1
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Seifu YW, Pukyšová V, Rýdza N, Bilanovičová V, Zwiewka M, Sedláček M, Nodzyński T. Mapping the membrane orientation of auxin homeostasis regulators PIN5 and PIN8 in Arabidopsis thaliana root cells reveals their divergent topology. PLANT METHODS 2024; 20:84. [PMID: 38825682 PMCID: PMC11145782 DOI: 10.1186/s13007-024-01182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/10/2024] [Indexed: 06/04/2024]
Abstract
PIN proteins establish the auxin concentration gradient, which coordinates plant growth. PIN1-4 and 7 localized at the plasma membrane (PM) and facilitate polar auxin transport while the endoplasmic reticulum (ER) localized PIN5 and PIN8 maintain the intracellular auxin homeostasis. Although an antagonistic activity of PIN5 and PIN8 proteins in regulating the intracellular auxin homeostasis and other developmental events have been reported, the membrane topology of these proteins, which might be a basis for their antagonistic function, is poorly understood. In this study we optimized digitonin based PM-permeabilizing protocols coupled with immunocytochemistry labeling to map the membrane topology of PIN5 and PIN8 in Arabidopsis thaliana root cells. Our results indicate that, except for the similarities in the orientation of the N-terminus, PIN5 and PIN8 have an opposite orientation of the central hydrophilic loop and the C-terminus, as well as an unequal number of transmembrane domains (TMDs). PIN8 has ten TMDs with groups of five alpha-helices separated by the central hydrophilic loop (HL) residing in the ER lumen, and its N- and C-terminals are positioned in the cytoplasm. However, the topology of PIN5 comprises nine TMDs. Its N-terminal end and the central HL face the cytoplasm while its C-terminus resides in the ER lumen. Overall, this study shows that PIN5 and PIN8 proteins have a divergent membrane topology while introducing a toolkit of methods for studying membrane topology of integral proteins including those localized at the ER membrane.
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Affiliation(s)
- Yewubnesh Wendimu Seifu
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Vendula Pukyšová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Nikola Rýdza
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Veronika Bilanovičová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Marta Zwiewka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Marek Sedláček
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Tomasz Nodzyński
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic.
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2
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Schoenmakers LLJ, den Uijl MJ, Postma JL, van den Akker TAP, Huck WTS, Driessen AJM. SecYEG-mediated translocation in a model synthetic cell. Synth Biol (Oxf) 2024; 9:ysae007. [PMID: 38807757 PMCID: PMC11131593 DOI: 10.1093/synbio/ysae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Giant unilamellar vesicles (GUVs) provide a powerful model compartment for synthetic cells. However, a key challenge is the incorporation of membrane proteins that allow for transport, energy transduction, compartment growth and division. Here, we have successfully incorporated the membrane protein complex SecYEG-the key bacterial translocase that is essential for the incorporation of newly synthesized membrane proteins-in GUVs. Our method consists of fusion of small unilamellar vesicles containing reconstituted SecYEG into GUVs, thereby forming SecGUVs. These are suitable for large-scale experiments while maintaining a high protein:lipid ratio. We demonstrate that incorporation of SecYEG into GUVs does not inhibit its translocation efficiency. Robust membrane protein functionalized proteo-GUVs are promising and flexible compartments for use in the formation and growth of synthetic cells.
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Affiliation(s)
- Ludo L J Schoenmakers
- Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Max J den Uijl
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jelle L Postma
- General Instrumentation, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Tim A P van den Akker
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Wilhelm T S Huck
- Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Arnold J M Driessen
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
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3
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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.
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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
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4
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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.
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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
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5
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Zhao Y, Dong Q, Geng Y, Ma C, Shao Q. Dynamic Regulation of Lipid Droplet Biogenesis in Plant Cells and Proteins Involved in the Process. Int J Mol Sci 2023; 24:ijms24087476. [PMID: 37108639 PMCID: PMC10138601 DOI: 10.3390/ijms24087476] [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: 03/11/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Lipid droplets (LDs) are ubiquitous, dynamic organelles found in almost all organisms, including animals, protists, plants and prokaryotes. The cell biology of LDs, especially biogenesis, has attracted increasing attention in recent decades because of their important role in cellular lipid metabolism and other newly identified processes. Emerging evidence suggests that LD biogenesis is a highly coordinated and stepwise process in animals and yeasts, occurring at specific sites of the endoplasmic reticulum (ER) that are defined by both evolutionarily conserved and organism- and cell type-specific LD lipids and proteins. In plants, understanding of the mechanistic details of LD formation is elusive as many questions remain. In some ways LD biogenesis differs between plants and animals. Several homologous proteins involved in the regulation of animal LD formation in plants have been identified. We try to describe how these proteins are synthesized, transported to the ER and specifically targeted to LD, and how these proteins participate in the regulation of LD biogenesis. Here, we review current work on the molecular processes that control LD formation in plant cells and highlight the proteins that govern this process, hoping to provide useful clues for future research.
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Affiliation(s)
- Yiwu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Qingdi Dong
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Yuhu Geng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Qun Shao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250358, China
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6
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Overduin M, Kervin TA, Klarenbach Z, Adra TRC, Bhat RK. Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL. Biophys Chem 2023; 295:106971. [PMID: 36801589 DOI: 10.1016/j.bpc.2023.106971] [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: 12/24/2022] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Structures can now be predicted for any protein using programs like AlphaFold and Rosetta, which rely on a foundation of experimentally determined structures of architecturally diverse proteins. The accuracy of such artificial intelligence and machine learning (AI/ML) approaches benefits from the specification of restraints which assist in navigating the universe of folds to converge on models most representative of a given protein's physiological structure. This is especially pertinent for membrane proteins, with structures and functions that depend on their presence in lipid bilayers. Structures of proteins in their membrane environments could conceivably be predicted from AI/ML approaches with user-specificized parameters that describe each element of the architecture of a membrane protein accompanied by its lipid environment. We propose the Classification Of Membrane Proteins based On Structures Engaging Lipids (COMPOSEL), which builds on existing nomenclature types for monotopic, bitopic, polytopic and peripheral membrane proteins as well as lipids. Functional and regulatory elements are also defined in the scripts, as shown with membrane fusing synaptotagmins, multidomain PDZD8 and Protrudin proteins that recognize phosphoinositide (PI) lipids, the intrinsically disordered MARCKS protein, caveolins, the β barrel assembly machine (BAM), an adhesion G-protein coupled receptor (aGPCR) and two lipid modifying enzymes - diacylglycerol kinase DGKε and fatty aldehyde dehydrogenase FALDH. This demonstrates how COMPOSEL communicates lipid interactivity as well as signaling mechanisms and binding of metabolites, drug molecules, polypeptides or nucleic acids to describe the operations of any protein. Moreover COMPOSEL can be scaled to express how genomes encode membrane structures and how our organs are infiltrated by pathogens such as SARS-CoV-2.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Trixie Rae C Adra
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Rakesh K Bhat
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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7
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Wu H, Hegde RS. Mechanism of signal-anchor triage during early steps of membrane protein insertion. Mol Cell 2023; 83:961-973.e7. [PMID: 36764302 PMCID: PMC10155758 DOI: 10.1016/j.molcel.2023.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/08/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023]
Abstract
Most membrane proteins use their first transmembrane domain, known as a signal anchor (SA), for co-translational targeting to the endoplasmic reticulum (ER) via the signal recognition particle (SRP). The SA then inserts into the membrane using either the Sec61 translocation channel or the ER membrane protein complex (EMC) insertase. How EMC and Sec61 collaborate to ensure SA insertion in the correct topology is not understood. Using site-specific crosslinking, we detect a pre-insertion SA intermediate adjacent to EMC. This intermediate forms after SA release from SRP but before ribosome transfer to Sec61. The polypeptide's N-terminal tail samples a cytosolic vestibule bordered by EMC3, from where it can translocate across the membrane concomitant with SA insertion. The ribosome then docks on Sec61, which has an opportunity to insert those SAs skipped by EMC. These results suggest that EMC acts between SRP and Sec61 to triage SAs for insertion during membrane protein biogenesis.
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Affiliation(s)
- Haoxi Wu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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8
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Sec61 channel subunit Sbh1/Sec61β promotes ER translocation of proteins with suboptimal targeting sequences and is fine-tuned by phosphorylation. J Biol Chem 2023; 299:102895. [PMID: 36639027 PMCID: PMC9947333 DOI: 10.1016/j.jbc.2023.102895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The highly conserved endoplasmic reticulum (ER) protein translocation channel contains one nonessential subunit, Sec61β/Sbh1, whose function is poorly understood so far. Its intrinsically unstructured cytosolic domain makes transient contact with ER-targeting sequences in the cytosolic channel vestibule and contains multiple phosphorylation sites suggesting a potential for regulating ER protein import. In a microscopic screen, we show that 12% of a GFP-tagged secretory protein library depends on Sbh1 for translocation into the ER. Sbh1-dependent proteins had targeting sequences with less pronounced hydrophobicity and often no charge bias or an inverse charge bias which reduces their insertion efficiency into the Sec61 channel. We determined that mutating two N-terminal, proline-flanked phosphorylation sites in the Sbh1 cytosolic domain to alanine phenocopied the temperature-sensitivity of a yeast strain lacking SBH1 and its ortholog SBH2. The phosphorylation site mutations reduced translocation into the ER of a subset of Sbh1-dependent proteins, including enzymes whose concentration in the ER lumen is critical for ER proteostasis. In addition, we found that ER import of these proteins depended on the activity of the phospho-S/T-specific proline isomerase Ess1 (PIN1 in mammals). We conclude that Sbh1 promotes ER translocation of substrates with suboptimal targeting sequences and that its activity can be regulated by a conformational change induced by N-terminal phosphorylation.
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9
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Itskanov S, Park E. Mechanism of Protein Translocation by the Sec61 Translocon Complex. Cold Spring Harb Perspect Biol 2023; 15:a041250. [PMID: 35940906 PMCID: PMC9808579 DOI: 10.1101/cshperspect.a041250] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The endoplasmic reticulum (ER) is a major site for protein synthesis, folding, and maturation in eukaryotic cells, responsible for production of secretory proteins and most integral membrane proteins. The universally conserved protein-conducting channel Sec61 complex mediates core steps in these processes by translocating hydrophilic polypeptide segments of client proteins across the ER membrane and integrating hydrophobic transmembrane segments into the membrane. The Sec61 complex associates with several other molecular machines and enzymes to enable substrate engagement with the channel and coordination of protein translocation with translation, protein folding, and/or post-translational modifications. Recent cryo-electron microscopy and functional studies of these translocon complexes have greatly advanced our mechanistic understanding of Sec61-dependent protein biogenesis at the ER. Here, we will review the current models for how the Sec61 channel performs its functions in coordination with partner complexes.
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Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program
- California Institute for Quantitative Biosciences
| | - Eunyong Park
- California Institute for Quantitative Biosciences
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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10
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O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
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Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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11
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Kawamala BK, Abrol R. Three-stage model of helical membrane protein folding: Role of membrane-water interface as the intermediate stage vestibule for TM helices during their in membrano assembly. Biochem Biophys Res Commun 2022; 624:1-7. [PMID: 35926384 PMCID: PMC10587497 DOI: 10.1016/j.bbrc.2022.07.006] [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: 06/18/2022] [Accepted: 07/02/2022] [Indexed: 11/22/2022]
Abstract
Integral membrane proteins (MPs) are dominated by transmembrane α-helical (TMH) proteins playing critical roles in cellular signaling processes. These proteins display a wide range of sizes from one TMH domain to at least 26 TMH domains and diverse structural folds. A common feature of most of these folds is the TM orientation of the helical domains and the approximately parallel packing of these domains into helical bundles of varying stability, however, it has been challenging to study the folding of these proteins experimentally. The contribution of helix stabilization in membrane and interface to the folding energy landscape are investigated here for the full range of TMH protein sizes containing 1 TM domain (1-TMH protein) to 24 TM domains (24-TMH protein) for all TMH proteins with available structures using structural bioinformatics based hydropathy analysis. The TM helix insertion stabilization energies from Water to membrane-water Interface (WAT→INT energies) are on average half of those insertion energies from water to transmembrane orientation (WAT→TM energies) for the whole polytopic helical membrane proteome (1-TMH to 24-TMH proteins). This suggests a potentially dominant role of the membrane-water interface as a viable holding vestibule for the TM helices during their release from the translocon. This provides proteome-level evidence for the broadly applicable four-step thermodynamic framework by White and co-workers as well as a natural extension of Popot and Engelman's original two-stage model of helical MP folding to a three-stage model, where, in the new intermediate stage, the membrane-water interface acts as a holding vestibule for the translated TM helices, reconciling the interface's critical role in MP folding seen in many previous studies. Support for this model is provided by showing the stability of hydrophobic TM helices at the membrane-water interface through several microsecond long molecular dynamics simulations of five hydrophobic helical domains and a helical hairpin pre-folded from the ribosomal exit vestibule.
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Affiliation(s)
- Bridget-K Kawamala
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, USA
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, USA.
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12
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Krämer LC, Wasser D, Haitz F, Sabel B, Büchel C. Heterologous expression of HUP1 glucose transporter enables low-light mediated growth on glucose in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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13
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Mercier E, Wang X, Bögeholz LAK, Wintermeyer W, Rodnina MV. Cotranslational Biogenesis of Membrane Proteins in Bacteria. Front Mol Biosci 2022; 9:871121. [PMID: 35573737 PMCID: PMC9099147 DOI: 10.3389/fmolb.2022.871121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/12/2022] [Indexed: 12/26/2022] Open
Abstract
Nascent polypeptides emerging from the ribosome during translation are rapidly scanned and processed by ribosome-associated protein biogenesis factors (RPBs). RPBs cleave the N-terminal formyl and methionine groups, assist cotranslational protein folding, and sort the proteins according to their cellular destination. Ribosomes translating inner-membrane proteins are recognized and targeted to the translocon with the help of the signal recognition particle, SRP, and SRP receptor, FtsY. The growing nascent peptide is then inserted into the phospholipid bilayer at the translocon, an inner-membrane protein complex consisting of SecY, SecE, and SecG. Folding of membrane proteins requires that transmembrane helices (TMs) attain their correct topology, the soluble domains are inserted at the correct (cytoplasmic or periplasmic) side of the membrane, and – for polytopic membrane proteins – the TMs find their interaction partner TMs in the phospholipid bilayer. This review describes the recent progress in understanding how growing nascent peptides are processed and how inner-membrane proteins are targeted to the translocon and find their correct orientation at the membrane, with the focus on biophysical approaches revealing the dynamics of the process. We describe how spontaneous fluctuations of the translocon allow diffusion of TMs into the phospholipid bilayer and argue that the ribosome orchestrates cotranslational targeting not only by providing the binding platform for the RPBs or the translocon, but also by helping the nascent chains to find their correct orientation in the membrane. Finally, we present the auxiliary role of YidC as a chaperone for inner-membrane proteins. We show how biophysical approaches provide new insights into the dynamics of membrane protein biogenesis and raise new questions as to how translation modulates protein folding.
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14
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Hsieh HH, Shan SO. Fidelity of Cotranslational Protein Targeting to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:ijms23010281. [PMID: 35008707 PMCID: PMC8745203 DOI: 10.3390/ijms23010281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 02/04/2023] Open
Abstract
Fidelity of protein targeting is essential for the proper biogenesis and functioning of organelles. Unlike replication, transcription and translation processes, in which multiple mechanisms to recognize and reject noncognate substrates are established in energetic and molecular detail, the mechanisms by which cells achieve a high fidelity in protein localization remain incompletely understood. Signal recognition particle (SRP), a conserved pathway to mediate the localization of membrane and secretory proteins to the appropriate cellular membrane, provides a paradigm to understand the molecular basis of protein localization in the cell. In this chapter, we review recent progress in deciphering the molecular mechanisms and substrate selection of the mammalian SRP pathway, with an emphasis on the key role of the cotranslational chaperone NAC in preventing protein mistargeting to the ER and in ensuring the organelle specificity of protein localization.
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15
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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16
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Jung SJ, Kim H. Emerging View on the Molecular Functions of Sec62 and Sec63 in Protein Translocation. Int J Mol Sci 2021; 22:ijms222312757. [PMID: 34884562 PMCID: PMC8657602 DOI: 10.3390/ijms222312757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022] Open
Abstract
Most secreted and membrane proteins are targeted to and translocated across the endoplasmic reticulum (ER) membrane through the Sec61 protein-conducting channel. Evolutionarily conserved Sec62 and Sec63 associate with the Sec61 channel, forming the Sec complex and mediating translocation of a subset of proteins. For the last three decades, it has been thought that ER protein targeting and translocation occur via two distinct pathways: signal recognition particle (SRP)-dependent co-translational or SRP-independent, Sec62/Sec63 dependent post-translational translocation pathway. However, recent studies have suggested that ER protein targeting and translocation through the Sec translocon are more intricate than previously thought. This review summarizes the current understanding of the molecular functions of Sec62/Sec63 in ER protein translocation.
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Affiliation(s)
| | - Hyun Kim
- Correspondence: ; Tel.: +82-2-880-4440; Fax: +82-2-872-1993
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17
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Take Me Home, Protein Roads: Structural Insights into Signal Peptide Interactions during ER Translocation. Int J Mol Sci 2021; 22:ijms222111871. [PMID: 34769302 PMCID: PMC8584900 DOI: 10.3390/ijms222111871] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Cleavable endoplasmic reticulum (ER) signal peptides (SPs) and other non-cleavable signal sequences target roughly a quarter of the human proteome to the ER. These short peptides, mostly located at the N-termini of proteins, are highly diverse. For most proteins targeted to the ER, it is the interactions between the signal sequences and the various ER targeting and translocation machineries such as the signal recognition particle (SRP), the protein-conducting channel Sec61, and the signal peptidase complex (SPC) that determine the proteins’ target location and provide translocation fidelity. In this review, we follow the signal peptide into the ER and discuss the recent insights that structural biology has provided on the governing principles of those interactions.
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18
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Rimal S, Li Y, Vartak R, Geng J, Tantray I, Li S, Huh S, Vogel H, Glabe C, Grinberg LT, Spina S, Seeley WW, Guo S, Lu B. Inefficient quality control of ribosome stalling during APP synthesis generates CAT-tailed species that precipitate hallmarks of Alzheimer's disease. Acta Neuropathol Commun 2021; 9:169. [PMID: 34663454 PMCID: PMC8522249 DOI: 10.1186/s40478-021-01268-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 11/25/2022] Open
Abstract
Amyloid precursor protein (APP) metabolism is central to Alzheimer's disease (AD) pathogenesis, but the key etiological driver remains elusive. Recent failures of clinical trials targeting amyloid-β (Aβ) peptides, the proteolytic fragments of amyloid precursor protein (APP) that are the main component of amyloid plaques, suggest that the proteostasis-disrupting, key pathogenic species remain to be identified. Previous studies suggest that APP C-terminal fragment (APP.C99) can cause disease in an Aβ-independent manner. The mechanism of APP.C99 pathogenesis is incompletely understood. We used Drosophila models expressing APP.C99 with the native ER-targeting signal of human APP, expressing full-length human APP only, or co-expressing full-length human APP and β-secretase (BACE), to investigate mechanisms of APP.C99 pathogenesis. Key findings are validated in mammalian cell culture models, mouse 5xFAD model, and postmortem AD patient brain materials. We find that ribosomes stall at the ER membrane during co-translational translocation of APP.C99, activating ribosome-associated quality control (RQC) to resolve ribosome collision and stalled translation. Stalled APP.C99 species with C-terminal extensions (CAT-tails) resulting from inadequate RQC are prone to aggregation, causing endolysosomal and autophagy defects and seeding the aggregation of amyloid β peptides, the main component of amyloid plaques. Genetically removing stalled and CAT-tailed APP.C99 rescued proteostasis failure, endolysosomal/autophagy dysfunction, neuromuscular degeneration, and cognitive deficits in AD models. Our finding of RQC factor deposition at the core of amyloid plaques from AD brains further supports the central role of defective RQC of ribosome collision and stalled translation in AD pathogenesis. These findings demonstrate that amyloid plaque formation is the consequence and manifestation of a deeper level proteostasis failure caused by inadequate RQC of translational stalling and the resultant aberrantly modified APP.C99 species, previously unrecognized etiological drivers of AD and newly discovered therapeutic targets.
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Affiliation(s)
- Suman Rimal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yu Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rasika Vartak
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ishaq Tantray
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shuangxi Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sungun Huh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Charles Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Lea T Grinberg
- Memory and Aging Center, Department of Neurology and Department of Pathology, University of California, San Francisco, CA, 94158, USA
| | - Salvatore Spina
- Memory and Aging Center, Department of Neurology and Department of Pathology, University of California, San Francisco, CA, 94158, USA
| | - William W Seeley
- Memory and Aging Center, Department of Neurology and Department of Pathology, University of California, San Francisco, CA, 94158, USA
| | - Su Guo
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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19
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Sicking M, Jung M, Lang S. Lights, Camera, Interaction: Studying Protein-Protein Interactions of the ER Protein Translocase in Living Cells. Int J Mol Sci 2021; 22:10358. [PMID: 34638699 PMCID: PMC8508666 DOI: 10.3390/ijms221910358] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Various landmark studies have revealed structures and functions of the Sec61/SecY complex in all domains of live demonstrating the conserved nature of this ancestral protein translocase. While the bacterial homolog of the Sec61 complex resides in the plasma membrane, the eukaryotic counterpart manages the transfer of precursor proteins into or across the membrane of the endoplasmic reticulum (ER). Sec61 complexes are accompanied by a set of dynamically recruited auxiliary proteins assisting the transport of certain precursor polypeptides. TRAP and Sec62/Sec63 are two auxiliary protein complexes in mammalian cells that have been characterized by structural and biochemical methods. Using these ER membrane protein complexes for our proof-of-concept study, we aimed to detect interactions of membrane proteins in living mammalian cells under physiological conditions. Bimolecular luminescence complementation and competition was used to demonstrate multiple protein-protein interactions of different topological layouts. In addition to the interaction of the soluble catalytic and regulatory subunits of the cytosolic protein kinase A, we detected interactions of ER membrane proteins that either belong to the same multimeric protein complex (intra-complex interactions: Sec61α-Sec61β, TRAPα-TRAPβ) or protein complexes in juxtaposition (inter-complex interactions: Sec61α-TRAPα, Sec61α-Sec63, and Sec61β-Sec63). In the process, we established further control elements like synthetic peptide complementation for expression profiling of fusion constructs and protease-mediated reporter degradation demonstrating the cytosolic localization of a reporter complementation. Ease of use and flexibility of the approach presented here will spur further research regarding the dynamics of protein-protein interactions in response to changing cellular conditions in living cells.
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Affiliation(s)
| | | | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (M.S.); (M.J.)
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20
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Efficient integration of transmembrane domains depends on the folding properties of the upstream sequences. Proc Natl Acad Sci U S A 2021; 118:2102675118. [PMID: 34373330 PMCID: PMC8379923 DOI: 10.1073/pnas.2102675118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The topology of membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. For each polypeptide segment of ∼20 residues entering the translocon, their combined hydrophobicities were previously shown to define membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect the hydrophobicity threshold. Sequences that are rapidly folding, intrinsically disordered, very short, or strongly binding chaperones allow efficient integration at low hydrophobicity. Folding deficient mutant domains and artificial sequences not binding chaperones interfered with membrane integration likely by remaining partially unfolded and exposing hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. Rapid folding or strong chaperone binding thus promote efficient integration. The topology of most membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. The translocon provides a pore for the transfer of polypeptide segments across the membrane while giving them lateral access to the lipid. For each polypeptide segment of ∼20 residues, the combined hydrophobicities of its constituent amino acids were previously shown to define the extent of membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect its hydrophobicity requirement for integration. Rapidly folding domains, sequences that are intrinsically disordered or very short or capable of binding chaperones with high affinity, allow for efficient transmembrane integration with low-hydrophobicity thresholds for both orientations in the membrane. In contrast, long protein fragments, folding-deficient mutant domains, and artificial sequences not binding chaperones interfered with membrane integration, requiring higher hydrophobicity. We propose that the latter sequences, as they compact on their hydrophobic residues, partially folded but unable to reach a native state, expose hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. The results suggest that rapid folding or strong chaperone binding is required for efficient transmembrane integration.
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21
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Dual topology of co-chaperones at the membrane of the endoplasmic reticulum. Cell Death Discov 2021; 7:203. [PMID: 34354047 PMCID: PMC8342575 DOI: 10.1038/s41420-021-00594-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Dual topologies of proteins at the ER membrane are known for a variety of proteins allowing the same protein to exert different functions according to the topology adopted. A dual topology of the co-chaperone ERdj4, which resides in the endoplasmic reticulum (ER), was proposed recently, a thesis that we found to align all published data and existing controversies into one whole picture. The aim of this review is to reassess all primary data available in the literature on ER-resident Hsp40 co-chaperones with respect to their topology. After careful and critical analyses of all experimental data published so far, we identified, next to ERdj4, two other co-chaperones, ERdj3 and ERdj6, that also display features of a dual topology at the ER membrane. We assume that during cellular stress subpools of some ER-resident J protein can alter their topology so that these proteins can exert different functions in order to adapt to cellular stress.
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22
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Seo DH, Lee A, Yu SG, Cui LH, Min HJ, Lee SE, Cho NH, Kim S, Bae H, Kim WT. OsPUB41, a U-box E3 ubiquitin ligase, acts as a negative regulator of drought stress response in rice (Oryza Sativa L.). PLANT MOLECULAR BIOLOGY 2021; 106:463-477. [PMID: 34100185 DOI: 10.1007/s11103-021-01158-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/20/2021] [Indexed: 05/29/2023]
Abstract
OsPUB41 plays a negative role in drought stress response through the mediation of OsUBC25 and interacts with OsCLC6, suggesting a putative substrate. The notable expansion of Plant U-Box E3 ligases (PUB), compared with those in mammals, implies that PUB proteins have evolved to perform plant-specific functions. OsPUB41, a potential ortholog of CMPG1, was recently reported to regulate the cell wall degrading enzyme (CWDE)-induced innate immune response in rice. Here, we characterized the OsPUB41 gene, which encodes a dual-localized cytosolic and nuclear U-box E3 ligase in rice. OsPUB41 expression was specifically induced by dehydration among various abiotic stresses and abscisic acid (ABA) treatments. Furthermore, we revealed that the core U-box motif of OsPUB41 possesses the E3 ligase activity that can be activated by OsUBC25 in rice. The Ubi:RNAi-OsPUB41 knock-down and ospub41 suppression mutant plants exhibited enhanced tolerance to drought stress compared with the wild-type rice plants in terms of transpirational water loss, long-term dehydration response, and chlorophyll content. Moreover, the knock-down or suppression of the OsPUB41 gene did not cause adverse effect on rice yield-related traits. Yeast two-hybrid and an in vitro pull-down analyses revealed that OsCLC6, a chloride channel, is a putative substrate of OsPUB41. Overall, these results suggest that OsPUB41 acts as a negative regulator of dehydration conditions and interacts with OsCLC6, implying that it is a substrate of OsPUB41.
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Affiliation(s)
- Dong Hye Seo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Andosung Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Seong Gwan Yu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Li Hua Cui
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hye Jo Min
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Seung Eun Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Na Hyun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sojung Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hansol Bae
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Woo Taek Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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23
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O’Keefe S, Zong G, Duah KB, Andrews LE, Shi WQ, High S. An alternative pathway for membrane protein biogenesis at the endoplasmic reticulum. Commun Biol 2021; 4:828. [PMID: 34211117 PMCID: PMC8249459 DOI: 10.1038/s42003-021-02363-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The heterotrimeric Sec61 complex is a major site for the biogenesis of transmembrane proteins (TMPs), accepting nascent TMP precursors that are targeted to the endoplasmic reticulum (ER) by the signal recognition particle (SRP). Unlike most single-spanning membrane proteins, the integration of type III TMPs is completely resistant to small molecule inhibitors of the Sec61 translocon. Using siRNA-mediated depletion of specific ER components, in combination with the potent Sec61 inhibitor ipomoeassin F (Ipom-F), we show that type III TMPs utilise a distinct pathway for membrane integration at the ER. Hence, following SRP-mediated delivery to the ER, type III TMPs can uniquely access the membrane insertase activity of the ER membrane complex (EMC) via a mechanism that is facilitated by the Sec61 translocon. This alternative EMC-mediated insertion pathway allows type III TMPs to bypass the Ipom-F-mediated blockade of membrane integration that is seen with obligate Sec61 clients.
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Affiliation(s)
- Sarah O’Keefe
- grid.5379.80000000121662407School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Guanghui Zong
- grid.164295.d0000 0001 0941 7177Department of Chemistry and Biochemistry, University of Maryland, College Park, MD USA
| | - Kwabena B. Duah
- grid.252754.30000 0001 2111 9017Department of Chemistry, Ball State University, Muncie, IN USA
| | - Lauren E. Andrews
- grid.252754.30000 0001 2111 9017Department of Chemistry, Ball State University, Muncie, IN USA
| | - Wei Q. Shi
- grid.252754.30000 0001 2111 9017Department of Chemistry, Ball State University, Muncie, IN USA
| | - Stephen High
- grid.5379.80000000121662407School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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24
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Jung SJ, Kim JEH, Junne T, Spiess M, Kim H. Cotranslational Targeting and Posttranslational Translocation can Cooperate in Spc3 Topogenesis. J Mol Biol 2021; 433:167109. [PMID: 34153287 DOI: 10.1016/j.jmb.2021.167109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/19/2022]
Abstract
Secretory and membrane proteins follow either the signal recognition particle (SRP)-dependent cotranslational translocation pathway or the SRP-independent Sec62/Sec63-dependent posttranslational pathway for their translocation across the endoplasmic reticulum (ER). However, increasing evidence suggests that most proteins are cotranslationally targeted to the ER, suggesting mixed mechanisms. It remains unclear how these two pathways cooperate. Previous studies have shown that Spc3, a signal-anchored protein, requires SRP and Sec62 for its biogenesis. This study investigated the targeting and topogenesis of Spc3 and the step at which SRP and Sec62 act using in vivo and in vitro translocation assays and co-immunoprecipitation. Our data suggest that Spc3 reaches its final topology in two steps: it enters the ER lumen head-first and then inverts its orientation. The first step is partially dependent on SRP, although independent of the Sec62/Sec63 complex. The second step is mediated by the Sec62/Sec63 complex. These data suggest that SRP and Sec62 act on a distinct step in the topogenesis of Spc3.
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Affiliation(s)
- Sung-Jun Jung
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Ji Eun Hani Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Tina Junne
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea.
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25
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Islam N, Krishnan HB, Natarajan S. Proteomic Profiling of Fast Neutron-Induced Soybean Mutant Unveiled Pathways Associated with Increased Seed Protein Content. J Proteome Res 2020; 19:3936-3944. [PMID: 32819100 DOI: 10.1021/acs.jproteome.0c00160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the FN mutant revealed 3,502 proteins, of which 206 proteins exhibited increased abundance and 214 proteins showed decreased abundance. Among the abundant proteins, basic 7S globulin increased fourfold, followed by vacuolar-sorting receptor and protein transporters. The differentially expressed proteins were mapped on the global metabolic pathways. It was observed that there was an enrichment of 29 ribosomal proteins, 16 endoplasmic reticular proteins, and several proteins in export metabolic pathways. The deletion of the sequence-specific DNA binding transcription factor along with 23 other genes may have altered the negative regulation of protein syntheses processes, resulting in an increase in the overall protein content of the mutant seed. This mutant is a valuable resource for researchers to understand the metabolic pathways that may affect an increase in seed protein content (the mass spectrometry data files were submitted to massive.ucsd.edu # MassIVE MSV000084228).
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Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, Missouri 65211, United States
| | - Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
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26
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Abstract
In eukaryotic cells, about one-third of the synthesized proteins are translocated into the endoplasmic reticulum; they are membrane or lumen resident proteins and proteins direct to the Golgi apparatus. The co-translational translocation takes place through the heterotrimeric protein-conducting channel Sec61 which is associated with the ribosome and many accessory components, such as the heterotetrameric translocon-associated protein (TRAP) complex. Recently, microscopic techniques, such as cryo-electron microscopy and cryo-electron tomography, have enabled the determination of the translocation machinery structure. However, at present, there is a lack of understanding regarding the roles of some of its components; indeed, the TRAP complex function during co-translational translocation needs to be established. In addition, TRAP may play a role during unfolded protein response, endoplasmic-reticulum-associated protein degradation and congenital disorder of glycosylation (ssr4 CDG). In this article, I describe the current understanding of the TRAP complex in the light of its possible function(s).
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Affiliation(s)
- Antonietta Russo
- Medical Biochemistry and Molecular Biology, UKS, University of Saarland, Homburg, Germany
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27
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Ito K, Shimokawa-Chiba N, Chiba S. Sec translocon has an insertase-like function in addition to polypeptide conduction through the channel. F1000Res 2020; 8. [PMID: 32025287 PMCID: PMC6971846 DOI: 10.12688/f1000research.21065.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 11/20/2022] Open
Abstract
The Sec translocon provides a polypeptide-conducting channel, which is insulated from the hydrophobic lipidic environment of the membrane, for translocation of hydrophilic passenger polypeptides. Its lateral gate allows a downstream hydrophobic segment (stop-transfer sequence) to exit the channel laterally for integration into the lipid phase. We note that this channel model only partly accounts for the translocon function. The other essential role of translocon is to facilitate de novo insertion of the N-terminal topogenic segment of a substrate polypeptide into the membrane. Recent structural studies suggest that de novo insertion does not use the polypeptide-conducting channel; instead, it takes place directly at the lateral gate, which is prone to opening. We propose that the de novo insertion process, in concept, is similar to that of insertases (such as YidC in bacteria and EMC3 in eukaryotes), in which an intramembrane surface of the machinery provides the halfway point of insertion.
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Affiliation(s)
- Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Naomi Shimokawa-Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
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28
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Knyazev DG, Kuttner R, Bondar AN, Zimmerman M, Siligan C, Pohl P. Voltage Sensing in Bacterial Protein Translocation. Biomolecules 2020; 10:E78. [PMID: 31947864 PMCID: PMC7023257 DOI: 10.3390/biom10010078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/25/2019] [Accepted: 01/01/2020] [Indexed: 01/04/2023] Open
Abstract
The bacterial channel SecYEG efficiently translocates both hydrophobic and hydrophilic proteins across the plasma membrane. Translocating polypeptide chains may dislodge the plug, a half helix that blocks the permeation of small molecules, from its position in the middle of the aqueous translocation channel. Instead of the plug, six isoleucines in the middle of the membrane supposedly seal the channel, by forming a gasket around the translocating polypeptide. However, this hypothesis does not explain how the tightness of the gasket may depend on membrane potential. Here, we demonstrate voltage-dependent closings of the purified and reconstituted channel in the presence of ligands, suggesting that voltage sensitivity may be conferred by motor protein SecA, ribosomes, signal peptides, and/or translocating peptides. Yet, the presence of a voltage sensor intrinsic to SecYEG was indicated by voltage driven closure of pores that were forced-open either by crosslinking the plug to SecE or by plug deletion. We tested the involvement of SecY's half-helix 2b (TM2b) in voltage sensing, since clearly identifiable gating charges are missing. The mutation L80D accelerated voltage driven closings by reversing TM2b's dipolar orientation. In contrast, the L80K mutation decelerated voltage induced closings by increasing TM2b's dipole moment. The observations suggest that TM2b is part of a larger voltage sensor. By partly aligning the combined dipole of this sensor with the orientation of the membrane-spanning electric field, voltage may drive channel closure.
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Affiliation(s)
- Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Roland Kuttner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Mirjam Zimmerman
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
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Guerriero CJ, Gomez YK, Daskivich GJ, Reutter KR, Augustine AA, Weiberth KF, Nakatsukasa K, Grabe M, Brodsky JL. Harmonizing Experimental Data with Modeling to Predict Membrane Protein Insertion in Yeast. Biophys J 2019; 117:668-678. [PMID: 31399214 DOI: 10.1016/j.bpj.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins must adopt their proper topologies within biological membranes, but achieving the correct topology is compromised by the presence of marginally hydrophobic transmembrane helices (TMHs). In this study, we report on a new model membrane protein in yeast that harbors two TMHs fused to an unstable nucleotide-binding domain. Because the second helix (TMH2) in this reporter has an unfavorable predicted free energy of insertion, we employed established methods to generate variants that alter TMH2 insertion free energy. We first found that altering TMH2 did not significantly affect the extent of protein degradation by the cellular quality control machinery. Next, we correlated predicted insertion free energies from a knowledge-based energy scale with the measured apparent free energies of TMH2 insertion. Although the predicted and apparent insertion energies showed a similar trend, the predicted free-energy changes spanned an unanticipated narrow range. By instead using a physics-based model, we obtained a broader range of free energies that agreed considerably better with the magnitude of the experimentally derived values. Nevertheless, some variants still inserted better in yeast than predicted from energy-based scales. Therefore, molecular dynamics simulations were performed and indicated that the corresponding mutations induced conformational changes within TMH2, which altered the number of stabilizing hydrogen bonds. Together, our results offer insight into the ability of the cellular quality control machinery to recognize conformationally distinct misfolded topomers, provide a model to assess TMH insertion in vivo, and indicate that TMH insertion energy scales may be limited depending on the specific protein and the mutation present.
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Affiliation(s)
| | - Yessica K Gomez
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Grant J Daskivich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Karl-Richard Reutter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew A Augustine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kurt F Weiberth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kunio Nakatsukasa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
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