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Ikeda T, Yamazaki K, Okumura F, Kamura T, Nakatsukasa K. Role of the San1 ubiquitin ligase in the heat stress-induced degradation of nonnative Nup1 in the nuclear pore complex. Genetics 2024; 226:iyae017. [PMID: 38302116 DOI: 10.1093/genetics/iyae017] [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: 11/21/2022] [Revised: 11/21/2022] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The nuclear pore complex (NPC) mediates the selective exchange of macromolecules between the nucleus and the cytoplasm. Neurodegenerative diseases such as amyotrophic lateral sclerosis are characterized by mislocalization of nucleoporins (Nups), transport receptors, and Ras-related nuclear proteins into nucleoplasmic or cytosolic aggregates, underscoring the importance of precise assembly of the NPC. The assembly state of large protein complexes is strictly monitored by the protein quality control system. The ubiquitin-proteasome system may eliminate aberrant, misfolded, and/or orphan components; however, the involvement of the ubiquitin-proteasome system in the degradation of nonnative Nups in the NPC remains unclear. Here, we show that in Saccharomyces cerevisiae, although Nup1 (the FG-Nup component of the central core of the NPC) was stable, C-terminally green fluorescent protein-tagged Nup1, which had been incorporated into the NPC, was degraded by the proteasome especially under heat stress conditions. The degradation was dependent on the San1 ubiquitin ligase and Cdc48/p97, as well as its cofactor Doa1. We also demonstrate that San1 weakly but certainly contributes to the degradation of nontagged endogenous Nup1 in cells defective in NPC biogenesis by the deletion of NUP120. In addition, the overexpression of SAN1 exacerbated the growth defect phenotype of nup120Δ cells, which may be caused by excess degradation of defective Nups due to the deletion of NUP120. These biochemical and genetic data suggest that San1 is involved in the degradation of nonnative Nups generated by genetic mutation or when NPC biogenesis is impaired.
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Affiliation(s)
- Takanari Ikeda
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
| | - Kenji Yamazaki
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Fukuoka 813-8529, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
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Flagg MP, Lam B, Lam DK, Le TM, Kao A, Slaiwa YI, Hampton RY. Exploring the "misfolding problem" by systematic discovery and analysis of functional-but-degraded proteins. Mol Biol Cell 2023; 34:ar125. [PMID: 37729018 PMCID: PMC10848938 DOI: 10.1091/mbc.e23-06-0248] [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: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
In both health and disease, the ubiquitin-proteasome system (UPS) degrades point mutants that retain partial function but have decreased stability compared with their wild-type counterparts. This class of UPS substrate includes routine translational errors and numerous human disease alleles, such as the most common cause of cystic fibrosis, ΔF508-CFTR. Yet, there is no systematic way to discover novel examples of these "minimally misfolded" substrates. To address that shortcoming, we designed a genetic screen to isolate functional-but-degraded point mutants, and we used the screen to study soluble, monomeric proteins with known structures. These simple parent proteins yielded diverse substrates, allowing us to investigate the structural features, cytotoxicity, and small-molecule regulation of minimal misfolding. Our screen can support numerous lines of inquiry, and it provides broad access to a class of poorly understood but biomedically critical quality-control substrates.
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Affiliation(s)
- Matthew P. Flagg
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Breanna Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Darren K. Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Tiffany M. Le
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Andy Kao
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Yousif I. Slaiwa
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
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3
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Bhaduri S, Aguayo A, Ohno Y, Proietto M, Jung J, Wang I, Kandel R, Singh N, Ibrahim I, Fulzele A, Bennett EJ, Kihara A, Neal SE. An ERAD-independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis. EMBO J 2023; 42:e112275. [PMID: 36350249 PMCID: PMC9929635 DOI: 10.15252/embj.2022112275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Nearly one-third of nascent proteins are initially targeted to the endoplasmic reticulum (ER), where they are correctly folded and assembled before being delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) removes these client proteins from the ER membrane to the cytosol in a process known as retrotranslocation. Our previous work demonstrated that rhomboid pseudoprotease Dfm1 is involved in the retrotranslocation of ubiquitinated membrane integral ERAD substrates. Herein, we found that Dfm1 associates with the SPOTS complex, which is composed of serine palmitoyltransferase (SPT) enzymes and accessory components that are critical for catalyzing the first rate-limiting step of the sphingolipid biosynthesis pathway. Furthermore, Dfm1 employs an ERAD-independent role for facilitating the ER export and endosome- and Golgi-associated degradation (EGAD) of Orm2, which is a major antagonist of SPT activity. Given that the accumulation of human Orm2 homologs, ORMDLs, is associated with various pathologies, our study serves as a molecular foothold for understanding how dysregulation of sphingolipid metabolism leads to various diseases.
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Affiliation(s)
- Satarupa Bhaduri
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Analine Aguayo
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Yusuke Ohno
- Laboratory of Biochemistry, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Marco Proietto
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Jasmine Jung
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Isabel Wang
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Rachel Kandel
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Narinderbir Singh
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Ikran Ibrahim
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Amit Fulzele
- Present address:
Institute of Molecular BiologyMainzGermany
| | - Eric J Bennett
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Sonya E Neal
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
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4
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Zhou D, Fu Y, Li F, Yang D, Wei L, Yue H, Dai Y, Jeon Y. Treatment of obese zebrafish with saringosterol acetate through AMP activated protein kinase pathway. Chem Biodivers 2022; 19:e202200495. [PMID: 35856892 DOI: 10.1002/cbdv.202200495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/18/2022] [Indexed: 11/06/2022]
Abstract
OBJECT Edible Brown Seaweed Sargassum fusiforme (Harvey) Setchell, 1931 abbreviated as Sargassum fusiforme was used for folk medical therapy in East Asia countries over five hundred years. Saringosterol acetate (SA) was isolated from S. fusiforme in our previous study and indicated various effects. However, anti-obesity activity of SA and its mechanism still unknown. Method: The inhibitory effect of SA, isolated from S. fusiforme , on adipogenesis in 3T3-L1 adipocytes was investigated in vitro and in zebrafish model. Cell toxicity, differentiation, signaling pathway, and lipid accumulation of SA treated 3T3-L1 adipocytes were determined. The body weight and triglyceride content of diet-induced obese (DIO) adult male zebrafish were measured from 12 to 17 weeks after fertilization. Result: SA attenuated the differentiation of cells and reduced lipid accumulation, and triglyceride content in the 3T3-L1 adipocytes. During the differentiation of adipocytes, SA suppressed fat accumulation and decreased the expression of signal factors responsible for adipogenesis. In SA-treated adipocytes, while fatty acid synthetase was downregulated, AMP-activated protein kinase (AMPK) was upregulated. Furthermore, SA suppressed body weight and triglyceride content in DIO zebrafish. CONCLUSION SA is a potential therapeutic agent in the management of metabolic disorders, such as obesity.
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Affiliation(s)
- DongYue Zhou
- Changchun University of Chinese Medicine, Jilin Ginseng Academy, Changchun 130117, Changchun, CHINA
| | - YunHua Fu
- Changchun University of Chinese Medicine, Jilin Ginseng Academy, Changchun 130117, Changchun, CHINA
| | - FangTong Li
- Changchun University of Chinese Medicine, Jilin Ginseng Academy, Changchun 130117, Changchun, CHINA
| | - Di Yang
- Changchun University of Chinese Medicine, Jilin Ginseng Academy, Changchun 130117, Changchun, CHINA
| | - LiNa Wei
- Changchun University of Chinese Medicine, Jilin Ginseng Academy, Changchun 130117, Changchun, CHINA
| | - Hao Yue
- Changchun University of Chinese Medicine, Jilin Ginseng Academy, Changchun 130117, Changchun, CHINA
| | - Yulin Dai
- Changchun University of Chinese Medicine, jilin ginseng academy, 1035# boshuo raod, 130117, Changchun, CHINA
| | - YouJin Jeon
- Jeju National University, Marine Science Institute, Jeju 63333, Jeju, KOREA, REPUBLIC OF
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5
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Lipid Dyshomeostasis and Inherited Cerebellar Ataxia. Mol Neurobiol 2022; 59:3800-3828. [PMID: 35420383 PMCID: PMC9148275 DOI: 10.1007/s12035-022-02826-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/01/2022] [Indexed: 12/04/2022]
Abstract
Cerebellar ataxia is a form of ataxia that originates from dysfunction of the cerebellum, but may involve additional neurological tissues. Its clinical symptoms are mainly characterized by the absence of voluntary muscle coordination and loss of control of movement with varying manifestations due to differences in severity, in the site of cerebellar damage and in the involvement of extracerebellar tissues. Cerebellar ataxia may be sporadic, acquired, and hereditary. Hereditary ataxia accounts for the majority of cases. Hereditary ataxia has been tentatively divided into several subtypes by scientists in the field, and nearly all of them remain incurable. This is mainly because the detailed mechanisms of these cerebellar disorders are incompletely understood. To precisely diagnose and treat these diseases, studies on their molecular mechanisms have been conducted extensively in the past. Accumulating evidence has demonstrated that some common pathogenic mechanisms exist within each subtype of inherited ataxia. However, no reports have indicated whether there is a common mechanism among the different subtypes of inherited cerebellar ataxia. In this review, we summarize the available references and databases on neurological disorders characterized by cerebellar ataxia and show that a subset of genes involved in lipid homeostasis form a new group that may cause ataxic disorders through a common mechanism. This common signaling pathway can provide a valuable reference for future diagnosis and treatment of ataxic disorders.
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Gu X, Zhuang A, Yu J, Chai P, Jia R, Ruan J. Phase separation drives tumor pathogenesis and evolution: all roads lead to Rome. Oncogene 2022; 41:1527-1535. [PMID: 35132182 DOI: 10.1038/s41388-022-02195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/10/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022]
Abstract
Cells coordinate numerous biochemical reactions in space and time, depending on the subdivision of the intracellular space into functional compartments. Compelling evidence has demonstrated that phase separation induces the formation of membrane-less compartments to partition intracellular substances in a strictly regulated manner and participates in various biological processes. Based on the strong association of cancer with the dysregulation of intracellular physiological processes and the occurrence of phase separation in cancer-associated condensates, phase separation undoubtedly plays a significant role in tumorigenesis. In this review, we summarize the drivers and functions of phase separation, elaborate on the roles of phase separation in tumor pathogenesis and evolution, and propose substantial research and therapeutic prospects for phase separation in cancer.
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Affiliation(s)
- Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, PR China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, PR China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, PR China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, PR China
| | - Jie Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, PR China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, PR China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, PR China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, PR China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, PR China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, PR China.
| | - Jing Ruan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, PR China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, PR China.
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7
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Nakatsukasa K, Wigge S, Takano Y, Kawarasaki T, Kamura T, Brodsky JL. A positive genetic selection for transmembrane domain mutations in HRD1 underscores the importance of Hrd1 complex integrity during ERAD. Curr Genet 2022; 68:227-242. [PMID: 35041076 PMCID: PMC9036396 DOI: 10.1007/s00294-022-01227-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/26/2022]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are retrotranslocated to the cytosol for ubiquitination and degradation by the proteasome. During this process, known as ER-associated degradation (ERAD), the ER-embedded Hrd1 ubiquitin ligase plays a central role in recognizing, ubiquitinating, and retrotranslocating scores of lumenal and integral membrane proteins. To better define the mechanisms underlying Hrd1 function in Saccharomyces cerevisiae, several model substrates have been developed. One substrate is Sec61-2, a temperature sensitive allele of the Sec61 translocation channel. Cells expressing Sec61-2 grow at 25 °C because the protein is stable, but sec61-2 yeast are inviable at 38 °C because the mutated protein is degraded in a Hrd1-dependent manner. Therefore, deleting HRD1 stabilizes Sec61-2 and hence sec61-2hrd1∆ double mutants are viable at 38 °C. This unique phenotype allowed us to perform a non-biased screen for loss-of-function alleles in HRD1. Based on its importance in mediating substrate retrotranslocation, the screen was also developed to focus on mutations in sequences encoding Hrd1's transmembrane-rich domain. Ultimately, a group of recessive mutations was identified in HRD1, including an ensemble of destabilizing mutations that resulted in the delivery of Hrd1 to the ERAD pathway. A more stable mutant resided in a buried transmembrane domain, yet the Hrd1 complex was disrupted in yeast expressing this mutant. Together, these data confirm the importance of Hrd1 complex integrity during ERAD, suggest that allosteric interactions between transmembrane domains regulate Hrd1 complex formation, and provide the field with new tools to define the dynamic interactions between ERAD components during substrate retrotranslocation.
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Affiliation(s)
- Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan.
| | - Sylvia Wigge
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, PA, 15260, USA
| | - Yuki Takano
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Tomoyuki Kawarasaki
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, PA, 15260, USA.
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8
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Smith CE, Tsai YC, Liang YH, Khago D, Mariano J, Li J, Tarasov SG, Gergel E, Tsai B, Villaneuva M, Clapp ME, Magidson V, Chari R, Byrd RA, Ji X, Weissman AM. A structurally conserved site in AUP1 binds the E2 enzyme UBE2G2 and is essential for ER-associated degradation. PLoS Biol 2021; 19:e3001474. [PMID: 34879065 PMCID: PMC8699718 DOI: 10.1371/journal.pbio.3001474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 12/23/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Endoplasmic reticulum–associated degradation (ERAD) is a protein quality control pathway of fundamental importance to cellular homeostasis. Although multiple ERAD pathways exist for targeting topologically distinct substrates, all pathways require substrate ubiquitination. Here, we characterize a key role for the UBE2G2 Binding Region (G2BR) of the ERAD accessory protein ancient ubiquitous protein 1 (AUP1) in ERAD pathways. This 27-amino acid (aa) region of AUP1 binds with high specificity and low nanomolar affinity to the backside of the ERAD ubiquitin-conjugating enzyme (E2) UBE2G2. The structure of the AUP1 G2BR (G2BRAUP1) in complex with UBE2G2 reveals an interface that includes a network of salt bridges, hydrogen bonds, and hydrophobic interactions essential for AUP1 function in cells. The G2BRAUP1 shares significant structural conservation with the G2BR found in the E3 ubiquitin ligase gp78 and in vitro can similarly allosterically activate ubiquitination in conjunction with ERAD E3s. In cells, AUP1 is uniquely required to maintain normal levels of UBE2G2; this is due to G2BRAUP1 binding to the E2 and preventing its rapid degradation. In addition, the G2BRAUP1 is required for both ER membrane recruitment of UBE2G2 and for its activation at the ER membrane. Thus, by binding to the backside of a critical ERAD E2, G2BRAUP1 plays multiple critical roles in ERAD. This study shows that a 27-amino acid domain that binds the ubiquitin conjugating enzyme UBE2G2, and which is found in two different proteins (AUP1 and gp78), is critical for endoplasmic reticulum-associated degradation (ERAD).
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Affiliation(s)
- Christopher E Smith
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Yu-He Liang
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Domarin Khago
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Jennifer Mariano
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Jess Li
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Sergey G Tarasov
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Emma Gergel
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Borong Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Matthew Villaneuva
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Michelle E Clapp
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Xinhua Ji
- Center for Structural Biology, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland, United States of America
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The Targeting of Native Proteins to the Endoplasmic Reticulum-Associated Degradation (ERAD) Pathway: An Expanding Repertoire of Regulated Substrates. Biomolecules 2021; 11:biom11081185. [PMID: 34439852 PMCID: PMC8393694 DOI: 10.3390/biom11081185] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 12/22/2022] Open
Abstract
All proteins are subject to quality control processes during or soon after their synthesis, and these cellular quality control pathways play critical roles in maintaining homeostasis in the cell and in organism health. Protein quality control is particularly vital for those polypeptides that enter the endoplasmic reticulum (ER). Approximately one-quarter to one-third of all proteins synthesized in eukaryotic cells access the ER because they are destined for transport to the extracellular space, because they represent integral membrane proteins, or because they reside within one of the many compartments of the secretory pathway. However, proteins that mature inefficiently are subject to ER-associated degradation (ERAD), a multi-step pathway involving the chaperone-mediated selection, ubiquitination, and extraction (or “retrotranslocation”) of protein substrates from the ER. Ultimately, these substrates are degraded by the cytosolic proteasome. Interestingly, there is an increasing number of native enzymes and metabolite and solute transporters that are also targeted for ERAD. While some of these proteins may transiently misfold, the ERAD pathway also provides a route to rapidly and quantitatively downregulate the levels and thus the activities of a variety of proteins that mature or reside in the ER.
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10
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Schumacher MM, DeBose-Boyd RA. Posttranslational Regulation of HMG CoA Reductase, the Rate-Limiting Enzyme in Synthesis of Cholesterol. Annu Rev Biochem 2021; 90:659-679. [PMID: 34153214 DOI: 10.1146/annurev-biochem-081820-101010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The polytopic, endoplasmic reticulum (ER) membrane protein 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase produces mevalonate, the key intermediate in the synthesis of cholesterol and many nonsterol isoprenoids including geranylgeranyl pyrophosphate (GGpp). Transcriptional, translational, and posttranslational feedback mechanisms converge on this reductase to ensure cells maintain a sufficient supply of essential nonsterol isoprenoids but avoid overaccumulation of cholesterol and other sterols. The focus of this review is mechanisms for the posttranslational regulation of HMG CoA reductase, which include sterol-accelerated ubiquitination and ER-associated degradation (ERAD) that is augmented by GGpp. We discuss how GGpp-induced ER-to-Golgi trafficking of the vitamin K2 synthetic enzyme UbiA prenyltransferase domain-containing protein-1 (UBIAD1) modulates HMG CoA reductase ERAD to balance the synthesis of sterol and nonsterol isoprenoids. We also summarize the characterization of genetically manipulated mice, which established that sterol-accelerated, UBIAD1-modulated ERAD plays a major role in regulation of HMG CoA reductase and cholesterol metabolism in vivo.
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Affiliation(s)
- Marc M Schumacher
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA;
| | - Russell A DeBose-Boyd
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA;
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11
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Erffelinck ML, Ribeiro B, Gryffroy L, Rai A, Pollier J, Goossens A. The Heat Shock Protein 40-Type Chaperone MASH Supports the Endoplasmic Reticulum-Associated Degradation E3 Ubiquitin Ligase MAKIBISHI1 in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:639625. [PMID: 33708234 PMCID: PMC7940691 DOI: 10.3389/fpls.2021.639625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/19/2021] [Indexed: 06/02/2023]
Abstract
Jasmonates (JA) are oxylipin-derived phytohormones that trigger the production of specialized metabolites that often serve in defense against biotic stresses. In Medicago truncatula, a JA-induced endoplasmic reticulum-associated degradation (ERAD)-type machinery manages the production of bioactive triterpenes and thereby secures correct plant metabolism, growth, and development. This machinery involves the conserved RING membrane-anchor (RMA)-type E3 ubiquitin ligase MAKIBISHI1 (MKB1). Here, we discovered two additional members of this protein control apparatus via a yeast-based protein-protein interaction screen and characterized their function. First, a cognate E2 ubiquitin-conjugating enzyme was identified that interacts with MKB1 to deliver activated ubiquitin and to mediate its ubiquitination activity. Second, we identified a heat shock protein 40 (HSP40) that interacts with MKB1 to support its activity and was therefore designated MKB1-supporting HSP40 (MASH). MASH expression was found to be co-regulated with that of MKB1. The presence of MASH is critical for MKB1 and ERAD functioning because the dramatic morphological, transcriptional, and metabolic phenotype of MKB1 knock-down M. truncatula hairy roots was phenocopied by silencing of MASH. Interaction was also observed between the Arabidopsis thaliana (Arabidopsis) homologs of MASH and MKB1, suggesting that MASH represents an essential and plant-specific component of this vital and conserved eukaryotic protein quality control machinery.
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Affiliation(s)
- Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bianca Ribeiro
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lore Gryffroy
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Avanish Rai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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12
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Kang JA, Jeon YJ. How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases. Int J Mol Sci 2021; 22:ijms22042078. [PMID: 33669844 PMCID: PMC7923238 DOI: 10.3390/ijms22042078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.
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Affiliation(s)
- Ji An Kang
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Young Joo Jeon
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Correspondence:
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13
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Abstract
Elimination of membrane proteins often requires recognition of their transmembrane domains (TMDs) in the lipid bilayer. In this issue, Arines et al. (2020. J. Cell Biol.https://doi.org/10.1083/jcb.202001116) show that in Saccharomyces cerevisiae, the vacuole-associated Rsp5 ubiquitin ligase uses a TMD in substrate adaptor Ssh4 to recognize membrane helices in Ypq1, which targets this lysine transporter for lysosomal degradation during lysine starvation.
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Affiliation(s)
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
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14
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Wangeline MA, Hampton RY. An autonomous, but INSIG-modulated, role for the sterol sensing domain in mallostery-regulated ERAD of yeast HMG-CoA reductase. J Biol Chem 2020; 296:100063. [PMID: 33184059 PMCID: PMC7948459 DOI: 10.1074/jbc.ra120.015910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/01/2020] [Accepted: 11/12/2020] [Indexed: 01/23/2023] Open
Abstract
HMG-CoA reductase (HMGR) undergoes feedback-regulated degradation as part of sterol pathway control. Degradation of the yeast HMGR isozyme Hmg2 is controlled by the sterol pathway intermediate GGPP, which causes misfolding of Hmg2, leading to degradation by the HRD pathway; we call this process mallostery. We evaluated the role of the Hmg2 sterol sensing domain (SSD) in mallostery, as well as the involvement of the highly conserved INSIG proteins. We show that the Hmg2 SSD is critical for regulated degradation of Hmg2 and required for mallosteric misfolding of GGPP as studied by in vitro limited proteolysis. The Hmg2 SSD functions independently of conserved yeast INSIG proteins, but its function was modulated by INSIG, thus imposing a second layer of control on Hmg2 regulation. Mutant analyses indicated that SSD-mediated mallostery occurred prior to and independent of HRD-dependent ubiquitination. GGPP-dependent misfolding was still extant but occurred at a much slower rate in the absence of a functional SSD, indicating that the SSD facilitates a physiologically useful rate of GGPP response and implying that the SSD is not a binding site for GGPP. Nonfunctional SSD mutants allowed us to test the importance of Hmg2 quaternary structure in mallostery: a nonresponsive Hmg2 SSD mutant strongly suppressed regulation of a coexpressed, normal Hmg2. Finally, we have found that GGPP-regulated misfolding occurred in detergent-solubilized Hmg2, a feature that will allow next-level analysis of the mechanism of this novel tactic of ligand-regulated misfolding.
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Affiliation(s)
- Margaret A Wangeline
- Division of Biological Sciences, the Section of Cell and Developmental Biology, UCSD, La Jolla, California, USA
| | - Randolph Y Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, UCSD, La Jolla, California, USA.
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15
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Charles KN, Shackelford JE, Faust PL, Fliesler SJ, Stangl H, Kovacs WJ. Functional Peroxisomes Are Essential for Efficient Cholesterol Sensing and Synthesis. Front Cell Dev Biol 2020; 8:560266. [PMID: 33240873 PMCID: PMC7677142 DOI: 10.3389/fcell.2020.560266] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/22/2020] [Indexed: 01/14/2023] Open
Abstract
Cholesterol biosynthesis is a multi-step process involving several subcellular compartments, including peroxisomes. Cells adjust their sterol content by both transcriptional and post-transcriptional feedback regulation, for which sterol regulatory element-binding proteins (SREBPs) are essential; such homeostasis is dysregulated in peroxisome-deficient Pex2 knockout mice. Here, we compared the regulation of cholesterol biosynthesis in Chinese hamster ovary (CHO-K1) cells and in three isogenic peroxisome-deficient CHO cell lines harboring Pex2 gene mutations. Peroxisome deficiency activated expression of cholesterogenic genes, however, cholesterol levels were unchanged. 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) protein levels were increased in mutant cells, whereas HMGCR activity was significantly decreased, resulting in reduced cholesterol synthesis. U18666A, an inhibitor of lysosomal cholesterol export, induced cholesterol biosynthetic enzymes; yet, cholesterol synthesis was still reduced. Interestingly, peroxisome deficiency promoted ER-to-Golgi SREBP cleavage-activating protein (SCAP) trafficking even when cells were cholesterol-loaded. Restoration of functional peroxisomes normalized regulation of cholesterol synthesis and SCAP trafficking. These results highlight the importance of functional peroxisomes for maintaining cholesterol homeostasis and efficient cholesterol synthesis.
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Affiliation(s)
- Khanichi N. Charles
- Department of Biology, San Diego State University, San Diego, CA, United States
| | | | - Phyllis L. Faust
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Steven J. Fliesler
- Departments of Ophthalmology and Biochemistry and Gradate Program in Neuroscience, University at Buffalo-The State University of New York (SUNY), Buffalo, NY, United States
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States
| | - Herbert Stangl
- Department of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Werner J. Kovacs
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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16
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Singh A, Vashistha N, Heck J, Tang X, Wipf P, Brodsky JL, Hampton RY. Direct involvement of Hsp70 ATP hydrolysis in Ubr1-dependent quality control. Mol Biol Cell 2020; 31:2669-2686. [PMID: 32966159 PMCID: PMC7927186 DOI: 10.1091/mbc.e20-08-0541] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Chaperones can mediate both protein folding and degradation. This process is referred to as protein triage, which demands study to reveal mechanisms of quality control for both basic scientific and translational purposes. In yeast, many misfolded proteins undergo chaperone-dependent ubiquitination by the action of the E3 ligases Ubr1 and San1, allowing detailed study of protein triage. In cells, both HSP70 and HSP90 mediated substrate ubiquitination, and the canonical ATP cycle was required for HSP70’s role: we have found that ATP hydrolysis by HSP70, the nucleotide exchange activity of Sse1, and the action of J-proteins are all needed for Ubr1-mediated quality control. To discern whether chaperones were directly involved in Ubr1-mediated ubiquitination, we developed a bead-based assay with covalently immobilized but releasable misfolded protein to obviate possible chaperone effects on substrate physical state or transport. In this in vitro assay, only HSP70 was required, along with its ATPase cycle and relevant cochaperones, for Ubr1-mediated ubiquitination. The requirement for the HSP70 ATP cycle in ubiquitination suggests a possible model of triage in which efficiently folded proteins are spared, while slow-folding or nonfolding proteins are iteratively tagged with ubiquitin for subsequent degradation.
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Affiliation(s)
- Amanjot Singh
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
| | - Nidhi Vashistha
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
| | - Jarrod Heck
- Adaptive Biotechnologies Corp., Seattle, WA 98102
| | - Xin Tang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Randolph Y Hampton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92103
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17
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Neal S, Syau D, Nejatfard A, Nadeau S, Hampton RY. HRD Complex Self-Remodeling Enables a Novel Route of Membrane Protein Retrotranslocation. iScience 2020; 23:101493. [PMID: 32891886 PMCID: PMC7481253 DOI: 10.1016/j.isci.2020.101493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/09/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022] Open
Abstract
ER-associated degradation (ERAD) targets misfolded ER proteins for degradation. Retrotranslocation, a key feature of ERAD, entails removal of ubiquitinated substrates into the cytosol for proteasomal destruction. Recently, it has been shown that the Hrd1 E3 ligase forms a retrotranslocation channel for luminal (ERAD-L) substrates. Conversely, our studies found that integral membrane (ERAD-M) substrates exit the ER through a distinct pathway mediated by the Dfm1 rhomboid protein. Those studies also revealed a second, Hrd1-dependent pathway of ERAD-M retrotranslocation can arise in dfm1Δ null. Here we show that, in the dfm1Δ null, the HRD complex undergoes remodeling to a form that mediates ERAD-M retrotranslocation. Specifically, Hrd1's normally present stochiometric partner Hrd3 is efficiently removed during suppressive remodeling, allowing Hrd1 to function in this novel capacity. Neither Hrd1 autoubiquitination nor its cytosolic domain is required for suppressive ERAD-M retrotranslocation. Thus, the HRD complex displays remarkable functional flexibility in response to ER stress.
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Affiliation(s)
- Sonya Neal
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Della Syau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Anahita Nejatfard
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Samantha Nadeau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Randolph Y Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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18
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Chua NK, Coates HW, Brown AJ. Squalene monooxygenase: a journey to the heart of cholesterol synthesis. Prog Lipid Res 2020; 79:101033. [DOI: 10.1016/j.plipres.2020.101033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
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19
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Hamazaki J, Murata S. ER-Resident Transcription Factor Nrf1 Regulates Proteasome Expression and Beyond. Int J Mol Sci 2020; 21:ijms21103683. [PMID: 32456207 PMCID: PMC7279161 DOI: 10.3390/ijms21103683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Protein folding is a substantively error prone process, especially when it occurs in the endoplasmic reticulum (ER). The highly exquisite machinery in the ER controls secretory protein folding, recognizes aberrant folding states, and retrotranslocates permanently misfolded proteins from the ER back to the cytosol; these misfolded proteins are then degraded by the ubiquitin–proteasome system termed as the ER-associated degradation (ERAD). The 26S proteasome is a multisubunit protease complex that recognizes and degrades ubiquitinated proteins in an ATP-dependent manner. The complex structure of the 26S proteasome requires exquisite regulation at the transcription, translation, and molecular assembly levels. Nuclear factor erythroid-derived 2-related factor 1 (Nrf1; NFE2L1), an ER-resident transcription factor, has recently been shown to be responsible for the coordinated expression of all the proteasome subunit genes upon proteasome impairment in mammalian cells. In this review, we summarize the current knowledge regarding the transcriptional regulation of the proteasome, as well as recent findings concerning the regulation of Nrf1 transcription activity in ER homeostasis and metabolic processes.
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20
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Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA. Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 2020; 368:368/6489/eaaz2449. [PMID: 32327568 DOI: 10.1126/science.aaz2449] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/18/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022]
Abstract
Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD-L is mediated by the Hrd1 complex (composed of Hrd1, Hrd3, Der1, Usa1, and Yos9), but the mechanism of retrotranslocation remains mysterious. Here, we report a structure of the active Hrd1 complex, as determined by cryo-electron microscopy analysis of two subcomplexes. Hrd3 and Yos9 jointly create a luminal binding site that recognizes glycosylated substrates. Hrd1 and the rhomboid-like Der1 protein form two "half-channels" with cytosolic and luminal cavities, respectively, and lateral gates facing one another in a thinned membrane region. These structures, along with crosslinking and molecular dynamics simulation results, suggest how a polypeptide loop of an ERAD-L substrate moves through the ER membrane.
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Affiliation(s)
- Xudong Wu
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marc Siggel
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Sergey Ovchinnikov
- Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Wei Mi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.,Present address: Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Vladimir Svetlov
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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21
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Oikonomou C, Hendershot LM. Disposing of misfolded ER proteins: A troubled substrate's way out of the ER. Mol Cell Endocrinol 2020; 500:110630. [PMID: 31669350 PMCID: PMC6911830 DOI: 10.1016/j.mce.2019.110630] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/19/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022]
Abstract
Secreted, plasma membrane, and resident proteins of the secretory pathway are synthesized in the endoplasmic reticulum (ER) where they undergo post-translational modifications, oxidative folding, and subunit assembly in tightly monitored processes. An ER quality control (ERQC) system oversees protein maturation and ensures that only those reaching their native state will continue trafficking into the secretory pathway to reach their final destinations. Those that fail must be recognized and eliminated to maintain ER homeostasis. Two cellular mechanisms have been identified to rid the ER of terminally unfolded, misfolded, and aggregated proteins. ER-associated degradation (ERAD) was discovered nearly 30 years ago and entails the identification of improperly matured secretory pathway proteins and their retrotranslocation to the cytosol for degradation by the ubiquitin-proteasome system. ER-phagy has been more recently described and caters to larger, more complex proteins and protein aggregates that are not readily handled by ERAD. This pathway has unique upstream components and relies on the same downstream effectors of autophagy used in other cellular processes to deliver clients to lysosomes for degradation. In this review, we describe the main elements of ERQC, ERAD, and ER-phagy and focus on recent advances in these fields.
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Affiliation(s)
- Christina Oikonomou
- St. Jude Children's Research Hospital, Memphis, TN, 38104, USA; The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Linda M Hendershot
- St. Jude Children's Research Hospital, Memphis, TN, 38104, USA; The University of Tennessee Health Science Center, Memphis, TN, USA.
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22
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Chua NK, Brown AJ. Mallostery: Filling a niche between quality and metabolic control. J Biol Chem 2019; 293:14951-14952. [PMID: 30242042 DOI: 10.1074/jbc.h118.005031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To be, or not to be … What determines the destruction of a protein in response to metabolic cues? In the current issue of JBC, Wangeline and Hampton shed new light on this existential question by studying the classic case of HMGCR (Hmg2 in yeast), the rate-limiting step in sterol synthesis, and find a metabolic cue that causes "allosteric misfolding" and subsequent destruction of the protein, a concept they name mallostery.
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Affiliation(s)
- Ngee Kiat Chua
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Andrew J Brown
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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23
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Sun Z, Brodsky JL. Protein quality control in the secretory pathway. J Cell Biol 2019; 218:3171-3187. [PMID: 31537714 PMCID: PMC6781448 DOI: 10.1083/jcb.201906047] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 12/23/2022] Open
Abstract
Protein folding is inherently error prone, especially in the endoplasmic reticulum (ER). Even with an elaborate network of molecular chaperones and protein folding facilitators, misfolding can occur quite frequently. To maintain protein homeostasis, eukaryotes have evolved a series of protein quality-control checkpoints. When secretory pathway quality-control pathways fail, stress response pathways, such as the unfolded protein response (UPR), are induced. In addition, the ER, which is the initial hub of protein biogenesis in the secretory pathway, triages misfolded proteins by delivering substrates to the proteasome or to the lysosome/vacuole through ER-associated degradation (ERAD) or ER-phagy. Some misfolded proteins escape the ER and are instead selected for Golgi quality control. These substrates are targeted for degradation after retrieval to the ER or delivery to the lysosome/vacuole. Here, we discuss how these guardian pathways function, how their activities intersect upon induction of the UPR, and how decisions are made to dispose of misfolded proteins in the secretory pathway.
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Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
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24
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Needham PG, Guerriero CJ, Brodsky JL. Chaperoning Endoplasmic Reticulum-Associated Degradation (ERAD) and Protein Conformational Diseases. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033928. [PMID: 30670468 DOI: 10.1101/cshperspect.a033928] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Misfolded proteins compromise cellular homeostasis. This is especially problematic in the endoplasmic reticulum (ER), which is a high-capacity protein-folding compartment and whose function requires stringent protein quality-control systems. Multiprotein complexes in the ER are able to identify, remove, ubiquitinate, and deliver misfolded proteins to the 26S proteasome for degradation in the cytosol, and these events are collectively termed ER-associated degradation, or ERAD. Several steps in the ERAD pathway are facilitated by molecular chaperone networks, and the importance of ERAD is highlighted by the fact that this pathway is linked to numerous protein conformational diseases. In this review, we discuss the factors that constitute the ERAD machinery and detail how each step in the pathway occurs. We then highlight the underlying pathophysiology of protein conformational diseases associated with ERAD.
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Affiliation(s)
- Patrick G Needham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | | | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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25
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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26
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Abstract
Elimination of misfolded proteins by endoplasmic reticulum (ER)-associated protein degradation (ERAD) ensures that proteins proceeding through the secretory pathway are correctly folded and processed, which is critical to minimize ER stress. All ERAD pathways include a protein translocation process termed retrotranslocation, in which ubiquitinated misfolded substrates are extracted from the ER and degraded by the cytosolic 26S proteasome. Despite being integral to ERAD, the retrotranslocation process has been largely obscure. Recently, an explosion of discoveries has provided key mechanistic insights into this novel route of protein transport. These advances were facilitated by the development of in vitro and in vivo assays that utilize components from the yeast Saccharomyces cerevisiae. The assays permit detailed study of the distinct steps in ERAD-linked retrotranslocation, including ubiquitination of selected ERAD substrates, substrate removal from the ER, maintenance of cytosolic substrate solubility in the cytosol, and substrate degradation. Here we provide detailed protocols for these assays that pertain to work on retrotranslocation of integral membrane proteins (ERAD-M substrates), with the expectation that these approaches can be adapted for many related biochemical processes.
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Affiliation(s)
- Sonya Neal
- Division of Biological Sciences, The Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, United States.
| | - Sascha H Duttke
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Randolph Y Hampton
- Division of Biological Sciences, The Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, United States
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27
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Menzies SA, Volkmar N, van den Boomen DJH, Timms RT, Dickson AS, Nathan JA, Lehner PJ. The sterol-responsive RNF145 E3 ubiquitin ligase mediates the degradation of HMG-CoA reductase together with gp78 and Hrd1. eLife 2018; 7:e40009. [PMID: 30543180 PMCID: PMC6292692 DOI: 10.7554/elife.40009] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/19/2018] [Indexed: 02/02/2023] Open
Abstract
Mammalian HMG-CoA reductase (HMGCR), the rate-limiting enzyme of the cholesterol biosynthetic pathway and the therapeutic target of statins, is post-transcriptionally regulated by sterol-accelerated degradation. Under cholesterol-replete conditions, HMGCR is ubiquitinated and degraded, but the identity of the E3 ubiquitin ligase(s) responsible for mammalian HMGCR turnover remains controversial. Using systematic, unbiased CRISPR/Cas9 genome-wide screens with a sterol-sensitive endogenous HMGCR reporter, we comprehensively map the E3 ligase landscape required for sterol-accelerated HMGCR degradation. We find that RNF145 and gp78 independently co-ordinate HMGCR ubiquitination and degradation. RNF145, a sterol-responsive ER-resident E3 ligase, is unstable but accumulates following sterol depletion. Sterol addition triggers RNF145 recruitment to HMGCR via Insigs, promoting HMGCR ubiquitination and proteasome-mediated degradation. In the absence of both RNF145 and gp78, Hrd1, a third UBE2G2-dependent E3 ligase, partially regulates HMGCR activity. Our findings reveal a critical role for the sterol-responsive RNF145 in HMGCR regulation and elucidate the complexity of sterol-accelerated HMGCR degradation. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Sam A Menzies
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Norbert Volkmar
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | | | - Richard T Timms
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Anna S Dickson
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - James A Nathan
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Paul J Lehner
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
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28
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Jiang H, Lin L, Tang W, Chen X, Zheng Q, Huang J, Yang T, Su L, Dong Y, Wang B, Wang Z. Putative Interaction Proteins of the Ubiquitin Ligase Hrd1 in Magnaporthe oryzae. Evol Bioinform Online 2018; 14:1176934318810990. [PMID: 30559593 PMCID: PMC6291861 DOI: 10.1177/1176934318810990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022] Open
Abstract
The endoplasmic reticulum (ER) is the entry portal of the conventional secretory pathway where the newly synthesized polypeptides fold, modify, and assemble. The ER responses to the unfolded proteins in its lumen (ER stress) by triggering intracellular signal transduction pathways include the ER-associated degradation (ERAD) pathway and the unfolded protein response (UPR) pathway. In yeast and mammals, the ubiquitin ligase Hrd1 is indispensable for the ERAD pathway, and also Hrd1-mediated ERAD pathway plays a crucial role in maintaining homeostasis and metabolism of human beings. However, the underlying physiological roles and regulatory mechanism of the Hrd1-involved ERAD pathway in the plant pathogenic fungi are still unclear. Here, we identified the Hrd1 orthologous proteins from 9 different fungi and noticed that these Hrd1 orthologs are conserved. Through identification of MoHrd1 putative interacting proteins by co-immunoprecipitation assays and enrichment analysis, we found that MoHrd1 is involved in the secretory pathway, energy synthesis, and metabolism. Taken together, our results suggest that MoHrd1 is conserved among fungi and play an important role in cellular metabolism and infection-related development. Our finding helps uncover the mechanism of Hrd1-involved ERAD pathway in fungi and sheds a new light to understand the pathogenic mechanism of Magnaporthe oryzae.
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Affiliation(s)
- Haolang Jiang
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Lianyu Lin
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Life Sciences, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Wei Tang
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Xuehang Chen
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Qiaojia Zheng
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Jun Huang
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Tao Yang
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Li Su
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | | | - Baohua Wang
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
| | - Zonghua Wang
- Fujian University Key Laboratory for
Plant-Microbe Interaction and College of Plant Protection, Fujian Agriculture and
Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang
University, Fuzhou, China
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29
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Clausen L, Abildgaard AB, Gersing SK, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Protein stability and degradation in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:61-83. [PMID: 30635086 DOI: 10.1016/bs.apcsb.2018.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cellular proteome performs highly varied functions to sustain life. Since most of these functions require proteins to fold properly, they can be impaired by mutations that affect protein structure, leading to diseases such as Alzheimer's disease, cystic fibrosis, and Lynch syndrome. The cell has evolved an intricate protein quality control (PQC) system that includes degradation pathways and a multitude of molecular chaperones and co-chaperones, all working together to catalyze the refolding or removal of aberrant proteins. Thus, the PQC system limits the harmful consequences of dysfunctional proteins, including those arising from disease-causing mutations. This complex system is still not fully understood. In particular the structural and sequence motifs that, when exposed, trigger degradation of misfolded proteins are currently under investigation. Moreover, several attempts are being made to activate or inhibit parts of the PQC system as a treatment for diseases. Here, we briefly review the present knowledge on the PQC system and list current strategies that are employed to exploit the system in disease treatment.
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Affiliation(s)
- Lene Clausen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah K Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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30
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Wangeline MA, Hampton RY. "Mallostery"-ligand-dependent protein misfolding enables physiological regulation by ERAD. J Biol Chem 2018; 293:14937-14950. [PMID: 30018140 DOI: 10.1074/jbc.ra118.001808] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
HMG-CoA reductase (HMGR) undergoes regulated degradation as part of feedback control of the sterol pathway. In yeast, the stability of the HMGR isozyme Hmg2 is controlled by the 20-carbon isoprenoid geranylgeranyl pyrophosphate (GGPP). Increasing GGPP levels cause more efficient degradation by the HMG-CoA reductase degradation (HRD) pathway, allowing for feedback regulation of HMGR. The HRD pathway is critical for the endoplasmic reticulum (ER)-associated degradation (ERAD) of misfolded ER proteins. Here, we have explored GGPP's role in HRD-dependent Hmg2 degradation. We found that GGPP potently regulates Hmg2 levels in vivo and causes reversible Hmg2 misfolding at nanomolar concentrations in vitro These GGPP-mediated effects were absent in several stabilized or nonregulated Hmg2 mutants. Consistent with its high potency, GGPP's effects were highly specific such that other structurally related molecules were ineffective in altering Hmg2 structure. For instance, two closely related GGPP analogues, 2F-GGPP and GGSPP, were completely inactive at all concentrations tested. Furthermore, GGSPP antagonized GGPP's effects in vivo and in vitro Chemical chaperones reversed GGPP's effects on Hmg2 structure and degradation, suggesting that GGPP causes selective Hmg2 misfolding. These results indicate that GGPP functions in a manner similar to an allosteric ligand, causing Hmg2 misfolding through interaction with a reversible, specific binding site. Consistent with this, the Hmg2 protein formed multimers, typical of allosteric proteins. We propose that this "allosteric misfolding," or mallostery, observed here for Hmg2 may be a widely used tactic of biological regulation with potential for development of therapeutic small molecules that induce selective misfolding.
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Affiliation(s)
- Margaret A Wangeline
- From the Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
| | - Randolph Y Hampton
- From the Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
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