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Liang Z, Ning R, Wang Z, Kong X, Yan Y, Cai Y, He Z, Liu XG, Zou Y, Zhou J. The emerging roles of UFMylation in the modulation of immune responses. Clin Transl Med 2024; 14:e70019. [PMID: 39259506 DOI: 10.1002/ctm2.70019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/21/2024] [Accepted: 09/01/2024] [Indexed: 09/13/2024] Open
Abstract
Post-translational modification is a rite of passage for cellular functional proteins and ultimately regulate almost all aspects of life. Ubiquitin-fold modifier 1 (UFM1) system represents a newly identified ubiquitin-like modification system with indispensable biological functions, and the underlying biological mechanisms remain largely undiscovered. The field has recently experienced a rapid growth of research revealing that UFMylation directly or indirectly regulates multiple immune processes. Here, we summarised important advances that how UFMylation system responds to intrinsic and extrinsic stresses under certain physiological or pathological conditions and safeguards immune homeostasis, providing novel perspectives into the regulatory framework and functions of UFMylation system, and its therapeutic applications in human diseases.
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Affiliation(s)
- Zhengyan Liang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Rongxuan Ning
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Zhaoxiang Wang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Xia Kong
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yubin Yan
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yafei Cai
- Key Laboratory for Epigenetics of Dongguan City, China-America Cancer Research Institute, Guangdong Medical University, Dongguan, China
| | - Zhiwei He
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xin-Guang Liu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yongkang Zou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Junzhi Zhou
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
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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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Wang X, Lv X, Ma J, Xu G. UFMylation: An integral post-translational modification for the regulation of proteostasis and cellular functions. Pharmacol Ther 2024; 260:108680. [PMID: 38878974 DOI: 10.1016/j.pharmthera.2024.108680] [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: 04/07/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is covalently conjugated to protein substrates via a cascade of enzymatic reactions, a process known as UFMylation. UFMylation orchestrates an array of vital biological functions, including maintaining endoplasmic reticulum (ER) homeostasis, facilitating protein biogenesis, promoting cellular differentiation, regulating DNA damage response, and participating in cancer-associated signaling pathways. UFMylation has rapidly evolved into one of the forefront research areas within the last few years, yet much remains to be uncovered. In this review, first, UFMylation and its cellular functions associated with diseases are briefly introduced. Then, we summarize the proteomic approaches for identifying UFMylation substrates and explore the impact of UFMylation on gene transcription, protein translation, and maintenance of ER homeostasis. Next, we highlight the intricate regulation between UFMylation and two protein degradation pathways, the ubiquitin-proteasome system and the autophagy-lysosome pathway, and explore the potential of UFMylation system as a drug target. Finally, we discuss emerging perspectives in the UFMylation field. This review may provide valuable insights for drug discovery targeting the UFMylation system.
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Affiliation(s)
- Xiaohui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Xiaowei Lv
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Jingjing Ma
- Department of Pharmacy, The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Medical Center of Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China; Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China.
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Liu Y, Niu M, Luo Y, Pan M, Hong S. DNA damage response and inflammatory response: Two traffic lights for HPVs on the road to transformation. J Med Virol 2024; 96:e29815. [PMID: 39073137 DOI: 10.1002/jmv.29815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/17/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
Human papillomaviruses (HPVs) are non-enveloped double-stranded DNA viruses. When HPV infection persists, infected tissues can develop many HPV-related diseases such as cervical cancer and head and neck squamous cell carcinoma. To establish their persistent infection, HPVs have evolved mechanisms to manipulate the host cellular processes such as DNA damage response (DDR), which includes homologous recombination, nonhomologous end joining, and microhomology-mediated end joining. Additionally, HPVs utilize host inflammatory processes to facilitate their life cycles. Here, we bridge the concepts of DDR and inflammatory response, and discuss how HPV proteins orchestrate a sophisticated manipulation of DDR and inflammation to promote their viral replication, ultimately fostering the progression of infected cells towards oncogenic transformation to malignancy.
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Affiliation(s)
- Yanfei Liu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Mengda Niu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Ying Luo
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Min Pan
- Department of Otorhinolaryngology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Shiyuan Hong
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
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Li G, Huang Y, Han W, Wei L, Huang H, Zhu Y, Xiao Q, Wang Z, Huang W, Duan R. Eg5 UFMylation promotes spindle organization during mitosis. Cell Death Dis 2024; 15:544. [PMID: 39085203 PMCID: PMC11291904 DOI: 10.1038/s41419-024-06934-w] [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: 12/14/2023] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
UFMylation is a highly conserved ubiquitin-like post-translational modification that catalyzes the covalent linkage of UFM1 to its target proteins. This modification plays a critical role in the maintenance of endoplasmic reticulum proteostasis, DNA damage response, autophagy, and transcriptional regulation. Mutations in UFM1, as well as in its specific E1 enzyme UBA5 and E2 enzyme UFC1, have been genetically linked to microcephaly. Our previous research unveiled the important role of UFMylation in regulating mitosis. However, the underlying mechanisms have remained unclear due to the limited identification of substrates. In this study, we identified Eg5, a motor protein crucial for mitotic spindle assembly and maintenance, as a novel substrate for UFMylation and identified Lys564 as the crucial UFMylation site. UFMylation did not alter its transcriptional level, phosphorylation level, or protein stability, but affected the mono-ubiquitination of Eg5. During mitosis, Eg5 and UFM1 co-localize at the centrosome and spindle apparatus, and defective UFMylation leads to diminished spindle localization of Eg5. Notably, the UFMylation-defective Eg5 mutant (K564R) exhibited shorter spindles, metaphase arrest, spindle checkpoint activation, and a failure of cell division in HeLa cells. Overall, Eg5 UFMylation is essential for proper spindle organization, mitotic progression, and cell proliferation.
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Affiliation(s)
- Guangxu Li
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Yuanjiang Huang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Wenbo Han
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Liyi Wei
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Hongjing Huang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Yingbao Zhu
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Qiao Xiao
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Zujia Wang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Wen Huang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Ranhui Duan
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China.
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Zohourian N, Coll E, Dever M, Sheahan A, Burns-Lane P, Brown JAL. Evaluating the Cellular Roles of the Lysine Acetyltransferase Tip60 in Cancer: A Multi-Action Molecular Target for Precision Oncology. Cancers (Basel) 2024; 16:2677. [PMID: 39123405 PMCID: PMC11312108 DOI: 10.3390/cancers16152677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/04/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Precision (individualized) medicine relies on the molecular profiling of tumors' dysregulated characteristics (genomic, epigenetic, transcriptomic) to identify the reliance on key pathways (including genome stability and epigenetic gene regulation) for viability or growth, and then utilises targeted therapeutics to disrupt these survival-dependent pathways. Non-mutational epigenetic changes alter cells' transcriptional profile and are a key feature found in many tumors. In contrast to genetic mutations, epigenetic changes are reversable, and restoring a normal epigenetic profile can inhibit tumor growth and progression. Lysine acetyltransferases (KATs or HATs) protect genome stability and integrity, and Tip60 is an essential acetyltransferase due to its roles as an epigenetic and transcriptional regulator, and as master regulator of the DNA double-strand break response. Tip60 is commonly downregulated and mislocalized in many cancers, and the roles that mislocalized Tip60 plays in cancer are not well understood. Here we categorize and discuss Tip60-regulated genes, evaluate Tip60-interacting proteins based on cellular localization, and explore the therapeutic potential of Tip60-targeting compounds as epigenetic inhibitors. Understanding the multiple roles Tip60 plays in tumorigenesis will improve our understanding of tumor progression and will inform therapeutic options, including informing potential combinatorial regimes with current chemotherapeutics, leading to improvements in patient outcomes.
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Affiliation(s)
- Nazanin Zohourian
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Erin Coll
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Muiread Dever
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Anna Sheahan
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Petra Burns-Lane
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - James A. L. Brown
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
- Limerick Digital Cancer Research Centre (LDCRC), Health Research Institute (HRI), University of Limerick, V94 T9PX Limerick, Ireland
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Xu D, Zhang D, Wei W, Zhang C. UBA5 inhibition restricts lung adenocarcinoma via blocking macrophage M2 polarization and cisplatin resistance. Exp Cell Res 2024; 440:114148. [PMID: 38936760 DOI: 10.1016/j.yexcr.2024.114148] [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: 04/09/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
UBA5, a ubiquitin-like activated enzyme involved in ufmylation and sumoylation, presents a viable target for pancreatic and breast cancer treatments, yet its role in lung adenocarcinoma (LUAD) remains underexplored. This study reveals UBA5's tumor-promoting effect in LUAD, as evidenced by its upregulation in patients and positive correlation with TNM stages. Elevated UBA5 levels predict poor outcomes for these patients. Pharmacological inhibition of UBA5 using DKM 2-93 significantly curtails the growth of A549, H1299, and cisplatin-resistant A549 (A549/DDP) LUAD cells in vitro. Additionally, UBA5 knockdown via shRNA lentivirus suppresses tumor growth both in vitro and in vivo. High UBA5 expression adversely alters the tumor immune microenvironment, affecting immunostimulators, MHC molecules, chemokines, receptors, and immune cell infiltration. Notably, UBA5 expression correlates positively with M2 macrophage infiltration, the predominant immune cells in LUAD. Co-culture experiments further demonstrate that UBA5 knockdown directly inhibits M2 macrophage polarization and lactate production in LUAD. Moreover, in vivo studies show reduced M2 macrophage infiltration following UBA5 knockdown. UBA5 expression is also associated with increased tumor heterogeneity, including tumor mutational burden, microsatellite instability, neoantigen presence, and homologous recombination deficiency. Experiments indicate that UBA5 overexpression promotes cisplatin resistance in vitro, whereas UBA5 inhibition enhances cisplatin sensitivity in both in vitro and in vivo settings. Overall, these findings suggest that targeting UBA5 inhibits LUAD by impeding cancer cell proliferation, M2 macrophage polarization, and cisplatin resistance.
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Affiliation(s)
- Dacai Xu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China.
| | - Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China
| | - Wenlu Wei
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China
| | - Chong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China
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Ran J, Guo G, Zhang S, Zhang Y, Zhang L, Li D, Wu S, Cong Y, Wang X, Xie S, Zhao H, Liu H, Ou G, Zhu X, Zhou J, Liu M. KIF11 UFMylation Maintains Photoreceptor Cilium Integrity and Retinal Homeostasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400569. [PMID: 38666385 PMCID: PMC11220646 DOI: 10.1002/advs.202400569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/01/2024] [Indexed: 07/04/2024]
Abstract
The photoreceptor cilium is vital for maintaining the structure and function of the retina. However, the molecular mechanisms underlying the photoreceptor cilium integrity and retinal homeostasis are largely unknown. Herein, it is shown that kinesin family member 11 (KIF11) localizes at the transition zone (connecting cilium) of the photoreceptor and plays a crucial role in orchestrating the cilium integrity. KIF11 depletion causes malformations of both the photoreceptor ciliary axoneme and membranous discs, resulting in photoreceptor degeneration and the accumulation of drusen-like deposits throughout the retina. Mechanistic studies show that the stability of KIF11 is regulated by an interplay between its UFMylation and ubiquitination; UFMylation of KIF11 at lysine 953 inhibits its ubiquitination by synoviolin 1 and thereby prevents its proteasomal degradation. The lysine 953-to-arginine mutant of KIF11 is more stable than wild-type KIF11 and also more effective in reversing the ciliary and retinal defects induced by KIF11 depletion. These findings identify a critical role for KIF11 UFMylation in the maintenance of photoreceptor cilium integrity and retinal homeostasis.
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Affiliation(s)
- Jie Ran
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Guizhi Guo
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Sai Zhang
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Yufei Zhang
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Liang Zhang
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Dengwen Li
- Department of Genetics and Cell BiologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Shian Wu
- Department of Genetics and Cell BiologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Yusheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceInstitute of Aging ResearchSchool of MedicineHangzhou Normal UniversityHangzhou310036China
| | - Xiaohong Wang
- Department of PharmacologyTianjin Key Laboratory of Inflammation BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Songbo Xie
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Huijie Zhao
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
| | - Hongbin Liu
- Center for Reproductive MedicineCheeloo College of MedicineKey Laboratory of Reproductive Endocrinology of Ministry of EducationShandong UniversityJinan250014China
| | - Guangshuo Ou
- Tsinghua‐Peking Center for Life SciencesMinistry of Education Key Laboratory for Protein ScienceSchool of Life SciencesTsinghua UniversityBeijing100084China
| | - Xueliang Zhu
- State Key Laboratory of Cell BiologyCAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
| | - Jun Zhou
- Center for Cell Structure and FunctionShandong Provincial Key Laboratory of Animal Resistance BiologyHaihe Laboratory of Cell EcosystemCollege of Life SciencesShandong Normal UniversityJinan250014China
- Department of Genetics and Cell BiologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Min Liu
- Laboratory of Tissue HomeostasisHaihe Laboratory of Cell EcosystemTianjin300462China
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Xu X, Huang W, Bryant CN, Dong Z, Li H, Wu G. The ufmylation cascade controls COPII recruitment, anterograde transport, and sorting of nascent GPCRs at ER. SCIENCE ADVANCES 2024; 10:eadm9216. [PMID: 38905340 PMCID: PMC11192079 DOI: 10.1126/sciadv.adm9216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Ufmylation is implicated in multiple cellular processes, but little is known about its functions and regulation in protein trafficking. Here, we demonstrate that the genetic depletion of core components of the ufmylation cascade, including ubiquitin-fold modifier 1 (UFM1), UFM1 activation enzyme 5, UFM1-specific ligase 1 (UFL1), UFM1-specific protease 2, and UFM1-binding protein 1 (UFBP1) each markedly inhibits the endoplasmic reticulum (ER)-Golgi transport, surface delivery, and recruitment to COPII vesicles of a subset of G protein-coupled receptors (GPCRs) and UFBP1's function partially relies on UFM1 conjugation. We also show that UFBP1 and UFL1 interact with GPCRs and UFBP1 localizes at COPII vesicles coated with specific Sec24 isoforms. Furthermore, the UFBP1/UFL1-binding domain identified in the receptors effectively converts non-GPCR protein transport into the ufmylation-dependent pathway. Collectively, these data reveal important functions for the ufmylation system in GPCR recruitment to COPII vesicles, biosynthetic transport, and sorting at ER via UFBP1 ufmylation and interaction directly.
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Affiliation(s)
- Xin Xu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Wei Huang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Christian N. Bryant
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Guangyu Wu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
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10
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Tan Q, Xu X. PTIP UFMylation promotes replication fork degradation in BRCA1-deficient cells. J Biol Chem 2024; 300:107312. [PMID: 38657865 PMCID: PMC11130726 DOI: 10.1016/j.jbc.2024.107312] [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: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
Homologous-recombination deficiency due to breast cancer 1/2 (BRCA1/2) mutations or mimicking BRCA1/2 mutations confer synthetic lethality with poly-(ADP)-ribose polymerase 1/2 inhibitors. The chromatin regulator Pax2 transactivation domain interacting protein (PTIP) promotes stalled replication fork degradation in BRCA1-deficient cells, but the underlying mechanism by which PTIP regulates stalled replication fork stability is unclear. Here, we performed a series of in vitro analyses to dissect the function of UFMylation in regulating fork stabilization in BRCA1-deficient cells. By denaturing co-immunoprecipitation, we first found that replication stress can induce PTIP UFMylation. Interestingly, this post-translational modification promotes end resection and degradation of nascent DNA at stalled replication forks in BRCA1-deficient cells. By cell viability assay, we found that PTIP-depleted and UFL1-depleted BRCA1 knockdown cells are less sensitive to poly-(ADP)-ribose polymerase inhibitors than the siRNA targeting negative control BRCA1-deficient cells. These results identify a new mechanism by which PTIP UFMylation confers chemoresistance in BRCA1-deficient cells.
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Affiliation(s)
- Qunsong Tan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 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, China.
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11
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Yan T, Heckman MG, Craver EC, Liu CC, Rawlinson BD, Wang X, Murray ME, Dickson DW, Ertekin-Taner N, Lou Z, Bu G, Springer W, Fiesel FC. The UFMylation pathway is impaired in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595755. [PMID: 38903110 PMCID: PMC11188091 DOI: 10.1101/2024.05.24.595755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Background Alzheimer's disease (AD) is characterized by the presence of neurofibrillary tangles made of hyperphosphorylated tau and senile plaques composed of beta-amyloid. These pathognomonic deposits have been implicated in the pathogenesis, although the molecular mechanisms and consequences remain undetermined. UFM1 is an important, but understudied ubiquitin-like protein that is covalently attached to substrates. This UFMylation has recently been identified as major modifier of tau aggregation upon seeding in experimental models. However, potential alterations of the UFM1 pathway in human AD brain have not been investigated yet. Methods Here we used frontal and temporal cortex samples from individuals with or without AD to measure the protein levels of the UFMylation pathway in human brain. We used multivariable regression analyses followed by Bonferroni correction for multiple testing to analyze associations of the UFMylation pathway with neuropathological characteristics, primary biochemical measurements of tau and additional biochemical markers from the same cases. We further studied associations of the UFMylation cascade with cellular stress pathways using Spearman correlations with bulk RNAseq expression data and functionally validated these interactions using gene-edited neurons that were generated by CRISPR-Cas9. Results Compared to controls, human AD brain had increased protein levels of UFM1. Our data further indicates that this increase mainly reflects conjugated UFM1 indicating hyperUFMylation in AD. UFMylation was strongly correlated with pathological tau in both AD-affected brain regions. In addition, we found that the levels of conjugated UFM1 were negatively correlated with soluble levels of the deUFMylation enzyme UFSP2. Functional analysis of UFM1 and/or UFSP2 knockout neurons revealed that the DNA damage response as well as the unfolded protein response are perturbed by changes in neuronal UFM1 signaling. Conclusions There are marked changes in the UFMylation pathway in human AD brain. These changes are significantly associated with pathological tau, supporting the idea that the UFMylation cascade might indeed act as a modifier of tau pathology in human brain. Our study further nominates UFSP2 as an attractive target to reduce the hyperUFMylation observed in AD brain but also underscores the critical need to identify risks and benefits of manipulating the UFMylation pathway as potential therapeutic avenue for AD.
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Affiliation(s)
- Tingxiang Yan
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Michael G. Heckman
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, FL, USA
| | - Emily C. Craver
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, FL, USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Xue Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
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12
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Gong Y, Wang Z, Zong W, Shi R, Sun W, Wang S, Peng B, Takeda S, Wang ZQ, Xu X. PARP1 UFMylation ensures the stability of stalled replication forks. Proc Natl Acad Sci U S A 2024; 121:e2322520121. [PMID: 38657044 PMCID: PMC11066985 DOI: 10.1073/pnas.2322520121] [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: 12/20/2023] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
The S-phase checkpoint involving CHK1 is essential for fork stability in response to fork stalling. PARP1 acts as a sensor of replication stress and is required for CHK1 activation. However, it is unclear how the activity of PARP1 is regulated. Here, we found that UFMylation is required for the efficient activation of CHK1 by UFMylating PARP1 at K548 during replication stress. Inactivation of UFL1, the E3 enzyme essential for UFMylation, delayed CHK1 activation and inhibits nascent DNA degradation during replication blockage as seen in PARP1-deficient cells. An in vitro study indicated that PARP1 is UFMylated at K548, which enhances its catalytic activity. Correspondingly, a PARP1 UFMylation-deficient mutant (K548R) and pathogenic mutant (F553L) compromised CHK1 activation, the restart of stalled replication forks following replication blockage, and chromosome stability. Defective PARP1 UFMylation also resulted in excessive nascent DNA degradation at stalled replication forks. Finally, we observed that PARP1 UFMylation-deficient knock-in mice exhibited increased sensitivity to replication stress caused by anticancer treatments. Thus, we demonstrate that PARP1 UFMylation promotes CHK1 activation and replication fork stability during replication stress, thus safeguarding genome integrity.
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Affiliation(s)
- Yamin Gong
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena07745, Germany
| | - Zhifeng Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Ruifeng Shi
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena07745, Germany
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Sijia Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Shunichi Takeda
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena07745, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
- Faculty of Biology and Pharmacy, Friedrich-Schiller University of Jena, Jena07743, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
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13
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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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14
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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15
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He C, Xing X, Chen HY, Gao M, Shi J, Xiang B, Xiao X, Sun Y, Yu H, Xu G, Yao Y, Xie Z, Xing Y, Budiarto BR, Chen SY, Gao Y, Lee YR, Zhang J. UFL1 ablation in T cells suppresses PD-1 UFMylation to enhance anti-tumor immunity. Mol Cell 2024; 84:1120-1138.e8. [PMID: 38377992 DOI: 10.1016/j.molcel.2024.01.024] [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: 05/30/2023] [Revised: 11/10/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024]
Abstract
UFMylation is an emerging ubiquitin-like post-translational modification that regulates various biological processes. Dysregulation of the UFMylation pathway leads to human diseases, including cancers. However, the physiological role of UFMylation in T cells remains unclear. Here, we report that mice with conditional knockout (cKO) Ufl1, a UFMylation E3 ligase, in T cells exhibit effective tumor control. Single-cell RNA sequencing analysis shows that tumor-infiltrating cytotoxic CD8+ T cells are increased in Ufl1 cKO mice. Mechanistically, UFL1 promotes PD-1 UFMylation to antagonize PD-1 ubiquitination and degradation. Furthermore, AMPK phosphorylates UFL1 at Thr536, disrupting PD-1 UFMylation to trigger its degradation. Of note, UFL1 ablation in T cells reduces PD-1 UFMylation, subsequently destabilizing PD-1 and enhancing CD8+ T cell activation. Thus, Ufl1 cKO mice bearing tumors have a better response to anti-CTLA-4 immunotherapy. Collectively, our findings uncover a crucial role of UFMylation in T cells and highlight UFL1 as a potential target for cancer treatment.
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Affiliation(s)
- Chuan He
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xixin Xing
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Hsin-Yi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Minling Gao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jie Shi
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Bolin Xiang
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangling Xiao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yishuang Sun
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Haisheng Yu
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Gaoshan Xu
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yingmeng Yao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Zuosong Xie
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yujie Xing
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Bugi Ratno Budiarto
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Yang Gao
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yu-Ru Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan.
| | - Jinfang Zhang
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China.
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16
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Wang L, Xu Y, Fukushige T, Saidi L, Wang X, Yu C, Lee JG, Krause M, Huang L, Ye Y. Mono-UFMylation promotes misfolding-associated secretion of α-synuclein. SCIENCE ADVANCES 2024; 10:eadk2542. [PMID: 38489364 PMCID: PMC10942102 DOI: 10.1126/sciadv.adk2542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Stressed cells secret misfolded proteins lacking signaling sequence via an unconventional protein secretion (UcPS) pathway, but how misfolded proteins are targeted selectively in UcPS is unclear. Here, we report that misfolded UcPS clients are subject to modification by a ubiquitin-like protein named ubiquitin-fold modifier 1 (UFM1). Using α-synuclein (α-Syn) as a UcPS model, we show that mutating the UFMylation sites in α-Syn or genetic inhibition of the UFMylation system mitigates α-Syn secretion, whereas overexpression of UFBP1, a component of the endoplasmic reticulum-associated UFMylation ligase complex, augments α-Syn secretion in mammalian cells and in model organisms. UFM1 itself is cosecreted with α-Syn, and the serum UFM1 level correlates with that of α-Syn. Because UFM1 can be directly recognized by ubiquitin specific peptidase 19 (USP19), a previously established UcPS stimulator known to associate with several chaperoning activities, UFMylation might facilitate substrate engagement by USP19, allowing stringent and regulated selection of misfolded proteins for secretion and proteotoxic stress alleviation.
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Affiliation(s)
- Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Layla Saidi
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Jin-Gu Lee
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Chen H, Wang YD, Blan AW, Almanza-Fuerte EP, Bonkowski ES, Bajpai R, Pruett-Miller SM, Mefford HC. Patient derived model of UBA5-associated encephalopathy identifies defects in neurodevelopment and highlights potential therapies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577254. [PMID: 38328212 PMCID: PMC10849720 DOI: 10.1101/2024.01.25.577254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
UBA5 encodes for the E1 enzyme of the UFMylation cascade, which plays an essential role in ER homeostasis. The clinical phenotypes of UBA5-associated encephalopathy include developmental delays, epilepsy and intellectual disability. To date, there is no humanized neuronal model to study the cellular and molecular consequences of UBA5 pathogenic variants. We developed and characterized patient-derived cortical organoid cultures and identified defects in GABAergic interneuron development. We demonstrated aberrant neuronal firing and microcephaly phenotypes in patient-derived organoids. Mechanistically, we show that ER homeostasis is perturbed along with exacerbated unfolded protein response pathway in cells and organoids expressing UBA5 pathogenic variants. We also assessed two gene expression modalities that augmented UBA5 expression to rescue aberrant molecular and cellular phenotypes. Our study provides a novel humanized model that allows further investigations of UBA5 variants in the brain and highlights novel systemic approaches to alleviate cellular aberrations for this rare, developmental disorder.
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Affiliation(s)
- Helen Chen
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Aidan W. Blan
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Edith P. Almanza-Fuerte
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Emily S. Bonkowski
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richa Bajpai
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Heather C. Mefford
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
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18
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Komatsu M, Inada T, Noda NN. The UFM1 system: Working principles, cellular functions, and pathophysiology. Mol Cell 2024; 84:156-169. [PMID: 38141606 DOI: 10.1016/j.molcel.2023.11.034] [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: 08/14/2023] [Revised: 10/21/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through UFMylation, a process similar to ubiquitylation. Growing lines of evidence regarding not only the structural basis of the components essential for UFMylation but also their biological properties shed light on crucial roles of the UFM1 system in the endoplasmic reticulum (ER), such as ER-phagy and ribosome-associated quality control at the ER, although there are some functions unrelated to the ER. Mouse genetics studies also revealed the indispensable roles of this system in hematopoiesis, liver development, neurogenesis, and chondrogenesis. Of critical importance, mutations of genes encoding core components of the UFM1 system in humans cause hereditary developmental epileptic encephalopathy and Schohat-type osteochondrodysplasia of the epiphysis. Here, we provide a multidisciplinary review of our current understanding of the mechanisms and cellular functions of the UFM1 system as well as its pathophysiological roles, and discuss issues that require resolution.
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Affiliation(s)
- Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan; Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan.
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19
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Zhou X, Mahdizadeh SJ, Le Gallo M, Eriksson LA, Chevet E, Lafont E. UFMylation: a ubiquitin-like modification. Trends Biochem Sci 2024; 49:52-67. [PMID: 37945409 DOI: 10.1016/j.tibs.2023.10.004] [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: 04/29/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein-protein interactions, protein stability, and thus the functions of their protein targets. Here, we focus on the most recently identified UBL, ubiquitin-fold modifier 1 (UFM1), and the machinery responsible for its transfer to substrates (UFMylation) or its removal (deUFMylation). We first highlight the biochemical peculiarities of these processes, then we develop on how UFMylation and its machinery control various intertwined cellular processes and we highlight some of the outstanding research questions in this emerging field.
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Affiliation(s)
- Xingchen Zhou
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Sayyed J Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Matthieu Le Gallo
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
| | - Elodie Lafont
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
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20
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. eLife 2023; 12:RP89891. [PMID: 38079206 PMCID: PMC10712953 DOI: 10.7554/elife.89891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and endoplasmic reticulum stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least 12 different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remain to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Albert N Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Michael W Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for ChildrenBostonUnited States
| | - Jenny L Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science UniversityPortlandUnited States
| | - Ruth J Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
- VA Portland Health Care SystemPortlandUnited States
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science UniversityPortlandUnited States
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
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21
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Millrine D, Peter JJ, Kulathu Y. A guide to UFMylation, an emerging posttranslational modification. FEBS J 2023; 290:5040-5056. [PMID: 36680403 PMCID: PMC10952357 DOI: 10.1111/febs.16730] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Ubiquitin Fold Modifier-1 (UFM1) is a ubiquitin-like modifier (UBL) that is posttranslationally attached to lysine residues on substrates via a dedicated system of enzymes conserved in most eukaryotes. Despite the structural similarity between UFM1 and ubiquitin, the UFMylation machinery employs unique mechanisms that ensure fidelity. While physiological triggers and consequences of UFMylation are not entirely clear, its biological importance is epitomized by mutations in the UFMylation pathway in human pathophysiology including musculoskeletal and neurodevelopmental diseases. Some of these diseases can be explained by the increased endoplasmic reticulum (ER) stress and disrupted translational homeostasis observed upon loss of UFMylation. The roles of UFM1 in these processes likely stem from its function at the ER where ribosomes are UFMylated in response to translational stalling. In addition, UFMylation has been implicated in other cellular processes including DNA damage response and telomere maintenance. Hence, the study of UFM1 pathway mechanics and its biological function will reveal insights into fundamental cell biology and is likely to afford new therapeutic opportunities for the benefit of human health. To this end, we herein provide a comprehensive guide to the current state of knowledge of UFM1 biogenesis, conjugation, and function with an emphasis on the underlying mechanisms.
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Affiliation(s)
- David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
| | - Joshua J. Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
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22
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Wang X, Xu X, Wang Z. The Post-Translational Role of UFMylation in Physiology and Disease. Cells 2023; 12:2543. [PMID: 37947621 PMCID: PMC10648299 DOI: 10.3390/cells12212543] [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: 08/30/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a newly identified ubiquitin-like protein that has been conserved during the evolution of multicellular organisms. In a similar manner to ubiquitin, UFM1 can become covalently linked to the lysine residue of a substrate via a dedicated enzymatic cascade. Although a limited number of substrates have been identified so far, UFM1 modification (UFMylation) has been demonstrated to play a vital role in a variety of cellular activities, including mammalian development, ribosome biogenesis, the DNA damage response, endoplasmic reticulum stress responses, immune responses, and tumorigenesis. In this review, we summarize what is known about the UFM1 enzymatic cascade and its biological functions, and discuss its recently identified substrates. We also explore the pathological role of UFMylation in human disease and the corresponding potential therapeutic targets and strategies.
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Affiliation(s)
| | - 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 518060, China;
| | - 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 518060, China;
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23
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.17.23292782. [PMID: 37502976 PMCID: PMC10371176 DOI: 10.1101/2023.07.17.23292782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and ER stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least twelve different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remains to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Albert N. Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Michael W. Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lauren C. Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A. Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Jenny L. Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ruth J. Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
- VA Portland Health Care System, Portland, OR 97239, USA
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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24
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Lu Y, Jiang X, Ai H, Li D, Khattak A, Zhang B, Liu X, Zhang H, Huang S. Characterization of a silkworm UFM1 homolog in regulating Bombyx mori unfolded protein response and nucleopolyhedrovirus replication. Biochem Biophys Res Commun 2023; 675:162-169. [PMID: 37478772 DOI: 10.1016/j.bbrc.2023.07.033] [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: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023]
Abstract
The Ubiquitin (Ub)-like molecules is essential for animal development and the physiopathology of multiple tissues in the vertebrate. Ubiquitin-fold modifier 1 (UFM1) is one of the newly-identified UBL, which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Bombyx mori nuclear polyhedrosis virus (BmNPV) is one of the main pathogens in sericulture, causing serious economic losses every year. However, there are no studies on UFMylation and the effect of UFMylation on BmNPV replication in silkworm. In this study, we identified BmUFM1 in the B. mori genome. Spatio-Temporal expression profiles showed that BmUFM1 expression was highly in hemocytes and response to various pathogenic stimuli. Furthermore, BmUFM1 is involved in the regulation of ER stress induced Unfolded Protein Response (UPR) and knockdown of BmUFM1 inhibited BmNPV replication. Overall, these results suggest that BmUFM1 plays an important role in facilitating BmNPV proliferation in silkworm. Our findings advance the understanding of UFM1's conjugation machinery, and also provides a potentially molecular target for BmNPV prevention and silkworm breeding.
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Affiliation(s)
- Yiting Lu
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei, 230036, China
| | - Xiaochun Jiang
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei, 230036, China
| | - Heng Ai
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei, 230036, China
| | - Danting Li
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei, 230036, China
| | - Afrasiyab Khattak
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei, 230036, China
| | - Bei Zhang
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xu Liu
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, 611130, China
| | - Hualing Zhang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, 611130, China
| | - Shoujun Huang
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei, 230036, China.
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25
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Cho UH, Hetzer MW. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife 2023; 12:RP89066. [PMID: 37665327 PMCID: PMC10476967 DOI: 10.7554/elife.89066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. 'Trimmed' NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.
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Affiliation(s)
- Ukrae H Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Institute of Science and Technology Austria (IST Austria)KlosterneuburgAustria
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26
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Mao Z, Ma X, Jing Y, Shen M, Ma X, Zhu J, Liu H, Zhang G, Chen F. Ufmylation on UFBP1 alleviates non-alcoholic fatty liver disease by modulating hepatic endoplasmic reticulum stress. Cell Death Dis 2023; 14:584. [PMID: 37660122 PMCID: PMC10475044 DOI: 10.1038/s41419-023-06095-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/06/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease characterized by lipid accumulation and endoplasmic reticulum (ER) stress, while effective therapies targeting the specific characteristics of NAFLD are limited. Ufmylation is a newly found post-translational modification process that involves the attachment of the Ubiquitin-fold modifier 1 (UFM1) protein to its substrates via ufmylation modification system. Ufmylation regulates ER stress via modifying UFM1 binding protein 1 (UFBP1), suggesting a potential role for ufmylation in NAFLD pathogenesis. However, the precise role of ufmylation in NAFLD remains unclear. Herein, we aim to elucidate the impact of ufmylation on UFBP1 in NAFLD and explore the underlying mechanisms involved. We observed increased expression of UFM1-conjugated proteins and ufmylation modification system components in livers with steatosis derived from NAFLD patients and NAFLD models. Upregulation of ufmylation on hepatic proteins appeared to be an adaptive response to hepatic ER stress in NAFLD. In vitro, knocking down UFBP1 resulted in increased lipid accumulation and lipogenesis in hepatocytes treated with free fatty acids (FFA), which could be rescued by wild-type UFBP1 (WT UFBP1) but not by a mutant form of UFBP1 lacking the main ufmylation site lys267 (UFBP1 K267R). In vivo, ufmylation on UFBP1 ameliorated obesity, hepatic steatosis, hepatic lipogenesis, dyslipidemia, insulin resistance and liver damage in mice with NAFLD induced by a high fat diet (HFD). We also demonstrated that the downregulation of UFBP1 induced ER stress, whereas the reintroduction or overexpression of UFBP1 alleviated ER stress in a manner dependent on ufmylation in NAFLD. This mechanism could be responsible for the amelioration of aberrant hepatic lipogenesis and insulin resistance in NAFLD. Our data reveal a protective role of ufmylation on UFBP1 against NAFLD and offer a specific target for NAFLD treatment.
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Affiliation(s)
- Ziming Mao
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China
| | - Xiaowen Ma
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China
| | - Yu Jing
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China
| | - Minyan Shen
- School of Graduate, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Xirui Ma
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China
| | - Jing Zhu
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China
| | - Huifang Liu
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China.
| | - Guangya Zhang
- Department of Cardiology, Shanghai Sixth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200233, China.
| | - Fengling Chen
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 201999, China.
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27
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Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. SCIENCE ADVANCES 2023; 9:eadh3635. [PMID: 37595036 PMCID: PMC10438457 DOI: 10.1126/sciadv.adh3635] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through ufmylation, similar to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control (RQC) at the ER (ER-RQC), and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here, we provide insights into the mechanism of the UFM1 E3 complex in not only ufmylation but also ER-RQC. The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1, UFM1 E2, and, subsequently, CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26. Upon disome formation, the E3 complex associated with ufmylated RPL26 on the 60S subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of the interaction between UFBP1 and ufmylated RPL26 attenuated ER-RQC. These results provide insights into not only the molecular basis of the ufmylation but also its role in proteostasis.
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Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sota Ito
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Gaoxin Mao
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan
- Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
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28
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Li SJ, Shi JJ, Mao CY, Zhang C, Xu YF, Fan Y, Hu ZW, Yu WK, Hao XY, Li MJ, Li JD, Ma DR, Guo MN, Zuo CY, Liang YY, Xu YM, Wu J, Sun SL, Wang YG, Shi CH. Identifying causal genes for migraine by integrating the proteome and transcriptome. J Headache Pain 2023; 24:111. [PMID: 37592229 PMCID: PMC10433568 DOI: 10.1186/s10194-023-01649-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND While previous genome-wide association studies (GWAS) have identified multiple risk variants for migraine, there is a lack of evidence about how these variants contribute to the development of migraine. We employed an integrative pipeline to efficiently transform genetic associations to identify causal genes for migraine. METHODS We conducted a proteome-wide association study (PWAS) by combining data from the migraine GWAS data with proteomic data from the human brain and plasma to identify proteins that may play a role in the risk of developing migraine. We also combined data from GWAS of migraine with a novel joint-tissue imputation (JTI) prediction model of 17 migraine-related human tissues to conduct transcriptome-wide association studies (TWAS) together with the fine mapping method FOCUS to identify disease-associated genes. RESULTS We identified 13 genes in the human brain and plasma proteome that modulate migraine risk by regulating protein abundance. In addition, 62 associated genes not reported in previous migraine TWAS studies were identified by our analysis of migraine using TWAS and fine mapping. Five genes including ICA1L, TREX1, STAT6, UFL1, and B3GNT8 showed significant associations with migraine at both the proteome and transcriptome, these genes are mainly expressed in ependymal cells, neurons, and glial cells, and are potential target genes for prevention of neuronal signaling and inflammatory responses in the pathogenesis of migraine. CONCLUSIONS Our proteomic and transcriptome findings have identified disease-associated genes that may give new insights into the pathogenesis and potential therapeutic targets for migraine.
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Affiliation(s)
- Shuang-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Jing-Jing Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Cheng-Yuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Chan Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Ya-Fang Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Yu Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Zheng-Wei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Wen-Kai Yu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Xiao-Yan Hao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Meng-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Jia-di Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Dong-Rui Ma
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Meng-Nan Guo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Chun-Yan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Yuan-Yuan Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Jun Wu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Shi-Lei Sun
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Yong-Gang Wang
- Headache Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, No.119 South Fourth Ring West Road, Fengtai District, Beijing, 100070, China.
| | - Chang-He Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450000, Henan, China.
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29
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Priya B, Ravi S, Kirubakaran S. Targeting ATM and ATR for cancer therapeutics: inhibitors in clinic. Drug Discov Today 2023:103662. [PMID: 37302542 DOI: 10.1016/j.drudis.2023.103662] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
The DNA Damage and Response (DDR) pathway ensures accurate information transfer from one generation to the next. Alterations in DDR functions have been connected to cancer predisposition, progression, and response to therapy. DNA double-strand break (DSB) is one of the most detrimental DNA defects, causing major chromosomal abnormalities such as translocations and deletions. ATR and ATM kinases recognize this damage and activate proteins involved in cell cycle checkpoint, DNA repair, and apoptosis. Cancer cells have a high DSB burden, and therefore rely on DSB repair for survival. Therefore, targeting DSB repair can sensitize cancer cells to DNA-damaging agents. This review focuses on ATM and ATR, their roles in DNA damage and repair pathways, challenges in targeting them, and inhibitors that are in current clinical trials.
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Affiliation(s)
- Bhanu Priya
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India
| | - Srimadhavi Ravi
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India
| | - Sivapriya Kirubakaran
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India.
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30
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Li H, Yu Z, Niu Z, Cheng Y, Wei Z, Cai Y, Ma F, Hu L, Zhu J, Zhang W. A neuroprotective role of Ufmylation through Atg9 in the aging brain of Drosophila. Cell Mol Life Sci 2023; 80:129. [PMID: 37086384 PMCID: PMC11073442 DOI: 10.1007/s00018-023-04778-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Ufmylation is a recently identified small ubiquitin-like modification, whose biological function and relevant cellular targets are poorly understood. Here we present evidence of a neuroprotective role for Ufmylation involving Autophagy-related gene 9 (Atg9) during Drosophila aging. The Ufm1 system ensures the health of aged neurons via Atg9 by coordinating autophagy and mTORC1, and maintaining mitochondrial homeostasis and JNK (c-Jun N-terminal kinase) activity. Neuron-specific expression of Atg9 suppresses the age-associated movement defect and lethality caused by loss of Ufmylation. Furthermore, Atg9 is identified as a conserved target of Ufm1 conjugation mediated by Ddrgk1, a critical regulator of Ufmylation. Mammalian Ddrgk1 was shown to be indispensable for the stability of endogenous Atg9A protein in mouse embryonic fibroblast (MEF) cells. Taken together, our findings might have important implications for neurodegenerative diseases in mammals.
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Affiliation(s)
- Huifang Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenghong Yu
- Department of Rheumatology and Immunology, Jinling Hospital, Affiliated Hosptial of Medical School, Nanjing University, Nanjing, 210002, China
| | - Zikang Niu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yun Cheng
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Zhenhao Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Ma
- College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Lanxin Hu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiejie Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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31
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Fukasawa T, Enomoto A, Yoshizaki-Ogawa A, Sato S, Miyagawa K, Yoshizaki A. The Role of Mammalian STK38 in DNA Damage Response and Targeting for Radio-Sensitization. Cancers (Basel) 2023; 15:cancers15072054. [PMID: 37046714 PMCID: PMC10093458 DOI: 10.3390/cancers15072054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Protein kinases, found in the nucleus and cytoplasm, play essential roles in a multitude of cellular processes, including cell division, proliferation, apoptosis, and signal transduction. STK38 is a member of the protein kinase A (PKA)/PKG/PKC family implicated in regulating cell division and morphogenesis in yeast and C. elegans. However, its function remained largely unknown in mammals. In recent years, advances in research on STK38 and the identification of its substrates has led to a better understanding of its function and role in mammals. This review discusses the structure, expression, and regulation of activity as a kinase, its role in the DNA damage response, cross-talk with other signaling pathways, and its application for radio-sensitization.
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32
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Zhou J, Ma X, He X, Chen B, Yuan J, Jin Z, Li L, Wang Z, Xiao Q, Cai Y, Zou Y. Dysregulation of PD-L1 by UFMylation imparts tumor immune evasion and identified as a potential therapeutic target. Proc Natl Acad Sci U S A 2023; 120:e2215732120. [PMID: 36893266 PMCID: PMC10089188 DOI: 10.1073/pnas.2215732120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/18/2023] [Indexed: 03/11/2023] Open
Abstract
Immunotherapy of PD-L1/PD-1 blockage elicited impressive clinical benefits for cancer treatment. However, the relative low response and therapy resistance highlight the need to better understand the molecular regulation of PD-L1 in tumors. Here, we report that PD-L1 is a target of UFMylation. UFMylation of PD-L1 destabilizes PD-L1 by synergizing its ubiquitination. Inhibition of PD-L1 UFMylation via silencing of UFL1 or Ubiquitin-fold modifier 1 (UFM1), or the defective UFMylation of PD-L1, stabilizes the PD-L1 in multiple human and murine cancer cells, and undermines antitumor immunity in vitro and mice, respectively. Clinically, UFL1 expression was decreased in multiple cancers and lower expression of UFL1 negatively correlated with the response of anti-PD1 therapy in melanoma patients. Moreover, we identified a covalent inhibitor of UFSP2 that promoted the UFMylation activity and contributed to the combination therapy with PD-1 blockade. Our findings identified a previously unrecognized regulator of PD-L1 and highlighted UFMylation as a potential therapeutic target.
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Affiliation(s)
- Junzhi Zhou
- School of Basic Medicine, Hangzhou Normal University, Hangzhou311121, China
| | - Xiaohe Ma
- School of Basic Medicine, Hangzhou Normal University, Hangzhou311121, China
| | - Xingrui He
- School of Pharmacy, Hangzhou Normal University, Hangzhou311121, China
| | - Beiying Chen
- School of Basic Medicine, Hangzhou Normal University, Hangzhou311121, China
| | - Jiao Yuan
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou510005, China
| | - Zhemin Jin
- Yongkang Maternity and Child Care hospital, Yongkang321300, China
| | - Lijing Li
- Yongkang Maternity and Child Care hospital, Yongkang321300, China
| | - Zhiguo Wang
- School of Basic Medicine, Hangzhou Normal University, Hangzhou311121, China
| | - Qian Xiao
- Rutgers Cancer Institute of New Jersey, New Jersey, NJ08901
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yongkang Zou
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen518107, China
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33
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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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34
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Wang L, Xu Y, Yun S, Yuan Q, Satpute-Krishnan P, Ye Y. SAYSD1 senses UFMylated ribosome to safeguard co-translational protein translocation at the endoplasmic reticulum. Cell Rep 2023; 42:112028. [PMID: 36848233 PMCID: PMC10010011 DOI: 10.1016/j.celrep.2023.112028] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/17/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Translocon clogging at the endoplasmic reticulum (ER) as a result of translation stalling triggers ribosome UFMylation, activating translocation-associated quality control (TAQC) to degrade clogged substrates. How cells sense ribosome UFMylation to initiate TAQC is unclear. We conduct a genome-wide CRISPR-Cas9 screen to identify an uncharacterized membrane protein named SAYSD1 that facilitates TAQC. SAYSD1 associates with the Sec61 translocon and also recognizes both ribosome and UFM1 directly, engaging a stalled nascent chain to ensure its transport via the TRAPP complex to lysosomes for degradation. Like UFM1 deficiency, SAYSD1 depletion causes the accumulation of translocation-stalled proteins at the ER and triggers ER stress. Importantly, disrupting UFM1- and SAYSD1-dependent TAQC in Drosophila leads to intracellular accumulation of translocation-stalled collagens, defective collagen deposition, abnormal basement membranes, and reduced stress tolerance. Thus, SAYSD1 acts as a UFM1 sensor that collaborates with ribosome UFMylation at the site of clogged translocon, safeguarding ER homeostasis during animal development.
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Affiliation(s)
- Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Quan Yuan
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prasanna Satpute-Krishnan
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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35
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Ahn HW, Worman ZF, Lechsinska A, Payer LM, Wang T, Malik N, Li W, Burns KH, Nath A, Levin HL. Retrotransposon insertions associated with risk of neurologic and psychiatric diseases. EMBO Rep 2023; 24:e55197. [PMID: 36367221 PMCID: PMC9827563 DOI: 10.15252/embr.202255197] [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: 04/08/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are active in neuronal cells raising the question whether TE insertions contribute to risk of neuropsychiatric disease. While genome-wide association studies (GWAS) serve as a tool to discover genetic loci associated with neuropsychiatric diseases, unfortunately GWAS do not directly detect structural variants such as TEs. To examine the role of TEs in psychiatric and neurologic disease, we evaluated 17,000 polymorphic TEs and find 76 are in linkage disequilibrium with disease haplotypes (P < 10-6 ) defined by GWAS. From these 76 polymorphic TEs, we identify potentially causal candidates based on having insertions in genomic regions of regulatory chromatin and on having associations with altered gene expression in brain tissues. We show that lead candidate insertions have regulatory effects on gene expression in human neural stem cells altering the activity of a minimal promoter. Taken together, we identify 10 polymorphic TE insertions that are potential candidates on par with other variants for having a causal role in neurologic and psychiatric disorders.
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Affiliation(s)
- Hyo Won Ahn
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Zelia F Worman
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
- Present address:
Seven BridgesCharlestownMAUSA
| | - Arianna Lechsinska
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Lindsay M Payer
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Tongguang Wang
- Translational Neuroscience CenterNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Nasir Malik
- Translational Neuroscience CenterNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Wenxue Li
- Section of Infections of the Nervous SystemNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Kathleen H Burns
- Department of Oncologic PathologyDana‐Farber Cancer InstituteBostonMAUSA
| | - Avindra Nath
- Translational Neuroscience CenterNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
- Section of Infections of the Nervous SystemNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Henry L Levin
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
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36
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Ozmen Yaylaci A, Canbek M. The role of ubiquitin signaling pathway on liver regeneration in rats. Mol Cell Biochem 2023; 478:131-147. [PMID: 35750978 DOI: 10.1007/s11010-022-04482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/18/2022] [Indexed: 01/17/2023]
Abstract
The ubiquitin signalling pathway is a large system associated with numerous intracellular mechanisms. However, its function in the liver regeneration process remains unknown. This particular study investigates the intracellular effect mechanisms of the ubiquitin signalling pathway. It also determines the differences in the expression of 88 genes belonging to the ubiquitin pathway using the RT-PCR array method. To conduct this research, three genes-that differed in the expression analysis were selected. Moreover, their proteins were analysed by western blot analysis while using Ki67 immunohistochemical analysis that determines proliferation rates by hour. It was determined that BRCA1 and BARD1, which are effective in DNA repair, play an active role at PH24. Similarly, Ube2t expression, which belongs to the Fanconi anaemia pathway associated with DNA repair, was also found to be high at PH12-72 h. In addition, it was revealed that the expressions of Anapc2, Anapc11, Cdc20 belonging to the APC/CCdc20 complex, which participate in cell cycle regulation, differed at different hours after PH. Expression of Mul1, which is involved in mitochondrial biogenesis and mitophagy mechanisms, peaked at PH12 under the observation. Considering the Mul1 gene expression difference, MUL1-mediated mitophagy and mitochondrial fission mechanism may be associated with liver regeneration. It was also determined that PARKIN-mediated mitophagy mechanisms are not active in 0-72 h of liver regeneration since PARKIN expression did not show a significant change in PH groups.
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Affiliation(s)
- Ayse Ozmen Yaylaci
- Department of Biology, Faculty of Arts and Science, Hitit University, 19030, Corum, Turkey.
| | - Mediha Canbek
- Department of Biology, Faculty of Arts and Science, Eskisehir Osmangazi University, 26480, Eskisehir, Turkey
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37
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UFL1 promotes antiviral immune response by maintaining STING stability independent of UFMylation. Cell Death Differ 2023; 30:16-26. [PMID: 35871231 PMCID: PMC9883236 DOI: 10.1038/s41418-022-01041-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/01/2023] Open
Abstract
The precise regulation of STING homeostasis is essential for its antiviral function. Post-translational modification, especially ubiquitination, is important for the regulation of STING homeostasis. Previous studies have focused on how STING is degraded, but little is known about its maintenance. Here, we show that UFM1 specific ligase UFL1 promotes innate immune response by maintaining STING expression independent of UFMylation. Mechanistically, UFL1 inhibits TRIM29 to interact with STING, thereby reducing its ubiquitination at K338/K347/K370 and subsequent proteasomal degradation. DNA virus infection reduces the UFL1 expression, which may promote STING degradation and facilitate viral expansion. Our study identifies UFL1 as a crucial regulator for the maintenance of STING stability and antiviral function, and provides novel insights into the mechanistic explanation for the immunological escape of DNA virus.
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Jiang Q, Wang Y, Xiang M, Hua J, Zhou T, Chen F, Lv X, Huang J, Cai Y. UFL1, a UFMylation E3 ligase, plays a crucial role in multiple cellular stress responses. Front Endocrinol (Lausanne) 2023; 14:1123124. [PMID: 36843575 PMCID: PMC9950256 DOI: 10.3389/fendo.2023.1123124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
The UFM1 conjugation system(UFMylation)is a novel type of ubiquitin-like system that plays an indispensable role in maintaining cell homeostasis under various cellular stress. Similar to ubiquitination, UFMylation consists of a three-step enzymatic reaction with E1-like enzymes ubiquitin-like modifier activating enzyme5 (UBA5), E2-like enzymes ubiquitin-fold modifier-conjugating enzyme 1(UFC1), and E3-like ligase UFM1-specific ligase 1 (UFL1). As the only identified E3 ligase, UFL1 is responsible for specific binding and modification of the substrates to mediate numerous hormone signaling pathways and endocrine regulation under different physiological or pathological stress, such as ER stress, genotoxic stress, oncogenic stress, and inflammation. Further elucidation of the UFL1 working mechanism in multiple cellular stress responses is essential for revealing the disease pathogenesis and providing novel potential therapeutic targets. In this short review, we summarize the recent advances in novel UFL1 functions and shed light on the potential challenges ahead, thus hopefully providing a better understanding of UFMylation-mediated cellular stress.
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Affiliation(s)
- Qiang Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yongsheng Wang
- Department of Respiratory Medicine, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Minghui Xiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jiamin Hua
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tianci Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fanghui Chen
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, United States
| | - Xiaoyang Lv
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou, China
| | - Jinming Huang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- *Correspondence: Yafei Cai, ; Jinming Huang,
| | - Yafei Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Yafei Cai, ; Jinming Huang,
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Mao M, Chen Y, Yang J, Cheng Y, Xu L, Ji F, Zhou J, Zhang X, Li Z, Chen C, Ju S, Zhang J, Wang L. Modification of PLAC8 by UFM1 affects tumorous proliferation and immune response by impacting PD-L1 levels in triple-negative breast cancer. J Immunother Cancer 2022; 10:jitc-2022-005668. [PMID: 36543379 PMCID: PMC9772693 DOI: 10.1136/jitc-2022-005668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer is characterized by a poor prognosis and lack of targeted treatments, and thus, new targeting markers and therapeutic strategies are urgently needed. We previously indicated that PLAC8 promotes tumorigenesis and exerts multidrug resistance in breast cancer. Therefore, we aimed to characterize the PLAC8-regulated network in triple-negative breast cancer. METHODS We measured the levels of PLAC8 in breast cancer cell lines and found that PLAC8 is post-translationally modified by ubiquitin-fold modifier 1 (UFM1). Then, we revealed a new regulatory system of PD-L1 by PLAC8 in triple-negative breast cancer. We also tested the molecular functions of PLAC8 in triple-negative breast cancer cell lines and measured the expression of PLAC8 and PD-L1 in breast cancer tissues. RESULTS PLAC8 was generally highly expressed in triple-negative breast cancer and could be modified by UFM1, which maintains PLAC8 protein stability. Moreover, PLAC8 could promote cancer cell proliferation and affect the immune response by regulating the level of PD-L1 ubiquitination. Additionally, among patients with breast cancer, the expression of PLAC8 was higher in triple-negative breast cancer than in non-triple-negative breast cancer and positively correlated with the level of PD-L1. CONCLUSIONS Our current study discoveries a new PLAC8-regulated network in triple-negative breast cancer and provides corresponding guidance for the clinical diagnosis and immunotherapy of triple-negative breast cancer.
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Affiliation(s)
- Misha Mao
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Yongxia Chen
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Jingjing Yang
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Yifan Cheng
- Department of Gastrointestinal Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China
| | - Ling Xu
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Feiyang Ji
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Jichun Zhou
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Xun Zhang
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Zhaoqing Li
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Cong Chen
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Siwei Ju
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Jiahang Zhang
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
| | - Linbo Wang
- Department of Surgical Oncology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Zhejiang, Hangzhou, China,Zhejiang university, Zhejiang, Hangzhou, China
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Ishimura R, El-Gowily AH, Noshiro D, Komatsu-Hirota S, Ono Y, Shindo M, Hatta T, Abe M, Uemura T, Lee-Okada HC, Mohamed TM, Yokomizo T, Ueno T, Sakimura K, Natsume T, Sorimachi H, Inada T, Waguri S, Noda NN, Komatsu M. The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Nat Commun 2022; 13:7857. [PMID: 36543799 PMCID: PMC9772183 DOI: 10.1038/s41467-022-35501-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Protein modification by ubiquitin-like proteins (UBLs) amplifies limited genome information and regulates diverse cellular processes, including translation, autophagy and antiviral pathways. Ubiquitin-fold modifier 1 (UFM1) is a UBL covalently conjugated with intracellular proteins through ufmylation, a reaction analogous to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control at the ER and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here we identify a UFM1 substrate, NADH-cytochrome b5 reductase 3 (CYB5R3), that localizes on the ER membrane. Ufmylation of CYB5R3 depends on the E3 components UFL1 and UFBP1 on the ER, and converts CYB5R3 into its inactive form. Ufmylated CYB5R3 is recognized by UFBP1 through the UFM1-interacting motif, which plays an important role in the further uyfmylation of CYB5R3. Ufmylated CYB5R3 is degraded in lysosomes, which depends on the autophagy-related protein Atg7- and the autophagy-adaptor protein CDK5RAP3. Mutations of CYB5R3 and genes involved in the UFM1 system cause hereditary developmental disorders, and ufmylation-defective Cyb5r3 knock-in mice exhibit microcephaly. Our results indicate that CYB5R3 ufmylation induces ER-phagy, which is indispensable for brain development.
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Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Afnan H El-Gowily
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Daisuke Noshiro
- Division of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasuko Ono
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Mayumi Shindo
- Advanced Technical Support Department, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Tomohisa Hatta
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan
| | - Takefumi Uemura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan
| | - Hyeon-Cheol Lee-Okada
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Takehiko Yokomizo
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan
| | - Tohru Natsume
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Hiroyuki Sorimachi
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, 108-8639, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan
| | - Nobuo N Noda
- Division of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
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41
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Song JX, Villagomes D, Zhao H, Zhu M. cGAS in nucleus: The link between immune response and DNA damage repair. Front Immunol 2022; 13:1076784. [PMID: 36591232 PMCID: PMC9797516 DOI: 10.3389/fimmu.2022.1076784] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
As the first barrier of host defense, innate immunity sets up the parclose to keep out external microbial or virus attacks. Depending on the type of pathogens, several cytoplasm pattern recognition receptors exist to sense the attacks from either foreign or host origins, triggering the immune response to battle with the infections. Among them, cGAS-STING is the major pathway that mainly responds to microbial DNA, DNA virus infections, or self-DNA, which mainly comes from genome instability by-product or released DNA from the mitochondria. cGAS was initially found functional in the cytoplasm, although intriguing evidence indicates that cGAS exists in the nucleus where it is involved in the DNA damage repair process. Because the close connection between DNA damage response and immune response and cGAS recognizes DNA in length-dependent but DNA sequence-independent manners, it is urgent to clear the function balance of cGAS in the nucleus versus cytoplasm and how it is shielded from recognizing the host origin DNA. Here, we outline the current conception of immune response and the regulation mechanism of cGAS in the nucleus. Furthermore, we will shed light on the potential mechanisms that are restricted to be taken away from self-DNA recognition, especially how post-translational modification regulates cGAS functions.
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Affiliation(s)
- Jia-Xian Song
- Institute for Translation Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Deana Villagomes
- Department of Molecular and Cellular Biology, University of California Davis, One Shields Avenue, Davis, CA, United States
| | - Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA, United States
| | - Min Zhu
- Institute for Translation Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China,*Correspondence: Min Zhu,
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42
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Molendijk J, Blazev R, Mills RJ, Ng YK, Watt KI, Chau D, Gregorevic P, Crouch PJ, Hilton JBW, Lisowski L, Zhang P, Reue K, Lusis AJ, Hudson JE, James DE, Seldin MM, Parker BL. Proteome-wide systems genetics identifies UFMylation as a regulator of skeletal muscle function. eLife 2022; 11:e82951. [PMID: 36472367 PMCID: PMC9833826 DOI: 10.7554/elife.82951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Improving muscle function has great potential to improve the quality of life. To identify novel regulators of skeletal muscle metabolism and function, we performed a proteomic analysis of gastrocnemius muscle from 73 genetically distinct inbred mouse strains, and integrated the data with previously acquired genomics and >300 molecular/phenotypic traits via quantitative trait loci mapping and correlation network analysis. These data identified thousands of associations between protein abundance and phenotypes and can be accessed online (https://muscle.coffeeprot.com/) to identify regulators of muscle function. We used this resource to prioritize targets for a functional genomic screen in human bioengineered skeletal muscle. This identified several negative regulators of muscle function including UFC1, an E2 ligase for protein UFMylation. We show UFMylation is up-regulated in a mouse model of amyotrophic lateral sclerosis, a disease that involves muscle atrophy. Furthermore, in vivo knockdown of UFMylation increased contraction force, implicating its role as a negative regulator of skeletal muscle function.
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Affiliation(s)
- Jeffrey Molendijk
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
- Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
- Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | | | - Yaan-Kit Ng
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
- Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Kevin I Watt
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
- Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Daryn Chau
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, IrvineIrvineUnited States
| | - Paul Gregorevic
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
- Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Peter J Crouch
- Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - James BW Hilton
- Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Leszek Lisowski
- Children's Medical Research Institute, University of SydneySydneyAustralia
- Military Institute of MedicineWarszawaPoland
| | - Peixiang Zhang
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Karen Reue
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Aldons J Lusis
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los AngelesLos AngelesUnited States
| | - James E Hudson
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Science, School of Medical Science, University of SydneySydneyAustralia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, IrvineIrvineUnited States
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
- Centre for Muscle Research, University of MelbourneMelbourneAustralia
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43
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Chung CH, Yoo HM. Emerging role of protein modification by UFM1 in cancer. Biochem Biophys Res Commun 2022; 633:61-63. [DOI: 10.1016/j.bbrc.2022.08.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 11/06/2022]
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44
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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45
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Peter JJ, Magnussen HM, DaRosa PA, Millrine D, Matthews SP, Lamoliatte F, Sundaramoorthy R, Kopito RR, Kulathu Y. A non-canonical scaffold-type E3 ligase complex mediates protein UFMylation. EMBO J 2022; 41:e111015. [PMID: 36121123 DOI: 10.15252/embj.2022111015] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Protein UFMylation, i.e., post-translational modification with ubiquitin-fold modifier 1 (UFM1), is essential for cellular and endoplasmic reticulum homeostasis. Despite its biological importance, we have a poor understanding of how UFM1 is conjugated onto substrates. Here, we use a rebuilding approach to define the minimal requirements of protein UFMylation. We find that the reported cognate E3 ligase UFL1 is inactive on its own and instead requires the adaptor protein UFBP1 to form an active E3 ligase complex. Structure predictions suggest the UFL1/UFBP1 complex to be made up of winged helix (WH) domain repeats. We show that UFL1/UFBP1 utilizes a scaffold-type E3 ligase mechanism that activates the UFM1-conjugating E2 enzyme, UFC1, for aminolysis. Further, we characterize a second adaptor protein CDK5RAP3 that binds to and forms an integral part of the ligase complex. Unexpectedly, we find that CDK5RAP3 inhibits UFL1/UFBP1 ligase activity in vitro. Results from reconstituting ribosome UFMylation suggest that CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26. In summary, our reconstitution approach reveals the biochemical basis of UFMylation and regulatory principles of this atypical E3 ligase complex.
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Affiliation(s)
- Joshua J Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Stephen P Matthews
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
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46
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Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet 2022; 23:563-580. [PMID: 35338361 DOI: 10.1038/s41576-022-00468-7] [Citation(s) in RCA: 297] [Impact Index Per Article: 148.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2022] [Indexed: 12/16/2022]
Abstract
Much has been learned since the early 1960s about histone post-translational modifications (PTMs) and how they affect DNA-templated processes at the molecular level. This understanding has been bolstered in the past decade by the identification of new types of histone PTM, the advent of new genome-wide mapping approaches and methods to deposit or remove PTMs in a locally and temporally controlled manner. Now, with the availability of vast amounts of data across various biological systems, the functional role of PTMs in important processes (such as transcription, recombination, replication, DNA repair and the modulation of genomic architecture) is slowly emerging. This Review explores the contribution of histone PTMs to the regulation of genome function by discussing when these modifications play a causative (or instructive) role in DNA-templated processes and when they are deposited as a consequence of such processes, to reinforce and record the event. Important advances in the field showing that histone PTMs can exert both direct and indirect effects on genome function are also presented.
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Affiliation(s)
- Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany.
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
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47
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Qin B, Yu J, Zhao F, Huang J, Zhou Q, Lou Z. Dynamic recruitment of UFM1-specific peptidase 2 to the DNA double-strand breaks regulated by WIP1. GENOME INSTABILITY & DISEASE 2022; 3:217-226. [PMID: 36042814 PMCID: PMC9418083 DOI: 10.1007/s42764-022-00076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/17/2022] [Accepted: 07/24/2022] [Indexed: 10/29/2022]
Abstract
The ufmylation ligase-UFL1 promotes ATM activation by monoufmylating H4 at K31 in a positive-feedback loop after double-strand breaks (DSB) occur, whereas UFM1 Specific Peptidase 2 (UfSP2) suppresses ATM activation, but the mechanism of recruitment of UfSP2 to the DSB finetuning DNA damage response is still not clear. Here, we report that UfSP2 foci formation is delayed compared to UFL1 foci formation following the radiation insult. Mechanistically, UfSP2 binds to the MRN complex in absence of DSB. Irradiation-induced phosphorylation of UfSP2 by ATM leads to the dissociation of UfSP2 from the MRN complex. This phosphorylation can be removed by the phosphatase WIP1, thereby UfSP2 is recruited to the DSBs, deufmylating H4 and suppressing ATM activation. In summary, we identify a mechanism of delicately negative modulation of ATM activation by UfSP2 and rewires ATM activation pathways.
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Affiliation(s)
- Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
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48
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Millrine D, Cummings T, Matthews SP, Peter JJ, Magnussen HM, Lange SM, Macartney T, Lamoliatte F, Knebel A, Kulathu Y. Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation. Cell Rep 2022; 40:111168. [PMID: 35926457 PMCID: PMC9638016 DOI: 10.1016/j.celrep.2022.111168] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/21/2022] [Accepted: 07/13/2022] [Indexed: 02/07/2023] Open
Abstract
An essential first step in the post-translational modification of proteins with UFM1, UFMylation, is the proteolytic cleavage of pro-UFM1 to expose a C-terminal glycine. Of the two UFM1-specific proteases (UFSPs) identified in humans, only UFSP2 is reported to be active, since the annotated sequence of UFSP1 lacks critical catalytic residues. Nonetheless, efficient UFM1 maturation occurs in cells lacking UFSP2, suggesting the presence of another active protease. We herein identify UFSP1 translated from a non-canonical start site to be this protease. Cells lacking both UFSPs show complete loss of UFMylation resulting from an absence of mature UFM1. While UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26, UFSP1 acts earlier in the pathway to mature UFM1 and cleave a potential autoinhibitory modification on UFC1, thereby controlling activation of UFMylation. In summary, our studies reveal important distinctions in substrate specificity and localization-dependent functions for the two proteases in regulating UFMylation.
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Affiliation(s)
- David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Thomas Cummings
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Stephen P Matthews
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Joshua J Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Helge M Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sven M Lange
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Thomas Macartney
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Frederic Lamoliatte
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Axel Knebel
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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49
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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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50
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Jing Y, Mao Z, Chen F. UFMylation System: An Emerging Player in Tumorigenesis. Cancers (Basel) 2022; 14:3501. [PMID: 35884562 PMCID: PMC9323365 DOI: 10.3390/cancers14143501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1), a newly identified ubiquitin-like molecule (UBLs), is evolutionarily expressed in multiple species except yeast. Similarly to ubiquitin, UFM1 is covalently attached to its substrates through a well-orchestrated three-step enzymatic reaction involving E1, the UFM1-activating enzyme (ubiquitin-like modifier-activating enzyme 5, UBA5); E2, the UFM1-conjugating enzyme 1 (UFC1); and E3, the UFM1-specific ligase 1 (UFL1). To date, numerous studies have shown that UFM1 modification is implicated in various cellular processes, including endoplasmic reticulum (ER) stress, DNA damage response and erythroid development. An abnormal UFM1 cascade is closely related to a variety of diseases, especially tumors. Herein, we summarize the process and functions of UFM1 modification, illustrating the relationship and mechanisms between aberrant UFMylation and diversified tumors, aiming to provide novel diagnostic biomarkers or therapeutic targets for cancer treatments.
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Affiliation(s)
| | | | - Fengling Chen
- Department of Endocrinology and Metabolism, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; (Y.J.); (Z.M.)
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