1
|
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.
Collapse
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
| |
Collapse
|
2
|
Lin M, Lian NZ, Cao LL, Huang CM, Zheng CH, Li P, Xie JW, Wang JB, Lu J, Chen QY, Li YH, Peng ZH, Zhang XY, Mei YX, Lin JX. Down-regulated expression of CDK5RAP3 and UFM1 suggests a poor prognosis in gastric cancer patients. Front Oncol 2022; 12:927751. [PMID: 36387125 PMCID: PMC9647057 DOI: 10.3389/fonc.2022.927751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2023] Open
Abstract
PURPOSE The relationship between the CDK5RAP3 and UFM1 expression and the prolonged outcomes of patients who underwent gastric cancer (GC) surgery was investigated. METHODS Single-sample gene set enrichment analysis (ssGSEA), unsupervised clustering and other methods were used to verify the relationship between CDK5RAP3 and UFM1 in GC through public databases. Additionally, CDK5RAP3 and UFM1 expression in cancerous and paracancerous tissues of GC was analysed in the context of patient prognosis. RESULTS CDK5RAP3 and UFM1 expression was downregulated synchronously, the interaction was observed between the two proteins, and UFM1 and CDK5RAP3 expression was found to be inversely associated to AKT pathway activation. Prognostic analysis showed that the prognosis is poorer for low CDK5RAP3 and UFM1 patients, than for high CDK5RAP3 and/or UFM1 (p<0.001) patients, and this expression pattern was an independent predictor for overall survival of GC. Coexpression of CDK5RAP3 and UFM1 combined with TNM staging can improve the accuracy of prognosis prediction for patients (p <0.001). CONCLUSIONS It is confirmed in our findings that a combination of CDK5RAP3 and UFM1 can produce a more precise prediction model for GC patients' survival.
Collapse
Affiliation(s)
- Mi Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Ning-Zi Lian
- Department of Gynecology, Fujian Obstetrics and Gynecology Hospital, Fuzhou, China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Ya-Han Li
- The Union Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Zhu-Huai Peng
- The Union Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiao-Yu Zhang
- The Union Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Yi-Xian Mei
- The Union Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| |
Collapse
|
3
|
Lehallier B, Shokhirev MN, Wyss‐Coray T, Johnson AA. Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. Aging Cell 2020; 19:e13256. [PMID: 33031577 PMCID: PMC7681068 DOI: 10.1111/acel.13256] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/21/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022] Open
Abstract
We previously identified 529 proteins that had been reported by multiple different studies to change their expression level with age in human plasma. In the present study, we measured the q-value and age coefficient of these proteins in a plasma proteomic dataset derived from 4263 individuals. A bioinformatics enrichment analysis of proteins that significantly trend toward increased expression with age strongly implicated diverse inflammatory processes. A literature search revealed that at least 64 of these 529 proteins are capable of regulating life span in an animal model. Nine of these proteins (AKT2, GDF11, GDF15, GHR, NAMPT, PAPPA, PLAU, PTEN, and SHC1) significantly extend life span when manipulated in mice or fish. By performing machine-learning modeling in a plasma proteomic dataset derived from 3301 individuals, we discover an ultra-predictive aging clock comprised of 491 protein entries. The Pearson correlation for this clock was 0.98 in the learning set and 0.96 in the test set while the median absolute error was 1.84 years in the learning set and 2.44 years in the test set. Using this clock, we demonstrate that aerobic-exercised trained individuals have a younger predicted age than physically sedentary subjects. By testing clocks associated with 1565 different Reactome pathways, we also show that proteins associated with signal transduction or the immune system are especially capable of predicting human age. We additionally generate a multitude of age predictors that reflect different aspects of aging. For example, a clock comprised of proteins that regulate life span in animal models accurately predicts age.
Collapse
Affiliation(s)
- Benoit Lehallier
- Department of Neurology and Neurological SciencesStanford UniversityStanfordCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford UniversityStanfordCaliforniaUSA
- Paul F. Glenn Center for the Biology of AgingStanford UniversityStanfordCaliforniaUSA
| | - Maxim N. Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics CoreThe Salk Institute for Biological StudiesLa JollaCaliforniaUSA
| | - Tony Wyss‐Coray
- Department of Neurology and Neurological SciencesStanford UniversityStanfordCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford UniversityStanfordCaliforniaUSA
- Paul F. Glenn Center for the Biology of AgingStanford UniversityStanfordCaliforniaUSA
- Department of Veterans AffairsVA Palo Alto Health Care SystemPalo AltoCaliforniaUSA
| | | |
Collapse
|
4
|
Lin JX, Xie XS, Weng XF, Qiu SL, Yoon C, Lian NZ, Xie JW, Wang JB, Lu J, Chen QY, Cao LL, Lin M, Tu RH, Yang YH, Huang CM, Zheng CH, Li P. UFM1 suppresses invasive activities of gastric cancer cells by attenuating the expres7sion of PDK1 through PI3K/AKT signaling. J Exp Clin Cancer Res 2019; 38:410. [PMID: 31533855 PMCID: PMC6751655 DOI: 10.1186/s13046-019-1416-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND UFM1 has been found to be involved in the regulation of tumor development. This study aims to clarify the role and potential molecular mechanisms of UFM1 in the invasion and metastasis of gastric cancer. METHODS Expression of UFM1 in gastric tumor and paired adjacent noncancerous tissues from 437 patients was analyzed by Western blotting, immunohistochemistry, and realtime PCR. Its correlation with the clinicopathological characteristics and prognosis of gastric cancer patients was analyzed. The effects of UFM1 on the invasion and migration of gastric cancer cells were determined by the wound and trans-well assays, and the effect of UFM1 on subcutaneous tumor formation was verified in nude mice. The potential downstream targets of UFM1 and related molecular mechanisms were clarified by the human protein kinase assay and co-immunoprecipitation technique. RESULTS Compared with the corresponding adjacent tissues, the transcription level and protein expression level of UFM1 in gastric cancer tissues were significantly downregulated (P < 0.05). The 5-year survival rate of gastric cancer patients with low UFM1 expression was significantly lower than the patients with high UFM1 expression (42.1% vs 63.0%, P < 0.05). The invasion and migration abilities of gastric cancer cells with stable UFM1 overexpression were significantly decreased, and the gastric cancer cells with UFM1 stable knockdown showed the opposite results; similar results were also obtained in the nude mouse model. Further studies have revealed that UFM1 could increase the ubiquitination level of PDK1 and decrease the expression of PDK1 at protein level, thereby inhibiting the phosphorylation level of AKT at Ser473. Additionally, the effect of UFM1 on gastric cancer cell function is dependent on the expression of PDK1. The expression level of UFM1 can improve the poor prognosis of PDK1 in patients with gastric cancer. CONCLUSION UFM1 suppresses the invasion and metastasis of gastric cancer by increasing the ubiquitination of PDK1 through negatively regulating PI3K/AKT signaling.
Collapse
Affiliation(s)
- Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Xin-Sheng Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Xiong-Feng Weng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Sheng-Liang Qiu
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
| | - Changhwan Yoon
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ning-Zi Lian
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Mi Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Ru-Hong Tu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Ying-Hong Yang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350108 Fujian Province China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350108 Fujian Province China
| |
Collapse
|
5
|
An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. J Mol Biol 2018; 431:463-478. [PMID: 30412706 DOI: 10.1016/j.jmb.2018.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/06/2023]
Abstract
Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.
Collapse
|
6
|
Gendron St-Marseille AF, Lord E, Véronneau PY, Brodeur J, Mimee B. Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode. FRONTIERS IN PLANT SCIENCE 2018; 9:987. [PMID: 30065735 PMCID: PMC6056837 DOI: 10.3389/fpls.2018.00987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Determining the adaptive potential of alien invasive species in a new environment is a key concern for risk assessment. As climate change is affecting local climatic conditions, widespread modifications in species distribution are expected. Therefore, the genetic mechanisms underlying local adaptations must be understood in order to predict future species distribution. The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a major pathogen of soybean that was accidentally introduced in most soybean-producing countries. In this study, we explored patterns of genetic exchange between North American populations of SCN and the effect of isolation by geographical distance. Genotyping-by-sequencing was used to sequence and compare 64 SCN populations from the United States and Canada. At large scale, only a weak correlation was found between genetic distance (Wright's fixation index, FST) and geographic distance, but local effects were strong in recently infested states. Our results also showed a high level of genetic differentiation within some populations, allowing them to adapt to new environments and become established in new soybean-producing areas. Bayesian genome scan methods identified 15 loci under selection for climatic or geographic co-variables. Among these loci, two non-synonymous mutations were detected in SMAD-4 (mothers against decapentaplegic homolog 4) and DOP-3 (dopamine receptor 3). High-impact variants linked to these loci by genetic hitchhiking were also highlighted as putatively involved in local adaptation of SCN populations to new environments. Overall, it appears that strong selective pressure by resistant cultivars is causing a large scale homogenization with virulent populations.
Collapse
Affiliation(s)
- Anne-Frédérique Gendron St-Marseille
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC, Canada
| | - Etienne Lord
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Pierre-Yves Véronneau
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Jacques Brodeur
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC, Canada
| | - Benjamin Mimee
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| |
Collapse
|
7
|
Al Saiqali M, Tangutur AD, Banoth C, Bhukya B. Antimicrobial and anticancer potential of low molecular weight polypeptides extracted and characterized from leaves of Azadirachta indica. Int J Biol Macromol 2018; 114:906-921. [DOI: 10.1016/j.ijbiomac.2018.03.169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/25/2018] [Accepted: 03/27/2018] [Indexed: 12/11/2022]
|
8
|
Mignon-Ravix C, Milh M, Kaiser CS, Daniel J, Riccardi F, Cacciagli P, Nagara M, Busa T, Liebau E, Villard L. Abnormal function of the UBA5 protein in a case of early developmental and epileptic encephalopathy with suppression-burst. Hum Mutat 2018; 39:934-938. [PMID: 29663568 DOI: 10.1002/humu.23534] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 01/19/2023]
Abstract
Early myoclonic epilepsy (EME) or Aicardi syndrome is one of the most severe epileptic syndromes affecting neonates. We performed whole exome sequencing in a sporadic case affected by EME and his parents. In the proband, we identified a homozygous missense variant in the ubiquitin-like modifier activating enzyme 5 (UBA5) gene, encoding a protein involved in post-translational modifications. Functional analysis of the UBA5 variant protein reveals that it is almost completely unable to perform its trans-thiolation activity. Although recessive variants in UBA5 have recently been associated with epileptic encephalopathy, variants in this gene have never been reported to cause EME. Our results further demonstrate the importance of post-translational modifications such as the addition of an ubiquitin-fold modifier 1 (UFM1) to target proteins (ufmylation) for normal neuronal networks activity, and reveal that the dysfunction of the ubiquitous UBA5 protein is a cause of EME.
Collapse
Affiliation(s)
- Cécile Mignon-Ravix
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France
| | - Mathieu Milh
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Service de Neurologie Pédiatrique, Hôpital d'Enfants de La Timone, Marseille, France
| | | | - Jens Daniel
- Department of Molecular Physiology, University of Muenster, Muenster, Germany
| | - Florence Riccardi
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - Pierre Cacciagli
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - Majdi Nagara
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France
| | - Tiffany Busa
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - Eva Liebau
- Department of Molecular Physiology, University of Muenster, Muenster, Germany
| | - Laurent Villard
- Aix Marseille Univ, Inserm, UMR-S 1251, MMG, Faculté de Médecine, Marseille, France.,Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| |
Collapse
|
9
|
Trans-Binding Mechanism of Ubiquitin-like Protein Activation Revealed by a UBA5-UFM1 Complex. Cell Rep 2018; 16:3113-3120. [PMID: 27653677 DOI: 10.1016/j.celrep.2016.08.067] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/07/2016] [Accepted: 08/19/2016] [Indexed: 01/14/2023] Open
Abstract
Modification of proteins by ubiquitin or ubiquitin-like proteins (UBLs) is a critical cellular process implicated in a variety of cellular states and outcomes. A prerequisite for target protein modification by a UBL is the activation of the latter by activating enzymes (E1s). Here, we present the crystal structure of the non-canonical homodimeric E1, UBA5, in complex with its cognate UBL, UFM1, and supporting biochemical experiments. We find that UBA5 binds to UFM1 via a trans-binding mechanism in which UFM1 interacts with distinct sites in both subunits of the UBA5 dimer. This binding mechanism requires a region C-terminal to the adenylation domain that brings UFM1 to the active site of the adjacent UBA5 subunit. We also find that transfer of UFM1 from UBA5 to the E2, UFC1, occurs via a trans mechanism, thereby requiring a homodimer of UBA5. These findings explicitly elucidate the role of UBA5 dimerization in UFM1 activation.
Collapse
|
10
|
Mashahreh B, Hassouna F, Soudah N, Cohen-Kfir E, Strulovich R, Haitin Y, Wiener R. Trans-binding of UFM1 to UBA5 stimulates UBA5 homodimerization and ATP binding. FASEB J 2018; 32:2794-2802. [PMID: 29295865 DOI: 10.1096/fj.201701057r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
All ubiquitin-like proteins (UBLs) undergo an activation process before their conjugation to target proteins. Although the steps required for the activation of UBLs are conserved and common to all UBLs, we have previously shown that the activation of the UBL, ubiquitin fold modifier 1 (UFM1) by the E1, Ufm1 modifier-activating enzyme 5 (UBA5) is executed in a trans-binding mechanism, not observed in any other E1. In this study, we explored the necessity of that mechanism for UFM1 activation and found that it is needed not only for UFM1 binding to UBA5 but also for stabilizing the UBA5 homodimer. Although UBA5 functions as a dimer, in solution it behaves as a weak dimer. Dimerization of UBA5 is required for ATP binding; therefore, stabilization of the dimer by UFM1 enhances ATP binding. Our results make a connection between the binding of UFM1 to UBA5 and the latter's affinity to ATP, so we propose a novel mechanism for the regulation of ATP's binding to E1.-Mashahreh, B., Hassouna, F., Soudah, N., Cohen-Kfir, E., Strulovich, R., Haitin, Y., Wiener, R. Trans-binding of UFM1 to UBA5 stimulates UBA5 homodimerization and ATP binding.
Collapse
Affiliation(s)
- Bayan Mashahreh
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Fouad Hassouna
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nadine Soudah
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Roi Strulovich
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
11
|
Wang Z, Zhu WG, Xu X. Ubiquitin-like modifications in the DNA damage response. Mutat Res 2017; 803-805:56-75. [PMID: 28734548 DOI: 10.1016/j.mrfmmm.2017.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/03/2017] [Accepted: 07/03/2017] [Indexed: 12/14/2022]
Abstract
Genomic DNA is damaged at an extremely high frequency by both endogenous and environmental factors. An improper response to DNA damage can lead to genome instability, accelerate the aging process and ultimately cause various human diseases, including cancers and neurodegenerative disorders. The mechanisms that underlie the cellular DNA damage response (DDR) are complex and are regulated at many levels, including at the level of post-translational modification (PTM). Since the discovery of ubiquitin in 1975 and ubiquitylation as a form of PTM in the early 1980s, a number of ubiquitin-like modifiers (UBLs) have been identified, including small ubiquitin-like modifiers (SUMOs), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), interferon-stimulated gene 15 (ISG15), human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), ubiquitin-fold modifier 1 (UFRM1), URM1 ubiquitin-related modifier-1 (URM1), autophagy-related protein 12 (ATG12), autophagy-related protein 8 (ATG8), fan ubiquitin-like protein 1 (FUB1) and histone mono-ubiquitylation 1 (HUB1). All of these modifiers have known roles in the cellular response to various forms of stress, and delineating their underlying molecular mechanisms and functions is fundamental in enhancing our understanding of human disease and longevity. To date, however, the molecular mechanisms and functions of these UBLs in the DDR remain largely unknown. This review summarizes the current status of PTMs by UBLs in the DDR and their implication in cancer diagnosis, therapy and drug discovery.
Collapse
Affiliation(s)
- Zhifeng Wang
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China; Beijing Key Laboratory of DNA Damage Response, Capital Normal University College of Life Sciences, Beijing 100048, China.
| |
Collapse
|
12
|
Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Sci Rep 2017; 7:508. [PMID: 28360427 PMCID: PMC5428781 DOI: 10.1038/s41598-017-00610-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/06/2017] [Indexed: 02/06/2023] Open
Abstract
The modification of proteins by ubiquitin-fold modifier 1 (UFM1) is implicated in many human diseases. Prior to conjugation, UFM1 undergoes activation by its cognate activating enzyme, UBA5. UBA5 is a non-canonical E1 activating enzyme that possesses an adenylation domain but lacks a distinct cysteine domain. Binding of UBA5 to UFM1 is mediated via an amino acid sequence, known as the UFM1-interacting sequence (UIS), located outside the adenylation domain that is required for UFM1 activation. However, the precise boundaries of the UIS are yet not clear and are still under debate. Here we revisit the interaction of UFM1 with UBA5 by determining the crystal structure of UFM1 fused to 13 amino acids of human UBA5. Using binding and activity assays, we found that His 336 of UBA5, previously not reported to be part of the UIS, occupies a negatively charged pocket on UFM1’s surface. This His is involved in UFM1 binding and if mutated perturbs activation of UFM1. Surprisingly, we also found that the interaction between two UFM1 molecules mimics how the UIS binds UFM1. Specifically, UFM1 His 70 resembles UBA5 His336 and enters a negatively charged pocked on the other UFM1 molecule. Our results refine our understanding of UFM1-UBA5 binding.
Collapse
|
13
|
Ishimura R, Obata M, Kageyama S, Daniel J, Tanaka K, Komatsu M. A novel approach to assess the ubiquitin-fold modifier 1-system in cells. FEBS Lett 2016; 591:196-204. [PMID: 27926783 DOI: 10.1002/1873-3468.12518] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 11/20/2016] [Accepted: 11/24/2016] [Indexed: 12/17/2022]
Abstract
The ubiquitin-fold modifier 1 (UFM1)-system, a ubiquitin-like protein conjugation system, is involved in the development of breast cancer and several hereditary neurological syndromes. However, the molecular mechanisms of UFM1-related pathogenesis remain unclear. Here, we show that in the absence of UFSP2, a deconjugating enzyme for UFM1, ectopic expression of both UFL1 and UFBP1, which serve as the E3-ligase complex for the UFM1-system, dramatically increases UFM1-conjugate formation at the endoplasmic reticulum. Utilizing this system, we were able to attribute disease-related isoforms of UBA5, the E1 enzyme for UFM1, to decreased UFM1-conjugate formation. Our procedure allows the assessment of UFM1-conjugate formation in cells and the identification of UFM1-targets, both of which are needed to clarify the pathophysiological role of the UFM1-system.
Collapse
Affiliation(s)
- Ryosuke Ishimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Japan.,Laboratory of Protein Metabolism, The Tokyo Metropolitan Institute of Medical Science, Japan
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Shun Kageyama
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Jens Daniel
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, The Tokyo Metropolitan Institute of Medical Science, Japan
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Japan
| |
Collapse
|
14
|
Multifunctional Thioredoxin-Like Protein from the Gastrointestinal Parasitic Nematodes Strongyloides ratti and Trichuris suis Affects Mucosal Homeostasis. J Parasitol Res 2016; 2016:8421597. [PMID: 27872753 PMCID: PMC5107843 DOI: 10.1155/2016/8421597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/30/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022] Open
Abstract
The cellular redox state is important for the regulation of multiple functions and is essential for the maintenance of cellular homeostasis and antioxidant defense. In the excretory/secretory (E/S) products of Strongyloides ratti and Trichuris suis sequences for thioredoxin (Trx) and Trx-like protein (Trx-lp) were identified. To characterize the antioxidant Trx-lp and its interaction with the parasite's mucosal habitat, S. ratti and T. suis Trx-lps were cloned and recombinantly expressed. The primary antioxidative activity was assured by reduction of insulin and IgM. Further analysis applying an in vitro mucosal 3D-cell culture model revealed that the secreted Trx-lps were able to bind to monocytic and intestinal epithelial cells and induce the time-dependent release of cytokines such as TNF-α, IL-22, and TSLP. In addition, the redox proteins also possessed chemotactic activity for monocytic THP-1 cells and fostered epithelial wound healing activity. These results confirm that the parasite-secreted Trx-lps are multifunctional proteins that can affect the host intestinal mucosa.
Collapse
|
15
|
Muona M, Ishimura R, Laari A, Ichimura Y, Linnankivi T, Keski-Filppula R, Herva R, Rantala H, Paetau A, Pöyhönen M, Obata M, Uemura T, Karhu T, Bizen N, Takebayashi H, McKee S, Parker MJ, Akawi N, McRae J, Hurles ME, Kuismin O, Kurki MI, Anttonen AK, Tanaka K, Palotie A, Waguri S, Lehesjoki AE, Komatsu M. Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy. Am J Hum Genet 2016; 99:683-694. [PMID: 27545674 DOI: 10.1016/j.ajhg.2016.06.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022] Open
Abstract
The ubiquitin fold modifier 1 (UFM1) cascade is a recently identified evolutionarily conserved ubiquitin-like modification system whose function and link to human disease have remained largely uncharacterized. By using exome sequencing in Finnish individuals with severe epileptic syndromes, we identified pathogenic compound heterozygous variants in UBA5, encoding an activating enzyme for UFM1, in two unrelated families. Two additional individuals with biallelic UBA5 variants were identified from the UK-based Deciphering Developmental Disorders study and one from the Northern Finland Intellectual Disability cohort. The affected individuals (n = 9) presented in early infancy with severe irritability, followed by dystonia and stagnation of development. Furthermore, the majority of individuals display postnatal microcephaly and epilepsy and develop spasticity. The affected individuals were compound heterozygous for a missense substitution, c.1111G>A (p.Ala371Thr; allele frequency of 0.28% in Europeans), and a nonsense variant or c.164G>A that encodes an amino acid substitution p.Arg55His, but also affects splicing by facilitating exon 2 skipping, thus also being in effect a loss-of-function allele. Using an in vitro thioester formation assay and cellular analyses, we show that the p.Ala371Thr variant is hypomorphic with attenuated ability to transfer the activated UFM1 to UFC1. Finally, we show that the CNS-specific knockout of Ufm1 in mice causes neonatal death accompanied by microcephaly and apoptosis in specific neurons, further suggesting that the UFM1 system is essential for CNS development and function. Taken together, our data imply that the combination of a hypomorphic p.Ala371Thr variant in trans with a loss-of-function allele in UBA5 underlies a severe infantile-onset encephalopathy.
Collapse
Affiliation(s)
- Mikko Muona
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00290, Finland; Folkhälsan Institute of Genetics, Helsinki 00290, Finland; Neuroscience Center, University of Helsinki, Helsinki 00290, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki 00290, Finland
| | - Ryosuke Ishimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan; Laboratory of Protein Metabolism, The Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Anni Laari
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland; Neuroscience Center, University of Helsinki, Helsinki 00290, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki 00290, Finland
| | - Yoshinobu Ichimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Tarja Linnankivi
- Department of Child Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
| | - Riikka Keski-Filppula
- PEDEGO Research Unit, University of Oulu, Oulu 90014, Finland; Medical Research Center Oulu, University of Oulu, Oulu 90014, Finland; Department of Clinical Genetics, Oulu University Hospital, Oulu 90029, Finland
| | - Riitta Herva
- Department of Pathology, Cancer and Translational Medicine Research Unit, Medical Research Center Oulu (MRC Oulu), Oulu University Hospital and University of Oulu, Oulu 90014, Finland
| | - Heikki Rantala
- PEDEGO Research Unit, University of Oulu, Oulu 90014, Finland; Medical Research Center Oulu, University of Oulu, Oulu 90014, Finland; Department of Children and Adolescents, Division of Paediatric Neurology, Oulu University Hospital, Oulu 90029, Finland
| | - Anders Paetau
- Department of Pathology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00290, Finland
| | - Minna Pöyhönen
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Takefumi Uemura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima 960-1295, Japan
| | - Thomas Karhu
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland; Neuroscience Center, University of Helsinki, Helsinki 00290, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki 00290, Finland
| | - Norihisa Bizen
- Division of Neurobiology and Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Shane McKee
- Department of Genetic Medicine, Belfast City Hospital, Belfast BT9 7AB, UK
| | - Michael J Parker
- Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield S10 2TH, UK
| | - Nadia Akawi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jeremy McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Outi Kuismin
- PEDEGO Research Unit, University of Oulu, Oulu 90014, Finland; Medical Research Center Oulu, University of Oulu, Oulu 90014, Finland; Department of Clinical Genetics, Oulu University Hospital, Oulu 90029, Finland
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00290, Finland; Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio 70029, Finland; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Anna-Kaisa Anttonen
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland; Neuroscience Center, University of Helsinki, Helsinki 00290, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki 00290, Finland; Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, The Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00290, Finland; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA; Program in Genetics and Genomics, Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02114, USA; Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima 960-1295, Japan
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki 00290, Finland; Neuroscience Center, University of Helsinki, Helsinki 00290, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki 00290, Finland.
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan.
| |
Collapse
|
16
|
Colin E, Daniel J, Ziegler A, Wakim J, Scrivo A, Haack TB, Khiati S, Denommé AS, Amati-Bonneau P, Charif M, Procaccio V, Reynier P, Aleck KA, Botto LD, Herper CL, Kaiser CS, Nabbout R, N'Guyen S, Mora-Lorca JA, Assmann B, Christ S, Meitinger T, Strom TM, Prokisch H, Miranda-Vizuete A, Hoffmann GF, Lenaers G, Bomont P, Liebau E, Bonneau D. Biallelic Variants in UBA5 Reveal that Disruption of the UFM1 Cascade Can Result in Early-Onset Encephalopathy. Am J Hum Genet 2016; 99:695-703. [PMID: 27545681 DOI: 10.1016/j.ajhg.2016.06.030] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/28/2016] [Indexed: 01/10/2023] Open
Abstract
Via whole-exome sequencing, we identified rare autosomal-recessive variants in UBA5 in five children from four unrelated families affected with a similar pattern of severe intellectual deficiency, microcephaly, movement disorders, and/or early-onset intractable epilepsy. UBA5 encodes the E1-activating enzyme of ubiquitin-fold modifier 1 (UFM1), a recently identified ubiquitin-like protein. Biochemical studies of mutant UBA5 proteins and studies in fibroblasts from affected individuals revealed that UBA5 mutations impair the process of ufmylation, resulting in an abnormal endoplasmic reticulum structure. In Caenorhabditis elegans, knockout of uba-5 and of human orthologous genes in the UFM1 cascade alter cholinergic, but not glutamatergic, neurotransmission. In addition, uba5 silencing in zebrafish decreased motility while inducing abnormal movements suggestive of seizures. These clinical, biochemical, and experimental findings support our finding of UBA5 mutations as a pathophysiological cause for early-onset encephalopathies due to abnormal protein ufmylation.
Collapse
Affiliation(s)
- Estelle Colin
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Jens Daniel
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany
| | - Alban Ziegler
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Jamal Wakim
- UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Aurora Scrivo
- Avenir-Atip team, INSERM U1051, Institute of Neurosciences of Montpellier, University of Montpellier, 34091 Montpellier Cedex 5, France
| | - Tobias B Haack
- Institute of Human Genetics, Technische Universität München, 81675 München, Germany
| | - Salim Khiati
- UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Anne-Sophie Denommé
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Patrizia Amati-Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Majida Charif
- UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Pascal Reynier
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Kyrieckos A Aleck
- Department of Genetics and Metabolism, Phoenix Children's Medical Group, Phoenix, AZ 85016, USA
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT 84132, USA
| | - Claudia Lena Herper
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany
| | - Charlotte Sophia Kaiser
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany
| | - Rima Nabbout
- Department of Pediatric Neurology, National Reference Center for Rare Epilepsies, University Hospital Necker-Enfants-Malades, 75015 Paris, France
| | - Sylvie N'Guyen
- Department of Pediatric Neurology, University Hospital, 49933 Angers Cedex 9, France
| | - José Antonio Mora-Lorca
- Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Birgit Assmann
- Department of General Pediatrics, Division of Pediatric Metabolic Medicine and Neuropediatrics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Stine Christ
- Department of General Pediatrics, Division of Pediatric Metabolic Medicine and Neuropediatrics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, 81675 München, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, 81675 München, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, 81675 München, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Antonio Miranda-Vizuete
- Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Georg F Hoffmann
- Department of General Pediatrics, Division of Pediatric Metabolic Medicine and Neuropediatrics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Guy Lenaers
- UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France
| | - Pascale Bomont
- Avenir-Atip team, INSERM U1051, Institute of Neurosciences of Montpellier, University of Montpellier, 34091 Montpellier Cedex 5, France
| | - Eva Liebau
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933 Angers Cedex 9, France; UMR CNRS 6214-INSERM 1083 and PREMMI, University of Angers, 49933 Angers Cedex 9, France.
| |
Collapse
|
17
|
The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity. Biochem Biophys Res Commun 2016; 476:450-456. [PMID: 27240952 DOI: 10.1016/j.bbrc.2016.05.143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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.
Collapse
|
18
|
Wei Y, Xu X. UFMylation: A Unique & Fashionable Modification for Life. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:140-146. [PMID: 27212118 PMCID: PMC4936604 DOI: 10.1016/j.gpb.2016.04.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 04/22/2016] [Indexed: 10/28/2022]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is one of the newly-identified ubiquitin-like proteins. Similar to ubiquitin, UFM1 is conjugated to its target proteins by a three-step enzymatic reaction. The UFM1-activating enzyme, ubiquitin-like modifier-activating enzyme 5 (UBA5), serves as the E1 to activate UFM1; UFM1-conjugating enzyme 1 (UFC1) acts as the E2 to transfer the activated UFM1 to the active site of the E2; and the UFM1-specific ligase 1 (UFL1) acts as the E3 to recognize its substrate, transfer, and ligate the UFM1 from E2 to the substrate. This process is called ufmylation. UFM1 chains can be cleaved from its target proteins by UFM1-specific proteases (UfSPs), suggesting that the ufmylation modification is reversible. UFM1 cascade is conserved among nearly all of the eukaryotic organisms, but not in yeast, and associated with several cellular activities including the endoplasmic reticulum stress response and hematopoiesis. Furthermore, the UFM1 cascade is closely related to a series of human diseases. In this review, we summarize the molecular details of this reversible modification process, the recent progress of its functional studies, as well as its implication in tumorigenesis and potential therapeutic targets for cancer.
Collapse
Affiliation(s)
- Ying Wei
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China.
| |
Collapse
|
19
|
Duan R, Shi Y, Yu L, Zhang G, Li J, Lin Y, Guo J, Wang J, Shen L, Jiang H, Wang G, Tang B. UBA5 Mutations Cause a New Form of Autosomal Recessive Cerebellar Ataxia. PLoS One 2016; 11:e0149039. [PMID: 26872069 PMCID: PMC4752235 DOI: 10.1371/journal.pone.0149039] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/26/2016] [Indexed: 12/19/2022] Open
Abstract
Autosomal recessive cerebellar ataxia (ARCA) comprises a large and heterogeneous group of neurodegenerative disorders. For many affected patients, the genetic cause remains undetermined. Through whole-exome sequencing, we identified compound heterozygous mutations in ubiquitin-like modifier activating enzyme 5 gene (UBA5) in two Chinese siblings presenting with ARCA. Moreover, copy number variations in UBA5 or ubiquitin-fold modifier 1 gene (UFM1) were documented with the phenotypes of global developmental delays and gait disturbances in the ClinVar database. UBA5 encodes UBA5, the ubiquitin-activating enzyme of UFM1. However, a crucial role for UBA5 in human neurological disease remains to be reported. Our molecular study of UBA5-R246X revealed a dramatically decreased half-life and loss of UFM1 activation due to the absence of the catalytic cysteine Cys250. UBA5-K310E maintained its interaction with UFM1, although with less stability, which may affect the ability of this UBA5 mutant to activate UFM1. Drosophila modeling revealed that UBA5 knockdown induced locomotive defects and a shortened lifespan accompanied by aberrant neuromuscular junctions (NMJs). Strikingly, we found that UFM1 and E2 cofactor knockdown induced markedly similar phenotypes. Wild-type UBA5, but not mutant UBA5, significantly restored neural lesions caused by the absence of UBA5. The finding of a UBA5 mutation in cerebellar ataxia suggests that impairment of the UFM1 pathway may contribute to the neurological phenotypes of ARCA.
Collapse
Affiliation(s)
- Ranhui Duan
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
- * E-mail: (RD); (BT)
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan province, China
| | - Li Yu
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
| | - Gehan Zhang
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
| | - Jia Li
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
| | - Yunting Lin
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan province, China
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
- The Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan province, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan province, China
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
- The Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan province, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan province, China
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
- The Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan province, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan province, China
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
- The Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan province, China
| | - Guanghui Wang
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu province, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan province, China
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan province, China
- The Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan province, China
- * E-mail: (RD); (BT)
| |
Collapse
|
20
|
Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Mol Cell Proteomics 2015; 14:2922-35. [PMID: 26392051 DOI: 10.1074/mcp.m115.049684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 01/05/2023] Open
Abstract
The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress.
Collapse
Affiliation(s)
| | - Aman Prasad
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | | | | | - Kelson Zawack
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | | | - Frank C Schroeder
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | - Judith Kimble
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Joshua J Coon
- From the Departments of ‡Chemistry, §Biomolecular Chemistry, ¶Genome Center,
| |
Collapse
|
21
|
Chaum E, Winborn CS, Bhattacharya S. Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium. Mamm Genome 2015; 26:210-21. [PMID: 25963977 DOI: 10.1007/s00335-015-9568-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/02/2015] [Indexed: 01/04/2023]
Abstract
The tumor suppressor p53 is a major regulator of genes important for cell cycle arrest, senescence, apoptosis, and innate immunity, and has recently been implicated in retinal aging. In this study we sought to identify the genetic networks that regulate p53 function in the retina using quantitative trait locus (QTL) analysis. First we examined age-associated changes in the activation and expression levels of p53; known p53 target proteins and markers of innate immune system activation in primary retinal pigment epithelial (RPE) cells that were harvested from young and aged human donors. We observed increased expression of p53, activated caspase-1, CDKN1A, CDKN2A (p16INK4a), TLR4, and IFNα in aged primary RPE cell lines. We used the Hamilton Eye Institute (HEI) retinal dataset ( www.genenetwork.org ) to identify genomic loci that modulate expression of genes in the p53 pathway in recombinant inbred BXD mouse strains using a QTL systems biology-based approach. We identified a significant trans-QTL on chromosome 1 (region 172-177 Mb) that regulates the expression of Cdkn1a. Many of the genes in this QTL locus are involved in innate immune responses, including Fc receptors, interferon-inducible family genes, and formin 2. Importantly, we found an age-related increase in FCGR3A and FMN2 and a decrease in IFI16 levels in RPE cultures. There is a complex multigenic innate immunity locus that controls expression of genes in the p53 pathway in the RPE, which may play an important role in modulating age-related changes in the retina.
Collapse
Affiliation(s)
- Edward Chaum
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA,
| | | | | |
Collapse
|
22
|
RCAD/Ufl1, a Ufm1 E3 ligase, is essential for hematopoietic stem cell function and murine hematopoiesis. Cell Death Differ 2015; 22:1922-34. [PMID: 25952549 DOI: 10.1038/cdd.2015.51] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 12/18/2022] Open
Abstract
The Ufm1 conjugation system is a novel ubiquitin-like modification system, consisting of Ufm1, Uba5 (E1), Ufc1 (E2) and poorly characterized E3 ligase(s). RCAD/Ufl1 (also known as KIAA0776, NLBP and Maxer) was reported to function as a Ufm1 E3 ligase in ufmylation (Ufm1-mediated conjugation) of DDRGK1 and ASC1 proteins. It has also been implicated in estrogen receptor signaling, unfolded protein response (UPR) and neurodegeneration, yet its physiological function remains completely unknown. In this study, we report that RCAD/Ufl1 is essential for embryonic development, hematopoietic stem cell (HSC) survival and erythroid differentiation. Both germ-line and somatic deletion of RCAD/Ufl1 impaired hematopoietic development, resulting in severe anemia, cytopenia and ultimately animal death. Depletion of RCAD/Ufl1 caused elevated endoplasmic reticulum stress and evoked UPR in bone marrow cells. In addition, loss of RCAD/Ufl1 blocked autophagic degradation, increased mitochondrial mass and reactive oxygen species, and led to DNA damage response, p53 activation and enhanced cell death of HSCs. Collectively, our study provides the first genetic evidence for the indispensable role of RCAD/Ufl1 in murine hematopoiesis and development. The finding of RCAD/Ufl1 as a key regulator of cellular stress response sheds a light into the role of a novel protein network including RCAD/Ufl1 and its associated proteins in regulating cellular homeostasis.
Collapse
|
23
|
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: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
24
|
Xie S. Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus-Ufc1 complex. Acta Crystallogr F Struct Biol Commun 2014; 70:1093-7. [PMID: 25084390 PMCID: PMC4118812 DOI: 10.1107/s2053230x14014502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Human Uba5, which contains an adenylation domain and a C-terminal region, is the smallest ubiquitin-like molecule-activating enzyme. The mechanism through which the enzyme recognizes Ufc1 and catalyzes the formation of the Ufc1-Ufm1 complex remains unknown. In this study, Uba5 residues 364-404 were demonstrated to be necessary for the transthiolation of Ufm1 to Ufc1, and Uba5 381-404 was identified to be the minimal region for Ufc1 recognition. The fusion protein between Uba5 381-404 and Ufc1 was cloned, expressed and purified, and exists as a homodimer in solution. Crystallization was performed at 293 K using PEG 4000 as precipitant; the optimized crystals diffracted to 3.0 Å resolution and had unit-cell parameters a = b = 82.49, c = 62.47 Å, α = β = 90, γ = 120°. With one fusion-protein molecule in the asymmetric unit, the Matthews coefficient and solvent content were calculated to be 2.55 Å(3) Da(-1) and 51.84%, respectively.
Collapse
Affiliation(s)
- Shutao Xie
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| |
Collapse
|
25
|
Daniel J, Liebau E. The ufm1 cascade. Cells 2014; 3:627-38. [PMID: 24921187 PMCID: PMC4092871 DOI: 10.3390/cells3020627] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 12/15/2022] Open
Abstract
The ubiquitin-fold modifier 1 (Ufm1) is a posttranslational modifier that belongs to the ubiquitin-like protein (UBL) family. Ufm1 is present in nearly all eukaryotic organisms, with the exception of fungi. It resembles ubiquitin in its ability to be ligated to other proteins, as well as in the mechanism of ligation. While the Ufm1 cascade has been implicated in endoplasmic reticulum functions and cell cycle control, its biological role still remains poorly understood. In this short review, we summarize the current state of Ufm1 research and its potential role in human diseases, like diabetes, ischemic heart disease and cancer.
Collapse
Affiliation(s)
- Jens Daniel
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Schlossplatz 8, D-48143 Münster, Germany.
| | - Eva Liebau
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Schlossplatz 8, D-48143 Münster, Germany.
| |
Collapse
|
26
|
Xie S. Characterization, crystallization and preliminary X-ray crystallographic analysis of the Uba5 fragment necessary for high-efficiency activation of Ufm1. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:765-8. [PMID: 24915089 DOI: 10.1107/s2053230x14008826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/17/2014] [Indexed: 12/18/2022]
Abstract
Uba5 is the smallest ubiquitin-like molecule-activating enzyme and contains an adenylation domain and a C-terminal region. This enzyme only exists in multicellular organisms. The mechanism through which the enzyme recognizes and activates ubiquitin-fold modifier 1 (Ufm1) remains unknown. In this study, Uba5 adenylation domains with different C-terminal region lengths were cloned, expressed and purified. The results of an in vitro truncation assay suggest that Uba5 residues 57-363 comprise the minimal fragment required for the high-efficiency activation of Ufm1. Crystallization of Uba5 residues 57-363 was performed at 277 K using PEG 3350 as the precipitant, and crystals optimized by microseeding diffracted to 2.95 Å resolution, with unit-cell parameters a=b=97.66, c=144.83 Å, α=β=90, γ=120°. There is one molecule in the asymmetric unit; the Matthews coefficient and the solvent content were calculated to be 2.93 Å3 Da(-1) and 58.1%, respectively.
Collapse
Affiliation(s)
- Shutao Xie
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| |
Collapse
|
27
|
An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. PLoS Genet 2014; 10:e1004082. [PMID: 24603482 PMCID: PMC3945108 DOI: 10.1371/journal.pgen.1004082] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 11/19/2013] [Indexed: 12/31/2022] Open
Abstract
Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4 and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene encodes a conserved tail-anchored transmembrane protein; the molecular identity of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4 also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding, maturation, or export from the ER. The physical interaction between human ODR4 and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues required for protease activity can rescue all odr-8 mutant phenotypes tested. Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia, either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and Ufm1-independent functions in GPCR biogenesis. Despite the importance of G-protein coupled receptors (GPCRs), we know little about their biogenesis. Olfactory receptors form a large and divergent group of GPCRs. We investigate their biogenesis in C. elegans. We show that maturation of a subset of these GPCRs, including the diacetyl receptor ODR-10, requires Ufm1 specific protease 2 (UfSP2), which corresponds to odr-8. Biochemical studies suggest mouse UfSP2 activates the Ubiquitin-like molecule Ufm1 and cleaves it from protein conjugates. However, neither the protease active site nor ufm-1 is required for UfSP2/ODR-8 to promote ODR-10 maturation. C. elegans UfSP2 is expressed in the same chemosensory neurons as ODR-4, a tail-anchored transmembrane protein also required for ODR-10 maturation. ODR-4 resides in the endoplasmic reticulum (ER); UfSP2 is cytosolic but associates with ER membranes. In odr-4 and odr-8 mutants ODR-10-GFP is retained in the ER, suggesting these genes are required to fold GPCRs or traffic them out of the ER. ODR-4 interacts biochemically with ODR-8 and ODR-10 to form an ER complex. ODR-4 and UfSP2 are conserved from plants to man, and human ODR4 can bind human UfSP2 and recruit it to ER membranes. Both proteins are expressed widely in mammals, suggesting a broader role in GPCR biogenesis.
Collapse
|
28
|
Ma L, Xie Y, Gu ZY, Wang BB, Li FC, Xu KZ, Shen WD, Li B. Characteristics of phoxim-exposed gene transcription in the silk gland of silkworms. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2013; 107:391-397. [PMID: 24267702 DOI: 10.1016/j.pestbp.2013.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 10/15/2013] [Accepted: 10/18/2013] [Indexed: 06/02/2023]
Abstract
Silkworm (Bombyx mori), a model Lepidoptera insect, is an important economic insect. Its silk gland is the important organ for silk protein synthesis and secretion. Phoxim exposure causes deficient cocooning of silkworm and has become one of the major negative factors for the silk industry. To study the impact of phoxim exposure on silk gland, using gene chip technology, we examined differentially expressed genes in silk gland after silkworms were exposed to phoxim (4.0μg/mL) for 24h. Functional annotation, classification and KEGG signaling pathway analysis were performed. The results showed that out of 3206 genes detected in silk gland after phoxim exposure, 270 were differentially expressed significantly, including 249 up-regulated genes and 21 down-regulated genes. These differentially expressed genes related to apoptosis, detoxification and protein degradation were selected. Using qRT-PCR, the expression levels of 9 genes involved in apoptosis, detoxification and protein degradation were validated. In addition, the expression profiles of three related fibroin synthesis genes (Fib-H, Fib-L and P25) were analyzed. Our results showed that phoxim exposure induced apoptosis of silk gland cells and inhibition of fibroin synthesis. This may be the cause of deficient silkworm cocooning.
Collapse
Affiliation(s)
- L Ma
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | | | | | | | | | | | | | | |
Collapse
|