1
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Panichnantakul P, Aguilar LC, Daynard E, Guest M, Peters C, Vogel J, Oeffinger M. Protein UFMylation regulates early events during ribosomal DNA-damage response. Cell Rep 2024; 43:114738. [PMID: 39277864 DOI: 10.1016/j.celrep.2024.114738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 07/03/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
The highly repetitive and transcriptionally active ribosomal DNA (rDNA) genes are exceedingly susceptible to genotoxic stress. Induction of DNA double-strand breaks (DSBs) in rDNA repeats is associated with ataxia-telangiectasia-mutated (ATM)-dependent rDNA silencing and nucleolar reorganization where rDNA is segregated into nucleolar caps. However, the regulatory events underlying this response remain elusive. Here, we identify protein UFMylation as essential for rDNA-damage response in human cells. We further show the only ubiquitin-fold modifier 1 (UFM1)-E3 ligase UFL1 and its binding partner DDRGK1 localize to nucleolar caps upon rDNA damage and that UFL1 loss impairs ATM activation and rDNA transcriptional silencing, leading to reduced rDNA segregation. Moreover, analysis of nuclear and nucleolar UFMylation targets in response to DSB induction further identifies key DNA-repair factors including ATM, in addition to chromatin and actin network regulators. Taken together, our data provide evidence of an essential role for UFMylation in orchestrating rDNA DSB repair.
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Affiliation(s)
- Pudchalaluck Panichnantakul
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Lisbeth C Aguilar
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Evan Daynard
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Mackenzie Guest
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Colten Peters
- Department of Biology, Faculty of Medicine, McGill University, Montréal, QC H3A 1B1, Canada
| | - Jackie Vogel
- Department of Biology, Faculty of Medicine, McGill University, Montréal, QC H3A 1B1, Canada
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H4A 3J1, Canada; Département de biochimie et médicine moléculaire, Faculté de Médicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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2
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Chen Y, Dai R, Cheng M, Wang W, Liu C, Cao Z, Ge Y, Wang Y, Zhang L. Status and role of the ubiquitin-proteasome system in renal fibrosis. Biomed Pharmacother 2024; 178:117210. [PMID: 39059348 DOI: 10.1016/j.biopha.2024.117210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024] Open
Abstract
The ubiquitin-proteasome system (UPS) is a basic regulatory mechanism in cells that is essential for maintaining cell homeostasis, stimulating signal transduction, and determining cell fate. These biological processes require coordinated signaling cascades across members of the UPS to achieve substrate ubiquitination and deubiquitination. The role of the UPS in fibrotic diseases has attracted widespread attention, and the aberrant expression of UPS members affects the fibrosis process. In this review, we provide an overview of the UPS and its relevance for fibrotic diseases. Moreover, for the first time, we explore in detail how the UPS promotes or inhibits renal fibrosis by regulating biological processes such as signaling pathways, inflammation, oxidative stress, and the cell cycle, emphasizing the status and role of the UPS in renal fibrosis. Further research on this system may reveal new strategies for preventing renal fibrosis.
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Affiliation(s)
- Yizhen Chen
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Rong Dai
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Meng Cheng
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Weili Wang
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Chuanjiao Liu
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Zeping Cao
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Yong Ge
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Yiping Wang
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
| | - Lei Zhang
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
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3
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Li G, Huang Y, Han W, Wei L, Huang H, Zhu Y, Xiao Q, Wang Z, Huang W, Duan R. Eg5 UFMylation promotes spindle organization during mitosis. Cell Death Dis 2024; 15:544. [PMID: 39085203 PMCID: PMC11291904 DOI: 10.1038/s41419-024-06934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
UFMylation is a highly conserved ubiquitin-like post-translational modification that catalyzes the covalent linkage of UFM1 to its target proteins. This modification plays a critical role in the maintenance of endoplasmic reticulum proteostasis, DNA damage response, autophagy, and transcriptional regulation. Mutations in UFM1, as well as in its specific E1 enzyme UBA5 and E2 enzyme UFC1, have been genetically linked to microcephaly. Our previous research unveiled the important role of UFMylation in regulating mitosis. However, the underlying mechanisms have remained unclear due to the limited identification of substrates. In this study, we identified Eg5, a motor protein crucial for mitotic spindle assembly and maintenance, as a novel substrate for UFMylation and identified Lys564 as the crucial UFMylation site. UFMylation did not alter its transcriptional level, phosphorylation level, or protein stability, but affected the mono-ubiquitination of Eg5. During mitosis, Eg5 and UFM1 co-localize at the centrosome and spindle apparatus, and defective UFMylation leads to diminished spindle localization of Eg5. Notably, the UFMylation-defective Eg5 mutant (K564R) exhibited shorter spindles, metaphase arrest, spindle checkpoint activation, and a failure of cell division in HeLa cells. Overall, Eg5 UFMylation is essential for proper spindle organization, mitotic progression, and cell proliferation.
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Affiliation(s)
- Guangxu Li
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Yuanjiang Huang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Wenbo Han
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Liyi Wei
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Hongjing Huang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Yingbao Zhu
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Qiao Xiao
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Zujia Wang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Wen Huang
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Ranhui Duan
- Furong Laboratory, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China.
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4
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Yan T, Heckman MG, Craver EC, Liu CC, Rawlinson BD, Wang X, Murray ME, Dickson DW, Ertekin-Taner N, Lou Z, Bu G, Springer W, Fiesel FC. The UFMylation pathway is impaired in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595755. [PMID: 38903110 PMCID: PMC11188091 DOI: 10.1101/2024.05.24.595755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Background Alzheimer's disease (AD) is characterized by the presence of neurofibrillary tangles made of hyperphosphorylated tau and senile plaques composed of beta-amyloid. These pathognomonic deposits have been implicated in the pathogenesis, although the molecular mechanisms and consequences remain undetermined. UFM1 is an important, but understudied ubiquitin-like protein that is covalently attached to substrates. This UFMylation has recently been identified as major modifier of tau aggregation upon seeding in experimental models. However, potential alterations of the UFM1 pathway in human AD brain have not been investigated yet. Methods Here we used frontal and temporal cortex samples from individuals with or without AD to measure the protein levels of the UFMylation pathway in human brain. We used multivariable regression analyses followed by Bonferroni correction for multiple testing to analyze associations of the UFMylation pathway with neuropathological characteristics, primary biochemical measurements of tau and additional biochemical markers from the same cases. We further studied associations of the UFMylation cascade with cellular stress pathways using Spearman correlations with bulk RNAseq expression data and functionally validated these interactions using gene-edited neurons that were generated by CRISPR-Cas9. Results Compared to controls, human AD brain had increased protein levels of UFM1. Our data further indicates that this increase mainly reflects conjugated UFM1 indicating hyperUFMylation in AD. UFMylation was strongly correlated with pathological tau in both AD-affected brain regions. In addition, we found that the levels of conjugated UFM1 were negatively correlated with soluble levels of the deUFMylation enzyme UFSP2. Functional analysis of UFM1 and/or UFSP2 knockout neurons revealed that the DNA damage response as well as the unfolded protein response are perturbed by changes in neuronal UFM1 signaling. Conclusions There are marked changes in the UFMylation pathway in human AD brain. These changes are significantly associated with pathological tau, supporting the idea that the UFMylation cascade might indeed act as a modifier of tau pathology in human brain. Our study further nominates UFSP2 as an attractive target to reduce the hyperUFMylation observed in AD brain but also underscores the critical need to identify risks and benefits of manipulating the UFMylation pathway as potential therapeutic avenue for AD.
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Affiliation(s)
- Tingxiang Yan
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Michael G. Heckman
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, FL, USA
| | - Emily C. Craver
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, FL, USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Xue Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
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5
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Kandel R, Jung J, Neal S. Proteotoxic stress and the ubiquitin proteasome system. Semin Cell Dev Biol 2024; 156:107-120. [PMID: 37734998 PMCID: PMC10807858 DOI: 10.1016/j.semcdb.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
The ubiquitin proteasome system maintains protein homeostasis by regulating the breakdown of misfolded proteins, thereby preventing misfolded protein aggregates. The efficient elimination is vital for preventing damage to the cell by misfolded proteins, known as proteotoxic stress. Proteotoxic stress can lead to the collapse of protein homeostasis and can alter the function of the ubiquitin proteasome system. Conversely, impairment of the ubiquitin proteasome system can also cause proteotoxic stress and disrupt protein homeostasis. This review examines two impacts of proteotoxic stress, 1) disruptions to ubiquitin homeostasis (ubiquitin stress) and 2) disruptions to proteasome homeostasis (proteasome stress). Here, we provide a mechanistic description of the relationship between proteotoxic stress and the ubiquitin proteasome system. This relationship is illustrated by findings from several protein misfolding diseases, mainly neurodegenerative diseases, as well as from basic biology discoveries from yeast to mammals. In addition, we explore the importance of the ubiquitin proteasome system in endoplasmic reticulum quality control, and how proteotoxic stress at this organelle is alleviated. Finally, we highlight how cells utilize the ubiquitin proteasome system to adapt to proteotoxic stress and how the ubiquitin proteasome system can be genetically and pharmacologically manipulated to maintain protein homeostasis.
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Affiliation(s)
- Rachel Kandel
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Jasmine Jung
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Sonya Neal
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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6
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Komatsu M, Inada T, Noda NN. The UFM1 system: Working principles, cellular functions, and pathophysiology. Mol Cell 2024; 84:156-169. [PMID: 38141606 DOI: 10.1016/j.molcel.2023.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/21/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through UFMylation, a process similar to ubiquitylation. Growing lines of evidence regarding not only the structural basis of the components essential for UFMylation but also their biological properties shed light on crucial roles of the UFM1 system in the endoplasmic reticulum (ER), such as ER-phagy and ribosome-associated quality control at the ER, although there are some functions unrelated to the ER. Mouse genetics studies also revealed the indispensable roles of this system in hematopoiesis, liver development, neurogenesis, and chondrogenesis. Of critical importance, mutations of genes encoding core components of the UFM1 system in humans cause hereditary developmental epileptic encephalopathy and Schohat-type osteochondrodysplasia of the epiphysis. Here, we provide a multidisciplinary review of our current understanding of the mechanisms and cellular functions of the UFM1 system as well as its pathophysiological roles, and discuss issues that require resolution.
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Affiliation(s)
- Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan; Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan.
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7
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Zhou X, Mahdizadeh SJ, Le Gallo M, Eriksson LA, Chevet E, Lafont E. UFMylation: a ubiquitin-like modification. Trends Biochem Sci 2024; 49:52-67. [PMID: 37945409 DOI: 10.1016/j.tibs.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein-protein interactions, protein stability, and thus the functions of their protein targets. Here, we focus on the most recently identified UBL, ubiquitin-fold modifier 1 (UFM1), and the machinery responsible for its transfer to substrates (UFMylation) or its removal (deUFMylation). We first highlight the biochemical peculiarities of these processes, then we develop on how UFMylation and its machinery control various intertwined cellular processes and we highlight some of the outstanding research questions in this emerging field.
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Affiliation(s)
- Xingchen Zhou
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Sayyed J Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Matthieu Le Gallo
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
| | - Elodie Lafont
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
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8
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. eLife 2023; 12:RP89891. [PMID: 38079206 PMCID: PMC10712953 DOI: 10.7554/elife.89891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and endoplasmic reticulum stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least 12 different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remain to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Albert N Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Michael W Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for ChildrenBostonUnited States
| | - Jenny L Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science UniversityPortlandUnited States
| | - Ruth J Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
- VA Portland Health Care SystemPortlandUnited States
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science UniversityPortlandUnited States
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
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9
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Millrine D, Peter JJ, Kulathu Y. A guide to UFMylation, an emerging posttranslational modification. FEBS J 2023; 290:5040-5056. [PMID: 36680403 PMCID: PMC10952357 DOI: 10.1111/febs.16730] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Ubiquitin Fold Modifier-1 (UFM1) is a ubiquitin-like modifier (UBL) that is posttranslationally attached to lysine residues on substrates via a dedicated system of enzymes conserved in most eukaryotes. Despite the structural similarity between UFM1 and ubiquitin, the UFMylation machinery employs unique mechanisms that ensure fidelity. While physiological triggers and consequences of UFMylation are not entirely clear, its biological importance is epitomized by mutations in the UFMylation pathway in human pathophysiology including musculoskeletal and neurodevelopmental diseases. Some of these diseases can be explained by the increased endoplasmic reticulum (ER) stress and disrupted translational homeostasis observed upon loss of UFMylation. The roles of UFM1 in these processes likely stem from its function at the ER where ribosomes are UFMylated in response to translational stalling. In addition, UFMylation has been implicated in other cellular processes including DNA damage response and telomere maintenance. Hence, the study of UFM1 pathway mechanics and its biological function will reveal insights into fundamental cell biology and is likely to afford new therapeutic opportunities for the benefit of human health. To this end, we herein provide a comprehensive guide to the current state of knowledge of UFM1 biogenesis, conjugation, and function with an emphasis on the underlying mechanisms.
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Affiliation(s)
- David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
| | - Joshua J. Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
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10
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Wang X, Xu X, Wang Z. The Post-Translational Role of UFMylation in Physiology and Disease. Cells 2023; 12:2543. [PMID: 37947621 PMCID: PMC10648299 DOI: 10.3390/cells12212543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a newly identified ubiquitin-like protein that has been conserved during the evolution of multicellular organisms. In a similar manner to ubiquitin, UFM1 can become covalently linked to the lysine residue of a substrate via a dedicated enzymatic cascade. Although a limited number of substrates have been identified so far, UFM1 modification (UFMylation) has been demonstrated to play a vital role in a variety of cellular activities, including mammalian development, ribosome biogenesis, the DNA damage response, endoplasmic reticulum stress responses, immune responses, and tumorigenesis. In this review, we summarize what is known about the UFM1 enzymatic cascade and its biological functions, and discuss its recently identified substrates. We also explore the pathological role of UFMylation in human disease and the corresponding potential therapeutic targets and strategies.
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Affiliation(s)
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China;
| | - Zhifeng Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China;
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11
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.17.23292782. [PMID: 37502976 PMCID: PMC10371176 DOI: 10.1101/2023.07.17.23292782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and ER stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least twelve different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remains to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Albert N. Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Michael W. Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lauren C. Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A. Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Jenny L. Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ruth J. Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
- VA Portland Health Care System, Portland, OR 97239, USA
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Yang X, Zhou T, Wang X, Xia Y, Cao X, Cheng X, Cao Y, Ma P, Ma H, Qin A, Zhao J. Loss of DDRGK1 impairs IRE1α UFMylation in spondyloepiphyseal dysplasia. Int J Biol Sci 2023; 19:4709-4725. [PMID: 37781516 PMCID: PMC10539710 DOI: 10.7150/ijbs.82765] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/27/2023] [Indexed: 10/03/2023] Open
Abstract
Spondyloepiphyseal dysplasia (SEMD) is a rare disease in which cartilage growth is disrupted, and the DDRGK1 mutation is one of the causative genes. In our study, we established Ddrgk1fl/fl, Col2a1-ERT Cre mice, which showed a thickened hypertrophic zone (HZ) in the growth plate, simulating the previous reported SEMD pathology in vivo. Instead of the classical modulation mechanism towards SOX9, our further mechanism study found that DDRGK1 stabilizes the stress sensor endoplasmic reticulum-to-nucleus signaling 1 (IRE1α) to maintain endoplasmic reticulum (ER) homoeostasis. The loss of DDRGK1 decreased the UFMylation and subsequently led to increased ubiquitylation-mediated IRE1α degradation, causing ER dysfunction and activating the PERK/CHOP/Caspase3 apoptosis pathway. Further DDRGK1 K268R-mutant mice revealed the importance of K268 UFMylation site in IRE1α degradation and subsequent ER dysfunction. In conclusion, DDRGK1 stabilizes IRE1α to ameliorate ER stress and following apoptosis in chondrocytes, which finally promote the normal chondrogenesis.
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Affiliation(s)
- Xiao Yang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tangjun Zhou
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Wang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Xia
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiankun Cao
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaofei Cheng
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Cao
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - An Qin
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zhao
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Kim HB, Bacik JP, Wu R, Jha RK, Hebron M, Triandafillou C, McCown JE, Baek NI, Kim JH, Kim YJ, Goulding CW, Strauss CEM, Schmidt JG, Shetye GS, Ryoo S, Jo EK, Jeon YH, Hung LW, Terwilliger TC, Kim CY. Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase. PLoS One 2022; 17:e0277670. [PMID: 36395154 PMCID: PMC9671377 DOI: 10.1371/journal.pone.0277670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.
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Affiliation(s)
- Heung-Bok Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - John-Paul Bacik
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Ruilian Wu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Michaeline Hebron
- Georgetown University Medical Center, Washington, D.C., United States of America
| | - Catherine Triandafillou
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, Illinois, United States of America
| | - Joseph E. McCown
- Array BioPharma Inc., Boulder, Colorado, United States of America
| | - Nam-In Baek
- Graduate School of Biotechnology and Department of Oriental Medicine Biotechnology, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jeong Han Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Jae Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, United States of America
| | - Charlie E. M. Strauss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Gauri S. Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois, Chicago, Illinois, United States of America
| | - Sungweon Ryoo
- Clinical Research Centre, Masan National Tuberculosis Hospital, Changwon-si, Gyeongsangnam-do, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Li-Wei Hung
- Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - Chang-Yub Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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14
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Jing Y, Mao Z, Chen F. UFMylation System: An Emerging Player in Tumorigenesis. Cancers (Basel) 2022; 14:3501. [PMID: 35884562 PMCID: PMC9323365 DOI: 10.3390/cancers14143501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1), a newly identified ubiquitin-like molecule (UBLs), is evolutionarily expressed in multiple species except yeast. Similarly to ubiquitin, UFM1 is covalently attached to its substrates through a well-orchestrated three-step enzymatic reaction involving E1, the UFM1-activating enzyme (ubiquitin-like modifier-activating enzyme 5, UBA5); E2, the UFM1-conjugating enzyme 1 (UFC1); and E3, the UFM1-specific ligase 1 (UFL1). To date, numerous studies have shown that UFM1 modification is implicated in various cellular processes, including endoplasmic reticulum (ER) stress, DNA damage response and erythroid development. An abnormal UFM1 cascade is closely related to a variety of diseases, especially tumors. Herein, we summarize the process and functions of UFM1 modification, illustrating the relationship and mechanisms between aberrant UFMylation and diversified tumors, aiming to provide novel diagnostic biomarkers or therapeutic targets for cancer treatments.
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Affiliation(s)
| | | | - Fengling Chen
- Department of Endocrinology and Metabolism, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; (Y.J.); (Z.M.)
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15
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Kumari S, Banerjee S, Kumar M, Hayashi A, Solaimuthu B, Cohen-Kfir E, Shaul YD, Rouvinski A, Wiener R. Overexpression of UBA5 in Cells Mimics the Phenotype of Cells Lacking UBA5. Int J Mol Sci 2022; 23:ijms23137445. [PMID: 35806453 PMCID: PMC9267032 DOI: 10.3390/ijms23137445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Ufmylation is a posttranslational modification in which the modifier UFM1 is attached to target proteins. This conjugation requires the concerted work of three enzymes named UBA5, UFC1, and UFL1. Initially, UBA5 activates UFM1 in a process that ends with UFM1 attached to UBA5’s active site Cys. Then, in a trans-thiolation reaction, UFM1 is transferred from UBA5 to UFC1, forming a thioester bond with the latter. Finally, with the help of UFL1, UFM1 is transferred to the final destination—a lysine residue on a target protein. Therefore, not surprisingly, deletion of one of these enzymes abrogates the conjugation process. However, how overexpression of these enzymes affects this process is not yet clear. Here we found, unexpectedly, that overexpression of UBA5, but not UFC1, damages the ability of cells to migrate, in a similar way to cells lacking UBA5 or UFC1. At the mechanistic level, we found that overexpression of UBA5 reverses the trans-thiolation reaction, thereby leading to a back transfer of UFM1 from UFC1 to UBA5. This, as seen in cells lacking UBA5, reduces the level of charged UFC1 and therefore harms the conjugation process. In contrast, co-expression of UBA5 with UFM1 abolishes this effect, suggesting that the reverse transfer of UFM1 from UFC1 to UBA5 depends on the level of free UFM1. Overall, our results propose that the cellular expression level of the UFM1 conjugation enzymes has to be tightly regulated to ensure the proper directionality of UFM1 transfer.
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Affiliation(s)
- Sujata Kumari
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
| | - Sayanika Banerjee
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
| | - Manoj Kumar
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
| | - Arata Hayashi
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
| | - Balakrishnan Solaimuthu
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
| | - Yoav D. Shaul
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.K.); (S.B.); (M.K.); (A.H.); (B.S.); (E.C.-K.); (Y.D.S.)
- Correspondence: ; Tel.: +972-2-6757327
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16
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Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism. J Struct Biol 2021; 213:107796. [PMID: 34508858 DOI: 10.1016/j.jsb.2021.107796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/17/2021] [Accepted: 09/05/2021] [Indexed: 11/21/2022]
Abstract
Ubiquitin fold modifier 1 (UFM1) is an ubiquitin-like protein (Ubl) involved especially in endoplasmic stress response. Activation occurs via a three-step mechanism like other Ubls. Data obtained reveal that UFM1 regulates the oligomeric state of ubiquitin activating enzyme 5 (UBA5) to initiate the activation step. Mixtures of homodimers and heterotrimers are observed in solution at the equilibrium state, demonstrating that the UBA5-UFM1 complex undergoes several concentration dependent oligomeric translational states to form a final functional complex. The oligomerization state of unbound UBA5 is also concentration dependent and shifts from the monomeric to the dimeric state. Data describing different oligomeric states are complemented with binding studies that reveal a negative cooperativity for the complex formation and thereby provide more detailed insights into the complex formation mechanism.
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17
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Wesch N, Löhr F, Rogova N, Dötsch V, Rogov VV. A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1. Int J Mol Sci 2021; 22:ijms22147390. [PMID: 34299007 PMCID: PMC8304084 DOI: 10.3390/ijms22147390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Natalia Rogova
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Correspondence: (V.D.); (V.V.R.)
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Correspondence: (V.D.); (V.V.R.)
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18
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Witting KF, Mulder MP. Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma. Biomolecules 2021; 11:biom11020255. [PMID: 33578803 PMCID: PMC7916544 DOI: 10.3390/biom11020255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.
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19
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Abstract
Post-translational modifications of cellular substrates with ubiquitin and ubiquitin-like proteins (UBLs), including ubiquitin, SUMOs, and neural precursor cell-expressed developmentally downregulated protein 8, play a central role in regulating many aspects of cell biology. The UBL conjugation cascade is initiated by a family of ATP-dependent enzymes termed E1 activating enzymes and executed by the downstream E2-conjugating enzymes and E3 ligases. Despite their druggability and their key position at the apex of the cascade, pharmacologic modulation of E1s with potent and selective drugs has remained elusive until 2009. Among the eight E1 enzymes identified so far, those initiating ubiquitylation (UBA1), SUMOylation (SAE), and neddylation (NAE) are the most characterized and are implicated in various aspects of cancer biology. To date, over 40 inhibitors have been reported to target UBA1, SAE, and NAE, including the NAE inhibitor pevonedistat, evaluated in more than 30 clinical trials. In this Review, we discuss E1 enzymes, the rationale for their therapeutic targeting in cancer, and their different inhibitors, with emphasis on the pharmacologic properties of adenosine sulfamates and their unique mechanism of action, termed substrate-assisted inhibition. Moreover, we highlight other less-characterized E1s-UBA6, UBA7, UBA4, UBA5, and autophagy-related protein 7-and the opportunities for targeting these enzymes in cancer. SIGNIFICANCE STATEMENT: The clinical successes of proteasome inhibitors in cancer therapy and the emerging resistance to these agents have prompted the exploration of other signaling nodes in the ubiquitin-proteasome system including E1 enzymes. Therefore, it is crucial to understand the biology of different E1 enzymes, their roles in cancer, and how to translate this knowledge into novel therapeutic strategies with potential implications in cancer treatment.
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Affiliation(s)
- Samir H Barghout
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
| | - Aaron D Schimmer
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
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20
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Banerjee S, Kumar M, Wiener R. Decrypting UFMylation: How Proteins Are Modified with UFM1. Biomolecules 2020; 10:E1442. [PMID: 33066455 PMCID: PMC7602216 DOI: 10.3390/biom10101442] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Besides ubiquitin (Ub), humans have a set of ubiquitin-like proteins (UBLs) that can also covalently modify target proteins. To date, less is known about UBLs than Ub and even less is known about the UBL called ubiquitin-fold modifier 1 (UFM1). Currently, our understanding of protein modification by UFM1 (UFMylation) is like a jigsaw puzzle with many missing pieces, and in some cases it is not even clear whether these pieces of data are in the right place. Here we review the current data on UFM1 from structural biology to biochemistry and cell biology. We believe that the physiological significance of protein modification by UFM1 is currently underestimated and there is more to it than meets the eye.
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Affiliation(s)
| | | | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; (S.B.); (M.K.)
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21
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Solution structure of TbUfm1 from Trypanosoma brucei and its binding to TbUba5. J Struct Biol 2020; 212:107580. [PMID: 32693018 DOI: 10.1016/j.jsb.2020.107580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/21/2022]
Abstract
Ubiquitin-like proteins are conserved in eukaryotes and involved in numerous cellular processes. Ufm1 is proved to play important roles in endoplasmic reticulum homeostasis, vesicle transportation and embryonic development. Enzyme cascade of Ufm1 is similar to that of ubiquitin. Mature Ufm1 is activated and conjugated to substrates by assistance of Ufm1 activating enzyme Uba5 (E1), Ufm1 conjugating enzyme Ufc1 (E2), and Ufm1 ligating enzyme Ufl1 (E3). Here, we determined the solution structure of TbUfm1 from Trypanosoma brucei (T. brucei) by NMR spectroscopy and explored the interactions between TbUfm1 and TbUba5/TbUfc1/TbUfl1. TbUfm1 adopts a typical β-grasp fold, which partially wraps a central α-helix and the other two helixes. NMR chemical shift perturbation indicated that TbUfm1 interacts with TbUba5 via a hydrophobic pocket formed by α1α2β1β2. Although the structure and Uba5-interaction mode of TbUfm1 are conserved in Ufm1 proteins, there are also some differences, which might reflect the potential diversity of Ufm1 in evolution and biological functions.
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22
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Ubiquitin-like proteins in the DNA damage response: the next generation. Essays Biochem 2020; 64:737-752. [DOI: 10.1042/ebc20190095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 12/29/2022]
Abstract
AbstractDNA suffers constant insult from a variety of endogenous and exogenous sources. To deal with the arising lesions, cells have evolved complex and coordinated pathways, collectively termed the DNA damage response (DDR). Importantly, an improper DDR can lead to genome instability, premature ageing and human diseases, including cancer as well as neurodegenerative disorders. As a crucial process for cell survival, regulation of the DDR is multi-layered and includes several post-translational modifications. Since the discovery of ubiquitin in 1975 and the ubiquitylation cascade in the early 1980s, a number of ubiquitin-like proteins (UBLs) have been identified as post-translational modifiers. However, while the importance of ubiquitin and the UBLs SUMO and NEDD8 in DNA damage repair and signalling is well established, the roles of the remaining UBLs in the DDR are only starting to be uncovered. Herein, we revise the current status of the UBLs ISG15, UBL5, FAT10 and UFM1 as emerging co-regulators of DDR processes. In fact, it is becoming clear that these post-translational modifiers play important pleiotropic roles in DNA damage and/or associated stress-related cellular responses. Expanding our understanding of the molecular mechanisms underlying these emerging UBL functions will be fundamental for enhancing our knowledge of the DDR and potentially provide new therapeutic strategies for various human diseases including cancer.
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23
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Huber J, Obata M, Gruber J, Akutsu M, Löhr F, Rogova N, Güntert P, Dikic I, Kirkin V, Komatsu M, Dötsch V, Rogov VV. An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5. Autophagy 2020; 16:256-270. [PMID: 30990354 PMCID: PMC6984602 DOI: 10.1080/15548627.2019.1606637] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
Short linear motifs, known as LC3-interacting regions (LIRs), interact with mactoautophagy/autophagy modifiers (Atg8/LC3/GABARAP proteins) via a conserved universal mechanism. Typically, this includes the occupancy of 2 hydrophobic pockets on the surface of Atg8-family proteins by 2 specific aromatic and hydrophobic residues within the LIR motifs. Here, we describe an alternative mechanism of Atg8-family protein interaction with the non-canonical UBA5 LIR, an E1-like enzyme of the ufmylation pathway that preferentially interacts with GABARAP but not LC3 proteins. By solving the structures of both GABARAP and GABARAPL2 in complex with the UBA5 LIR, we show that in addition to the binding to the 2 canonical hydrophobic pockets (HP1 and HP2), a conserved tryptophan residue N-terminal of the LIR core sequence binds into a novel hydrophobic pocket on the surface of GABARAP proteins, which we term HP0. This mode of action is unique for UBA5 and accompanied by large rearrangements of key residues including the side chains of the gate-keeping K46 and the adjacent K/R47 in GABARAP proteins. Swapping mutations in LC3B and GABARAPL2 revealed that K/R47 is the key residue in the specific binding of GABARAP proteins to UBA5, with synergetic contributions of the composition and dynamics of the loop L3. Finally, we elucidate the physiological relevance of the interaction and show that GABARAP proteins regulate the localization and function of UBA5 on the endoplasmic reticulum membrane in a lipidation-independent manner.Abbreviations: ATG: AuTophaGy-related; EGFP: enhanced green fluorescent protein; GABARAP: GABA-type A receptor-associated protein; ITC: isothermal titration calorimetry; KO: knockout; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NMR: nuclear magnetic resonance; RMSD: root-mean-square deviation of atomic positions; TKO: triple knockout; UBA5: ubiquitin like modifier activating enzyme 5.
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Affiliation(s)
- Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jens Gruber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Natalia Rogova
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
- Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Ivan Dikic
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
- Institute of Biochemistry II, School of Medicine, Frankfurt am Main, Germany
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
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24
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Gerakis Y, Quintero M, Li H, Hetz C. The UFMylation System in Proteostasis and Beyond. Trends Cell Biol 2019; 29:974-986. [PMID: 31703843 PMCID: PMC6917045 DOI: 10.1016/j.tcb.2019.09.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications are at the apex of cellular communication and eventually regulate every aspect of life. The identification of new post-translational modifiers is opening alternative avenues in understanding fundamental cell biology processes and may ultimately provide novel therapeutic opportunities. The ubiquitin-fold modifier 1 (UFM1) is a post-translational modifier discovered a decade ago but its biological significance has remained mostly unknown. The field has recently witnessed an explosion of research uncovering the implications of the pathway to cellular homeostasis in living organisms. We overview recent advances in the function and regulation of the UFM1 pathway, and its implications for cell physiology and disease.
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Affiliation(s)
- Yannis Gerakis
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP (Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias) Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Michaela Quintero
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP (Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias) Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA; Cellular and Molecular Biology Program, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.
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25
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Bio-Guided Fractionation of Ethanol Extract of Leaves of Esenbeckia alata Kunt (Rutaceae) Led to the Isolation of Two Cytotoxic Quinoline Alkaloids: Evidence of Selectivity Against Leukemia Cells. Biomolecules 2019; 9:biom9100585. [PMID: 31597257 PMCID: PMC6843300 DOI: 10.3390/biom9100585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/23/2022] Open
Abstract
Bio-guided fractionation performed on the leaves-derived ethanol extract of Esenbeckia alata (Rutaceae), a plant used in traditional medicine, led to the isolation of two alkaloids, kokusaginine 1 and flindersiamine 2, as main cytotoxic agents. Primary ethanolic extract and raw fractions exhibited cell inhibition against five cancer cell lines at different levels (25-97% inhibition at 50 µg/mL) as well as isolated alkaloids 1-2 (30-90% inhibition at 20 µM). Although alkaloid 2 generally was the most active compound, both alkaloids showed a selective effect on K562, a human chronic myelogenous leukemia cell line. The E1-like ubiquitin-activating enzymes (e.g., UBA5) have been recently described as important targets for future treatment of cancer progression, such as leukemia, among others. Therefore, as a rationale to the observed cytotoxic selectivity, an in-silico evaluation by molecular docking and molecular dynamics was also explored. Compounds 1-2 exhibited good performance on the interaction within the active site of UBA5.
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26
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Closing the gap of ubiquitin activation. Proc Natl Acad Sci U S A 2019; 116:15319-15321. [PMID: 31278148 DOI: 10.1073/pnas.1909868116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Abstract
Posttranslational protein modification by ubiquitin (Ub) regulates aspects of biology, including protein turnover and the cell cycle. Proteins and enzymes that promote Ub conjugation are therapeutic targets because they are sometimes dysregulated in cancer, neurodegenerative diseases, and other disorders. Ub conjugation is initiated by a Ub-activating enzyme that adopts different conformations to catalyze Ub activation, Ub-activating enzyme thioester bond formation, and thioester bond transfer to Ub-conjugating enzymes. Here, we illuminate 2 uncharacterized states for Ub-activating enzyme, one bound to pyrophosphate prior to thioester bond formation and one captured during thioester bond formation. These structures reveal key differences and similarities among activating enzymes for Ub and SUMO with respect to conformational changes that accompany thioester formation. The ubiquitin (Ub) and Ub-like (Ubl) protein-conjugation cascade is initiated by E1 enzymes that catalyze Ub/Ubl activation through C-terminal adenylation, thioester bond formation with an E1 catalytic cysteine, and thioester bond transfer to Ub/Ubl E2 conjugating enzymes. Each of these reactions is accompanied by conformational changes of the E1 domain that contains the catalytic cysteine (Cys domain). Open conformations of the Cys domain are associated with adenylation and thioester transfer to E2s, while a closed conformation is associated with pyrophosphate release and thioester bond formation. Several structures are available for Ub E1s, but none has been reported in the open state before pyrophosphate release or in the closed state. Here, we describe the structures of Schizosaccharomyces pombe Ub E1 in these two states, captured using semisynthetic Ub probes. In the first, with a Ub-adenylate mimetic (Ub-AMSN) bound, the E1 is in an open conformation before release of pyrophosphate. In the second, with a Ub-vinylsulfonamide (Ub-AVSN) bound covalently to the catalytic cysteine, the E1 is in a closed conformation required for thioester bond formation. These structures provide further insight into Ub E1 adenylation and thioester bond formation. Conformational changes that accompany Cys-domain rotation are conserved for SUMO and Ub E1s, but changes in Ub E1 involve additional surfaces as mutational and biochemical analysis of residues within these surfaces alter Ub E1 activities.
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28
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shaun K Olsen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.
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29
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Lv Z, Yuan L, Atkison JH, Williams KM, Vega R, Sessions EH, Divlianska DB, Davies C, Chen Y, Olsen SK. Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme. Nat Commun 2018; 9:5145. [PMID: 30514846 PMCID: PMC6279746 DOI: 10.1038/s41467-018-07015-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
E1 enzymes activate ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in the first step of Ub/Ubl conjugation cascades and represent potential targets for therapeutic intervention in cancer and other life-threatening diseases. Here, we report the crystal structure of the E1 enzyme for the Ubl SUMO in complex with a recently discovered and highly specific covalent allosteric inhibitor (COH000). The structure reveals that COH000 targets a cryptic pocket distinct from the active site that is completely buried in all previous SUMO E1 structures and that COH000 binding to SUMO E1 is accompanied by a network of structural changes that altogether lock the enzyme in a previously unobserved inactive conformation. These structural changes include disassembly of the active site and a 180° rotation of the catalytic cysteine-containing SCCH domain, relative to conformational snapshots of SUMO E1 poised to catalyze adenylation. Altogether, our study provides a molecular basis for the inhibitory mechanism of COH000 and its SUMO E1 specificity, and also establishes a framework for potential development of molecules targeting E1 enzymes for other Ubls at a cryptic allosteric site.
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA
| | - Lingmin Yuan
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA
| | - James H Atkison
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA
| | - Katelyn M Williams
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA
| | - Ramir Vega
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, 91010, CA, USA
| | - E Hampton Sessions
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, 32827, FL, USA
| | - Daniela B Divlianska
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, 32827, FL, USA
| | - Christopher Davies
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA
| | - Yuan Chen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, 91010, CA, USA.
| | - Shaun K Olsen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA.
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30
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An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. J Mol Biol 2018; 431:463-478. [PMID: 30412706 DOI: 10.1016/j.jmb.2018.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/06/2023]
Abstract
Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.
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31
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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.
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32
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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.
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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
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33
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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.
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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.
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34
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Misra M, Kuhn M, Löbel M, An H, Statsyuk AV, Sotriffer C, Schindelin H. Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Structure 2017; 25:1120-1129.e3. [PMID: 28578874 DOI: 10.1016/j.str.2017.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/27/2017] [Accepted: 05/05/2017] [Indexed: 12/29/2022]
Abstract
Targeting the activating enzymes (E1) of ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) has emerged as a promising anti-cancer strategy, possibly overcoming the ineffectiveness of proteasome inhibitors against solid tumors. Here, we report crystal structures of the yeast ubiquitin E1 (Uba1) with three adenosyl sulfamate inhibitors exhibiting different E1 specificities, which are all covalently linked to ubiquitin. The structures illustrate how the chemically diverse inhibitors are accommodated within the adenylation active site. When compared with the previously reported structures of various E1 enzymes, our structures provide the basis of the preferences of these inhibitors for different Ub/Ubl-activating enzymes. In vitro inhibition assays and molecular dynamics simulations validated the specificities of the inhibitors as deduced from the structures. Taken together, the structures establish a framework for the development of additional compounds targeting E1 enzymes, which will display higher potency and selectivity.
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Affiliation(s)
- Mohit Misra
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany; Institute of Pharmacy and Food Chemistry, Department of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Maximilian Kuhn
- Institute of Pharmacy and Food Chemistry, Department of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mark Löbel
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Heeseon An
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Alexander V Statsyuk
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Department of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Hermann Schindelin
- Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
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35
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Roberts AM, Miyamoto DK, Huffman TR, Bateman LA, Ives AN, Akopian D, Heslin MJ, Contreras CM, Rape M, Skibola CF, Nomura DK. Chemoproteomic Screening of Covalent Ligands Reveals UBA5 As a Novel Pancreatic Cancer Target. ACS Chem Biol 2017; 12:899-904. [PMID: 28186401 DOI: 10.1021/acschembio.7b00020] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chemical genetic screening of small-molecule libraries has been a promising strategy for discovering unique and novel therapeutic compounds. However, identifying the targets of lead molecules that arise from these screens has remained a major bottleneck in understanding the mechanism of action of these compounds. Here, we have coupled the screening of a cysteine-reactive fragment-based covalent ligand library with an isotopic tandem orthogonal proteolysis-enabled activity-based protein profiling (isoTOP-ABPP) chemoproteomic platform to rapidly couple the discovery of lead small molecules that impair pancreatic cancer pathogenicity with the identification of druggable hotspots for potential cancer therapy. Through this coupled approach, we have discovered a covalent ligand DKM 2-93 that impairs pancreatic cancer cell survival and in vivo tumor growth through covalently modifying the catalytic cysteine of the ubiquitin-like modifier activating enzyme 5 (UBA5), thereby inhibiting its activity as a protein that activates the ubiquitin-like protein UFM1 to UFMylate proteins. We show that UBA5 is a novel pancreatic cancer therapeutic target and show DKM 2-93 as a relatively selective lead inhibitor of UBA5. Our results underscore the utility of coupling the screening of covalent ligand libraries with isoTOP-ABPP platforms for mining the proteome for druggable hotspots for cancer therapy.
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Affiliation(s)
- Allison M. Roberts
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - David K. Miyamoto
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Tucker R. Huffman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Leslie A. Bateman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ashley N. Ives
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - David Akopian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Martin J. Heslin
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Carlo M. Contreras
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christine F. Skibola
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Daniel K. Nomura
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
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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: 23] [Impact Index Per Article: 3.3] [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.
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Abstract
Ubiquitin-like proteins (Ubl's) are conjugated to target proteins or lipids to regulate their activity, stability, subcellular localization, or macromolecular interactions. Similar to ubiquitin, conjugation is achieved through a cascade of activities that are catalyzed by E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. In this review, we will summarize structural and mechanistic details of enzymes and protein cofactors that participate in Ubl conjugation cascades. Precisely, we will focus on conjugation machinery in the SUMO, NEDD8, ATG8, ATG12, URM1, UFM1, FAT10, and ISG15 pathways while referring to the ubiquitin pathway to highlight common or contrasting themes. We will also review various strategies used to trap intermediates during Ubl activation and conjugation.
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Affiliation(s)
- Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States.,Howard Hughes Medical Institute, Sloan Kettering Institute , New York, New York 10021, United States
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38
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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.
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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.
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39
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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: 57] [Impact Index Per Article: 7.1] [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.
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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)
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40
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An H, Statsyuk AV. Facile synthesis of covalent probes to capture enzymatic intermediates during E1 enzyme catalysis. Chem Commun (Camb) 2015; 52:2477-80. [PMID: 26575161 DOI: 10.1039/c5cc08592f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report a facile synthetic strategy to prepare UBL-AMP electrophilic probes that form a covalent bond with the catalytic cysteine of cognate E1s, mimicking the tetrahedral intermediate of the E1-UBL-AMP complex. These probes enable the structural and biochemical study of both canonical- and non-canonical E1s.
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Affiliation(s)
- Heeseon An
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University, Silverman Hall, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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41
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da Silva SR, Paiva SL, Bancerz M, Geletu M, Lewis AM, Chen J, Cai Y, Lukkarila JL, Li H, Gunning PT. A selective inhibitor of the UFM1-activating enzyme, UBA5. Bioorg Med Chem Lett 2015; 26:4542-4547. [PMID: 27520940 DOI: 10.1016/j.bmcl.2015.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 11/18/2022]
Abstract
Protein conjugation with ubiquitin and ubiquitin-like small molecules, such as UFM1, is important for promoting cancer cell survival and proliferation. Herein, the development of the first selective micromolar inhibitor of the UBA5 E1 enzyme that initiates UFM1 protein conjugation is described. This organometallic inhibitor incorporates adenosine and zinc(II)cyclen within its core scaffold and inhibits UBA5 noncompetitively and selectively over other E1 enzymes and a panel of human kinases. Furthermore, this compound selectively impedes the cellular proliferation (above 50μM) of cancer cells containing higher levels of UBA5. This inhibitor may be used to further probe the intracellular role of the UFM1 pathway in disease progression.
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Affiliation(s)
- Sara R da Silva
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Stacey-Lynn Paiva
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Matthew Bancerz
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Mulu Geletu
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Andrew M Lewis
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jijun Chen
- Department of Biochemistry and Molecular Biology, Georgia Regents University Cancer Center, Augusta, GA 30912, USA
| | - Yafei Cai
- Department of Biochemistry and Molecular Biology, Georgia Regents University Cancer Center, Augusta, GA 30912, USA
| | - Julie L Lukkarila
- Department of Biochemistry and Molecular Biology, Georgia Regents University Cancer Center, Augusta, GA 30912, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Georgia Regents University Cancer Center, Augusta, GA 30912, USA
| | - Patrick T Gunning
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada.
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42
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Yoo HM, Park JH, Jeon YJ, Chung CH. Ubiquitin-fold modifier 1 acts as a positive regulator of breast cancer. Front Endocrinol (Lausanne) 2015; 6:36. [PMID: 25852645 PMCID: PMC4367433 DOI: 10.3389/fendo.2015.00036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 03/03/2015] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptor-α (ERα) is a steroid hormone-sensitive transcription factor that plays a critical role in development of breast cancer. The binding of estrogen to ERα triggers the recruitment of transcriptional co-activators as well as chromatin remodeling factors to estrogen-responsive elements (ERE) of ERα target genes. This process is tightly associated with post-translational modifications (PTMs) of ERα and its co-activators for promotion of transcriptional activation, which leads to proliferation of a large subset of breast tumor cells. These PTMs include phosphorylation, acetylation, methylation, and conjugation by ubiquitin and ubiquitin-like proteins. Ubiquitin-fold modifier 1 (UFM1), one of ubiquitin-like proteins, has recently been shown to be ligated to activating signal co-integrator 1 (ASC1), which acts as a transcriptional co-activator of nuclear receptors. Here, we discuss the mechanistic connection between ASC1 modification by UFM1 and ERα transactivation, and highlight how the interplay of these processes is involved in development of breast cancer. We also discuss potential use of UFM1-conjugating system as therapeutic targets against not only breast cancer but also other nuclear receptor-mediated cancers.
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Affiliation(s)
- Hee Min Yoo
- Institute for Protein Metabolism, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jong Ho Park
- Institute for Protein Metabolism, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Young Joo Jeon
- Institute for Protein Metabolism, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Chin Ha Chung
- Institute for Protein Metabolism, School of Biological Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Chin Ha Chung, Institute for Protein Metabolism, School of Biological Sciences, Seoul National University, 56-1 Shillim-dong, Gwanak-gu, Seoul 151-742, South Korea e-mail:
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43
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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: 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.
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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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44
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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.
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Affiliation(s)
- Shutao Xie
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
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45
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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.
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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.
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46
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Xie ST. Expression, purification, and crystal structure of N-terminal domains of human ubiquitin-activating enzyme (E1). Biosci Biotechnol Biochem 2014; 78:1542-9. [PMID: 25209502 DOI: 10.1080/09168451.2014.923301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Ubiquitin-activating enzyme (E1) is a key regulator in protein ubiquitination, which lies on the upstream of the ubiquitin-related pathways and determines the activation of the downstream enzyme cascade. Thus far, no structural information about the human ubiquitin-activating enzyme has been reported. We expressed and purified the N-terminal domains of human E1 and determined their crystal structures, which contain inactive adenylation domain (IAD) and the first catalytic cysteine half-domain (FCCH). This study presents the crystal structure of human E1 fragment for the first time. The main structure of both IAD and FCCH superimposed well with their corresponding domains in yeast Uba1, but their relative positions vary significantly. This work provides new structural insights in understanding the mechanisms of ubiquitin activation in humans.
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Affiliation(s)
- Shu-Tao Xie
- a MOE Key Laboratory of Protein Sciences and Tsinghua-Peking Center for Life Sciences , School of Life Sciences, Tsinghua University , Beijing , China
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47
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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.
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Affiliation(s)
- Shutao Xie
- MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
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da Silva SR, Paiva SL, Lukkarila JL, Gunning PT. Exploring a new frontier in cancer treatment: targeting the ubiquitin and ubiquitin-like activating enzymes. J Med Chem 2013; 56:2165-77. [PMID: 23360215 DOI: 10.1021/jm301420b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The labeling of proteins with small ubiquitin (Ub) and ubiquitin-like (Ubl) modifiers regulates a plethora of activities within the cell, such as protein recycling, cell cycle modifications, and protein translocation. These processes are often overactive in diseased cells, leading to unregulated cell growth and disease progression. Therefore, in systems where Ub/Ubl protein labeling is dysregulated, the development of drugs to selectively and potently disrupt Ub/Ubl protein labeling offers a targeted molecular approach for sensitizing these diseased cells. This Perspective outlines the progress that has been made in the context of inhibitor development for targeting Ub/Ubl pathways.
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Affiliation(s)
- Sara R da Silva
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
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Hertel P, Daniel J, Stegehake D, Vaupel H, Kailayangiri S, Gruel C, Woltersdorf C, Liebau E. The ubiquitin-fold modifier 1 (Ufm1) cascade of Caenorhabditis elegans. J Biol Chem 2013; 288:10661-71. [PMID: 23449979 DOI: 10.1074/jbc.m113.458000] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Ufm1 (ubiquitin-fold modifier 1) is the most recently identified member of the ubiquitin-like protein family. We characterized the Ufm1 cascade of the model organism Caenorhabditis elegans in terms of function and analyzed interactions of the involved proteins in vitro and in vivo. Furthermore, we investigated the phenotypes of the deletion mutants uba5(ok3364) (activating enzyme of Ufm1) and ufc1(tm4888) (conjugating enzyme of Ufm1). The viable deletion mutants showed a decrease in reproduction, development, life span, and a reduced survival under heavy metal stress. However, an increased survival rate under pathogenic, oxidative, heat, and endoplasmic reticulum stress was observed. We propose that the Ufm1 cascade negatively regulates the IRE1-mediated unfolded protein response.
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Affiliation(s)
- Patrick Hertel
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany
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Caldecott KW. Tyrosyl DNA phosphodiesterase 2, an enzyme fit for purpose. Nat Struct Mol Biol 2013; 19:1212-3. [PMID: 23211766 DOI: 10.1038/nsmb.2455] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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