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Kamada Y, Ohnishi Y, Nakashima C, Fujii A, Terakawa M, Hamano I, Nakayamada U, Katoh S, Hirata N, Tateishi H, Fukuda R, Takahashi H, Lukacs GL, Okiyoneda T. HERC3 facilitates ERAD of select membrane proteins by recognizing membrane-spanning domains. J Cell Biol 2024; 223:e202308003. [PMID: 38722278 PMCID: PMC11082371 DOI: 10.1083/jcb.202308003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant proteins located in the endoplasmic reticulum (ER) undergo rapid ubiquitination by multiple ubiquitin (Ub) E3 ligases and are retrotranslocated to the cytosol as part of the ER-associated degradation (ERAD). Despite several ERAD branches involving different Ub E3 ligases, the molecular machinery responsible for these ERAD branches in mammalian cells remains not fully understood. Through a series of multiplex knockdown/knockout experiments with real-time kinetic measurements, we demonstrate that HERC3 operates independently of the ER-embedded ubiquitin ligases RNF5 and RNF185 (RNF5/185) to mediate the retrotranslocation and ERAD of misfolded CFTR. While RNF5/185 participates in the ERAD process of both misfolded ABCB1 and CFTR, HERC3 uniquely promotes CFTR ERAD. In vitro assay revealed that HERC3 directly interacts with the exposed membrane-spanning domains (MSDs) of CFTR but not with the MSDs embedded in liposomes. Therefore, HERC3 could play a role in the quality control of MSDs in the cytoplasm and might be crucial for the ERAD pathway of select membrane proteins.
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Affiliation(s)
- Yuka Kamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Yuko Ohnishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Chikako Nakashima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Aika Fujii
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Mana Terakawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ikuto Hamano
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Uta Nakayamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Saori Katoh
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Noriaki Hirata
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hazuki Tateishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), Ehime University, Matsuyama, Japan
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, Canada
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
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Katsuki R, Kanuka M, Ohta R, Yoshida S, Tamura T. Turnover of EDEM1, an ERAD-enhancing factor, is mediated by multiple degradation routes. Genes Cells 2024; 29:486-502. [PMID: 38682256 PMCID: PMC11163939 DOI: 10.1111/gtc.13117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 05/01/2024]
Abstract
Quality-based protein production and degradation in the endoplasmic reticulum (ER) are essential for eukaryotic cell survival. During protein maturation in the ER, misfolded or unassembled proteins are destined for disposal through a process known as ER-associated degradation (ERAD). EDEM1 is an ERAD-accelerating factor whose gene expression is upregulated by the accumulation of aberrant proteins in the ER, known as ER stress. Although the role of EDEM1 in ERAD has been studied in detail, the turnover of EDEM1 by intracellular degradation machinery, including the proteasome and autophagy, is not well understood. To clarify EDEM1 regulation in the protein level, degradation mechanism of EDEM1 was examined. Our results indicate that both ERAD and autophagy degrade EDEM1 alike misfolded degradation substrates, although each degradation machinery targets EDEM1 in different folded states of proteins. We also found that ERAD factors, including the SEL1L/Hrd1 complex, YOD1, XTP3B, ERdj3, VIMP, BAG6, and JB12, but not OS9, are involved in EDEM1 degradation in a mannose-trimming-dependent and -independent manner. Our results suggest that the ERAD accelerating factor, EDEM1, is turned over by the ERAD itself, similar to ERAD clients.
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Affiliation(s)
- Riko Katsuki
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Mai Kanuka
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Ren Ohta
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Shusei Yoshida
- Department of Life Science, Faculty of Engineering ScienceAkita UniversityAkitaJapan
| | - Taku Tamura
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
- Department of Life Science, Faculty of Engineering ScienceAkita UniversityAkitaJapan
- Present address:
Biococoon Laboratories Inc.4‐3‐5, UedaMoriokaJapan
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Purificação ADD, Debbas V, Tanaka LY, Gabriel GVDM, Wosniak Júnior J, De Bessa TC, Garcia-Rosa S, Laurindo FRM, Oliveira PVS. DNAJB12 and DNJB14 are non-redundant Hsp40 redox chaperones involved in endoplasmic reticulum protein reflux. Biochim Biophys Acta Gen Subj 2024; 1868:130502. [PMID: 37925033 DOI: 10.1016/j.bbagen.2023.130502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 10/19/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND The endoplasmic reticulum (ER) transmembrane chaperones DNAJB12(B12) and DNAJB14(B14) are cofactors that cooperate with cytosolic Heat Shock-70 protein (HSC70) facilitating folding/degradation of nascent membrane proteins and supporting the ER-membrane penetration of viral particles. Here, we assessed structural/functional features of B12/B14 with respect to their regulation by ER stress and their involvement in ER stress-mediated protein reflux. METHODS We investigated the effect of Unfolded Protein Response(UPR)-eliciting drugs on the expression/regulation of B12-B14 and their roles in ER-to-cytosol translocation of Protein Disulfide Isomerase-A1(PDI). RESULTS We show that B12 and B14 are similar but do not seem redundant. They share predicted structural features and show high homology of their cytosolic J-domains, while their ER-lumen DUF1977 domains are quite dissimilar. Interactome analysis suggested that B12/B14 associate with different biological processes. UPR activation did not significantly impact on B12 gene expression, while B14 transcripts were up-regulated. Meanwhile, B12 and B14 (33.4 kDa isoform) protein levels were degraded by the proteasome upon acute reductive challenge. Also, B12 degradation was impaired upon sulfenic-acid trapping by dimedone. We originally report that knockdown of B12/B14 and their cytosolic partner SGTA in ER-stressed cells significantly impaired the amount of the ER redox-chaperone PDI in a cytosolic-enriched fraction. Additionally, B12 but not B14 overexpression increased PDI relocalization in non-stressed cells. CONCLUSIONS AND GENERAL SIGNIFICANCE Our findings reveal that B12/B14 regulation involves thiol redox processes that may impact on their stability and possibly on physiological effects. Furthermore, we provide novel evidence that these proteins are involved in UPR-induced ER protein reflux.
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Affiliation(s)
- Aline Dias da Purificação
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Victor Debbas
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Leonardo Yuji Tanaka
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Gabriele Verônica de Mello Gabriel
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - João Wosniak Júnior
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Tiphany Coralie De Bessa
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Sheila Garcia-Rosa
- Brazilian Bioscience National Laboratory - LNBio, National Center Research in Energy and material - CNPEM, Campinas, Brazil
| | - Francisco Rafael Martins Laurindo
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Percillia Victoria Santos Oliveira
- Laboratorio de Biologia Vascular, LIM-64 (Biologia Cardiovascular Translacional), Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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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: 18] [Impact Index Per Article: 18.0] [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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5
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Chen G, Wei T, Ju F, Li H. Protein quality control and aggregation in the endoplasmic reticulum: From basic to bedside. Front Cell Dev Biol 2023; 11:1156152. [PMID: 37152279 PMCID: PMC10154544 DOI: 10.3389/fcell.2023.1156152] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Endoplasmic reticulum (ER) is the largest membrane-bound compartment in all cells and functions as a key regulator in protein biosynthesis, lipid metabolism, and calcium balance. Mammalian endoplasmic reticulum has evolved with an orchestrated protein quality control system to handle defective proteins and ensure endoplasmic reticulum homeostasis. Nevertheless, the accumulation and aggregation of misfolded proteins in the endoplasmic reticulum may occur during pathological conditions. The inability of endoplasmic reticulum quality control system to clear faulty proteins and aggregates from the endoplasmic reticulum results in the development of many human disorders. The efforts to comprehensively understand endoplasmic reticulum quality control network and protein aggregation will benefit the diagnostics and therapeutics of endoplasmic reticulum storage diseases. Herein, we overview recent advances in mammalian endoplasmic reticulum protein quality control system, describe protein phase transition model, and summarize the approaches to monitor protein aggregation. Moreover, we discuss the therapeutic applications of enhancing endoplasmic reticulum protein quality control pathways in endoplasmic reticulum storage diseases.
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Affiliation(s)
- Guofang Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tingyi Wei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Furong Ju
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Sha Tin, Hong kong SAR, China
| | - Haisen Li
- School of Life Sciences, Fudan University, Shanghai, China
- AoBio Medical, Shanghai, China
- *Correspondence: Haisen Li,
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Wang L, Li J, Wang Q, Ge MX, Ji J, Liu D, Wang Z, Cao Y, Zhang Y, Zhang ZR. TMUB1 is an endoplasmic reticulum-resident escortase that promotes the p97-mediated extraction of membrane proteins for degradation. Mol Cell 2022; 82:3453-3467.e14. [PMID: 35961308 DOI: 10.1016/j.molcel.2022.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 05/15/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023]
Abstract
Membrane protein clients of endoplasmic reticulum (ER)-associated degradation must be retrotranslocated from the ER membrane by the AAA-ATPase p97 for proteasomal degradation. Before direct engagement with p97, client transmembrane domains (TMDs) that have partially or fully crossed the membrane must be constantly shielded to avoid non-native interactions. How client TMDs are seamlessly escorted from the membrane to p97 is unknown. Here, we identified ER-anchored TMUB1 as a TMD-specific escortase. TMUB1 interacts with the TMD of clients within the membrane and holds ∼10-14 residues of a hydrophobic sequence that is exposed out of membrane, using its transmembrane and cytosolic regions, respectively. The ubiquitin-like domain of TMUB1 recruits p97, which can pull client TMDs from bound TMUB1 into the cytosol. The disruption of TMUB1 escortase activity impairs retrotranslocation and stabilizes retrotranslocating intermediates of client proteins within the ER membrane. Thus, TMUB1 promotes TMD segregation by safeguarding the TMD movement from the membrane to p97.
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Affiliation(s)
- Linhan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qingchen Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Di Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yang Cao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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7
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Hill J, Nyathi Y. USP5 enhances SGTA mediated protein quality control. PLoS One 2022; 17:e0257786. [PMID: 35895711 PMCID: PMC9328565 DOI: 10.1371/journal.pone.0257786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/11/2022] [Indexed: 11/18/2022] Open
Abstract
Mislocalised membrane proteins (MLPs) present a risk to the cell due to exposed hydrophobic amino acids which cause MLPs to aggregate. Previous studies identified SGTA as a key component of the machinery that regulates the quality control of MLPs. Overexpression of SGTA promotes deubiqutination of MLPs resulting in their accumulation in cytosolic inclusions, suggesting SGTA acts in collaboration with deubiquitinating enzymes (DUBs) to exert these effects. However, the DUBs that play a role in this process have not been identified. In this study we have identified the ubiquitin specific peptidase 5 (USP5) as a DUB important in regulating the quality control of MLPs. We show that USP5 is in complex with SGTA, and this association is increased in the presence of an MLP. Overexpression of SGTA results in an increase in steady-state levels of MLPs suggesting a delay in proteasomal degradation of substrates. However, our results show that this effect is strongly dependent on the presence of USP5. We find that in the absence of USP5, the ability of SGTA to increase the steady state levels of MLPs is compromised. Moreover, knockdown of USP5 results in a reduction in the steady state levels of MLPs, while overexpression of USP5 increases the steady state levels. Our findings suggest that the interaction of SGTA with USP5 enables specific MLPs to escape proteasomal degradation allowing selective modulation of MLP quality control. These findings progress our understanding of aggregate formation, a hallmark in a range of neurodegenerative diseases and type II diabetes, as well as physiological processes of aggregate clearance.
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Affiliation(s)
- Jake Hill
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, Lincoln, United Kingdom
- School of Chemistry and Bioscience, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
| | - Yvonne Nyathi
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, Lincoln, United Kingdom
- School of Chemistry and Bioscience, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
- * E-mail:
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Song H, Chen D, Bai R, Feng Y, Wu S, Wang T, Xia X, Li J, Miao YL, Zuo B, Li F. BCL2-associated athanogene 6 exon24 contributes to testosterone synthesis and male fertility in mammals. Cell Prolif 2022; 55:e13281. [PMID: 35688694 PMCID: PMC9251057 DOI: 10.1111/cpr.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/10/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022] Open
Abstract
Objectives BCL2‐associated athanogene 6 (BAG6) plays critical roles in spermatogenesis by maintaining testicular cell survival. Our previous data showed porcine BAG6 exon24‐skipped transcript is highly expressed in immature testes compared with mature testes. The objective of this study is to reveal the functional significance of BAG6 exon24 in mammalian spermatogenesis. Materials and Methods CRISPR/Cas9 system was used to generate Bag6 exon24 knockout mice. Testes and cauda epididymal sperm were collected from mice. TMT proteomics analysis was used to discover the protein differences induced by Bag6 exon24 deletion. Testosterone enanthate was injected into mice to generate a high‐testosterone mice model. H&E staining, qRT‐PCR, western blotting, vector/siRNA transfection, immunofluorescence, immunoprecipitation, transmission electron microscopy, TUNEL and ELISA were performed to investigate the phenotypes and molecular basis. Results Bag6 exon24 knockout mice show sub‐fertility along with partially impaired blood‐testis barrier, increased apoptotic testicular cell rate and abnormal sperm morphology. Endoplasmic reticulum stress occurs in Bag6 exon24‐deficient testes and sterol regulatory element‐binding transcription factor 2 is activated; as a result, cytochrome P450 family 51 subfamily A member 1 expression is up‐regulated, which causes a high serum testosterone level. Additionally, serine/arginine‐rich splicing factor 1 down‐regulates BAG6 exon24‐skipped transcripts in porcine Sertoli cells by binding to 35–51 nt on BAG6 exon24 via its N‐terminal RNA‐recognition domain. Conclusions Our findings reveal the critical roles of BAG6 exon24 in testosterone biosynthesis and male fertility, which provides new insights into the regulation of spermatogenesis and pathogenesis of subfertility in mammals.
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Affiliation(s)
- Huibin Song
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Dake Chen
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rong Bai
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yue Feng
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shang Wu
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Tiansu Wang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xuanyan Xia
- College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jialian Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yi-Liang Miao
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Zuo
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Fenge Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
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9
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Culver JA, Li X, Jordan M, Mariappan M. A second chance for protein targeting/folding: Ubiquitination and deubiquitination of nascent proteins. Bioessays 2022; 44:e2200014. [PMID: 35357021 PMCID: PMC9133216 DOI: 10.1002/bies.202200014] [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: 01/18/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/07/2022]
Abstract
Molecular chaperones in cells constantly monitor and bind to exposed hydrophobicity in newly synthesized proteins and assist them in folding or targeting to cellular membranes for insertion. However, proteins can be misfolded or mistargeted, which often causes hydrophobic amino acids to be exposed to the aqueous cytosol. Again, chaperones recognize exposed hydrophobicity in these proteins to prevent nonspecific interactions and aggregation, which are harmful to cells. The chaperone-bound misfolded proteins are then decorated with ubiquitin chains denoting them for proteasomal degradation. It remains enigmatic how molecular chaperones can mediate both maturation of nascent proteins and ubiquitination of misfolded proteins solely based on their exposed hydrophobic signals. In this review, we propose a dynamic ubiquitination and deubiquitination model in which ubiquitination of newly synthesized proteins serves as a "fix me" signal for either refolding of soluble proteins or retargeting of membrane proteins with the help of chaperones and deubiquitinases. Such a model would provide additional time for aberrant nascent proteins to fold or route for membrane insertion, thus avoiding excessive protein degradation and saving cellular energy spent on protein synthesis. Also see the video abstract here: https://youtu.be/gkElfmqaKG4.
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Affiliation(s)
- Jacob A. Culver
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Matthew Jordan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
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10
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Roboti P, Lawless C, High S. Mitochondrial antiviral-signalling protein is a client of the BAG6 protein quality control complex. J Cell Sci 2022; 135:275354. [PMID: 35543156 PMCID: PMC9264363 DOI: 10.1242/jcs.259596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
The heterotrimeric BAG6 complex coordinates the direct handover of newly synthesised tail-anchored (TA) membrane proteins from an SGTA-bound preloading complex to the endoplasmic reticulum (ER) delivery component TRC40. In contrast, defective precursors, including aberrant TA proteins, form a stable complex with this cytosolic protein quality control factor, enabling such clients to be either productively re-routed or selectively degraded. We identify the mitochondrial antiviral-signalling protein (MAVS) as an endogenous TA client of both SGTA and the BAG6 complex. Our data suggest that the BAG6 complex binds to a cytosolic pool of MAVS before its misinsertion into the ER membrane, from where it can subsequently be removed via ATP13A1-mediated dislocation. This BAG6-associated fraction of MAVS is dynamic and responds to the activation of an innate immune response, suggesting that BAG6 may modulate the pool of MAVS that is available for coordinating the cellular response to viral infection. Summary: Mitochondrial antiviral-signalling protein (MAVS) is a favoured client of the cytosolic BAG6 complex. We discuss how this dynamic interaction may modulate MAVS biogenesis at signalling membranes.
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Affiliation(s)
- Peristera Roboti
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Craig Lawless
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Stephen High
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
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11
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BAG6 prevents the aggregation of neurodegeneration-associated fragments of TDP43. iScience 2022; 25:104273. [PMID: 35542047 PMCID: PMC9079172 DOI: 10.1016/j.isci.2022.104273] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/23/2021] [Accepted: 04/14/2022] [Indexed: 11/24/2022] Open
Abstract
Neurodegeneration is associated with the aggregation of proteins bearing solvent-exposed hydrophobicity as a result of their misfolding and/or proteolytic cleavage. An understanding of the cellular protein quality control mechanisms which prevent protein aggregation is fundamental to understanding the etiology of neurodegeneration. By examining the metabolism of disease-linked C-terminal fragments of the TAR DNA-binding protein 43 (TDP43), we found that the Bcl-2 associated athanogene 6 (BAG6) functions as a sensor of proteolytic fragments bearing exposed hydrophobicity and prevents their intracellular aggregation. In addition, BAG6 facilitates the ubiquitylation of TDP43 fragments by recruiting the Ub-ligase, Ring finger protein 126 (RNF126). Authenticating its role in preventing aggregation, we found that TDP43 fragments form intracellular aggregates in the absence of BAG6. Finally, we found that BAG6 could interact with and solubilize additional neurodegeneration-associated proteolytic fragments. Therefore, BAG6 plays a general role in preventing intracellular aggregation associated with neurodegeneration. Proteolytic cleavage generates protein fragments bearing exposed hydrophobicity BAG6 maintains the solubility and directs the degradation of protein fragments BAG6 prevents intracellular aggregation associated with neurodegeneration
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12
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Li X, Yang G, Zhang W, Qin B, Ye Z, Shi H, Zhao X, Chen Y, Song B, Mei Z, Zhao Q, Wang F. USP13: Multiple Functions and Target Inhibition. Front Cell Dev Biol 2022; 10:875124. [PMID: 35445009 PMCID: PMC9014248 DOI: 10.3389/fcell.2022.875124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
As a deubiquitination (DUB) enzyme, ubiquitin-specific protease 13 (USP13) is involved in a myriad of cellular processes, such as mitochondrial energy metabolism, autophagy, DNA damage response, and endoplasmic reticulum-associated degradation (ERAD), by regulating the deubiquitination of diverse key substrate proteins. Thus, dysregulation of USP13 can give rise to the occurrence and development of plenty of diseases, in particular malignant tumors. Given its implications in the stabilization of disease-related proteins and oncology targets, considerable efforts have been committed to the discovery of inhibitors targeting USP13. Here, we summarize an overview of the recent advances of the structure, function of USP13, and its relations to diseases, as well as discovery and development of inhibitors, aiming to provide the theoretical basis for investigation of the molecular mechanism of USP13 action and further development of more potent druggable inhibitors.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Wenyao Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Biying Qin
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Zifan Ye
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Huijing Shi
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Xinmeng Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yihang Chen
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Bowei Song
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Ziqing Mei
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | | | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
- *Correspondence: Feng Wang,
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13
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Christianson JC, Carvalho P. Order through destruction: how ER-associated protein degradation contributes to organelle homeostasis. EMBO J 2022; 41:e109845. [PMID: 35170763 PMCID: PMC8922271 DOI: 10.15252/embj.2021109845] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 12/24/2022] Open
Abstract
The endoplasmic reticulum (ER) is a large, dynamic, and multifunctional organelle. ER protein homeostasis is essential for the coordination of its diverse functions and depends on ER-associated protein degradation (ERAD). The latter process selects target proteins in the lumen and membrane of the ER, promotes their ubiquitination, and facilitates their delivery into the cytosol for degradation by the proteasome. Originally characterized for a role in the degradation of misfolded proteins and rate-limiting enzymes of sterol biosynthesis, the many branches of ERAD now appear to control the levels of a wider range of substrates and influence more broadly the organization and functions of the ER, as well as its interactions with adjacent organelles. Here, we discuss recent mechanistic advances in our understanding of ERAD and of its consequences for the regulation of ER functions.
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Affiliation(s)
- John C Christianson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesBotnar Research CentreUniversity of OxfordOxfordUK
| | - Pedro Carvalho
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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14
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Kumar T, Maitra S, Rahman A, Bhattacharjee S. A conserved guided entry of tail-anchored pathway is involved in the trafficking of a subset of membrane proteins in Plasmodium falciparum. PLoS Pathog 2021; 17:e1009595. [PMID: 34780541 PMCID: PMC8629386 DOI: 10.1371/journal.ppat.1009595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/29/2021] [Accepted: 10/19/2021] [Indexed: 01/22/2023] Open
Abstract
Tail-anchored (TA) proteins are defined by the absence of N-terminus signal sequence and the presence of a single transmembrane domain (TMD) proximal to their C-terminus. They play fundamental roles in cellular processes including vesicular trafficking, protein translocation and quality control. Some of the TA proteins are post-translationally integrated by the Guided Entry of TA (GET) pathway to the cellular membranes; with their N-terminus oriented towards the cytosol and C-terminus facing the organellar lumen. The TA repertoire and the GET machinery have been extensively characterized in the yeast and mammalian systems, however, they remain elusive in the human malaria parasite Plasmodium falciparum. In this study, we bioinformatically predicted a total of 63 TA proteins in the P. falciparum proteome and revealed the association of a subset with the P. falciparum homolog of Get3 (PfGet3). In addition, our proximity labelling studies either definitively identified or shortlisted the other eligible GET constituents, and our in vitro association studies validated associations between PfGet3 and the corresponding homologs of Get4 and Get2 in P. falciparum. Collectively, this study reveals the presence of proteins with hallmark TA signatures and the involvement of evolutionary conserved GET trafficking pathway for their targeted delivery within the parasite. Tail-anchored (TA) membrane proteins are known to play essential cellular functions in the eukaryotes. These proteins are trafficked to their respective destinations by post-translational translocation pathways that are evolutionarily conserved from yeast to human. However, they remain unidentified in the malaria parasite Plasmodium falciparum. We have used bioinformatic prediction algorithms in conjunction with functional validation studies to identify the candidate TA repertoire and some of the homologs of the trafficking machinery in P. falciparum. Initially, we predicted the presence of 63 putative TA proteins localized to distinct compartments within this parasite, including a few confirmed TA homologs in other eukaryotic systems. We then identified and characterized PfGet3 as a central component in the Guided-Entry of TA (GET) translocation machinery, and our bacterial co-expression and pulldown assays with two selected recombinant TA proteins, PfBOS1 and PfUSE1, showed co-association with PfGet3. We also identified PfGet2 and PfGet4 as the other two components of the GET machinery in P. falciparum using proximity biotinylation followed by mass spectrometry. Interestingly, we also found six TA proteins in the parasite enriched in this fraction. We further validated the direct interactions between a few TA candidates, PfGet4 and PfGet2 with PfGet3 using recombinant-based pulldown studies. In conclusion, this study classified a subset of membrane proteins with the TA nomenclature and implicated a previously unidentified GET pathway for their translocation in this apicomplexan parasite.
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Affiliation(s)
- Tarkeshwar Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Satarupa Maitra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Abdur Rahman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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15
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Lemberg MK, Strisovsky K. Maintenance of organellar protein homeostasis by ER-associated degradation and related mechanisms. Mol Cell 2021; 81:2507-2519. [PMID: 34107306 DOI: 10.1016/j.molcel.2021.05.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
Protein homeostasis mechanisms are fundamentally important to match cellular needs and to counteract stress conditions. A fundamental challenge is to understand how defective proteins are recognized and extracted from cellular organelles to be degraded in the cytoplasm. The endoplasmic reticulum (ER)-associated degradation (ERAD) pathway is the best-understood organellar protein quality control system. Here, we review new insights into the mechanism of recognition and retrotranslocation of client proteins in ERAD. In addition to the membrane-integral ERAD E3 ubiquitin ligases, we highlight one protein family that is remarkably often involved in various aspects of membrane protein quality control and protein dislocation: the rhomboid superfamily, which includes derlins and intramembrane serine proteases. Rhomboid-like proteins have been found to control protein homeostasis in the ER, but also in other eukaryotic organelles and in bacteria, pointing toward conserved principles of membrane protein quality control across organelles and evolution.
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Affiliation(s)
- Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany.
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czechia.
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16
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Quel NG, Fernando de C Rodrigues L, Aragão AZB, Pinheiro GMS, Camacho RP, Souto DEP, Kubota LT, Barbosa LRS, Ramos CHI. Insights into the structure and function of the C-terminus of SGTs (small glutamine-rich TPR-containing proteins): A study of the Aedes aegypti homolog. Biochimie 2021; 187:131-143. [PMID: 34082040 DOI: 10.1016/j.biochi.2021.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
SGTs (small glutamine-rich TPR-containing proteins) are dimeric proteins that belong to the class of co-chaperones characterized by the presence of TPR domains (containing tetratricopeptide repeats). Human (SGTA) and yeast (Sgt2) SGTs are characterized by three distinct domains: an N-terminal dimerization domain, a central TPR-domain important for binding to other proteins (chaperones included) and a C-terminal domain involved in hydrophobic interactions. Both these SGTs are involved in the cellular PQC (protein quality control) system, as they interact with chaperones and have functions that aid stress recovery. However, there are differences between them, such as structural features and binding specificities, that could be better understood if other orthologous proteins were studied. Therefore, we produced and characterized a putative SGT protein, designated AaSGT, from the mosquito Aedes aegypti, which is a vector of several diseases, such as dengue and Zika. The protein was produced as a folded dimer which was stable up to 40 °C and was capable of binding to AaHsp90 and fully protecting a model protein, α-synuclein, from aggregation. The conformation of AaSGT was investigated by biophysical tools and small angle X-ray scattering, which showed that the protein had an elongated conformation and that its C-terminal domain was mainly disordered. The results with a C-terminal deletion mutant supported these observations. Altogether, these results are consistent with those from other functional SGT proteins and add to the understanding of the PQC system in Aedes aegypti, an important aim that may help to develop inhibitory strategies against this vector of neglected diseases.
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Affiliation(s)
- Natália G Quel
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil; National Institute of Science & Technology of Structural Biology and Bioimage (INCTBEB), Brazil
| | | | - Annelize Z B Aragão
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Glaucia M S Pinheiro
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Rafael P Camacho
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Denio E P Souto
- Department of Chemistry, Federal University of Paraná-UFPR, Curitiba PR, 81530-900, Brazil
| | - Lauro T Kubota
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil; National Institute of Science & Technology of Bioanalytics (INCTBio), Brazil
| | - Leandro R S Barbosa
- Institute of Physics, University of São Paulo, São Paulo SP, 05508-090 Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil; National Institute of Science & Technology of Structural Biology and Bioimage (INCTBEB), Brazil.
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17
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Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Sci 2021; 30:882-898. [PMID: 33620121 PMCID: PMC7980504 DOI: 10.1002/pro.4049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/05/2023]
Abstract
STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - William M. Clemons
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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18
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SGTA associates with intracellular aggregates in neurodegenerative diseases. Mol Brain 2021; 14:59. [PMID: 33757575 PMCID: PMC7986274 DOI: 10.1186/s13041-021-00770-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/15/2021] [Indexed: 11/24/2022] Open
Abstract
Intracellular aggregates are a common pathological hallmark of neurodegenerative diseases such as polyglutamine (polyQ) diseases, amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), and multiple system atrophy (MSA). Aggregates are mainly formed by aberrant disease-specific proteins and are accompanied by accumulation of other aggregate-interacting proteins. Although aggregate-interacting proteins have been considered to modulate the formation of aggregates and to be involved in molecular mechanisms of disease progression, the components of aggregate-interacting proteins remain unknown. In this study, we showed that small glutamine-rich tetratricopeptide repeat-containing protein alfa (SGTA) is an aggregate-interacting protein in neurodegenerative diseases. Immunohistochemistry showed that SGTA interacted with intracellular aggregates in Huntington disease (HD) cell models and neurons of HD model mice. We also revealed that SGTA colocalized with intracellular aggregates in postmortem brains of patients with polyQ diseases including spinocerebellar ataxia (SCA)1, SCA2, SCA3, and dentatorubral–pallidoluysian atrophy. In addition, SGTA colocalized with glial cytoplasmic inclusions in the brains of MSA patients, whereas no accumulation of SGTA was observed in neurons of PD and ALS patients. In vitro study showed that SGTA bound to polyQ aggregates through its C-terminal domain and SGTA overexpression reduced intracellular aggregates. These results suggest that SGTA may play a role in the formation of aggregates and may act as potential modifier of molecular pathological mechanisms of polyQ diseases and MSA.
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19
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Kang JA, Jeon YJ. How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases. Int J Mol Sci 2021; 22:ijms22042078. [PMID: 33669844 PMCID: PMC7923238 DOI: 10.3390/ijms22042078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.
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Affiliation(s)
- Ji An Kang
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Young Joo Jeon
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Correspondence:
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20
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Zhang R, Cui D, Xue T, Lang Y, Zhang Y, Li L, Sun H, Kuang Y, Li G, Tang J. HLA-B-associated transcript 3 (Bat3) stabilizes and activates p53 in a HAUSP-dependent manner. J Mol Cell Biol 2021; 12:99-112. [PMID: 31647545 PMCID: PMC7109604 DOI: 10.1093/jmcb/mjz102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/12/2019] [Accepted: 08/26/2019] [Indexed: 01/06/2023] Open
Abstract
The p53 pathway is a highly complex signaling network including several key regulators. HAUSP is a critical component of the p53 pathway acting as a deubiquitinase for both p53 and its key repressor Mdm2. Here, we identified a novel HAUSP-interacting protein, HLA-B-associated transcript 3 (Bat3) and found it to be capable of inducing p53 stabilization and activation via a HAUSP-dependent mechanism, resulting in cell growth inhibition. Surprisingly, the deubiquitylating enzymatic activity of HAUSP was not required for this phenomenon. Co-immunoprecipitation showed that p53 coexisted in a complex with Bat3 and HAUSP in vivo, and HAUSP may serve as a binding mediator to enhance the interaction between p53 and Bat3. Further studies revealed that formation of this three-protein complex interfered with the binding of p53 to its proteasome receptor S5a and promoted the accumulation of p53 in nucleus. Notably, Mdm2 protein abundance is also regulated by Bat3 in the presence of HAUSP. Overexpression of Bat3 and HAUSP increases Mdm2 protein levels without influencing the p53–Mdm2 interaction and Mdm2-mediated p53 ubiquitination, indicating that Bat3–HAUSP-mediated protein stabilization is not specific to p53 and different mechanisms may be involved in Bat3-mediated regulation of p53–Mdm2 pathway. Together, our study unravels a novel mechanism by which p53 is stabilized and activated by HAUSP-mediated interaction with Bat3 and implies that Bat3 might function as a tumor suppressor through the stabilization of p53.
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Affiliation(s)
- Rui Zhang
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Di Cui
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Teng Xue
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yue Lang
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yunfan Zhang
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Lianjie Li
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Haili Sun
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yu Kuang
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Gebin Li
- Department of Clinical Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jun Tang
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
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21
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Lin KF, Fry MY, Saladi SM, Clemons WM. Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2. J Biol Chem 2021; 296:100441. [PMID: 33610544 PMCID: PMC8010706 DOI: 10.1016/j.jbc.2021.100441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 02/08/2023] Open
Abstract
The targeting and insertion of tail-anchored (TA) integral membrane proteins (IMPs) into the correct membrane is critical for cellular homeostasis. The fungal protein Sgt2, and its human homolog SGTA, is the entry point for clients to the guided entry of tail-anchored protein (GET) pathway, which targets endoplasmic reticulum-bound TA IMPs. Consisting of three structurally independent domains, the C terminus of Sgt2 binds to the hydrophobic transmembrane domain (TMD) of clients. However, the exact binding interface within Sgt2 and molecular details that underlie its binding mechanism and client preference are not known. Here, we reveal the mechanism of Sgt2 binding to hydrophobic clients, including TA IMPs. Through sequence analysis, biophysical characterization, and a series of capture assays, we establish that the Sgt2 C-terminal domain is flexible but conserved and sufficient for client binding. A molecular model for this domain reveals a helical hand forming a hydrophobic groove approximately 15 Å long that is consistent with our observed higher affinity for client TMDs with a hydrophobic face and a minimal length of 11 residues. This work places Sgt2 into a broader family of TPR-containing cochaperone proteins, demonstrating structural and sequence-based similarities to the DP domains in the yeast Hsp90 and Hsp70 coordinating protein, Sti1.
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Affiliation(s)
- Ku-Feng Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Michelle Y Fry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
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22
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Zhang H, Zhao Y, Yao Q, Ye Z, Mañas A, Xiang J. Ubl4A is critical for mitochondrial fusion process under nutrient deprivation stress. PLoS One 2020; 15:e0242700. [PMID: 33211772 PMCID: PMC7676689 DOI: 10.1371/journal.pone.0242700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/08/2020] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial fusion and fission are dynamic processes regulated by the cellular microenvironment. Under nutrient starvation conditions, mitochondrial fusion is strengthened for energy conservation. We have previously shown that newborns of Ubl4A-deficient mice were more sensitive to starvation stress with a higher rate of mortality than their wild-type littermates. Ubl4A binds with the actin-related protein Arp2/3 complex to synergize the actin branching process. Here, we showed that deficiency in Ubl4A resulted in mitochondrial fragmentation and apoptosis. A defect in the fusion process was the main cause of the mitochondrial fragmentation and resulted from a shortage of primed Arp2/3 complex pool around the mitochondria in the Ubl4A-deficient cells compared to the wild-type cells. As a result, the mitochondrial fusion process was not undertaken quickly enough to sustain starvation stress-induced cell death. Consequently, fragmented mitochondria lost their membrane integrity and ROS was accumulated to trigger caspase 9-dependent apoptosis before autophagic rescue. Furthermore, the wild-type Ubl4A, but not the Arp2/3-binding deficient mutant, could rescue the starvation-induced mitochondrial fragmentation phenotype. These results suggest that Ubl4A promotes the mitochondrial fusion process via Arp2/3 complex during the initial response to nutrient deprivation for cell survival.
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Affiliation(s)
- Huaiyuan Zhang
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Yu Zhao
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Qi Yao
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Zijing Ye
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Adriana Mañas
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
- * E-mail:
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23
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Off and On Again: De- and Reubiquitination during Membrane Protein Degradation. Mol Cell 2020; 79:203-204. [PMID: 32679074 DOI: 10.1016/j.molcel.2020.06.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this issue of Molecular Cell, Hu et al. (2020) show that the cytosolic E3 ligase RNF126 reubiquitinates membrane proteins after their extraction from the membrane of the endoplasmic reticulum to target them for proteasomal degradation.
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Sulkshane P, Duek I, Ram J, Thakur A, Reis N, Ziv T, Glickman MH. Inhibition of proteasome reveals basal mitochondrial ubiquitination. J Proteomics 2020; 229:103949. [PMID: 32882436 DOI: 10.1016/j.jprot.2020.103949] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Strict quality control for mitochondrial proteins is necessary to ensure cell homeostasis. Two cellular pathways-Ubiquitin Proteasome System (UPS) and autophagy-contribute to mitochondrial homeostasis under stressful conditions. Here, we investigate changes to the mitochondria proteome and to the ubiquitin landscape at mitochondria in response to proteasome inhibition. Treatment of HeLa cells devoid of Parkin, the primary E3 ligase responsible for mitophagy, with proteasome inhibitor MG132 for a few hours caused mitochondrial oxidative stress and fragmentation, reduced energy output, and increased mitochondrial ubiquitination without inducing mitophagy. Overexpression of Parkin did not show any induction of mitophagy in response to MG132 treatment. Analysis of ubiquitin chains on isolated mitochondria revealed predominance of K48, K29 and K63-linked polyubiquitin. Interestingly, of all ubiquitinated mitochondrial proteins detected in response to MG132 treatment, a majority (≥90%) were intramitochondrial irrespective of Parkin expression. However, overall levels of these ubiquitinated mitochondrial proteins did not change significantly upon proteasome inhibition when evaluated by quantitative proteomics (LFQ and SILAC), suggesting that only a small portion are ubiquitinated under basal conditions. Another aspect of proteasome inhibition is significant enrichment of UPS, lysosomal and phagosomal components, and other heat shock proteins associated with isolated mitochondria. Taken together, our study highlights a critical role of UPS for ubiquitinating and removing imported proteins as part of a basal mitochondrial quality control system independent of Parkin. SIGNIFICANCE: As centers of cellular bioenergetics, numerous metabolic pathways and signaling cascades, the health of mitochondria is of utmost importance for ensuring cell survival. Due to their unique physiology, mitochondria are constantly subjected to damaging oxidative radicals (ROS) and protein import-related stress due to buildup of unfolded aggregate-prone proteins. Thus, for quality control purposes, mitochondria are constantly under surveillance by Autophagy and the Ubiquitin Proteasome System (UPS), both of which share ubiquitin as a common signal. The ubiquitin landscape of mitochondria has been studied in detail under stressful conditions, however, little is known about basal mitochondrial ubiquitination. Our study reveals that the extent of ubiquitination at mitochondria greatly increases upon proteasome inhibition, pointing to a large number of potential substrates for proteasomal degradation. Interestingly, most of the ubiquitination occurs on intramitochondrial proteins, components of the electron transport chain (ETC) and matrix-resident metabolic enzymes in particular. Moreover, numerous cytosolic UPS components, chaperones and autophagy-lysosomal proteins were recruited to mitochondria upon proteasome inhibition. Taken together, this suggests that the levels and functions of mitochondrial proteins are constantly regulated through ubiquitin-dependent proteasomal degradation even under basal conditions. Unclogging mitochondrial import channels may provide a mechanism to alleviate stress associated with mitochondrial protein import or to adapt cells according to their metabolic needs. Therefore, targeting the mitochondrial ubiquitination/deubiquitination machinery, such as improving the therapeutic potency of proteasome inhibitors, may provide an additional therapeutic arsenal against tumors.
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Affiliation(s)
- Prasad Sulkshane
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Inbar Duek
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Jonathan Ram
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Anita Thakur
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Noa Reis
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Tamar Ziv
- The Smoler Protein Research Center, Technion Israel Institute of Technology, Haifa 32000, Israel.
| | - Michael H Glickman
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel.
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25
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Abildgaard AB, Gersing SK, Larsen-Ledet S, Nielsen SV, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome. Biomolecules 2020; 10:biom10081141. [PMID: 32759676 PMCID: PMC7463752 DOI: 10.3390/biom10081141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis (proteostasis) is essential for the cell and is maintained by a highly conserved protein quality control (PQC) system, which triages newly synthesized, mislocalized and misfolded proteins. The ubiquitin-proteasome system (UPS), molecular chaperones, and co-chaperones are vital PQC elements that work together to facilitate degradation of misfolded and toxic protein species through the 26S proteasome. However, the underlying mechanisms are complex and remain partly unclear. Here, we provide an overview of the current knowledge on the co-chaperones that directly take part in targeting and delivery of PQC substrates for degradation. While J-domain proteins (JDPs) target substrates for the heat shock protein 70 (HSP70) chaperones, nucleotide-exchange factors (NEFs) deliver HSP70-bound substrates to the proteasome. So far, three NEFs have been established in proteasomal delivery: HSP110 and the ubiquitin-like (UBL) domain proteins BAG-1 and BAG-6, the latter acting as a chaperone itself and carrying its substrates directly to the proteasome. A better understanding of the individual delivery pathways will improve our ability to regulate the triage, and thus regulate the fate of aberrant proteins involved in cell stress and disease, examples of which are given throughout the review.
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Affiliation(s)
- Amanda B. Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sarah K. Gersing
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sven Larsen-Ledet
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sofie V. Nielsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Amelie Stein
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
- Correspondence:
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26
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Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4256301. [PMID: 32685484 PMCID: PMC7345912 DOI: 10.1155/2020/4256301] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
Coronaviruses are specific crown-shaped viruses that were first identified in the 1960s, and three typical examples of the most recent coronavirus disease outbreaks include severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and COVID-19. Particularly, COVID-19 is currently causing a worldwide pandemic, threatening the health of human beings globally. The identification of viral pathogenic mechanisms is important for further developing effective drugs and targeted clinical treatment methods. The delayed revelation of viral infectious mechanisms is currently one of the technical obstacles in the prevention and treatment of infectious diseases. In this study, we proposed a random walk model to identify the potential pathological mechanisms of COVID-19 on a virus–human protein interaction network, and we effectively identified a group of proteins that have already been determined to be potentially important for COVID-19 infection and for similar SARS infections, which help further developing drugs and targeted therapeutic methods against COVID-19. Moreover, we constructed a standard computational workflow for predicting the pathological biomarkers and related pharmacological targets of infectious diseases.
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27
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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: 0.3] [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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Schmidt CC, Vasic V, Stein A. Doa10 is a membrane protein retrotranslocase in ER-associated protein degradation. eLife 2020; 9:56945. [PMID: 32588820 PMCID: PMC7319771 DOI: 10.7554/elife.56945] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
In endoplasmic reticulum-associated protein degradation (ERAD), membrane proteins are ubiquitinated, extracted from the membrane, and degraded by the proteasome. The cytosolic ATPase Cdc48 drives extraction by pulling on polyubiquitinated substrates. How hydrophobic transmembrane (TM) segments are moved from the phospholipid bilayer into cytosol, often together with hydrophilic and folded ER luminal protein parts, is not known. Using a reconstituted system with purified proteins from Saccharomyces cerevisiae, we show that the ubiquitin ligase Doa10 (Teb-4/MARCH6 in animals) is a retrotranslocase that facilitates membrane protein extraction. A substrate’s TM segment interacts with the membrane-embedded domain of Doa10 and then passively moves into the aqueous phase. Luminal substrate segments cross the membrane in an unfolded state. Their unfolding occurs on the luminal side of the membrane by cytoplasmic Cdc48 action. Our results reveal how a membrane-bound retrotranslocase cooperates with the Cdc48 ATPase in membrane protein extraction. The inside of a cell contains many different compartments called organelles, which are separated by membranes. Each organelle is composed of a unique set of proteins and performs specific roles in the cell. The endoplasmic reticulum, or ER for short, is an organelle where many proteins are produced. Most of these proteins are then released from the cell or sorted to other organelles. The ER has a strict quality control system that ensures any faulty proteins are quickly marked for the cell to destroy. However, the destruction process itself does not happen in the ER, so faulty proteins first need to leave this organelle. This is achieved by a group of proteins known as endoplasmic reticulum-associated protein degradation machinery (or ERAD for short). To extract a faulty protein from the ER, proteins of the ER and outside the ER cooperate. First, an ERAD protein called Doa10 attaches a small protein tag called ubiquitin to the faulty proteins to mark them for destruction. Then, outside of the ER, a protein called Cdc48 ‘grabs’ the ubiquitin tag and pulls. But that is only part of the story. Many of the proteins made by the ER have tethers that anchor them firmly to the membrane, making them much harder to remove. To get a better idea of how the extraction works, Schmidt et al. rebuilt the ERAD machinery in a test tube. This involved purifying proteins from yeast and inserting them into artificial membranes, allowing closer study of each part of the process. This revealed that attaching ubiquitin tags to faulty proteins is only one part of Doa10's role; it also participates in the extraction itself. Part of Doa10 resides within the membrane, and this ‘membrane-spanning domain’ can interact with faulty proteins, loosening their membrane anchors. At the same time, Cdc48 pulls from the outside. This pulling force causes the faulty proteins to unfold, allowing them to pass through the membrane. Given these findings, the next step is to find out exactly how Doa10 works by looking at its three-dimensional structure. This could have implications not only for the study of ERAD, but of similar quality control processes in other organelles too. A build-up of faulty proteins can cause diseases like neurodegeneration, so understanding how cells remove faulty proteins could help future medical research.
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Affiliation(s)
- Claudia C Schmidt
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vedran Vasic
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander Stein
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Leznicki P, High S. SGTA associates with nascent membrane protein precursors. EMBO Rep 2020; 21:e48835. [PMID: 32216016 PMCID: PMC7202230 DOI: 10.15252/embr.201948835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 01/15/2023] Open
Abstract
The endoplasmic reticulum (ER) is a major site for membrane protein synthesis in eukaryotes. The majority of integral membrane proteins are delivered to the ER membrane via the co‐translational, signal recognition particle (SRP)‐dependent route. However, tail‐anchored proteins employ an alternative, post‐translational route(s) that relies on distinct factors such as a cytosolic protein quality control component, SGTA. We now show that SGTA is selectively recruited to ribosomes synthesising a diverse range of membrane proteins, suggesting that its biosynthetic client base also includes precursors on the co‐translational ER delivery pathway. Strikingly, SGTA is recruited to nascent membrane proteins before their transmembrane domain emerges from the ribosome. Hence, SGTA is ideally placed to capture these aggregation prone regions shortly after their synthesis. For nascent membrane proteins on the co‐translational pathway, SGTA complements the role of SRP by reducing the co‐translational ubiquitination of clients with multiple hydrophobic signal sequences. On this basis, we propose that SGTA acts to mask specific transmembrane domains located in complex membrane proteins until they can engage the ER translocon and become membrane inserted.
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Affiliation(s)
- Pawel Leznicki
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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30
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Abstract
One-fourth of eukaryotic genes code for integral membrane proteins, nearly all of which are inserted and assembled at the endoplasmic reticulum (ER). The defining feature of membrane proteins is one or more transmembrane domains (TMDs). During membrane protein biogenesis, TMDs are selectively recognized, shielded, and chaperoned into the lipid bilayer, where they often assemble with other TMDs. If maturation fails, exposed TMDs serve as a cue for engagement of degradation pathways. Thus, TMD-recognition factors in the cytosol and ER are essential for membrane protein biogenesis and quality control. Here, we discuss the growing assortment of cytosolic and membrane-embedded TMD-recognition factors, the pathways within which they operate, and mechanistic principles of recognition.
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31
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Peng SJ, Yao RR, Yu SS, Chen HY, Pang X, Zhang Y, Zhang J. UBL4A Augments Innate Immunity by Promoting the K63-Linked Ubiquitination of TRAF6. THE JOURNAL OF IMMUNOLOGY 2019; 203:1943-1951. [PMID: 31451677 DOI: 10.4049/jimmunol.1800750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/24/2019] [Indexed: 12/25/2022]
Abstract
Human UBL4A/GdX, encoding an ubiquitin-like protein, was shown in this study to be upregulated by viral infection and IFN stimulation. Then the functions of UBL4A in antiviral immune response were characterized. Overexpression of UBL4A promoted RNA virus-induced ISRE or IFN-β or NF-κB activation, leading to enhanced type I IFN transcription and reduced virus replication. Consistently, knockdown of UBL4A resulted in reduced type I IFN transcription and enhanced virus replication. Additionally, overexpression of UBL4A promoted virus-induced phosphorylation of TBK1, IRF3, and IKKα/β. Knockdown of UBL4A inhibited virus-induced phosphorylation of TBK1, IRF3, and IKKα/β. Coimmunoprecipitation showed that UBL4A interacted with TRAF6, and this interaction was enhanced upon viral infection. Ubiquitination assays showed that UBL4A promoted the K63-linked ubiquitination of TRAF6. Therefore, we reveal a novel positive feedback regulation of UBL4A in innate immune response combating virus invasion by enhancing the K63-linked ubiquitination of TRAF6.
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Affiliation(s)
- Shu-Jie Peng
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
| | - Ran-Ran Yao
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
| | - Shuang-Shuang Yu
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
| | - Hong-Yan Chen
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
| | - Xuewen Pang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
| | - Jun Zhang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing 100191, China
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Balancing the Photoreceptor Proteome: Proteostasis Network Therapeutics for Inherited Retinal Disease. Genes (Basel) 2019; 10:genes10080557. [PMID: 31344897 PMCID: PMC6722924 DOI: 10.3390/genes10080557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
The light sensing outer segments of photoreceptors (PRs) are renewed every ten days due to their high photoactivity, especially of the cones during daytime vision. This demands a tremendous amount of energy, as well as a high turnover of their main biosynthetic compounds, membranes, and proteins. Therefore, a refined proteostasis network (PN), regulating the protein balance, is crucial for PR viability. In many inherited retinal diseases (IRDs) this balance is disrupted leading to protein accumulation in the inner segment and eventually the death of PRs. Various studies have been focusing on therapeutically targeting the different branches of the PR PN to restore the protein balance and ultimately to treat inherited blindness. This review first describes the different branches of the PN in detail. Subsequently, insights are provided on how therapeutic compounds directed against the different PN branches might slow down or even arrest the appalling, progressive blinding conditions. These insights are supported by findings of PN modulators in other research disciplines.
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33
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Liu C, Zhou Y, Li M, Wang Y, Yang L, Yang S, Feng Y, Wang Y, Wang Y, Ren F, Li J, Dong Z, Chin YE, Fu X, Wu L, Chang Z. Absence of GdX/UBL4A Protects against Inflammatory Diseases by Regulating NF-кB Signaling in Macrophages and Dendritic Cells. Am J Cancer Res 2019; 9:1369-1384. [PMID: 30867837 PMCID: PMC6401509 DOI: 10.7150/thno.32451] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/29/2022] Open
Abstract
Nuclear factor-kappa B (NF-κB) activation is critical for innate immune responses. However, cellular-intrinsic regulation of NF-κB activity during inflammatory diseases remains incompletely understood. Ubiquitin-like protein 4A (UBL4A, GdX) is a small adaptor protein involved in protein folding, biogenesis and transcription. Yet, whether GdX has a role during innate immune response is largely unknown. Methods: To investigate the involvement of GdX in innate immunity, we challenged GdX-deficient mice with lipopolysaccharides (LPS). To investigate the underlying mechanism, we performed RNA sequencing, real-time PCR, ELISA, luciferase reporter assay, immunoprecipitation and immunoblot analyses, flow cytometry, and structure analyses. To investigate whether GdX functions in inflammatory bowel disease, we generated dendritic cell (DC), macrophage (Mφ), epithelial-cell specific GdX-deficient mice and induced colitis with dextran sulfate sodium. Results: GdX enhances DC and Mφ-mediated innate immune defenses by positively regulating NF-κB signaling. GdX-deficient mice were resistant to LPS-induced endotoxin shock and DSS-induced colitis. DC- or Mφ- specific GdX-deficient mice displayed alleviated mucosal inflammation. The production of pro-inflammatory cytokines by GdX-deficient DCs and Mφ was reduced. Mechanistically, we found that tyrosine-protein phosphatase non-receptor type 2 (PTPN2, TC45) and protein phosphatase 2A (PP2A) form a complex with RelA (p65) to mediate its dephosphorylation whereas GdX interrupts the TC45/PP2A/p65 complex formation and restrict p65 dephosphorylation by trapping TC45. Conclusion: Our study provides a mechanism by which NF-κB signaling is positively regulated by an adaptor protein GdX in DC or Mφ to maintain the innate immune response. Targeting GdX could be a strategy to reduce over-activated immune response in inflammatory diseases.
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Benarroch R, Austin JM, Ahmed F, Isaacson RL. The roles of cytosolic quality control proteins, SGTA and the BAG6 complex, in disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 114:265-313. [PMID: 30635083 PMCID: PMC7102839 DOI: 10.1016/bs.apcsb.2018.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SGTA is a co-chaperone that, in collaboration with the complex of BAG6/UBL4A/TRC35, facilitates the biogenesis and quality control of hydrophobic proteins, protecting them from the aqueous cytosolic environment. This work includes targeting tail-anchored proteins to their resident membranes, sorting of membrane and secretory proteins that mislocalize to the cytoplasm and endoplasmic reticulum-associated degradation of misfolded proteins. Since these functions are all vital for the cell's continued proteostasis, their disruption poses a threat to the cell, with a particular risk of protein aggregation, a phenomenon that underpins many diseases. Although the specific disease implications of machinery involved in quality control of hydrophobic substrates are poorly understood, here we summarize much of the available information on this topic.
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Affiliation(s)
- Rashi Benarroch
- Department of Chemistry, King's College London, London, United Kingdom
| | - Jennifer M Austin
- Department of Chemistry, King's College London, London, United Kingdom
| | - Fahmeda Ahmed
- Department of Chemistry, King's College London, London, United Kingdom
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, London, United Kingdom.
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35
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Moon HW, Han HG, Jeon YJ. Protein Quality Control in the Endoplasmic Reticulum and Cancer. Int J Mol Sci 2018; 19:E3020. [PMID: 30282948 PMCID: PMC6213883 DOI: 10.3390/ijms19103020] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/22/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is an essential compartment of the biosynthesis, folding, assembly, and trafficking of secretory and transmembrane proteins, and consequently, eukaryotic cells possess specialized machineries to ensure that the ER enables the proteins to acquire adequate folding and maturation for maintaining protein homeostasis, a process which is termed proteostasis. However, a large variety of physiological and pathological perturbations lead to the accumulation of misfolded proteins in the ER, which is referred to as ER stress. To resolve ER stress and restore proteostasis, cells have evolutionary conserved protein quality-control machineries of the ER, consisting of the unfolded protein response (UPR) of the ER, ER-associated degradation (ERAD), and autophagy. Furthermore, protein quality-control machineries of the ER play pivotal roles in the control of differentiation, progression of cell cycle, inflammation, immunity, and aging. Therefore, severe and non-resolvable ER stress is closely associated with tumor development, aggressiveness, and response to therapies for cancer. In this review, we highlight current knowledge in the molecular understanding and physiological relevance of protein quality control of the ER and discuss new insights into how protein quality control of the ER is implicated in the pathogenesis of cancer, which could contribute to therapeutic intervention in cancer.
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Affiliation(s)
- Hye Won Moon
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Hye Gyeong Han
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Young Joo Jeon
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
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36
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Martínez-Lumbreras S, Krysztofinska EM, Thapaliya A, Spilotros A, Matak-Vinkovic D, Salvadori E, Roboti P, Nyathi Y, Muench JH, Roessler MM, Svergun DI, High S, Isaacson RL. Structural complexity of the co-chaperone SGTA: a conserved C-terminal region is implicated in dimerization and substrate quality control. BMC Biol 2018; 16:76. [PMID: 29996828 PMCID: PMC6042327 DOI: 10.1186/s12915-018-0542-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/20/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Protein quality control mechanisms are essential for cell health and involve delivery of proteins to specific cellular compartments for recycling or degradation. In particular, stray hydrophobic proteins are captured in the aqueous cytosol by a co-chaperone, the small glutamine-rich, tetratricopeptide repeat-containing protein alpha (SGTA), which facilitates the correct targeting of tail-anchored membrane proteins, as well as the sorting of membrane and secretory proteins that mislocalize to the cytosol and endoplasmic reticulum-associated degradation. Full-length SGTA has an unusual elongated dimeric structure that has, until now, evaded detailed structural analysis. The C-terminal region of SGTA plays a key role in binding a broad range of hydrophobic substrates, yet in contrast to the well-characterized N-terminal and TPR domains, there is a lack of structural information on the C-terminal domain. In this study, we present new insights into the conformation and organization of distinct domains of SGTA and show that the C-terminal domain possesses a conserved region essential for substrate processing in vivo. RESULTS We show that the C-terminal domain region is characterized by α-helical propensity and an intrinsic ability to dimerize independently of the N-terminal domain. Based on the properties of different regions of SGTA that are revealed using cell biology, NMR, SAXS, Native MS, and EPR, we observe that its C-terminal domain can dimerize in the full-length protein and propose that this reflects a closed conformation of the substrate-binding domain. CONCLUSION Our results provide novel insights into the structural complexity of SGTA and provide a new basis for mechanistic studies of substrate binding and release at the C-terminal region.
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Affiliation(s)
| | - Ewelina M Krysztofinska
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Arjun Thapaliya
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Alessandro Spilotros
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany
| | - Dijana Matak-Vinkovic
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Enrico Salvadori
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, UK
| | - Peristera Roboti
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yvonne Nyathi
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Present Address: School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, LN6 7DL, UK
| | - Janina H Muench
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK.
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Abstract
Proper localization of membrane proteins is essential for the function of biological membranes and for the establishment of organelle identity within a cell. Molecular machineries that mediate membrane protein biogenesis need to not only achieve a high degree of efficiency and accuracy, but also prevent off-pathway aggregation events that can be detrimental to cells. The posttranslational targeting of tail-anchored proteins (TAs) provides tractable model systems to probe these fundamental issues. Recent advances in understanding TA-targeting pathways reveal sophisticated molecular machineries that drive and regulate these processes. These findings also suggest how an interconnected network of targeting factors, cochaperones, and quality control machineries together ensures robust membrane protein biogenesis.
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Affiliation(s)
- Un Seng Chio
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| | - Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
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Ju LG, Lin X, Yan D, Li QL, Wu M, Li LY. Characterization of WDR20: A new regulator of the ERAD machinery. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:970-980. [PMID: 29655804 DOI: 10.1016/j.bbamcr.2018.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 01/01/2023]
Abstract
ERAD is an important process of protein quality control that eliminates misfolded or unassembled proteins from ER. Before undergoing proteasome degradation, the misfolded proteins are dislocated from ER membrane into cytosol, which requires the AAA ATPase p97/VCP and its cofactor, the NPL4-UFD1 dimer. Here, we performed a CRISPR-based screen and identify many candidates for ERAD regulation. We further confirmed four proteins, FBOX2, TRIM6, UFL1 and WDR20, are novel regulators for ERAD. Then the molecular mechanism for WDR20 in ERAD is further characterized. Depletion of WDR20 inhibits the degradation of TCRα, a typical ERAD substrate, while WDR20 overexpression reduces TCRα protein level. WDR20 associates with TCRα and central regulators of the ERAD system, p97, GP78 and HRD1. A portion of WDR20 localizes to the ER-containing microsomal membrane. WDR20 expression increases TCRα ubiquitination, and HRD1 E3 ligase is essential for the process. WDR20 seems to serve as an adaptor protein to mediate the interaction between p97 and TCRα. Our study provides novel candidates and reveals an unexpected role of WDR20 in ERAD regulation.
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Affiliation(s)
- Lin-Gao Ju
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiang Lin
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Dong Yan
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Qing-Lan Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Lian-Yun Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.
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Liang J, Li J, Fu Y, Ren F, Xu J, Zhou M, Li P, Feng H, Wang Y. GdX/UBL4A null mice exhibit mild kyphosis and scoliosis accompanied by dysregulation of osteoblastogenesis and chondrogenesis. Cell Biochem Funct 2018; 36:129-136. [DOI: 10.1002/cbf.3324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Jiao Liang
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
| | - Jun Li
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
| | - Yanxia Fu
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
- Tsinghua University-Perking University Joint Center for Life Sciences; Beijing China
| | - Fangli Ren
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
| | - Jiake Xu
- School of Biomedical Sciences; University of Western Australia; Perth Western Australia Australia
| | - Mengyu Zhou
- Department of Dentistry; The First Affiliated Hospital of Guangxi Medical University; Nanning China
| | - Peiyu Li
- The General Hospital of the People's Liberation Army; Beijing China
| | - Haotian Feng
- Research Centre for Regenerative Medicine; Guangxi Medical University; Nanning China
| | - Yinyin Wang
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
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40
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Yoo YS, Han HG, Jeon YJ. Unfolded Protein Response of the Endoplasmic Reticulum in Tumor Progression and Immunogenicity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2969271. [PMID: 29430279 PMCID: PMC5752989 DOI: 10.1155/2017/2969271] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is a pivotal regulator of folding, quality control, trafficking, and targeting of secreted and transmembrane proteins, and accordingly, eukaryotic cells have evolved specialized machinery to ensure that the ER enables these proteins to acquire adequate folding and maturation in the presence of intrinsic and extrinsic insults. This adaptive capacity of the ER to intrinsic and extrinsic perturbations is important for maintaining protein homeostasis, which is termed proteostasis. Failure in adaptation to these perturbations leads to accumulation of misfolded or unassembled proteins in the ER, which is termed ER stress, resulting in the activation of unfolded protein response (UPR) of the ER and the execution of ER-associated degradation (ERAD) to restore homeostasis. Furthermore, both of the two axes play key roles in the control of tumor progression, inflammation, immunity, and aging. Therefore, understanding UPR of the ER and subsequent ERAD will provide new insights into the pathogenesis of many human diseases and contribute to therapeutic intervention in these diseases.
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Affiliation(s)
- Yoon Seon Yoo
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Hye Gyeong Han
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Young Joo Jeon
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
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41
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Shao S, Rodrigo-Brenni MC, Kivlen MH, Hegde RS. Mechanistic basis for a molecular triage reaction. Science 2017; 355:298-302. [PMID: 28104892 DOI: 10.1126/science.aah6130] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/22/2016] [Indexed: 01/24/2023]
Abstract
Newly synthesized proteins are triaged between biosynthesis and degradation to maintain cellular homeostasis, but the decision-making mechanisms are unclear. We reconstituted the core reactions for membrane targeting and ubiquitination of nascent tail-anchored membrane proteins to understand how their fate is determined. The central six-component triage system is divided into an uncommitted client-SGTA complex, a self-sufficient targeting module, and an embedded but self-sufficient quality control module. Client-SGTA engagement of the targeting module induces rapid, private, and committed client transfer to TRC40 for successful biosynthesis. Commitment to ubiquitination is dictated primarily by comparatively slower client dissociation from SGTA and nonprivate capture by the BAG6 subunit of the quality control module. Our results provide a paradigm for how priority and time are encoded within a multichaperone triage system.
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Affiliation(s)
- Sichen Shao
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Monica C Rodrigo-Brenni
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Maryann H Kivlen
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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42
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SGTA-Dependent Regulation of Hsc70 Promotes Cytosol Entry of Simian Virus 40 from the Endoplasmic Reticulum. J Virol 2017; 91:JVI.00232-17. [PMID: 28356524 DOI: 10.1128/jvi.00232-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/24/2017] [Indexed: 01/01/2023] Open
Abstract
Membrane penetration by nonenveloped viruses remains enigmatic. In the case of the nonenveloped polyomavirus simian virus 40 (SV40), the virus penetrates the endoplasmic reticulum (ER) membrane to reach the cytosol and then traffics to the nucleus to cause infection. We previously demonstrated that the cytosolic Hsc70-SGTA-Hsp105 complex is tethered to the ER membrane, where Hsp105 and SGTA facilitate the extraction of SV40 from the ER and transport of the virus into the cytosol. We now find that Hsc70 also ejects SV40 from the ER into the cytosol in a step regulated by SGTA. Although SGTA's N-terminal domain, which mediates homodimerization and recruits cellular adaptors, is dispensable during ER-to-cytosol transport of SV40, this domain appears to exert an unexpected post-ER membrane translocation function during SV40 entry. Our study thus establishes a critical function of Hsc70 within the Hsc70-SGTA-Hsp105 complex in promoting SV40 ER-to-cytosol membrane penetration and unveils a role of SGTA in controlling this step.IMPORTANCE How a nonenveloped virus transports across a biological membrane to cause infection remains mysterious. One enigmatic step is whether host cytosolic components are co-opted to transport the viral particle into the cytosol. During ER-to-cytosol membrane transport of the nonenveloped polyomavirus SV40, a decisive infection step, a cytosolic complex composed of Hsc70-SGTA-Hsp105 was previously shown to associate with the ER membrane. SGTA and Hsp105 have been shown to extract SV40 from the ER and transport the virus into the cytosol. We demonstrate here a critical role of Hsc70 in SV40 ER-to-cytosol penetration and reveal how SGTA controls Hsc70 to impact this process.
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43
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Deficiency in ubiquitin-like protein Ubl4A impairs migration of fibroblasts and macrophages. Biochem Biophys Res Commun 2016; 483:617-623. [PMID: 27998771 DOI: 10.1016/j.bbrc.2016.12.094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/14/2016] [Indexed: 11/24/2022]
Abstract
Ubiquitin-like protein Ubl4A is a small, multi-functional protein with no ubiquitination activity. We have previously demonstrated that Ubl4A directly interacts with actin-related protein 2/3 complex (Arp2/3) and promotes Arp2/3-dependent actin branching, thereby accelerating plasma membrane translocation of protein kinase Akt upon insulin stimulation. Here, we show that Ubl4A is critical for plasma membrane protrusion and cell migration. Ubl4A, F-actin and Arp2/3 are co-localized at the cell leading edges during wound closure. Knockout of Ubl4A significantly reduces actin-mediated membrane protrusion and delays wound healing by primary mouse embryonic fibroblasts. Consistently, the ability of fibroblasts to migrate out of corneal tissue ex vivo is also impaired in Ubl4A-deficient mice. Furthermore, cell motility, but not phagocytosis, is significantly decreased in Ubl4A-deficient macrophages compared with wild-type controls. These results imply an important role for Ubl4A in cell migration-associated pathophysiological processes.
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44
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Thapaliya A, Nyathi Y, Martínez-Lumbreras S, Krysztofinska EM, Evans NJ, Terry IL, High S, Isaacson RL. SGTA interacts with the proteasomal ubiquitin receptor Rpn13 via a carboxylate clamp mechanism. Sci Rep 2016; 6:36622. [PMID: 27827410 PMCID: PMC5101480 DOI: 10.1038/srep36622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022] Open
Abstract
The fate of secretory and membrane proteins that mislocalize to the cytosol is decided by a collaboration between cochaperone SGTA (small, glutamine-rich, tetratricopeptide repeat protein alpha) and the BAG6 complex, whose operation relies on multiple transient and subtly discriminated interactions with diverse binding partners. These include chaperones, membrane-targeting proteins and ubiquitination enzymes. Recently a direct interaction was discovered between SGTA and the proteasome, mediated by the intrinsic proteasomal ubiquitin receptor Rpn13. Here, we structurally and biophysically characterize this binding and identify a region of the Rpn13 C-terminal domain that is necessary and sufficient to facilitate it. We show that the contact occurs through a carboxylate clamp-mediated molecular recognition event with the TPR domain of SGTA, and provide evidence that the interaction can mediate the association of Rpn13 and SGTA in a cellular context.
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Affiliation(s)
- Arjun Thapaliya
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Yvonne Nyathi
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, U.K
| | | | - Ewelina M. Krysztofinska
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Nicola J. Evans
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Isabelle L. Terry
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, U.K
| | - Rivka L. Isaacson
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
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45
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How Polyomaviruses Exploit the ERAD Machinery to Cause Infection. Viruses 2016; 8:v8090242. [PMID: 27589785 PMCID: PMC5035956 DOI: 10.3390/v8090242] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
To infect cells, polyomavirus (PyV) traffics from the cell surface to the endoplasmic reticulum (ER) where it hijacks elements of the ER-associated degradation (ERAD) machinery to penetrate the ER membrane and reach the cytosol. From the cytosol, the virus transports to the nucleus, enabling transcription and replication of the viral genome that leads to lytic infection or cellular transformation. How PyV exploits the ERAD machinery to cross the ER membrane and access the cytosol, a decisive infection step, remains enigmatic. However, recent studies have slowly unraveled many aspects of this process. These emerging insights should advance our efforts to develop more effective therapies against PyV-induced human diseases.
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46
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Abstract
The endoplasmic reticulum is the port of entry for proteins into the secretory pathway and the site of synthesis for several important lipids, including cholesterol, triacylglycerol, and phospholipids. Protein production within the endoplasmic reticulum is tightly regulated by a cohort of resident machinery that coordinates the folding, modification, and deployment of secreted and integral membrane proteins. Proteins failing to attain their native conformation are degraded through the endoplasmic reticulum-associated degradation (ERAD) pathway via a series of tightly coupled steps: substrate recognition, dislocation, and ubiquitin-dependent proteasomal destruction. The same ERAD machinery also controls the flux through various metabolic pathways by coupling the turnover of metabolic enzymes to the levels of key metabolites. We review the current understanding and biological significance of ERAD-mediated regulation of lipid metabolism in mammalian cells.
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Affiliation(s)
- Julian Stevenson
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - Edmond Y Huang
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - James A Olzmann
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
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47
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Krysztofinska EM, Martínez-Lumbreras S, Thapaliya A, Evans NJ, High S, Isaacson RL. Structural and functional insights into the E3 ligase, RNF126. Sci Rep 2016; 6:26433. [PMID: 27193484 PMCID: PMC4872217 DOI: 10.1038/srep26433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/03/2016] [Indexed: 12/14/2022] Open
Abstract
RNF126 is an E3 ubiquitin ligase that collaborates with the BAG6 sortase complex to ubiquitinate hydrophobic substrates in the cytoplasm that are destined for proteasomal recycling. Composed of a trimeric complex of BAG6, TRC35 and UBL4A the BAG6 sortase is also associated with SGTA, a co-chaperone from which it can obtain hydrophobic substrates. Here we solve the solution structure of the RNF126 zinc finger domain in complex with the BAG6 UBL domain. We also characterise an interaction between RNF126 and UBL4A and analyse the competition between SGTA and RNF126 for the N-terminal BAG6 binding site. This work sheds light on the sorting mechanism of the BAG6 complex and its accessory proteins which, together, decide the fate of stray hydrophobic proteins in the aqueous cytoplasm.
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Affiliation(s)
- Ewelina M. Krysztofinska
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | | | - Arjun Thapaliya
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Nicola J. Evans
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Stephen High
- Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Rivka L. Isaacson
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, UK
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48
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The Vpu-interacting Protein SGTA Regulates Expression of a Non-glycosylated Tetherin Species. Sci Rep 2016; 6:24934. [PMID: 27103333 PMCID: PMC4840321 DOI: 10.1038/srep24934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/07/2016] [Indexed: 01/02/2023] Open
Abstract
The HIV-1 accessory protein Vpu enhances virus release by counteracting the host restriction factor tetherin. To further understand the role of host cell proteins in Vpu function, we carried out yeast two-hybrid screening and identified a previously reported Vpu-interacting host factor, small glutamine-rich tetratricopeptide repeat-containing protein (SGTA). While RNAi-mediated depletion of SGTA did not significantly affect levels of tetherin or virus release efficiency, we observed that overexpression of SGTA inhibited HIV-1 release in a Vpu- and tetherin-independent manner. Overexpression of SGTA in the presence of Vpu, but not in its absence, resulted in a marked stabilization and cytosolic relocalization of a 23-kDa, non-glycosylated tetherin species. Coimmunoprecipitation studies indicated that non-glycosylated tetherin is stabilized through the formation of a ternary SGTA/Vpu/tetherin complex. This accumulation of non-glycosylated tetherin is due to inhibition of its degradation, independent of the ER-associated degradation (ERAD) pathway. Because the SGTA-stabilized tetherin species is partially localized to the cytosol, we propose that overexpression of SGTA in the presence of Vpu blocks the translocation of tetherin across the ER membrane, resulting in cytosolic accumulation of a non-glycosylated tetherin species. Although our results do not provide support for a physiological function of SGTA in HIV-1 replication, they demonstrate that SGTA overexpression regulates tetherin expression and stability, thus providing insights into the function of SGTA in ER translocation and protein degradation.
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49
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Nakatsukasa K, Kamura T. Subcellular Fractionation Analysis of the Extraction of Ubiquitinated Polytopic Membrane Substrate during ER-Associated Degradation. PLoS One 2016; 11:e0148327. [PMID: 26849222 PMCID: PMC4743956 DOI: 10.1371/journal.pone.0148327] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/15/2016] [Indexed: 11/21/2022] Open
Abstract
During ER-associated degradation (ERAD), misfolded polytopic membrane proteins are ubiquitinated and retrotranslocated to the cytosol for proteasomal degradation. However, our understanding as to how polytopic membrane proteins are extracted from the ER to the cytosol remains largely unclear. To better define the localization and physical properties of ubiquitinated polytopic membrane substrates in vivo, we performed subcellular fractionation analysis of Ste6*, a twelve transmembrane protein that is ubiquitinated primarily by Doa10 E3 ligase in yeast. Consistent with previous in vitro studies, ubiquitinated Ste6* was extracted from P20 (20,000 g pellet) fraction to S20 (20,000 g supernatant) fraction in a Cdc48/p97-dependent manner. Similarly, Ubx2p, which recruits Cdc48/p97 to the ER, facilitated the extraction of Ste6*. By contrast, lipid droplet formation, which was suggested to be dispensable for the degradation of Hrd1-substrates in yeast, was not required for the degradation of Ste6*. Intriguingly, we found that ubiquitinated Ste6* in the S20 fraction could be enriched by further centrifugation at 100,000 g. Although it is currently uncertain whether ubiquitinated Ste6* in P100 fraction is completely free from any lipids, membrane flotation analysis suggested the existence of two distinct populations of ubiquitinated Ste6* with different states of membrane association. Together, these results imply that ubiquitinated Ste6* may be sequestered into a putative quality control sub-structure by Cdc48/p97. Fractionation assays developed in the present study provide a means to further dissect the ill-defined post-ubiquitination step during ERAD of polytopic membrane substrates.
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Affiliation(s)
- Kunio Nakatsukasa
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- * E-mail: (KN); (TK)
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- * E-mail: (KN); (TK)
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50
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Tanaka H, Takahashi T, Xie Y, Minami R, Yanagi Y, Hayashishita M, Suzuki R, Yokota N, Shimada M, Mizushima T, Kuwabara N, Kato R, Kawahara H. A conserved island of BAG6/Scythe is related to ubiquitin domains and participates in short hydrophobicity recognition. FEBS J 2015; 283:662-77. [PMID: 26663859 DOI: 10.1111/febs.13618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/19/2015] [Accepted: 12/02/2015] [Indexed: 11/27/2022]
Abstract
BAG6 (also called Scythe) interacts with the exposed hydrophobic regions of newly synthesized proteins and escorts them to the degradation machinery through mechanisms that remain to be elucidated. In this study, we provide evidence that BAG6 physically interacts with the model defective protein substrate CL1 in a manner that depends directly on its short hydrophobicity. We found that the N terminus of BAG6 contains an evolutionarily conserved island tentatively designated the BAG6 ubiquitin-linked domain. Partial deletion of this domain in the BAG6 N-terminal fragment abolished in cell recognition of polyubiquitinated polypeptides as well as the hydrophobicity-mediated recognition of the CL1 degron in cell and in vitro. These observations suggest a mechanism whereby the BAG6 ubiquitin-linked domain provides a platform for discriminating substrates with shorter hydrophobicity stretches as a signal for defective proteins.
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Affiliation(s)
- Hirofumi Tanaka
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Toshiki Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Yiming Xie
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Ryosuke Minami
- Department of Biological Sciences, Tokyo Metropolitan University, Japan.,Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yuko Yanagi
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | | | - Rigel Suzuki
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Naoto Yokota
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Masumi Shimada
- Department of Biological Sciences, Tokyo Metropolitan University, Japan.,Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Tsunehiro Mizushima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Japan
| | - Naoyuki Kuwabara
- Structural Biology Research Center, Photon Factory, IMSS, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Ryuichi Kato
- Structural Biology Research Center, Photon Factory, IMSS, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Hiroyuki Kawahara
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
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