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Wang Z, Xiong S, Wu Z, Wang X, Gong Y, Zhu WG, Xu X. VCP/p97 UFMylation stabilizes BECN1 and facilitates the initiation of autophagy. Autophagy 2024; 20:2041-2054. [PMID: 38762759 PMCID: PMC11346537 DOI: 10.1080/15548627.2024.2356488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 05/05/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
Macroautophagy/autophagy is essential for the degradation and recycling of cytoplasmic materials. The initiation of this process is determined by phosphatidylinositol-3-kinase (PtdIns3K) complex, which is regulated by factor BECN1 (beclin 1). UFMylation is a novel ubiquitin-like modification that has been demonstrated to modulate several cellular activities. However, the role of UFMylation in regulating autophagy has not been fully elucidated. Here, we found that VCP/p97 is UFMylated on K109 by the E3 UFL1 (UFM1 specific ligase 1) and this modification promotes BECN1 stabilization and assembly of the PtdIns3K complex, suggesting a role for VCP/p97 UFMylation in autophagy initiation. Mechanistically, VCP/p97 UFMylation stabilizes BECN1 through ATXN3 (ataxin 3)-mediated deubiquitination. As a key component of the PtdIns3K complex, stabilized BECN1 facilitates assembly of this complex. Re-expression of VCP/p97, but not the UFMylation-defective mutant, rescued the VCP/p97 depletion-induced increase in MAP1LC3B/LC3B protein expression. We also showed that several pathogenic VCP/p97 mutations identified in a variety of neurological disorders and cancers were associated with reduced UFMylation, thus implicating VCP/p97 UFMylation as a potential therapeutic target for these diseases. Abbreviation: ATG14:autophagy related 14; Baf A1:bafilomycin A1;CMT2Y: Charcot-Marie-Toothdisease, axonal, 2Y; CYB5R3: cytochromeb5 reductase 3; DDRGK1: DDRGK domain containing 1; DMEM:Dulbecco'smodified Eagle's medium;ER:endoplasmic reticulum; FBS:fetalbovine serum;FTDALS6:frontotemporaldementia and/or amyotrophic lateral sclerosis 6; IBMPFD1:inclusion bodymyopathy with early-onset Paget disease with or withoutfrontotemporal dementia 1; LC-MS/MS:liquid chromatography tandem mass spectrometry; MAP1LC3B/LC3B:microtubule associated protein 1 light chain 3 beta; MS: massspectrometry; NPLOC4: NPL4 homolog, ubiquitin recognition factor;PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3;PIK3R4: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K:phosphatidylinositol 3-kinase; RPL26: ribosomal protein L26; RPN1:ribophorin I; SQSTM1/p62: sequestosome 1; UBA5: ubiquitin likemodifier activating enzyme 5; UFC1: ubiquitin-fold modifierconjugating enzyme 1; UFD1: ubiquitin recognition factor in ERassociated degradation 1; UFL1: UFM1 specific ligase 1; UFM1:ubiquitin fold modifier 1; UFSP2: UFM1 specific peptidase 2; UVRAG:UV radiation resistance associated; VCP/p97: valosin containingprotein; WT: wild-type.
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Affiliation(s)
- Zhifeng Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Shuhui Xiong
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhaoyi Wu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Xingde Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Yamin Gong
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
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2
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Chen J, Zhao H, Liu M, Chen L. A new perspective on the autophagic and non-autophagic functions of the GABARAP protein family: a potential therapeutic target for human diseases. Mol Cell Biochem 2024; 479:1415-1441. [PMID: 37440122 DOI: 10.1007/s11010-023-04800-5] [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: 03/16/2023] [Accepted: 06/24/2023] [Indexed: 07/14/2023]
Abstract
Mammalian autophagy-related protein Atg8, including the LC3 subfamily and GABARAP subfamily. Atg8 proteins play a vital role in autophagy initiation, autophagosome formation and transport, and autophagy-lysosome fusion. GABARAP subfamily proteins (GABARAPs) share a high degree of homology with LC3 family proteins, and their unique roles are often overlooked. GABARAPs are as indispensable as LC3 in autophagy. Deletion of GABARAPs fails autophagy flux induction and autophagy lysosomal fusion, which leads to the failure of autophagy. GABARAPs are also involved in the transport of selective autophagy receptors. They are engaged in various particular autophagy processes, including mitochondrial autophagy, endoplasmic reticulum autophagy, Golgi autophagy, centrosome autophagy, and dorphagy. Furthermore, GABARAPs are closely related to the transport and delivery of the inhibitory neurotransmitter γ-GABAA and the angiotensin II AT1 receptor (AT1R), tumor growth, metastasis, and prognosis. GABARAPs also have been confirmed to be involved in various diseases, such as cancer, cardiovascular disease, and neurodegenerative diseases. In order to better understand the role and therapeutic potential of GABARAPs, this article comprehensively reviews the autophagic and non-autophagic functions of GABARAPs, as well as the research progress of the role and mechanism of GABARAPs in cancer, cardiovascular diseases and neurodegenerative diseases. It emphasizes the significance of GABARAPs in the clinical prevention and treatment of diseases, and may provide new therapeutic ideas and targets for human diseases. GABARAP and GABARAPL1 in the serum of cancer patients are positively correlated with the prognosis of patients, which can be used as a clinical biomarker, predictor and potential therapeutic target.
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Affiliation(s)
- Jiawei Chen
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Hong Zhao
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- School of Nursing, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Meiqing Liu
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China.
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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3
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Zhuo R, Zhang Z, Chen Y, Li G, Du S, Guo X, Yang R, Tao Y, Li X, Fang F, Xie Y, Wu D, Yang Y, Yang C, Yin H, Qian G, Wang H, Yu J, Jia S, Zhu F, Feng C, Wang J, Xu Y, Li Z, Shi L, Wang X, Pan J, Wang J. CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma. Cancer Lett 2024; 591:216882. [PMID: 38636893 DOI: 10.1016/j.canlet.2024.216882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/30/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Super enhancers (SEs) are genomic regions comprising multiple closely spaced enhancers, typically occupied by a high density of cell-type-specific master transcription factors (TFs) and frequently enriched in key oncogenes in various tumors, including neuroblastoma (NB), one of the most prevalent malignant solid tumors in children originating from the neural crest. Cyclin-dependent kinase 5 regulatory subunit-associated protein 3 (CDK5RAP3) is a newly identified super-enhancer-driven gene regulated by master TFs in NB; however, its function in NB remains unclear. Through an integrated study of publicly available datasets and microarrays, we observed a significantly elevated CDK5RAP3 expression level in NB, associated with poor patient prognosis. Further research demonstrated that CDK5RAP3 promotes the growth of NB cells, both in vitro and in vivo. Mechanistically, defective CDK5RAP3 interfered with the UFMylation system, thereby triggering endoplasmic reticulum (ER) phagy. Additionally, we provide evidence that CDK5RAP3 maintains the stability of MEIS2, a master TF in NB, and in turn, contributes to the high expression of CDK5RAP3. Overall, our findings shed light on the molecular mechanisms by which CDK5RAP3 promotes tumor progression and suggest that its inhibition may represent a novel therapeutic strategy for NB.
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Affiliation(s)
- Ran Zhuo
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China; Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, China
| | - Zimu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yanling Chen
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Gen Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Shibei Du
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xinyi Guo
- Department of Infection Management, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Randong Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China; Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, China
| | - Yanfang Tao
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xiaolu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yi Xie
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Di Wu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yang Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Chun Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Hongli Yin
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Guanghui Qian
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Hairong Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Juanjuan Yu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Siqi Jia
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Frank Zhu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, China
| | - Chenxi Feng
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Jianwei Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yunyun Xu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Zhiheng Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Lei Shi
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, China
| | - Xiaodong Wang
- Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China.
| | - Jian Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China; Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, China.
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4
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Li W, Lin Y, Wang X, Yang H, Ding Y, Chen Z, He Z, Zhang J, Zhao L, Jiao P. Chicken UFL1 Restricts Avian Influenza Virus Replication by Disrupting the Viral Polymerase Complex and Facilitating Type I IFN Production. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1479-1492. [PMID: 38477617 DOI: 10.4049/jimmunol.2300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024]
Abstract
During avian influenza virus (AIV) infection, host defensive proteins promote antiviral innate immunity or antagonize viral components to limit viral replication. UFM1-specific ligase 1 (UFL1) is involved in regulating innate immunity and DNA virus replication in mammals, but the molecular mechanism by which chicken (ch)UFL1 regulates AIV replication is unclear. In this study, we first identified chUFL1 as a negative regulator of AIV replication by enhancing innate immunity and disrupting the assembly of the viral polymerase complex. Mechanistically, chUFL1 interacted with chicken stimulator of IFN genes (chSTING) and contributed to chSTING dimerization and the formation of the STING-TBK1-IRF7 complex. We further demonstrated that chUFL1 promoted K63-linked polyubiquitination of chSTING at K308 to facilitate chSTING-mediated type I IFN production independent of UFMylation. Additionally, chUFL1 expression was upregulated in response to AIV infection. Importantly, chUFL1 also interacted with the AIV PA protein to inhibit viral polymerase activity. Furthermore, chUFL1 impeded the nuclear import of the AIV PA protein and the assembly of the viral polymerase complex to suppress AIV replication. Collectively, these findings demonstrate that chUFL1 restricts AIV replication by disrupting the viral polymerase complex and facilitating type I IFN production, which provides new insights into the regulation of AIV replication in chickens.
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Affiliation(s)
- Weiqiang Li
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
| | - Yu Lin
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Xiyi Wang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Huixing Yang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Yangbao Ding
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Zuxian Chen
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Zhuoliang He
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Junsheng Zhang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Luxiang Zhao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Peirong Jiao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
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5
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Tian T, Chen J, Zhao H, Li Y, Xia F, Huang J, Han J, Liu T. UFL1 triggers replication fork degradation by MRE11 in BRCA1/2-deficient cells. Nat Chem Biol 2024:10.1038/s41589-024-01611-7. [PMID: 38649452 DOI: 10.1038/s41589-024-01611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
The stabilization of stalled forks has emerged as a crucial mechanism driving resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient tumors. Here, we identify UFL1, a UFM1-specific E3 ligase, as a pivotal regulator of fork stability and the response to PARP inhibitors in BRCA1/2-deficient cells. On replication stress, UFL1 localizes to stalled forks and catalyzes the UFMylation of PTIP, a component of the MLL3/4 methyltransferase complex, specifically at lysine 148. This modification facilitates the assembly of the PTIP-MLL3/4 complex, resulting in the enrichment of H3K4me1 and H3K4me3 at stalled forks and subsequent recruitment of the MRE11 nuclease. Consequently, loss of UFL1, disruption of PTIP UFMylation or overexpression of the UFM1 protease UFSP2 protects nascent DNA strands from extensive degradation and confers resistance to PARP inhibitors in BRCA1/2-deficient cells. These findings provide mechanistic insights into the processes underlying fork instability in BRCA1/2-deficient cells and offer potential therapeutic avenues for the treatment of BRCA1/2-deficient tumors.
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Affiliation(s)
- Tian Tian
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junliang Chen
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Huacun Zhao
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yulin Li
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Feiyu Xia
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Huang
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jinhua Han
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ting Liu
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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6
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Santhosh Kumar S, Naseri NN, Pather SR, Hallacli E, Ndayisaba A, Buenaventura C, Acosta K, Roof J, Fazelinia H, Spruce LA, Luk K, Khurana V, Rhoades E, Shalem O. Sequential CRISPR screening reveals partial NatB inhibition as a strategy to mitigate alpha-synuclein levels in human neurons. SCIENCE ADVANCES 2024; 10:eadj4767. [PMID: 38335281 PMCID: PMC10857481 DOI: 10.1126/sciadv.adj4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Alpha-synuclein (αSyn) protein levels correlate with the risk and severity of Parkinson's disease and related neurodegenerative diseases. Lowering αSyn is being actively investigated as a therapeutic modality. Here, we systematically map the regulatory network that controls endogenous αSyn using sequential CRISPR-knockout and -interference screens in an αSyn gene (SNCA)-tagged cell line and induced pluripotent stem cell-derived neurons (iNeurons). We uncover αSyn modifiers at multiple regulatory layers, with amino-terminal acetyltransferase B (NatB) enzymes being the most potent endogenous αSyn modifiers in both cell lines. Amino-terminal acetylation protects the cytosolic αSyn from rapid degradation by the proteasome in a Ube2w-dependent manner. Moreover, we show that pharmacological inhibition of methionyl-aminopeptidase 2, a regulator of NatB complex formation, attenuates endogenous αSyn in iNeurons carrying SNCA triplication. Together, our study reveals several gene networks that control endogenous αSyn, identifies mechanisms mediating the degradation of nonacetylated αSyn, and illustrates potential therapeutic pathways for decreasing αSyn levels in synucleinopathies.
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Affiliation(s)
- Saranya Santhosh Kumar
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nima N. Naseri
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarshan R. Pather
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erinc Hallacli
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Buenaventura
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen Acosta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Roof
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A. Spruce
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelvin Luk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Picchianti L, Sánchez de Medina Hernández V, Zhan N, Irwin NA, Groh R, Stephani M, Hornegger H, Beveridge R, Sawa-Makarska J, Lendl T, Grujic N, Naumann C, Martens S, Richards TA, Clausen T, Ramundo S, Karagöz GE, Dagdas Y. Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy. EMBO J 2023; 42:e112053. [PMID: 36762703 PMCID: PMC10183829 DOI: 10.15252/embj.2022112053] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
UFMylation involves the covalent modification of substrate proteins with UFM1 (Ubiquitin-fold modifier 1) and is important for maintaining ER homeostasis. Stalled translation triggers the UFMylation of ER-bound ribosomes and activates C53-mediated autophagy to clear toxic polypeptides. C53 contains noncanonical shuffled ATG8-interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. However, the mechanistic basis of sAIM-mediated ATG8 interaction remains unknown. Here, we show that C53 and sAIMs are conserved across eukaryotes but secondarily lost in fungi and various algal lineages. Biochemical assays showed that the unicellular alga Chlamydomonas reinhardtii has a functional UFMylation pathway, refuting the assumption that UFMylation is linked to multicellularity. Comparative structural analyses revealed that both UFM1 and ATG8 bind sAIMs in C53, but in a distinct way. Conversion of sAIMs into canonical AIMs impaired binding of C53 to UFM1, while strengthening ATG8 binding. Increased ATG8 binding led to the autoactivation of the C53 pathway and sensitization of Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral role of sAIMs in UFMylation-dependent fine-tuning of C53-mediated autophagy activation.
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Affiliation(s)
- Lorenzo Picchianti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Víctor Sánchez de Medina Hernández
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ni Zhan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nicholas At Irwin
- Department of Zoology, University of Oxford, Oxford, UK.,Merton College, University of Oxford, Oxford, UK
| | - Roan Groh
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Madlen Stephani
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Harald Hornegger
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Justyna Sawa-Makarska
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Lendl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Nenad Grujic
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sascha Martens
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | | | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Silvia Ramundo
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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8
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Eisenack TJ, Trentini DB. Ending a bad start: Triggers and mechanisms of co-translational protein degradation. Front Mol Biosci 2023; 9:1089825. [PMID: 36660423 PMCID: PMC9846516 DOI: 10.3389/fmolb.2022.1089825] [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: 11/04/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis-the state of proteome balance-cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.
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Affiliation(s)
- Tom Joshua Eisenack
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Débora Broch Trentini
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany,*Correspondence: Débora Broch Trentini,
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9
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Hong X, Wu Z, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Cong L, Wang H, Wu X, Liu Y, Gao W, Li L. Longitudinal Association of DNA Methylation With Type 2 Diabetes and Glycemic Traits: A 5-Year Cross-Lagged Twin Study. Diabetes 2022; 71:2804-2817. [PMID: 36170668 DOI: 10.2337/db22-0513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Investigators of previous cross-sectional epigenome-wide association studies (EWAS) in adults have reported hundreds of 5'-cytosine-phosphate-guanine-3' (CpG) sites associated with type 2 diabetes mellitus (T2DM) and glycemic traits. However, the results from EWAS have been inconsistent, and longitudinal observations of these associations are scarce. Furthermore, few studies have investigated whether DNA methylation (DNAm) could be modified by smoking, drinking, and glycemic traits, which have broad impacts on genome-wide DNAm and result in altering the risk of T2DM. Twin studies provide a valuable tool for epigenetic studies, as twins are naturally matched for genetic information. In this study, we conducted a systematic literature search in PubMed and Embase for EWAS, and 214, 33, and 117 candidate CpG sites were selected for T2DM, HbA1c, and fasting blood glucose (FBG). Based on 1,070 twins from the Chinese National Twin Registry, 67, 17, and 16 CpG sites from previous studies were validated for T2DM, HbA1c, and FBG. Longitudinal review and blood sampling for phenotypic information and DNAm were conducted twice in 2013 and 2018 for 308 twins. A cross-lagged analysis was performed to examine the temporal relationship between DNAm and T2DM or glycemic traits in the longitudinal data. A total of 11 significant paths from T2DM to subsequent DNAm and 15 paths from DNAm to subsequent T2DM were detected, suggesting both directions of associations. For glycemic traits, we detected 17 cross-lagged associations from baseline glycemic traits to subsequent DNAm, and none were from the other cross-lagged direction, indicating that CpG sites may be the consequences, not the causes, of glycemic traits. Finally, a longitudinal mediation analysis was performed to explore the mediation effects of DNAm on the associations of smoking, drinking, and glycemic traits with T2DM. No significant mediations of DNAm in the associations linking smoking and drinking with T2DM were found. In contrast, our study suggested a potential role of DNAm of cg19693031, cg00574958, and cg04816311 in mediating the effect of altered glycemic traits on T2DM.
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Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhiyu Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Liming Cong
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
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10
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Zhu J, Ma X, Jing Y, Zhang G, Zhang D, Mao Z, Ma X, Liu H, Chen F. P4HB UFMylation regulates mitochondrial function and oxidative stress. Free Radic Biol Med 2022; 188:277-286. [PMID: 35753586 DOI: 10.1016/j.freeradbiomed.2022.06.237] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
UFMylation is a ubiquitin-like modification which attaches the ubiquitin-fold modifier 1 to target proteins. To date, only a few UFMylation targets have been identified. In the current study, we demonstrated that P4HB is a new target protein for UFMylation and it can be UFMylated at three lysine residues in the form of mono-UFMylation. P4HB has oxidoreductase, chaperone and isomerase effects. It presents in the endoplasmic reticulum, mitochondria and cytosol. Next, we generated a stable HepG2 cell line, the hepatocellular cells, with defective P4HB UFMylation. Our data show that P4HB UFMylation defect promotes P4HB protein degradation via the ubiquitin-proteasome pathway. Defective P4HB UFMylation causes mitochondrial function damage, oxidative stress, and endoplasmic reticulum stress in HepG2 cells. These effects are more obvious when treating HepG2 cells with palmitic acid, which is frequently used as one of the cell models of non-alcoholic fatty liver disease (NAFLD). Our results identify UFMylation as a key post-translational modification for the maintenance of P4HB stability and biological functions in HepG2 cells, and point to P4HB UFMylation as a potential direction in the study of NAFLD.
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Affiliation(s)
- Jing Zhu
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xirui Ma
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Jing
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guangya Zhang
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dandan Zhang
- Department of Endocrinology, Xi'an No. 1 Hospital, First Affiliated Hospital of Northwestern University, Xi'an, Shaanxi Province, China
| | - Ziming Mao
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaowen Ma
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huifang Liu
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fengling Chen
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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11
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Yoo HM, Park JH, Kim JY, Chung CH. Modification of ERα by UFM1 Increases Its Stability and Transactivity for Breast Cancer Development. Mol Cells 2022; 45:425-434. [PMID: 35680375 PMCID: PMC9200662 DOI: 10.14348/molcells.2022.0029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
The post-translational modification (e.g., phosphorylation) of estrogen receptor α (ERα) plays a role in controlling the expression and subcellular localization of ERα as well as its sensitivity to hormone response. Here, we show that ERα is also modified by UFM1 and this modification (ufmylation) plays a crucial role in promoting the stability and transactivity of ERα, which in turn promotes breast cancer development. The elevation of ufmylation via the knockdown of UFSP2 (the UFM1-deconjugating enzyme in humans) dramatically increases ERα stability by inhibiting ubiquitination. In contrast, ERα stability is decreased by the prevention of ufmylation via the silencing of UBA5 (the UFM1-activating E1 enzyme). Lys171 and Lys180 of ERα were identified as the major UFM1 acceptor sites, and the replacement of both Lys residues by Arg (2KR mutation) markedly reduced ERα stability. Moreover, the 2KR mutation abrogated the 17β-estradiol-induced transactivity of ERα and the expression of its downstream target genes, including pS2, cyclin D1, and c-Myc; this indicates that ERα ufmylation is required for its transactivation function. In addition, the 2KR mutation prevented anchorage-independent colony formation by MCF7 cells. Most notably, the expression of UFM1 and its conjugating machinery (i.e., UBA5, UFC1, UFL1, and UFBP1) were dramatically upregulated in ERα-positive breast cancer cell lines and tissues. Collectively, these findings implicate a critical role attributed to ERα ufmylation in breast cancer development by ameliorating its stability and transactivity.
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Affiliation(s)
- Hee Min Yoo
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Jong Ho Park
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae Yeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Chin Ha Chung
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- The Second Division of Natural Sciences, Korea National Academy of Sciences, Seoul 06579, Korea
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12
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Tolmachova K, Farnung J, Liang JR, Corn JE, Bode JW. Facile Preparation of UFMylation Activity-Based Probes by Chemoselective Installation of Electrophiles at the C-Terminus of Recombinant UFM1. ACS CENTRAL SCIENCE 2022; 8:756-762. [PMID: 35756382 PMCID: PMC9228560 DOI: 10.1021/acscentsci.2c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Indexed: 05/17/2023]
Abstract
Aberrations in protein modification with ubiquitin-fold modifier (UFM1) are associated with a range of diseases, but the biological function and regulation of this post-translational modification, known as UFMylation, remain enigmatic. To provide activity-based probes for UFMylation, we have developed a new method for the installation of electrophilic warheads at the C-terminus of recombinant UFM1. A C-terminal UFM1 acyl hydrazide was readily produced by selective intein cleavage and chemoselectively acylated by a variety of carboxylic acid anhydrides at pH 3, without detriment to the folded protein or reactions at unprotected amino acid side chains. The resulting UFM1 activity-based probes show a range of tunable reactivity and high selectivity for proteins involved in UFMylation processes; structurally related E1s, E2s, and proteases associated with Ub or other Ubls were unreactive. The UFM1 probes were active both in cell lysates and in living cells. A previously inaccessible α-chloroacetyl probe was remarkably selective for covalent modification of the active-site cysteine of de-UFMylase UFSP2 in cellulo.
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Affiliation(s)
- Kateryna
A. Tolmachova
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jakob Farnung
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jin Rui Liang
- Institute
of Molecular Health Sciences, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jacob E. Corn
- Institute
of Molecular Health Sciences, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
- E-mail:
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13
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Liang Q, Jin Y, Xu S, Zhou J, Mao J, Ma X, Wang M, Cong YS. Human UFSP1 translated from an upstream near-cognate initiation codon functions as an active UFM1-specific protease. J Biol Chem 2022; 298:102016. [PMID: 35525273 PMCID: PMC9168615 DOI: 10.1016/j.jbc.2022.102016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a recently identified ubiquitin-like posttranslational modification with important biological functions. However, the regulatory mechanisms governing UFM1 modification of target proteins (UFMylation) and the cellular processes controlled by UFMylation remain largely unknown. It has been previously shown that a UFM1-specific protease (UFSP2) mediates the maturation of the UFM1 precursor and drives the de-UFMylation reaction. Furthermore, it has long been thought that UFSP1, an ortholog of UFSP2, is inactive in many organisms, including human, because it lacks an apparent protease domain when translated from the canonical start codon (445AUG). Here, we demonstrate using the combination of site-directed mutagenesis, CRISPR/Cas9–mediated genome editing, and mass spectrometry approaches that translation of human UFSP1 initiates from an upstream near-cognate codon, 217CUG, via eukaryotic translation initiation factor eIF2A-mediated translational initiation rather than from the annotated 445AUG, revealing the presence of a catalytic protease domain containing a Cys active site. Moreover, we show that both UFSP1 and UFSP2 mediate maturation of UFM1 and de-UFMylation of target proteins. This study demonstrates that human UFSP1 functions as an active UFM1-specific protease, thus contributing to our understanding of the UFMylation/de-UFMylation process.
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Affiliation(s)
- Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yaqi Jin
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Shiwen Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xiaohe Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
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14
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Snider DL, Park M, Murphy KA, Beachboard DC, Horner SM. Signaling from the RNA sensor RIG-I is regulated by ufmylation. Proc Natl Acad Sci U S A 2022; 119:e2119531119. [PMID: 35394863 PMCID: PMC9169834 DOI: 10.1073/pnas.2119531119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/28/2022] [Indexed: 01/23/2023] Open
Abstract
The RNA-binding protein RIG-I is a key initiator of the antiviral innate immune response. The signaling that mediates the antiviral response downstream of RIG-I is transduced through the adaptor protein MAVS and results in the induction of type I and III interferons (IFNs). This signal transduction occurs at endoplasmic reticulum (ER)–mitochondrial contact sites, to which RIG-I and other signaling proteins are recruited following their activation. RIG-I signaling is highly regulated to prevent aberrant activation of this pathway and dysregulated induction of IFN. Previously, we identified UFL1, the E3 ligase of the ubiquitin-like modifier conjugation system called ufmylation, as one of the proteins recruited to membranes at ER–mitochondrial contact sites in response to RIG-I activation. Here, we show that UFL1, as well as the process of ufmylation, promote IFN induction in response to RIG-I activation. We found that following RNA virus infection, UFL1 is recruited to the membrane-targeting protein 14–3-3ε and that this complex is then recruited to activated RIG-I to promote downstream innate immune signaling. Importantly, we found that 14–3-3ε has an increase in UFM1 conjugation following RIG-I activation. Additionally, loss of cellular ufmylation prevents the interaction of 14–3-3ε with RIG-I, which abrogates the interaction of RIG-I with MAVS and thus the downstream signal transduction that induces IFN. Our results define ufmylation as an integral regulatory component of the RIG-I signaling pathway and as a posttranslational control for IFN induction.
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Affiliation(s)
- Daltry L. Snider
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Moonhee Park
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Kristen A. Murphy
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Dia C. Beachboard
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Stacy M. Horner
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
- Department of Medicine, Duke University Medical Center, Durham, NC 27710
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15
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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16
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Li W, Li F, Zhang X, Lin HK, Xu C. Insights into the post-translational modification and its emerging role in shaping the tumor microenvironment. Signal Transduct Target Ther 2021; 6:422. [PMID: 34924561 PMCID: PMC8685280 DOI: 10.1038/s41392-021-00825-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
More and more in-depth studies have revealed that the occurrence and development of tumors depend on gene mutation and tumor heterogeneity. The most important manifestation of tumor heterogeneity is the dynamic change of tumor microenvironment (TME) heterogeneity. This depends not only on the tumor cells themselves in the microenvironment where the infiltrating immune cells and matrix together forming an antitumor and/or pro-tumor network. TME has resulted in novel therapeutic interventions as a place beyond tumor beds. The malignant cancer cells, tumor infiltrate immune cells, angiogenic vascular cells, lymphatic endothelial cells, cancer-associated fibroblastic cells, and the released factors including intracellular metabolites, hormonal signals and inflammatory mediators all contribute actively to cancer progression. Protein post-translational modification (PTM) is often regarded as a degradative mechanism in protein destruction or turnover to maintain physiological homeostasis. Advances in quantitative transcriptomics, proteomics, and nuclease-based gene editing are now paving the global ways for exploring PTMs. In this review, we focus on recent developments in the PTM area and speculate on their importance as a critical functional readout for the regulation of TME. A wealth of information has been emerging to prove useful in the search for conventional therapies and the development of global therapeutic strategies.
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Affiliation(s)
- Wen Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China
| | - Feifei Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, 530021, Nanning, Guangxi, China
| | - Xia Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Chuan Xu
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China.
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA.
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17
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Al-Saady ML, Kaiser CS, Wakasuqui F, Korenke GC, Waisfisz Q, Polstra A, Pouwels PJW, Bugiani M, van der Knaap MS, Lunsing RJ, Liebau E, Wolf NI. Homozygous UBA5 Variant Leads to Hypomyelination with Thalamic Involvement and Axonal Neuropathy. Neuropediatrics 2021; 52:489-494. [PMID: 33853163 DOI: 10.1055/s-0041-1724130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The enzyme ubiquitin-like modifier activating enzyme 5 (UBA5) plays an important role in activating ubiquitin-fold modifier 1 (UFM1) and its associated cascade. UFM1 is widely expressed and known to facilitate the post-translational modification of proteins. Variants in UBA5 and UFM1 are involved in neurodevelopmental disorders with early-onset epileptic encephalopathy as a frequently seen disease manifestation. Using whole exome sequencing, we detected a homozygous UBA5 variant (c.895C > T p. [Pro299Ser]) in a patient with severe global developmental delay and epilepsy, the latter from the age of 4 years. Magnetic resonance imaging showed hypomyelination with atrophy and T2 hyperintensity of the thalamus. Histology of the sural nerve showed axonal neuropathy with decreased myelin. Functional analyses confirmed the effect of the Pro299Ser variant on UBA5 protein function, showing 58% residual protein activity. Our findings indicate that the epilepsy currently associated with UBA5 variants may present later in life than previously thought, and that radiological signs include hypomyelination and thalamic involvement. The data also reinforce recently reported associations between UBA5 variants and peripheral neuropathy.
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Affiliation(s)
- Murtadha L Al-Saady
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Charlotte S Kaiser
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Felipe Wakasuqui
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | | | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center Amsterdam, The Netherlands
| | - Abeltje Polstra
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center Amsterdam, The Netherlands
| | - Petra J W Pouwels
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - Marianna Bugiani
- Department of Pathology, Amsterdam Leukodystrophy Center, VU University Medical Center and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Marjo S van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Roelineke J Lunsing
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eva Liebau
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
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18
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Lee L, Perez Oliva AB, Martinez-Balsalobre E, Churikov D, Peter J, Rahmouni D, Audoly G, Azzoni V, Audebert S, Camoin L, Mulero V, Cayuela ML, Kulathu Y, Geli V, Lachaud C. UFMylation of MRE11 is essential for telomere length maintenance and hematopoietic stem cell survival. SCIENCE ADVANCES 2021; 7:eabc7371. [PMID: 34559557 PMCID: PMC8462904 DOI: 10.1126/sciadv.abc7371] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is involved in neural and erythroid development, yet its biological roles in these processes are unknown. Here, we generated zebrafish models deficient in Ufm1 and Ufl1 that exhibited telomere shortening associated with developmental delay, impaired hematopoiesis and premature aging. We further report that HeLa cells lacking UFL1 have instability of telomeres replicated by leading-strand synthesis. We uncover that MRE11 UFMylation is necessary for the recruitment of the phosphatase PP1-α leading to dephosphorylation of NBS1. In the absence of UFMylation, NBS1 remains phosphorylated, thereby reducing MRN recruitment to telomeres. The absence of MRN at telomeres favors the formation of the TRF2-Apollo/SNM1 complex consistent with the loss of leading telomeres. These results suggest that MRE11-UFMylation may serve as module to recruit PP1-α. Last, zebrafish expressing Mre11 that cannot be UFMylated phenocopy Ufm1-deficient zebrafish, demonstrating that UFMylation of MRE11 is a previously undescribed evolutionarily conserved mechanisms regulating telomere length.
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Affiliation(s)
- Lara Lee
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Ana Belen Perez Oliva
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Elena Martinez-Balsalobre
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Dmitri Churikov
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Joshua Peter
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Dalicya Rahmouni
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Gilles Audoly
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Violette Azzoni
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Stephane Audebert
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Victoriano Mulero
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Maria L. Cayuela
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vincent Geli
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Christophe Lachaud
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
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19
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Wesch N, Löhr F, Rogova N, Dötsch V, Rogov VV. A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1. Int J Mol Sci 2021; 22:ijms22147390. [PMID: 34299007 PMCID: PMC8304084 DOI: 10.3390/ijms22147390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Natalia Rogova
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Correspondence: (V.D.); (V.V.R.)
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Correspondence: (V.D.); (V.V.R.)
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20
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Yang J, Zhou Y, Xie S, Wang J, Li Z, Chen L, Mao M, Chen C, Huang A, Chen Y, Zhang X, Khan NUH, Wang L, Zhou J. Metformin induces Ferroptosis by inhibiting UFMylation of SLC7A11 in breast cancer. J Exp Clin Cancer Res 2021; 40:206. [PMID: 34162423 PMCID: PMC8223374 DOI: 10.1186/s13046-021-02012-7] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ferroptosis is a newly defined form of regulated cell death characterized by the iron-dependent accumulation of lipid peroxidation and is involved in various pathophysiological conditions, including cancer. Targeting ferroptosis is considered to be a novel anti-cancer strategy. The identification of FDA-approved drugs as ferroptosis inducers is proposed to be a new promising approach for cancer treatment. Despite a growing body of evidence indicating the potential efficacy of the anti-diabetic metformin as an anti-cancer agent, the exact mechanism underlying this efficacy has not yet been fully elucidated. METHODS The UFMylation of SLC7A11 is detected by immunoprecipitation and the expression of UFM1 and SLC7A11 in tumor tissues was detected by immunohistochemical staining. The level of ferroptosis is determined by the level of free iron, total/lipid Ros and GSH in the cells and the morphological changes of mitochondria are observed by transmission electron microscope. The mechanism in vivo was verified by in situ implantation tumor model in nude mice. RESULTS Metformin induces ferroptosis in an AMPK-independent manner to suppress tumor growth. Mechanistically, we demonstrate that metformin increases the intracellular Fe2+ and lipid ROS levels. Specifically, metformin reduces the protein stability of SLC7A11, which is a critical ferroptosis regulator, by inhibiting its UFMylation process. Furthermore, metformin combined with sulfasalazine, the system xc- inhibitor, can work in a synergistic manner to induce ferroptosis and inhibit the proliferation of breast cancer cells. CONCLUSIONS This study is the first to demonstrate that the ability of metformin to induce ferroptosis may be a novel mechanism underlying its anti-cancer effect. In addition, we identified SLC7A11 as a new UFMylation substrate and found that targeting the UFM1/SLC7A11 pathway could be a promising cancer treatment strategy.
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Affiliation(s)
- Jingjing Yang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Yulu Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Shuduo Xie
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Ji Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Zhaoqing Li
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Lini Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Misha Mao
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Cong Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Aihua Huang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Yongxia Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | - Xun Zhang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China
| | | | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China.
| | - Jichun Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310000, Zhejiang, China.
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21
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Tsaban T, Stupp D, Sherill-Rofe D, Bloch I, Sharon E, Schueler-Furman O, Wiener R, Tabach Y. CladeOScope: functional interactions through the prism of clade-wise co-evolution. NAR Genom Bioinform 2021; 3:lqab024. [PMID: 33928243 PMCID: PMC8057497 DOI: 10.1093/nargab/lqab024] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
Mapping co-evolved genes via phylogenetic profiling (PP) is a powerful approach to uncover functional interactions between genes and to associate them with pathways. Despite many successful endeavors, the understanding of co-evolutionary signals in eukaryotes remains partial. Our hypothesis is that 'Clades', branches of the tree of life (e.g. primates and mammals), encompass signals that cannot be detected by PP using all eukaryotes. As such, integrating information from different clades should reveal local co-evolution signals and improve function prediction. Accordingly, we analyzed 1028 genomes in 66 clades and demonstrated that the co-evolutionary signal was scattered across clades. We showed that functionally related genes are frequently co-evolved in only parts of the eukaryotic tree and that clades are complementary in detecting functional interactions within pathways. We examined the non-homologous end joining pathway and the UFM1 ubiquitin-like protein pathway and showed that both demonstrated distinguished co-evolution patterns in specific clades. Our research offers a different way to look at co-evolution across eukaryotes and points to the importance of modular co-evolution analysis. We developed the 'CladeOScope' PP method to integrate information from 16 clades across over 1000 eukaryotic genomes and is accessible via an easy to use web server at http://cladeoscope.cs.huji.ac.il.
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Affiliation(s)
- Tomer Tsaban
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Doron Stupp
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Elad Sharon
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada and Hadassah Medical School,The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada and Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
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22
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Cao Y, Li R, Shen M, Li C, Zou Y, Jiang Q, Liu S, Lu C, Li H, Liu H, Cai Y. DDRGK1, a crucial player of ufmylation system, is indispensable for autophagic degradation by regulating lysosomal function. Cell Death Dis 2021; 12:416. [PMID: 33879777 PMCID: PMC8058061 DOI: 10.1038/s41419-021-03694-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/21/2023]
Abstract
DDRGK domain-containing protein 1 (DDRGK1) is an important component of the newly discovered ufmylation system and its absence has been reported to induce extensive endoplasmic reticulum (ER) stress. Recently, emerging evidence indicates that the ufmylation system is correlated with autophagy, although the exact mechanism remains largely unknown. To explore the regulation mechanism of DDRGK1 on autophagy, in this study, we established an immortalized mouse embryonic fibroblast (MEF) cell lines harvested from the DDRGK1F/F:ROSA26-CreERT2 mice, in which DDRGK1 depletion can be induced by 4-hydroxytamoxifen (4-OHT) treatment. Here, we show that DDRGK1 deficiency in MEFs has a dual effect on autophagy, which leads to a significant accumulation of autophagosomes. On one hand, it promotes autophagy induction by impairing mTOR signaling; on the other hand, it blocks autophagy degradation by inhibiting autophagosome-lysosome fusion. This dual effect of DDRGK1 depletion on autophagy ultimately aggravates apoptosis in MEFs. Further studies reveal that DDRGK1 loss is correlated with suppressed lysosomal function, including impaired Cathepsin D (CTSD) expression, aberrant lysosomal pH, and v-ATPase accumulation, which might be a potential trigger for impairment in autophagy process. Hence, this study confirms a crucial role of DDRGK1 as an autophagy regulator by controlling lysosomal function. It may provide a theoretical basis for the treatment strategies of various physiological diseases caused by DDRGK1 deficiency.
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Affiliation(s)
- Yan Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Rongyang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ming Shen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Chengyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yan Zou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qiang Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shuo Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Chunwan Lu
- School of life sciences, Tianjin University, 300072, Tianjin, China
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Yafei Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China.
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23
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Witting KF, Mulder MP. Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma. Biomolecules 2021; 11:biom11020255. [PMID: 33578803 PMCID: PMC7916544 DOI: 10.3390/biom11020255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.
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24
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Gingerich DJ, Hellmann H, Christians MJ, Stone SL. Editorial: Structure, Function, and Evolution of E3 Ligases and Targets. FRONTIERS IN PLANT SCIENCE 2021; 12:767281. [PMID: 34707634 PMCID: PMC8542714 DOI: 10.3389/fpls.2021.767281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 05/09/2023]
Affiliation(s)
- Derek J. Gingerich
- Department of Biology, University of Wisconsin-Eau Claire, Eau Claire, WI, United States
- *Correspondence: Derek J. Gingerich
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Matthew J. Christians
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, United States
| | - Sophia L. Stone
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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25
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Ubiquitin fold modifier 1 activates NF-κB pathway by down-regulating LZAP expression in the macrophage of diabetic mouse model. Biosci Rep 2020; 40:221481. [PMID: 31829413 PMCID: PMC6944655 DOI: 10.1042/bsr20191672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/25/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022] Open
Abstract
Inflammatory response is closely related with the development of many serious health problems worldwide including diabetes mellitus (DM). Ubiquitin-fold modifer 1 (Ufm1) is a newly discovered ubiquitin-like protein, while its function remains poorly investigated, especially in inflammatory response and DM. In the present study, we analyzed the role of Ufm1 on inflammatory response in DM, and found that the proinflammatory cytokine levels (tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and IL-1β) and Ufm1 expression were highly increased both in the peritoneal macrophages of db/db mice and Raw264.7 cells induced by lipopolysaccharide (LPS). Western blot and luciferase reporter assay showed that NF-κB pathway was obviously activated in macrophages and the expression of LZAP, an inhibitor of NF-κB pathway, was down-regulated. With the LZAP knockdown plasmid and activation plasmid, we demonstrated that NF-κB/p65 activation was inhibited by LZAP in macrophages. The interaction of Ufm1 and LZAP was further proved with co-immunoprecipitation assay in HEK293 and Raw264.7 cells. The LZAP expression was also related with the presence of Ufm1 demonstrated by Ufm1 knockdown plasmid and activation plasmid. Besides that, we finally proved that the expression and activation of Ufm1 induced by LPS were regulated by JNK/ATF2 and JNK/c-Jun pathway with the use of SP600125. In conclusion, the present study demonstrated that Ufm 1 could activate NF-κB pathway by down-regulating LZAP in macrophage of diabetes, and its expression and activation were regulated by JNK/ATF2 and c-Jun pathway.
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26
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Abstract
Post-translational modifications of cellular substrates with ubiquitin and ubiquitin-like proteins (UBLs), including ubiquitin, SUMOs, and neural precursor cell-expressed developmentally downregulated protein 8, play a central role in regulating many aspects of cell biology. The UBL conjugation cascade is initiated by a family of ATP-dependent enzymes termed E1 activating enzymes and executed by the downstream E2-conjugating enzymes and E3 ligases. Despite their druggability and their key position at the apex of the cascade, pharmacologic modulation of E1s with potent and selective drugs has remained elusive until 2009. Among the eight E1 enzymes identified so far, those initiating ubiquitylation (UBA1), SUMOylation (SAE), and neddylation (NAE) are the most characterized and are implicated in various aspects of cancer biology. To date, over 40 inhibitors have been reported to target UBA1, SAE, and NAE, including the NAE inhibitor pevonedistat, evaluated in more than 30 clinical trials. In this Review, we discuss E1 enzymes, the rationale for their therapeutic targeting in cancer, and their different inhibitors, with emphasis on the pharmacologic properties of adenosine sulfamates and their unique mechanism of action, termed substrate-assisted inhibition. Moreover, we highlight other less-characterized E1s-UBA6, UBA7, UBA4, UBA5, and autophagy-related protein 7-and the opportunities for targeting these enzymes in cancer. SIGNIFICANCE STATEMENT: The clinical successes of proteasome inhibitors in cancer therapy and the emerging resistance to these agents have prompted the exploration of other signaling nodes in the ubiquitin-proteasome system including E1 enzymes. Therefore, it is crucial to understand the biology of different E1 enzymes, their roles in cancer, and how to translate this knowledge into novel therapeutic strategies with potential implications in cancer treatment.
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Affiliation(s)
- Samir H Barghout
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
| | - Aaron D Schimmer
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
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Yang S, Yang R, Wang H, Huang Y, Jia Y. CDK5RAP3 Deficiency Restrains Liver Regeneration after Partial Hepatectomy Triggering Endoplasmic Reticulum Stress. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:2403-2416. [PMID: 32926856 DOI: 10.1016/j.ajpath.2020.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022]
Abstract
CDK5 regulatory subunit-associated protein 3 (CDK5RAP3) plays a crucial role in mammalian liver development and hepatic function by controlling hepatocyte proliferation and differentiation, glucose and lipid metabolism, UFMylation, and endoplasmic reticulum homeostasis. However, the role of CDK5RAP3 in liver regeneration remains unknown. A liver-specific Cdk5rap3 knockout (CKO) mouse model was used to study the function of CDK5RAP3 during liver regeneration induced by standard two-thirds partial hepatectomy (PHx). Twenty-four hours after PHx, the liver-to-body weight ratio was markedly higher in CKO mice than in wild-type mice. However, this ratio did not increase significantly and gradually over time after PHx in CKO mice. Hepatocyte proliferation was significantly delayed in CKO mice compared with wild-type mice. Meanwhile, CDK5RAP3 deficiency increased lipid accumulation, impaired glycogen synthesis, and lowered blood glucose levels after PHx. Critically, the absence of CDK5RAP3 seemed to promote an inflammatory response and induce apoptosis at a late stage of liver regeneration. In addition, CDK5RAP3 deficiency disrupted UFMylation homeostasis and aggravated endoplasmic reticulum stress in hepatocytes after PHx. Taken together, these data suggest that CDK5RAP3 enhances liver regeneration, at least partially via controlling cell cycle and glucose and lipid metabolism.
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Affiliation(s)
- Shuchun Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huanmin Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuyan Jia
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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28
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Liu J, Guan D, Dong M, Yang J, Wei H, Liang Q, Song L, Xu L, Bai J, Liu C, Mao J, Zhang Q, Zhou J, Wu X, Wang M, Cong YS. UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nat Cell Biol 2020; 22:1056-1063. [PMID: 32807901 DOI: 10.1038/s41556-020-0559-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Abstract
p53 is the most intensively studied tumour suppressor1. The regulation of p53 homeostasis is essential for its tumour-suppressive function2,3. Although p53 is regulated by an array of post-translational modifications, both during normal homeostasis and in stress-induced responses2-4, how p53 maintains its homeostasis remains unclear. UFMylation is a recently identified ubiquitin-like modification with essential biological functions5-7. Deficiency in this modification leads to embryonic lethality in mice and disease in humans8-12. Here, we report that p53 can be covalently modified by UFM1 and that this modification stabilizes p53 by antagonizing its ubiquitination and proteasome degradation. Mechanistically, UFL1, the UFM1 ligase6, competes with MDM2 to bind to p53 for its stabilization. Depletion of UFL1 or DDRGK1, the critical regulator of UFMylation6,13, decreases p53 stability and in turn promotes cell growth and tumour formation in vivo. Clinically, UFL1 and DDRGK1 expression are downregulated and positively correlated with levels of p53 in a high percentage of renal cell carcinomas. Our results identify UFMylation as a crucial post-translational modification for maintenance of p53 stability and tumour-suppressive function, and point to UFMylation as a promising therapeutic target in cancer.
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Affiliation(s)
- Jiang Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Di Guan
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Maogong Dong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Yang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Haibin Wei
- Institute of Cancer and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lizhi Song
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lu Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Junjie Bai
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Cui Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Qian Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Xiaoying Wu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China.
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29
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Zhang G, Tang S, Wang H, Pan H, Zhang W, Huang Y, Kong J, Wang Y, Gu J, Wang Y. UFSP2-related spondyloepimetaphyseal dysplasia: A confirmatory report. Eur J Med Genet 2020; 63:104021. [PMID: 32755715 DOI: 10.1016/j.ejmg.2020.104021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 06/12/2020] [Accepted: 07/20/2020] [Indexed: 12/27/2022]
Abstract
Spondyloepimetaphyseal dysplasias (SEMDs), which comprise a heterogeneous group of autosomal-dominant, autosomal-recessive and X-linked recessive disorders, are characterized by anomalies of the spine, the epiphyses and metaphyses of the long bones, resulting in short stature and osteoarthritic changes of the joints. UFSP2 gene encodes a highly conserved cysteine protease which cleaves two C-terminal residues from ubiquitin-fold modifier 1, an ubiquitin-like post-translational modifier protein. In 2018, Di Rocco, M reported for the first time that a novel heterozygous variant exon 11: c.1277A > C of the UFSP2 gene was the cause to spondyloepimetaphyseal dysplasia mainly manifested as: short stature, anterior vertebral dysplasia, hip dysplasia, flat vertebra, spinal metaphyseal dysplasia, irregular acetabular apex, distal femoral metaphyseal dysplasia, proximal tibial metaphyseal dysplasia, osteoarthritis and so on. In this report, we describe a boy with spondyloepimetaphyseal dysplasia due to a novel mutation exon 11: c.1283A > G (leading to p. H428R) of the UFSP2 gene. This is the second report to describe children with SEMDs associated with an UFSP2 variant. However, it is the first to describe a UFSP2 gene mutation exon 11: c.1283A > G (leading to p. H428R). Our findings of a novel heterozygous mutation of UFSP2 gene add to the list of 2 reported heterozygous mutations of UFSP2 which led to hereditary osteopathy.
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Affiliation(s)
- Guiping Zhang
- Department of Paediatrics, Affiliated Hospital of Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Shiwei Tang
- Department of Pharmacy, The People's Hospital of Dujiangyan, Sichuan, 611830, China.
| | - Hongli Wang
- Department of Pediatrics, The First People's Hospital of Bijie, Guizhou, 551700, China.
| | - Huan Pan
- Outpatient Department of Pediatrics, Affiliated Hospital of Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Wei Zhang
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Yi Huang
- Department of Pharmacy, Affiliated Hospital of Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Jing Kong
- Department of Pharmacy, Affiliated Hospital of Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Yongtao Wang
- Department of Imaging, Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Juan Gu
- Department of Pharmacy, Affiliated Hospital of Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
| | - Yuhe Wang
- Department of Pharmacy, Affiliated Hospital of Affiliated Hospital of Zunyi Medical University, Guizhou, 563003, China.
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30
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Solution structure of TbUfm1 from Trypanosoma brucei and its binding to TbUba5. J Struct Biol 2020; 212:107580. [PMID: 32693018 DOI: 10.1016/j.jsb.2020.107580] [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] [Received: 01/11/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/21/2022]
Abstract
Ubiquitin-like proteins are conserved in eukaryotes and involved in numerous cellular processes. Ufm1 is proved to play important roles in endoplasmic reticulum homeostasis, vesicle transportation and embryonic development. Enzyme cascade of Ufm1 is similar to that of ubiquitin. Mature Ufm1 is activated and conjugated to substrates by assistance of Ufm1 activating enzyme Uba5 (E1), Ufm1 conjugating enzyme Ufc1 (E2), and Ufm1 ligating enzyme Ufl1 (E3). Here, we determined the solution structure of TbUfm1 from Trypanosoma brucei (T. brucei) by NMR spectroscopy and explored the interactions between TbUfm1 and TbUba5/TbUfc1/TbUfl1. TbUfm1 adopts a typical β-grasp fold, which partially wraps a central α-helix and the other two helixes. NMR chemical shift perturbation indicated that TbUfm1 interacts with TbUba5 via a hydrophobic pocket formed by α1α2β1β2. Although the structure and Uba5-interaction mode of TbUfm1 are conserved in Ufm1 proteins, there are also some differences, which might reflect the potential diversity of Ufm1 in evolution and biological functions.
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31
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UFM1-Specific Ligase 1 Ligating Enzyme 1 Mediates Milk Protein and Fat Synthesis-Related Gene Expression via the JNK Signaling Pathway in Mouse Mammary Epithelial Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:4045674. [PMID: 32655766 PMCID: PMC7321527 DOI: 10.1155/2020/4045674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/04/2020] [Accepted: 04/30/2020] [Indexed: 01/25/2023]
Abstract
Ubiquitin-like modifier 1 ligating enzyme 1 (UFL1) has been characterized as a ubiquitin-like (Ubl) protein that affects a range of cellular processes across various pathways. In this study, mouse mammary epithelial cells (HC11 cell line) and UFL1 knockout (KO) mice were used to establish UFL1 knockdown models to explore the influence of UFL1 on milk protein and fat synthesis in the mouse mammary gland and the underlying mechanisms. This is the first study to show UFL1 localization in mouse mammary epithelial cells. UFL1 depletion by transfected UFL1 siRNA (siUFL1) caused aggravated apoptosis. In addition, UFL1 depletion suppressed milk protein synthesis-related protein level in vivo and in vitro. Conversely, ACACA and FASN expressions increased in UFL1-deficient mice. Moreover, UFL1 depletion increased triglyceride synthesis levels and inhibited the p-JNK expression. Importantly, the expression of proteins related to milk protein synthesis was decreased in JNK- and UFL1-deficient cells, whereas proteins related to milk fat synthesis showed the opposite trend, indicating that UFL1 affects milk protein and fat synthesis via the suppression of JNK activation. Overall, our findings indicate that UFL1 plays a key role in mammary milk and fat synthesis via JNK activation.
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32
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Ubiquitin-like proteins in the DNA damage response: the next generation. Essays Biochem 2020; 64:737-752. [DOI: 10.1042/ebc20190095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 12/29/2022]
Abstract
AbstractDNA suffers constant insult from a variety of endogenous and exogenous sources. To deal with the arising lesions, cells have evolved complex and coordinated pathways, collectively termed the DNA damage response (DDR). Importantly, an improper DDR can lead to genome instability, premature ageing and human diseases, including cancer as well as neurodegenerative disorders. As a crucial process for cell survival, regulation of the DDR is multi-layered and includes several post-translational modifications. Since the discovery of ubiquitin in 1975 and the ubiquitylation cascade in the early 1980s, a number of ubiquitin-like proteins (UBLs) have been identified as post-translational modifiers. However, while the importance of ubiquitin and the UBLs SUMO and NEDD8 in DNA damage repair and signalling is well established, the roles of the remaining UBLs in the DDR are only starting to be uncovered. Herein, we revise the current status of the UBLs ISG15, UBL5, FAT10 and UFM1 as emerging co-regulators of DDR processes. In fact, it is becoming clear that these post-translational modifiers play important pleiotropic roles in DNA damage and/or associated stress-related cellular responses. Expanding our understanding of the molecular mechanisms underlying these emerging UBL functions will be fundamental for enhancing our knowledge of the DDR and potentially provide new therapeutic strategies for various human diseases including cancer.
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33
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Cabrera-Serrano M, Coote DJ, Azmanov D, Goullee H, Andersen E, McLean C, Davis M, Ishimura R, Stark Z, Vallat JM, Komatsu M, Kornberg A, Ryan M, Laing NG, Ravenscroft G. A homozygous UBA5 pathogenic variant causes a fatal congenital neuropathy. J Med Genet 2020; 57:835-842. [PMID: 32179706 DOI: 10.1136/jmedgenet-2019-106496] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND UBA5 is the activating enzyme of UFM1 in the ufmylation post-translational modification system. Different neurological phenotypes have been associated with UBA5 pathogenic variants including epilepsy, intellectual disability, movement disorders and ataxia. METHODS AND RESULTS We describe a large multigenerational consanguineous family presenting with a severe congenital neuropathy causing early death in infancy. Whole exome sequencing and linkage analysis identified a novel homozygous UBA5 NM_024818.3 c.31C>T (p.Arg11Trp) mutation. Protein expression assays in mouse tissue showed similar levels of UBA5 in peripheral nerves to the central nervous system. CRISPR-Cas9 edited HEK (human embrionic kidney) cells homozygous for the UBA5 p.Arg11Trp mutation showed reduced levels of UBA5 protein compared with the wild-type. The mutant p.Arg11Trp UBA5 protein shows reduced ability to activate UFM1. CONCLUSION This report expands the phenotypical spectrum of UBA5 mutations to include fatal peripheral neuropathy.
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Affiliation(s)
- Macarena Cabrera-Serrano
- Department of Neurology, Neuromuscular Unit and Instituto de Biomedicina de Sevilla/CSIC, Hospital Universitario Virgen del Rocío, Sevilla, Spain.,Centre of Medical Research, The University of Western Australia and the Harry Perkins Institute for Medical Research, Perth, Western Australia, Australia.,Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - David Joseph Coote
- Centre of Medical Research, The University of Western Australia and the Harry Perkins Institute for Medical Research, Perth, Western Australia, Australia
| | - Dimitar Azmanov
- Centre of Medical Research, The University of Western Australia and the Harry Perkins Institute for Medical Research, Perth, Western Australia, Australia.,Department of Diagnostic Genomics, PathWest, QEII Medical Centre, Perth, Western Australia, Australia
| | - Hayley Goullee
- Centre of Medical Research, The University of Western Australia and the Harry Perkins Institute for Medical Research, Perth, Western Australia, Australia
| | - Erik Andersen
- Pediatrics, University of Otago Wellington, Wellington, New Zealand.,Department of Neurology and Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Catriona McLean
- Anatomical Pathology, Alfred Health, Melbourne, Victoria, Australia
| | - Mark Davis
- Department of Diagnostic Genomics, PathWest, QEII Medical Centre, Perth, Western Australia, Australia
| | - Ryosuke Ishimura
- Department of Physiology, Juntendo University School of Medicine Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Jean-Michel Vallat
- Reference center for peripheral neuropathies, University Hospital, Limoges, France
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University School of Medicine Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Andrew Kornberg
- Department of Neurology and Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Monique Ryan
- Department of Neurology and Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Nigel G Laing
- Centre of Medical Research, The University of Western Australia and the Harry Perkins Institute for Medical Research, Perth, Western Australia, Australia
| | - Gina Ravenscroft
- Centre of Medical Research, The University of Western Australia and the Harry Perkins Institute for Medical Research, Perth, Western Australia, Australia
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34
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Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Cell 2020; 180:1160-1177.e20. [PMID: 32160526 DOI: 10.1016/j.cell.2020.02.017] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
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Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thao Luong
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthias Muhar
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Truc Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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35
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Huber J, Obata M, Gruber J, Akutsu M, Löhr F, Rogova N, Güntert P, Dikic I, Kirkin V, Komatsu M, Dötsch V, Rogov VV. An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5. Autophagy 2020; 16:256-270. [PMID: 30990354 PMCID: PMC6984602 DOI: 10.1080/15548627.2019.1606637] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
Short linear motifs, known as LC3-interacting regions (LIRs), interact with mactoautophagy/autophagy modifiers (Atg8/LC3/GABARAP proteins) via a conserved universal mechanism. Typically, this includes the occupancy of 2 hydrophobic pockets on the surface of Atg8-family proteins by 2 specific aromatic and hydrophobic residues within the LIR motifs. Here, we describe an alternative mechanism of Atg8-family protein interaction with the non-canonical UBA5 LIR, an E1-like enzyme of the ufmylation pathway that preferentially interacts with GABARAP but not LC3 proteins. By solving the structures of both GABARAP and GABARAPL2 in complex with the UBA5 LIR, we show that in addition to the binding to the 2 canonical hydrophobic pockets (HP1 and HP2), a conserved tryptophan residue N-terminal of the LIR core sequence binds into a novel hydrophobic pocket on the surface of GABARAP proteins, which we term HP0. This mode of action is unique for UBA5 and accompanied by large rearrangements of key residues including the side chains of the gate-keeping K46 and the adjacent K/R47 in GABARAP proteins. Swapping mutations in LC3B and GABARAPL2 revealed that K/R47 is the key residue in the specific binding of GABARAP proteins to UBA5, with synergetic contributions of the composition and dynamics of the loop L3. Finally, we elucidate the physiological relevance of the interaction and show that GABARAP proteins regulate the localization and function of UBA5 on the endoplasmic reticulum membrane in a lipidation-independent manner.Abbreviations: ATG: AuTophaGy-related; EGFP: enhanced green fluorescent protein; GABARAP: GABA-type A receptor-associated protein; ITC: isothermal titration calorimetry; KO: knockout; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NMR: nuclear magnetic resonance; RMSD: root-mean-square deviation of atomic positions; TKO: triple knockout; UBA5: ubiquitin like modifier activating enzyme 5.
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Affiliation(s)
- Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jens Gruber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Natalia Rogova
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
- Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Ivan Dikic
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
- Institute of Biochemistry II, School of Medicine, Frankfurt am Main, Germany
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
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36
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Kuang M, Li L, Li C, Wang G. Protective effects of UFL1 against endoplasmic reticulum stress-induced autophagy in bovine mammary epithelial cells. Cell Stress Chaperones 2019; 24:1115-1125. [PMID: 31721015 PMCID: PMC6883021 DOI: 10.1007/s12192-019-01033-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1)-specific ligase 1 (UFL1) is an important component of the UFM1 conjugation system, which is required for various cellular processes including protein translation, apoptosis, autophagy, and signal transduction. However, both, the expression of UFL1 in mammary cells and its role in endoplasmic reticulum (ER) stress in bovine mammary epithelial cells (BMECs) remain to be fully elucidated. Here, we characterized the potential roles of UFL1 in BMECs. Amino acid sequence comparison indicated that bovine UFL1 shares a high level of sequence identity with the UFL1 of other ruminant species. Notably, UFL1 expression in BMECs was increased by endoplasmic reticulum (ER) stress induced by treatment with tunicamycin (TM). ER stress-related gene expression was further increased in UFL1 knockdown cells upon TM treatment. Moreover, UFL1 overexpression inhibited TM-stimulated ER stress and alleviated ER stress-induced autophagy. Together, our results indicated that UFL1 is a novel ER stress-responsive protein in BMECs. Thus, our study provides a basis for further research into ER stress-related processes in bovine mammary tissues and potential targets for alleviating ER stress in these cells.
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Affiliation(s)
- Meiqian Kuang
- College of Animal Science and Technology, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 Jiangsu China
| | - Lian Li
- College of Animal Science and Technology, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 Jiangsu China
| | - Chengmin Li
- College of Animal Science and Technology, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 Jiangsu China
| | - Genlin Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 Jiangsu China
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37
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Geng S, Wang J, Zhang X, Zhang JJ, Wu F, Pang Y, Zhong Y, Wang J, Wang W, Lyu X, Huang Y, Jing H. Single-cell RNA sequencing reveals chemokine self-feeding of myeloma cells promotes extramedullary metastasis. FEBS Lett 2019; 594:452-465. [PMID: 31561267 DOI: 10.1002/1873-3468.13623] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/20/2022]
Abstract
In this study, we aimed to determine the mechanisms underlying the initial extramedullary translocation of myeloma cells from bone marrow into peripheral blood. We found that clonal circulating plasma cells (cPCs) are more frequently detected by flow cytometry in extramedullary plasmacytoma (EMP) patients and worsen their prognosis. It is technically much easier to collect single cPCs using FACS than it is to perform EMP biopsy. Therefore, combining EMP imaging with cPC detection may be a promising strategy for prognostic stratification. Here, using single-cell transcriptome analysis, we found that the chemokine CXCL12, a key molecule involved in CXCR4-dependent cell retention in the bone marrow, is abnormally upregulated in cPCs and might initially enable cPCs to evade bone marrow retention and translocate into the bloodstream.
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Affiliation(s)
- Shuang Geng
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jing Wang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China
| | - Xiannian Zhang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jia-Jia Zhang
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yuhong Pang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yuping Zhong
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wenming Wang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China
| | - Xiaoqing Lyu
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yanyi Huang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hongmei Jing
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China
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Li J, Johnson JA, Su H. Ubiquitin and Ubiquitin-like proteins in cardiac disease and protection. Curr Drug Targets 2019; 19:989-1002. [PMID: 26648080 DOI: 10.2174/1389450117666151209114608] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 11/01/2015] [Indexed: 01/10/2023]
Abstract
Post-translational modification represents an important mechanism to regulate protein function in cardiac cells. Ubiquitin (Ub) and ubiquitin-like proteins (UBLs) are a family of protein modifiers that share a certain extent of sequence and structure similarity. Conjugation of Ub or UBLs to target proteins is dynamically regulated by a set of UBL-specific enzymes and modulates the physical and physiological properties of protein substrates. Ub and UBLs control a strikingly wide spectrum of cellular processes and not surprisingly are involved in the development of multiple human diseases including cardiac diseases. Further identification of novel UBL targets will expand our understanding of the functional diversity of UBL pathways in physiology and pathology. Here we review recent findings on the mechanisms, proteome and functions of a subset of UBLs and highlight their potential impacts on the development and progression of various forms of cardiac diseases.
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Affiliation(s)
- Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - John A Johnson
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States.,Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, United States
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Li J, Yue G, Ma W, Zhang A, Zou J, Cai Y, Tang X, Wang J, Liu J, Li H, Su H. Ufm1-Specific Ligase Ufl1 Regulates Endoplasmic Reticulum Homeostasis and Protects Against Heart Failure. Circ Heart Fail 2019; 11:e004917. [PMID: 30354401 DOI: 10.1161/circheartfailure.118.004917] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Defects in protein homeostasis are sufficient to provoke cardiac remodeling and dysfunction. Although posttranslational modifications by ubiquitin and ubiquitin-like proteins are emerging as an important regulatory mechanism of protein function, the role of Ufm1 (ubiquitin-fold modifier 1)-a novel ubiquitin-like protein-has not been explored in either the normal or stressed heart. METHODS AND RESULTS Western blotting revealed that Ufl1 (Ufm1-specific E3 ligase 1)-an enzyme essential for Ufm1 modification-was increased in hypertrophic mouse hearts but reduced in the failing hearts of patients with dilated cardiomyopathy. To determine the functional role of Ufl1 in the heart, we generated a cardiac-specific knockout mouse and showed that Ufl1-deficient mice developed age-dependent cardiomyopathy and heart failure, as indicated by elevated cardiac fetal gene expression, increased fibrosis, and impaired cardiac contractility. When challenged with pressure overload, Ufl1-deficient hearts exhibited remarkably greater hypertrophy, exacerbated fibrosis, and worsened cardiac contractility compared with control counterparts. Transcriptome analysis identified that genes associated with the endoplasmic reticulum (ER) function were dysregulated in Ufl1-deficient hearts. Biochemical analysis revealed that excessive ER stress preceded and deteriorated along with the development of cardiomyopathy in Ufl1-deficient hearts. Mechanistically, Ufl1 depletion impaired (PKR-like ER-resident kinase) signaling and aggravated cardiomyocyte cell death after ER stress. Administration of the chemical ER chaperone tauroursodeoxycholic acid to Ufl1-deficient mice alleviated ER stress and attenuated pressure overload-induced cardiac dysfunction. CONCLUSIONS Our results advance a novel concept that the Ufm1 system is essential for cardiac homeostasis through regulation of ER function and that upregulation of myocardial Ufl1 could be protective against heart failure.
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Affiliation(s)
- Jie Li
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University
| | - Guihua Yue
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University.,Guangxi Medical College, Nanning, China (G.Y.)
| | - Wenxia Ma
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University
| | - Aizhen Zhang
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University.,Affiliated Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning (A.Z.)
| | - Jianqiu Zou
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, China (Y.C.)
| | - Xiaoli Tang
- Department of Biochemistry, School of Medicine, Nanchang University, Jiangxi, China (X.T.)
| | - Jun Wang
- Department of Basic Research Laboratories, Center for Stem Cell Engineering, Texas Heart Institute, Houston (J.W.)
| | - Jinbao Liu
- Protein Modification and Degradation Lab, School of Basic Medical Sciences, Guangzhou Medical University, China (J.L., H.S.)
| | - Honglin Li
- Department of Biochemistry and Molecular Biology (H.L.), Medical College of Georgia, Augusta University
| | - Huabo Su
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University.,Department of Pharmacology and Toxicology (H.S.), Medical College of Georgia, Augusta University.,Protein Modification and Degradation Lab, School of Basic Medical Sciences, Guangzhou Medical University, China (J.L., H.S.)
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40
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Osorio H, Jara C, Fuenzalida K, Rey-Jurado E, Vásquez M. High-efficiency nuclear transformation of the microalgae Nannochloropsis oceanica using Tn5 Transposome for the generation of altered lipid accumulation phenotypes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:134. [PMID: 31168324 PMCID: PMC6545213 DOI: 10.1186/s13068-019-1475-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND One of the major problems in the production of lipids for biotechnological purposes using microalgae is maintaining a high productivity of these molecules without reducing cellular biomass. High production rates are usually obtained by cultivating microalgae under different stress conditions. However, many of these changes usually result in lower biomass productivity. Therefore, the optimization of the culture conditions and genetic modification techniques in these organisms is needed to generate robust new strains for profitable economic use. RESULTS In this work, we describe a new strategy for random mutation of genomic DNA in the microalgae Nannochloropsis oceanica by insertion of a Transposome complex Tn5. This complex contains an antibiotic-resistance cassette commanded by a CMV viral promoter that allows high efficiency of transformation and the generation of mutants. This strategy, complemented with a large-scale identification and selection system for mutants, such as flow cytometry with cell selection, allowed us to obtain clonal cultures of mutants with altered phenotypes in the accumulation of intracellular lipids. The characterization of some of these mutants uncovered new genes that are likely to be involved in the regulation of lipid synthesis, revealing possible cellular responses that influence the intracellular homeostasis of lipids. CONCLUSION The strategies proposed here are easy to implement in different types of microalgae and provide a promising scenario for improving biotechnological applications.
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Affiliation(s)
- Hector Osorio
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Carol Jara
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Karen Fuenzalida
- Departamento de Fisiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Emma Rey-Jurado
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Mónica Vásquez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
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Xie Z, Fang Z, Pan Z. Ufl1/RCAD, a Ufm1 E3 ligase, has an intricate connection with ER stress. Int J Biol Macromol 2019; 135:760-767. [PMID: 31129212 DOI: 10.1016/j.ijbiomac.2019.05.170] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/11/2022]
Abstract
Ufmylation is a type of post-translational modification that deals with complex and fine-tuned cellular activities. This modification proceeds mainly through a three-step enzymatic reaction with ubiquitin-fold modifier 1 (Ufm1), ubiquitin-like modifier-activating enzyme 5 (Uba5), Ufm1-conjugating enzyme 1 (Ufc1) and Ufm1-specific ligase 1 (Ufl1). Ufl1 has previously been reported to function as a Ufm1 E3 ligase in the ufmylation system, but knowledge of its physiological functions remains poor. At the subcellular level, Ufl1 is enriched in the endoplasmic reticulum (ER), implying that it may regulate events closely associated with the ER and ER functions, such as protein synthesis, folding, and secretion, compounding lipids or sterols, and maintaining calcium homeostasis. Different physiological or pathological stress circumstances can, however, disrupt ER homeostasis, giving rise to an incongruous condition that is harmful to cellular activity and ultimately causes ER stress. Understanding the relationship between Ufl1 and ER stress in physiology and pathology may reveal the pathogenesis of some diseases and provide new guidance to create a therapeutic method. Herein, we review the current literature and discuss the relationship between Ufl1 and ER stress (in hematopoietic disease, heart disease, etc.), thus providing insight into additional diseases.
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Affiliation(s)
- Zheng Xie
- Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Zhi Fang
- Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Zezheng Pan
- Faculty of Basic Medical Science, Jiangxi Medical College, Nanchang University, Nanchang 330006, China.
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42
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Jiang Y, Lin X, Kapoor A, He L, Wei F, Gu Y, Mei W, Zhao K, Yang H, Tang D. FAM84B promotes prostate tumorigenesis through a network alteration. Ther Adv Med Oncol 2019; 11:1758835919846372. [PMID: 31205500 PMCID: PMC6535720 DOI: 10.1177/1758835919846372] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 01/04/2023] Open
Abstract
Background: The aim of this study was to investigate the contributions of FAM84B in prostate tumorigenesis and progression. Methods: A FAM84B mutant with deletion of its HRASLS domain (ΔHRASLS) was constructed. DU145 prostate cancer (PC) cells stably expressing an empty vector (EV), FAM84B, or FAM84B (ΔHRASLS) were produced. These lines were examined for proliferation, invasion, and growth in soft agar in vitro. DU145 EV and FAM84B cells were investigated for tumor growth and lung metastasis in NOD/SCID mice. The transcriptome of DU145 EV xenografts (n = 2) and DU145 FAM84B tumors (n = 2) was determined using RNA sequencing, and analyzed for pathway alterations. The FAM84B-affected network was evaluated for an association with PC recurrence. Results: FAM84B but not FAM84B (ΔHRASLS) increased DU145 cell invasion and growth in soft agar. Co-immunoprecipitation and co-localization analyses revealed an interaction between FAM84B and FAM84B (ΔHRASLS), suggesting an intramolecular association among FAM84B molecules. FAM84B significantly enhanced DU145 cell-derived xenografts and lung metastasis. In comparison with DU145 EV cell-produced tumors, those generated by DU145 FAM84B cells showed a large number of differentially expressed genes (DEGs; n = 4976). A total of 51 pathways were enriched in these DEGs, which function in the Golgi-to-endoplasmic reticulum processes, cell cycle checkpoints, mitochondrial events, and protein translation. A novel 27-gene signature (SigFAM) was derived from these DEGs; SigFAM robustly stratifies PC recurrence in two large PC populations (n = 490, p = 0; n = 140, p = 4e−11), and remains an independent risk factor of PC recurrence after adjusting for age at diagnosis, Gleason scores, surgical margin, and tumor stages. Conclusions: FAM84B promotes prostate tumorigenesis through a complex network that predicts PC recurrence.
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Affiliation(s)
- Yanzhi Jiang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan, China Department of Medicine, McMaster University, Hamilton, ON, Canada Father Sean O'Sullivan Research Institute, St. Joseph's Hospital, Hamilton, ON. Canada Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON, Canada Hamilton Urologic Urological Cancer Center for Research and Innovation (UCCRI), St. Joseph's Hospital, Hamilton, ON, Canada
| | - Xiaozeng Lin
- Department of Medicine, McMaster University, Hamilton, ON, Canada Father Sean O'Sullivan Research Institute, St. Joseph's Hospital/Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON, Canada Urological Cancer Center for Research and Innovation (UCCRI), St. Joseph's Hospital, Hamilton, ON, Canada
| | - Anil Kapoor
- Father Sean O'Sullivan Research Institute, St. Joseph's Hospital, Hamilton, ON, Canada Urological Cancer Center for Research and Innovation (UCCRI), St. Joseph's Hospital, Hamilton, ON, Canada Department of Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Lizhi He
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Fengxiang Wei
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital, Longgang District, Shenzhen, Guangdong, China
| | - Yan Gu
- Department of Medicine, McMaster University, Hamilton, ON, Canada Father Sean O'Sullivan Research Institute, St. Joseph's Hospital/Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON, Canada Urological Cancer Center for Research and Innovation (UCCRI), St. Joseph's Hospital, Hamilton, ON, Canada
| | - Wenjuan Mei
- Department of Medicine, McMaster University, Hamilton, ON, Canada Father Sean O'Sullivan Research Institute, St. Joseph's Hospital Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON, Canada Urological Cancer Center for Research and Innovation (UCCRI), St. Joseph's Hospital, Hamilton, ON, Canada Department of Nephrology, The First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Kuncheng Zhao
- Department of Medicine, McMaster University, Hamilton, ON, Canada Father Sean O'Sullivan Research Institute, St. Joseph's Hospital/Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON, Canada Urological Cancer Center for Research and Innovation (UCCRI), St. Joseph's Hospital, Hamilton, ON, Canada
| | - Huixiang Yang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Damu Tang
- Department of Medicine, McMaster University, T3310, St. Joseph's Hospital, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
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UFL1 Alleviates Lipopolysaccharide-Induced Cell Damage and Inflammation via Regulation of the TLR4/NF- κB Pathway in Bovine Mammary Epithelial Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:6505373. [PMID: 30881595 PMCID: PMC6387704 DOI: 10.1155/2019/6505373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/09/2018] [Accepted: 11/27/2018] [Indexed: 12/25/2022]
Abstract
In recent studies, UFL1 (ubiquitin-like modifier 1 ligating enzyme 1) has been identified as a significant regulator of NF-κB signaling and cellular stress response, yet its physiological function in LPS-stimulated bovine mammary epithelial cells (BMECs) remains unknown. In this study, we investigated the modulating effect of UFL1 on the regulation of LPS-induced inflammation and cell damage, with a focus on apoptosis, ER stress, autophagy, oxidative stress, and the TLR4/NF-κB signaling pathway. The results showed that UFL1 depletion aggravated the LPS-induced inflammatory response and cell damage by positively regulating the TLR4/NF-κB pathway (increased the expression of TLR4, NF-κB P65 in nuclear, and phospho-IκBα), exacerbating LPS-induced ER stress (increased the expression of CHOP, Hsp70, and GRP78), apoptosis (increased the expression of Bax/Bcl-2 and activity of caspase-3), autophagy (increased LC3-II and decreased P62 expression), and oxidative stress (decreased SOD and CAT levels and increased MDA levels). Overexpression of UFL1 suppressed the activation of the TLR4/NF-κB pathway and relieved the LPS-induced ER stress, apoptosis, autophagy, and oxidative stress, thereby alleviating the inflammatory response and cell damage. Collectively, UFL1 may play an important role during the inflammatory response and thereby acts as a potential therapeutic target for bovine mastitis.
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Yang R, Wang H, Kang B, Chen B, Shi Y, Yang S, Sun L, Liu Y, Xiao W, Zhang T, Yang J, Zhang Y, Zhu M, Xu P, Chang Y, Jia Y, Huang Y. CDK5RAP3, a UFL1 substrate adaptor, is crucial for liver development. Development 2019; 146:dev.169235. [PMID: 30635284 DOI: 10.1242/dev.169235] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 01/04/2019] [Indexed: 12/21/2022]
Abstract
Protein modification by ubiquitin and ubiquitin-like proteins (UBLs) regulates numerous biological functions. The UFM1 system, a novel UBL conjugation system, is implicated in mouse development and hematopoiesis. However, its broad biological functions and working mechanisms remain largely elusive. CDK5RAP3, a possible ufmylation substrate, is essential for epiboly and gastrulation in zebrafish. Herein, we report a crucial role of CDK5RAP3 in liver development and hepatic functions. Cdk5rap3 knockout mice displayed prenatal lethality with severe liver hypoplasia, as characterized by delayed proliferation and compromised differentiation. Hepatocyte-specific Cdk5rap3 knockout mice suffered post-weaning lethality, owing to serious hypoglycemia and impaired lipid metabolism. Depletion of CDK5RAP3 triggered endoplasmic reticulum stress and activated unfolded protein responses in hepatocytes. We detected the in vivo interaction of CDK5RAP3 with UFL1, the defined E3 ligase in ufmylation. Notably, loss of CDK5RAP3 altered the ufmylation profile in liver cells, suggesting that CDK5RAP3 serves as a novel substrate adaptor for this UBL modification. Collectively, our study identifies CDK5RAP3 as an important regulator of ufmylation and suggests the involvement of ufmylation in mammalian development.
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Affiliation(s)
- Rui Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Huanmin Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Boxi Kang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Bin Chen
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yaoyao Shi
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100005, China
| | - Shuchun Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Lihong Sun
- Center for Experimental Animal Research, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yufang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Weidi Xiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Juntao Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Ye Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Mingzhao Zhu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100005, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yongsheng Chang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.,Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yuyan Jia
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China .,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China .,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
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Abstract
Ubiquitin fold modifier 1 (UFM1) is a small, metazoan-specific, ubiquitin-like protein modifier that is essential for embryonic development. Although loss-of-function mutations in UFM1 conjugation are linked to endoplasmic reticulum (ER) stress, neither the biological function nor the relevant cellular targets of this protein modifier are known. Here, we show that a largely uncharacterized ribosomal protein, RPL26, is the principal target of UFM1 conjugation. RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes tethered to the cytoplasmic surface of the ER and UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes. Biochemical analysis and structural modeling establish that UFMylated RPL26 and the UFMylation machinery are in close proximity to the SEC61 translocon, suggesting that this modification plays a direct role in cotranslational protein translocation into the ER. These data suggest that UFMylation is a ribosomal modification specialized to facilitate metazoan-specific protein biogenesis at the ER.
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46
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An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. J Mol Biol 2018; 431:463-478. [PMID: 30412706 DOI: 10.1016/j.jmb.2018.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/06/2023]
Abstract
Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.
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47
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Nahorski MS, Maddirevula S, Ishimura R, Alsahli S, Brady AF, Begemann A, Mizushima T, Guzmán-Vega FJ, Obata M, Ichimura Y, Alsaif HS, Anazi S, Ibrahim N, Abdulwahab F, Hashem M, Monies D, Abouelhoda M, Meyer BF, Alfadhel M, Eyaid W, Zweier M, Steindl K, Rauch A, Arold ST, Woods CG, Komatsu M, Alkuraya FS. Biallelic UFM1 and UFC1 mutations expand the essential role of ufmylation in brain development. Brain 2018; 141:1934-1945. [PMID: 29868776 PMCID: PMC6022668 DOI: 10.1093/brain/awy135] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/03/2018] [Accepted: 03/23/2018] [Indexed: 12/31/2022] Open
Abstract
The post-translational modification of proteins through the addition of UFM1, also known as ufmylation, plays a critical developmental role as revealed by studies in animal models. The recent finding that biallelic mutations in UBA5 (the E1-like enzyme for ufmylation) cause severe early-onset encephalopathy with progressive microcephaly implicates ufmylation in human brain development. More recently, a homozygous UFM1 variant was proposed as a candidate aetiology of severe early-onset encephalopathy with progressive microcephaly. Here, we establish a locus for severe early-onset encephalopathy with progressive microcephaly based on two families, and map the phenotype to a novel homozygous UFM1 mutation. This mutation has a significantly diminished capacity to form thioester intermediates with UBA5 and with UFC1 (the E2-like enzyme for ufmylation), with resulting impaired ufmylation of cellular proteins. Remarkably, in four additional families where eight children have severe early-onset encephalopathy with progressive microcephaly, we identified two biallelic UFC1 mutations, which impair UFM1-UFC1 intermediate formation with resulting widespread reduction of cellular ufmylation, a pattern similar to that observed with UFM1 mutation. The striking resemblance between UFM1- and UFC1-related clinical phenotype and biochemical derangements strongly argues for an essential role for ufmylation in human brain development. The hypomorphic nature of UFM1 and UFC1 mutations and the conspicuous depletion of biallelic null mutations in the components of this pathway in human genome databases suggest that it is necessary for embryonic survival, which is consistent with the embryonic lethal nature of knockout models for the orthologous genes.
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Affiliation(s)
- Michael S Nahorski
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building Addenbrookes Hospital, Hills Rd, Cambridge, UK
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ryosuke Ishimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Angela F Brady
- North West Thames Genetics Service, Level 8V, St Mark’s Hospital, Northwick Park Hospital Watford Road, Harrow, UK
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Tsunehiro Mizushima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Francisco J Guzmán-Vega
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Yoshinobu Ichimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Wafa Eyaid
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building Addenbrookes Hospital, Hills Rd, Cambridge, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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48
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Low KJ, Baptista J, Babiker M, Caswell R, King C, Ellard S, Scurr I. Hemizygous UBA5 missense mutation unmasks recessive disorder in a patient with infantile-onset encephalopathy, acquired microcephaly, small cerebellum, movement disorder and severe neurodevelopmental delay. Eur J Med Genet 2018; 62:97-102. [PMID: 29902590 DOI: 10.1016/j.ejmg.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/28/2018] [Accepted: 06/10/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Karen J Low
- Department of Clinical Genetics, St Michael's Hospital, Bristol, UK.
| | - J Baptista
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK; Institute for Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - M Babiker
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, UK
| | - R Caswell
- Institute for Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - C King
- Department of Clinical Genetics, St Michael's Hospital, Bristol, UK
| | - S Ellard
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK; Institute for Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - I Scurr
- Department of Clinical Genetics, St Michael's Hospital, Bristol, UK
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49
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Mignon-Ravix C, Milh M, Kaiser CS, Daniel J, Riccardi F, Cacciagli P, Nagara M, Busa T, Liebau E, Villard L. Abnormal function of the UBA5 protein in a case of early developmental and epileptic encephalopathy with suppression-burst. Hum Mutat 2018; 39:934-938. [PMID: 29663568 DOI: 10.1002/humu.23534] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 01/19/2023]
Abstract
Early myoclonic epilepsy (EME) or Aicardi syndrome is one of the most severe epileptic syndromes affecting neonates. We performed whole exome sequencing in a sporadic case affected by EME and his parents. In the proband, we identified a homozygous missense variant in the ubiquitin-like modifier activating enzyme 5 (UBA5) gene, encoding a protein involved in post-translational modifications. Functional analysis of the UBA5 variant protein reveals that it is almost completely unable to perform its trans-thiolation activity. Although recessive variants in UBA5 have recently been associated with epileptic encephalopathy, variants in this gene have never been reported to cause EME. Our results further demonstrate the importance of post-translational modifications such as the addition of an ubiquitin-fold modifier 1 (UFM1) to target proteins (ufmylation) for normal neuronal networks activity, and reveal that the dysfunction of the ubiquitous UBA5 protein is a cause of EME.
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Affiliation(s)
- Cécile Mignon-Ravix
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France
| | - Mathieu Milh
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Service de Neurologie Pédiatrique, Hôpital d'Enfants de La Timone, Marseille, France
| | | | - Jens Daniel
- Department of Molecular Physiology, University of Muenster, Muenster, Germany
| | - Florence Riccardi
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - Pierre Cacciagli
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - Majdi Nagara
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France
| | - Tiffany Busa
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - Eva Liebau
- Department of Molecular Physiology, University of Muenster, Muenster, Germany
| | - Laurent Villard
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
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50
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Kwasna D, Abdul Rehman SA, Natarajan J, Matthews S, Madden R, De Cesare V, Weidlich S, Virdee S, Ahel I, Gibbs-Seymour I, Kulathu Y. Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability. Mol Cell 2018; 70:150-164.e6. [PMID: 29576527 PMCID: PMC5896202 DOI: 10.1016/j.molcel.2018.02.023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 01/17/2023]
Abstract
Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.
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Affiliation(s)
- Dominika Kwasna
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jayaprakash Natarajan
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Stephen Matthews
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ross Madden
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ivan Ahel
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Ian Gibbs-Seymour
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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