1
|
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
|
2
|
Li M, Zhang C, Xu Y, Li S, Huang C, Wu J, Lei M. Structural insights into human EMC and its interaction with VDAC. Aging (Albany NY) 2024; 16:5501-5525. [PMID: 38517390 PMCID: PMC11006472 DOI: 10.18632/aging.205660] [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: 11/06/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.
Collapse
Affiliation(s)
- Mingyue Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chunli Zhang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Yuntao Xu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Shaobai Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chenhui Huang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Jian Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Ming Lei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| |
Collapse
|
3
|
Kok M, Hartnett-Scott K, Happe CL, MacDonald ML, Aizenman E, Brodsky JL. The expression system influences stability, maturation efficiency, and oligomeric properties of the potassium-chloride co-transporter KCC2. Neurochem Int 2024; 174:105695. [PMID: 38373478 PMCID: PMC10923169 DOI: 10.1016/j.neuint.2024.105695] [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: 09/08/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024]
Abstract
The neuron-specific K+/Cl- co-transporter 2, KCC2, which is critical for brain development, regulates γ-aminobutyric acid-dependent inhibitory neurotransmission. Consistent with its function, mutations in KCC2 are linked to neurodevelopmental disorders, including epilepsy, schizophrenia, and autism. KCC2 possesses 12 transmembrane spans and forms an intertwined dimer. Based on its complex architecture and function, reduced cell surface expression and/or activity have been reported when select disease-associated mutations are present in the gene encoding the protein, SLC12A5. These data suggest that KCC2 might be inherently unstable, as seen for other complex polytopic ion channels, thus making it susceptible to cellular quality control pathways that degrade misfolded proteins. To test these hypotheses, we examined KCC2 stability and/or maturation in five model systems: yeast, HEK293 cells, primary rat neurons, and rat and human brain synaptosomes. Although studies in yeast revealed that KCC2 is selected for endoplasmic reticulum-associated degradation (ERAD), experiments in HEK293 cells supported a more subtle role for ERAD in maintaining steady-state levels of KCC2. Nevertheless, this system allowed for an analysis of KCC2 glycosylation in the ER and Golgi, which serves as a read-out for transport through the secretory pathway. In turn, KCC2 was remarkably stable in primary rat neurons, suggesting that KCC2 folds efficiently in more native systems. Consistent with these data, the mature glycosylated form of KCC2 was abundant in primary rat neurons as well as in rat and human brain. Together, this work details the first insights into the influence that the cellular and membrane environments have on several fundamental KCC2 properties, acknowledges the advantages and disadvantages of each system, and helps set the stage for future experiments to assess KCC2 in a normal or disease setting.
Collapse
Affiliation(s)
- Morgan Kok
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karen Hartnett-Scott
- Department of Neurobiology and the Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cassandra L Happe
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew L MacDonald
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elias Aizenman
- Department of Neurobiology and the Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
4
|
McDonald EF, Meiler J, Plate L. CFTR Folding: From Structure and Proteostasis to Cystic Fibrosis Personalized Medicine. ACS Chem Biol 2023; 18:2128-2143. [PMID: 37730207 PMCID: PMC10595991 DOI: 10.1021/acschembio.3c00310] [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: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023]
Abstract
Cystic fibrosis (CF) is a lethal genetic disease caused by mutations in the chloride ion channel cystic fibrosis transmembrane conductance regulator (CFTR). Class-II mutants of CFTR lack intermolecular interactions important for CFTR structural stability and lead to misfolding. Misfolded CFTR is detected by a diverse suite of proteostasis factors that preferentially bind and route mutant CFTR toward premature degradation, resulting in reduced plasma membrane CFTR levels and impaired chloride ion conductance associated with CF. CF treatment has been vastly improved over the past decade by the availability of small molecules called correctors. Correctors directly bind CFTR, stabilize its structure by conferring thermodynamically favorable interactions that compensate for mutations, and thereby lead to downstream folding fidelity. However, each of over 100 Class-II CF causing mutations causes unique structural defects and shows a unique response to drug treatment, described as theratype. Understanding CFTR structural defects, the proteostasis factors evaluating those defects, and the stabilizing effects of CFTR correctors will illuminate a path toward personalized medicine for CF. Here, we review recent advances in our understanding of CFTR folding, focusing on structure, corrector binding sites, the mechanisms of proteostasis factors that evaluate CFTR, and the implications for CF personalized medicine.
Collapse
Affiliation(s)
- Eli Fritz McDonald
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Institute
for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Lars Plate
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| |
Collapse
|
5
|
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
|
6
|
Bai L, Li H. Structural insights into the membrane chaperones for multi-pass membrane protein biogenesis. Curr Opin Struct Biol 2023; 79:102563. [PMID: 36863267 DOI: 10.1016/j.sbi.2023.102563] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/22/2023] [Accepted: 01/28/2023] [Indexed: 03/04/2023]
Abstract
Certain transmembrane α-helices of multi-pass membrane proteins line substrate transport paths or catalytic pockets and, therefore, are partially hydrophilic. Sec61 alone is insufficient to insert these less hydrophobic segments into the membrane and needs to work with dedicated membrane chaperones. Three such membrane chaperones have been described in the literature-the endoplasmic reticulum membrane protein complex (EMC), the TMCO1 complex, and the PAT complex. Recent structural studies on these membrane chaperones have revealed their overall architecture, multi-subunit assembly, putative substrate transmembrane helix-binding pockets, and cooperative mechanisms with the ribosome and Sec61 translocon. These structures are providing initial insights into the poorly understood processes of multi-pass membrane protein biogenesis.
Collapse
Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, 49503, United States.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Whittsette AL, Wang YJ, Mu TW. The endoplasmic reticulum membrane complex promotes proteostasis of GABA A receptors. iScience 2022; 25:104754. [PMID: 35938049 PMCID: PMC9352529 DOI: 10.1016/j.isci.2022.104754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
The endoplasmic reticulum membrane complex (EMC) plays a critical role in the biogenesis of tail-anchored proteins and a subset of multi-pass membrane proteins in the endoplasmic reticulum (ER). However, because of nearly exclusive expression of neurotransmitter-gated ion channels in the central nervous system (CNS), the role of the EMC in their biogenesis is not well understood. In this study, we demonstrated that the EMC positively regulates the surface trafficking and thus function of endogenous γ-aminobutyric acid type A (GABAA) receptors, the primary inhibitory ion channels in the mammalian brain. Moreover, among ten EMC subunits, EMC3 and EMC6 have the most prominent effect, and overexpression of EMC3 or EMC6 is sufficient to restore the function of epilepsy-associated GABAA receptor variants. In addition, EMC3 and EMC6 demonstrate endogenous interactions with major neuroreceptors, which depends on their transmembrane domains, suggesting a general role of the EMC in the biogenesis of neuroreceptors.
Collapse
Affiliation(s)
- Angela L. Whittsette
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ya-Juan Wang
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| |
Collapse
|
9
|
The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei. PLoS Pathog 2022; 18:e1009717. [PMID: 35500022 PMCID: PMC9113592 DOI: 10.1371/journal.ppat.1009717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 05/17/2022] [Accepted: 04/03/2022] [Indexed: 11/19/2022] Open
Abstract
The endoplasmic reticulum membrane complex (EMC) is a versatile complex that plays a key role in membrane protein biogenesis in the ER. Deletion of the complex has wide-ranging consequences including ER stress, disturbance in lipid transport and organelle tethering, among others. Here we report the function and organization of the evolutionarily conserved EMC (TbEMC) in the highly diverged eukaryote, Trypanosoma brucei. Using (co-) immunoprecipitation experiments in combination with mass spectrometry and whole cell proteomic analyses of parasites after depletion of select TbEMC subunits, we demonstrate that the TbEMC is composed of 9 subunits that are present in a high molecular mass complex localizing to the mitochondrial-endoplasmic reticulum interface. Knocking out or knocking down of single TbEMC subunits led to growth defects of T. brucei procyclic forms in culture. Interestingly, we found that depletion of individual TbEMC subunits lead to disruption of de novo synthesis of phosphatidylcholine (PC) or phosphatidylethanolamine (PE), the two most abundant phospholipid classes in T. brucei. Downregulation of TbEMC1 or TbEMC3 inhibited formation of PC while depletion of TbEMC8 inhibited PE synthesis, pointing to a role of the TbEMC in phospholipid synthesis. In addition, we found that in TbEMC7 knock-out parasites, TbEMC3 is released from the complex, implying that TbEMC7 is essential for the formation or the maintenance of the TbEMC.
Collapse
|
10
|
Prins S, Corradi V, Sheppard DN, Tieleman DP, Vergani P. Can two wrongs make a right? F508del-CFTR ion channel rescue by second-site mutations in its transmembrane domains. J Biol Chem 2022; 298:101615. [PMID: 35065958 PMCID: PMC8861112 DOI: 10.1016/j.jbc.2022.101615] [Citation(s) in RCA: 4] [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: 09/01/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/20/2022] Open
Abstract
Deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is the most common cause of cystic fibrosis. The F508 residue is located on nucleotide-binding domain 1 (NBD1) in contact with the cytosolic extensions of the transmembrane helices, in particular intracellular loop 4 (ICL4). To investigate how absence of F508 at this interface impacts the CFTR protein, we carried out a mutagenesis scan of ICL4 by introducing second-site mutations at 11 positions in cis with F508del. Using an image-based fluorescence assay, we measured how each mutation affected membrane proximity and ion-channel function. The scan strongly validated the effectiveness of R1070W at rescuing F508del defects. Molecular dynamics simulations highlighted two features characterizing the ICL4/NBD1 interface of F508del/R1070W-CFTR: flexibility, with frequent transient formation of interdomain hydrogen bonds, and loosely stacked aromatic sidechains (F1068, R1070W, and F1074, mimicking F1068, F508, and F1074 in WT CFTR). F508del-CFTR displayed a distorted aromatic stack, with F1068 displaced toward the space vacated by F508, while in F508del/R1070F-CFTR, which largely retained F508del defects, R1070F could not form hydrogen bonds and the interface was less flexible. Other ICL4 second-site mutations which partially rescued F508del-CFTR included F1068M and F1074M. Methionine side chains allow hydrophobic interactions without the steric rigidity of aromatic rings, possibly conferring flexibility to accommodate the absence of F508 and retain a dynamic interface. These studies highlight how both hydrophobic interactions and conformational flexibility might be important at the ICL4/NBD1 interface, suggesting possible structural underpinnings of F508del-induced dysfunction.
Collapse
Affiliation(s)
- Stella Prins
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Valentina Corradi
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - D Peter Tieleman
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Paola Vergani
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
| |
Collapse
|
11
|
Iazzi M, Astori A, St-Germain J, Raught B, Gupta GD. Proximity Profiling of the CFTR Interaction Landscape in Response to Orkambi. Int J Mol Sci 2022; 23:2442. [PMID: 35269585 PMCID: PMC8910062 DOI: 10.3390/ijms23052442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Deletion of phenylalanine 508 (∆F508) of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) anion channel protein is the leading cause of Cystic Fibrosis (CF). Here, we report the analysis of CFTR and ∆F508-CFTR interactomes using BioID (proximity-dependent biotin identification), a technique that can also detect transient associations. We identified 474 high-confidence CFTR proximity-interactors, 57 of which have been previously validated, with the remainder representing novel interaction space. The ∆F508 interactome, comprising 626 proximity-interactors was markedly different from its wild type counterpart, with numerous alterations in protein associations categorized in membrane trafficking and cellular stress functions. Furthermore, analysis of the ∆F508 interactome in cells treated with Orkambi identified several interactions that were altered as a result of this drug therapy. We examined two candidate CFTR proximity interactors, VAPB and NOS1AP, in functional assays designed to assess surface delivery and overall chloride efflux. VAPB depletion impacted both CFTR surface delivery and chloride efflux, whereas NOS1AP depletion only affected the latter. The wild type and ∆F508-CFTR interactomes represent rich datasets that could be further mined to reveal additional candidates for the functional rescue of ∆F508-CFTR.
Collapse
Affiliation(s)
- Melissa Iazzi
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada;
| | - Audrey Astori
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A1, Canada; (A.A.); (J.S.-G.); (B.R.)
| | - Jonathan St-Germain
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A1, Canada; (A.A.); (J.S.-G.); (B.R.)
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A1, Canada; (A.A.); (J.S.-G.); (B.R.)
| | - Gagan D. Gupta
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada;
| |
Collapse
|
12
|
Abstract
The endoplasmic reticulum (ER) is the site of membrane protein insertion, folding, and assembly in eukaryotes. Over the past few years, a combination of genetic and biochemical studies have implicated an abundant factor termed the ER membrane protein complex (EMC) in several aspects of membrane protein biogenesis. This large nine-protein complex is built around a deeply conserved core formed by the EMC3-EMC6 subcomplex. EMC3 belongs to the universally conserved Oxa1 superfamily of membrane protein transporters, whereas EMC6 is an ancient, widely conserved obligate partner. EMC has an established role in the insertion of transmembrane domains (TMDs) and less understood roles during the later steps of membrane protein folding and assembly. Several recent structures suggest hypotheses about the mechanism(s) of TMD insertion by EMC, with various biochemical and proteomics studies beginning to reveal the range of EMC's membrane protein substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
| |
Collapse
|
13
|
Gaspar CJ, Vieira LC, Santos CC, Christianson JC, Jakubec D, Strisovsky K, Adrain C, Domingos PM. EMC is required for biogenesis of Xport-A, an essential chaperone of Rhodopsin-1 and the TRP channel. EMBO Rep 2022; 23:e53210. [PMID: 34918864 PMCID: PMC8728618 DOI: 10.15252/embr.202153210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/26/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
The ER membrane protein complex (EMC) is required for the biogenesis of a subset of tail anchored (TA) and polytopic membrane proteins, including Rhodopsin-1 (Rh1) and the TRP channel. To understand the physiological implications of EMC-dependent membrane protein biogenesis, we perform a bioinformatic identification of Drosophila TA proteins. From 254 predicted TA proteins, screening in larval eye discs identified two proteins that require EMC for their biogenesis: fan and Xport-A. Fan is required for male fertility in Drosophila and we show that EMC is also required for this process. Xport-A is essential for the biogenesis of both Rh1 and TRP, raising the possibility that disruption of Rh1 and TRP biogenesis in EMC mutants is secondary to the Xport-A defect. We show that EMC is required for Xport-A TMD membrane insertion and that EMC-independent Xport-A mutants rescue Rh1 and TRP biogenesis in EMC mutants. Finally, our work also reveals a role for Xport-A in a glycosylation-dependent triage mechanism during Rh1 biogenesis in the endoplasmic reticulum.
Collapse
Affiliation(s)
- Catarina J Gaspar
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
- Membrane Traffic LabInstituto Gulbenkian de Ciência (IGC)OeirasPortugal
| | - Lígia C Vieira
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
- Present address:
Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Cristiana C Santos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
| | - John C Christianson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesBotnar Research CentreUniversity of OxfordOxfordUK
| | - David Jakubec
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
| | - Colin Adrain
- Membrane Traffic LabInstituto Gulbenkian de Ciência (IGC)OeirasPortugal
- Patrick G Johnston Centre for Cancer ResearchQueen’s UniversityBelfastUK
| | - Pedro M Domingos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
| |
Collapse
|
14
|
Bai L, Li H. Cryo-EM structures of the endoplasmic reticulum membrane complex. FEBS J 2022; 289:102-112. [PMID: 33629497 PMCID: PMC8382784 DOI: 10.1111/febs.15786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 01/03/2023]
Abstract
The transmembrane α-helices of membrane proteins are in general highly hydrophobic, and they enter the lipid bilayer through a lateral gate in the Sec61 translocon. However, some transmembrane α-helices are less hydrophobic and form membrane channels or substrate-binding pockets. Insertion of these amphipathic transmembrane α-helices into the membrane requires the specific membrane-embedded insertase called the endoplasmic reticulum membrane complex (EMC), which is a multi-subunit chaperone distinct from the GET insertase complex. Four recent cryo-electron microscopy studies on the eukaryotic EMC have revealed their remarkable architectural conservation from yeast to humans; a general consensus on the substrate transmembrane helix-binding pocket; and the evolutionary link to the prokaryotic insertases of the tail-anchored membrane proteins. These structures provide a solid framework for future mechanistic investigation.
Collapse
Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing 100083, China
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
The ER membrane protein complex subunit Emc3 controls angiogenesis via the FZD4/WNT signaling axis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1868-1883. [PMID: 34128175 DOI: 10.1007/s11427-021-1941-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) regulates the synthesis and quality control of membrane proteins with multiple transmembrane domains. One of the membrane spanning subunits, EMC3, is a core member of the EMC complex that provides essential hydrophilic vestibule for substrate insertion. Here, we show that the EMC subunit Emc3 plays critical roles in the retinal vascular angiogenesis by regulating Norrin/Wnt signaling. Postnatal endothelial cell (EC)-specific deletion of Emc3 led to retarded retinal vascular development with a hyperpruned vascular network, the appearance of blunt-ended, aneurysm-like tip endothelial cells (ECs) with reduced numbers of filopodia and leakage of erythrocytes at the vascular front. Diminished tube formation and cell proliferation were also observed in EMC3 depleted human retinal endothelial cells (HRECs). We then discovered a critical role for EMC3 in expression of FZD4 receptor of β-catenin signaling using RNA sequencing, real-time quantitative PCR (RT-qPCR) and luciferase reporter assay. Moreover, augmentation of Wnt activity via lithium chloride (LiCl) treatment remarkably enhanced β-catenin signaling and cell proliferation of HRECs. Additionally, LiCl partially reversed the angiogenesis defects in Emc3-cKO mice. Our data reveal that Emc3 plays essential roles in angiogenesis through direct control of FZD4 expression and Norrin/β-catenin signaling.
Collapse
|
17
|
Phillips BP, Miller EA. Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum. J Cell Sci 2020; 133:133/22/jcs251983. [PMID: 33247003 PMCID: PMC7116877 DOI: 10.1242/jcs.251983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.
Collapse
Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | |
Collapse
|
18
|
Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS. Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. eLife 2020; 9:e62611. [PMID: 33236988 PMCID: PMC7785296 DOI: 10.7554/elife.62611] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.
Collapse
Affiliation(s)
- Lakshmi E Miller-Vedam
- Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Katerina D Popova
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Nicole T Schirle Oakdale
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica L Bonnar
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jesuraj R Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Elizabeth A Boydston
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Matthew J Shurtleff
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| |
Collapse
|
19
|
Santos SM, Laflin S, Broadway A, Burnet C, Hartheimer J, Rodgers J, Smith DL, Hartman JL. High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability. GeroScience 2020; 43:941-964. [PMID: 33015753 PMCID: PMC8110628 DOI: 10.1007/s11357-020-00265-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
Yeast cells survive in stationary phase culture by entering quiescence, which is measured by colony-forming capacity upon nutrient re-exposure. Yeast chronological lifespan (CLS) studies, employing the comprehensive collection of gene knockout strains, have correlated weakly between independent laboratories, which is hypothesized to reflect differential interaction between the deleted genes, auxotrophy, media composition, and other assay conditions influencing quiescence. This hypothesis was investigated by high-throughput quiescence profiling of the parental prototrophic strain, from which the gene deletion strain libraries were constructed, and all possible auxotrophic allele combinations in that background. Defined media resembling human cell culture media promoted long-term quiescence and was used to assess effects of glucose, ammonium sulfate, auxotrophic nutrient availability, target of rapamycin signaling, and replication stress. Frequent, high-replicate measurements of colony-forming capacity from cultures aged past 60 days provided profiles of quiescence phenomena such as gasping and hormesis. Media acidification was assayed in parallel to assess correlation. Influences of leucine, methionine, glucose, and ammonium sulfate metabolism were clarified, and a role for lysine metabolism newly characterized, while histidine and uracil perturbations had less impact. Interactions occurred between glucose, ammonium sulfate, auxotrophy, auxotrophic nutrient limitation, aeration, TOR signaling, and/or replication stress. Weak correlation existed between media acidification and maintenance of quiescence. In summary, experimental factors, uncontrolled across previous genome-wide yeast CLS studies, influence quiescence and interact extensively, revealing quiescence as a complex metabolic and developmental process that should be studied in a prototrophic context, omitting ammonium sulfate from defined media, and employing highly replicable protocols.
Collapse
Affiliation(s)
- Sean M Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samantha Laflin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Audrie Broadway
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cosby Burnet
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joline Hartheimer
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Rodgers
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel L Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John L Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
20
|
Papouskova K, Moravcova M, Masrati G, Ben-Tal N, Sychrova H, Zimmermannova O. C5 conserved region of hydrophilic C-terminal part of Saccharomyces cerevisiae Nha1 antiporter determines its requirement of Erv14 COPII cargo receptor for plasma-membrane targeting. Mol Microbiol 2020; 115:41-57. [PMID: 32864748 DOI: 10.1111/mmi.14595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/23/2020] [Accepted: 08/22/2020] [Indexed: 01/03/2023]
Abstract
Erv14, a conserved cargo receptor of COPII vesicles, helps the proper trafficking of many but not all transporters to the yeast plasma membrane, for example, three out of five alkali-metal-cation transporters in Saccharomyces cerevisiae. Among them, the Nha1 cation/proton antiporter, which participates in cell cation and pH homeostasis, is a large membrane protein (985 aa) possessing a long hydrophilic C-terminus (552 aa) containing six conserved regions (C1-C6) with unknown function. A short Nha1 version, lacking almost the entire C-terminus, still binds to Erv14 but does not need it to be targeted to the plasma membrane. Comparing the localization and function of ScNha1 variants shortened at its C-terminus in cells with or without Erv14 reveals that only ScNha1 versions possessing the complete C5 region are dependent on Erv14. In addition, our broad evolutionary conservation analysis of fungal Na+ /H+ antiporters identified new conserved regions in their C-termini, and our experiments newly show C5 and other, so far unknown, regions of the C-terminus, to be involved in the functionality and substrate specificity of ScNha1. Taken together, our results reveal that also relatively small hydrophilic parts of some yeast membrane proteins underlie their need to interact with the Erv14 cargo receptor.
Collapse
Affiliation(s)
- Klara Papouskova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Michaela Moravcova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Hana Sychrova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Olga Zimmermannova
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| |
Collapse
|
21
|
Tian S, Wu Q, Zhou B, Choi MY, Ding B, Yang W, Dong M. Proteomic Analysis Identifies Membrane Proteins Dependent on the ER Membrane Protein Complex. Cell Rep 2020; 28:2517-2526.e5. [PMID: 31484065 PMCID: PMC6749609 DOI: 10.1016/j.celrep.2019.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/18/2019] [Accepted: 07/30/2019] [Indexed: 02/04/2023] Open
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is a key contributor to biogenesis and membrane integration of transmembrane proteins, but our understanding of its mechanisms and the range of EMC-dependent proteins remains incomplete. Here, we carried out an unbiased mass spectrometry (MS)-based quantitative proteomic analysis comparing membrane proteins in EMC-deficient cells to wild-type (WT) cells and identified 36 EMC-dependent membrane proteins and 171 EMC-independent membrane proteins. Of these, six EMC-dependent and six EMC-independent proteins were further independently validated. We found that a common feature among EMC-dependent proteins is that they contain transmembrane domains (TMDs) with polar and/or charged residues. Mutagenesis studies demonstrate that EMC dependency can be converted in cells by removing or introducing polar and/or charged residues within TMDs. Our studies expand the list of validated EMC-dependent and EMC-independent proteins and suggest that the EMC is involved in handling TMDs with residues challenging for membrane integration. The endoplasmic reticulum membrane protein complex (EMC) contributes to the biogenesis of transmembrane proteins. Using mass spectrometry-based quantitative proteomic analysis, Tian et al. identify EMC-dependent and EMC-independent proteins. The authors find evidence that the EMC is involved in handling transmembrane domains with polar and/or charged residues that are challenging for membrane integration.
Collapse
Affiliation(s)
- Songhai Tian
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Quan Wu
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, People's Republic of China
| | - Bo Zhou
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mei Yuk Choi
- Division of Genetics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Bo Ding
- Bonacept LLC, San Diego, CA 92122, USA
| | - Wei Yang
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
22
|
Oliver KE, Rauscher R, Mijnders M, Wang W, Wolpert MJ, Maya J, Sabusap CM, Kesterson RA, Kirk KL, Rab A, Braakman I, Hong JS, Hartman JL, Ignatova Z, Sorscher EJ. Slowing ribosome velocity restores folding and function of mutant CFTR. J Clin Invest 2020; 129:5236-5253. [PMID: 31657788 DOI: 10.1172/jci124282] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/28/2019] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR), with approximately 90% of patients harboring at least one copy of the disease-associated variant F508del. We utilized a yeast phenomic system to identify genetic modifiers of F508del-CFTR biogenesis, from which ribosomal protein L12 (RPL12/uL11) emerged as a molecular target. In the present study, we investigated mechanism(s) by which suppression of RPL12 rescues F508del protein synthesis and activity. Using ribosome profiling, we found that rates of translation initiation and elongation were markedly slowed by RPL12 silencing. However, proteolytic stability and patch-clamp assays revealed RPL12 depletion significantly increased F508del-CFTR steady-state expression, interdomain assembly, and baseline open-channel probability. We next evaluated whether Rpl12-corrected F508del-CFTR could be further enhanced with concomitant pharmacologic repair (e.g., using clinically approved modulators lumacaftor and tezacaftor) and demonstrated additivity of these treatments. Rpl12 knockdown also partially restored maturation of specific CFTR variants in addition to F508del, and WT Cftr biogenesis was enhanced in the pancreas, colon, and ileum of Rpl12 haplosufficient mice. Modulation of ribosome velocity therefore represents a robust method for understanding both CF pathogenesis and therapeutic response.
Collapse
Affiliation(s)
| | - Robert Rauscher
- Institute for Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marjolein Mijnders
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Wei Wang
- Gregory Fleming James Cystic Fibrosis Research Center and
| | | | - Jessica Maya
- Gregory Fleming James Cystic Fibrosis Research Center and
| | | | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Kevin L Kirk
- Gregory Fleming James Cystic Fibrosis Research Center and
| | - Andras Rab
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jeong S Hong
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - John L Hartman
- Gregory Fleming James Cystic Fibrosis Research Center and.,Department of Genetics, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Zoya Ignatova
- Institute for Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | | |
Collapse
|
23
|
O'Donnell JP, Phillips BP, Yagita Y, Juszkiewicz S, Wagner A, Malinverni D, Keenan RJ, Miller EA, Hegde RS. The architecture of EMC reveals a path for membrane protein insertion. eLife 2020; 9:e57887. [PMID: 32459176 PMCID: PMC7292650 DOI: 10.7554/elife.57887] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022] Open
Abstract
Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been implicated in membrane protein biogenesis, but its mechanism of action is poorly understood. Here, we define the composition and architecture of human EMC using biochemical assays, crystallography of individual subunits, site-specific photocrosslinking, and cryo-EM reconstruction. Our results suggest that EMC's cytosolic domain contains a large, moderately hydrophobic vestibule that can bind a substrate's transmembrane domain (TMD). The cytosolic vestibule leads into a lumenally-sealed, lipid-exposed intramembrane groove large enough to accommodate a single substrate TMD. A gap between the cytosolic vestibule and intramembrane groove provides a potential path for substrate egress from EMC. These findings suggest how EMC facilitates energy-independent membrane insertion of TMDs, explain why only short lumenal domains are translocated by EMC, and constrain models of EMC's proposed chaperone function.
Collapse
Affiliation(s)
| | - Ben P Phillips
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Yuichi Yagita
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | | | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | | | | |
Collapse
|
24
|
Volkmar N, Christianson JC. Squaring the EMC - how promoting membrane protein biogenesis impacts cellular functions and organismal homeostasis. J Cell Sci 2020; 133:133/8/jcs243519. [PMID: 32332093 PMCID: PMC7188443 DOI: 10.1242/jcs.243519] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Integral membrane proteins play key functional roles at organelles and the plasma membrane, necessitating their efficient and accurate biogenesis to ensure appropriate targeting and activity. The endoplasmic reticulum membrane protein complex (EMC) has recently emerged as an important eukaryotic complex for biogenesis of integral membrane proteins by promoting insertion and stability of atypical and sub-optimal transmembrane domains (TMDs). Although confirmed as a bona fide complex almost a decade ago, light is just now being shed on the mechanism and selectivity underlying the cellular responsibilities of the EMC. In this Review, we revisit the myriad of functions attributed the EMC through the lens of these new mechanistic insights, to address questions of the cellular and organismal roles the EMC has evolved to undertake. Summary: The EMC is an important factor facilitating membrane protein biogenesis. Here we discuss the broad cellular and organismal responsibilities overseen by client proteins requiring the EMC for maturation.
Collapse
Affiliation(s)
- Norbert Volkmar
- Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - John C Christianson
- Oxford Centre for Translational Myeloma Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Headington, Oxford OX3 7LD, UK
| |
Collapse
|
25
|
Abstract
Due to their topology tail-anchored (TA) proteins must target to the membrane independently of the co-translational route defined by the signal sequence recognition particle (SRP), its receptor and the translocon Sec61. More than a decade of work has extensively characterized a highly conserved pathway, the yeast GET or mammalian TRC40 pathway, which is capable of countering the biogenetic challenge posed by the C-terminal TA anchor. In this review we briefly summarize current models of this targeting route and focus on emerging aspects such as the intricate interplay with the proteostatic network of cells and with other targeting pathways. Importantly, we consider the lessons provided by the in vivo analysis of the pathway in different model organisms and by the consideration of its full client spectrum in more recent studies. This analysis of the state of the field highlights directions in which the current models may be experimentally probed and conceptually extended.
Collapse
Affiliation(s)
- Nica Borgese
- Institute of Neuroscience and BIOMETRA Department, Consiglio Nazionale delle Ricerche and Università degli Studi di Milano, via Vanvitelli 32, 20129, Milan, Italy.
| | - Javier Coy-Vergara
- Department of Molecular Biology, University of Göttingen Medical Centre, Humboldtallee 23, 37073, Göttingen, Germany
| | - Sara Francesca Colombo
- Institute of Neuroscience and BIOMETRA Department, Consiglio Nazionale delle Ricerche and Università degli Studi di Milano, via Vanvitelli 32, 20129, Milan, Italy
| | - Blanche Schwappach
- Department of Molecular Biology, University of Göttingen Medical Centre, Humboldtallee 23, 37073, Göttingen, Germany.
| |
Collapse
|
26
|
Lakshminarayan R, Phillips BP, Binnian IL, Gomez-Navarro N, Escudero-Urquijo N, Warren AJ, Miller EA. Pre-emptive Quality Control of a Misfolded Membrane Protein by Ribosome-Driven Effects. Curr Biol 2020; 30:854-864.e5. [PMID: 31956032 PMCID: PMC7063571 DOI: 10.1016/j.cub.2019.12.060] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/02/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022]
Abstract
Cells possess multiple mechanisms that protect against the accumulation of toxic aggregation-prone proteins. Here, we identify a pre-emptive pathway that reduces synthesis of membrane proteins that have failed to properly assemble in the endoplasmic reticulum (ER). We show that loss of the ER membrane complex (EMC) or mutation of the Sec61 translocon causes reduced synthesis of misfolded forms of the yeast ABC transporter Yor1. Synthesis defects are rescued by various ribosomal mutations, as well as by reducing cellular ribosome abundance. Genetic and biochemical evidence point to a ribosome-associated quality-control pathway triggered by ribosome collisions when membrane domain insertion and/or folding fails. In support of this model, translation initiation also contributes to synthesis defects, likely by modulating ribosome abundance on the message. Examination of translation efficiency across the yeast membrane proteome revealed that polytopic membrane proteins have relatively low ribosome abundance, providing evidence for translational tuning to balance protein synthesis and folding. We propose that by modulating translation rates of poorly folded proteins, cells can pre-emptively protect themselves from potentially toxic aberrant transmembrane proteins. Yor1-ΔF shows synthesis defects when Sec61 or EMC function is compromised Synthesis defects are suppressed by ribosomal and RQC mutants Translation initiation is a second point of potential regulation Pre-emptive quality control on the ER might protect the cell from aberrant proteins
Collapse
Affiliation(s)
- Ramya Lakshminarayan
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Ave., New York, NY 10027, USA
| | - Ben P Phillips
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave., Cambridge CB2 0QH, UK
| | - Imogen L Binnian
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave., Cambridge CB2 0QH, UK
| | - Natalia Gomez-Navarro
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave., Cambridge CB2 0QH, UK
| | - Norberto Escudero-Urquijo
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Haematology, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Puddicomb Way, Cambridge CB2 0AW, UK
| | - Alan J Warren
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Haematology, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Puddicomb Way, Cambridge CB2 0AW, UK
| | - Elizabeth A Miller
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Ave., New York, NY 10027, USA; Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave., Cambridge CB2 0QH, UK.
| |
Collapse
|
27
|
Santos SM, Hartman JL. A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin. Cancer Metab 2019; 7:9. [PMID: 31660150 PMCID: PMC6806529 DOI: 10.1186/s40170-019-0201-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/03/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. METHODS Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. RESULTS Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. We analyzed human homologs of yeast genes exhibiting gene-doxorubicin interaction in cancer pharmacogenomics data to predict causality for differential gene expression associated with doxorubicin cytotoxicity in cancer cells. This analysis suggested conserved cellular responses to doxorubicin due to influences of homologous recombination, sphingolipid homeostasis, telomere tethering at nuclear periphery, actin cortical patch localization, and other gene functions. CONCLUSIONS Warburg status alters the genetic network required for yeast to buffer doxorubicin toxicity. Integration of yeast phenomic and cancer pharmacogenomics data suggests evolutionary conservation of gene-drug interaction networks and provides a new experimental approach to model their influence on chemotherapy response. Thus, yeast phenomic models could aid the development of precision oncology algorithms to predict efficacious cytotoxic drugs for cancer, based on genetic and metabolic profiles of individual tumors.
Collapse
Affiliation(s)
- Sean M. Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL USA
| | - John L. Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL USA
| |
Collapse
|
28
|
Abstract
One-fourth of eukaryotic genes code for integral membrane proteins, nearly all of which are inserted and assembled at the endoplasmic reticulum (ER). The defining feature of membrane proteins is one or more transmembrane domains (TMDs). During membrane protein biogenesis, TMDs are selectively recognized, shielded, and chaperoned into the lipid bilayer, where they often assemble with other TMDs. If maturation fails, exposed TMDs serve as a cue for engagement of degradation pathways. Thus, TMD-recognition factors in the cytosol and ER are essential for membrane protein biogenesis and quality control. Here, we discuss the growing assortment of cytosolic and membrane-embedded TMD-recognition factors, the pathways within which they operate, and mechanistic principles of recognition.
Collapse
|
29
|
A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
Collapse
|
30
|
Hiramatsu N, Tago T, Satoh T, Satoh AK. ER membrane protein complex is required for the insertions of late-synthesized transmembrane helices of Rh1 in Drosophila photoreceptors. Mol Biol Cell 2019; 30:2890-2900. [PMID: 31553680 PMCID: PMC6822582 DOI: 10.1091/mbc.e19-08-0434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Most membrane proteins are synthesized on and inserted into the membrane of the endoplasmic reticulum (ER), in eukaryote. The widely conserved ER membrane protein complex (EMC) facilitates the biogenesis of a wide range of membrane proteins. In this study, we investigated the EMC function using Drosophila photoreceptor as a model system. We found that the EMC was necessary only for the biogenesis of a subset of multipass membrane proteins such as rhodopsin (Rh1), TRP, TRPL, Csat, Cni, SERCA, and Na+K+ATPase α, but not for that of secretory or single-pass membrane proteins. Additionally, in EMC-deficient cells, Rh1 was translated to its C terminus but degraded independently from ER-associated degradation. Thus, EMC exerted its effect after translation but before or during the membrane integration of transmembrane domains (TMDs). Finally, we found that EMC was not required for the stable expression of the first three TMDs of Rh1 but was required for that of the fourth and fifth TMDs. Our results suggested that EMC is required for the ER membrane insertion of succeeding TMDs of multipass membrane proteins.
Collapse
Affiliation(s)
- Naoki Hiramatsu
- Program of Life and Environmental Sciences, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Tatsuya Tago
- Program of Life and Environmental Sciences, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Takunori Satoh
- Program of Life and Environmental Sciences, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akiko K Satoh
- Program of Life and Environmental Sciences, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| |
Collapse
|
31
|
Erv14 cargo receptor participates in regulation of plasma-membrane potential, intracellular pH and potassium homeostasis via its interaction with K+-specific transporters Trk1 and Tok1. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1376-1388. [DOI: 10.1016/j.bbamcr.2019.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/31/2022]
|
32
|
Talbot BE, Vandorpe DH, Stotter BR, Alper SL, Schlondorff JS. Transmembrane insertases and N-glycosylation critically determine synthesis, trafficking, and activity of the nonselective cation channel TRPC6. J Biol Chem 2019; 294:12655-12669. [PMID: 31266804 PMCID: PMC6709635 DOI: 10.1074/jbc.ra119.008299] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/28/2019] [Indexed: 12/12/2022] Open
Abstract
Transient receptor potential cation channel subfamily C member 6 (TRPC6) is a widely expressed ion channel. Gain-of-function mutations in the human TRPC6 channel cause autosomal-dominant focal segmental glomerulosclerosis, but the molecular components involved in disease development remain unclear. Here, we found that overexpression of gain-of-function TRPC6 channel variants is cytotoxic in cultured cells. Exploiting this phenotype in a genome-wide CRISPR/Cas screen for genes whose inactivation rescues cells from TRPC6-associated cytotoxicity, we identified several proteins essential for TRPC6 protein expression, including the endoplasmic reticulum (ER) membrane protein complex transmembrane insertase. We also identified transmembrane protein 208 (TMEM208), a putative component of a signal recognition particle-independent (SND) ER protein-targeting pathway, as being necessary for expression of TRPC6 and several other ion channels and transporters. TRPC6 expression was also diminished by loss of the previously uncharacterized WD repeat domain 83 opposite strand (WDR83OS), which interacted with both TRPC6 and TMEM208. Additionally enriched among the screen hits were genes involved in N-linked protein glycosylation. Deletion of the mannosyl (α-1,3-)-glycoprotein β-1,2-N-acetylglucosaminyltransferase (MGAT1), necessary for the generation of complex N-linked glycans, abrogated TRPC6 gain-of-function variant-mediated Ca2+ influx and extracellular signal-regulated kinase activation in HEK cells, but failed to diminish cytotoxicity in cultured podocytes. However, mutating the two TRPC6 N-glycosylation sites abrogated the cytotoxicity of mutant TRPC6 and reduced its surface expression. These results expand the targets of TMEM208-mediated ER translocation to include multipass transmembrane proteins and suggest that TRPC6 N-glycosylation plays multiple roles in modulating channel trafficking and activity.
Collapse
Affiliation(s)
- Brianna E Talbot
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - David H Vandorpe
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Brian R Stotter
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Seth L Alper
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Johannes S Schlondorff
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| |
Collapse
|
33
|
Barrows NJ, Anglero-Rodriguez Y, Kim B, Jamison SF, Le Sommer C, McGee CE, Pearson JL, Dimopoulos G, Ascano M, Bradrick SS, Garcia-Blanco MA. Dual roles for the ER membrane protein complex in flavivirus infection: viral entry and protein biogenesis. Sci Rep 2019; 9:9711. [PMID: 31273220 PMCID: PMC6609633 DOI: 10.1038/s41598-019-45910-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/27/2019] [Indexed: 12/16/2022] Open
Abstract
Hundreds of cellular host factors are required to support dengue virus infection, but their identity and roles are incompletely characterized. Here, we identify human host dependency factors required for efficient dengue virus-2 (DENV2) infection of human cells. We focused on two, TTC35 and TMEM111, which we previously demonstrated to be required for yellow fever virus (YFV) infection and others subsequently showed were also required by other flaviviruses. These proteins are components of the human endoplasmic reticulum membrane protein complex (EMC), which has roles in ER-associated protein biogenesis and lipid metabolism. We report that DENV, YFV and Zika virus (ZIKV) infections were strikingly inhibited, while West Nile virus infection was unchanged, in cells that lack EMC subunit 4. Furthermore, targeted depletion of EMC subunits in live mosquitoes significantly reduced DENV2 propagation in vivo. Using a novel uncoating assay, which measures interactions between host RNA-binding proteins and incoming viral RNA, we show that EMC is required at or prior to virus uncoating. Importantly, we uncovered a second and important role for the EMC. The complex is required for viral protein accumulation in a cell line harboring a ZIKV replicon, indicating that EMC participates in the complex process of viral protein biogenesis.
Collapse
Affiliation(s)
- Nicholas J Barrows
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA
| | - Yesseinia Anglero-Rodriguez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Byungil Kim
- Department of Biochemistry, Vanderbilt University, Nashville, USA
| | - Sharon F Jamison
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA
| | - Caroline Le Sommer
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA
| | | | - James L Pearson
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University, Nashville, USA
| | - Shelton S Bradrick
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA. .,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA.
| | - Mariano A Garcia-Blanco
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA. .,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA. .,Programme of Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| |
Collapse
|
34
|
Campos RK, Garcia-Blanco MA, Bradrick SS. Roles of Pro-viral Host Factors in Mosquito-Borne Flavivirus Infections. Curr Top Microbiol Immunol 2019; 419:43-67. [PMID: 28688087 DOI: 10.1007/82_2017_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Identification and analysis of viral host factors is a growing area of research which aims to understand the how viruses molecularly interface with the host cell. Investigations into flavivirus-host interactions has led to new discoveries in viral and cell biology, and will potentially bolster strategies to control the important diseases caused by these pathogens. Here, we address the current knowledge of prominent host factors required for the flavivirus life-cycle and mechanisms by which they promote infection.
Collapse
Affiliation(s)
- Rafael K Campos
- Department of Molecular Genetics and Microbiology, Center for RNA Biology, Duke University, Durham, NC, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. .,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
35
|
Chitwood PJ, Hegde RS. The Role of EMC during Membrane Protein Biogenesis. Trends Cell Biol 2019; 29:371-384. [PMID: 30826214 DOI: 10.1016/j.tcb.2019.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/11/2022]
Abstract
Ten years ago, high-throughput genetic interaction analyses revealed an abundant and widely conserved protein complex residing in the endoplasmic reticulum (ER) membrane. Dubbed the ER membrane protein complex (EMC), its disruption has since been found to affect wide-ranging processes, including protein trafficking, organelle communication, ER stress, viral maturation, lipid homeostasis, and others. However, its molecular function has remained enigmatic. Recent studies suggest a role for EMC during membrane protein biogenesis. Biochemical reconstitution experiments show that EMC can directly mediate the insertion of transmembrane domains (TMDs) into the lipid bilayer. Given the large proportion of genes encoding membrane proteins, a central role for EMC as a TMD insertion factor can explain its high abundance, wide conservation, and pleiotropic phenotypes.
Collapse
Affiliation(s)
- Patrick J Chitwood
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB20QH, UK
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB20QH, UK.
| |
Collapse
|
36
|
Volkmar N, Thezenas ML, Louie SM, Juszkiewicz S, Nomura DK, Hegde RS, Kessler BM, Christianson JC. The ER membrane protein complex promotes biogenesis of sterol-related enzymes maintaining cholesterol homeostasis. J Cell Sci 2019; 132:jcs.223453. [PMID: 30578317 PMCID: PMC6362398 DOI: 10.1242/jcs.223453] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022] Open
Abstract
The eukaryotic endoplasmic reticulum (ER) membrane contains essential complexes that oversee protein biogenesis and lipid metabolism, impacting nearly all aspects of cell physiology. The ER membrane protein complex (EMC) is a newly described transmembrane domain (TMD) insertase linked with various phenotypes, but whose clients and cellular responsibilities remain incompletely understood. We report that EMC deficiency limits the cellular boundaries defining cholesterol tolerance, reflected by diminished viability with limiting or excessive extracellular cholesterol. Lipidomic and proteomic analyses revealed defective biogenesis and concomitant loss of the TMD-containing ER-resident enzymes sterol-O-acyltransferase 1 (SOAT1) and squalene synthase (SQS, also known as FDFT1), which serve strategic roles in the adaptation of cells to changes in cholesterol availability. Insertion of the weakly hydrophobic tail-anchor (TA) of SQS into the ER membrane by the EMC ensures sufficient flux through the sterol biosynthetic pathway while biogenesis of polytopic SOAT1 promoted by the EMC provides cells with the ability to store free cholesterol as inert cholesteryl esters. By facilitating insertion of TMDs that permit essential mammalian sterol-regulating enzymes to mature accurately, the EMC is an important biogenic determinant of cellular robustness to fluctuations in cholesterol availability. This article has an associated First Person interview with the first author of the paper. Highlighted Article: The ER membrane protein complex promotes biogenesis of key membrane-bound enzymes responsible for regulation of cholesterol biosynthesis and storage, an important determinant of mammalian cell viability.
Collapse
Affiliation(s)
- Norbert Volkmar
- Ludwig Institute for Cancer Research, University of Oxford, ORCRB, Headington, Oxford, OX3 7DQ, UK
| | - Maria-Laetitia Thezenas
- Target Discovery Institute (TDI) Mass Spectrometry Laboratory, Nuffield Department of Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Sharon M Louie
- Dept. of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Szymon Juszkiewicz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniel K Nomura
- Dept. of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Benedikt M Kessler
- Target Discovery Institute (TDI) Mass Spectrometry Laboratory, Nuffield Department of Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - John C Christianson
- Ludwig Institute for Cancer Research, University of Oxford, ORCRB, Headington, Oxford, OX3 7DQ, UK .,Oxford Centre for Translational Myeloma Research, NDORMS, University of Oxford, Botnar Research Centre, Headington, Oxford, OX3 7LD, UK
| |
Collapse
|
37
|
EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. Cell 2018; 175:1507-1519.e16. [PMID: 30415835 PMCID: PMC6269167 DOI: 10.1016/j.cell.2018.10.009] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/15/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Mammals encode ∼5,000 integral membrane proteins that need to be inserted in a defined topology at the endoplasmic reticulum (ER) membrane by mechanisms that are incompletely understood. Here, we found that efficient biogenesis of β1-adrenergic receptor (β1AR) and other G protein-coupled receptors (GPCRs) requires the conserved ER membrane protein complex (EMC). Reconstitution studies of β1AR biogenesis narrowed the EMC requirement to the co-translational insertion of the first transmembrane domain (TMD). Without EMC, a proportion of TMD1 inserted in an inverted orientation or failed altogether. Purified EMC and SRP receptor were sufficient for correctly oriented TMD1 insertion, while the Sec61 translocon was necessary for insertion of the next TMD. Enforcing TMD1 topology with an N-terminal signal peptide bypassed the EMC requirement for insertion in vitro and restored efficient biogenesis of multiple GPCRs in EMC-knockout cells. Thus, EMC inserts TMDs co-translationally and cooperates with the Sec61 translocon to ensure accurate topogenesis of many membrane proteins. Efficient biogenesis of many GPCRs requires EMC, the ER membrane protein complex Without EMC, correct topology and insertion of the first transmembrane domain fails Purified EMC is sufficient for insertion of the first transmembrane domain of GPCRs The Sec61 complex is required for insertion of subsequent transmembrane domains
Collapse
|
38
|
Kudze T, Mendez-Dorantes C, Jalloh CS, McClellan AJ. Evidence for interaction between Hsp90 and the ER membrane complex. Cell Stress Chaperones 2018; 23:1101-1115. [PMID: 29808299 PMCID: PMC6111080 DOI: 10.1007/s12192-018-0908-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/24/2018] [Accepted: 05/27/2018] [Indexed: 01/04/2023] Open
Abstract
Numerous putative heat shock protein 90 (Hsp90)-interacting proteins, which could represent novel folding clients or co-chaperones, have been identified in recent years. Two separate high-throughput screens in yeast uncovered genetic effects between Hsp90 and components of the ER membrane complex (EMC), which is required for tolerance to unfolded protein response stress in yeast. Herein, we provide the first experimental evidence supporting that there is a genuine interaction of Hsp90 with the EMC. We demonstrate genetic interactions between EMC2 and the known Hsp90 co-chaperone encoded by STI1, as well as Hsp90 point mutant allele-specific differences in inherent growth and Hsp90 inhibitor tolerance in the absence and presence of EMC2. In co-precipitation experiments, Hsp90 interacts with Emc2p, whether or not Emc2p contains amino acid sequences designated as a tetratricopeptide repeat motif. Yeast with multiple EMC gene deletions exhibit increased sensitivity to Hsp90 inhibitor as well as defective folding of the well-established Hsp90 folding client, the glucocorticoid receptor. Altogether, our evidence of physical, genetic, and functional interaction of Hsp90 with the EMC, as well as bioinformatic analysis of shared interactors, supports that there is a legitimate interaction between them in vivo.
Collapse
Affiliation(s)
- Tambudzai Kudze
- Division of Science and Mathematics, Bennington College, Bennington, VT, USA
| | | | | | - Amie J McClellan
- Division of Science and Mathematics, Bennington College, Bennington, VT, USA.
| |
Collapse
|
39
|
Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky JL, Frost A, Borner GH, Weissman JS. The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. eLife 2018; 7:37018. [PMID: 29809151 PMCID: PMC5995541 DOI: 10.7554/elife.37018] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/26/2018] [Indexed: 12/20/2022] Open
Abstract
The endoplasmic reticulum (ER) supports biosynthesis of proteins with diverse transmembrane domain (TMD) lengths and hydrophobicity. Features in transmembrane domains such as charged residues in ion channels are often functionally important, but could pose a challenge during cotranslational membrane insertion and folding. Our systematic proteomic approaches in both yeast and human cells revealed that the ER membrane protein complex (EMC) binds to and promotes the biogenesis of a range of multipass transmembrane proteins, with a particular enrichment for transporters. Proximity-specific ribosome profiling demonstrates that the EMC engages clients cotranslationally and immediately following clusters of TMDs enriched for charged residues. The EMC can remain associated after completion of translation, which both protects clients from premature degradation and allows recruitment of substrate-specific and general chaperones. Thus, the EMC broadly enables the biogenesis of multipass transmembrane proteins containing destabilizing features, thereby mitigating the trade-off between function and stability.
Collapse
Affiliation(s)
- Matthew J Shurtleff
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Nicole T Schirle Oakdale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Elizabeth A Costa
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Martin Jonikas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jimena Weibezahn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Katerina D Popova
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Calvin H Jan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Pavel Sinitcyn
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Shruthi S Vembar
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Hilda Hernandez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Georg Hh Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
40
|
Abstract
Precision medicine is an integrative approach to cardiovascular disease prevention and treatment that considers an individual's genetics, lifestyle, and exposures as determinants of their cardiovascular health and disease phenotypes. This focus overcomes the limitations of reductionism in medicine, which presumes that all patients with the same signs of disease share a common pathophenotype and, therefore, should be treated similarly. Precision medicine incorporates standard clinical and health record data with advanced panomics (ie, transcriptomics, epigenomics, proteomics, metabolomics, and microbiomics) for deep phenotyping. These phenotypic data can then be analyzed within the framework of molecular interaction (interactome) networks to uncover previously unrecognized disease phenotypes and relationships between diseases, and to select pharmacotherapeutics or identify potential protein-drug or drug-drug interactions. In this review, we discuss the current spectrum of cardiovascular health and disease, population averages and the response of extreme phenotypes to interventions, and population-based versus high-risk treatment strategies as a pretext to understanding a precision medicine approach to cardiovascular disease prevention and therapeutic interventions. We also consider the search for resilience and Mendelian disease genes and argue against the theory of a single causal gene/gene product as a mediator of the cardiovascular disease phenotype, as well as an Erlichian magic bullet to solve cardiovascular disease. Finally, we detail the importance of deep phenotyping and interactome networks and the use of this information for rational polypharmacy. These topics highlight the urgent need for precise phenotyping to advance precision medicine as a strategy to improve cardiovascular health and prevent disease.
Collapse
Affiliation(s)
- Jane A Leopold
- From the Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Joseph Loscalzo
- From the Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
| |
Collapse
|
41
|
Guna A, Volkmar N, Christianson JC, Hegde RS. The ER membrane protein complex is a transmembrane domain insertase. Science 2018; 359:470-473. [PMID: 29242231 PMCID: PMC5788257 DOI: 10.1126/science.aao3099] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/26/2017] [Accepted: 11/27/2017] [Indexed: 12/26/2022]
Abstract
Insertion of proteins into membranes is an essential cellular process. The extensive biophysical and topological diversity of membrane proteins necessitates multiple insertion pathways that remain incompletely defined. Here we found that known membrane insertion pathways fail to effectively engage tail-anchored membrane proteins with moderately hydrophobic transmembrane domains. These proteins are instead shielded in the cytosol by calmodulin. Dynamic release from calmodulin allowed sampling of the endoplasmic reticulum (ER), where the conserved ER membrane protein complex (EMC) was shown to be essential for efficient insertion in vitro and in cells. Purified EMC in synthetic liposomes catalyzed the insertion of its substrates in a reconstituted system. Thus, EMC is a transmembrane domain insertase, a function that may explain its widely pleiotropic membrane-associated phenotypes across organisms.
Collapse
Affiliation(s)
- Alina Guna
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Norbert Volkmar
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK
| | - John C Christianson
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK
| | - Ramanujan S Hegde
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| |
Collapse
|
42
|
|
43
|
Oliver KE, Han ST, Sorscher EJ, Cutting GR. Transformative therapies for rare CFTR missense alleles. Curr Opin Pharmacol 2017; 34:76-82. [PMID: 29032041 DOI: 10.1016/j.coph.2017.09.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 01/09/2023]
Abstract
With over 1900 variants reported in the cystic fibrosis transmembrane conductance regulator (CFTR), enhanced understanding of cystic fibrosis (CF) genotype-phenotype correlation represents an important and expanding area of research. The potentiator Ivacaftor has proven an effective treatment for a subset of individuals carrying missense variants, particularly those that impact CFTR gating. Therapeutic efforts have recently focused on correcting the basic defect resulting from the common F508del variant, as well as many less frequent missense alleles. Modest enhancement of F508del-CFTR function has been achieved by combining Ivacaftor with Lumacaftor, a compound that aids maturational processing of misfolded CFTR. Continued development of in silico and in vitro models will facilitate CFTR variant characterization and drug testing, thereby elucidating heterogeneity in the molecular pathogenesis, phenotype, and modulator responsiveness of CF.
Collapse
Affiliation(s)
- Kathryn E Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Sangwoo T Han
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
44
|
Xavier BM, Hildebrandt E, Jiang F, Ding H, Kappes JC, Urbatsch IL. Substitution of Yor1p NBD1 residues improves the thermal stability of Human Cystic Fibrosis Transmembrane Conductance Regulator. Protein Eng Des Sel 2017; 30:729-741. [PMID: 29053845 PMCID: PMC5914393 DOI: 10.1093/protein/gzx054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 01/05/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a plasma membrane chloride channel protein that regulates vertebrate fluid homeostasis. The inefficiency of wild type human CFTR protein folding/trafficking is exacerbated by genetic mutations that can cause protein misfolding in the endoplasmic reticulum (ER) and subsequent degradation. This project investigates small changes in protein sequence that can alter the thermal stability of the large multi-domain CFTR protein. We target a conserved 70-residue α-subdomain located in the first nucleotide-binding domain that hosts the common misfolding mutation ∆F508. To investigate substitutions that can stabilize this domain, we constructed chimeras between human CFTR and its closest yeast homolog Yor1p. The α-subdomain of Yor1p was replaced with that of CFTR in Saccharomyces cerevisiae. Cellular localization of green fluorescence protein-tagged Yor1p-CFTR chimeras was analyzed by fluorescence microscopy and quantitative multispectral imaging flow cytometry, steady-state protein levels were compared by SDS-PAGE and protein function probed by a phenotypic oligomycin resistance assay. The chimeras exhibited ER retention in yeast characteristic of defective protein folding/processing. Substitution of seven CFTR α-subdomain residues that are highly conserved in Yor1p and other transporters but differ in CFTR (S495P/R516K/F533L/A534P/K536G/I539T/R553K) improved Yor1p-CFTR chimera localization to the yeast plasma membrane. When introduced into human CFTR expressed in mammalian cells, the same substitutions improve the purified protein thermal stability. This stabilized human CFTR protein will be directly useful for structural and biophysical studies that have been limited by the thermal sensitivity of wild type CFTR. The insights into critical structural residues within CFTR could facilitate development of effective therapeutics for CF-causing mutations.
Collapse
Affiliation(s)
- B M Xavier
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - E Hildebrandt
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - F Jiang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - H Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - J C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Veterans Affairs Medical Center, Research Service, Birmingham, AL 35294, USA
| | - I L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| |
Collapse
|
45
|
Farinha CM, Miller E, McCarty N. Protein and lipid interactions - Modulating CFTR trafficking and rescue. J Cyst Fibros 2017; 17:S9-S13. [PMID: 28887112 DOI: 10.1016/j.jcf.2017.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 08/28/2017] [Indexed: 12/26/2022]
Abstract
Different levels of CFTR regulation in the cell contribute to a stringent control of chloride secretion in epithelia. Tuning of chloride transport is achieved by modulating CFTR biogenesis, exit from the endoplasmic reticulum, trafficking, membrane stability and channel activity. In this short review, we summarize recent findings identifying interactions with other proteins - directly or through membrane lipids - and briefly discuss how these observations can provide clues to the design of better therapeutic approaches.
Collapse
Affiliation(s)
- Carlos M Farinha
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal.
| | | | - Nael McCarty
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| |
Collapse
|
46
|
Smith DL, Maharrey CH, Carey CR, White RA, Hartman JL. Gene-nutrient interaction markedly influences yeast chronological lifespan. Exp Gerontol 2016; 86:113-123. [PMID: 27125759 PMCID: PMC5079838 DOI: 10.1016/j.exger.2016.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 02/01/2023]
Abstract
PURPOSE Research into the genetic mechanisms of aging has expanded rapidly over the past two decades. This has in part been the result of the use of model organisms (particularly yeast, worms and flies) and high-throughput technologies, combined with a growing interest in aging research. Despite this progress, widespread consensus regarding the pathways that are fundamental to the modulation of cellular aging and lifespan for all organisms has been limited due to discrepancies between different studies. We have compared results from published genome-wide, chronological lifespan (CLS) screens of individual gene deletion strains in Saccharomyces cerevisiae in order to identify gene deletion strains with consistent influences on longevity as possible indicators of fundamental aging processes from this single-celled, eukaryotic model organism. METHODS Three previous reports have described genetic modifiers of chronological aging in the budding yeast (S. cerevisiae) using the yeast gene deletion strain collection. We performed a comparison among the data sets using correlation and decile distribution analysis to describe concordance between screens and identify strains that consistently increased or decreased CLS. We used gene enrichment analysis in an effort to understand the biology underlying genes identified in multiple studies. We attempted to replicate the different experimental conditions employed by the screens to identify potential sources of variability in CLS worth further investigating. RESULTS Among 3209 strains present in all three screens, nine deletions strains were in common in the longest-lived decile (2.80%) and thirteen were in common in the shortest-lived decile (4.05%) of all three screens. Similarly, pairwise overlap between screens was low. When the same comparison was extended to three deciles to include more mutants studied in common between the three screens, enrichment of cellular processes based on gene ontology analysis in the long-lived strains remained very limited. To test the hypothesis that different parental strain auxotrophic requirements or media formulations employed by the respective genome-wide screens might contribute to the lack of concordance, different CLS assay conditions were assessed in combination with strains having different ploidy and auxotrophic requirements (all relevant to differences in the way the three genome-wide CLS screens were performed). This limited but systematic analysis of CLS with respect to auxotrophy, ploidy, and media revealed several instances of gene-nutrient interaction. CONCLUSIONS There is surprisingly little overlap between the results of three independently performed genome-wide screens of CLS in S. cerevisiae. However, differences in strain genetic background (ploidy and specific auxotrophic requirements) were present, as well as different media and experimental conditions (e.g., aeration and pooled vs. individual culturing), which, along with stochastic effects such as genetic drift or selection of secondary mutations that suppress the loss of function from gene deletion, could in theory account for some of the lack of consensus between results. Considering the lack of overlap in CLS phenotypes among the set of genes reported by all three screens, and the results of a CLS experiment that systematically tested (incorporating extensive controls) for interactions between variables existing between the screens, we propose that discrepancies can be reconciled through deeper understanding of the influence of cell intrinsic factors such as auxotrophic requirements ploidy status, extrinsic factors such as media composition and aeration, as well as interactions that may occur between them, for example as a result of different pooling vs. individually aging cultures. Such factors may have a more significant impact on CLS outcomes than previously realized. Future studies that systematically account for these contextual factors, and can thus clarify the interactions between genetic and nutrient factors that alter CLS phenotypes, should aid more complete understanding of the underlying biology so that genetic principles of CLS in yeast can be extrapolated to differential cellular aging observed in animal models.
Collapse
Affiliation(s)
- Daniel L Smith
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Crystal H Maharrey
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christopher R Carey
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Richard A White
- Department of Statistics and Michael Smith Laboratories, University of British Columbia,3182 Earth Sciences Building, 2207 Main Mall, Vancouver BC V6T-1Z4, Canada
| | - John L Hartman
- Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
47
|
Veit G, Oliver K, Apaja PM, Perdomo D, Bidaud-Meynard A, Lin ST, Guo J, Icyuz M, Sorscher EJ, Hartman JL, Lukacs GL. Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect. PLoS Biol 2016; 14:e1002462. [PMID: 27168400 PMCID: PMC4864299 DOI: 10.1371/journal.pbio.1002462] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/14/2016] [Indexed: 01/05/2023] Open
Abstract
The most common cystic fibrosis (CF) causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del), results in functional expression defect of the CF transmembrane conductance regulator (CFTR) at the apical plasma membrane (PM) of secretory epithelia, which is attributed to the degradation of the misfolded channel at the endoplasmic reticulum (ER). Deletion of phenylalanine 670 (ΔF670) in the yeast oligomycin resistance 1 gene (YOR1, an ABC transporter) of Saccharomyces cerevisiae phenocopies the ΔF508-CFTR folding and trafficking defects. Genome-wide phenotypic (phenomic) analysis of the Yor1-ΔF670 biogenesis identified several modifier genes of mRNA processing and translation, which conferred oligomycin resistance to yeast. Silencing of orthologues of these candidate genes enhanced the ΔF508-CFTR functional expression at the apical PM in human CF bronchial epithelia. Although knockdown of RPL12, a component of the ribosomal stalk, attenuated the translational elongation rate, it increased the folding efficiency as well as the conformational stability of the ΔF508-CFTR, manifesting in 3-fold augmented PM density and function of the mutant. Combination of RPL12 knockdown with the corrector drug, VX-809 (lumacaftor) restored the mutant function to ~50% of the wild-type channel in primary CFTRΔF508/ΔF508 human bronchial epithelia. These results and the observation that silencing of other ribosomal stalk proteins partially rescue the loss-of-function phenotype of ΔF508-CFTR suggest that the ribosomal stalk modulates the folding efficiency of the mutant and is a potential therapeutic target for correction of the ΔF508-CFTR folding defect. Reducing the rate of translational elongation by silencing ribosomal stalk proteins ameliorates the folding and stability defect of the cystic fibrosis mutant protein ΔF508-CFTR, partially restoring the plasma membrane chloride conductance. Cystic fibrosis (CF) is one of the most common autosomal recessive diseases in Caucasians. It is caused by mutations in the CF transmembrane conductance regulator (CFTR), which functions as an anion channel at the apical plasma membrane of secretory epithelia. The most common CF mutation, a deletion of the phenylalanine residue at position 508 (ΔF508), results in the channel misfolding and subsequent intracellular degradation. Our previous genome-wide phenotypic screens, using a yeast variant, have predicted modifier genes for ΔF508-CFTR biogenesis. Here, we show that silencing of one of these candidate genes, RPL12, a component of the ribosomal stalk, increased the folding and stabilization of ΔF508-CFTR, resulting in its increased plasma membrane expression and function. Our data suggest that reducing the translational elongation rate via RPL12 silencing can partially reverse the ΔF508-CFTR folding defect. Importantly, RPL12 silencing in combination with the corrector drug VX-809 (lumacaftor), increased the mutant function to 50% of the wild-type CFTR channel, suggesting that the ribosomal stalk perturbation may represent a therapeutic target for rescuing the ΔF508-CFTR biogenesis defect.
Collapse
Affiliation(s)
- Guido Veit
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Kathryn Oliver
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Pirjo M. Apaja
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Doranda Perdomo
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | | | - Sheng-Ting Lin
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Jingyu Guo
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Mert Icyuz
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - John L. Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail: (JLH); (GLL)
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, Quebec, Canada
- Department of Biochemistry, McGill University, Montréal, Quebec, Canada
- Groupe de Recherche Axé sur la Structure des Protéines (GRASP), McGill University, Montréal, Quebec, Canada
- * E-mail: (JLH); (GLL)
| |
Collapse
|
48
|
Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nat Biotechnol 2016; 34:531-8. [PMID: 27065010 DOI: 10.1038/nbt.3514] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022]
Abstract
Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we describe a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. A comprehensive screen of 874 genes in 589,306 genomes led to the identification of 13 adults harboring mutations for 8 severe Mendelian conditions, with no reported clinical manifestation of the indicated disease. Our findings demonstrate the promise of broadening genetic studies to systematically search for well individuals who are buffering the effects of rare, highly penetrant, deleterious mutations. They also indicate that incomplete penetrance for Mendelian diseases is likely more common than previously believed. The identification of resilient individuals may provide a first step toward uncovering protective genetic variants that could help elucidate the mechanisms of Mendelian diseases and new therapeutic strategies.
Collapse
Affiliation(s)
- Rong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jörg Hakenberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Om Prakash
- Department of Clinical Sciences, Diabetes &Endocrinology, Lund University Diabetes Center, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patrick Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wei-Yi Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Menachem Fromer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Matthew A Deardorff
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jason R Bobe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Elissa Levin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Leif Groop
- Department of Clinical Sciences, Diabetes &Endocrinology, Lund University Diabetes Center, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen H Friend
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sage Bionetworks, Seattle, Washington, USA
| |
Collapse
|
49
|
Abstract
Cytoplasmic coat protein complexes perform central roles in sorting protein constituents within the endomembrane system. A new study reveals that the COPII coat operates through dual recognition of signals in a sorting receptor and its bound cargo to promote efficient export from the endoplasmic reticulum.
Collapse
Affiliation(s)
- Charles Barlowe
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| |
Collapse
|
50
|
Wei S, Roessler BC, Icyuz M, Chauvet S, Tao B, Hartman JL, Kirk KL. Long-range coupling between the extracellular gates and the intracellular ATP binding domains of multidrug resistance protein pumps and cystic fibrosis transmembrane conductance regulator channels. FASEB J 2015; 30:1247-62. [PMID: 26606940 DOI: 10.1096/fj.15-278382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/16/2015] [Indexed: 12/22/2022]
Abstract
The ABCC transporter subfamily includes pumps, the long and short multidrug resistance proteins (MRPs), and an ATP-gated anion channel, the cystic fibrosis transmembrane conductance regulator (CFTR). We show that despite their thermodynamic differences, these ABCC transporter subtypes use broadly similar mechanisms to couple their extracellular gates to the ATP occupancies of their cytosolic nucleotide binding domains. A conserved extracellular phenylalanine at this gate was a prime location for producing gain of function (GOF) mutants of a long MRP in yeast (Ycf1p cadmium transporter), a short yeast MRP (Yor1p oligomycin exporter), and human CFTR channels. Extracellular gate mutations rescued ATP binding mutants of the yeast MRPs and CFTR by increasing ATP sensitivity. Control ATPase-defective MRP mutants could not be rescued by this mechanism. A CFTR double mutant with an extracellular gate mutation plus a cytosolic GOF mutation was highly active (single-channel open probability >0.3) in the absence of ATP and protein kinase A, each normally required for CFTR activity. We conclude that all 3 ABCC transporter subtypes use similar mechanisms to couple their extracellular gates to ATP occupancy, and highly active CFTR channels that bypass defects in ATP binding or phosphorylation can be produced.
Collapse
Affiliation(s)
- Shipeng Wei
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bryan C Roessler
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mert Icyuz
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sylvain Chauvet
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Binli Tao
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - John L Hartman
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin L Kirk
- *Department of Cell, Developmental, and Integrative Biology, Department of Genetics, and Department of Neurobiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|