in vitro experiments verified that ERVW-1 indeed increased ATF6 and XBP1 expression while decreasing GANAB expression. Additionally, the confocal microscope experiment suggested that ERVW-1 could impact the shape of the ER, leading to ER stress. GANAB was found to participate in ER stress regulated by ERVW-1. In conclusion, ERVW-1 induced ER stress by suppressing GANAB expression, thereby upregulating the expression of ATF6 and XBP1 and ultimately contributing to the development of schizophrenia.
Collapse
Affiliation(s)
- Xing Xue
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.X.); (X.W.); (L.L.)
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.X.); (X.W.); (L.L.)
| | - Lijuan Liu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.X.); (X.W.); (L.L.)
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, China
| | | | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; (X.X.); (X.W.); (L.L.)
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, China
| |
Collapse
|
50
|
Jaskolowski M, Jomaa A, Gamerdinger M, Shrestha S, Leibundgut M, Deuerling E, Ban N. Molecular basis of the TRAP complex function in ER protein biogenesis. Nat Struct Mol Biol 2023:10.1038/s41594-023-00990-0. [PMID: 37170030 DOI: 10.1038/s41594-023-00990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
The translocon-associated protein (TRAP) complex resides in the endoplasmic reticulum (ER) membrane and interacts with the Sec translocon and the ribosome to facilitate biogenesis of secretory and membrane proteins. TRAP plays a key role in the secretion of many hormones, including insulin. Here we reveal the molecular architecture of the mammalian TRAP complex and how it engages the translating ribosome associated with Sec61 translocon on the ER membrane. The TRAP complex is anchored to the ribosome via a long tether and its position is further stabilized by a finger-like loop. This positions a cradle-like lumenal domain of TRAP below the translocon for interactions with translocated nascent chains. Our structure-guided TRAP mutations in Caenorhabditis elegans lead to growth deficits associated with increased ER stress and defects in protein hormone secretion. These findings elucidate the molecular basis of the TRAP complex in the biogenesis and translocation of proteins at the ER.
Collapse
Affiliation(s)
- Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
- Department of Molecular Physiology and Biological Physics and the Center for Cell and Membrane Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Sandeep Shrestha
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany.
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|