1
|
Wang X, Lv X, Ma J, Xu G. UFMylation: An integral post-translational modification for the regulation of proteostasis and cellular functions. Pharmacol Ther 2024; 260:108680. [PMID: 38878974 DOI: 10.1016/j.pharmthera.2024.108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is covalently conjugated to protein substrates via a cascade of enzymatic reactions, a process known as UFMylation. UFMylation orchestrates an array of vital biological functions, including maintaining endoplasmic reticulum (ER) homeostasis, facilitating protein biogenesis, promoting cellular differentiation, regulating DNA damage response, and participating in cancer-associated signaling pathways. UFMylation has rapidly evolved into one of the forefront research areas within the last few years, yet much remains to be uncovered. In this review, first, UFMylation and its cellular functions associated with diseases are briefly introduced. Then, we summarize the proteomic approaches for identifying UFMylation substrates and explore the impact of UFMylation on gene transcription, protein translation, and maintenance of ER homeostasis. Next, we highlight the intricate regulation between UFMylation and two protein degradation pathways, the ubiquitin-proteasome system and the autophagy-lysosome pathway, and explore the potential of UFMylation system as a drug target. Finally, we discuss emerging perspectives in the UFMylation field. This review may provide valuable insights for drug discovery targeting the UFMylation system.
Collapse
Affiliation(s)
- Xiaohui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Xiaowei Lv
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Jingjing Ma
- Department of Pharmacy, The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Medical Center of Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China; Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Merino-Cacho L, Barroso-Gomila O, Hernández-Sánchez S, Ramirez J, Mayor U, Sutherland JD, Barrio R. Biotin-Based Strategies to Explore the World of Ubiquitin and Ubiquitin-Like Modifiers. Chembiochem 2024; 25:e202300746. [PMID: 38081789 DOI: 10.1002/cbic.202300746] [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: 10/31/2023] [Revised: 12/07/2023] [Indexed: 01/06/2024]
Abstract
A complex code of cellular signals is mediated by ubiquitin and ubiquitin-like (Ub/UbL) modifications on substrate proteins. The so-called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non-modified cellular substrates, and protease-mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin-based tools developed for this purpose (for example BioUbLs, UbL-ID, BioE3, BioID), taking advantage of the strong affinity of biotin-streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass-spectrometry-based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL-ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.
Collapse
Affiliation(s)
- Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Sandra Hernández-Sánchez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| |
Collapse
|
4
|
Yamamoto-Hino M, Ariura M, Tanaka M, Iwasaki YW, Kawaguchi K, Shimamoto Y, Goto S. PIGB maintains nuclear lamina organization in skeletal muscle of Drosophila. J Cell Biol 2024; 223:e202301062. [PMID: 38261271 PMCID: PMC10808031 DOI: 10.1083/jcb.202301062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 10/09/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
The nuclear lamina (NL) plays various roles and participates in nuclear integrity, chromatin organization, and transcriptional regulation. Lamin proteins, the main components of the NL, form a homogeneous meshwork structure under the nuclear envelope. Lamins are essential, but it is unknown whether their homogeneous distribution is important for nuclear function. Here, we found that PIGB, an enzyme involved in glycosylphosphatidylinositol (GPI) synthesis, is responsible for the homogeneous lamin meshwork in Drosophila. Loss of PIGB resulted in heterogeneous distributions of B-type lamin and lamin-binding proteins in larval muscles. These phenotypes were rescued by expression of PIGB lacking GPI synthesis activity. The PIGB mutant exhibited changes in lamina-associated domains that are large heterochromatic genomic regions in the NL, reduction of nuclear stiffness, and deformation of muscle fibers. These results suggest that PIGB maintains the homogeneous meshwork of the NL, which may be essential for chromatin distribution and nuclear mechanical properties.
Collapse
Affiliation(s)
- Miki Yamamoto-Hino
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Masaru Ariura
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Masahito Tanaka
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Yuka W. Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
- Laboratory for Functional Non-Coding Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan
| | - Kohei Kawaguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Yuta Shimamoto
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Satoshi Goto
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| |
Collapse
|
5
|
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: 20] [Impact Index Per Article: 20.0] [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.
Collapse
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.
| |
Collapse
|
6
|
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: 17] [Impact Index Per Article: 17.0] [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.
Collapse
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.
| |
Collapse
|
7
|
Barroso-Gomila O, Merino-Cacho L, Muratore V, Perez C, Taibi V, Maspero E, Azkargorta M, Iloro I, Trulsson F, Vertegaal ACO, Mayor U, Elortza F, Polo S, Barrio R, Sutherland JD. BioE3 identifies specific substrates of ubiquitin E3 ligases. Nat Commun 2023; 14:7656. [PMID: 37996419 PMCID: PMC10667490 DOI: 10.1038/s41467-023-43326-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Hundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.
Collapse
Affiliation(s)
- Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Coralia Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Vincenzo Taibi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Fredrik Trulsson
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Ugo Mayor
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940, Leioa, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di oncologia ed emato-oncologia, Università degli Studi di Milano, Milan, Italy
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| |
Collapse
|
8
|
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: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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.
Collapse
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;
| |
Collapse
|
9
|
Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. SCIENCE ADVANCES 2023; 9:eadh3635. [PMID: 37595036 PMCID: PMC10438457 DOI: 10.1126/sciadv.adh3635] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through ufmylation, similar to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control (RQC) at the ER (ER-RQC), and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here, we provide insights into the mechanism of the UFM1 E3 complex in not only ufmylation but also ER-RQC. The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1, UFM1 E2, and, subsequently, CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26. Upon disome formation, the E3 complex associated with ufmylated RPL26 on the 60S subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of the interaction between UFBP1 and ufmylated RPL26 attenuated ER-RQC. These results provide insights into not only the molecular basis of the ufmylation but also its role in proteostasis.
Collapse
Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sota Ito
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Gaoxin Mao
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan
- Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| |
Collapse
|
10
|
Wang K, Papadopoulos N, Hamidi A, Lennartsson J, Heldin CH. SUMOylation of PDGF receptor α affects signaling via PLCγ and STAT3, and cell proliferation. BMC Mol Cell Biol 2023; 24:19. [PMID: 37193980 DOI: 10.1186/s12860-023-00481-6] [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: 12/29/2022] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND The platelet-derived growth factor (PDGF) family of ligands exerts their cellular effects by binding to α- and β-tyrosine kinase receptors (PDGFRα and PDGFRβ, respectively). SUMOylation is an important posttranslational modification (PTM) which regulates protein stability, localization, activation and protein interactions. A mass spectrometry screen has demonstrated SUMOylation of PDGFRα. However, the functional role of SUMOylation of PDGFRα has remained unknown. RESULTS In the present study, we validated that PDGFRα is SUMOylated on lysine residue 917 as was previously reported using a mass spectrometry approach. Mutation of lysine residue 917 to arginine (K917R) in PDGFRα substantially decreased SUMOylation, indicating that this amino acid residue is a major SUMOylation site. Whereas no difference in the stability of wild-type and mutant receptor was observed, the K917R mutant PDGFRα was less ubiquitinated than wild-type PDGFRα. The internalization and trafficking of the receptor to early and late endosomes were not affected by the mutation, neither was the localization of the PDGFRα to Golgi. However, the K917R mutant PDGFRα showed delayed activation of PLC-γ and enhanced activation of STAT3. Functional assays showed that the mutation of K917 of PDGFRα decreased cell proliferation in response to PDGF-BB stimulation. CONCLUSIONS SUMOylation of PDGFRα decreases ubiquitination of the receptor and affects ligand-induced signaling and cell proliferation.
Collapse
Affiliation(s)
- Kehuan Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Box 582, Sweden
| | - Natalia Papadopoulos
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Box 582, Sweden
| | - Anahita Hamidi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Box 582, Sweden
| | - Johan Lennartsson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Box 582, Sweden.
| |
Collapse
|
11
|
Kumarasinghe L, Garcia-Gimeno MA, Ramirez J, Mayor U, Zugaza JL, Sanz P. P-Rex1 is a novel substrate of the E3 ubiquitin ligase Malin associated with Lafora disease. Neurobiol Dis 2023; 177:105998. [PMID: 36638890 PMCID: PMC10682699 DOI: 10.1016/j.nbd.2023.105998] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Laforin and Malin are two proteins that are encoded by the genes EPM2A and EPM2B, respectively. Laforin is a glucan phosphatase and Malin is an E3-ubiquitin ligase, and these two proteins function as a complex. Mutations occurring at the level of one of the two genes lead to the accumulation of an aberrant form of glycogen meant to cluster in polyglucosans that go under the name of Lafora bodies. Individuals affected by the appearance of these polyglucosans, especially at the cerebral level, experience progressive neurodegeneration and several episodes of epilepsy leading to the manifestation of a fatal form of a rare disease called Lafora disease (LD), for which, to date, no treatment is available. Despite the different dysfunctions described for this disease, many molecular aspects still demand elucidation. An effective way to unknot some of the nodes that prevent the achievement of better knowledge of LD is to focus on the substrates that are ubiquitinated by the E3-ubiquitin ligase Malin. Some substrates have already been provided by previous studies based on protein-protein interaction techniques and have been associated with some alterations that mark the disease. In this work, we have used an unbiased alternative approach based on the activity of Malin as an E3-ubiquitin ligase. We report the discovery of novel bonafide substrates of Malin and have characterized one of them more deeply, namely PIP3-dependent Rac exchanger 1 (P-Rex1). The analysis conducted upon this substrate sets the genesis of the delineation of a molecular pathway that leads to altered glucose uptake, which could be one of the origin of the accumulation of the polyglucosans present in the disease.
Collapse
Affiliation(s)
- L Kumarasinghe
- Instituto de Biomedicina de Valencia, IBV-CSIC, 46010, Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 28029 Madrid, Spain
| | - M A Garcia-Gimeno
- Department of Biotechnology, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politécnica de València, 46022, Valencia, Spain
| | - J Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, Leioa, Bizkaia, Spain
| | - U Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, Leioa, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 48009 Bilbao, Spain
| | - J L Zugaza
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 48009 Bilbao, Spain; Achucarro Basque Center for Neuroscience, Scientific Park UPV/EHU, 48940 Leioa, Bizkaia, Spain; Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Bizkaia, Spain
| | - P Sanz
- Instituto de Biomedicina de Valencia, IBV-CSIC, 46010, Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 28029 Madrid, Spain.
| |
Collapse
|
12
|
Zou J, Wang W, Lu Y, Ayala J, Dong K, Zhou H, Wang J, Chen W, Weintraub NL, Zhou J, Li J, Su H. Neddylation is required for perinatal cardiac development through stimulation of metabolic maturation. Cell Rep 2023; 42:112018. [PMID: 36662623 PMCID: PMC10029150 DOI: 10.1016/j.celrep.2023.112018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/23/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Cardiac maturation is crucial for postnatal cardiac development and is increasingly known to be regulated by a series of transcription factors. However, post-translational mechanisms regulating this process remain unclear. Here we report the indispensable role of neddylation in cardiac maturation. Mosaic deletion of NAE1, an essential enzyme for neddylation, in neonatal hearts results in the rapid development of cardiomyopathy and heart failure. NAE1 deficiency disrupts transverse tubule formation, inhibits physiological hypertrophy, and represses fetal-to-adult isoform switching, thus culminating in cardiomyocyte immaturation. Mechanistically, we find that neddylation is needed for the perinatal metabolic transition from glycolytic to oxidative metabolism in cardiomyocytes. Further, we show that HIF1α is a putative neddylation target and that inhibition of neddylation accumulates HIF1α and impairs fatty acid utilization and bioenergetics in cardiomyocytes. Together, our data show neddylation is required for cardiomyocyte maturation through promoting oxidative metabolism in the developing heart.
Collapse
Affiliation(s)
- Jianqiu Zou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Wenjuan Wang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Yi Lu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Juan Ayala
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Kunzhe Dong
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Hongyi Zhou
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jinxi Wang
- Department of Medicine, University of Iowa, 200 Hawkins Drive, CBRB 2270B, Iowa City, IA 52242, USA
| | - Weiqin Chen
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Neal L Weintraub
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jiliang Zhou
- Department of Medicine, University of Iowa, 200 Hawkins Drive, CBRB 2270B, Iowa City, IA 52242, USA
| | - Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Division of Cardiology, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| |
Collapse
|
13
|
Matthiesen R, Rodriguez MS, Carvalho AS. A Computational Tool for Analysis of Mass Spectrometry Data of Ubiquitin-Enriched Samples. Methods Mol Biol 2023; 2602:205-214. [PMID: 36446977 DOI: 10.1007/978-1-0716-2859-1_15] [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] [Indexed: 06/16/2023]
Abstract
Mass spectrometry data on ubiquitin and ubiquitin-like modifiers are becoming increasingly more accessible, and the coverage progressively deepen as methodologies mature. This type of mass spectrometry data is linked to specific data analysis pipelines for ubiquitin. This chapter describes a computational tool to facilitate analysis of mass spectrometry data obtained on ubiquitin-enriched samples. For example, the analysis of ubiquitin branch site statistics and functional enrichment analysis against ubiquitin proteasome system protein sets are completed with a few functional calls. We foresee that the proposed computational methodology can aid in proximity drug design by, for example, elucidating the expression of E3 ligases and other factors related to the ubiquitin proteasome system.
Collapse
Affiliation(s)
- Rune Matthiesen
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, Lisbon, Portugal.
| | | | - Ana Sofia Carvalho
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, Lisbon, Portugal
| |
Collapse
|
14
|
Barroso-Gomila O, Mayor U, Barrio R, Sutherland JD. SUMO-ID: A Strategy for the Identification of SUMO-Dependent Proximal Interactors. Methods Mol Biol 2023; 2602:177-189. [PMID: 36446975 DOI: 10.1007/978-1-0716-2859-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications by the ubiquitin-like family (UbL) of proteins determine the biological fate of a substrate, including new interaction partners. In the case of the small ubiquitin-like modifier (SUMO), this is achieved in part through its non-covalent interaction with SUMO-interacting motifs (SIMs) found in some proteins. Investigating such partner-complex formation is particularly challenging due to the fast dynamics and reversibility of SUMO modifications and the low affinity of SUMO-SIM interactions. Here, we present a detailed protocol of SUMO-ID, a technology that merges promiscuous proximity biotinylation by TurboID enzyme and protein-fragment complementation strategy to specifically biotinylate SUMO-dependent interactors of particular substrates. When coupled to streptavidin-affinity purification and mass spectrometry, SUMO-ID efficiently identifies SUMO-dependent interactors of a given protein. The methodology describes all the steps from SUMO-ID cell line generation to LC-MS sample preparation to study SUMO-dependent interactors of a particular protein. The protocol is generic and therefore adaptable to study other UbL-dependent interactors, such as ubiquitin.
Collapse
Affiliation(s)
- Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ugo Mayor
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| |
Collapse
|
15
|
Garvin AJ, Lanz AJ, Morris JR. SUMO monoclonal antibodies vary in sensitivity, specificity, and ability to detect types of SUMO conjugate. Sci Rep 2022; 12:21343. [PMID: 36494414 PMCID: PMC9734647 DOI: 10.1038/s41598-022-25665-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Monoclonal antibodies (MAb) to members of the Small Ubiquitin-like modifier (SUMO) family are essential tools in the study of cellular SUMOylation. However, many anti-SUMO MAbs are poorly validated, and antibody matching to detection format is without an evidence base. Here we test the specificity and sensitivity of twenty-four anti-SUMO MAbs towards monomeric and polymeric SUMO1-4 in dot-blots, immunoblots, immunofluorescence and immunoprecipitation. We find substantial variability between SUMO MAbs for different conjugation states, for detecting increased SUMOylation in response to thirteen different stress agents, and as enrichment reagents for SUMOylated RanGAP1 or KAP1. All four anti-SUMO4 monoclonal antibodies tested cross-reacted wit SUMO2/3, and several SUMO2/3 monoclonal antibodies cross-reacted with SUMO4. These data characterize the specificity of twenty-four anti-SUMO antibodies across commonly used assays, creating an enabling resource for the SUMO research community.
Collapse
Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Alexander J Lanz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
16
|
Studying the ubiquitin code through biotin-based labelling methods. Semin Cell Dev Biol 2022; 132:109-119. [PMID: 35181195 DOI: 10.1016/j.semcdb.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
Collapse
|
17
|
Tsefou E, Ketteler R. Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin. Int J Mol Sci 2022; 23:12105. [PMID: 36292958 PMCID: PMC9603086 DOI: 10.3390/ijms232012105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
The quality control of mitochondria is critical for the survival of cells, and defects in the pathways required for this quality control can lead to severe disease. A key quality control mechanism in cells is mitophagy, which functions to remove damaged mitochondria under conditions of various stresses. Defective mitophagy can lead to a number of diseases including neurodegeneration. It has been proposed that an enhancement of mitophagy can improve cell survival, enhance neuronal function in neurodegeneration and extend health and lifespans. In this review, we highlight the role of deubiquitinating enzymes (DUBs) in the regulation of mitophagy. We summarise the current knowledge on DUBs that regulate mitophagy as drug targets and provide a list of small molecule inhibitors that are valuable tools for the further development of therapeutic strategies targeting the mitophagy pathway in neurodegeneration.
Collapse
Affiliation(s)
- Eliona Tsefou
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- UCL:Eisai Therapeutic Innovation Group, Translational Research Office, University College London, London W1T 7NF, UK
| | - Robin Ketteler
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| |
Collapse
|
18
|
Hegde S, Sreejan A, Gadgil CJ, Ratnaparkhi GS. SUMOylation of Dorsal attenuates Toll/NF-κB signaling. Genetics 2022; 221:iyac081. [PMID: 35567478 PMCID: PMC9252280 DOI: 10.1093/genetics/iyac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
In Drosophila, Toll/NF-κB signaling plays key roles in both animal development and in host defense. The activation, intensity, and kinetics of Toll signaling are regulated by posttranslational modifications such as phosphorylation, SUMOylation, or ubiquitination that target multiple proteins in the Toll/NF-κB cascade. Here, we have generated a CRISPR-Cas9 edited Dorsal (DL) variant that is SUMO conjugation resistant. Intriguingly, embryos laid by dlSCR mothers overcome dl haploinsufficiency and complete the developmental program. This ability appears to be a result of higher transcriptional activation by DLSCR. In contrast, SUMOylation dampens DL transcriptional activation, ultimately conferring robustness to the dorso-ventral program. In the larval immune response, dlSCR animals show an increase in crystal cell numbers, stronger activation of humoral defense genes, and high cactus levels. A mathematical model that evaluates the contribution of the small fraction of SUMOylated DL (1-5%) suggests that it acts to block transcriptional activation, which is driven primarily by DL that is not SUMO conjugated. Our findings define SUMO conjugation as an important regulator of the Toll signaling cascade, in both development and host defense. Our results broadly suggest that SUMO attenuates DL at the level of transcriptional activation. Furthermore, we hypothesize that SUMO conjugation of DL may be part of a Ubc9-dependent mechanism that restrains Toll/NF-κB signaling.
Collapse
Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research, Pune 411008, India
| | - Ashley Sreejan
- Chemical Engineering and Process Development Division, CSIR—National Chemical Laboratory, Pune 411008, India
| | - Chetan J Gadgil
- Chemical Engineering and Process Development Division, CSIR—National Chemical Laboratory, Pune 411008, India
- CSIR—Institute of Genomics and Integrative Biology, New Delhi 110020, India
| | | |
Collapse
|
19
|
The Next Frontier: Translational Development of Ubiquitination, SUMOylation, and NEDDylation in Cancer. Int J Mol Sci 2022; 23:ijms23073480. [PMID: 35408841 PMCID: PMC8999128 DOI: 10.3390/ijms23073480] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/01/2023] Open
Abstract
Post-translational modifications of proteins ensure optimized cellular processes, including proteostasis, regulated signaling, cell survival, and stress adaptation to maintain a balanced homeostatic state. Abnormal post-translational modifications are associated with cellular dysfunction and the occurrence of life-threatening diseases, such as cancer and neurodegenerative diseases. Therefore, some of the frequently seen protein modifications have been used as disease markers, while others are targeted for developing specific therapies. The ubiquitin and ubiquitin-like post-translational modifiers, namely, small ubiquitin-like modifier (SUMO) and neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8), share several features, such as protein structures, enzymatic cascades mediating the conjugation process, and targeted amino acid residues. Alterations in the regulatory mechanisms lead to aberrations in biological processes during tumorigenesis, including the regulation of tumor metabolism, immunological modulation of the tumor microenvironment, and cancer stem cell stemness, besides many more. Novel insights into ubiquitin and ubiquitin-like pathways involved in cancer biology reveal a potential interplay between ubiquitination, SUMOylation, and NEDDylation. This review outlines the current understandings of the regulatory mechanisms and assay capabilities of ubiquitination, SUMOylation, and NEDDylation. It will further highlight the role of ubiquitination, SUMOylation, and NEDDylation in tumorigenesis.
Collapse
|
20
|
Cheng Y, Niu Z, Cai Y, Zhang W. Emerging role of UFMylation in secretory cells involved in the endocrine system by maintaining ER proteostasis. Front Endocrinol (Lausanne) 2022; 13:1085408. [PMID: 36743909 PMCID: PMC9894094 DOI: 10.3389/fendo.2022.1085408] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/13/2022] [Indexed: 01/21/2023] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like molecule (UBL) discovered almost two decades ago, but our knowledge about the cellular and molecular mechanisms of this novel protein post-translational modification is still very fragmentary. In this review, we first summarize the core enzymes and factors involved in the UFMylation cascade, which, similar to ubiquitin, is consecutively catalyzed by UFM1-activating enzyme 5 (UBA5), UFM1-conjugating enzyme 1 (UFC1) and UFM1-specific ligase 1 (UFL1). Inspired by the substantial implications of UFM1 machinery in the secretory pathway, we next concentrate on the puzzling role of UFMylation in maintaining ER protein homeostasis, intending to illustrate the underlying mechanisms and future perspectives. At last, given a robust ER network is a hallmark of healthy endocrine secretory cells, we emphasize the function of UFM1 modification in physiology and pathology in the context of endocrine glands pancreas and female ovaries, aiming to provide precise insight into other internal glands of the endocrine system.
Collapse
Affiliation(s)
- Yun Cheng
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zikang Niu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Wei Zhang,
| |
Collapse
|
21
|
Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
Collapse
Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
22
|
Barroso-Gomila O, Trulsson F, Muratore V, Canosa I, Merino-Cacho L, Cortazar AR, Pérez C, Azkargorta M, Iloro I, Carracedo A, Aransay AM, Elortza F, Mayor U, Vertegaal ACO, Barrio R, Sutherland JD. Identification of proximal SUMO-dependent interactors using SUMO-ID. Nat Commun 2021; 12:6671. [PMID: 34795231 PMCID: PMC8602451 DOI: 10.1038/s41467-021-26807-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
The fast dynamics and reversibility of posttranslational modifications by the ubiquitin family pose significant challenges for research. Here we present SUMO-ID, a technology that merges proximity biotinylation by TurboID and protein-fragment complementation to find SUMO-dependent interactors of proteins of interest. We develop an optimized split-TurboID version and show SUMO interaction-dependent labelling of proteins proximal to PML and RANGAP1. SUMO-dependent interactors of PML are involved in transcription, DNA damage, stress response and SUMO modification and are highly enriched in SUMO Interacting Motifs, but may only represent a subset of the total PML proximal proteome. Likewise, SUMO-ID also allow us to identify interactors of SUMOylated SALL1, a less characterized SUMO substrate. Furthermore, using TP53 as a substrate, we identify SUMO1, SUMO2 and Ubiquitin preferential interactors. Thus, SUMO-ID is a powerful tool that allows to study the consequences of SUMO-dependent interactions, and may further unravel the complexity of the ubiquitin code.
Collapse
Affiliation(s)
- Orhi Barroso-Gomila
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Fredrik Trulsson
- grid.10419.3d0000000089452978Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Veronica Muratore
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Iñigo Canosa
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Laura Merino-Cacho
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Ana Rosa Cortazar
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Coralia Pérez
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Mikel Azkargorta
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Ibon Iloro
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Arkaitz Carracedo
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain ,grid.11480.3c0000000121671098Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940 Leioa, Spain
| | - Ana M. Aransay
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Felix Elortza
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Ugo Mayor
- grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain ,grid.11480.3c0000000121671098Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940 Leioa, Spain
| | - Alfred C. O. Vertegaal
- grid.10419.3d0000000089452978Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Spain.
| | - James D. Sutherland
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| |
Collapse
|
23
|
Nayak P, Kejriwal A, Ratnaparkhi GS. SUMOylation of Arginyl tRNA Synthetase Modulates the Drosophila Innate Immune Response. Front Cell Dev Biol 2021; 9:695630. [PMID: 34660574 PMCID: PMC8514731 DOI: 10.3389/fcell.2021.695630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
SUMO conjugation of a substrate protein can modify its activity, localization, interaction or function. A large number of SUMO targets in cells have been identified by Proteomics, but biological roles for SUMO conjugation for most targets remains elusive. The multi-aminoacyl tRNA synthetase complex (MARS) is a sensor and regulator of immune signaling. The proteins of this 1.2 MDa complex are targets of SUMO conjugation, in response to infection. Arginyl tRNA Synthetase (RRS), a member of the sub-complex II of MARS, is one such SUMO conjugation target. The sites for SUMO conjugation are Lys 147 and 383. Replacement of these residues by Arg (RRS K147R,K383R ), creates a SUMO conjugation resistant variant (RRS SCR ). Transgenic Drosophila lines for RRS WT and RRS SCR were generated by expressing these variants in a RRS loss of function (lof) animal, using the UAS-Gal4 system. The RRS-lof line was itself generated using CRISPR/Cas9 genome editing. Expression of both RRS WT and RRS SCR rescue the RRS-lof lethality. Adult animals expressing RRS WT and RRS SCR are compared and contrasted for their response to bacterial infection by gram positive M. luteus and gram negative Ecc15. We find that RRS SCR , when compared to RRS WT , shows modulation of the transcriptional response, as measured by quantitative 3' mRNA sequencing. Our study uncovers a possible non-canonical role for SUMOylation of RRS, a member of the MARS complex, in host-defense.
Collapse
Affiliation(s)
- Prajna Nayak
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - Aarti Kejriwal
- Indian Institute of Science Education and Research (IISER), Pune, India
| | | |
Collapse
|
24
|
Giordano I, Pirone L, Muratore V, Landaluze E, Pérez C, Lang V, Garde-Lapido E, Gonzalez-Lopez M, Barroso-Gomila O, Vertegaal ACO, Aransay AM, Rodriguez JA, Rodriguez MS, Sutherland JD, Barrio R. SALL1 Modulates CBX4 Stability, Nuclear Bodies, and Regulation of Target Genes. Front Cell Dev Biol 2021; 9:715868. [PMID: 34621739 PMCID: PMC8490708 DOI: 10.3389/fcell.2021.715868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Development is orchestrated through a complex interplay of multiple transcription factors. The comprehension of this interplay will help us to understand developmental processes. Here we analyze the relationship between two key transcription factors: CBX4, a member of the Polycomb Repressive Complex 1 (PRC1), and SALL1, a member of the Spalt-like family with important roles in embryogenesis and limb development. Both proteins localize to nuclear bodies and are modified by the small ubiquitin-like modifier (SUMO). Our results show that CBX4 and SALL1 interact in the nucleoplasm and that increased SALL1 expression reduces ubiquitination of CBX4, enhancing its stability. This is accompanied by an increase in the number and size of CBX4-containing Polycomb bodies, and by a greater repression of CBX4 target genes. Thus, our findings uncover a new way of SALL1-mediated regulation of Polycomb bodies through modulation of CBX4 stability, with consequences in the regulation of its target genes, which could have an impact in cell differentiation and development.
Collapse
Affiliation(s)
- Immacolata Giordano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Lucia Pirone
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Eukene Landaluze
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Coralia Pérez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Valerie Lang
- Viralgen Vector Core, Parque Científico y Tecnológico de Guipúzcoa, San Sebastián, Spain
| | - Elisa Garde-Lapido
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Monika Gonzalez-Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ana M Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination-CNRS, Paul Sabatier: Université Toulouse III, Toulouse, France
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| |
Collapse
|
25
|
UFL1 regulates milk protein and fat synthesis-related gene expression of bovine mammary epithelial cells probably via the mTOR signaling pathway. In Vitro Cell Dev Biol Anim 2021; 57:550-559. [PMID: 34081293 DOI: 10.1007/s11626-021-00587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
UFL1 is an ufmylation (a novel post-translational modification) E3 ligase, mainly located in the endoplasmic reticulum (ER), that has emerged as a significant regulator of several physiological and pathological processes. Yet its physiological function in milk synthesis in bovine mammary epithelial cells (BMECs) remains unknown. In this study, we investigated the effects of UFL1 in milk protein and fat synthesis-related gene expression, with a particular emphasis on the role of UFL1 in LPS-treated BMECs. Results showed that UFL1 depletion significantly reduced the expression of milk protein and fat synthesis-related gene and mTOR phosphorylation in both normal and LPS-treated BMECs. Overexpression of UFL1 enhanced the activation of the mTOR and milk protein and fat synthesis-related gene expression. Collectively, these above results strongly demonstrate that UFL1 could regulate milk protein and fat synthesis-related gene expression of BMECs probably via the mTOR signaling pathway.
Collapse
|
26
|
The role of SUMOylation during development. Biochem Soc Trans 2021; 48:463-478. [PMID: 32311032 PMCID: PMC7200636 DOI: 10.1042/bst20190390] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022]
Abstract
During the development of multicellular organisms, transcriptional regulation plays an important role in the control of cell growth, differentiation and morphogenesis. SUMOylation is a reversible post-translational process involved in transcriptional regulation through the modification of transcription factors and through chromatin remodelling (either modifying chromatin remodelers or acting as a ‘molecular glue’ by promoting recruitment of chromatin regulators). SUMO modification results in changes in the activity, stability, interactions or localization of its substrates, which affects cellular processes such as cell cycle progression, DNA maintenance and repair or nucleocytoplasmic transport. This review focuses on the role of SUMO machinery and the modification of target proteins during embryonic development and organogenesis of animals, from invertebrates to mammals.
Collapse
|
27
|
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: 3.0] [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.
Collapse
|
28
|
Li J, Zou J, Littlejohn R, Liu J, Su H. Neddylation, an Emerging Mechanism Regulating Cardiac Development and Function. Front Physiol 2020; 11:612927. [PMID: 33391028 PMCID: PMC7773599 DOI: 10.3389/fphys.2020.612927] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022] Open
Abstract
Defects in protein quality control have been increasingly recognized as pathogenic factors in the development of heart failure, a persistent devastating disease lacking efficacious therapies. Ubiquitin and ubiquitin-like proteins, a family of post-translational modifying polypeptides, play important roles in controlling protein quality by maintaining the stability and functional diversity of the proteome. NEDD8 (neural precursor cell expressed, developmentally downregulated 8), a small ubiquitin-like protein, was discovered two decades ago but until recently the biological significance of NEDD8 modifications (neddylation) in the heart has not been appreciated. In this review, we summarize the current knowledge of the biology of neddylation, highlighting several mechanisms by which neddylation regulates the function of its downstream targets, and discuss the expanding roles for neddylation in cardiac physiology and disease, with an emphasis on cardiac protein quality control. Finally, we outline challenges linked to the study of neddylation in health and disease.
Collapse
Affiliation(s)
- Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Jianqiu Zou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Rodney Littlejohn
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Jinbao Liu
- Protein Modification and Degradation Lab, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| |
Collapse
|
29
|
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: 7.2] [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.
Collapse
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.)
| |
Collapse
|
30
|
Folci A, Mirabella F, Fossati M. Ubiquitin and Ubiquitin-Like Proteins in the Critical Equilibrium between Synapse Physiology and Intellectual Disability. eNeuro 2020; 7:ENEURO.0137-20.2020. [PMID: 32719102 PMCID: PMC7544190 DOI: 10.1523/eneuro.0137-20.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 01/04/2023] Open
Abstract
Posttranslational modifications (PTMs) represent a dynamic regulatory system that precisely modulates the functional organization of synapses. PTMs consist in target modifications by small chemical moieties or conjugation of lipids, sugars or polypeptides. Among them, ubiquitin and a large family of ubiquitin-like proteins (UBLs) share several features such as the structure of the small protein modifiers, the enzymatic cascades mediating the conjugation process, and the targeted aminoacidic residue. In the brain, ubiquitination and two UBLs, namely sumoylation and the recently discovered neddylation orchestrate fundamental processes including synapse formation, maturation and plasticity, and their alteration is thought to contribute to the development of neurological disorders. Remarkably, emerging evidence suggests that these pathways tightly interplay to modulate the function of several proteins that possess pivotal roles for brain homeostasis as well as failure of this crosstalk seems to be implicated in the development of brain pathologies. In this review, we outline the role of ubiquitination, sumoylation, neddylation, and their functional interplay in synapse physiology and discuss their implication in the molecular pathogenesis of intellectual disability (ID), a neurodevelopmental disorder that is frequently comorbid with a wide spectrum of brain pathologies. Finally, we propose a few outlooks that might contribute to better understand the complexity of these regulatory systems in regard to neuronal circuit pathophysiology.
Collapse
Affiliation(s)
- Alessandra Folci
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089, Rozzano (MI), Italy
| | - Filippo Mirabella
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve 9 Emanuele - Milan, Italy
| | - Matteo Fossati
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089, Rozzano (MI), Italy
- CNR-Institute of Neuroscience, via Manzoni 56, 20089, Rozzano (MI), Italy
| |
Collapse
|
31
|
Bozal-Basterra L, Gonzalez-Santamarta M, Muratore V, Bermejo-Arteagabeitia A, Da Fonseca C, Barroso-Gomila O, Azkargorta M, Iloro I, Pampliega O, Andrade R, Martín-Martín N, Branon TC, Ting AY, Rodríguez JA, Carracedo A, Elortza F, Sutherland JD, Barrio R. LUZP1, a novel regulator of primary cilia and the actin cytoskeleton, is a contributing factor in Townes-Brocks Syndrome. eLife 2020; 9:e55957. [PMID: 32553112 PMCID: PMC7363444 DOI: 10.7554/elife.55957] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022] Open
Abstract
Primary cilia are sensory organelles crucial for cell signaling during development and organ homeostasis. Cilia arise from centrosomes and their formation and function is governed by numerous factors. Through our studies on Townes-Brocks Syndrome (TBS), a rare disease linked to abnormal cilia formation in human fibroblasts, we uncovered the leucine-zipper protein LUZP1 as an interactor of truncated SALL1, a dominantly-acting protein causing the disease. Using TurboID proximity labeling and pulldowns, we show that LUZP1 associates with factors linked to centrosome and actin filaments. Here, we show that LUZP1 is a cilia regulator. It localizes around the centrioles and to actin cytoskeleton. Loss of LUZP1 reduces F-actin levels, facilitates ciliogenesis and alters Sonic Hedgehog signaling, pointing to a key role in cytoskeleton-cilia interdependency. Truncated SALL1 increases the ubiquitin proteasome-mediated degradation of LUZP1. Together with other factors, alterations in LUZP1 may be contributing to TBS etiology.
Collapse
Affiliation(s)
- Laura Bozal-Basterra
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - María Gonzalez-Santamarta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Aitor Bermejo-Arteagabeitia
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Carolina Da Fonseca
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERehd, Instituto de Salud Carlos IIIMadridSpain
- ProteoRed-ISCIII, Instituto de Salud Carlos IIIMadridSpain
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERehd, Instituto de Salud Carlos IIIMadridSpain
- ProteoRed-ISCIII, Instituto de Salud Carlos IIIMadridSpain
| | - Olatz Pampliega
- Department of Neurosciences, University of the Basque Country, Achucarro Basque Center for Neuroscience-UPV/EHULeioaSpain
| | - Ricardo Andrade
- Analytical & High Resolution Biomedical Microscopy Core Facility, University of the Basque Country (UPV/EHU)LeioaSpain
| | - Natalia Martín-Martín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Tess C Branon
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Departments of Genetics, Chemistry and Biology, Stanford UniversityStanfordUnited States
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Departments of Genetics, Chemistry and Biology, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Jose A Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU)LeioaSpain
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERONC, Instituto de Salud Carlos IIIMadridSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU)BilbaoSpain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERehd, Instituto de Salud Carlos IIIMadridSpain
- ProteoRed-ISCIII, Instituto de Salud Carlos IIIMadridSpain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| |
Collapse
|
32
|
Raducanu VS, Tehseen M, Shirbini A, Raducanu DV, Hamdan SM. Two chromatographic schemes for protein purification involving the biotin/avidin interaction under native conditions. J Chromatogr A 2020; 1621:461051. [DOI: 10.1016/j.chroma.2020.461051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/13/2020] [Accepted: 03/15/2020] [Indexed: 11/25/2022]
|
33
|
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: 1.4] [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.
Collapse
|
34
|
Yau TY, Molina O, Courey AJ. SUMOylation in development and neurodegeneration. Development 2020; 147:147/6/dev175703. [PMID: 32188601 DOI: 10.1242/dev.175703] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In essentially all eukaryotes, proteins can be modified by the attachment of small ubiquitin-related modifier (SUMO) proteins to lysine side chains to produce branched proteins. This process of 'SUMOylation' plays essential roles in plant and animal development by altering protein function in spatially and temporally controlled ways. In this Primer, we explain the process of SUMOylation and summarize how SUMOylation regulates a number of signal transduction pathways. Next, we discuss multiple roles of SUMOylation in the epigenetic control of transcription. In addition, we evaluate the role of SUMOylation in the etiology of neurodegenerative disorders, focusing on Parkinson's disease and cerebral ischemia. Finally, we discuss the possibility that SUMOylation may stimulate survival and neurogenesis of neuronal stem cells.
Collapse
Affiliation(s)
- Tak-Yu Yau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Oscar Molina
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Albert J Courey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
| |
Collapse
|
35
|
Hegde S, Soory A, Kaduskar B, Ratnaparkhi GS. SUMO conjugation regulates immune signalling. Fly (Austin) 2020; 14:62-79. [PMID: 32777975 PMCID: PMC7714519 DOI: 10.1080/19336934.2020.1808402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) are critical drivers and attenuators for proteins that regulate immune signalling cascades in host defence. In this review, we explore functional roles for one such PTM, the small ubiquitin-like modifier (SUMO). Very few of the SUMO conjugation targets identified by proteomic studies have been validated in terms of their roles in host defence. Here, we compare and contrast potential SUMO substrate proteins in immune signalling for flies and mammals, with an emphasis on NFκB pathways. We discuss, using the few mechanistic studies that exist for validated targets, the effect of SUMO conjugation on signalling and also explore current molecular models that explain regulation by SUMO. We also discuss in detail roles of evolutionary conservation of mechanisms, SUMO interaction motifs, crosstalk of SUMO with other PTMs, emerging concepts such as group SUMOylation and finally, the potentially transforming roles for genome-editing technologies in studying the effect of PTMs.
Collapse
Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
| | - Amarendranath Soory
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
| | | | | |
Collapse
|
36
|
Huang Q, Zhang X. Emerging Roles and Research Tools of Atypical Ubiquitination. Proteomics 2020; 20:e1900100. [PMID: 31930661 DOI: 10.1002/pmic.201900100] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/02/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a posttranslational modification characterized by the covalent attachment of ubiquitin molecules to protein substrates. The ubiquitination modification process is reversible, dynamic, and involved in the regulation of various biological processes, such as autophagy, inflammatory responses, and DNA damage responses. The forms of ubiquitin modification are very diverse, incorporating either a single ubiquitin molecule or a complicated ubiquitin polymer, and different types of ubiquitination usually elicit corresponding cellular responses. The development of research tools and strategies has afforded more detailed insight into atypical ubiquitin signaling pathways that were previously poorly understood. Here, an update on the understanding of atypical ubiquitin chain signaling pathways is provided and the recent development of representative research tools for ubiquitin systems is discussed. In addition, the future challenges in ubiquitin research are reflected on and summarized.
Collapse
Affiliation(s)
- Qiuling Huang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaofei Zhang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510530, China
| |
Collapse
|
37
|
Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle. Cell Rep 2019; 23:2273-2282. [PMID: 29791839 DOI: 10.1016/j.celrep.2018.04.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/10/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Circadian clocks have evolved as time-measuring molecular devices to help organisms adapt their physiology to daily changes in light and temperature. Transcriptional oscillations account for a large fraction of rhythmic protein abundance. However, cycling of various posttranslational modifications, such as ubiquitylation, also contributes to shape the rhythmic protein landscape. In this study, we used an in vivo ubiquitin labeling assay to investigate the circadian ubiquitylated proteome of Drosophila melanogaster. We find that cyclic ubiquitylation affects MEGATOR (MTOR), a chromatin-associated nucleoporin that, in turn, feeds back to regulate the core molecular oscillator. Furthermore, we show that the ubiquitin ligase subunits CULLIN-3 (CUL-3) and SUPERNUMERARY LIMBS (SLMB) cooperate for ubiquitylating the TIMELESS protein. These findings stress the importance of ubiquitylation pathways in the Drosophila circadian clock and reveal a key component of this system.
Collapse
|
38
|
Yu L, Li G, Deng J, Jiang X, Xue J, Zhu Y, Huang W, Tang B, Duan R. The UFM1 cascade times mitosis entry associated with microcephaly. FASEB J 2019; 34:1319-1330. [PMID: 31914610 DOI: 10.1096/fj.201901751r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/15/2019] [Accepted: 11/14/2019] [Indexed: 02/02/2023]
Abstract
Posttranslational modifications enhance the functional diversity of the proteome by modifying the substrates. The UFM1 cascade is a novel ubiquitin-like modification system. The mutations in UFM1, its E1 (UBA5) and E2 (UFC1), have been identified in patients with microcephaly. However, its pathological mechanisms remain unclear. Herein, we observed the disruption of the UFM1 cascade in Drosophila neuroblasts (NBs) decreased the number of NBs, leading to a smaller brain size. The lack of ufmylation in NBs resulted in an increased mitotic index and an extended G2/M phase, indicating a defect in mitotic progression. In addition, live imaging of the embryos revealed an impaired E3 ligase (Ufl1) function resulted in premature entry into mitosis and failed cellularization. Even worse, the embryonic lethality occurred as early as within the first few mitotic cycles following the depletion of Ufm1. Knockdown of ufmylation in the fixed embryos exhibited severe phenotypes, including detached centrosomes, defective microtubules, and DNA bridge. Furthermore, we observed that the UFM1 cascade could alter the level of phosphorylation on tyrosine-15 of CDK1 (pY15-CDK1), which is a negative regulator of the G2 to M transition. These findings yield unambiguous evidence suggesting that the UFM1 cascade is a microcephaly-causing factor that regulates the progression of the cell cycle at mitosis phase entry.
Collapse
Affiliation(s)
- Li Yu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Guangxu Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Jing Deng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Xuan Jiang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Jin Xue
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Yingbao Zhu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Beisha Tang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Ranhui Duan
- 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
| |
Collapse
|
39
|
Li J, Yue G, Ma W, Zhang A, Zou J, Cai Y, Tang X, Wang J, Liu J, Li H, Su H. Ufm1-Specific Ligase Ufl1 Regulates Endoplasmic Reticulum Homeostasis and Protects Against Heart Failure. Circ Heart Fail 2019; 11:e004917. [PMID: 30354401 DOI: 10.1161/circheartfailure.118.004917] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Defects in protein homeostasis are sufficient to provoke cardiac remodeling and dysfunction. Although posttranslational modifications by ubiquitin and ubiquitin-like proteins are emerging as an important regulatory mechanism of protein function, the role of Ufm1 (ubiquitin-fold modifier 1)-a novel ubiquitin-like protein-has not been explored in either the normal or stressed heart. METHODS AND RESULTS Western blotting revealed that Ufl1 (Ufm1-specific E3 ligase 1)-an enzyme essential for Ufm1 modification-was increased in hypertrophic mouse hearts but reduced in the failing hearts of patients with dilated cardiomyopathy. To determine the functional role of Ufl1 in the heart, we generated a cardiac-specific knockout mouse and showed that Ufl1-deficient mice developed age-dependent cardiomyopathy and heart failure, as indicated by elevated cardiac fetal gene expression, increased fibrosis, and impaired cardiac contractility. When challenged with pressure overload, Ufl1-deficient hearts exhibited remarkably greater hypertrophy, exacerbated fibrosis, and worsened cardiac contractility compared with control counterparts. Transcriptome analysis identified that genes associated with the endoplasmic reticulum (ER) function were dysregulated in Ufl1-deficient hearts. Biochemical analysis revealed that excessive ER stress preceded and deteriorated along with the development of cardiomyopathy in Ufl1-deficient hearts. Mechanistically, Ufl1 depletion impaired (PKR-like ER-resident kinase) signaling and aggravated cardiomyocyte cell death after ER stress. Administration of the chemical ER chaperone tauroursodeoxycholic acid to Ufl1-deficient mice alleviated ER stress and attenuated pressure overload-induced cardiac dysfunction. CONCLUSIONS Our results advance a novel concept that the Ufm1 system is essential for cardiac homeostasis through regulation of ER function and that upregulation of myocardial Ufl1 could be protective against heart failure.
Collapse
Affiliation(s)
- Jie Li
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University
| | - Guihua Yue
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University.,Guangxi Medical College, Nanning, China (G.Y.)
| | - Wenxia Ma
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University
| | - Aizhen Zhang
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University.,Affiliated Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning (A.Z.)
| | - Jianqiu Zou
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, China (Y.C.)
| | - Xiaoli Tang
- Department of Biochemistry, School of Medicine, Nanchang University, Jiangxi, China (X.T.)
| | - Jun Wang
- Department of Basic Research Laboratories, Center for Stem Cell Engineering, Texas Heart Institute, Houston (J.W.)
| | - Jinbao Liu
- Protein Modification and Degradation Lab, School of Basic Medical Sciences, Guangzhou Medical University, China (J.L., H.S.)
| | - Honglin Li
- Department of Biochemistry and Molecular Biology (H.L.), Medical College of Georgia, Augusta University
| | - Huabo Su
- Vascular Biology Center (J.L., G.Y., W.M., A.Z., J.Z., H.S.), Medical College of Georgia, Augusta University.,Department of Pharmacology and Toxicology (H.S.), Medical College of Georgia, Augusta University.,Protein Modification and Degradation Lab, School of Basic Medical Sciences, Guangzhou Medical University, China (J.L., H.S.)
| |
Collapse
|
40
|
Fang Z, Pan Z. Essential Role of Ubiquitin-Fold Modifier 1 Conjugation in DNA Damage Response. DNA Cell Biol 2019; 38:1030-1039. [PMID: 31368785 DOI: 10.1089/dna.2019.4861] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Both endogenous and exogenous factors can cause DNA damage that compromises genomic integrity and cell viability. A proper DNA damage response (DDR) plays a role in maintaining genome stability and preventing tumorigenesis. DNA double-strand breaks (DSBs) are the most toxic DNA lesion, whose response is dominated by the ataxia-telangiectasia mutated (ATM) protein kinase. After being activated by the sensor Mre11-Rad50-Nbs1 (MRN) complex or acetyltransferase Tip60, ATM rapidly phosphorylates downstream targets to launch DDR signaling when DNA is damaged. However, the exact mechanism of DDR is complex and ambiguous. Ufmylation, one type of ubiquitin-like modification, proceeds mainly through a three-step enzymatic reaction to help ubiquitin-fold modifier 1 (Ufm1), attach to substrates with ubiquitin-like modifier-activating enzyme 5 (Uba5), Ufm1-conjugating enzyme 1 (Ufc1) and Ufm1-specific ligase 1 (Ufl1). Although ubiquitination is essential to the DSBs response, the potential function of ufmylation in DDR is largely unknown. Herein, we review the relationship between ufmylation and DDR to elucidate the function and mechanism of ufmylation in DDR, which would reveal the pathogenesis of some diseases and provide new guidance to create a therapeutic method.
Collapse
Affiliation(s)
- Zhi Fang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zezheng Pan
- Faculty of Basic Medical Science, Jiangxi Medical College, Nanchang University, Nanchang, China
| |
Collapse
|
41
|
Post-Translational Modifications of the Mini-Chromosome Maintenance Proteins in DNA Replication. Genes (Basel) 2019; 10:genes10050331. [PMID: 31052337 PMCID: PMC6563057 DOI: 10.3390/genes10050331] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
The eukaryotic mini-chromosome maintenance (MCM) complex, composed of MCM proteins 2-7, is the core component of the replisome that acts as the DNA replicative helicase to unwind duplex DNA and initiate DNA replication. MCM10 tightly binds the cell division control protein 45 homolog (CDC45)/MCM2-7/ DNA replication complex Go-Ichi-Ni-San (GINS) (CMG) complex that stimulates CMG helicase activity. The MCM8-MCM9 complex may have a non-essential role in activating the pre-replicative complex in the gap 1 (G1) phase by recruiting cell division cycle 6 (CDC6) to the origin recognition complex (ORC). Each MCM subunit has a distinct function achieved by differential post-translational modifications (PTMs) in both DNA replication process and response to replication stress. Such PTMs include phosphorylation, ubiquitination, small ubiquitin-like modifier (SUMO)ylation, O-N-acetyl-D-glucosamine (GlcNAc)ylation, and acetylation. These PTMs have an important role in controlling replication progress and genome stability. Because MCM proteins are associated with various human diseases, they are regarded as potential targets for therapeutic development. In this review, we summarize the different PTMs of the MCM proteins, their involvement in DNA replication and disease development, and the potential therapeutic implications.
Collapse
|
42
|
Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
Collapse
Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
| |
Collapse
|
43
|
Abstract
Ubiquitin fold modifier 1 (UFM1) is a small, metazoan-specific, ubiquitin-like protein modifier that is essential for embryonic development. Although loss-of-function mutations in UFM1 conjugation are linked to endoplasmic reticulum (ER) stress, neither the biological function nor the relevant cellular targets of this protein modifier are known. Here, we show that a largely uncharacterized ribosomal protein, RPL26, is the principal target of UFM1 conjugation. RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes tethered to the cytoplasmic surface of the ER and UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes. Biochemical analysis and structural modeling establish that UFMylated RPL26 and the UFMylation machinery are in close proximity to the SEC61 translocon, suggesting that this modification plays a direct role in cotranslational protein translocation into the ER. These data suggest that UFMylation is a ribosomal modification specialized to facilitate metazoan-specific protein biogenesis at the ER.
Collapse
|
44
|
Bakos G, Yu L, Gak IA, Roumeliotis TI, Liakopoulos D, Choudhary JS, Mansfeld J. An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. Nat Commun 2018; 9:4776. [PMID: 30429481 PMCID: PMC6235928 DOI: 10.1038/s41467-018-07251-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to many biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we present an E2-thioester-driven identification (E2~dID) method for the targeted identification of substrates of specific E2 and E3 enzyme pairs. E2~dID exploits the central position of E2-conjugating enzymes in the ubiquitination cascade and provides in vitro generated biotinylated E2~ubiquitin thioester conjugates as the sole source for ubiquitination in extracts. This enables purification and mass spectrometry-based identification of modified proteins under stringent conditions independently of the biological source of the extract. We demonstrate the sensitivity and specificity of E2-dID by identifying and validating substrates of APC/C in human cells. Finally, we perform E2~dID with SUMO in S. cerevisiae, showing that this approach can be easily adapted to other ubiquitin-like modifiers and experimental models.
Collapse
Affiliation(s)
- Gábor Bakos
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | | | - Dimitris Liakopoulos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 34293, Montpellier Cedex 05, France
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany.
| |
Collapse
|
45
|
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: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/06/2023]
Abstract
Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.
Collapse
|
46
|
Probing ubiquitin and SUMO conjugation and deconjugation. Biochem Soc Trans 2018; 46:423-436. [PMID: 29588386 DOI: 10.1042/bst20170086] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 12/24/2022]
Abstract
Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins including small Ubl modifier (SUMO) are small proteins which are covalently linked to target proteins to regulate their functions. In this review, we discuss the current state of the art and point out what we feel this field urgently needs in order to delineate the wiring of the system. We discuss what is needed to unravel the connections between different components of the conjugation machineries for ubiquitylation and SUMOylation, and to unravel the connections between the conjugation machineries and their substrates. Chemical probes are key tools to probe signal transduction by these small proteins that may help understand their action. This rapidly moving field has resulted in various small molecules that will help us to further understand Ub and SUMO function and that may lead to the development of new drugs.
Collapse
|
47
|
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: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
All ubiquitin-like proteins (UBLs) undergo an activation process before their conjugation to target proteins. Although the steps required for the activation of UBLs are conserved and common to all UBLs, we have previously shown that the activation of the UBL, ubiquitin fold modifier 1 (UFM1) by the E1, Ufm1 modifier-activating enzyme 5 (UBA5) is executed in a trans-binding mechanism, not observed in any other E1. In this study, we explored the necessity of that mechanism for UFM1 activation and found that it is needed not only for UFM1 binding to UBA5 but also for stabilizing the UBA5 homodimer. Although UBA5 functions as a dimer, in solution it behaves as a weak dimer. Dimerization of UBA5 is required for ATP binding; therefore, stabilization of the dimer by UFM1 enhances ATP binding. Our results make a connection between the binding of UFM1 to UBA5 and the latter's affinity to ATP, so we propose a novel mechanism for the regulation of ATP's binding to E1.-Mashahreh, B., Hassouna, F., Soudah, N., Cohen-Kfir, E., Strulovich, R., Haitin, Y., Wiener, R. Trans-binding of UFM1 to UBA5 stimulates UBA5 homodimerization and ATP binding.
Collapse
Affiliation(s)
- Bayan Mashahreh
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Fouad Hassouna
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nadine Soudah
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Roi Strulovich
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
48
|
Berndt N, Seib E, Kim S, Troost T, Lyga M, Langenbach J, Haensch S, Kalodimou K, Delidakis C, Klein T. Ubiquitylation-independent activation of Notch signalling by Delta. eLife 2017; 6:27346. [PMID: 28960177 PMCID: PMC5675594 DOI: 10.7554/elife.27346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/28/2017] [Indexed: 12/29/2022] Open
Abstract
Ubiquitylation (ubi) by the E3-ligases Mindbomb1 (Mib1) and Neuralized (Neur) is required for activation of the DSL ligands Delta (Dl) and Serrate (Ser) to activate Notch signalling. These ligases transfer ubiquitin to lysines of the ligands' intracellular domains (ICDs), which sends them into an Epsin-dependent endocytic pathway. Here, we have tested the requirement of ubi of Dl for signalling. We found that Dl requires ubi for its full function, but can also signal in two ubi-independent modes, one dependent and one independent of Neur. We identified two neural lateral specification processes where Dl signals in an ubi-independent manner. Neur, which is needed for these processes, was shown to be able to activate Dl in an ubi-independent manner. Our analysis suggests that one important role of DSL protein ubi by Mib1 is their release from cis-inhibitory interactions with Notch, enabling them to trans-activate Notch on adjacent cells.
Collapse
Affiliation(s)
- Nicole Berndt
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| | - Ekaterina Seib
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| | - Soya Kim
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany.,Molekulare Zellbiologie, Institut I für Anatomie, Uniklinik Köln, Universität zu Köln, Köln, Germany
| | - Tobias Troost
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| | - Marvin Lyga
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| | - Jessica Langenbach
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| | - Sebastian Haensch
- Center of Advanced Imaging, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| | - Konstantina Kalodimou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - Thomas Klein
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Duesseldorf, Germany
| |
Collapse
|
49
|
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: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/03/2017] [Accepted: 07/03/2017] [Indexed: 12/14/2022]
Abstract
Genomic DNA is damaged at an extremely high frequency by both endogenous and environmental factors. An improper response to DNA damage can lead to genome instability, accelerate the aging process and ultimately cause various human diseases, including cancers and neurodegenerative disorders. The mechanisms that underlie the cellular DNA damage response (DDR) are complex and are regulated at many levels, including at the level of post-translational modification (PTM). Since the discovery of ubiquitin in 1975 and ubiquitylation as a form of PTM in the early 1980s, a number of ubiquitin-like modifiers (UBLs) have been identified, including small ubiquitin-like modifiers (SUMOs), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), interferon-stimulated gene 15 (ISG15), human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), ubiquitin-fold modifier 1 (UFRM1), URM1 ubiquitin-related modifier-1 (URM1), autophagy-related protein 12 (ATG12), autophagy-related protein 8 (ATG8), fan ubiquitin-like protein 1 (FUB1) and histone mono-ubiquitylation 1 (HUB1). All of these modifiers have known roles in the cellular response to various forms of stress, and delineating their underlying molecular mechanisms and functions is fundamental in enhancing our understanding of human disease and longevity. To date, however, the molecular mechanisms and functions of these UBLs in the DDR remain largely unknown. This review summarizes the current status of PTMs by UBLs in the DDR and their implication in cancer diagnosis, therapy and drug discovery.
Collapse
Affiliation(s)
- Zhifeng Wang
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China; Beijing Key Laboratory of DNA Damage Response, Capital Normal University College of Life Sciences, Beijing 100048, China.
| |
Collapse
|
50
|
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: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/06/2017] [Indexed: 02/06/2023] Open
Abstract
The modification of proteins by ubiquitin-fold modifier 1 (UFM1) is implicated in many human diseases. Prior to conjugation, UFM1 undergoes activation by its cognate activating enzyme, UBA5. UBA5 is a non-canonical E1 activating enzyme that possesses an adenylation domain but lacks a distinct cysteine domain. Binding of UBA5 to UFM1 is mediated via an amino acid sequence, known as the UFM1-interacting sequence (UIS), located outside the adenylation domain that is required for UFM1 activation. However, the precise boundaries of the UIS are yet not clear and are still under debate. Here we revisit the interaction of UFM1 with UBA5 by determining the crystal structure of UFM1 fused to 13 amino acids of human UBA5. Using binding and activity assays, we found that His 336 of UBA5, previously not reported to be part of the UIS, occupies a negatively charged pocket on UFM1’s surface. This His is involved in UFM1 binding and if mutated perturbs activation of UFM1. Surprisingly, we also found that the interaction between two UFM1 molecules mimics how the UIS binds UFM1. Specifically, UFM1 His 70 resembles UBA5 His336 and enters a negatively charged pocked on the other UFM1 molecule. Our results refine our understanding of UFM1-UBA5 binding.
Collapse
|