Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients

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 di...

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Published ineLife Vol. 9
Main Authors Miller-Vedam, Lakshmi E, Bräuning, Bastian, Popova, Katerina D, Schirle Oakdale, Nicole T, Bonnar, Jessica L, Prabu, Jesuraj R, Boydston, Elizabeth A, Sevillano, Natalia, Shurtleff, Matthew J, Stroud, Robert M, Craik, Charles S, Schulman, Brenda A, Frost, Adam, Weissman, Jonathan S
Format Journal Article
LanguageEnglish
Published England eLife Sciences Publications, Ltd 25.11.2020
eLife Sciences Publications Ltd
Subjects
Blotting, Western
Cell Biology
chaperone holdase
electron microscopy
EMC
endoplasmic reticulum
Endoplasmic Reticulum - metabolism
Humans
insertase
Intracellular Membranes - metabolism
membrane protein biogenesis
Membrane Proteins - biosynthesis
Membrane Proteins - genetics
Membrane Proteins - metabolism
Protein Structure, Tertiary
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae Proteins - biosynthesis
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
Sequence Alignment
Structural Biology and Molecular Biophysics
cell biology
chaperone holdase
electron microscopy
membrane protein biogenesis
EMC
structural biology
molecular biophysics
human
endoplasmic reticulum
S. cerevisiae
insertase
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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.
AbstractList 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.
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. Cells are surrounded and contained by a plasma membrane consisting of a double layer of fats and proteins. These proteins monitor and facilitate the movement of food, oxygen and messages in and out of the cell, and help neighboring cells communicate. Membrane proteins are manufactured in a cell compartment called the endoplasmic reticulum. Cellular machines called ribosomes visit this compartment’s membrane to manufacture proteins that need to be secreted or embedded into the cell’s membranes. As these proteins are made, they are pulled into the endoplasmic reticulum so they can be folded correctly and inserted in the membrane. A cellular machine in this compartment’s membrane that aids this process is the endoplasmic reticulum membrane protein complex (EMC). Many steps can go wrong during protein assembly, so to control protein quality, the EMC has to accommodate the variety of complex physical features that proteins can have. To explore the activity of the EMC, Miller-Vedam, Bräuning, Popova et al. studied the normal structure of the EMC in both yeast and human cells grown in the lab. These snapshots of the complex in different species had a lot in common, including how the complex was arranged within and around the membrane. Next, Miller-Vedam, Bräuning, Popova et al. generated 50 mutant versions of the EMC in human cells to determine how changing different parts of the complex affected the production of three proteins that rely on the EMC to fold correctly. These proteins were an enzyme called squalene synthase, a signaling protein called the beta adrenergic receptor and sigma intracellular receptor 2, a protein involved in the regulation of cholesterol levels. Mutations in the section of the EMC outside of the endoplasmic reticulum, within the main cellular compartment, negatively impacted the stability of squalene synthase. This section of the EMC provides a platform where proteins can associate before entering the membrane. The part of EMC that spans the membrane contains both a fat-filled cavity and a cavity with a ‘door’ that is either open or closed. Mutations in this section disrupted the insertion of both squalene synthase and the beta adrenergic receptor into the membrane, a role performed by the cavity with the door. The specific role of the fat-filled cavity is still not fully understood, but a mutation affecting this cavity disrupts the correct production of all three proteins studied. The largest section of the complex, which sits inside the endoplasmic reticulum, protected proteins as they folded, ensuring they were not destroyed for being folded incorrectly before they were fully formed. Mutations in this part of the EMC negatively impacted the stability of sigma intracellular receptor 2 without negatively affecting the other proteins. This molecular dissection of the activity of the EMC provides insights into how membrane proteins are manufactured, stabilized, coordinated, and monitored for quality. These findings could contribute towards the development of new treatments for certain congenital diseases. For example, cystic fibrosis, retinitis pigmentosa, and Charcot-Marie-Tooth disease are all thought to be caused by mutations within membrane proteins that require the EMC during their production.
Author Stroud, Robert M
Miller-Vedam, Lakshmi E
Sevillano, Natalia
Popova, Katerina D
Bräuning, Bastian
Schirle Oakdale, Nicole T
Prabu, Jesuraj R
Boydston, Elizabeth A
Shurtleff, Matthew J
Schulman, Brenda A
Bonnar, Jessica L
Frost, Adam
Weissman, Jonathan S
Craik, Charles S
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/33236988$$D View this record in MEDLINE/PubMed
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Keywords cell biology
chaperone holdase
electron microscopy
membrane protein biogenesis
EMC
structural biology
molecular biophysics
human
endoplasmic reticulum
S. cerevisiae
insertase
Language English
License 2020, Miller-Vedam et al.
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
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Lycia Therapeutics, South San Francisco, San Francisco, United States.
These authors contributed equally to this work.
Gilead Sciences, Foster City, United States.
Whitehead Institute, MIT, Cambridge, United States.
FairJourney Biologics, Porto, Portugal.
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0000-0001-7704-9185
OpenAccessLink https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7785296/
PMID 33236988
PQID 2464194423
PQPubID 23479
ParticipantIDs doaj_primary_oai_doaj_org_article_4aa84c6d7fa149a6bde470da7aa51b54
pubmedcentral_primary_oai_pubmedcentral_nih_gov_7785296
proquest_miscellaneous_2464194423
crossref_primary_10_7554_eLife_62611
pubmed_primary_33236988
PublicationCentury 2000
PublicationDate 2020-11-25
PublicationDateYYYYMMDD 2020-11-25
PublicationDate_xml – month: 11
  year: 2020
  text: 2020-11-25
  day: 25
PublicationDecade 2020
PublicationPlace England
PublicationPlace_xml – name: England
PublicationTitle eLife
PublicationTitleAlternate Elife
PublicationYear 2020
Publisher eLife Sciences Publications, Ltd
eLife Sciences Publications Ltd
Publisher_xml – name: eLife Sciences Publications, Ltd
– name: eLife Sciences Publications Ltd
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SSID ssj0000748819
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Snippet Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved...
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SubjectTerms Blotting, Western
Cell Biology
chaperone holdase
electron microscopy
EMC
endoplasmic reticulum
Endoplasmic Reticulum - metabolism
Humans
insertase
Intracellular Membranes - metabolism
membrane protein biogenesis
Membrane Proteins - biosynthesis
Membrane Proteins - genetics
Membrane Proteins - metabolism
Protein Structure, Tertiary
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae Proteins - biosynthesis
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
Sequence Alignment
Structural Biology and Molecular Biophysics
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Title Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients
URI https://www.ncbi.nlm.nih.gov/pubmed/33236988
https://search.proquest.com/docview/2464194423
https://pubmed.ncbi.nlm.nih.gov/PMC7785296
https://doaj.org/article/4aa84c6d7fa149a6bde470da7aa51b54
Volume 9
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