1
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Tushi NJ, Zhang Z, Sun S. The ER-associated Degradation Adaptor SEL1L is Dispensable for ER Homeostasis and the Differentiation of Spermatogenic Cells. J Biol Chem 2025:110283. [PMID: 40412517 DOI: 10.1016/j.jbc.2025.110283] [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: 03/31/2025] [Revised: 05/01/2025] [Accepted: 05/15/2025] [Indexed: 05/27/2025] Open
Abstract
The SEL1L-HRD1 complex is a critical component of the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway, essential for maintaining ER homeostasis and cellular function. While the crucial roles of SEL1L and HRD1 in various physiological processes have been reported in mice and humans, their specific functions in male germ cells remain unexplored. Here, we show that, while SEL1L is highly expressed in spermatogenic cells, it is dispensable for their differentiation and ER homeostasis. SEL1L deletion in these cells does not affect sperm count, motility, male fertility, or testicular histology. Mechanistically, our data show that SEL1L loss reduces HRD1 protein levels in spermatids but unexpectedly, not in spermatocytes. Furthermore, SEL1L deficiency does not induce overt ER stress response, ER dilation, or cell death in the testes. Collectively, these findings indicate that SEL1L is not required for ER homeostasis or the differentiation of male germ cells.
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Affiliation(s)
- Nusrat Jahan Tushi
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
| | - Zhibing Zhang
- Department of Physiology and Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Shengyi Sun
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA.
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2
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Podolsky MJ, Kheyfets B, Pandey M, Beigh AH, Yang CD, Lizama CO, Datta R, Lin LL, Wang Z, Wolters PJ, McManus MT, Qi L, Atabai K. Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover. Nat Commun 2024; 15:1531. [PMID: 38378719 PMCID: PMC10879544 DOI: 10.1038/s41467-024-45817-8] [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: 01/14/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
Accumulating evidence has implicated impaired extracellular matrix (ECM) clearance as a key factor in fibrotic disease. Despite decades of research elucidating the effectors of ECM clearance, relatively little is understood regarding the upstream regulation of this process. Collagen is the most abundant constituent of normal and fibrotic ECM in mammalian tissues. Its catabolism occurs through extracellular proteolysis and cell-mediated uptake of collagen fragments for intracellular degradation. Given the paucity of information regarding the regulation of this latter process, here we execute unbiased genome-wide screens to understand the molecular underpinnings of cell-mediated collagen clearance. Using this approach, we discover a mechanism through which collagen biosynthesis is sensed by cells internally and directly regulates clearance of extracellular collagen. The sensing mechanism appears to be dependent on endoplasmic reticulum-resident protein SEL1L and occurs via a noncanonical function of this protein. This pathway functions as a homeostatic negative feedback loop that limits collagen accumulation in tissues. In human fibrotic lung disease, the induction of this collagen clearance pathway by collagen synthesis is impaired, thereby contributing to the pathological accumulation of collagen in lung tissue. Thus, we describe cell-autonomous, rheostatic collagen clearance as an important pathway of tissue homeostasis.
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Affiliation(s)
- Michael J Podolsky
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Benjamin Kheyfets
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Monika Pandey
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Afaq H Beigh
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher D Yang
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Carlos O Lizama
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Ritwik Datta
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Liangguang L Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhihong Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Paul J Wolters
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael T McManus
- Department of Microbiology and Immunology and UCSF Diabetes Center, University of California, San Francisco, CA, USA
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kamran Atabai
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Lung Biology Center, University of California, San Francisco, CA, USA.
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3
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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.
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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.
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4
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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.
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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.
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5
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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.
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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
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6
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Weis D, Lin LL, Wang HH, Li ZJ, Kusikova K, Ciznar P, Wolf HM, Leiss-Piller A, Wang Z, Wei X, Weis S, Skalicka K, Hrckova G, Danisovic L, Soltysova A, Yang TT, Feichtinger RG, Mayr JA, Qi L. Biallelic Cys141Tyr variant of SEL1L is associated with neurodevelopmental disorders, agammaglobulinemia, and premature death. J Clin Invest 2024; 134:e170882. [PMID: 37943617 PMCID: PMC10786703 DOI: 10.1172/jci170882] [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: 03/29/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Suppressor of lin-12-like-HMG-CoA reductase degradation 1 (SEL1L-HRD1) ER-associated degradation (ERAD) plays a critical role in many physiological processes in mice, including immunity, water homeostasis, and energy metabolism; however, its relevance and importance in humans remain unclear, as no disease variant has been identified. Here, we report a biallelic SEL1L variant (p. Cys141Tyr) in 5 patients from a consanguineous Slovakian family. These patients presented with not only ERAD-associated neurodevelopmental disorders with onset in infancy (ENDI) syndromes, but infantile-onset agammaglobulinemia with no mature B cells, resulting in frequent infections and early death. This variant disrupted the formation of a disulfide bond in the luminal fibronectin II domain of SEL1L, largely abolishing the function of the SEL1L-HRD1 ERAD complex in part via proteasomal-mediated self destruction by HRD1. This study reports a disease entity termed ENDI-agammaglobulinemia (ENDI-A) syndrome and establishes an inverse correlation between SEL1L-HRD1 ERAD functionality and disease severity in humans.
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Affiliation(s)
- Denisa Weis
- Department of Medical Genetics, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
- Department of Pediatrics, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, Bratislava, Slovakia
| | - Liangguang L. Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Huilun H. Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Zexin Jason Li
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katarina Kusikova
- Department of Pediatric Neurology, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, Bratislava, Slovakia
| | - Peter Ciznar
- Department of Pediatrics, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, Bratislava, Slovakia
| | - Hermann M. Wolf
- Immunology Outpatient Clinic, Vienna, Austria
- Sigmund Freud Private University–Medical School, Vienna, Austria
| | | | - Zhihong Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Xiaoqiong Wei
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Serge Weis
- Division of Neuropathology, Neuromed Campus, Department of Pathology and Molecular Pathology, Kepler University Hospital, Johannes Kepler University, Linz, Austria
| | - Katarina Skalicka
- Department of Pediatrics, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, Bratislava, Slovakia
| | - Gabriela Hrckova
- Department of Pediatrics, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, Bratislava, Slovakia
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, and
| | - Andrea Soltysova
- Faculty of Natural Sciences, Department of Molecular Biology, Comenius University, Bratislava, Slovakia
- Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - René Günther Feichtinger
- University Children’s Hospital, Salzburger Landeskliniken Universitätsklinikum (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes A. Mayr
- University Children’s Hospital, Salzburger Landeskliniken Universitätsklinikum (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, 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
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7
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Hayashi Y, Takatori S, Warsame WY, Tomita T, Fujisawa T, Ichijo H. TOLLIP acts as a cargo adaptor to promote lysosomal degradation of aberrant ER membrane proteins. EMBO J 2023; 42:e114272. [PMID: 37929762 PMCID: PMC10690474 DOI: 10.15252/embj.2023114272] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Endoplasmic reticulum (ER) proteostasis is maintained by various catabolic pathways. Lysosomes clear entire ER portions by ER-phagy, while proteasomes selectively clear misfolded or surplus aberrant proteins by ER-associated degradation (ERAD). Recently, lysosomes have also been implicated in the selective clearance of aberrant ER proteins, but the molecular basis remains unclear. Here, we show that the phosphatidylinositol-3-phosphate (PI3P)-binding protein TOLLIP promotes selective lysosomal degradation of aberrant membrane proteins, including an artificial substrate and motoneuron disease-causing mutants of VAPB and Seipin. These cargos are recognized by TOLLIP through its misfolding-sensing intrinsically disordered region (IDR) and ubiquitin-binding CUE domain. In contrast to ER-phagy receptors, which clear both native and aberrant proteins by ER-phagy, TOLLIP selectively clears aberrant cargos by coupling them with the PI3P-dependent lysosomal trafficking without promoting bulk ER turnover. Moreover, TOLLIP depletion augments ER stress after ERAD inhibition, indicating that TOLLIP and ERAD cooperatively safeguard ER proteostasis. Our study identifies TOLLIP as a unique type of cargo-specific adaptor dedicated to the clearance of aberrant ER cargos and provides insights into molecular mechanisms underlying lysosome-mediated quality control of membrane proteins.
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Affiliation(s)
- Yuki Hayashi
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | | | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Takao Fujisawa
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Hidenori Ichijo
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
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8
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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.
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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.
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9
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Baier D, Mendrina T, Schoenhacker‐Alte B, Pirker C, Mohr T, Rusz M, Regner B, Schaier M, Sgarioto N, Raynal NJ, Nowikovsky K, Schmidt WM, Heffeter P, Meier‐Menches SM, Koellensperger G, Keppler BK, Berger W. The Lipid Metabolism as Target and Modulator of BOLD-100 Anticancer Activity: Crosstalk with Histone Acetylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301939. [PMID: 37752764 PMCID: PMC10646284 DOI: 10.1002/advs.202301939] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/18/2023] [Indexed: 09/28/2023]
Abstract
The leading first-in-class ruthenium-complex BOLD-100 currently undergoes clinical phase-II anticancer evaluation. Recently, BOLD-100 is identified as anti-Warburg compound. The present study shows that also deregulated lipid metabolism parameters characterize acquired BOLD-100-resistant colon and pancreatic carcinoma cells. Acute BOLD-100 treatment reduces lipid droplet contents of BOLD-100-sensitive but not -resistant cells. Despite enhanced glycolysis fueling lipid accumulation, BOLD-100-resistant cells reveal diminished lactate secretion based on monocarboxylate transporter 1 (MCT1) loss mediated by a frame-shift mutation in the MCT1 chaperone basigin. Glycolysis and lipid catabolism converge in the production of protein/histone acetylation substrate acetyl-coenzymeA (CoA). Mass spectrometric and nuclear magnetic resonance analyses uncover spontaneous cell-free BOLD-100-CoA adduct formation suggesting acetyl-CoA depletion as mechanism bridging BOLD-100-induced lipid metabolism alterations and histone acetylation-mediated gene expression deregulation. Indeed, BOLD-100 treatment decreases histone acetylation selectively in sensitive cells. Pharmacological targeting confirms histone de-acetylation as central mode-of-action of BOLD-100 and metabolic programs stabilizing histone acetylation as relevant Achilles' heel of acquired BOLD-100-resistant cell and xenograft models. Accordingly, histone gene expression changes also predict intrinsic BOLD-100 responsiveness. Summarizing, BOLD-100 is identified as epigenetically active substance acting via targeting several onco-metabolic pathways. Identification of the lipid metabolism as driver of acquired BOLD-100 resistance opens novel strategies to tackle therapy failure.
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Affiliation(s)
- Dina Baier
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Institute of Inorganic ChemistryUniversity of ViennaWaehringer Str. 42Vienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
| | - Theresa Mendrina
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Institute of Inorganic ChemistryUniversity of ViennaWaehringer Str. 42Vienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
| | - Beatrix Schoenhacker‐Alte
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Institute of Inorganic ChemistryUniversity of ViennaWaehringer Str. 42Vienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
| | - Christine Pirker
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
| | - Thomas Mohr
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Joint Metabolome FacilityUniversity of Vienna and Medical University of ViennaWaehringer Str. 38Vienna1090Austria
- ScienceConsultGuntramsdorf2351Austria
| | - Mate Rusz
- Institute of Inorganic ChemistryUniversity of ViennaWaehringer Str. 42Vienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
- Institute of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 38Vienna1090Austria
| | - Benedict Regner
- Anna Spiegel Center of Translational ResearchDepartment of Medicine IMedical University ViennaLazarettgasse 14Vienna1090Austria
| | - Martin Schaier
- Institute of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 38Vienna1090Austria
| | - Nicolas Sgarioto
- Départment de pharmacologie et physiologieFaculté de médecineCentre de recherché de l hôpitalUniversité de MontréalSaint‐Justine (7.17.020), 3175 Chemin de la Côte Ste‐CatherineQuebecH3T1C5Canada
| | - Noël J.‐M. Raynal
- Départment de pharmacologie et physiologieFaculté de médecineCentre de recherché de l hôpitalUniversité de MontréalSaint‐Justine (7.17.020), 3175 Chemin de la Côte Ste‐CatherineQuebecH3T1C5Canada
| | - Karin Nowikovsky
- Unit of Physiology and BiophysicsDepartment of Biomedical SciencesUniversity of Veterinary Medicine ViennaVeterinaerplatz 1Vienna1210Austria
| | - Wolfgang M. Schmidt
- Neuromuscular Research DepartmentCenter for Anatomy and Cell BiologyMedical University of ViennaWähringer Str. 13Vienna1090Austria
| | - Petra Heffeter
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
| | - Samuel M. Meier‐Menches
- Institute of Inorganic ChemistryUniversity of ViennaWaehringer Str. 42Vienna1090Austria
- Joint Metabolome FacilityUniversity of Vienna and Medical University of ViennaWaehringer Str. 38Vienna1090Austria
- Institute of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 38Vienna1090Austria
| | - Gunda Koellensperger
- Institute of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 38Vienna1090Austria
| | - Bernhard K. Keppler
- Institute of Inorganic ChemistryUniversity of ViennaWaehringer Str. 42Vienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
| | - Walter Berger
- Center for Cancer Research and Comprehensive Cancer CenterMedical University ViennaBorschkegasse 8aVienna1090Austria
- Research Cluster “Translational Cancer Therapy Research”Vienna1090Austria
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10
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Miura K, Katsuki R, Yoshida S, Ohta R, Tamura T. Identification of EGF Receptor and Thrombospondin-1 as Endogenous Targets of ER-Associated Degradation Enhancer EDEM1 in HeLa Cells. Int J Mol Sci 2023; 24:12171. [PMID: 37569550 PMCID: PMC10418772 DOI: 10.3390/ijms241512171] [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: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Secretory and membrane proteins are vital for cell activities, including intra- and intercellular communication. Therefore, protein quality control in the endoplasmic reticulum (ER) is an essential and crucial process for eukaryotic cells. Endoplasmic reticulum-associated degradation (ERAD) targets misfolded proteins during the protein maturation process in the ER and leads to their disposal. This process maintains the ER productive function and prevents misfolded protein stress (i.e., ER stress). The ERAD-stimulating factor ER degradation-enhancing α mannosidase-like 1 protein (EDEM1) acts on misfolded proteins to accelerate ERAD, thereby maintaining the productivity of the ER. However, the detail mechanism underlying the function of EDEM1 in ERAD is not completely understood due to a lack of established physiological substrate proteins. In this study, we attempted to identify substrate proteins for EDEM1 using siRNA. The matrix component thrombospondin-1 (TSP1) and epidermal growth factor receptor (EGFR) were identified as candidate targets of EDEM1. Their protein maturation status and cellular localization were markedly affected by knockdown of EDEM1. We also showed that EDEM1 physically associates with EGFR and enhances EGFR degradation via ERAD. Our data highlight the physiological role of EDEM1 in maintaining specific target proteins and provide a potential approach to the regulation of expression of clinically important proteins.
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Affiliation(s)
- Kohta Miura
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Riko Katsuki
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Shusei Yoshida
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Ren Ohta
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Taku Tamura
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan
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11
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Vilen Z, Joeh E, Lee E, Huang ML. Surfaceome Profiling Identifies Basigin-Chaperoned Protein Clients. Chembiochem 2023; 24:e202300073. [PMID: 36973167 PMCID: PMC10424708 DOI: 10.1002/cbic.202300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]
Abstract
The surface proteome or "surfaceome" is a critical mediator of cellular biology, facilitating cell-to-cell interactions and communication with extracellular biomolecules. Constituents of the surfaceome can serve as biomarkers for changing cell states and as targets for pharmacological intervention. While some pathways of cell surface trafficking are well characterized to allow prediction of surface localization, some non-canonical trafficking mechanisms do not. Basigin (Bsg), a cell surface glycoprotein, has been shown to chaperone protein clients to the cell surface. However, understanding which proteins are served by Bsg is not always straightforward. To accelerate such identification, we applied a surfaceome proximity labeling method that is integrated with quantitative mass spectrometry-based proteomics to discern changes in the surfaceome of hepatic stellate cells that occur in response to the genetic loss of Bsg. Using this strategy, we observed that the loss of Bsg leads to corresponding reductions in the cell surface expression of monocarboxylate transporters MCT1 and MCT4. We also found that these relationships were unique to Bsg and not found in neuroplastin (Nptn), a related family member. These results establish the utility of the surfaceome proximity labeling method to determine clients of cell surface chaperone proteins.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Eugene Joeh
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Elizabeth Lee
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Mia L. Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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12
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Munteanu CVA, Chirițoiu GN, Petrescu AJ, Petrescu ȘM. Defining the altered glycoproteomic space of the early secretory pathway by class I mannosidase pharmacological inhibition. Front Mol Biosci 2023; 9:1064868. [PMID: 36699698 PMCID: PMC9869281 DOI: 10.3389/fmolb.2022.1064868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
N-glycosylation is a key process for various biological functions like protein folding, maturation and sorting for the conventional secretory compartment, cell-cell communication and immune response. This is usually accomplished by a complex system of mannosidases in which those from class I have an outstanding role, commonly involved in the early protein sorting associated to the Endoplasmic Reticulum (ER) in the N-glycan dependent quality control (ERQC) and ER-associated degradation (ERAD). Although these are vital processes in maintaining cellular homeostasis, large-scale analysis studies for this pool of molecules, further denoted as proteins from the early secretory pathway (ESP), were limited addressed. Here, using a custom workflow employing a combination of glycomics and deglycoproteomics analyses, using lectin affinity and selective Endoglycosidase H (Endo H) digestion, we scrutinize the steady-state oligomannosidic glycoprotein load and delineate ESP fraction in melanoma cells. All of these were assessed by applying our workflow for glycosite relative quantification of both the peptide chain and carbohydrate structure in cells with inhibited activity of class I mannosidases after kifunensine treatment. We found that most of the ESP are transient clients involved in cell communication via extracellular matrix, particularly integrin-mediated communication which adopt Man9 N-glycans in kifunensine-treated cells. Moreover, our results reveal that core-fucosylation is decreased subsequent inhibition of class I mannosidases and this could be explained by a general lower protein level of FUT8, the enzyme responsible for fucosylation. By comparing our data with results obtained following downregulation of a key mannosidase in misfolded protein degradation, we mapped both novel and previously suggested endogenous substrate candidates like PCDH2, HLA-B, LAMB2 or members of the integrin family of proteins such as ITGA1 and ITGA4, thus validating the findings obtained using our workflow regarding accumulation and characterization of ESP transitory members following mannosidase class I inhibition. This workflow and the associated dataset not only allowed us to investigate the oligomannosidic glycoprotein fraction but also to delineate differences mediated at glycosite-level upon kifunensine treatment and outline the potential associated cellular responses.
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Affiliation(s)
- Cristian V A Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Gabriela N Chirițoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Ștefana M Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
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13
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The protective effect of low-dose minocycline on brain microvascular ultrastructure in a rodent model of subarachnoid hemorrhage. Histochem Cell Biol 2023; 159:91-114. [PMID: 36153470 PMCID: PMC9899762 DOI: 10.1007/s00418-022-02150-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 02/07/2023]
Abstract
The multifaceted nature of subarachnoid hemorrhage (SAH) pathogenesis is poorly understood. To date, no pharmacological agent has been found to be efficacious for the prevention of brain injury when used for acute SAH intervention. This study was undertaken to evaluate the beneficial effects of low-dose neuroprotective agent minocycline on brain microvascular ultrastructures that have not been studied in detail. We studied SAH brain injury using an in vivo prechiasmatic subarachnoid hemorrhage rodent model. We analyzed the qualitative and quantitative ultrastructural morphology of capillaries and surrounding neuropil in the rodent brains with SAH and/or minocycline administration. Here, we report that low-dose minocycline (1 mg/kg) displayed protective effects on capillaries and surrounding cells from significant SAH-induced changes. Ultrastructural morphology analysis revealed also that minocycline stopped endothelial cells from abnormal production of vacuoles and vesicles that compromise blood-brain barrier (BBB) transcellular transport. The reported ultrastructural abnormalities as well as neuroprotective effects of minocycline during SAH were not directly mediated by inhibition of MMP-2, MMP-9, or EMMPRIN. However, SAH brain tissue treated with minocycline was protected from development of other morphological features associated with oxidative stress and the presence of immune cells in the perivascular space. These data advance the knowledge on the effect of SAH on brain tissue ultrastructure in an SAH rodent model and the neuroprotective effect of minocycline when administered in low doses.
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14
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Asgari R, Vaisi-Raygani A, Aleagha MSE, Mohammadi P, Bakhtiari M, Arghiani N. CD147 and MMPs as key factors in physiological and pathological processes. Biomed Pharmacother 2023; 157:113983. [PMID: 36370522 DOI: 10.1016/j.biopha.2022.113983] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Cluster of differentiation 147 (CD147) or extracellular matrix metalloproteinase inducer (EMMPRIN) is a transmembrane glycoprotein that induces the synthesis of matrix metalloproteinases (MMPs). MMPs, as zinc-dependent proteases and versatile enzymes, play critical roles in the degradation of the extracellular matrix (ECM) components, cleaving of the receptors of cellular surfaces, signaling molecules, and other precursor proteins, which may lead to attenuation or activation of such targets. CD147 and MMPs play essential roles in physiological and pathological conditions and any disorder in the expression, synthesis, or function of CD147 and MMPs may be associated with various types of disease. In this review, we have focused on the roles of CD147 and MMPs in some major physiological and pathological processes.
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Affiliation(s)
- Rezvan Asgari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Asad Vaisi-Raygani
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Sajad Emami Aleagha
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pantea Mohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mitra Bakhtiari
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Nahid Arghiani
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; School of Life Science, Department of Biochemistry and Biomedicine, University of Sussex, Brighton, United Kingdom.
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15
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Yu W, Lin Z, Woo CM, Baskin JM. A Chemoproteomics Approach to Profile Phospholipase D-Derived Phosphatidyl Alcohol Interactions. ACS Chem Biol 2022; 17:3276-3283. [PMID: 34908404 DOI: 10.1021/acschembio.1c00584] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alcohol consumption leads to formation of phosphatidylethanol (PEth) via the transphosphatidylation activity of phospholipase D (PLD) enzymes. Though this non-natural phospholipid routinely serves as a biomarker of chronic alcoholism, its pathophysiological roles remain unknown. We use a minimalist diazirine alkyne alcohol as an ethanol surrogate to generate clickable, photoaffinity lipid reporters of PEth localization and lipid-protein interactions via PLD-mediated transphosphatidylation. We use these tools to visualize phosphatidyl alcohols in a manner compatible with standard permeabilization and immunofluorescence methods. We also use click chemistry tagging, enrichment, and proteomics analysis to define the phosphatidyl alcohol interactome. Our analysis reveals an enrichment of putative interactors at various membrane locations, and we validate one such interaction with the single-pass transmembrane protein basigin/CD147. This study provides a comprehensive view of the molecular interactions of phosphatidyl alcohols with the cellular proteome and points to future work to connect such interactions to potential pathophysiological roles of PEth.
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Affiliation(s)
- Weizhi Yu
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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16
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Krshnan L, van de Weijer ML, Carvalho P. Endoplasmic Reticulum-Associated Protein Degradation. Cold Spring Harb Perspect Biol 2022; 14:a041247. [PMID: 35940909 PMCID: PMC9732900 DOI: 10.1101/cshperspect.a041247] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Misfolded, potentially toxic proteins in the lumen and membrane of the endoplasmic reticulum (ER) are eliminated by proteasomes in the cytosol through ER-associated degradation (ERAD). The ERAD process involves the recognition of substrates in the lumen and membrane of the ER, their translocation into the cytosol, ubiquitination, and delivery to the proteasome for degradation. These ERAD steps are performed by membrane-embedded ubiquitin-ligase complexes of different specificity that together cover a wide range of substrates. Besides misfolded proteins, ERAD further contributes to quality control by targeting unassembled and mislocalized proteins. ERAD also targets a restricted set of folded proteins to influence critical ER functions such as sterol biosynthesis, calcium homeostasis, or ER contacts with other organelles. This review describes the ubiquitin-ligase complexes and the principles guiding protein degradation by ERAD.
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Affiliation(s)
- Logesvaran Krshnan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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17
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Padovani C, Jevtić P, Rapé M. Quality control of protein complex composition. Mol Cell 2022; 82:1439-1450. [PMID: 35316660 DOI: 10.1016/j.molcel.2022.02.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/26/2022] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
Eukaryotic cells possess hundreds of protein complexes that contain multiple subunits and must be formed at the correct time and place during development. Despite specific assembly pathways, cells frequently encounter complexes with missing or aberrant subunits that can disrupt important signaling events. Cells, therefore, employ several ubiquitin-dependent quality control pathways that can prevent, correct, or degrade flawed complexes. In this review, we will discuss our emerging understanding of such quality control of protein complex composition.
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Affiliation(s)
- Chris Padovani
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Predrag Jevtić
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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18
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Li H, Sun S. Protein Aggregation in the ER: Calm behind the Storm. Cells 2021; 10:cells10123337. [PMID: 34943844 PMCID: PMC8699410 DOI: 10.3390/cells10123337] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
As one of the largest organelles in eukaryotic cells, the endoplasmic reticulum (ER) plays a vital role in the synthesis, folding, and assembly of secretory and membrane proteins. To maintain its homeostasis, the ER is equipped with an elaborate network of protein folding chaperones and multiple quality control pathways whose cooperative actions safeguard the fidelity of protein biogenesis. However, due to genetic abnormalities, the error-prone nature of protein folding and assembly, and/or defects or limited capacities of the protein quality control systems, nascent proteins may become misfolded and fail to exit the ER. If not cleared efficiently, the progressive accumulation of misfolded proteins within the ER may result in the formation of toxic protein aggregates, leading to the so-called “ER storage diseases”. In this review, we first summarize our current understanding of the protein folding and quality control networks in the ER, including chaperones, unfolded protein response (UPR), ER-associated protein degradation (ERAD), and ER-selective autophagy (ER-phagy). We then survey recent research progress on a few ER storage diseases, with a focus on the role of ER quality control in the disease etiology, followed by a discussion on outstanding questions and emerging concepts in the field.
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Affiliation(s)
- Haisen Li
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
| | - Shengyi Sun
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence:
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19
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Can ND, Basturk E, Kizilboga T, Akcay IM, Dingiloglu B, Tatli O, Acar S, Ozfiliz Kilbas P, Elbeyli E, Muratcioglu S, Jannuzzi AT, Gursoy A, Keskin O, Doganay HL, Karademir Yilmaz B, Dinler Doganay G. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation. PLoS One 2021; 16:e0256640. [PMID: 34428256 PMCID: PMC8384158 DOI: 10.1371/journal.pone.0256640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022] Open
Abstract
Bag-1 is a multifunctional protein that regulates Hsp70 chaperone activity, apoptosis, and proliferation. The three major Bag-1 isoforms have different subcellular localizations and partly non-overlapping functions. To identify the detailed interaction network of each isoform, we utilized mass spectrometry-based proteomics and found that interactomes of Bag-1 isoforms contained many common proteins, with variations in their abundances. Bag-1 interactomes were enriched with proteins involved in protein processing and degradation pathways. Novel interaction partners included VCP/p97; a transitional ER ATPase, Rad23B; a shuttling factor for ubiquitinated proteins, proteasome components, and ER-resident proteins, suggesting a role for Bag-1 also in ER-associated protein degradation (ERAD). Bag-1 pull-down from cells and tissues from breast cancer patients validated these interactions and showed cancer-related prominence. Using in silico predictions we detected hotspot residues of Bag-1. Mutations of these residues caused loss of binding to protein quality control elements and impaired proteasomal activity in MCF-7 cells. Following CD147 glycosylation pattern, we showed that Bag-1 downregulated VCP/p97-dependent ERAD. Overall, our data extends the interaction map of Bag-1, and broadens its role in protein homeostasis. Targeting the interaction surfaces revealed in this study might be an effective strategy in the treatment of cancer.
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Affiliation(s)
- Nisan Denizce Can
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
| | - Ezgi Basturk
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
| | - Tugba Kizilboga
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
| | - Izzet Mehmet Akcay
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
| | - Baran Dingiloglu
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Tatli
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
- Molecular Biology and Genetics Department, Istanbul Medeniyet University, Istanbul, Turkey
| | - Sevilay Acar
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
| | - Pelin Ozfiliz Kilbas
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Istanbul Kultur University, Istanbul, Turkey
| | - Efe Elbeyli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Ayse Tarbin Jannuzzi
- Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Istanbul University, Istanbul, Turkey
| | - Attila Gursoy
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | | | - Betul Karademir Yilmaz
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology—Genetics and Biotechnology, Istanbul Technical University, Istanbul, Turkey
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Fenech EJ, Ben-Dor S, Schuldiner M. Double the Fun, Double the Trouble: Paralogs and Homologs Functioning in the Endoplasmic Reticulum. Annu Rev Biochem 2021; 89:637-666. [PMID: 32569522 DOI: 10.1146/annurev-biochem-011520-104831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of eukaryotic genomes has been propelled by a series of gene duplication events, leading to an expansion in new functions and pathways. While duplicate genes may retain some functional redundancy, it is clear that to survive selection they cannot simply serve as a backup but rather must acquire distinct functions required for cellular processes to work accurately and efficiently. Understanding these differences and characterizing gene-specific functions is complex. Here we explore different gene pairs and families within the context of the endoplasmic reticulum (ER), the main cellular hub of lipid biosynthesis and the entry site for the secretory pathway. Focusing on each of the ER functions, we highlight specificities of related proteins and the capabilities conferred to cells through their conservation. More generally, these examples suggest why related genes have been maintained by evolutionary forces and provide a conceptual framework to experimentally determine why they have survived selection.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
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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
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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
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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.
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Discovery and Biological Evaluation of CD147 N-Glycan Inhibitors: A New Direction in the Treatment of Tumor Metastasis. Molecules 2020; 26:molecules26010033. [PMID: 33374805 PMCID: PMC7794696 DOI: 10.3390/molecules26010033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
N-glycosylation is instrumental to the regulation of CD147 functions, including the maturation of CD147, secretion of matrix metalloproteinases (MMPs), and promotion of tumor metastasis. Glycosylated CD147 is highly expressed in various cancer types, participates in metastasis, and is associated with the poor prognosis of malignant tumors. However, to date, there has been little development of target-specific inhibitors for CD147 glycosylation. In this work, we report a strategy for discovering CD147 glycosylation inhibitors through computer-aided screening and inhibition assays. Four compounds were screened as potential CD147 glycosylation inhibitors. Of these, compound 72 was finally identified as the best candidate. Further experiments confirmed that compound 72 inhibited the production of MMPs and the metastasis of cancer cells in the Hela cell line. Results further suggest that compound 72 could promote the expression of E-cadherin by targeting CD147, thereby inhibiting tumor migration. Finally, the structures of the other potential CD147 N-glycosylation inhibitors may eventually provide guidance for future optimization.
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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.
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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.
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Xu J, Zhao H, Wang T. Suppression of retinal degeneration by two novel ERAD ubiquitin E3 ligases SORDD1/2 in Drosophila. PLoS Genet 2020; 16:e1009172. [PMID: 33137101 PMCID: PMC7660902 DOI: 10.1371/journal.pgen.1009172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/12/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations in the gene rhodopsin are one of the major causes of autosomal dominant retinitis pigmentosa (adRP). Mutant forms of Rhodopsin frequently accumulate in the endoplasmic reticulum (ER), cause ER stress, and trigger photoreceptor cell degeneration. Here, we performed a genome-wide screen to identify suppressors of retinal degeneration in a Drosophila model of adRP, carrying a point mutation in the major rhodopsin, Rh1 (Rh1G69D). We identified two novel E3 ubiquitin ligases SORDD1 and SORDD2 that effectively suppressed Rh1G69D-induced photoreceptor dysfunction and retinal degeneration. SORDD1/2 promoted the ubiquitination and degradation of Rh1G69D through VCP (valosin containing protein) and independent of processes reliant on the HRD1 (HMG-CoA reductase degradation protein 1)/HRD3 complex. We further demonstrate that SORDD1/2 and HRD1 function in parallel and in a redundant fashion to maintain rhodopsin homeostasis and integrity of photoreceptor cells. These findings identify a new ER-associated protein degradation (ERAD) pathway and suggest that facilitating SORDD1/2 function may be a therapeutic strategy to treat adRP. Misfolded rhodopsins accumulated in endoplasmic reticulum (ER) could disrupt the homeostasis of the ER and cause ER stress. Chronic ER stress would finally lead to photoreceptor cell death and retinal degeneration. To diminish the stress and sustain homeostasis cells develop alternative strategies to clear the misfolded rhodopsins. Previous studies have suggested that ubiquitin E3 ligase HRD1 is involved in the degradation of misfolded rhodopsins. In this study, we define novel ubiquitin E3 ligase SORDD1/2 based on a genetic screen and demonstrate that SORDD1/2 promotes the degradation of misfolded rhodopsins through ER-associated degradation (ERAD) pathway. Furthermore, we demonstrate that SORDD1/2 function independently of HRD1 in misfolded rhodopsins degradation. We also show SORDD1/2 and HRD1 play redundant roles in rhodopsin homeostasis. Finally, we demonstrate that SORDD1 works well in a Drosophila disease model. Our studies identify a novel ERAD pathway that acts in parallel to HRD1, and suggest that SORDD1 is a good candidate therapeutic target.
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Affiliation(s)
- Jaiwei Xu
- College of Biological Sciences, China Agricultural University, China
- National Institute of Biological Sciences, China
| | - Haifang Zhao
- National Institute of Biological Sciences, China
| | - Tao Wang
- National Institute of Biological Sciences, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, China
- * E-mail:
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27
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Buck TM, Zeng X, Cantrell PS, Cattley RT, Hasanbasri Z, Yates ME, Nguyen D, Yates NA, Brodsky JL. The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation. Mol Cell Proteomics 2020; 19:1896-1909. [PMID: 32868373 DOI: 10.1074/mcp.ra120.002050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/06/2020] [Indexed: 01/13/2023] Open
Abstract
Studies in the yeast Saccharomyces cerevisiae have helped define mechanisms underlying the activity of the ubiquitin-proteasome system (UPS), uncover the proteasome assembly pathway, and link the UPS to the maintenance of cellular homeostasis. However, the spectrum of UPS substrates is incompletely defined, even though multiple techniques-including MS-have been used. Therefore, we developed a substrate trapping proteomics workflow to identify previously unknown UPS substrates. We first generated a yeast strain with an epitope tagged proteasome subunit to which a proteasome inhibitor could be applied. Parallel experiments utilized inhibitor insensitive strains or strains lacking the tagged subunit. After affinity isolation, enriched proteins were resolved, in-gel digested, and analyzed by high resolution liquid chromatography-tandem MS. A total of 149 proteasome partners were identified, including all 33 proteasome subunits. When we next compared data between inhibitor sensitive and resistant cells, 27 proteasome partners were significantly enriched. Among these proteins were known UPS substrates and proteins that escort ubiquitinated substrates to the proteasome. We also detected Erg25 as a high-confidence partner. Erg25 is a methyl oxidase that converts dimethylzymosterol to zymosterol, a precursor of the plasma membrane sterol, ergosterol. Because Erg25 is a resident of the endoplasmic reticulum (ER) and had not previously been directly characterized as a UPS substrate, we asked whether Erg25 is a target of the ER associated degradation (ERAD) pathway, which most commonly mediates proteasome-dependent destruction of aberrant proteins. As anticipated, Erg25 was ubiquitinated and associated with stalled proteasomes. Further, Erg25 degradation depended on ERAD-associated ubiquitin ligases and was regulated by sterol synthesis. These data expand the cohort of lipid biosynthetic enzymes targeted for ERAD, highlight the role of the UPS in maintaining ER function, and provide a novel tool to uncover other UPS substrates via manipulations of our engineered strain.
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Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA
| | - Pamela S Cantrell
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA
| | - Richard T Cattley
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA
| | - Zikri Hasanbasri
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Megan E Yates
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Diep Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nathan A Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, Pennsylvania, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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Min X, Zhang X, Li Y, Cao X, Cheng H, Li Y, Li C, Kong Q, Mao Q, Peng P, Ni Y, Li J, Duan Y, Liu L, Ding Z. HSPA12A unstabilizes CD147 to inhibit lactate export and migration in human renal cell carcinoma. Am J Cancer Res 2020; 10:8573-8590. [PMID: 32754264 PMCID: PMC7392002 DOI: 10.7150/thno.44321] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Metastasis accounts for 90% of cancer-associated mortality in patients with renal cell carcinoma (RCC). However, the clinical management of RCC metastasis is challenging. Lactate export is known to play an important role in cancer cell migration. This study investigated the role of heat shock protein A12A (HSPA12A) in RCC migration. Methods: HSPA12A expression was examined in 82 pairs of matched RCC tumors and corresponding normal kidney tissues from patients by immunoblotting and immunofluorescence analyses. The proliferation of RCC cells was analyzed using MTT and EdU incorporation assays. The migration of RCC cells was evaluated by wound healing and Transwell migration assays. Extracellular acidification was examined using Seahorse technology. Protein stability was determined following treatment with protein synthesis inhibitor cycloheximide and proteasome inhibitor MG132. Mass spectrometry, immunoprecipitation, and immunoblotting were employed to examine protein-protein interactions. Results: RCC tumors from patients showed downregulation of HSPA12A, which was associated with advanced tumor node metastasis stage. Intriguingly, overexpression of HSPA12A in RCC cells inhibited migration, whereas HSPA12A knockdown had the opposite effect. Lactate export, glycolysis rate, and CD147 protein abundance were also inhibited by HSPA12A overexpression but promoted by HSPA12A knockdown. An interaction of HSPA12A with HRD1 ubiquitin E3 ligase was detected in RCC cells. Further studies demonstrated that CD147 ubiquitination and proteasomal degradation were promoted by HSPA12A overexpression whereas inhibited by HSPA12A knockdown. Notably, the HSPA12A overexpression-induced inhibition of lactate export and migration were abolished by CD147 overexpression. Conclusion: Human RCC shows downregulation of HSPA12A. Overexpression of HSPA12A in RCC cells unstabilizes CD147 through increasing its ubiquitin-proteasome degradation, thereby inhibits lactate export and glycolysis, and ultimately suppresses RCC cell migration. Our results demonstrate that overexpression of HSPA12A might represent a viable strategy for managing RCC metastasis.
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29
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Qin X, Denton WD, Huiting LN, Smith KS, Feng H. Unraveling the regulatory role of endoplasmic-reticulum-associated degradation in tumor immunity. Crit Rev Biochem Mol Biol 2020; 55:322-353. [PMID: 32633575 DOI: 10.1080/10409238.2020.1784085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During malignant transformation and cancer progression, tumor cells face both intrinsic and extrinsic stress, endoplasmic reticulum (ER) stress in particular. To survive and proliferate, tumor cells use multiple stress response pathways to mitigate ER stress, promoting disease aggression and treatment resistance. Among the stress response pathways is ER-associated degradation (ERAD), which consists of multiple components and steps working together to ensure protein quality and quantity. In addition to its established role in stress responses and tumor cell survival, ERAD has recently been shown to regulate tumor immunity. Here we summarize current knowledge on how ERAD promotes protein degradation, regulates immune cell development and function, participates in antigen presentation, exerts paradoxical roles on tumorigenesis and immunity, and thus impacts current cancer therapy. Collectively, ERAD is a critical protein homeostasis pathway intertwined with cancer development and tumor immunity. Of particular importance is the need to further unveil ERAD's enigmatic roles in tumor immunity to develop effective targeted and combination therapy for successful treatment of cancer.
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Affiliation(s)
- Xiaodan Qin
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - William D Denton
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Leah N Huiting
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Kaylee S Smith
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Hui Feng
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
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30
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Fenech EJ, Lari F, Charles PD, Fischer R, Laétitia-Thézénas M, Bagola K, Paton AW, Paton JC, Gyrd-Hansen M, Kessler BM, Christianson JC. Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling. eLife 2020; 9:e57306. [PMID: 32614325 PMCID: PMC7332293 DOI: 10.7554/elife.57306] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/11/2020] [Indexed: 12/25/2022] Open
Abstract
Ubiquitin ligases (E3s) embedded in the endoplasmic reticulum (ER) membrane regulate essential cellular activities including protein quality control, calcium flux, and sterol homeostasis. At least 25 different, transmembrane domain (TMD)-containing E3s are predicted to be ER-localised, but for most their organisation and cellular roles remain poorly defined. Using a comparative proteomic workflow, we mapped over 450 protein-protein interactions for 21 stably expressed, full-length E3s. Bioinformatic analysis linked ER-E3s and their interactors to multiple homeostatic, regulatory, and metabolic pathways. Among these were four membrane-embedded interactors of RNF26, a polytopic E3 whose abundance is auto-regulated by ubiquitin-proteasome dependent degradation. RNF26 co-assembles with TMEM43, ENDOD1, TMEM33 and TMED1 to form a complex capable of modulating innate immune signalling through the cGAS-STING pathway. This RNF26 complex represents a new modulatory axis of STING and innate immune signalling at the ER membrane. Collectively, these data reveal the broad scope of regulation and differential functionalities mediated by ER-E3s for both membrane-tethered and cytoplasmic processes.
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Affiliation(s)
- Emma J Fenech
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Federica Lari
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Philip D Charles
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Marie Laétitia-Thézénas
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Katrin Bagola
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of AdelaideAdelaideAustralia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of AdelaideAdelaideAustralia
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - John C Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research CentreOxfordUnited Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Botnar Research CentreOxfordUnited Kingdom
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31
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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.
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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
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32
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Valosin-containing protein mediates the ERAD of squalene monooxygenase and its cholesterol-responsive degron. Biochem J 2019; 476:2545-2560. [DOI: 10.1042/bcj20190418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/17/2022]
Abstract
AbstractSqualene monooxygenase (SM) is an essential rate-limiting enzyme in cholesterol synthesis. SM degradation is accelerated by excess cholesterol, and this requires the first 100 amino acids of SM (SM N100). This process is part of a protein quality control pathway called endoplasmic reticulum-associated degradation (ERAD). In ERAD, SM is ubiquitinated by MARCH6, an E3 ubiquitin ligase located in the endoplasmic reticulum (ER). However, several details of the ERAD process for SM remain elusive, such as the extraction mechanism from the ER membrane. Here, we used SM N100 fused to GFP (SM N100-GFP) as a model degron to investigate the extraction process of SM in ERAD. We showed that valosin-containing protein (VCP) is important for the cholesterol-accelerated degradation of SM N100-GFP and SM. In addition, we revealed that VCP acts following ubiquitination of SM N100-GFP by MARCH6. We demonstrated that the amphipathic helix (Gln62–Leu73) of SM N100-GFP is critical for regulation by VCP and MARCH6. Replacing this amphipathic helix with hydrophobic re-entrant loops promoted degradation in a VCP-dependent manner. Finally, we showed that inhibiting VCP increases cellular squalene and cholesterol levels, indicating a functional consequence for VCP in regulating the cholesterol synthesis pathway. Collectively, we established VCP plays a key role in ERAD that contributes to the cholesterol-mediated regulation of SM.
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33
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Gottlieb CD, Thompson ACS, Ordureau A, Harper JW, Kopito RR. Acute unfolding of a single protein immediately stimulates recruitment of ubiquitin protein ligase E3C (UBE3C) to 26S proteasomes. J Biol Chem 2019; 294:16511-16524. [PMID: 31375563 DOI: 10.1074/jbc.ra119.009654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
The intracellular accumulation of aggregated misfolded proteins is a cytopathological hallmark of neurodegenerative diseases. However, the functional relationship between protein misfolding or aggregation and the cellular proteostasis network that monitors and maintains proteome health is poorly understood. Previous studies have associated translational suppression and transcriptional remodeling with the appearance of protein aggregates, but whether these responses are induced by aggregates or their misfolded monomeric or oligomeric precursors remains unclear. Because aggregation in cells is rapid, nonlinear, and asynchronous, it has not been possible to deconvolve these kinetically linked processes to determine the earliest cellular responses to misfolded proteins. Upon removal of the synthetic, biologically inert ligand shield-1 (S1), AgDD, an engineered variant FK506-binding protein (FKBP1A), rapidly (t ½ ∼5 min) unfolds and self-associates, forming detergent-insoluble, microscopic cytoplasmic aggregates. Using global diglycine-capture (K-GG) proteomics, we found here that this solubility transition is associated with immediate increases in ubiquitylation of AgDD itself, along with that of endogenous proteins that are components of the ribosome and the 26S proteasome. We also found that the earliest cellular responses to acute S1 removal include recruitment of ubiquitin protein ligase E3C (UBE3C) to the 26S proteasome and ubiquitylation of two key proteasomal ubiquitin receptors, 26S proteasome regulatory subunit RPN10 (RPN10) and Rpn13 homolog (RPN13 or ADRM1). We conclude that these proteasomal responses are due to AgDD protein misfolding and not to the presence of detergent-insoluble aggregates.
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Affiliation(s)
- Colin D Gottlieb
- Department of Biology, Stanford University, Stanford, California 94305
| | | | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, California 94305
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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.
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35
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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: 98] [Impact Index Per Article: 14.0] [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.
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Menzies SA, Volkmar N, van den Boomen DJH, Timms RT, Dickson AS, Nathan JA, Lehner PJ. The sterol-responsive RNF145 E3 ubiquitin ligase mediates the degradation of HMG-CoA reductase together with gp78 and Hrd1. eLife 2018; 7:e40009. [PMID: 30543180 PMCID: PMC6292692 DOI: 10.7554/elife.40009] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/19/2018] [Indexed: 02/02/2023] Open
Abstract
Mammalian HMG-CoA reductase (HMGCR), the rate-limiting enzyme of the cholesterol biosynthetic pathway and the therapeutic target of statins, is post-transcriptionally regulated by sterol-accelerated degradation. Under cholesterol-replete conditions, HMGCR is ubiquitinated and degraded, but the identity of the E3 ubiquitin ligase(s) responsible for mammalian HMGCR turnover remains controversial. Using systematic, unbiased CRISPR/Cas9 genome-wide screens with a sterol-sensitive endogenous HMGCR reporter, we comprehensively map the E3 ligase landscape required for sterol-accelerated HMGCR degradation. We find that RNF145 and gp78 independently co-ordinate HMGCR ubiquitination and degradation. RNF145, a sterol-responsive ER-resident E3 ligase, is unstable but accumulates following sterol depletion. Sterol addition triggers RNF145 recruitment to HMGCR via Insigs, promoting HMGCR ubiquitination and proteasome-mediated degradation. In the absence of both RNF145 and gp78, Hrd1, a third UBE2G2-dependent E3 ligase, partially regulates HMGCR activity. Our findings reveal a critical role for the sterol-responsive RNF145 in HMGCR regulation and elucidate the complexity of sterol-accelerated HMGCR degradation. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Sam A Menzies
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Norbert Volkmar
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | | | - Richard T Timms
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Anna S Dickson
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - James A Nathan
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Paul J Lehner
- Department of MedicineCambridge Institute for Medical ResearchCambridgeUnited Kingdom
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Ye Y, Baek SH, Ye Y, Zhang T. Proteomic characterization of endogenous substrates of mammalian ubiquitin ligase Hrd1. Cell Biosci 2018; 8:46. [PMID: 30167107 PMCID: PMC6103995 DOI: 10.1186/s13578-018-0245-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/14/2018] [Indexed: 11/23/2022] Open
Abstract
Background Endoplasmic reticulum (ER)-associated degradation (ERAD) regulates protein homeostasis in the secretory pathway by targeting misfolded or unassembled proteins for degradation by the proteasome. Hrd1 is a conserved multi-spanning membrane bound ubiquitin ligase required for ubiquitination of many aberrant ER proteins, but few endogenous substrates of Hrd1 have been identified to date. Methods Using a SILAC-based quantitative proteomic approach combined with CRISPR-mediated gene silencing, we searched for endogenous physiological substrates of Hrd1. We used RNA microarray, immunoblotting, cycloheximide chase combined with chemical genetics to define the role of Hrd1 in regulating the stability of endogenous ERAD substrates. Results We identified 58 proteins whose levels are consistently upregulated in Hrd1 null HEK293 cells. Many of these proteins function in pathways involved in stress adaptation or immune surveillance. We validated OS9, a lectin required for ERAD of glycoproteins as a highly upregulated protein in Hrd1 deficient cells. Moreover, the abundance of OS9 is inversely correlated with Hrd1 level in clinical synovium samples isolated from osteoarthritis and rheumatoid arthritis patients. Intriguingly, immunoblotting detects two OS9 variants, both of which are upregulated when Hrd1 is inactivated. However, only one of these variants is subject to proteasome dependent degradation that requires Hrd1 and the AAA (ATPase associated with diverse cellular activities) ATPase p97. The stability of the other variant on the other hand is influenced by a lysosomal inhibitor. Conclusion Hrd1 regulates the stability of proteins involved in ER stress response and immune activation by both proteasome dependent and independent mechanisms. Electronic supplementary material The online version of this article (10.1186/s13578-018-0245-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yilin Ye
- 1Department of Orthopedics, Peking University First Hospital, Beijing, 100034 China
| | - Suk-Hwan Baek
- 2Department of Biochemistry & Molecular Biology, College of Medicine, Yeungnam University, Gyeongsan, 38541 South Korea
| | - Yihong Ye
- 3Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ting Zhang
- 3Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA.,SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055 China
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Stefanovic-Barrett S, Dickson AS, Burr SP, Williamson JC, Lobb IT, van den Boomen DJ, Lehner PJ, Nathan JA. MARCH6 and TRC8 facilitate the quality control of cytosolic and tail-anchored proteins. EMBO Rep 2018; 19:e45603. [PMID: 29519897 PMCID: PMC5934766 DOI: 10.15252/embr.201745603] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/26/2022] Open
Abstract
Misfolded or damaged proteins are typically targeted for destruction by proteasome-mediated degradation, but the mammalian ubiquitin machinery involved is incompletely understood. Here, using forward genetic screens in human cells, we find that the proteasome-mediated degradation of the soluble misfolded reporter, mCherry-CL1, involves two ER-resident E3 ligases, MARCH6 and TRC8. mCherry-CL1 degradation is routed via the ER membrane and dependent on the hydrophobicity of the substrate, with complete stabilisation only observed in double knockout MARCH6/TRC8 cells. To identify a more physiological correlate, we used quantitative mass spectrometry and found that TRC8 and MARCH6 depletion altered the turnover of the tail-anchored protein heme oxygenase-1 (HO-1). These E3 ligases associate with the intramembrane cleaving signal peptide peptidase (SPP) and facilitate the degradation of HO-1 following intramembrane proteolysis. Our results highlight how ER-resident ligases may target the same substrates, but work independently of each other, to optimise the protein quality control of selected soluble and tail-anchored proteins.
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Affiliation(s)
- Sandra Stefanovic-Barrett
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Anna S Dickson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Stephen P Burr
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - James C Williamson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Ian T Lobb
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Dick Jh van den Boomen
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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van der Goot AT, Pearce MMP, Leto DE, Shaler TA, Kopito RR. Redundant and Antagonistic Roles of XTP3B and OS9 in Decoding Glycan and Non-glycan Degrons in ER-Associated Degradation. Mol Cell 2018; 70:516-530.e6. [PMID: 29706535 DOI: 10.1016/j.molcel.2018.03.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 02/15/2018] [Accepted: 03/21/2018] [Indexed: 12/25/2022]
Abstract
Glycoproteins engaged in unproductive folding in the ER are marked for degradation by a signal generated by progressive demannosylation of substrate N-glycans that is decoded by ER lectins, but how the two lectins, OS9 and XTP3B, contribute to non-glycosylated protein triage is unknown. We generated cell lines with homozygous deletions of both lectins individually and in combination. We found that OS9 and XTP3B redundantly promote glycoprotein degradation and stabilize the SEL1L/HRD1 dislocon complex, that XTP3B profoundly inhibits the degradation of non-glycosylated proteins, and that OS9 antagonizes this inhibition. The relative expression of OS9 and XTP3B and the distribution of glycan and non-glycan degrons within the same protein contribute to the fidelity and processivity of glycoprotein triage and, therefore, determine the fates of newly synthesized proteins in the early secretory pathway.
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Affiliation(s)
| | | | - Dara E Leto
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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40
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Huang EY, To M, Tran E, Dionisio LTA, Cho HJ, Baney KLM, Pataki CI, Olzmann JA. A VCP inhibitor substrate trapping approach (VISTA) enables proteomic profiling of endogenous ERAD substrates. Mol Biol Cell 2018. [PMID: 29514927 PMCID: PMC5921570 DOI: 10.1091/mbc.e17-08-0514] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A new substrate trapping strategy that couples VCP inhibition and quantitative ubiquitin proteomics identifies endogenous ERAD substrates, expanding the available toolbox of strategies for global analysis of the ERAD substrate landscape. Endoplasmic reticulum (ER)–associated degradation (ERAD) mediates the proteasomal clearance of proteins from the early secretory pathway. In this process, ubiquitinated substrates are extracted from membrane-embedded dislocation complexes by the AAA ATPase VCP and targeted to the cytosolic 26S proteasome. In addition to its well-established role in the degradation of misfolded proteins, ERAD also regulates the abundance of key proteins such as enzymes involved in cholesterol synthesis. However, due to the lack of generalizable methods, our understanding of the scope of proteins targeted by ERAD remains limited. To overcome this obstacle, we developed a VCP inhibitor substrate trapping approach (VISTA) to identify endogenous ERAD substrates. VISTA exploits the small-molecule VCP inhibitor CB5083 to trap ERAD substrates in a membrane-associated, ubiquitinated form. This strategy, coupled with quantitative ubiquitin proteomics, identified previously validated (e.g., ApoB100, Insig2, and DHCR7) and novel (e.g., SCD1 and RNF5) ERAD substrates in cultured human hepatocellular carcinoma cells. Moreover, our results indicate that RNF5 autoubiquitination on multiple lysine residues targets it for ubiquitin and VCP-dependent clearance. Thus, VISTA provides a generalizable discovery method that expands the available toolbox of strategies to elucidate the ERAD substrate landscape.
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Affiliation(s)
- Edmond Y Huang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Milton To
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Erica Tran
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Lorraine T Ador Dionisio
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Hyejin J Cho
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Katherine L M Baney
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Camille I Pataki
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
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41
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Bersuker K, Peterson CWH, To M, Sahl SJ, Savikhin V, Grossman EA, Nomura DK, Olzmann JA. A Proximity Labeling Strategy Provides Insights into the Composition and Dynamics of Lipid Droplet Proteomes. Dev Cell 2017; 44:97-112.e7. [PMID: 29275994 DOI: 10.1016/j.devcel.2017.11.020] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 01/06/2023]
Abstract
Lipid droplet (LD) functions are regulated by a complement of integral and peripheral proteins that associate with the bounding LD phospholipid monolayer. Defining the composition of the LD proteome has remained a challenge due to the presence of contaminating proteins in LD-enriched buoyant fractions. To overcome this limitation, we developed a proximity labeling strategy that exploits LD-targeted APEX2 to biotinylate LD proteins in living cells. Application of this approach to two different cell types identified the vast majority of previously validated LD proteins, excluded common contaminating proteins, and revealed new LD proteins. Moreover, quantitative analysis of LD proteome dynamics uncovered a role for endoplasmic reticulum-associated degradation in controlling the composition of the LD proteome. These data provide an important resource for future LD studies and demonstrate the utility of proximity labeling to study the regulation of LD proteomes.
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Affiliation(s)
- Kirill Bersuker
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Clark W H Peterson
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Milton To
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Steffen J Sahl
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Victoria Savikhin
- SLAC National Accelerator Center, SSRL, Menlo Park, CA 94025, USA; Stanford Electrical Engineering Department, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth A Grossman
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
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42
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Wang T, Wang B, Huang H, Zhang C, Zhu Y, Pei B, Cheng C, Sun L, Wang J, Jin Q, Zhao Z. Enterovirus 71 protease 2Apro and 3Cpro differentially inhibit the cellular endoplasmic reticulum-associated degradation (ERAD) pathway via distinct mechanisms, and enterovirus 71 hijacks ERAD component p97 to promote its replication. PLoS Pathog 2017; 13:e1006674. [PMID: 28985237 PMCID: PMC5650186 DOI: 10.1371/journal.ppat.1006674] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 10/20/2017] [Accepted: 09/28/2017] [Indexed: 11/19/2022] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is an important function for cellular homeostasis. The mechanism of how picornavirus infection interferes with ERAD remains unclear. In this study, we demonstrated that enterovirus 71 (EV71) infection significantly inhibits cellular ERAD by targeting multiple key ERAD molecules with its proteases 2Apro and 3Cpro using different mechanisms. Ubc6e was identified as the key E2 ubiquitin-conjugating enzyme in EV71 disturbed ERAD. EV71 3Cpro cleaves Ubc6e at Q219G, Q260S, and Q273G. EV71 2Apro mainly inhibits the de novo synthesis of key ERAD molecules Herp and VIMP at the protein translational level. Herp differentially participates in the degradation of different glycosylated ERAD substrates α-1 antitrypsin Null Hong Kong (NHK) and the C-terminus of sonic hedgehog (SHH-C) via unknown mechanisms. p97 was identified as a host factor in EV71 replication; it redistributed and co-exists with the viral protein and other known replication-related molecules in EV71-induced replication organelles. Electron microscopy and multiple-color confocal assays also showed that EV71-induced membranous vesicles were closely associated with the endoplasmic reticulum (ER), and the ER membrane molecule RTN3 was redistributed to the viral replication complex during EV71 infection. Therefore, we propose that EV71 rearranges ER membranes and hijacks p97 from cellular ERAD to benefit its replication. These findings add to our understanding of how viruses disturb ERAD and provide potential anti-viral targets for EV71 infection.
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Affiliation(s)
- Tao Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Bei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - He Huang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Chongyang Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Yuanmei Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Bin Pei
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Chaofei Cheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Lei Sun
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- * E-mail: (JWW); (QJ); (ZDZ)
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- * E-mail: (JWW); (QJ); (ZDZ)
| | - Zhendong Zhao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Center of Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- CAMS-Oxford University International Center for Translational Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- * E-mail: (JWW); (QJ); (ZDZ)
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43
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Schulz J, Avci D, Queisser MA, Gutschmidt A, Dreher LS, Fenech EJ, Volkmar N, Hayashi Y, Hoppe T, Christianson JC. Conserved cytoplasmic domains promote Hrd1 ubiquitin ligase complex formation for ER-associated degradation (ERAD). J Cell Sci 2017; 130:3322-3335. [PMID: 28827405 DOI: 10.1242/jcs.206847] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/16/2017] [Indexed: 12/20/2022] Open
Abstract
The mammalian ubiquitin ligase Hrd1 is the central component of a complex facilitating degradation of misfolded proteins during the ubiquitin-proteasome-dependent process of ER-associated degradation (ERAD). Hrd1 associates with cofactors to execute ERAD, but their roles and how they assemble with Hrd1 are not well understood. Here, we identify crucial cofactor interaction domains within Hrd1 and report a previously unrecognised evolutionarily conserved segment within the intrinsically disordered cytoplasmic domain of Hrd1 (termed the HAF-H domain), which engages complementary segments in the cofactors FAM8A1 and Herp (also known as HERPUD1). This domain is required by Hrd1 to interact with both FAM8A1 and Herp, as well as to assemble higher-order Hrd1 complexes. FAM8A1 enhances binding of Herp to Hrd1, an interaction that is required for ERAD. Our findings support a model of Hrd1 complex formation, where the Hrd1 cytoplasmic domain and FAM8A1 have a central role in the assembly and activity of this ERAD machinery.
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Affiliation(s)
- Jasmin Schulz
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Dönem Avci
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Markus A Queisser
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Aljona Gutschmidt
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Lena-Sophie Dreher
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Emma J Fenech
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Norbert Volkmar
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Yuki Hayashi
- Department of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - John C Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
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Printsev I, Curiel D, Carraway KL. Membrane Protein Quantity Control at the Endoplasmic Reticulum. J Membr Biol 2017; 250:379-392. [PMID: 27743014 PMCID: PMC5392169 DOI: 10.1007/s00232-016-9931-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023]
Abstract
The canonical function of the endoplasmic reticulum-associated degradation (ERAD) system is to enforce quality control among membrane-associated proteins by targeting misfolded secreted, intra-organellar, and intramembrane proteins for degradation. However, increasing evidence suggests that ERAD additionally functions in maintaining appropriate levels of a subset of membrane-associated proteins. In this 'quantity control' capacity, ERAD responds to environmental cues to regulate the proteasomal degradation of specific ERAD substrates according to cellular need. In this review, we discuss in detail seven proteins that are targeted by the ERAD quantity control system. Not surprisingly, ERAD-mediated protein degradation is a key regulatory feature of a variety of ER-resident proteins, including HMG-CoA reductase, cytochrome P450 3A4, IP3 receptor, and type II iodothyronine deiodinase. In addition, the ERAD quantity control system plays roles in maintaining the proper stoichiometry of multi-protein complexes by mediating the degradation of components that are produced in excess of the limiting subunit. Perhaps somewhat unexpectedly, recent evidence suggests that the ERAD quantity control system also contributes to the regulation of plasma membrane-localized signaling receptors, including the ErbB3 receptor tyrosine kinase and the GABA neurotransmitter receptors. For these substrates, a proportion of the newly synthesized yet properly folded receptors are diverted for degradation at the ER, and are unable to traffic to the plasma membrane. Given that receptor abundance or concentration within the plasma membrane plays key roles in determining signaling efficiency, these observations may point to a novel mechanism for modulating receptor-mediated cellular signaling.
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Affiliation(s)
- Ignat Printsev
- Department of Biochemistry and Molecular Medicine, and UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, Research Building III, Room 1100B, 4645 2nd Avenue, Sacramento, CA, 95817, USA
| | - Daniel Curiel
- Department of Biochemistry and Molecular Medicine, and UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, Research Building III, Room 1100B, 4645 2nd Avenue, Sacramento, CA, 95817, USA
| | - Kermit L Carraway
- Department of Biochemistry and Molecular Medicine, and UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, Research Building III, Room 1100B, 4645 2nd Avenue, Sacramento, CA, 95817, USA.
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45
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The evolving role of ubiquitin modification in endoplasmic reticulum-associated degradation. Biochem J 2017; 474:445-469. [PMID: 28159894 DOI: 10.1042/bcj20160582] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022]
Abstract
The endoplasmic reticulum (ER) serves as a warehouse for factors that augment and control the biogenesis of nascent proteins entering the secretory pathway. In turn, this compartment also harbors the machinery that responds to the presence of misfolded proteins by targeting them for proteolysis via a process known as ER-associated degradation (ERAD). During ERAD, substrates are selected, modified with ubiquitin, removed from the ER, and then degraded by the cytoplasmic 26S proteasome. While integral membrane proteins can directly access the ubiquitination machinery that resides in the cytoplasm or on the cytoplasmic face of the ER membrane, soluble ERAD substrates within the lumen must be retrotranslocated from this compartment. In either case, nearly all ERAD substrates are tagged with a polyubiquitin chain, a modification that represents a commitment step to degrade aberrant proteins. However, increasing evidence indicates that the polyubiquitin chain on ERAD substrates can be further modified, serves to recruit ERAD-requiring factors, and may regulate the ERAD machinery. Amino acid side chains other than lysine on ERAD substrates can also be modified with ubiquitin, and post-translational modifications that affect substrate ubiquitination have been observed. Here, we summarize these data and provide an overview of questions driving this field of research.
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46
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Bersuker K, Olzmann JA. Establishing the lipid droplet proteome: Mechanisms of lipid droplet protein targeting and degradation. Biochim Biophys Acta Mol Cell Biol Lipids 2017. [PMID: 28627435 DOI: 10.1016/j.bbalip.2017.06.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipid droplets (LDs) are ubiquitous, endoplasmic reticulum (ER)-derived organelles that mediate the sequestration of neutral lipids (e.g. triacylglycerol and sterol esters), providing a dynamic cellular storage depot for rapid lipid mobilization in response to increased cellular demands. LDs have a unique ultrastructure, consisting of a core of neutral lipids encircled by a phospholipid monolayer that is decorated with integral and peripheral proteins. The LD proteome contains numerous lipid metabolic enzymes, regulatory scaffold proteins, proteins involved in LD clustering and fusion, and other proteins of unknown functions. The cellular role of LDs is inherently determined by the composition of its proteome and alteration of the LD protein coat provides a powerful mechanism to adapt LDs to fluctuating metabolic states. Here, we review the current understanding of the molecular mechanisms that govern LD protein targeting and degradation. This article is part of a Special Issue entitled: Recent Advances in Lipid Droplet Biology edited by Rosalind Coleman and Matthijs Hesselink.
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Affiliation(s)
- Kirill Bersuker
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA.
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47
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Hwang J, Walczak CP, Shaler TA, Olzmann JA, Zhang L, Elias JE, Kopito RR. Characterization of protein complexes of the endoplasmic reticulum-associated degradation E3 ubiquitin ligase Hrd1. J Biol Chem 2017; 292:9104-9116. [PMID: 28411238 PMCID: PMC5454095 DOI: 10.1074/jbc.m117.785055] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/05/2017] [Indexed: 12/20/2022] Open
Abstract
Hrd1 is the core structural component of a large endoplasmic reticulum membrane-embedded protein complex that coordinates the destruction of folding-defective proteins in the early secretory pathway. Defining the composition, dynamics, and ultimately, the structure of the Hrd1 complex is a crucial step in understanding the molecular basis of glycoprotein quality control but has been hampered by the lack of suitable techniques to interrogate this complex under native conditions. In this study we used genome editing to generate clonal HEK293 (Hrd1.KI) cells harboring a homozygous insertion of a small tandem affinity tag knocked into the endogenous Hrd1 locus. We found that steady-state levels of tagged Hrd1 in these cells are indistinguishable from those of Hrd1 in unmodified cells and that the tagged variant is functional in supporting the degradation of well characterized luminal and membrane substrates. Analysis of detergent-solubilized Hrd1.KI cells indicates that the composition and stoichiometry of Hrd1 complexes are strongly influenced by Hrd1 expression levels. Analysis of affinity-captured Hrd1 complexes from these cells by size-exclusion chromatography, immunodepletion, and absolute quantification mass spectrometry identified two major high-molecular-mass complexes with distinct sets of interacting proteins and variable stoichiometries, suggesting a hitherto unrecognized heterogeneity in the functional units of Hrd1-mediated protein degradation.
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Affiliation(s)
| | | | | | | | - Lichao Zhang
- Chemical and Systems Biology, Stanford University, Stanford, California 94305 and
| | - Joshua E Elias
- Chemical and Systems Biology, Stanford University, Stanford, California 94305 and
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48
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Ward BK, Rea SL, Magno AL, Pedersen B, Brown SJ, Mullin S, Arulpragasam A, Ingley E, Conigrave AD, Ratajczak T. The endoplasmic reticulum-associated protein, OS-9, behaves as a lectin in targeting the immature calcium-sensing receptor. J Cell Physiol 2017; 233:38-56. [PMID: 28419469 DOI: 10.1002/jcp.25957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 04/13/2017] [Indexed: 11/07/2022]
Abstract
The mechanisms responsible for the processing and quality control of the calcium-sensing receptor (CaSR) in the endoplasmic reticulum (ER) are largely unknown. In a yeast two-hybrid screen of the CaSR C-terminal tail (residues 865-1078), we identified osteosarcoma-9 (OS-9) protein as a binding partner. OS-9 is an ER-resident lectin that targets misfolded glycoproteins to the ER-associated degradation (ERAD) pathway through recognition of specific N-glycans by its mannose-6-phosphate receptor homology (MRH) domain. We show by confocal microscopy that the CaSR and OS-9 co-localize in the ER in COS-1 cells. In immunoprecipitation studies with co-expressed OS-9 and CaSR, OS-9 specifically bound the immature form of wild-type CaSR in the ER. OS-9 also bound the immature forms of a CaSR C-terminal deletion mutant and a C677A mutant that remains trapped in the ER, although binding to neither mutant was favored over wild-type receptor. OS-9 binding to immature CaSR required the MRH domain of OS-9 indicating that OS-9 acts as a lectin most likely to target misfolded CaSR to ERAD. Our results also identify two distinct binding interactions between OS-9 and the CaSR, one involving both C-terminal domains of the two proteins and the other involving both N-terminal domains. This suggests the possibility of more than one functional interaction between OS-9 and the CaSR. When we investigated the functional consequences of altered OS-9 expression, neither knockdown nor overexpression of OS-9 was found to have a significant effect on CaSR cell surface expression or CaSR-mediated ERK1/2 phosphorylation.
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Affiliation(s)
- Bryan K Ward
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Laboratory for Molecular Endocrinology, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Sarah L Rea
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Laboratory for Molecular Endocrinology, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Aaron L Magno
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Laboratory for Molecular Endocrinology, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Bernadette Pedersen
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Laboratory for Molecular Endocrinology, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Shelby Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Ajanthy Arulpragasam
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Laboratory for Molecular Endocrinology, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Evan Ingley
- Cell Signalling Group, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Arthur D Conigrave
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, New South Wales, Australia
| | - Thomas Ratajczak
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Laboratory for Molecular Endocrinology, Harry Perkins Institute of Medical Research and the Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
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49
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Qi L, Tsai B, Arvan P. New Insights into the Physiological Role of Endoplasmic Reticulum-Associated Degradation. Trends Cell Biol 2017; 27:430-440. [PMID: 28131647 DOI: 10.1016/j.tcb.2016.12.002] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/04/2016] [Accepted: 12/23/2016] [Indexed: 12/13/2022]
Abstract
Many human diseases are associated with mutations causing protein misfolding and aggregation in the endoplasmic reticulum (ER). ER-associated degradation (ERAD) is a principal quality-control mechanism responsible for targeting misfolded ER proteins for cytosolic degradation. However, despite years of effort, the physiological role of ERAD in vivo remains largely unknown. Several recent studies have reported intriguing phenotypes of mice deficient for ERAD function in specific cell types. These studies highlight that mammalian ERAD has been designed to perform a wide-range of cell-type-specific functions in vivo in a substrate-dependent manner.
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Affiliation(s)
- Ling Qi
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA.
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| | - Peter Arvan
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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50
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To M, Peterson CWH, Roberts MA, Counihan JL, Wu TT, Forster MS, Nomura DK, Olzmann JA. Lipid disequilibrium disrupts ER proteostasis by impairing ERAD substrate glycan trimming and dislocation. Mol Biol Cell 2016; 28:270-284. [PMID: 27881664 PMCID: PMC5231896 DOI: 10.1091/mbc.e16-07-0483] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/09/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
The endoplasmic reticulum (ER) mediates the folding, maturation, and deployment of the secretory proteome. Proteins that fail to achieve their native conformation are retained in the ER and targeted for clearance by ER-associated degradation (ERAD), a sophisticated process that mediates the ubiquitin-dependent delivery of substrates to the 26S proteasome for proteolysis. Recent findings indicate that inhibition of long-chain acyl-CoA synthetases with triacsin C, a fatty acid analogue, impairs lipid droplet (LD) biogenesis and ERAD, suggesting a role for LDs in ERAD. However, whether LDs are involved in the ERAD process remains an outstanding question. Using chemical and genetic approaches to disrupt diacylglycerol acyltransferase (DGAT)-dependent LD biogenesis, we provide evidence that LDs are dispensable for ERAD in mammalian cells. Instead, our results suggest that triacsin C causes global alterations in the cellular lipid landscape that disrupt ER proteostasis by interfering with the glycan trimming and dislocation steps of ERAD. Prolonged triacsin C treatment activates both the IRE1 and PERK branches of the unfolded protein response and ultimately leads to IRE1-dependent cell death. These findings identify an intimate relationship between fatty acid metabolism and ER proteostasis that influences cell viability.
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Affiliation(s)
- Milton To
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Clark W H Peterson
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Melissa A Roberts
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Jessica L Counihan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Tiffany T Wu
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Mercedes S Forster
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
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