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Jiajia H, Ziyao Y, Jiaqi Z, Yanli C, Xiaotao Z, Ming S. Screening UFMylation-associated genes in heart tissues of Ufm1-transgenic mice. BMC Cardiovasc Disord 2023; 23:567. [PMID: 37980507 PMCID: PMC10657630 DOI: 10.1186/s12872-023-03563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 10/15/2023] [Indexed: 11/20/2023] Open
Abstract
UFMylation is a ubiquitination-like modification that is related to endoplasmic reticulum stress and unfolded protein response. A recent study reported that Ufl1, a key enzyme of UFMylation, protects against heart failure, indicating that UFMylation may be associated with heart function regulation. In the present study, we initially constructed a Flag-6×His-tagged Ufm1ΔSC transgenic (Tg-Ufm1) mouse model that enables UFMylation studies in vivo. Tg-Ufm1 mice showed significant activation of UFMylation in hearts. By using this model, we identified 38 potential Ufm1-binding proteins in heart tissues through LC‒MS/MS methods. We found that these proteins were associated with mitochondria, metabolism and chaperone binding. By using transcriptomic screening, we identified Tnfaip2 as a novel UFMylation-associated gene. Overexpression of Ufm1 significantly upregulated the protein expression of Tnfaip2, whereas isoproterenol treatment decreased Tnfaip2 expression in Tg-Ufm1 mice. These data may provide novel clues for UFMylation in cardiac hypertrophy.
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Affiliation(s)
- Hu Jiajia
- Department of Clinical Laboratory, Peking University People's Hospital, No.11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yang Ziyao
- Department of Blood Transfusion, Peking University First Hospital, Beijing, China
| | - Zheng Jiaqi
- Department of Clinical Laboratory, Peking University People's Hospital, No.11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Chen Yanli
- Department of Clinical Laboratory, Peking University People's Hospital, No.11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Zhao Xiaotao
- Department of Clinical Laboratory, Peking University People's Hospital, No.11 Xizhimen South Street, Xicheng District, Beijing, 100044, China.
| | - Su Ming
- Department of Clinical Laboratory, Peking University People's Hospital, No.11 Xizhimen South Street, Xicheng District, Beijing, 100044, China.
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China.
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Ha BH, Kim KH, Yoo HM, Lee W, EunKyeong Kim E. The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity. Biochem Biophys Res Commun 2016; 476:450-6. [PMID: 27240952 DOI: 10.1016/j.bbrc.2016.05.143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 05/27/2016] [Indexed: 02/05/2023]
Abstract
Ubiquitin-fold modifier 1 (Ufm1) specific protease (UfSP) is a novel cysteine protease that activates Ufm1 from its precursor by processing the C-terminus to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. There are two forms: UfSP1 and UfSP2, the later with an additional domain at the N-terminus. Ufm1 and both the conjugating and deconjugating enzymes are highly conserved. However, in Caenorhabditis elegans there is one UfSP which has extra 136 residues at the N terminus compared to UfSP2. The crystal structure of cUfSP reveals that these additional residues display a MPN fold while the rest of the structure mimics that of UfSP2. The MPN domain does not have the metalloprotease activity found in some MPN-domain containing protein, rather it is required for the recognition and deufmylation of the substrate of cUfSP, UfBP1. In addition, the MPN domain is also required for localization to the endoplasmic reticulum.
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Abstract
The origin of the eukaryotic cell is one of the most important transitions in the history of life. However, the emergence and early evolution of eukaryotes remains poorly understood. Recent data have shown that the last eukaryotic common ancestor (LECA) was much more complex than previously thought. The LECA already had the genetic machinery encoding the endomembrane apparatus, spliceosome, nuclear pore, and myosin and kinesin cytoskeletal motors. It is unclear, however, when the functional regulation of these cellular components evolved. Here, we address this question by analyzing the origin and evolution of the ubiquitin (Ub) signaling system, one of the most important regulatory layers in eukaryotes. We delineated the evolution of the whole Ub, Small-Ub-related MOdifier (SUMO), and Ub-fold modifier 1 (Ufm1) signaling networks by analyzing representatives from all major eukaryotic, bacterial, and archaeal lineages. We found that the Ub toolkit had a pre-eukaryotic origin and is present in three extant archaeal groups. The pre-eukaryotic Ub toolkit greatly expanded during eukaryogenesis, through massive gene innovation and diversification of protein domain architectures. This resulted in a LECA with essentially all of the Ub-related genes, including the SUMO and Ufm1 Ub-like systems. Ub and SUMO signaling further expanded during eukaryotic evolution, especially labeling and delabeling enzymes responsible for substrate selection. Additionally, we analyzed protein domain architecture evolution and found that multicellular lineages have the most complex Ub systems in terms of domain architectures. Together, we demonstrate that the Ub system predates the origin of eukaryotes and that a burst of innovation during eukaryogenesis led to a LECA with complex posttranslational regulation.
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Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain Departament de Genètica, Universitat de Barcelona, Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Gavin JM, Hoar K, Xu Q, Ma J, Lin Y, Chen J, Chen W, Bruzzese FJ, Harrison S, Mallender WD, Bump NJ, Sintchak MD, Bence NF, Li P, Dick LR, Gould AE, Chen JJ. Mechanistic study of Uba5 enzyme and the Ufm1 conjugation pathway. J Biol Chem 2014; 289:22648-22658. [PMID: 24966333 PMCID: PMC4132772 DOI: 10.1074/jbc.m114.573972] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
E1 enzymes activate ubiquitin or ubiquitin-like proteins (Ubl) via an adenylate intermediate and initiate the enzymatic cascade of Ubl conjugation to target proteins or lipids. Ubiquitin-fold modifier 1 (Ufm1) is activated by the E1 enzyme Uba5, and this pathway is proposed to play an important role in the endoplasmic reticulum (ER) stress response. However, the mechanisms of Ufm1 activation by Uba5 and subsequent transfer to the conjugating enzyme (E2), Ufc1, have not been studied in detail. In this work, we found that Uba5 activated Ufm1 via a two-step mechanism and formed a binary covalent complex of Uba5∼Ufm1 thioester. This feature contrasts with the three-step mechanism and ternary complex formation in ubiquitin-activating enzyme Uba1. Uba5 displayed random ordered binding with Ufm1 and ATP, and its ATP-pyrophosphate (PPi) exchange activity was inhibited by both AMP and PPi. Ufm1 activation and Uba5∼Ufm1 thioester formation were stimulated in the presence of Ufc1. Furthermore, binding of ATP to Uba5∼Ufm1 thioester was required for efficient transfer of Ufm1 from Uba5 to Ufc1 via transthiolation. Consistent with the two-step activation mechanism, the mechanism-based pan-E1 inhibitor, adenosine 5'-sulfamate (ADS), reacted with the Uba5∼Ufm1 thioester and formed a covalent, tight-binding Ufm1-ADS adduct in the active site of Uba5, which prevented further substrate binding or catalysis. ADS was also shown to inhibit the Uba5 conjugation pathway in the HCT116 cells through formation of the Ufm1-ADS adduct. This suggests that further development of more selective Uba5 inhibitors could be useful in interrogating the roles of the Uba5 pathway in cells.
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Affiliation(s)
- James M Gavin
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139.
| | - Kara Hoar
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Qing Xu
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Jingya Ma
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Yafang Lin
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Jiejin Chen
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Wei Chen
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Frank J Bruzzese
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Sean Harrison
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - William D Mallender
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Nancy J Bump
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Michael D Sintchak
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Neil F Bence
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Ping Li
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Lawrence R Dick
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Alexandra E Gould
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Jesse J Chen
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139.
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Liu H, Li J, Tillman B, French BA, French SW. Ufmylation and FATylation pathways are downregulated in human alcoholic and nonalcoholic steatohepatitis, and mice fed DDC, where Mallory-Denk bodies (MDBs) form. Exp Mol Pathol 2014; 97:81-8. [PMID: 24893112 DOI: 10.1016/j.yexmp.2014.05.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 05/30/2014] [Indexed: 12/19/2022]
Abstract
We previously reported the mechanisms involved in the formation of Mallory-Denk bodies (MDBs) in mice fed DDC. To further provide clinical evidence as to how ubiquitin-like protein (Ubls) modification, gene transcript expression in Ufmylation and FATylation were investigated in human archived formalin-fixed, paraffin-embedded (FFPE) liver biopsies and frozen liver sections from DDC re-fed mice were used. Real-time PCR analysis showed that all Ufmylation molecules (Ufm1, Uba5, Ufc1, Ufl1 and UfSPs) were significantly downregulated, both in DDC re-fed mice livers and patients' livers where MDBs had formed, indicating that gene transcript changes were limited to MDB-forming livers where the protein quality control system was downregulated. FAT10 and subunits of the immunoproteasome (LMP2 and LMP7) were both upregulated as previously shown. An approximate 176- and 5-fold upregulation (respectively) of FAT10 was observed in the DDC re-fed mice liver and in the livers of human alcoholic hepatitis with MDBs present, implying that there was an important role played by this gene. The FAT10-specific E1 and E2 enzymes Uba6 and USE1, however, were found to be downregulated both in patients' livers and in the liver of DDC re-fed mice. Interestedly, the downregulation of mRNA levels was proportionate to MDB abundance in the liver tissues. Our results show the first systematic demonstration of transcript regulation of Ufmylation and FATylation in the liver of patients who form MDBs, where protein quality control is downregulated. This was also shown in the livers of DDC re-fed mice where MDBs had formed.
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Affiliation(s)
- H Liu
- Department of Pathology, LABioMed at Harbor UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90509, USA
| | - J Li
- Department of Pathology, LABioMed at Harbor UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90509, USA
| | - B Tillman
- Department of Pathology, LABioMed at Harbor UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90509, USA
| | - B A French
- Department of Pathology, LABioMed at Harbor UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90509, USA
| | - S W French
- Department of Pathology, LABioMed at Harbor UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90509, USA.
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