1
|
Guay KP, Chou WC, Canniff NP, Paul KB, Hebert DN. N-glycan-dependent protein maturation and quality control in the ER. Nat Rev Mol Cell Biol 2025:10.1038/s41580-025-00855-y. [PMID: 40389697 DOI: 10.1038/s41580-025-00855-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2025] [Indexed: 05/21/2025]
Abstract
The vast majority of proteins that traverse the mammalian secretory pathway become N-glycosylated in the endoplasmic reticulum (ER). The bulky glycan protein modifications, which are conserved in fungi and humans, act as maturation and quality-control tags. In this Review, we discuss findings published in the past decade that have rapidly expanded our understanding of the transfer and processing of N-glycans, as well as their role in protein maturation, quality control and trafficking in the ER, facilitated by structural insights into the addition of N-glycans by the oligosaccharyltransferases A and B (OST-A and OST-B). These findings suggest that N-glycans serve as reporters of the folding status of secretory proteins as they traverse the ER, enabling the lectin chaperones to guide their maturation. We also explore how the emergence of co-translational glycosylation and the expansion of the glycoproteostasis network in metazoans has expanded the role of N-glycans in early protein-maturation events and quality control.
Collapse
Affiliation(s)
- Kevin P Guay
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA.
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
| | - Wen-Chuan Chou
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Nathan P Canniff
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Kylie B Paul
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Daniel N Hebert
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|
2
|
Ninagawa S, Matsuo M, Ying D, Oshita S, Aso S, Matsushita K, Taniguchi M, Fueki A, Yamashiro M, Sugasawa K, Saito S, Imami K, Kizuka Y, Sakuma T, Yamamoto T, Yagi H, Kato K, Mori K. UGGT1-mediated reglucosylation of N-glycan competes with ER-associated degradation of unstable and misfolded glycoproteins. eLife 2024; 12:RP93117. [PMID: 39654396 PMCID: PMC11630818 DOI: 10.7554/elife.93117] [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] [Indexed: 12/12/2024] Open
Abstract
How the fate (folding versus degradation) of glycoproteins is determined in the endoplasmic reticulum (ER) is an intriguing question. Monoglucosylated glycoproteins are recognized by lectin chaperones to facilitate their folding, whereas glycoproteins exposing well-trimmed mannoses are subjected to glycoprotein ER-associated degradation (gpERAD); we have elucidated how mannoses are sequentially trimmed by EDEM family members (George et al., 2020; 2021 eLife). Although reglucosylation by UGGT was previously reported to have no effect on substrate degradation, here we directly tested this notion using cells with genetically disrupted UGGT1/2. Strikingly, the results showed that UGGT1 delayed the degradation of misfolded substrates and unstable glycoproteins including ATF6α. An experiment with a point mutant of UGGT1 indicated that the glucosylation activity of UGGT1 was required for the inhibition of early glycoprotein degradation. These and overexpression-based competition experiments suggested that the fate of glycoproteins is determined by a tug-of-war between structure formation by UGGT1 and degradation by EDEMs. We further demonstrated the physiological importance of UGGT1, since ATF6α cannot function properly without UGGT1. Thus, our work strongly suggests that UGGT1 is a central factor in ER protein quality control via the regulation of both glycoprotein folding and degradation.
Collapse
Affiliation(s)
- Satoshi Ninagawa
- Biosignal Research Center, Kobe UniversityKobeJapan
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe UniversityKobeJapan
| | - Masaki Matsuo
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe UniversityKobeJapan
| | - Deng Ying
- Department of Biophysics, Graduate School of Science, Kyoto UniversityKyotoJapan
| | - Shuichiro Oshita
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe UniversityKobeJapan
| | - Shinya Aso
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe UniversityKobeJapan
| | - Kazutoshi Matsushita
- Department of Biophysics, Graduate School of Science, Kyoto UniversityKyotoJapan
| | - Mai Taniguchi
- Department of Biophysics, Graduate School of Science, Kyoto UniversityKyotoJapan
| | - Akane Fueki
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe UniversityKobeJapan
| | - Moe Yamashiro
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe UniversityKobeJapan
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe UniversityKobeJapan
- Graduate School of Science, Kobe UniversityKobeJapan
| | - Shunsuke Saito
- Department of Biophysics, Graduate School of Science, Kyoto UniversityKyotoJapan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Yasuhiko Kizuka
- Laboratory of Glycobiochemistry, Institute for Glyco-core Research (iGCORE), Gifu UniversityGifuJapan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima UniversityHiroshimaJapan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima UniversityHiroshimaJapan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City UniversityNagoyaJapan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural SciencesOkazakiJapan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City UniversityNagoyaJapan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural SciencesOkazakiJapan
- Institute for Molecular Science (IMS), National Institutes of Natural SciencesOkazakiJapan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto UniversityKyotoJapan
- Institute for Advanced Study, Kyoto UniversityKyotoJapan
| |
Collapse
|
3
|
Lu Y, Zhou J, Wang H, Gao H, Ning E, Shao Z, Hao Y, Yang X. Endoplasmic reticulum stress-mediated apoptosis and autophagy in osteoarthritis: From molecular mechanisms to therapeutic applications. Cell Stress Chaperones 2024; 29:805-830. [PMID: 39571722 DOI: 10.1016/j.cstres.2024.11.005] [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: 09/04/2024] [Revised: 11/08/2024] [Accepted: 11/16/2024] [Indexed: 12/09/2024] Open
Abstract
Osteoarthritis (OA) is characterized primarily by the degeneration of articular cartilage, with a high prevalence and disability rate. The functional phenotype of chondrocytes, as the sole cell type within cartilage, is vital for OA progression. Due to the avascular nature of cartilage and its limited regenerative capacity, repair following injury poses significant challenges. Various cellular stressors, including hypoxia, nutrient deprivation, oxidative stress, and collagen mutations, can lead to the accumulation of misfolded proteins in the endoplasmic reticulum (ER), resulting in ER stress (ERS). In response to restore ER homeostasis as well as cellular vitality and function, a series of adaptive mechanisms are triggered, including the unfolded protein response, ER-associated degradation, and ER-phagy. Prolonged or severe ERS may exceed the adaptive capacity of cells, leading to dysregulation in apoptosis and autophagy-key pathogenic factors contributing to chondrocyte damage and OA progression. This review examines the relationship between ERS in OA chondrocytes and both apoptosis and autophagy in order to identify potential therapeutic targets and strategies for prevention and treatment of OA.
Collapse
Affiliation(s)
- Yifan Lu
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China
| | - Jing Zhou
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China
| | - Hong Wang
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China
| | - Hua Gao
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China
| | - Eryu Ning
- Gusu School, Nanjing Medical University, Suzhou, PR China; Department of Sports Rehabilitation, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China
| | - Zhiqiang Shao
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China
| | - Yuefeng Hao
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China.
| | - Xing Yang
- Orthopedics and Sports Medicine Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, PR China; Gusu School, Nanjing Medical University, Suzhou, PR China.
| |
Collapse
|
4
|
Hendershot LM, Buck TM, Brodsky JL. The Essential Functions of Molecular Chaperones and Folding Enzymes in Maintaining Endoplasmic Reticulum Homeostasis. J Mol Biol 2024; 436:168418. [PMID: 38143019 PMCID: PMC12015986 DOI: 10.1016/j.jmb.2023.168418] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
It has been estimated that up to one-third of the proteins encoded by the human genome enter the endoplasmic reticulum (ER) as extended polypeptide chains where they undergo covalent modifications, fold into their native structures, and assemble into oligomeric protein complexes. The fidelity of these processes is critical to support organellar, cellular, and organismal health, and is perhaps best underscored by the growing number of disease-causing mutations that reduce the fidelity of protein biogenesis in the ER. To meet demands encountered by the diverse protein clientele that mature in the ER, this organelle is populated with a cadre of molecular chaperones that prevent protein aggregation, facilitate protein disulfide isomerization, and lower the activation energy barrier of cis-trans prolyl isomerization. Components of the lectin (glycan-binding) chaperone system also reside within the ER and play numerous roles during protein biogenesis. In addition, the ER houses multiple homologs of select chaperones that can recognize and act upon diverse peptide signatures. Moreover, redundancy helps ensure that folding-compromised substrates are unable to overwhelm essential ER-resident chaperones and enzymes. In contrast, the ER in higher eukaryotic cells possesses a single member of the Hsp70, Hsp90, and Hsp110 chaperone families, even though several homologs of these molecules reside in the cytoplasm. In this review, we discuss specific functions of the many factors that maintain ER quality control, highlight some of their interactions, and describe the vulnerabilities that arise from the absence of multiple members of some chaperone families.
Collapse
Affiliation(s)
- Linda M Hendershot
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
| | - Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| |
Collapse
|
5
|
Mu W, Zhi Y, Zhou J, Wang C, Chai K, Fan Z, Lv G. Endoplasmic reticulum stress and quality control in relation to cisplatin resistance in tumor cells. Front Pharmacol 2024; 15:1419468. [PMID: 38948460 PMCID: PMC11211601 DOI: 10.3389/fphar.2024.1419468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024] Open
Abstract
The endoplasmic reticulum (ER) is a crucial organelle that orchestrates key cellular functions like protein folding and lipid biosynthesis. However, it is highly sensitive to disturbances that lead to ER stress. In response, the unfolded protein response (UPR) activates to restore ER homeostasis, primarily through three sensors: IRE1, ATF6, and PERK. ERAD and autophagy are crucial in mitigating ER stress, yet their dysregulation can lead to the accumulation of misfolded proteins. Cisplatin, a commonly used chemotherapy drug, induces ER stress in tumor cells, activating complex signaling pathways. Resistance to cisplatin stems from reduced drug accumulation, activation of DNA repair, and anti-apoptotic mechanisms. Notably, cisplatin-induced ER stress can dualistically affect tumor cells, promoting either survival or apoptosis, depending on the context. ERAD is crucial for degrading misfolded proteins, whereas autophagy can protect cells from apoptosis or enhance ER stress-induced apoptosis. The complex interaction between ER stress, cisplatin resistance, ERAD, and autophagy opens new avenues for cancer treatment. Understanding these processes could lead to innovative strategies that overcome chemoresistance, potentially improving outcomes of cisplatin-based cancer treatments. This comprehensive review provides a multifaceted perspective on the complex mechanisms of ER stress, cisplatin resistance, and their implications in cancer therapy.
Collapse
Affiliation(s)
| | | | | | | | | | - Zhongqi Fan
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|
6
|
Katsuki R, Kanuka M, Ohta R, Yoshida S, Tamura T. Turnover of EDEM1, an ERAD-enhancing factor, is mediated by multiple degradation routes. Genes Cells 2024; 29:486-502. [PMID: 38682256 PMCID: PMC11163939 DOI: 10.1111/gtc.13117] [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: 11/09/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 05/01/2024]
Abstract
Quality-based protein production and degradation in the endoplasmic reticulum (ER) are essential for eukaryotic cell survival. During protein maturation in the ER, misfolded or unassembled proteins are destined for disposal through a process known as ER-associated degradation (ERAD). EDEM1 is an ERAD-accelerating factor whose gene expression is upregulated by the accumulation of aberrant proteins in the ER, known as ER stress. Although the role of EDEM1 in ERAD has been studied in detail, the turnover of EDEM1 by intracellular degradation machinery, including the proteasome and autophagy, is not well understood. To clarify EDEM1 regulation in the protein level, degradation mechanism of EDEM1 was examined. Our results indicate that both ERAD and autophagy degrade EDEM1 alike misfolded degradation substrates, although each degradation machinery targets EDEM1 in different folded states of proteins. We also found that ERAD factors, including the SEL1L/Hrd1 complex, YOD1, XTP3B, ERdj3, VIMP, BAG6, and JB12, but not OS9, are involved in EDEM1 degradation in a mannose-trimming-dependent and -independent manner. Our results suggest that the ERAD accelerating factor, EDEM1, is turned over by the ERAD itself, similar to ERAD clients.
Collapse
Affiliation(s)
- Riko Katsuki
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Mai Kanuka
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Ren Ohta
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Shusei Yoshida
- Department of Life Science, Faculty of Engineering ScienceAkita UniversityAkitaJapan
| | - Taku Tamura
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
- Department of Life Science, Faculty of Engineering ScienceAkita UniversityAkitaJapan
- Present address:
Biococoon Laboratories Inc.4‐3‐5, UedaMoriokaJapan
| |
Collapse
|
7
|
Sarkar R, Chhabra S, Tanwar M, Agarwal N, Kalia M. Japanese encephalitis virus hijacks ER-associated degradation regulators for its replication. J Gen Virol 2024; 105. [PMID: 38787366 DOI: 10.1099/jgv.0.001995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
Flaviviruses target their replication on membranous structures derived from the ER, where both viral and host proteins play crucial structural and functional roles. Here, we have characterized the involvement of the ER-associated degradation (ERAD) pathway core E3 ligase complex (SEL1L-HRD1) regulator proteins in the replication of Japanese encephalitis virus (JEV). Through high-resolution immunofluorescence imaging of JEV-infected HeLa cells, we observe that the virus replication complexes marked by NS1 strongly colocalize with the ERAD adapter SEL1L, lectin OS9, ER-membrane shuttle factor HERPUD1, E3 ubiquitin ligase HRD1 and rhomboid superfamily member DERLIN1. NS5 positive structures also show strong overlap with SEL1L. While these effectors show significant transcriptional upregulation, their protein levels remain largely stable in infected cells. siRNA mediated depletion of OS9, SEL1L, HERPUD1 and HRD1 significantly inhibit viral RNA replication and titres, with SEL1L depletion showing the maximum attenuation of replication. By performing protein translation arrest experiments, we show that SEL1L, and OS9 are stabilised upon JEV infection. Overall results from this study suggest that these ERAD effector proteins are crucial host-factors for JEV replication.
Collapse
Affiliation(s)
- Riya Sarkar
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
- Centre for Tuberculosis Research, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
- Present address: Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Simran Chhabra
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Mukesh Tanwar
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Nisheeth Agarwal
- Centre for Tuberculosis Research, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Manjula Kalia
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| |
Collapse
|
8
|
Lin LL, Wang HH, Pederson B, Wei X, Torres M, Lu Y, Li ZJ, Liu X, Mao H, Wang H, Zhou LE, Zhao Z, Sun S, Qi L. SEL1L-HRD1 interaction is required to form a functional HRD1 ERAD complex. Nat Commun 2024; 15:1440. [PMID: 38365914 PMCID: PMC10873344 DOI: 10.1038/s41467-024-45633-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
The SEL1L-HRD1 protein complex represents the most conserved branch of endoplasmic reticulum (ER)-associated degradation (ERAD). Despite recent advances in both mouse models and humans, in vivo evidence for the importance of SEL1L in the ERAD complex formation and its (patho-)physiological relevance in mammals remains limited. Here we report that SEL1L variant p.Ser658Pro (SEL1LS658P) is a pathogenic hypomorphic mutation, causing partial embryonic lethality, developmental delay, and early-onset cerebellar ataxia in homozygous mice carrying the bi-allelic variant. Biochemical analyses reveal that SEL1LS658P variant not only reduces the protein stability of SEL1L, but attenuates the SEL1L-HRD1 interaction, likely via electrostatic repulsion between SEL1L F668 and HRD1 Y30 residues. Proteomic screens of SEL1L and HRD1 interactomes reveal that SEL1L-HRD1 interaction is a prerequisite for the formation of a functional HRD1 ERAD complex, as SEL1L is required for the recruitment of E2 enzyme UBE2J1 as well as DERLIN to HRD1. These data not only establish the disease relevance of SEL1L-HRD1 ERAD, but also provide additional insight into the formation of a functional HRD1 ERAD complex.
Collapse
Affiliation(s)
- Liangguang Leo Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Huilun Helen Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Brent Pederson
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Xiaoqiong Wei
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Mauricio Torres
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - You Lu
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Zexin Jason Li
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Xiaodan Liu
- Zilkha Neurogenetic Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90033, USA
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Hancheng Mao
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Hui Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Linyao Elina Zhou
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Zhen Zhao
- Zilkha Neurogenetic Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90033, USA
| | - Shengyi Sun
- Department of Pharmacology, University of Virginia, School of Medicine, Charlottesville, VA, 22908, USA.
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA.
| |
Collapse
|
9
|
Wei X, Lu Y, Lin LL, Zhang C, Chen X, Wang S, Wu SA, Li ZJ, Quan Y, Sun S, Qi L. Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis. Nat Commun 2024; 15:659. [PMID: 38253565 PMCID: PMC10803770 DOI: 10.1038/s41467-024-44948-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) plays indispensable roles in many physiological processes; however, the nature of endogenous substrates remains largely elusive. Here we report a proteomics strategy based on the intrinsic property of the SEL1L-HRD1 ERAD complex to identify endogenous ERAD substrates both in vitro and in vivo. Following stringent filtering using a machine learning algorithm, over 100 high-confidence potential substrates are identified in human HEK293T and mouse brown adipose tissue, among which ~88% are cell type-specific. One of the top shared hits is the catalytic subunit of the glycosylphosphatidylinositol (GPI)-transamidase complex, PIGK. Indeed, SEL1L-HRD1 ERAD attenuates the biogenesis of GPI-anchored proteins by specifically targeting PIGK for proteasomal degradation. Lastly, several PIGK disease variants in inherited GPI deficiency disorders are also SEL1L-HRD1 ERAD substrates. This study provides a platform and resources for future effort to identify proteome-wide endogenous substrates in vivo, and implicates SEL1L-HRD1 ERAD in many cellular processes including the biogenesis of GPI-anchored proteins.
Collapse
Affiliation(s)
- Xiaoqiong Wei
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - You Lu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Liangguang Leo Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Xinxin Chen
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Siwen Wang
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Shuangcheng Alivia Wu
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Zexin Jason Li
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Yujun Quan
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Shengyi Sun
- Department of Pharmacology, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, 22903, USA.
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA.
| |
Collapse
|
10
|
Wang HH, Lin LL, Li ZJ, Wei X, Askander O, Cappuccio G, Hashem MO, Hubert L, Munnich A, Alqahtani M, Pang Q, Burmeister M, Lu Y, Poirier K, Besmond C, Sun S, Brunetti-Pierri N, Alkuraya FS, Qi L. Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders. J Clin Invest 2024; 134:e170054. [PMID: 37943610 PMCID: PMC10786691 DOI: 10.1172/jci170054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Recent studies using cell type-specific knockout mouse models have improved our understanding of the pathophysiological relevance of suppressor of lin-12-like-HMG-CoA reductase degradation 1 (SEL1L-HRD1) endoplasmic reticulum-associated (ER-associated) degradation (ERAD); however, its importance in humans remains unclear, as no disease variant has been identified. Here, we report the identification of 3 biallelic missense variants of SEL1L and HRD1 (or SYVN1) in 6 children from 3 independent families presenting with developmental delay, intellectual disability, microcephaly, facial dysmorphisms, hypotonia, and/or ataxia. These SEL1L (p.Gly585Asp, p.Met528Arg) and HRD1 (p.Pro398Leu) variants were hypomorphic and impaired ERAD function at distinct steps of ERAD, including substrate recruitment (SEL1L p.Gly585Asp), SEL1L-HRD1 complex formation (SEL1L p.Met528Arg), and HRD1 activity (HRD1 p.Pro398Leu). Our study not only provides insights into the structure-function relationship of SEL1L-HRD1 ERAD, but also establishes the importance of SEL1L-HRD1 ERAD in humans.
Collapse
Affiliation(s)
- Huilun H. Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Liangguang L. Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Zexin J. Li
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Xiaoqiong Wei
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Omar Askander
- Hopital Cheik Zaïd, Hopital Universitaire International RABAT, Morocco
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Mais O. Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Laurence Hubert
- Imagine Institute, INSERM UMR1163, Paris, France
- Université Paris Cité, Paris, France
| | | | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Margit Burmeister
- Michigan Neuroscience Institute and Departments of Computational Medicine & Bioinformatics, Psychiatry, and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - You Lu
- Department of Molecular & Integrative Physiology and
| | | | | | - Shengyi Sun
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
11
|
Christianson JC, Jarosch E, Sommer T. Mechanisms of substrate processing during ER-associated protein degradation. Nat Rev Mol Cell Biol 2023; 24:777-796. [PMID: 37528230 DOI: 10.1038/s41580-023-00633-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 08/03/2023]
Abstract
Maintaining proteome integrity is essential for long-term viability of all organisms and is overseen by intrinsic quality control mechanisms. The secretory pathway of eukaryotes poses a challenge for such quality assurance as proteins destined for secretion enter the endoplasmic reticulum (ER) and become spatially segregated from the cytosolic machinery responsible for disposal of aberrant (misfolded or otherwise damaged) or superfluous polypeptides. The elegant solution provided by evolution is ER-membrane-bound ubiquitylation machinery that recognizes misfolded or surplus proteins or by-products of protein biosynthesis in the ER and delivers them to 26S proteasomes for degradation. ER-associated protein degradation (ERAD) collectively describes this specialized arm of protein quality control via the ubiquitin-proteasome system. But, instead of providing a single strategy to remove defective or unwanted proteins, ERAD represents a collection of independent processes that exhibit distinct yet overlapping selectivity for a wide range of substrates. Not surprisingly, ER-membrane-embedded ubiquitin ligases (ER-E3s) act as central hubs for each of these separate ERAD disposal routes. In these processes, ER-E3s cooperate with a plethora of specialized factors, coordinating recognition, transport and ubiquitylation of undesirable secretory, membrane and cytoplasmic proteins. In this Review, we focus on substrate processing during ERAD, highlighting common threads as well as differences between the many routes via ERAD.
Collapse
Affiliation(s)
- John C Christianson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
| | - Ernst Jarosch
- Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany
| | - Thomas Sommer
- Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
12
|
Chen S, Wang Q, Wang H, Xia S. Endoplasmic reticulum stress in T cell-mediated diseases. Scand J Immunol 2023; 98:e13307. [PMID: 38441291 DOI: 10.1111/sji.13307] [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: 01/17/2023] [Revised: 05/23/2023] [Accepted: 06/18/2023] [Indexed: 03/07/2024]
Abstract
T cells synthesize a large number of proteins during their development, activation, and differentiation. The build-up of misfolded and unfolded proteins in the endoplasmic reticulum, however, causes endoplasmic reticulum (ER) stress. Thus, T cells can maintain ER homeostasis via endoplasmic reticulum-associated degradation, unfolded protein response, and autophagy. In T cell-mediated diseases, such as rheumatoid arthritis, systemic lupus erythematosus, Sjogren's syndrome, type 1 diabetes and vitiligo, ER stress caused by changes in the internal microenvironment can cause disease progression by affecting T cell homeostasis. This review discusses ER stress in T cell formation, activation, differentiation, and T cell-mediated illnesses, and may offer new perspectives on the involvement of T cells in autoimmune disorders and cancer.
Collapse
Affiliation(s)
- Shaodan Chen
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Qiulei Wang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hui Wang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Sheng Xia
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| |
Collapse
|
13
|
Badawi S, Mohamed FE, Varghese DS, Ali BR. Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models. Traffic 2023; 24:312-333. [PMID: 37188482 DOI: 10.1111/tra.12902] [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: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.
Collapse
Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
| |
Collapse
|
14
|
Scavone F, Gumbin S, Da Rosa P, Kopito R. RPL26/uL24 UFMylation is essential for ribosome-associated quality control at the endoplasmic reticulum. Proc Natl Acad Sci U S A 2023; 120:e2220340120. [PMID: 37036982 PMCID: PMC10120006 DOI: 10.1073/pnas.2220340120] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
Ribosomes that stall while translating cytosolic proteins are incapacitated by incomplete nascent chains, termed "arrest peptides" (APs) that are destroyed by the ubiquitin proteasome system (UPS) via a process known as the ribosome-associated quality control (RQC) pathway. By contrast, APs on ribosomes that stall while translocating secretory proteins into the endoplasmic reticulum (ER-APs) are shielded from cytosol by the ER membrane and the tightly sealed ribosome-translocon junction (RTJ). How this junction is breached to enable access of cytosolic UPS machinery and 26S proteasomes to translocon- and ribosome-obstructing ER-APs is not known. Here, we show that UPS and RQC-dependent degradation of ER-APs strictly requires conjugation of the ubiquitin-like (Ubl) protein UFM1 to 60S ribosomal subunits at the RTJ. Therefore, UFMylation of translocon-bound 60S subunits modulates the RTJ to promote access of proteasomes and RQC machinery to ER-APs.
Collapse
Affiliation(s)
| | - Samantha C. Gumbin
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Paul A. Da Rosa
- Department of Biology, Stanford University, Stanford, CA94305
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA94305
| |
Collapse
|
15
|
Erzurumlu Y, Catakli D, Dogan HK. Circadian Oscillation Pattern of Endoplasmic Reticulum Quality Control (ERQC) Components in Human Embryonic Kidney HEK293 Cells. J Circadian Rhythms 2023; 21:1. [PMID: 37033333 PMCID: PMC10077977 DOI: 10.5334/jcr.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
The circadian clock regulates the “push-pull” of the molecular signaling mechanisms that arrange the rhythmic organization of the physiology to maintain cellular homeostasis. In mammals, molecular clock genes tightly arrange cellular rhythmicity. It has been shown that this circadian clock optimizes various biological processes, including the cell cycle and autophagy. Hence, we explored the dynamic crosstalks between the circadian rhythm and endoplasmic reticulum (ER)-quality control (ERQC) mechanisms. ER-associated degradation (ERAD) is one of the most important parts of the ERQC system and is an elaborate surveillance system that eliminates misfolded proteins. It regulates the steady-state levels of several physiologically crucial proteins, such as 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) and the metastasis suppressor KAI1/CD82. However, the circadian oscillation of ERQC members and their roles in cellular rhythmicity requires further investigation. In the present study, we provided a thorough investigation of the circadian rhythmicity of the fifteen crucial ERQC members, including gp78, Hrd1, p97/VCP, SVIP, Derlin1, Ufd1, Npl4, EDEM1, OS9, XTP3B, Sel1L, Ufd2, YOD1, VCIP135 and FAM8A1 in HEK293 cells. We found that mRNA and protein accumulation of the ubiquitin conjugation, binding and processing factors, retrotranslocation-dislocation, substrate recognition and targeting components of ERQC exhibit oscillation under the control of the circadian clock. Moreover, we found that Hrd1 and gp78 have a possible regulatory function on Bmal1 turnover. The findings of the current study indicated that the expression level of ERQC components is fine-tuned by the circadian clock and major ERAD E3 ligases, Hrd1 and gp78, may influence the regulation of circadian oscillation by modulation of Bmal1 stability.
Collapse
|
16
|
Gugliandolo A, Blando S, Salamone S, Caprioglio D, Pollastro F, Mazzon E, Chiricosta L. Δ8-THC Protects against Amyloid Beta Toxicity Modulating ER Stress In Vitro: A Transcriptomic Analysis. Int J Mol Sci 2023; 24:ijms24076598. [PMID: 37047608 PMCID: PMC10095455 DOI: 10.3390/ijms24076598] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Alzheimer’s disease (AD) represents the most common form of dementia, characterized by amyloid β (Aβ) plaques and neurofibrillary tangles (NFTs). It is characterized by neuroinflammation, the accumulation of misfolded protein, ER stress and neuronal apoptosis. It is of main importance to find new therapeutic strategies because AD prevalence is increasing worldwide. Cannabinoids are arising as promising neuroprotective phytocompounds. In this study, we evaluated the neuroprotective potential of Δ8-THC pretreatment in an in vitro model of AD through transcriptomic analysis. We found that Δ8-THC pretreatment restored the loss of cell viability in retinoic acid-differentiated neuroblastoma SH-SY5Y cells treated with Aβ1-42. Moreover, the transcriptomic analysis provided evidence that the enriched biological processes of gene ontology were related to ER functions and proteostasis. In particular, Aβ1-42 upregulated genes involved in ER stress and unfolded protein response, leading to apoptosis as demonstrated by the increase in Bax and the decrease in Bcl-2 both at gene and protein expression levels. Moreover, genes involved in protein folding and degradation were also deregulated. On the contrary, Δ8-THC pretreatment reduced ER stress and, as a consequence, neuronal apoptosis. Then, the results demonstrated that Δ8-THC might represent a new neuroprotective agent in AD.
Collapse
Affiliation(s)
- Agnese Gugliandolo
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy
| | - Santino Blando
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy
| | - Stefano Salamone
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Largo Donegani 2, 28100 Novara, Italy
- PlantaChem Srls, Via Amico Canobio 4/6, 28100 Novara, Italy
| | - Diego Caprioglio
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Largo Donegani 2, 28100 Novara, Italy
- PlantaChem Srls, Via Amico Canobio 4/6, 28100 Novara, Italy
| | - Federica Pollastro
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Largo Donegani 2, 28100 Novara, Italy
- PlantaChem Srls, Via Amico Canobio 4/6, 28100 Novara, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy
| | - Luigi Chiricosta
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy
| |
Collapse
|
17
|
Scavone F, Gumbin SC, DaRosa PA, Kopito RR. RPL26/uL24 UFMylation is essential for ribosome-associated quality control at the endoplasmic reticulum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531792. [PMID: 36945571 PMCID: PMC10028864 DOI: 10.1101/2023.03.08.531792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Ribosomes that stall while translating cytosolic proteins are incapacitated by incomplete nascent chains, termed "arrest peptides" (APs) that are destroyed by the ubiquitin proteasome system (UPS) via a process known as the ribosome-associated quality control (RQC) pathway. By contrast, APs on ribosomes that stall while translocating secretory proteins into the endoplasmic reticulum (ER-APs) are shielded from cytosol by the ER membrane and the tightly sealed ribosome-translocon junction (RTJ). How this junction is breached to enable access of cytosolic UPS machinery and 26S proteasomes to translocon- and ribosome-obstructing ER-APs is not known. Here, we show that UPS and RQC-dependent degradation of ER-APs strictly requires conjugation of the ubiquitin-like (Ubl) protein UFM1 to 60S ribosomal subunits at the RTJ. Therefore, UFMylation of translocon-bound 60S subunits modulates the RTJ to promote access of proteasomes and RQC machinery to ER-APs. Significance Statement UFM1 is a ubiquitin-like protein that is selectively conjugated to the large (60S) subunit of ribosomes bound to the endoplasmic reticulum (ER), but the specific biological function of this modification is unclear. Here, we show that UFMylation facilitates proteasome-mediated degradation of arrest polypeptides (APs) which are generated following splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. We propose that UFMylation weakens the tightly sealed ribosome-translocon junction, thereby allowing the cytosolic ubiquitin-proteasome and ribosome-associated quality control machineries to access ER-APs.
Collapse
Affiliation(s)
| | - Samantha C Gumbin
- Department of Molecular and Cellular Physiology, Stanford School of Medicine, Stanford CA, 94305
| | - Paul A DaRosa
- Department of Biology, Stanford University, Stanford CA, 94305
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford CA, 94305
| |
Collapse
|
18
|
Fung C, Wilding B, Schittenhelm RB, Bryson-Richardson RJ, Bird PI. Expression of the Z Variant of α1-Antitrypsin Suppresses Hepatic Cholesterol Biosynthesis in Transgenic Zebrafish. Int J Mol Sci 2023; 24:ijms24032475. [PMID: 36768797 PMCID: PMC9917206 DOI: 10.3390/ijms24032475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
Individuals homozygous for the Pi*Z allele of SERPINA1 (ZAAT) are susceptible to lung disease due to insufficient α1-antitrypsin secretion into the circulation and may develop liver disease due to compromised protein folding that leads to inclusion body formation in the endoplasmic reticulum (ER) of hepatocytes. Transgenic zebrafish expressing human ZAAT show no signs of hepatic accumulation despite displaying serum insufficiency, suggesting the defect in ZAAT secretion occurs independently of its tendency to form inclusion bodies. In this study, proteomic, transcriptomic, and biochemical analysis provided evidence of suppressed Srebp2-mediated cholesterol biosynthesis in the liver of ZAAT-expressing zebrafish. To investigate the basis for this perturbation, CRISPR/Cas9 gene editing was used to manipulate ER protein quality control factors. Mutation of erlec1 resulted in a further suppression in the cholesterol biosynthesis pathway, confirming a role for this ER lectin in targeting misfolded ZAAT for ER-associated degradation (ERAD). Mutation of the two ER mannosidase homologs enhanced ZAAT secretion without inducing hepatic accumulation. These insights into hepatic ZAAT processing suggest potential therapeutic targets to improve secretion and alleviate serum insufficiency in this form of the α1-antitrypsin disease.
Collapse
Affiliation(s)
- Connie Fung
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Correspondence: (C.F.); (P.I.B.)
| | - Brendan Wilding
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash University, Melbourne 3800, Australia
| | | | - Phillip I. Bird
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Correspondence: (C.F.); (P.I.B.)
| |
Collapse
|
19
|
Harada Y, Ohkawa Y, Maeda K, Taniguchi N. Glycan quality control in and out of the endoplasmic reticulum of mammalian cells. FEBS J 2022; 289:7147-7162. [PMID: 34492158 DOI: 10.1111/febs.16185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/23/2021] [Accepted: 09/06/2021] [Indexed: 01/13/2023]
Abstract
The endoplasmic reticulum (ER) is equipped with multiple quality control systems (QCS) that are necessary for shaping the glycoproteome of eukaryotic cells. These systems facilitate the productive folding of glycoproteins, eliminate defective products, and function as effectors to evoke cellular signaling in response to various cellular stresses. These ER functions largely depend on glycans, which contain sugar-based codes that, when needed, function to recruit carbohydrate-binding proteins that determine the fate of glycoproteins. To ensure their functionality, the biosynthesis of such glycans is therefore strictly monitored by a system that selectively degrades structurally defective glycans before adding them to proteins. This system, which is referred to as the glycan QCS, serves as a mechanism to reduce the risk of abnormal glycosylation under conditions where glycan biosynthesis is genetically or metabolically stalled. On the other hand, glycan QCS increases the risk of global hypoglycosylation by limiting glycan availability, which can lead to protein misfolding and the activation of unfolded protein response to maintaining cell viability or to initiate cell death programs. This review summarizes the current state of our knowledge of the mechanisms underlying glycan QCS in mammals and its physiological and pathological roles in embryogenesis, tumor progression, and congenital disorders associated with abnormal glycosylation.
Collapse
Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| |
Collapse
|
20
|
Murase R, Yamamoto A, Hirata Y, Oh-Hashi K. Expression analysis and functional characterization of thioredoxin domain-containing protein 11. Mol Biol Rep 2022; 49:10541-10556. [PMID: 36152228 DOI: 10.1007/s11033-022-07932-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUNDS The endoplasmic reticulum (ER) is a crucial organelle that regulates both the folding, modification and transport of many proteins and senses certain stimuli inside and outside of cells. ER-associated degradation (ERAD), including SEL1L is a crucial mechanism to maintain homeostasis. In this study, we performed comparative proteome analysis in wild-type (wt) and SEL1L-deficient cells. METHODS AND RESULTS We found constitutively high expression of thioredoxin domain-containing protein 11 (TXNDC11) mRNA and protein in our SEL1L-deficient HEK293 cells by RT-PCR and Western blot analysis. The TXNDC11 gene possesses a well-conserved unfolded protein response element (UPRE) around its transcription start site, and ER stress increased TXNDC11 mRNA and luciferase reporter activity via this putative UPRE in HEK293 cells. The amounts of TXNDC11 protein in wild-type and SEL1L-deficient cells with or without thapsigargin (Tg) treatment were parallel to their mRNAs in these cells, which was almost proportional to spliced XBP1 (sXBP1) mRNA expression. The establishment and characterization of TXNDC11-deficient HEK293 cells revealed that the expression of three different ER resident stress sensors, ATF6α, CREB3 and CREB3L2, is regulated by TXNDC11. The rate of disappearance of the three proteins by CHX treatment in wt cells was remarkably different, and the full-length CREB3L2 protein was almost completely degraded within 15 min after CHX treatment. TXNDC11 deficiency increased the expression of each full-length form under resting conditions and delayed their disappearance by CHX treatment. Interestingly, the degree of increase in full-length CREB3/CREB3L2 by TXNDC11 deficiency was apparently higher than that in full-length ATF6α. The increase in these proteins by TXNDC11 deficiency was hardly correlated with the expression of each mRNA. Treatment with ER stress inducers influenced each full-length mature form, and the difference in each full-length form observed in wt and TXNDC11-deficient cells was smaller. CONCLUSION This study demonstrated that TXNDC11 is an ER stress-inducible gene regulated by the IRE1-sXBP1 pathway. In addition, TXNDC11 is involved in the regulation of ATF6α, CREB3 and CREB3L2 protein expression, although the contribution to the stability of these proteins is quite variable. Therefore, its further characterization will provide new insights for understanding protein homeostasis in ER physiology and pathology.
Collapse
Affiliation(s)
- Ryoichi Murase
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Ayumi Yamamoto
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yoko Hirata
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kentaro Oh-Hashi
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
| |
Collapse
|
21
|
De Masi R, Orlando S. GANAB and N-Glycans Substrates Are Relevant in Human Physiology, Polycystic Pathology and Multiple Sclerosis: A Review. Int J Mol Sci 2022; 23:7373. [PMID: 35806376 PMCID: PMC9266668 DOI: 10.3390/ijms23137373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Glycans are one of the four fundamental macromolecular components of living matter, and they are highly regulated in the cell. Their functions are metabolic, structural and modulatory. In particular, ER resident N-glycans participate with the Glc3Man9GlcNAc2 highly conserved sequence, in protein folding process, where the physiological balance between glycosylation/deglycosylation on the innermost glucose residue takes place, according GANAB/UGGT concentration ratio. However, under abnormal conditions, the cell adapts to the glucose availability by adopting an aerobic or anaerobic regimen of glycolysis, or to external stimuli through internal or external recognition patterns, so it responds to pathogenic noxa with unfolded protein response (UPR). UPR can affect Multiple Sclerosis (MS) and several neurological and metabolic diseases via the BiP stress sensor, resulting in ATF6, PERK and IRE1 activation. Furthermore, the abnormal GANAB expression has been observed in MS, systemic lupus erythematous, male germinal epithelium and predisposed highly replicating cells of the kidney tubules and bile ducts. The latter is the case of Polycystic Liver Disease (PCLD) and Polycystic Kidney Disease (PCKD), where genetically induced GANAB loss affects polycystin-1 (PC1) and polycystin-2 (PC2), resulting in altered protein quality control and cyst formation phenomenon. Our topics resume the role of glycans in cell physiology, highlighting the N-glycans one, as a substrate of GANAB, which is an emerging key molecule in MS and other human pathologies.
Collapse
Affiliation(s)
- Roberto De Masi
- Complex Operative Unit of Neurology, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy;
- Laboratory of Neuroproteomics, Multiple Sclerosis Centre, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy
| | - Stefania Orlando
- Laboratory of Neuroproteomics, Multiple Sclerosis Centre, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy
| |
Collapse
|
22
|
Wiseman RL, Mesgarzadeh JS, Hendershot LM. Reshaping endoplasmic reticulum quality control through the unfolded protein response. Mol Cell 2022; 82:1477-1491. [PMID: 35452616 PMCID: PMC9038009 DOI: 10.1016/j.molcel.2022.03.025] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/28/2022] [Accepted: 03/18/2022] [Indexed: 01/09/2023]
Abstract
Endoplasmic reticulum quality control (ERQC) pathways comprising chaperones, folding enzymes, and degradation factors ensure the fidelity of ER protein folding and trafficking to downstream secretory environments. However, multiple factors, including tissue-specific secretory proteomes, environmental and genetic insults, and organismal aging, challenge ERQC. Thus, a key question is: how do cells adapt ERQC to match the diverse, ever-changing demands encountered during normal physiology and in disease? The answer lies in the unfolded protein response (UPR), a signaling mechanism activated by ER stress. In mammals, the UPR comprises three signaling pathways regulated downstream of the ER membrane proteins IRE1, ATF6, and PERK. Upon activation, these UPR pathways remodel ERQC to alleviate cellular stress and restore ER function. Here, we describe how UPR signaling pathways adapt ERQC, highlighting their importance for maintaining ER function across tissues and the potential for targeting the UPR to mitigate pathologies associated with protein misfolding diseases.
Collapse
Affiliation(s)
- R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037,To whom correspondences should be addressed: Linda Hendershot, ; R. Luke Wiseman,
| | - Jaleh S. Mesgarzadeh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Linda M. Hendershot
- Department of Tumor Biology, St Jude Children’s Research Hospital, Memphis, TN 38105,To whom correspondences should be addressed: Linda Hendershot, ; R. Luke Wiseman,
| |
Collapse
|
23
|
Lemberg MK, Strisovsky K. Maintenance of organellar protein homeostasis by ER-associated degradation and related mechanisms. Mol Cell 2021; 81:2507-2519. [PMID: 34107306 DOI: 10.1016/j.molcel.2021.05.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
Protein homeostasis mechanisms are fundamentally important to match cellular needs and to counteract stress conditions. A fundamental challenge is to understand how defective proteins are recognized and extracted from cellular organelles to be degraded in the cytoplasm. The endoplasmic reticulum (ER)-associated degradation (ERAD) pathway is the best-understood organellar protein quality control system. Here, we review new insights into the mechanism of recognition and retrotranslocation of client proteins in ERAD. In addition to the membrane-integral ERAD E3 ubiquitin ligases, we highlight one protein family that is remarkably often involved in various aspects of membrane protein quality control and protein dislocation: the rhomboid superfamily, which includes derlins and intramembrane serine proteases. Rhomboid-like proteins have been found to control protein homeostasis in the ER, but also in other eukaryotic organelles and in bacteria, pointing toward conserved principles of membrane protein quality control across organelles and evolution.
Collapse
Affiliation(s)
- Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany.
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czechia.
| |
Collapse
|
24
|
Ninagawa S. N-glycan Dependent Protein Quality Control System in the Endoplasmic Reticulum. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2108.2e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University
| |
Collapse
|
25
|
Ninagawa S. N-glycan Dependent Protein Quality Control System in the Endoplasmic Reticulum. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2108.2j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University
| |
Collapse
|
26
|
Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
Collapse
Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| |
Collapse
|
27
|
Hattori T, Hanafusa K, Wada I, Hosokawa N. SEL1L degradation intermediates stimulate cytosolic aggregation of polyglutamine-expanded protein. FEBS J 2021; 288:4637-4654. [PMID: 33576152 DOI: 10.1111/febs.15761] [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: 09/21/2020] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 12/01/2022]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are degraded by ER-associated degradation (ERAD). In mammalian cells, the HRD1-SEL1L membrane ubiquitin ligase complex plays a central role in this process. However, SEL1L is inherently unstable, and excess SEL1L is also degraded by ERAD. Accordingly, when proteasome activity is inhibited, multiple degradation intermediates of SEL1L appear in the cytosol. In this study, we searched for factors that inhibit SEL1L degradation and identified OS-9 and XTP3-B, two ER lectins that regulate glycoprotein ERAD. SEL1L degradation was characterized by a ladder of degradation products, and the C-terminal Pro-rich region of SEL1L was responsible for generation of this pattern. In the cytosol, these degradation intermediates stimulated aggregation of polyglutamine-expanded Huntingtin protein (Htt-polyQ-GFP) by interacting with aggregation-prone proteins, including Htt-polyQ-GFP. Collectively, our findings indicate that peptide fragments of ER proteins generated during ERAD may affect protein aggregation in the cytosol, revealing the interconnection of protein homeostasis across subcellular compartments.
Collapse
Affiliation(s)
- Tokuya Hattori
- Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Japan
| | - Ken Hanafusa
- Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Japan
| | - Ikuo Wada
- Department of Cell Science, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Japan
| | - Nobuko Hosokawa
- Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Japan
| |
Collapse
|
28
|
Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
Collapse
|
29
|
Ninagawa S, George G, Mori K. Mechanisms of productive folding and endoplasmic reticulum-associated degradation of glycoproteins and non-glycoproteins. Biochim Biophys Acta Gen Subj 2020; 1865:129812. [PMID: 33316349 DOI: 10.1016/j.bbagen.2020.129812] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The quality of proteins destined for the secretory pathway is ensured by two distinct mechanisms in the endoplasmic reticulum (ER): productive folding of newly synthesized proteins, which is assisted by ER-localized molecular chaperones and in most cases also by disulfide bond formation and transfer of an oligosaccharide unit; and ER-associated degradation (ERAD), in which proteins unfolded or misfolded in the ER are recognized and processed for delivery to the ER membrane complex, retrotranslocated through the complex with simultaneous ubiquitination, extracted by AAA-ATPase to the cytosol, and finally degraded by the proteasome. SCOPE OF REVIEW We describe the mechanisms of productive folding and ERAD, with particular attention to glycoproteins versus non-glycoproteins, and to yeast versus mammalian systems. MAJOR CONCLUSION Molecular mechanisms of the productive folding of glycoproteins and non-glycoproteins mediated by molecular chaperones and protein disulfide isomerases are well conserved from yeast to mammals. Additionally, mammals have gained an oligosaccharide structure-dependent folding cycle for glycoproteins. The molecular mechanisms of ERAD are also well conserved from yeast to mammals, but redundant expression of yeast orthologues in mammals has been encountered, particularly for components involved in recognition and processing of glycoproteins and components of the ER membrane complex involved in retrotranslocation and simultaneous ubiquitination of glycoproteins and non-glycoproteins. This may reflect an evolutionary consequence of increasing quantity or quality needs toward mammals. GENERAL SIGNIFICANCE The introduction of innovative genome editing technology into analysis of the mechanisms of mammalian ERAD, as exemplified here, will provide new insights into the pathogenesis of various diseases.
Collapse
Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| |
Collapse
|
30
|
Chiritoiu M, Chiritoiu GN, Munteanu CVA, Pastrama F, Ivessa NE, Petrescu SM. EDEM1 Drives Misfolded Protein Degradation via ERAD and Exploits ER-Phagy as Back-Up Mechanism When ERAD Is Impaired. Int J Mol Sci 2020; 21:ijms21103468. [PMID: 32423001 PMCID: PMC7279049 DOI: 10.3390/ijms21103468] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 01/20/2023] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is the main mechanism of targeting ER proteins for degradation to maintain homeostasis, and perturbations of ERAD lead to pathological conditions. ER-degradation enhancing α-mannosidase-like (EDEM1) was proposed to extract terminally misfolded proteins from the calnexin folding cycle and target them for degradation by ERAD. Here, using mass-spectrometry and biochemical methods, we show that EDEM1 is found in auto-regulatory complexes with ERAD components. Moreover, the N-terminal disordered region of EDEM1 mediates protein–protein interaction with misfolded proteins, whilst the absence of this domain significantly impairs their degradation. We also determined that overexpression of EDEM1 can induce degradation, even when proteasomal activity is severely impaired, by promoting the formation of aggregates, which can be further degraded by autophagy. Therefore, we propose that EDEM1 maintains ER homeostasis and mediates ERAD client degradation via autophagy when either dislocation or proteasomal degradation are impaired.
Collapse
Affiliation(s)
- Marioara Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Gabriela N. Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Cristian V. A. Munteanu
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - Florin Pastrama
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - N. Erwin Ivessa
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, A-1030 Vienna, Austria;
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
- Correspondence: ; Tel.: +40-2-1223-9069
| |
Collapse
|
31
|
George G, Ninagawa S, Yagi H, Saito T, Ishikawa T, Sakuma T, Yamamoto T, Imami K, Ishihama Y, Kato K, Okada T, Mori K. EDEM2 stably disulfide-bonded to TXNDC11 catalyzes the first mannose trimming step in mammalian glycoprotein ERAD. eLife 2020; 9:53455. [PMID: 32065582 PMCID: PMC7039678 DOI: 10.7554/elife.53455] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/07/2020] [Indexed: 01/05/2023] Open
Abstract
Sequential mannose trimming of N-glycan (Man9GlcNAc2 -> Man8GlcNAc2 -> Man7GlcNAc2) facilitates endoplasmic reticulum-associated degradation of misfolded glycoproteins (gpERAD). Our gene knockout experiments in human HCT116 cells have revealed that EDEM2 is required for the first step. However, it was previously shown that purified EDEM2 exhibited no α1,2-mannosidase activity toward Man9GlcNAc2 in vitro. Here, we found that EDEM2 was stably disulfide-bonded to TXNDC11, an endoplasmic reticulum protein containing five thioredoxin (Trx)-like domains. C558 present outside of the mannosidase homology domain of EDEM2 was linked to C692 in Trx5, which solely contains the CXXC motif in TXNDC11. This covalent bonding was essential for mannose trimming and subsequent gpERAD in HCT116 cells. Furthermore, EDEM2-TXNDC11 complex purified from transfected HCT116 cells converted Man9GlcNAc2 to Man8GlcNAc2(isomerB) in vitro. Our results establish the role of EDEM2 as an initiator of gpERAD, and represent the first clear demonstration of in vitro mannosidase activity of EDEM family proteins.
Collapse
Affiliation(s)
- Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Taiki Saito
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Tokiro Ishikawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Tetsuya Okada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
32
|
Wang Y, Maeda Y, Liu YS, Takada Y, Ninomiya A, Hirata T, Fujita M, Murakami Y, Kinoshita T. Cross-talks of glycosylphosphatidylinositol biosynthesis with glycosphingolipid biosynthesis and ER-associated degradation. Nat Commun 2020; 11:860. [PMID: 32054864 PMCID: PMC7018848 DOI: 10.1038/s41467-020-14678-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 01/27/2020] [Indexed: 12/21/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins and glycosphingolipids interact with each other in the mammalian plasma membranes, forming dynamic microdomains. How their interaction starts in the cells has been unclear. Here, based on a genome-wide CRISPR-Cas9 genetic screen for genes required for GPI side-chain modification by galactose in the Golgi apparatus, we report that β1,3-galactosyltransferase 4 (B3GALT4), the previously characterized GM1 ganglioside synthase, additionally functions in transferring galactose to the N-acetylgalactosamine side-chain of GPI. Furthermore, B3GALT4 requires lactosylceramide for the efficient GPI side-chain galactosylation. Thus, our work demonstrates previously unexpected functional relationships between GPI-anchored proteins and glycosphingolipids in the Golgi. Through the same screening, we also show that GPI biosynthesis in the endoplasmic reticulum (ER) is severely suppressed by ER-associated degradation to prevent GPI accumulation when the transfer of synthesized GPI to proteins is defective. Our data demonstrates cross-talks of GPI biosynthesis with glycosphingolipid biosynthesis and the ER quality control system. Glycosylphosphatidylinositol (GPI) anchors are found on many cell surface proteins but their biosynthesis is not fully understood. Here, the authors identify genes involved in GPI galactosylation and reveal functional connections between GPI processing, glycosphingolipid biosynthesis and ER-associated degradation.
Collapse
Affiliation(s)
- Yicheng Wang
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yoko Takada
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Akinori Ninomiya
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuya Hirata
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu-City, Gifu 501-1193, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan. .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
33
|
Bhattacharya A, Qi L. ER-associated degradation in health and disease - from substrate to organism. J Cell Sci 2019; 132:132/23/jcs232850. [PMID: 31792042 DOI: 10.1242/jcs.232850] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The recent literature has revolutionized our view on the vital importance of endoplasmic reticulum (ER)-associated degradation (ERAD) in health and disease. Suppressor/enhancer of Lin-12-like (Sel1L)-HMG-coA reductase degradation protein 1 (Hrd1)-mediated ERAD has emerged as a crucial determinant of normal physiology and as a sentinel against disease pathogenesis in the body, in a largely substrate- and cell type-specific manner. In this Review, we highlight three features of ERAD, constitutive versus inducible ERAD, quality versus quantity control of ERAD and ERAD-mediated regulation of nuclear gene transcription, through which ERAD exerts a profound impact on a number of physiological processes.
Collapse
Affiliation(s)
- Asmita Bhattacharya
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA.,Graduate Program of Genetics, Genomics and Development, Cornell University, Ithaca, NY 14853, USA
| | - Ling Qi
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA .,Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| |
Collapse
|
34
|
Sicari D, Igbaria A, Chevet E. Control of Protein Homeostasis in the Early Secretory Pathway: Current Status and Challenges. Cells 2019; 8:E1347. [PMID: 31671908 PMCID: PMC6912474 DOI: 10.3390/cells8111347] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
: Discrimination between properly folded proteins and those that do not reach this state is necessary for cells to achieve functionality. Eukaryotic cells have evolved several mechanisms to ensure secretory protein quality control, which allows efficiency and fidelity in protein production. Among the actors involved in such process, both endoplasmic reticulum (ER) and the Golgi complex play prominent roles in protein synthesis, biogenesis and secretion. ER and Golgi functions ensure that only properly folded proteins are allowed to flow through the secretory pathway while improperly folded proteins have to be eliminated to not impinge on cellular functions. Thus, complex quality control and degradation machineries are crucial to prevent the toxic accumulation of improperly folded proteins. However, in some instances, improperly folded proteins can escape the quality control systems thereby contributing to several human diseases. Herein, we summarize how the early secretory pathways copes with the accumulation of improperly folded proteins, and how insufficient handling can cause the development of several human diseases. Finally, we detail the genetic and pharmacologic approaches that could be used as potential therapeutic tools to treat these diseases.
Collapse
Affiliation(s)
- Daria Sicari
- Proteostasis & Cancer Team INSERM U1242 « Chemistry, Oncogenesis Stress Signaling », Université de Rennes, CEDEX, 35042 Rennes, France.
- Centre de Lutte contre le Cancer Eugène Marquis, CEDEX, 35042 Rennes, France.
| | - Aeid Igbaria
- Proteostasis & Cancer Team INSERM U1242 « Chemistry, Oncogenesis Stress Signaling », Université de Rennes, CEDEX, 35042 Rennes, France.
- Centre de Lutte contre le Cancer Eugène Marquis, CEDEX, 35042 Rennes, France.
| | - Eric Chevet
- Proteostasis & Cancer Team INSERM U1242 « Chemistry, Oncogenesis Stress Signaling », Université de Rennes, CEDEX, 35042 Rennes, France.
- Centre de Lutte contre le Cancer Eugène Marquis, CEDEX, 35042 Rennes, France.
| |
Collapse
|
35
|
Tax G, Lia A, Santino A, Roversi P. Modulation of ERQC and ERAD: A Broad-Spectrum Spanner in the Works of Cancer Cells? JOURNAL OF ONCOLOGY 2019; 2019:8384913. [PMID: 31662755 PMCID: PMC6791201 DOI: 10.1155/2019/8384913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022]
Abstract
Endoplasmic reticulum glycoprotein folding quality control (ERQC) and ER-associated degradation (ERAD) preside over cellular glycoprotein secretion and maintain steady glycoproteostasis. When cells turn malignant, cancer cell plasticity is affected and supported either by point mutations, preferential isoform selection, altered expression levels, or shifts to conformational equilibria of a secreted glycoprotein. Such changes are crucial in mediating altered extracellular signalling, metabolic behavior, and adhesion properties of cancer cells. It is therefore conceivable that interference with ERQC and/or ERAD can be used to selectively damage cancers. Indeed, inhibitors of the late stages of ERAD are already in the clinic against cancers such as multiple myeloma. Here, we review recent advances in our understanding of the complex relationship between glycoproteostasis and cancer biology and discuss the potential of ERQC and ERAD modulators for the selective targeting of cancer cell plasticity.
Collapse
Affiliation(s)
- Gábor Tax
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
| | - Andrea Lia
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, I-73100 Lecce, Italy
| | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, I-73100 Lecce, Italy
| | - Pietro Roversi
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
| |
Collapse
|
36
|
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: 260] [Impact Index Per Article: 43.3] [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.
Collapse
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
| |
Collapse
|
37
|
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: 88] [Impact Index Per Article: 14.7] [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.
Collapse
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
| |
Collapse
|
38
|
Abstract
The site of protein folding and maturation for the majority of proteins that are secreted, localized to the plasma membrane or targeted to endomembrane compartments is the endoplasmic reticulum (ER). It is essential that proteins targeted to the ER are properly folded in order to carry out their function, as well as maintain protein homeostasis, as accumulation of misfolded proteins could lead to the formation of cytotoxic aggregates. Because protein folding is an error-prone process, the ER contains protein quality control networks that act to optimize proper folding and trafficking of client proteins. If a protein is unable to reach its native state, it is targeted for ER retention and subsequent degradation. The protein quality control networks of the ER that oversee this evaluation or interrogation process that decides the fate of maturing nascent chains is comprised of three general types of families: the classical chaperones, the carbohydrate-dependent system, and the thiol-dependent system. The cooperative action of these families promotes protein quality control and protein homeostasis in the ER. This review will describe the families of the ER protein quality control network and discuss the functions of individual members.
Collapse
Affiliation(s)
- Benjamin M Adams
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 240 Thatcher Road, Amherst, MA, 01003, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Michela E Oster
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 240 Thatcher Road, Amherst, MA, 01003, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 240 Thatcher Road, Amherst, MA, 01003, USA.
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
| |
Collapse
|
39
|
Shenkman M, Lederkremer GZ. Compartmentalization and Selective Tagging for Disposal of Misfolded Glycoproteins. Trends Biochem Sci 2019; 44:827-836. [PMID: 31133362 DOI: 10.1016/j.tibs.2019.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 01/08/2023]
Abstract
The ability of mammalian cells to correctly identify and degrade misfolded secretory proteins, most of them bearing N-glycans, is crucial for their correct function and survival. An inefficient disposal mechanism results in the accumulation of misfolded proteins and consequent endoplasmic reticulum (ER) stress. N-glycan processing creates a code that reveals the folding status of each molecule, enabling continued folding attempts or targeting of the doomed glycoprotein for disposal. We review here the main steps involved in the accurate processing of unfolded glycoproteins. We highlight recent data suggesting that the processing is not stochastic, but that there is selective accelerated glycan trimming on misfolded glycoprotein molecules.
Collapse
Affiliation(s)
- Marina Shenkman
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gerardo Z Lederkremer
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
40
|
Vitale M, Bakunts A, Orsi A, Lari F, Tadè L, Danieli A, Rato C, Valetti C, Sitia R, Raimondi A, Christianson JC, van Anken E. Inadequate BiP availability defines endoplasmic reticulum stress. eLife 2019; 8:41168. [PMID: 30869076 PMCID: PMC6417858 DOI: 10.7554/elife.41168] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/13/2019] [Indexed: 12/16/2022] Open
Abstract
How endoplasmic reticulum (ER) stress leads to cytotoxicity is ill-defined. Previously we showed that HeLa cells readjust homeostasis upon proteostatically driven ER stress, triggered by inducible bulk expression of secretory immunoglobulin M heavy chain (μs) thanks to the unfolded protein response (UPR; Bakunts et al., 2017). Here we show that conditions that prevent that an excess of the ER resident chaperone (and UPR target gene) BiP over µs is restored lead to µs-driven proteotoxicity, i.e. abrogation of HRD1-mediated ER-associated degradation (ERAD), or of the UPR, in particular the ATF6α branch. Such conditions are tolerated instead upon removal of the BiP-sequestering first constant domain (CH1) from µs. Thus, our data define proteostatic ER stress to be a specific consequence of inadequate BiP availability, which both the UPR and ERAD redeem.
Collapse
Affiliation(s)
- Milena Vitale
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Anush Bakunts
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Orsi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.,Università Vita-Salute San Raffaele, Milan, Italy
| | - Federica Lari
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Laura Tadè
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Alberto Danieli
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Rato
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Caterina Valetti
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Roberto Sitia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.,Università Vita-Salute San Raffaele, Milan, Italy
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
| | - John C Christianson
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Eelco van Anken
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.,Università Vita-Salute San Raffaele, Milan, Italy
| |
Collapse
|
41
|
Abstract
Ubiquitin fold modifier 1 (UFM1) is a small, metazoan-specific, ubiquitin-like protein modifier that is essential for embryonic development. Although loss-of-function mutations in UFM1 conjugation are linked to endoplasmic reticulum (ER) stress, neither the biological function nor the relevant cellular targets of this protein modifier are known. Here, we show that a largely uncharacterized ribosomal protein, RPL26, is the principal target of UFM1 conjugation. RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes tethered to the cytoplasmic surface of the ER and UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes. Biochemical analysis and structural modeling establish that UFMylated RPL26 and the UFMylation machinery are in close proximity to the SEC61 translocon, suggesting that this modification plays a direct role in cotranslational protein translocation into the ER. These data suggest that UFMylation is a ribosomal modification specialized to facilitate metazoan-specific protein biogenesis at the ER.
Collapse
|
42
|
Genome-wide CRISPR Analysis Identifies Substrate-Specific Conjugation Modules in ER-Associated Degradation. Mol Cell 2018; 73:377-389.e11. [PMID: 30581143 DOI: 10.1016/j.molcel.2018.11.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/08/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023]
Abstract
The ubiquitin proteasome system (UPS) maintains the integrity of the proteome by selectively degrading misfolded or mis-assembled proteins, but the rules that govern how conformationally defective proteins in the secretory pathway are selected from the structurally and topologically diverse constellation of correctly folded membrane and secretory proteins for efficient degradation by cytosolic proteasomes is not well understood. Here, we combine parallel pooled genome-wide CRISPR-Cas9 forward genetic screening with a highly quantitative and sensitive protein turnover assay to discover a previously undescribed collaboration between membrane-embedded cytoplasmic ubiquitin E3 ligases to conjugate heterotypic branched or mixed ubiquitin (Ub) chains on substrates of endoplasmic-reticulum-associated degradation (ERAD). These findings demonstrate that parallel CRISPR analysis can be used to deconvolve highly complex cell biological processes and identify new biochemical pathways in protein quality control.
Collapse
|