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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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Cao X, Cui H, Ji X, Li B, Lu R, Zhang Y, Chen J. Determining the Potential Roles of Branched-Chain Amino Acids in the Regulation of Muscle Growth in Common Carp ( Cyprinus carpio) Based on Transcriptome and MicroRNA Sequencing. Aquac Nutr 2023; 2023:7965735. [PMID: 37303609 PMCID: PMC10257547 DOI: 10.1155/2023/7965735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023]
Abstract
Branched-chain amino acids (BCAAs) can be critically involved in skeletal muscle growth and body energy homeostasis. Skeletal muscle growth is a complex process; some muscle-specific microRNAs (miRNAs) are involved in the regulation of muscle thickening and muscle mass. Additionally, the regulatory network between miRNA and messenger RNA (mRNA) in the modulation of the role of BCAAs on skeletal muscle growth in fish has not been studied. In this study, common carp was starved for 14 days, followed by a 14-day gavage therapy with BCAAs, to investigate some of the miRNAs and genes that contribute to the regulation of normal growth and maintenance of skeletal muscle in response to short-term BCAA starvation stress. Subsequently, the transcriptome and small RNAome sequencing of carp skeletal muscle were performed. A total of 43,414 known and 1,112 novel genes were identified, in addition to 142 known and 654 novel miRNAs targeting 22,008 and 33,824 targets, respectively. Based on their expression profiles, 2,146 differentially expressed genes (DEGs) and 84 differentially expressed miRNA (DEMs) were evaluated. Kyoto Encyclopedia of Genes and Genome pathways, including the proteasome, phagosome, autophagy in animals, proteasome activator complex, and ubiquitin-dependent protein catabolic process, were enriched for these DEGs and DEMs. Our findings revealed the role of atg5, map1lc3c, ctsl, cdc53, psma6, psme2, myl9, and mylk in skeletal muscle growth, protein synthesis, and catabolic metabolism. Furthermore, miR-135c, miR-192, miR-194, and miR-203a may play key roles in maintaining the normal activities of the organism by regulating genes related to muscle growth, protein synthesis, and catabolism. This study on transcriptome and miRNA reveals the potential molecular mechanisms underlying the regulation of muscle protein deposition and provides new insights into genetic engineering techniques to improve common carp muscle development.
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Affiliation(s)
- Xianglin Cao
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Han Cui
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Xinyu Ji
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Baohua Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Yuru Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Jianjun Chen
- College of Life Science, Henan Normal University, Xinxiang 453007, China
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Adinolfi S, Patinen T, Jawahar Deen A, Pitkänen S, Härkönen J, Kansanen E, Küblbeck J, Levonen AL. The KEAP1-NRF2 pathway: Targets for therapy and role in cancer. Redox Biol 2023; 63:102726. [PMID: 37146513 DOI: 10.1016/j.redox.2023.102726] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
The KEAP1-NRF2 pathway is the key regulator of cellular defense against both extrinsic and intrinsic oxidative and electrophilic stimuli. Since its discovery in the 1990s, its seminal role in various disease pathologies has become well appreciated, motivating research to elucidate the intricacies of NRF2 signaling and its downstream effects to identify novel targets for therapy. In this graphical review, we present an updated overview of the KEAP1-NRF2 signaling, focusing on the progress made within the past ten years. Specifically, we highlight the advances made in understanding the mechanism of activation of NRF2, resulting in novel discoveries in its therapeutic targeting. Furthermore, we will summarize new findings in the rapidly expanding field of NRF2 in cancer, with important implications for its diagnostics and treatment.
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Affiliation(s)
- Simone Adinolfi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Tommi Patinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Ashik Jawahar Deen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Sini Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Jouni Härkönen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland; Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Emilia Kansanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland; Science Service Center, Kuopio University Hospital, Kuopio, Finland
| | - Jenni Küblbeck
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Anna-Liisa Levonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland.
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Black HH, Hanson JL, Roberts JE, Leslie SN, Campodonico W, Ebmeier CC, Holling GA, Tay JW, Matthews AM, Ung E, Lau CI, Whiteley AM. UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS. eLife 2023; 12:e79452. [PMID: 36951542 PMCID: PMC10076021 DOI: 10.7554/elife.79452] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/15/2023] [Indexed: 03/24/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron dysfunction and loss. A portion of ALS cases are caused by mutation of the proteasome shuttle factor Ubiquilin 2 (UBQLN2), but the molecular pathway leading from UBQLN2 dysfunction to disease remains unclear. Here, we demonstrate that UBQLN2 regulates the domesticated gag-pol retrotransposon 'paternally expressed gene 10 (PEG10)' in human cells and tissues. In cells, the PEG10 gag-pol protein cleaves itself in a mechanism reminiscent of retrotransposon self-processing to generate a liberated 'nucleocapsid' fragment, which uniquely localizes to the nucleus and changes the expression of genes involved in axon remodeling. In spinal cord tissue from ALS patients, PEG10 gag-pol is elevated compared to healthy controls. These findings implicate the retrotransposon-like activity of PEG10 as a contributing mechanism in ALS through the regulation of gene expression, and restraint of PEG10 as a primary function of UBQLN2.
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Affiliation(s)
- Holly H Black
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Jessica L Hanson
- Institute for Behavioral Genetics, University of Colorado BoulderBoulderUnited States
| | - Julia E Roberts
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Shannon N Leslie
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Will Campodonico
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | | | - G Aaron Holling
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Jian Wei Tay
- Biofrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Autumn M Matthews
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Elizabeth Ung
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Cristina I Lau
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
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Nakatsukasa K, Fujisawa M, Yang X, Kawarasaki T, Okumura F, Kamura T. Triacylglycerol lipase Tgl4 is a stable protein and its dephosphorylation is regulated in a cell cycle-dependent manner in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2022; 626:85-91. [PMID: 35981421 DOI: 10.1016/j.bbrc.2022.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Triacylglycerols (TGs) serve as reservoirs for diacylglycerols and fatty acids, which play important roles in synthesizing energy and membrane lipids that are required for cell cycle progression. In the yeast, Saccharomyces cerevisiae, Tgl4, the functional ortholog of murine adipose triacylglycerol lipase (ATGL), is activated by Cdk1/Cdc28-mediated phosphorylation and facilitates the G1/S transition. However, little is known about how Tgl4 is inactivated during the cell cycle. To monitor the phosphorylation status and the stability of endogenous Tgl4, we raised a specific antibody against Tgl4. We found that in contrast to the previous suggestion, Tgl4 was a stable protein throughout the cell cycle. We also showed that Tgl4 was dephosphorylated upon entry into G1 phase. These results suggest that Tgl4 is a stable protein and is inactivated during G1 phase by dephosphorylation.
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Affiliation(s)
- Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan.
| | - Munetaka Fujisawa
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Xiaotan Yang
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Tomoyuki Kawarasaki
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, 813-8582, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
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Basu B, Ghosh MK. Ubiquitination and deubiquitination in the regulation of epithelial-mesenchymal transition in cancer: Shifting gears at the molecular level. Biochim Biophys Acta Mol Cell Res 2022; 1869:119261. [PMID: 35307468 DOI: 10.1016/j.bbamcr.2022.119261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The process of conversion of non-motile epithelial cells to their motile mesenchymal counterparts is known as epithelial-mesenchymal transition (EMT), which is a fundamental event during embryonic development, tissue repair, and for the maintenance of stemness. However, this crucial process is hijacked in cancer and becomes the means by which cancer cells acquire further malignant properties such as increased invasiveness, acquisition of stem cell-like properties, increased chemoresistance, and immune evasion ability. The switch from epithelial to mesenchymal phenotype is mediated by a wide variety of effector molecules such as transcription factors, epigenetic modifiers, post-transcriptional and post-translational modifiers. Ubiquitination and de-ubiquitination are two post-translational processes that are fundamental to the ubiquitin-proteasome system (UPS) of the cell, and the shift in equilibrium between these two processes during cancer dictates the suppression or activation of different intracellular processes, including EMT. Here, we discuss the complex and dynamic relationship between components of the UPS and EMT in cancer.
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Affiliation(s)
- Bhaskar Basu
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.
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7
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Bartas M, Slychko K, Brázda V, Červeň J, Beaudoin CA, Blundell TL, Pečinka P. Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. Int J Mol Sci 2022; 23:768. [PMID: 35054954 DOI: 10.3390/ijms23020768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.
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Abstract
Ubiquitin-proteasome mediated protein turnover is an important regulatory mechanism of cellular function in eukaryotes. Extensive studies have linked the ubiquitin-proteasome system (UPS) to human diseases, and an array of proteasome inhibitors have been successfully developed for cancer therapy. Although still an emerging field, research on UPS regulation of fungal development and virulence has been rapidly advancing and has generated considerable excitement in its potential as a target for novel drugs. In this review, we summarize UPS composition and regulatory function in pathogenic fungi, especially in stress responses, host adaption, and fungal pathogenesis. Emphasis will be given to UPS regulation of pathogenic factors that are important for fungal pathogenesis. We also discuss future potential therapeutic strategies for fungal infections based on targeting UPS pathways.
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Affiliation(s)
- Chengjun Cao
- Public Health Research Institute, Rutgers University, New Brunswick, NJ, United States
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, New Brunswick, NJ, United States
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, United States
- Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ, United States
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9
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St-Cyr D, Ceccarelli DF, Orlicky S, van der Sloot AM, Tang X, Kelso S, Moore S, James C, Posternak G, Coulombe-Huntington J, Bertomeu T, Marinier A, Sicheri F, Tyers M. Identification and optimization of molecular glue compounds that inhibit a noncovalent E2 enzyme-ubiquitin complex. Sci Adv 2021; 7:eabi5797. [PMID: 34705497 PMCID: PMC10763754 DOI: 10.1126/sciadv.abi5797] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Pharmacological control of the ubiquitin-proteasome system (UPS) is of intense interest in drug discovery. Here, we report the development of chemical inhibitors of the ubiquitin-conjugating (E2) enzyme CDC34A (also known as UBE2R1), which donates activated ubiquitin to the cullin-RING ligase (CRL) family of ubiquitin ligase (E3) enzymes. A FRET-based interaction assay was used to screen for novel compounds that stabilize the noncovalent complex between CDC34A and ubiquitin, and thereby inhibit the CDC34A catalytic cycle. An isonipecotamide hit compound was elaborated into analogs with ~1000-fold increased potency in stabilizing the CDC34A-ubiquitin complex. These analogs specifically inhibited CDC34A-dependent ubiquitination in vitro and stabilized an E2~ubiquitin thioester reaction intermediate in cells. The x-ray crystal structure of a CDC34A-ubiquitin-inhibitor complex uncovered the basis for analog structure-activity relationships. The development of chemical stabilizers of the CDC34A-ubiquitin complex illustrates a general strategy for de novo discovery of molecular glue compounds that stabilize weak protein interactions.
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Affiliation(s)
- Daniel St-Cyr
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Derek F. Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Stephen Orlicky
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Almer M. van der Sloot
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Xiaojing Tang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Susan Kelso
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Susan Moore
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Clint James
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Ganna Posternak
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
- Department of Chemistry, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
- Department of Medicine, University of Montreal, Montreal, Québec H3C 3J7, Canada
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Abstract
Cullin-RING ubiquitin ligases (CRLs) are dynamic modular platforms that regulate myriad biological processes through target-specific ubiquitylation. Our knowledge of this system emerged from the F-box hypothesis, posited a quarter century ago: Numerous interchangeable F-box proteins confer specific substrate recognition for a core CUL1-based RING E3 ubiquitin ligase. This paradigm has been expanded through the evolution of a superfamily of analogous modular CRLs, with five major families and over 200 different substrate-binding receptors in humans. Regulation is achieved by numerous factors organized in circuits that dynamically control CRL activation and substrate ubiquitylation. CRLs also serve as a vast landscape for developing small molecules that reshape interactions and promote targeted ubiquitylation-dependent turnover of proteins of interest. Here, we review molecular principles underlying CRL function, the role of allosteric and conformational mechanisms in controlling substrate timing and ubiquitylation, and how the dynamics of substrate receptor interchange drives the turnover of selected target proteins to promote cellular decision-making.
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Affiliation(s)
- J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany;
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Parveen A, Rahim MS, Sharma A, Mishra A, Kumar P, Fandade V, Kumar P, Bhandawat A, Verma SK, Roy J. Genome-wide analysis of RING-type E3 ligase family identifies potential candidates regulating high amylose starch biosynthesis in wheat (Triticum aestivum L.). Sci Rep 2021; 11:11461. [PMID: 34075092 DOI: 10.1038/s41598-021-90685-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/10/2021] [Indexed: 12/02/2022] Open
Abstract
In ubiquitin-mediated post-translational modifications, RING finger families are emerged as important E3 ligases in regulating biological processes. Amylose and amylopectin are two major constituents of starch in wheat seed endosperm. Studies have been found the beneficial effects of high amylose or resistant starch on health. The ubiquitin-mediated post-translational regulation of key enzymes for amylose/amylopectin biosynthesis (GBSSI and SBEII) is still unknown. In this study, the genome-wide analysis identified 1272 RING domains in 1255 proteins in wheat, which is not reported earlier. The identified RING domains classified into four groups—RING-H2, RING-HC, RING-v, RING-G, based on the amino acid residues (Cys, His) at metal ligand positions and the number of residues between them with the predominance of RING-H2 type. A total of 1238 RING protein genes were found to be distributed across all 21 wheat chromosomes. Among them, 1080 RING protein genes were identified to show whole genome/segmental duplication within the hexaploid wheat genome. In silico expression analysis using transcriptome data revealed 698 RING protein genes, having a possible role in seed development. Based on differential gene expression and correlation analysis of 36 RING protein genes in diverse (high and low) amylose mutants and parent, 10 potential RING protein genes found to be involved in high amylose biosynthesis and significantly associated with two starch biosynthesis genes; GBSSI and SBEIIa. Characterization of mutant lines using next-generation sequencing method identified unique mutations in 698 RING protein genes. This study signifies the putative role of RING-type E3 ligases in amylose biosynthesis and this information will be helpful for further functional validation and its role in other biological processes in wheat.
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Gai W, Peng Z, Liu CH, Zhang L, Jiang H. Advances in Cancer Treatment by Targeting the Neddylation Pathway. Front Cell Dev Biol 2021; 9:653882. [PMID: 33898451 PMCID: PMC8060460 DOI: 10.3389/fcell.2021.653882] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Developmental down-regulation protein 8 (NEDD8), expressed by neural progenitors, is a ubiquitin-like protein that conjugates to and regulates the biological function of its substrates. The main target of NEDD8 is cullin-RING E3 ligases. Upregulation of the neddylation pathway is closely associated with the progression of various tumors, and MLN4924, which inhibits NEDD8-activating enzyme (NAE), is a promising new antitumor compound for combination therapy. Here, we summarize the latest progress in anticancer strategies targeting the neddylation pathway and their combined applications, providing a theoretical reference for developing antitumor drugs and combination therapies.
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Affiliation(s)
- Wenbin Gai
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Zhiqiang Peng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lingqiang Zhang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,Peixian People's Hospital, Xuzhou, China
| | - Hong Jiang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
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13
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Wu Y, Zhang W. The Role of E3s in Regulating Pluripotency of Embryonic Stem Cells and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:1168. [PMID: 33503896 PMCID: PMC7865285 DOI: 10.3390/ijms22031168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are derived from early embryos and can differentiate into any type of cells in living organisms. Induced pluripotent stem cells (iPSCs) resemble ESCs, both of which serve as excellent sources to study early embryonic development and realize cell replacement therapies for age-related degenerative diseases and other cell dysfunction-related illnesses. To achieve these valuable applications, comprehensively understanding of the mechanisms underlying pluripotency maintenance and acquisition is critical. Ubiquitination modifies proteins with Ubiquitin (Ub) at the post-translational level to monitor protein stability and activity. It is extensively involved in pluripotency-specific regulatory networks in ESCs and iPSCs. Ubiquitination is achieved by sequential actions of the Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. Compared with E1s and E2s, E3s are most abundant, responsible for substrate selectivity and functional diversity. In this review, we focus on E3 ligases to discuss recent progresses in understanding how they regulate pluripotency and somatic cell reprogramming through ubiquitinating core ESC regulators.
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Affiliation(s)
| | - Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China;
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14
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Bungsy M, Palmer MCL, Jeusset LM, Neudorf NM, Lichtensztejn Z, Nachtigal MW, McManus KJ. Reduced RBX1 expression induces chromosome instability and promotes cellular transformation in high-grade serous ovarian cancer precursor cells. Cancer Lett 2020; 500:194-207. [PMID: 33290867 DOI: 10.1016/j.canlet.2020.11.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
Despite high-grade serous ovarian cancer (HGSOC) being the most common and lethal gynecological cancer in women, the early etiological events driving disease development remain largely unknown. Emerging evidence now suggests that chromosome instability (CIN; ongoing changes in chromosome numbers) may play a central role in the development and progression of HGSOC. Importantly, genomic amplification of the Cyclin E1 gene (CCNE1) contributes to HGSOC pathogenesis in ~20% of patients, while Cyclin E1 overexpression induces CIN in model systems. Cyclin E1 levels are normally regulated by the SCF (SKP1-CUL1-FBOX) complex, an E3 ubiquitin ligase that includes RBX1 as a core component. Interestingly, RBX1 is heterozygously lost in ~80% of HGSOC cases and reduced expression corresponds with worse outcomes, suggesting it may be a pathogenic event. Using both short (siRNA) and long (CRISPR/Cas9) term approaches, we show that reduced RBX1 expression corresponds with significant increases in CIN phenotypes in fallopian tube secretory epithelial cells, a cellular precursor of HGSOC. Moreover, reduced RBX1 expression corresponds with increased Cyclin E1 levels and anchorage-independent growth. Collectively, these data identify RBX1 as a novel CIN gene with pathogenic implications for HGSOC.
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Affiliation(s)
- Manisha Bungsy
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Michaela C L Palmer
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Lucile M Jeusset
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Nicole M Neudorf
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Mark W Nachtigal
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Obstetrics, Gynecology & Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J McManus
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada.
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15
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Dhakal S, Macreadie I. Protein Homeostasis Networks and the Use of Yeast to Guide Interventions in Alzheimer's Disease. Int J Mol Sci 2020; 21:E8014. [PMID: 33126501 PMCID: PMC7662794 DOI: 10.3390/ijms21218014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's Disease (AD) is a progressive multifactorial age-related neurodegenerative disorder that causes the majority of deaths due to dementia in the elderly. Although various risk factors have been found to be associated with AD progression, the cause of the disease is still unresolved. The loss of proteostasis is one of the major causes of AD: it is evident by aggregation of misfolded proteins, lipid homeostasis disruption, accumulation of autophagic vesicles, and oxidative damage during the disease progression. Different models have been developed to study AD, one of which is a yeast model. Yeasts are simple unicellular eukaryotic cells that have provided great insights into human cell biology. Various yeast models, including unmodified and genetically modified yeasts, have been established for studying AD and have provided significant amount of information on AD pathology and potential interventions. The conservation of various human biological processes, including signal transduction, energy metabolism, protein homeostasis, stress responses, oxidative phosphorylation, vesicle trafficking, apoptosis, endocytosis, and ageing, renders yeast a fascinating, powerful model for AD. In addition, the easy manipulation of the yeast genome and availability of methods to evaluate yeast cells rapidly in high throughput technological platforms strengthen the rationale of using yeast as a model. This review focuses on the description of the proteostasis network in yeast and its comparison with the human proteostasis network. It further elaborates on the AD-associated proteostasis failure and applications of the yeast proteostasis network to understand AD pathology and its potential to guide interventions against AD.
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Affiliation(s)
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia;
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16
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Subudhi AK, O'Donnell AJ, Ramaprasad A, Abkallo HM, Kaushik A, Ansari HR, Abdel-Haleem AM, Ben Rached F, Kaneko O, Culleton R, Reece SE, Pain A. Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms. Nat Commun 2020; 11:2763. [PMID: 32488076 DOI: 10.1038/s41467-020-16593-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 05/04/2020] [Indexed: 01/23/2023] Open
Abstract
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 6% of Plasmodium falciparum genes show 24 h rhythms in expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a 24 h transcriptional rhythm and disrupting it in rodent malaria parasites shortens the IDC by 2-3 h; (v) Multiple processes including DNA replication, and the ubiquitin and proteasome pathways, are affected by loss of coordination with host rhythms and by disruption of SR10. Our results reveal malaria parasites are at least partly responsible for scheduling the IDC and coordinating their development with host daily rhythms. The mechanism underlying periodicity of Plasmodium’s intra-erythrocytic developmental cycle (IDC) is unclear. Here, Subudhi et al. show that serpentine receptor 10 (SR10) plays a role in regulating the schedule of the IDC in line with the timing of host daily rhythms.
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17
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Asmamaw MD, Liu Y, Zheng YC, Shi XJ, Liu HM. Skp2 in the ubiquitin-proteasome system: A comprehensive review. Med Res Rev 2020; 40:1920-1949. [PMID: 32391596 DOI: 10.1002/med.21675] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/26/2020] [Accepted: 04/27/2020] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system (UPS) is a complex process that regulates protein stability and activity by the sequential actions of E1, E2 and E3 enzymes to influence diverse aspects of eukaryotic cells. However, due to the diversity of proteins in cells, substrate selection is a highly critical part of the process. As a key player in UPS, E3 ubiquitin ligases recruit substrates for ubiquitination specifically. Among them, RING E3 ubiquitin ligases which are the most abundant E3 ubiquitin ligases contribute to diverse cellular processes. The multisubunit cullin-RING ligases (CRLs) are the largest family of RING E3 ubiquitin ligases with tremendous plasticity in substrate specificity and regulate a vast array of cellular functions. The F-box protein Skp2 is a component of CRL1 (the prototype of CRLs) which is expressed in many tissues and participates in multiple cellular functions such as cell proliferation, metabolism, and tumorigenesis by contributing to the ubiquitination and subsequent degradation of several specific tumor suppressors. Most importantly, Skp2 plays a pivotal role in a plethora of cancer-associated signaling pathways. It enhances cell growth, accelerates cell cycle progression, promotes migration and invasion, and inhibits cell apoptosis among others. Hence, targeting Skp2 may represent a novel and attractive strategy for the treatment of different human cancers overexpressing this oncogene. In this review article, we summarized the known roles of Skp2 both in health and disease states in relation to the UPS.
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Affiliation(s)
- Moges Dessale Asmamaw
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Ying Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Xiao-Jing Shi
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
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18
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Matsuda N, Yamano K. Two sides of a coin: Physiological significance and molecular mechanisms for damage-induced mitochondrial localization of PINK1 and Parkin. Neurosci Res 2020; 159:16-24. [PMID: 32201358 DOI: 10.1016/j.neures.2020.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022]
Abstract
In 1998, PARKIN was reported as a causal gene for hereditary recessive Parkinsonism by Kitada, Mizuno, Hattori, and Shimizu et al. Later in 2004, PINK1 was also reported as a causal gene for hereditary recessive Parkinsonism by Valente, Auburger, and Wood et al. Although many unsolved mysteries still remain, our knowledge of PINK1 and Parkin function has increased dramatically since then. Despite a number of milestone studies that advanced the PINK1 and Parkin research field, a critical turning point was undoubtedly the determination that their genuine subcellular localization was on depolarized mitochondria. In this review, we outline the key studies that have contributed to our current model for mitochondrial localization of PINK1 and Parkin. Interestingly, like two sides of a coin, our attempts to elucidate the mechanisms underlying the localization of PINK1 and Parkin were inextricably tied to the identification of the PINK1 substrate and molecular dissection of the Parkin activation mechanism.
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Affiliation(s)
- Noriyuki Matsuda
- The Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Room N-202, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Koji Yamano
- The Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Room N-202, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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19
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Jaskolka MC, Kane PM. Interaction between the yeast RAVE complex and Vph1-containing V o sectors is a central glucose-sensitive interaction required for V-ATPase reassembly. J Biol Chem 2020; 295:2259-2269. [PMID: 31941791 DOI: 10.1074/jbc.ra119.011522] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Indexed: 12/12/2022] Open
Abstract
The yeast vacuolar H+-ATPase (V-ATPase) of budding yeast (Saccharomyces cerevisiae) is regulated by reversible disassembly. Disassembly inhibits V-ATPase activity under low-glucose conditions by releasing peripheral V1 subcomplexes from membrane-bound Vo subcomplexes. V-ATPase reassembly and reactivation requires intervention of the conserved regulator of H+-ATPase of vacuoles and endosomes (RAVE) complex, which binds to cytosolic V1 subcomplexes and assists reassembly with integral membrane Vo complexes. Consistent with its role, the RAVE complex itself is reversibly recruited to the vacuolar membrane by glucose, but the requirements for its recruitment are not understood. We demonstrate here that RAVE recruitment to the membrane does not require an interaction with V1 Glucose-dependent RAVE localization to the vacuolar membrane required only intact Vo complexes containing the Vph1 subunit, suggesting that the RAVE-Vo interaction is glucose-dependent. We identified a short conserved sequence in the center of the RAVE subunit Rav1 that is essential for the interaction with Vph1 in vivo and in vitro Mutations in this region resulted in the temperature- and pH-dependent growth phenotype characteristic of ravΔ mutants. However, this region did not account for glucose sensitivity of the Rav1-Vph1 interaction. We quantitated glucose-dependent localization of a GFP-tagged RAVE subunit to the vacuolar membrane in several mutants previously implicated in altering V-ATPase assembly state or glucose-induced assembly. RAVE localization did not correlate with V-ATPase assembly levels reported previously in these mutants, highlighting both the catalytic nature of RAVE's role in V-ATPase assembly and the likelihood of glucose signaling to RAVE independently of V1.
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Affiliation(s)
- Michael C Jaskolka
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210.
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20
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Sui X, Li YM. Development of Ubiquitin Tools for Studies of Complex Ubiquitin Processing Protein Machines. CURR ORG CHEM 2020. [DOI: 10.2174/1385272823666191113161511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Ubiquitination is one of the most extensive post-translational modifications in
eukaryotes and is involved in various physiological processes such as protein degradation,
autophagy, protein interaction, and protein localization. The ubiquitin (Ub)-related protein
machines include Ub-activating enzymes (E1s), Ub-conjugating enzymes (E2s), Ub ligases
(E3s), deubiquitinating enzymes (DUBs), p97, and the proteasomes. In recent years,
the role of DUBs has been extensively studied and relatively well understood. On the
other hand, the functional mechanisms of the other more complex ubiquitin-processing
protein machines (e.g., E3, p97, and proteasomes) are still to be sufficiently well explored
due to their intricate nature. One of the hurdles facing the studies of these complex protein
machines is the challenge of developing tailor-designed structurally defined model substrates,
which unfortunately cannot be directly obtained using recombinant technology. Consequently, the acquisition
and synthesis of the ubiquitin tool molecules are essential for the elucidation of the functions and
structures of the complex ubiquitin-processing protein machines. This paper aims to highlight recent studies on
these protein machines based on the synthetic ubiquitin tool molecules.
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Affiliation(s)
- Xin Sui
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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21
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Gong L, Cui D, Xiong X, Zhao Y. Targeting Cullin-RING Ubiquitin Ligases and the Applications in PROTACs. Advances in Experimental Medicine and Biology 2020. [DOI: 10.1007/978-981-15-1025-0_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Ding Z, Ejendal KFK, Soto-Velasquez M, Hayes MP, Santoro N, Larsen MJ, Watts VJ. Genome-Wide Small Interfering RNA Screening Reveals a Role for Cullin3-Really Interesting New Gene Ligase Signaling in Heterologous Sensitization of Adenylyl Cyclase. J Pharmacol Exp Ther 2019; 372:267-276. [PMID: 31857349 DOI: 10.1124/jpet.119.261255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022] Open
Abstract
Heterologous sensitization of adenylyl cyclase (AC) is revealed as enhanced or exaggerated AC/cAMP signaling that occurs following persistent activation of Gα i/o-coupled receptors. This paradoxical phenomenon was discovered more than 40 years ago and was proposed as a cellular mechanism to explain the adaptive changes that occur following chronic exposure to drugs of abuse. However, the underlying molecular mechanisms of heterologous sensitization of AC remain largely unknown. In the present study, we performed a genome-wide cell-based RNA interference screen as an unbiased approach to identify genes associated with heterologous sensitization of AC. Following a series of validation and confirmation assays, three genes that form an E3 ligase complex, cullin3 (CUL3), neural precursor-cell-expressed and developmentally downregulated 8 (NEDD8), and really interesting new gene (RING)-box protein 1 (RBX1), were identified as specific modulators of heterologous sensitization of AC. Furthermore, based on the downstream actions of these genes, we evaluated the activity of proteasome inhibitors as well as the specific NEDD8-activating enzyme inhibitor, MLN4924 (Pevonedistat), in AC sensitization. We demonstrate that MG-132 and bortezomib treatments could mimic the inhibitory effects observed with gene knockdown, and MLN4924 was potent and efficacious in blocking the development of heterologous sensitization of endogenous and recombinant AC isoforms, including AC1, AC2, AC5, and AC6. Together, by using genetic and pharmacological approaches, we identified, for the first time, cullin3-RING ligases and the protein degradation pathway as essential modulators for heterologous sensitization of AC. SIGNIFICANCE STATEMENT: Through a genome-wide cell-based RNA interference screening, we identified three genes that form an E3 ligase complex, cullin3, neural precursor-cell-expressed and developmentally downregulated 8 (NEDD8), and really interesting new gene-box protein 1, as specific modulators of heterologous sensitization of AC. The effect of cullin3, NEDD8, or really interesting new gene-box protein 1 small interfering RNAs on heterologous sensitization was recapitulated by proteasome inhibitors, MG132 and bortezomib, and the specific NEDD8-activating enzyme inhibitor, MLN4924. These results suggest a novel hypothesis in which protein degradation is involved in the sensitization of AC signaling that occurs following chronic activation of Gαi/o-coupled receptors.
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Affiliation(s)
- Zhong Ding
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
| | - Karin F K Ejendal
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
| | - Monica Soto-Velasquez
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
| | - Michael P Hayes
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
| | - Nicholas Santoro
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
| | - Martha J Larsen
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology (Z.D., K.F.K.E., M.S.-V., M.P.H., V.J.W.), Purdue Institute for Drug Discovery (V.J.W.), and Purdue Institute for Integrative Neuroscience (V.J.W.), Purdue University, West Lafayette, Indiana; and Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (N.S., M.J.L.)
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Maurya S, Mary B, Jayandharan GR. Rational Engineering and Preclinical Evaluation of Neddylation and SUMOylation Site Modified Adeno-Associated Virus Vectors in Murine Models of Hemophilia B and Leber Congenital Amaurosis. Hum Gene Ther 2019; 30:1461-1476. [PMID: 31642343 PMCID: PMC6919284 DOI: 10.1089/hum.2019.164] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synthetic engineering of viral vectors such as adeno-associated virus (AAV) is crucial to overcome host transduction barriers observed during clinical gene therapy. We reasoned that exploring the role of cellular ubiquitin-like modifiers (UBLs) such as Neddylation or SUMOylation during AAV transduction could be beneficial. Using a combination of in silico biochemical and molecular engineering strategies, we have studied the impact of these UBLs during AAV2 infection and further developed Neddylation or SUMOylation site–modified AAV vectors and validated them in multiple disease models in vitro and in vivo. Hepatic gene transfer of two novel vectors developed, K105Q (SUMOylation-site mutant) and K665Q (Neddylation-site mutant), demonstrated a significantly improved human coagulation factor (F) IX expression (up to two-fold) in a murine model of hemophilia B. Furthermore, subretinal gene transfer of AAV2-K105Q vector expressing RPE65 gene demonstrated visual correction in a murine model of a retinal degenerative disease (rd12 mice). These vectors did not have any adverse immunogenic events in vivo. Taken together, we demonstrate that gene delivery vectors specifically engineered at UBLs can improve the therapeutic outcome during AAV-mediated ocular or hepatic gene therapy.
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Affiliation(s)
- Shubham Maurya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Bertin Mary
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Giridhara R Jayandharan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
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24
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Nakade H, Migita K, Matsumoto S, Wakatsuki K, Kunishige T, Miyao S, Sho M. Overexpression of Cullin4A correlates with a poor prognosis and tumor progression in esophageal squamous cell carcinoma. Int J Clin Oncol 2019; 25:446-455. [PMID: 31535245 DOI: 10.1007/s10147-019-01547-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cullin4A (CUL4A), which is a component of E3 ubiquitin ligase, is implicated in many cellular events. Although the altered expression of CUL4A has been reported in several human cancers, the role of CUL4A in esophageal cancer remains unknown. METHODS We investigated the CUL4A expression in primary esophageal squamous cell carcinoma (ESCC) tissue specimens from 120 patients by immunohistochemistry and explored its clinical relevance and prognostic value. Furthermore, the effect of the expression of CUL4A on cancer cell proliferation was analyzed in vitro using an siRNA silencing technique. RESULTS The higher expression of CUL4A was significantly associated with a deeper depth of tumor invasion (P < 0.001) and the presence of venous invasion (P = 0.014). The disease-specific survival (DSS) rate in patients with tumors that showed high CUL4A expression levels was significantly lower than that in patients whose tumors showed low CUL4A expression levels (P = 0.001). Importantly, the CUL4A status was identified as an independent prognostic factor for DSS (P = 0.045). Our results suggested that the CUL4A expression has significant prognostic value in ESCC. Furthermore, CUL4A gene silencing significantly inhibited the proliferation of ESCC cells in vitro. In addition, the knockdown of the CUL4A expression induced G1 phase arrest and increased the p21 and p27 protein levels. CONCLUSIONS CUL4A might play an important role in regulating the proliferation of ESCC cells and promoting the development of postoperative recurrence.
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Affiliation(s)
- Hiroshi Nakade
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan.
| | - Kazuhiro Migita
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Sohei Matsumoto
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Kohei Wakatsuki
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Tomohiro Kunishige
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Shintaro Miyao
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Masayuki Sho
- Department of Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
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25
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Williams KM, Qie S, Atkison JH, Salazar-Arango S, Alan Diehl J, Olsen SK. Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Nat Commun 2019; 10:3296. [PMID: 31341161 PMCID: PMC6656757 DOI: 10.1038/s41467-019-11061-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/20/2019] [Indexed: 12/14/2022] Open
Abstract
Ubiquitin (Ub) signaling requires the sequential interactions and activities of three enzymes, E1, E2, and E3. Cdc34 is an E2 that plays a key role in regulating cell cycle progression and requires unique structural elements to function. The molecular basis by which Cdc34 engages its E1 and the structural mechanisms by which its unique C-terminal extension functions in Cdc34 activity are unknown. Here, we present crystal structures of Cdc34 alone and in complex with E1, and a Cdc34~Ub thioester mimetic that represents the product of Uba1-Cdc34 Ub transthiolation. These structures reveal conformational changes in Uba1 and Cdc34 and a unique binding mode that are required for transthiolation. The Cdc34~Ub structure reveals contacts between the Cdc34 C-terminal extension and Ub that stabilize Cdc34~Ub in a closed conformation and are critical for Ub discharge. Altogether, our structural, biochemical, and cell-based studies provide insights into the molecular mechanisms by which Cdc34 function in cells.
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Affiliation(s)
- Katelyn M Williams
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Shuo Qie
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - James H Atkison
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Sabrina Salazar-Arango
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - J Alan Diehl
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Shaun K Olsen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
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26
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Münzner U, Klipp E, Krantz M. A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae. Nat Commun 2019; 10:1308. [PMID: 30899000 PMCID: PMC6428898 DOI: 10.1038/s41467-019-08903-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Understanding how cellular functions emerge from the underlying molecular mechanisms is a key challenge in biology. This will require computational models, whose predictive power is expected to increase with coverage and precision of formulation. Genome-scale models revolutionised the metabolic field and made the first whole-cell model possible. However, the lack of genome-scale models of signalling networks blocks the development of eukaryotic whole-cell models. Here, we present a comprehensive mechanistic model of the molecular network that controls the cell division cycle in Saccharomyces cerevisiae. We use rxncon, the reaction-contingency language, to neutralise the scalability issues preventing formulation, visualisation and simulation of signalling networks at the genome-scale. We use parameter-free modelling to validate the network and to predict genotype-to-phenotype relationships down to residue resolution. This mechanistic genome-scale model offers a new perspective on eukaryotic cell cycle control, and opens up for similar models-and eventually whole-cell models-of human cells.
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Affiliation(s)
- Ulrike Münzner
- Humboldt-Universität zu Berlin, Institute of Biology, Theoretical Biophysics, Berlin, 10099, Germany
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Edda Klipp
- Humboldt-Universität zu Berlin, Institute of Biology, Theoretical Biophysics, Berlin, 10099, Germany
| | - Marcus Krantz
- Humboldt-Universität zu Berlin, Institute of Biology, Theoretical Biophysics, Berlin, 10099, Germany.
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27
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Abstract
Ubiquitin (Ub)-mediated protein degradation is a key cellular defense mechanism that detects and eliminates defective proteins. A major intracellular site of protein quality control degradation is the endoplasmic reticulum (ER), hence the term ER-associated degradation, or endoplasmic reticulum-associated degradation (ERAD). Yeast ERAD is composed of three Ub-protein conjugation complexes, named according to their E3 Ub-protein ligase components, Hrd1, Doa10, and the Asi complex, which resides at the nuclear envelope (NE). These ER/NE membrane-associated RING-type E3 ligases recognize and ubiquitylate defective proteins in cooperation with the E2 conjugating enzyme Ubc7 and the obligatory Ubc7 cofactor Cue1. Interaction of Ubc7 with the RING domains of its cognate E3 Ub-protein ligases stimulates the formation of isopeptide (amide) Ub-Ub linkages. Each isopeptide bond is formed by transfer of an Ubc7-linked activated Ub to a lysine side chain of an acceptor Ub. Multiple Ub transfer reactions form a poly-Ub chain that targets the conjugated protein for degradation by the proteasome. To study the mechanism of Ub-Ub bond formation, this reaction is reconstituted in a cell-free system consisting of recombinant E1, Ub, Ubc7, its cofactor Cue1, and the RING domain of either Doa10 or Hrd1. Here we provide detailed protocols for the purification of the required recombinant proteins and for the reactions that produce an Ub-Ub bond, specifically, the formation of an Ubc7~Ub thiolester (Ub charging) and subsequent formation of the isopeptide Ub-Ub linkage (Ub transfer). These protocols also provide a useful guideline for similar in vitro ubiquitylation reactions intended to explore the mechanism of other Ub-conjugation systems.
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Affiliation(s)
- Bayan Mashahreh
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Reiss
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | - Tommer Ravid
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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28
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Bramasole L, Sinha A, Gurevich S, Radzinski M, Klein Y, Panat N, Gefen E, Rinaldi T, Jimenez-Morales D, Johnson J, Krogan NJ, Reis N, Reichmann D, Glickman MH, Pick E. Proteasome lid bridges mitochondrial stress with Cdc53/Cullin1 NEDDylation status. Redox Biol 2019; 20:533-543. [PMID: 30508698 PMCID: PMC6279957 DOI: 10.1016/j.redox.2018.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Cycles of Cdc53/Cullin1 rubylation (a.k.a NEDDylation) protect ubiquitin-E3 SCF (Skp1-Cullin1-F-box protein) complexes from self-destruction and play an important role in mediating the ubiquitination of key protein substrates involved in cell cycle progression, development, and survival. Cul1 rubylation is balanced by the COP9 signalosome (CSN), a multi-subunit derubylase that shows 1:1 paralogy to the 26S proteasome lid. The turnover of SCF substrates and their relevance to various diseases is well studied, yet, the extent by which environmental perturbations influence Cul1 rubylation/derubylation cycles per se is still unclear. In this study, we show that the level of cellular oxidation serves as a molecular switch, determining Cullin1 rubylation/derubylation ratio. We describe a mutant of the proteasome lid subunit, Rpn11 that exhibits accumulated levels of Cullin1-Rub1 conjugates, a characteristic phenotype of csn mutants. By dissecting between distinct phenotypes of rpn11 mutants, proteasome and mitochondria dysfunction, we were able to recognize the high reactive oxygen species (ROS) production during the transition of cells into mitochondrial respiration, as a checkpoint of Cullin1 rubylation in a reversible manner. Thus, the study adds the rubylation cascade to the list of cellular pathways regulated by redox homeostasis.
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Affiliation(s)
- L Bramasole
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - A Sinha
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - S Gurevich
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - M Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - Y Klein
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - N Panat
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - E Gefen
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - T Rinaldi
- Department of Biology and Biotechnology, University of Rome ''La Sapienza'', Rome 00185, Italy
| | - D Jimenez-Morales
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - J Johnson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N Reis
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - D Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - M H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - E Pick
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel.
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29
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Bulatov E, Valiullina A, Sayarova R, Rizvanov A. Promising new therapeutic targets for regulation of inflammation and immunity: RING-type E3 ubiquitin ligases. Immunol Lett 2018; 202:44-51. [PMID: 30099009 DOI: 10.1016/j.imlet.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/24/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023]
Abstract
Ubiquitin-proteasome system (UPS) is a primary signaling pathway for regulation of protein turnover and removal of misfolded proteins in eukaryotic cells. Enzymes of the UPS pathway - E1 activating, E2 conjugating, E3 ligating - act together to covalently tag substrate proteins with a chain of ubiquitins, small regulatory proteins. The poly-ubiquitin chain then serves as a recognition motif for 26S proteasome to recognize and degrade the substrate. In recent years UPS has emerged as attractive enzymatic cascade for development of novel therapeutics against various human diseases. Building on the previous success of targeting this pathway in cancer - the broader scientific community is currently looking for ways to elucidate functions of E3 ligases, substrate-specific members of the UPS. RING-type E3 ubiquitin ligases, the largest class of E3s, represent prospective targets for small molecule modulation and their importance is reinforced by ever growing evidence of playing role in non-cancer diseases, primarily associated with inflammatory and immune disorders. In this review, we aim to briefly cover the current knowledge of biological functions of RING-type E3 ligases in inflammation and immunity.
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Affiliation(s)
- Emil Bulatov
- Kazan Federal University, Kazan, Russian Federation.
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30
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Bulatov E, Zagidullin A, Valiullina A, Sayarova R, Rizvanov A. Small Molecule Modulators of RING-Type E3 Ligases: MDM and Cullin Families as Targets. Front Pharmacol 2018; 9:450. [PMID: 29867461 PMCID: PMC5951978 DOI: 10.3389/fphar.2018.00450] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/18/2018] [Indexed: 12/14/2022] Open
Abstract
Ubiquitin-proteasome system (UPS) is a primary signaling pathway for regulation of intracellular protein levels. E3 ubiquitin ligases, substrate-specific members of the UPS, represent highly attractive protein targets for drug discovery. The importance of E3 ligases as prospective targets for small molecule modulation is reinforced by ever growing evidence of their role in cancer and other diseases. To date the number of potent compounds targeting E3 ligases remains rather low and their rational design constitutes a challenging task. To successfully address this problem one must take into consideration the multi-subunit nature of many E3 ligases that implies multiple druggable pockets and protein-protein interfaces. In this review, we briefly cover the current state of drug discovery in the field of RING-type E3 ligases with focus on MDM and Cullin families as targets. We also provide an overview of small molecule chimeras that induce RING-type E3-mediated proteasomal degradation of substrate proteins of interest.
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Affiliation(s)
- Emil Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Almaz Zagidullin
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - Aygul Valiullina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Regina Sayarova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
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31
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Zhou L, Zhang W, Sun Y, Jia L. Protein neddylation and its alterations in human cancers for targeted therapy. Cell Signal 2018; 44:92-102. [PMID: 29331584 DOI: 10.1016/j.cellsig.2018.01.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/27/2017] [Accepted: 01/08/2018] [Indexed: 01/05/2023]
Abstract
Neddylation, a post-translational modification that conjugates an ubiquitin-like protein NEDD8 to substrate proteins, is an important biochemical process that regulates protein function. The best-characterized substrates of neddylation are the cullin subunits of Cullin-RING ligases (CRLs), which, as the largest family of E3 ubiquitin ligases, control many important biological processes, including tumorigenesis, through promoting ubiquitylation and subsequent degradation of a variety of key regulatory proteins. Recently, increasing pieces of experimental evidence strongly indicate that the process of protein neddylation modification is elevated in multiple human cancers, providing sound rationale for its targeting as an attractive anticancer therapeutic strategy. Indeed, neddylation inactivation by MLN4924 (also known as pevonedistat), a small molecule inhibitor of E1 NEDD8-activating enzyme currently in phase I/II clinical trials, exerts significant anticancer effects by inducing cell cycle arrest, apoptosis, senescence and autophagy in a cell-type and context dependent manner. Here, we summarize the latest progresses in the field with a major focus on preclinical studies in validation of neddylation modification as a promising anticancer target.
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32
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Reitsma JM, Liu X, Reichermeier KM, Moradian A, Sweredoski MJ, Hess S, Deshaies RJ. Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases. Cell 2017; 171:1326-1339.e14. [PMID: 29103612 DOI: 10.1016/j.cell.2017.10.016] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/17/2017] [Accepted: 10/12/2017] [Indexed: 12/17/2022]
Abstract
SCF (Skp1-Cullin-F-box) ubiquitin ligases comprise several dozen modular enzymes that have diverse roles in biological regulation. SCF enzymes share a common catalytic core containing Cul1⋅Rbx1, which is directed toward different substrates by a variable substrate receptor (SR) module comprising 1 of 69 F-box proteins bound to Skp1. Despite the broad cellular impact of SCF enzymes, important questions remain about the architecture and regulation of the SCF repertoire, including whether SRs compete for Cul1 and, if so, how this competition is managed. Here, we devise methods that preserve the in vivo assemblages of SCF complexes and apply quantitative mass spectrometry to perform a census of these complexes (the "SCFome") in various states. We show that Nedd8 conjugation and the SR exchange factor Cand1 have a profound effect on shaping the SCFome. Together, these factors enable rapid remodeling of SCF complexes to promote biased assembly of SR modules bound to substrate.
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33
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Rojas F, Koszela J, Búa J, Llorente B, Burchmore R, Auer M, Mottram JC, Téllez-Iñón MT. The ubiquitin-conjugating enzyme CDC34 is essential for cytokinesis in contrast to putative subunits of a SCF complex in Trypanosoma brucei. PLoS Negl Trop Dis 2017; 11:e0005626. [PMID: 28609481 PMCID: PMC5507466 DOI: 10.1371/journal.pntd.0005626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 07/11/2017] [Accepted: 05/06/2017] [Indexed: 12/31/2022] Open
Abstract
The ubiquitin-proteasome system is a post-translational regulatory pathway for controlling protein stability and activity that underlies many fundamental cellular processes, including cell cycle progression. Target proteins are tagged with ubiquitin molecules through the action of an enzymatic cascade composed of E1 ubiquitin activating enzymes, E2 ubiquitin conjugating enzymes, and E3 ubiquitin ligases. One of the E3 ligases known to be responsible for the ubiquitination of cell cycle regulators in eukaryotes is the SKP1-CUL1-F-box complex (SCFC). In this work, we identified and studied the function of homologue proteins of the SCFC in the life cycle of Trypanosoma brucei, the causal agent of the African sleeping sickness. Depletion of trypanosomal SCFC components TbRBX1, TbSKP1, and TbCDC34 by RNAi resulted in decreased growth rate and contrasting cell cycle abnormalities for both procyclic (PCF) and bloodstream (BSF) forms. Depletion of TbRBX1 in PCF cells interfered with kinetoplast replication, whilst depletion of TbSKP1 arrested PCF and BSF cells in the G1/S transition. Silencing of TbCDC34 in BSF cells resulted in a block in cytokinesis and caused rapid clearance of parasites from infected mice. We also show that TbCDC34 is able to conjugate ubiquitin in vitro and in vivo, and that its activity is necessary for T. brucei infection progression in mice. This study reveals that different components of a putative SCFC have contrasting phenotypes once depleted from the cells, and that TbCDC34 is essential for trypanosome replication, making it a potential target for therapeutic intervention. African sleeping sickness is a neglected tropical disease caused by infection with the protozoan parasite Trypanosoma brucei, which is transmitted to humans by tsetse flies (Glossina genus). Treatment of the disease is complex and relies on limited pharmaceutical options. Understanding how T. brucei regulates cell cycle progression at a molecular level when alternating between the mammalian host and the insect vector could lead to better therapies. In this study, we examined different T. brucei proteins with homology to components of the SKP1-CUL1-F-box ubiquitin ligase complex (SCFC), previously characterized in other eukaryotes as a regulator of cell cycle progression. We found that depletion of the homologues of a putative SCFC cause T. brucei to develop abnormally, generating different phenotypes of the mammalian and insect stages. Interestingly, depletion of the ubiquitin conjugating enzyme TbCDC34 arrest cells in a pre-cytokinesis stage, indicating that this protein is essential for cytokinesis. In addition to improving our fundamental understanding of the molecular regulation underlying the sophisticated life cycle of T. brucei, this work pinpoints a potential target for drug development against trypanosomiasis.
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Affiliation(s)
- Federico Rojas
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
- * E-mail:
| | - Joanna Koszela
- Institute of Quantitative Biology Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Jacqueline Búa
- Instituto Nacional de Parasitología ‘Dr. M. Fatala Chabén’, A.N.L.I.S., ‘Dr. Carlos G. Malbrán’, Buenos Aires, Argentina
| | - Briardo Llorente
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Manfred Auer
- Institute of Quantitative Biology Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Jeremy C. Mottram
- Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom
| | - María Teresa Téllez-Iñón
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
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Tao T, Zhou CJ, Wang Q, Chen XR, Sun Q, Zhao TY, Ye JC, Wang Y, Zhang ZY, Zhang YL, Guo ZJ, Wang XB, Li DW, Yu JL, Han CG. Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway. PLoS One 2017; 12:e0177518. [PMID: 28494021 PMCID: PMC5426791 DOI: 10.1371/journal.pone.0177518] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/29/2017] [Indexed: 11/18/2022] Open
Abstract
As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1) plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA), jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV), a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK) proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2) from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection.
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Affiliation(s)
- Tao Tao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Cui-Ji Zhou
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Qian Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong Province, People's Republic of China
| | - Xiang-Ru Chen
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Qian Sun
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Tian-Yu Zhao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Jian-Chun Ye
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Ying Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Zong-Ying Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Yong-Liang Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Ze-Jian Guo
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Xian-Bing Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Da-Wei Li
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Jia-Lin Yu
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Cheng-Gui Han
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, People's Republic of China
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35
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Abstract
Solid-support resins are critical components of AP-MS experiments, but their interactions with experimental conditions are underappreciated.
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Affiliation(s)
- Spencer Havis
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| | - Wilna J. Moree
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| | - Sujina Mali
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
| | - Steven J. Bark
- Department of Biology and Biochemistry
- The University of Houston
- Houston
- USA
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36
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Mali S, Moree WJ, Mitchell M, Widger W, Bark SJ. Observations on different resin strategies for affinity purification mass spectrometry of a tagged protein. Anal Biochem 2016; 515:26-32. [DOI: 10.1016/j.ab.2016.09.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/22/2016] [Accepted: 09/28/2016] [Indexed: 02/06/2023]
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37
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Abstract
Abundance of substrate receptor subunits of Cullin-RING ubiquitin ligases (CRLs) is tightly controlled to maintain the full repertoire of CRLs. Unbalanced levels can lead to sequestration of CRL core components by a few overabundant substrate receptors. Numerous diseases, including cancer, have been associated with misregulation of substrate receptor components, particularly for the largest class of CRLs, the SCF ligases. One relevant mechanism that controls abundance of their substrate receptors, the F-box proteins, is autocatalytic ubiquitylation by intact SCF complex followed by proteasome-mediated degradation. Here we describe an additional pathway for regulation of F-box proteins on the example of yeast Met30. This ubiquitylation and degradation pathway acts on Met30 that is dissociated from Skp1. Unexpectedly, this pathway required the cullin component Cdc53/Cul1 but was independent of the other central SCF component Skp1. We demonstrated that this non-canonical degradation pathway is critical for chromosome stability and effective defense against heavy metal stress. More importantly, our results assign important biological functions to a sub-complex of cullin-RING ligases that comprises Cdc53/Rbx1/Cdc34, but is independent of Skp1. Protein ubiquitylation is the covalent attachment of the small protein ubiquitin onto other proteins and is a key regulatory pathway for most biological processes. The central components of the ubiquitylation process are the E3 ligases, which recognize substrate proteins. The best-studied E3 complexes are the SCF ligases, which are composed of 3 core components—Cdc53, Skp1, Rbx1—that assemble to the functional ligase complex by binding to one of the multiple substrate adaptors—the F-box proteins. Maintaining a balanced repertoire of diverse SCF complexes that represent the entire cellular panel of substrate adapters is challenging. Depending on the cell type, hundreds of different F-box proteins can compete for the single binding site on the common SCF core complex. Rapid degradation of F-box proteins helps in maintaining a critical level of unoccupied Cdc53/Skp1/Rbx1 core, complexes and alterations in levels of F-box proteins has been linked to diseases including cancer. Studying the yeast F-box protein Met30 as a model, we have uncovered a novel mechanism for degradation of F-box proteins. This pathway targets free F-box proteins and requires part of the SCF core. These findings add an additional layer to our understanding of regulation of multisubunit E3 ligase.
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Affiliation(s)
- Radhika Mathur
- Department of Biological Chemistry, College of Medicine, University of California Irvine, Irvine, California, United States of America
| | - James L. Yen
- Department of Biological Chemistry, College of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Peter Kaiser
- Department of Biological Chemistry, College of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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38
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Smardon AM, Nasab ND, Tarsio M, Diakov TT, Kane PM. Molecular Interactions and Cellular Itinerary of the Yeast RAVE (Regulator of the H+-ATPase of Vacuolar and Endosomal Membranes) Complex. J Biol Chem 2015; 290:27511-23. [PMID: 26405040 DOI: 10.1074/jbc.m115.667634] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 12/11/2022] Open
Abstract
The RAVE complex (regulator of the H(+)-ATPase of vacuolar and endosomal membranes) is required for biosynthetic assembly and glucose-stimulated reassembly of the yeast vacuolar H(+)-ATPase (V-ATPase). Yeast RAVE contains three subunits: Rav1, Rav2, and Skp1. Rav1 is the largest subunit, and it binds Rav2 and Skp1 of RAVE; the E, G, and C subunits of the V-ATPase peripheral V1 sector; and Vph1 of the membrane Vo sector. We identified Rav1 regions required for interaction with its binding partners through deletion analysis, co-immunoprecipitation, two-hybrid assay, and pulldown assays with expressed proteins. We find that Skp1 binding requires sequences near the C terminus of Rav1, V1 subunits E and C bind to a conserved region in the C-terminal half of Rav1, and the cytosolic domain of Vph1 binds near the junction of the Rav1 N- and C-terminal halves. In contrast, Rav2 binds to the N-terminal domain of Rav1, which can be modeled as a double β-propeller. Only the V1 C subunit binds to both Rav1 and Rav2. Using GFP-tagged RAVE subunits in vivo, we demonstrate glucose-dependent association of RAVE with the vacuolar membrane, consistent with its role in glucose-dependent V-ATPase assembly. It is known that V1 subunit C localizes to the V1-Vo interface in assembled V-ATPase complexes and is important in regulated disassembly of V-ATPases. We propose that RAVE cycles between cytosol and vacuolar membrane in a glucose-dependent manner, positioning V1 and V0 subcomplexes and orienting the V1 C subunit to promote assembly.
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Affiliation(s)
- Anne M Smardon
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Negin Dehdar Nasab
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Maureen Tarsio
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Theodore T Diakov
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Patricia M Kane
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
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39
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Bulatov E, Ciulli A. Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation. Biochem J 2015; 467:365-86. [PMID: 25886174 DOI: 10.1042/BJ20141450] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the last decade, the ubiquitin–proteasome system has emerged as a valid target for the development of novel therapeutics. E3 ubiquitin ligases are particularly attractive targets because they confer substrate specificity on the ubiquitin system. CRLs [Cullin–RING (really interesting new gene) E3 ubiquitin ligases] draw particular attention, being the largest family of E3s. The CRLs assemble into functional multisubunit complexes using a repertoire of substrate receptors, adaptors, Cullin scaffolds and RING-box proteins. Drug discovery targeting CRLs is growing in importance due to mounting evidence pointing to significant roles of these enzymes in diverse biological processes and human diseases, including cancer, where CRLs and their substrates often function as tumour suppressors or oncogenes. In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity. A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included. This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.
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40
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Ibeawuchi SRC, Agbor LN, Quelle FW, Sigmund CD. Hypertension-causing Mutations in Cullin3 Protein Impair RhoA Protein Ubiquitination and Augment the Association with Substrate Adaptors. J Biol Chem 2015; 290:19208-17. [PMID: 26100637 DOI: 10.1074/jbc.m115.645358] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 11/06/2022] Open
Abstract
Cullin-Ring ubiquitin ligases regulate protein turnover by promoting the ubiquitination of substrate proteins, targeting them for proteasomal degradation. It has been shown previously that mutations in Cullin3 (Cul3) causing deletion of 57 amino acids encoded by exon 9 (Cul3Δ9) cause hypertension. Moreover, RhoA activity contributes to vascular constriction and hypertension. We show that ubiquitination and degradation of RhoA is dependent on Cul3 in HEK293T cells in which Cul3 expression is ablated by either siRNA or by CRISPR-Cas9 genome editing. The latter was used to generate a Cul3-null cell line (HEK293T(Cul3KO)). When expressed in these cells, Cul3Δ9 supported reduced ubiquitin ligase activity toward RhoA compared with equivalent levels of wild-type Cul3 (Cul3WT). Consistent with its reduced activity, binding of Cul3Δ9 to the E3 ubiquitin ligase Rbx1 and neddylation of Cul3Δ9 were impaired significantly compared with Cul3WT. Conversely, Cul3Δ9 bound to substrate adaptor proteins more efficiently than Cul3WT. Cul3Δ9 also forms unstable dimers with Cul3WT, disrupting dimers of Cul3WT complexes that are required for efficient ubiquitination of some substrates. Indeed, coexpression of Cul3WT and Cul3Δ9 in HEK293T(Cul3KO) cells resulted in a decrease in the active form of Cul3WT. We conclude that Cul3Δ9-associated ubiquitin ligase activity toward RhoA is impaired and suggest that Cul3Δ9 mutations may act dominantly by sequestering substrate adaptors and disrupting Cul3WT complexes.
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Affiliation(s)
| | - Larry N Agbor
- From the Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242
| | - Frederick W Quelle
- From the Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242
| | - Curt D Sigmund
- From the Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242
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41
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Migita K, Takayama T, Matsumoto S, Wakatsuki K, Tanaka T, Ito M, Nishiwada S, Nakajima Y. Prognostic impact of RING box protein-1 (RBX1) expression in gastric cancer. Gastric Cancer 2014; 17:601-9. [PMID: 24292229 DOI: 10.1007/s10120-013-0318-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/10/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND RING box protein-1 (RBX1) is an essential component of the E3 ubiquitin ligase Skp1/Cullin/RBX1/F-box protein complex. Although an altered expression of RBX1 has been reported in several human cancers, the role of RBX1 in gastric cancer remains unknown. METHODS We investigated the RBX1 expression in primary gastric cancer tissues from 145 patients by immunohistochemistry, and explored its clinical relevance and prognostic value. Furthermore, the effect of RBX1 expression on cancer cell proliferation was analyzed in vitro using a siRNA silencing technique. RESULTS The RBX1 expression was abundant in gastric cancer tissues. There was a significant difference in the expression level of RBX1 in terms of the tumor depth (P = 0.008), presence of distant metastasis (P = 0.016) and venous invasion (P = 0.005). The postoperative overall (P < 0.001) and relapse-free survival (P < 0.001) rates were significantly poorer in patients with RBX1-high tumors than in patients with RBX1-low tumors. There was a significant correlation of the RBX1 status with postoperative hematogenous recurrence (P = 0.013). Importantly, the RBX1 status was identified as an independent prognostic factor for gastric cancer (P = 0.002). Furthermore, RBX1 gene silencing significantly inhibited the proliferation of gastric cancer cells in vitro. CONCLUSIONS The RBX1 expression has a significant prognostic value in gastric cancer. RBX1 might play an important role in regulating the proliferation of gastric cancer cells and promoting the development of postoperative recurrence. Our data provide a rationale for developing a novel therapy targeting RBX1 for gastric cancer.
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Affiliation(s)
- Kazuhiro Migita
- Department of Surgery, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan,
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42
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Liu J, Ma J. Dampened regulates the activating potency of Bicoid and the embryonic patterning outcome in Drosophila. Nat Commun 2014; 4:2968. [PMID: 24336107 PMCID: PMC3902774 DOI: 10.1038/ncomms3968] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 11/18/2013] [Indexed: 01/26/2023] Open
Abstract
The Drosophila morphogen gradient of Bicoid (Bcd) initiates anterior-posterior (AP) patterning, but it is poorly understood how its ability to activate a target gene may impact this process. Here we report an F-box protein, Dampened (Dmpd) as a nuclear co-factor of Bcd that can enhance its activating potency. We establish a quantitative platform to specifically investigate two parameters of a Bcd target gene response, expression amplitude and boundary position. We show that embryos lacking Dmpd have a reduced amplitude of Bcd-activated hunchback (hb) expression at a critical time of development. This is due to a reduced Bcd-dependent transcribing probability. This defect is faithfully propagated further downstream of the AP patterning network to alter the spatial characteristics of even-skipped (eve) stripes. Thus, unlike another Bcd-interacting F-box protein Fates-shifted (Fsd), which controls AP patterning through regulating the Bcd gradient profile, Dmpd achieves its patterning role through regulating the activating potency of Bcd.
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Affiliation(s)
- Junbo Liu
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA
| | - Jun Ma
- 1] Division of Biomedical Informatics, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA [2] Division of Developmental Biology, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio, USA
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43
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Huang H, Ceccarelli DF, Orlicky S, St-Cyr DJ, Ziemba A, Garg P, Plamondon S, Auer M, Sidhu S, Marinier A, Kleiger G, Tyers M, Sicheri F. E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin. Nat Chem Biol 2014; 10:156-163. [PMID: 24316736 PMCID: PMC3905752 DOI: 10.1038/nchembio.1412] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/31/2013] [Indexed: 11/09/2022]
Abstract
Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.
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Affiliation(s)
- Hao Huang
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
| | - Derek F Ceccarelli
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
| | - Stephen Orlicky
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
| | - Daniel J. St-Cyr
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Amy Ziemba
- Department of Chemistry, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV, 89154
| | - Pankaj Garg
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Serge Plamondon
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Manfred Auer
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR United Kingdom
| | - Sachdev Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
- Department of Chemistry, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Gary Kleiger
- Department of Chemistry, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV, 89154
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
- Department of Medicine, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Frank Sicheri
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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44
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Li H, Tan M, Jia L, Wei D, Zhao Y, Chen G, Xu J, Zhao L, Thomas D, Beer DG, Sun Y. Inactivation of SAG/RBX2 E3 ubiquitin ligase suppresses KrasG12D-driven lung tumorigenesis. J Clin Invest 2014; 124:835-46. [PMID: 24430184 PMCID: PMC3904615 DOI: 10.1172/jci70297] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 11/07/2013] [Indexed: 12/20/2022] Open
Abstract
Cullin-RING ligases (CRLs) are a family of E3 ubiquitin ligase complexes that rely on either RING-box 1 (RBX1) or sensitive to apoptosis gene (SAG), also known as RBX2, for activity. RBX1 and SAG are both overexpressed in human lung cancer; however, their contribution to patient survival and lung tumorigenesis is unknown. Here, we report that overexpression of SAG, but not RBX1, correlates with poor patient prognosis and more advanced disease. We found that SAG is overexpressed in murine KrasG12D-driven lung tumors and that Sag deletion suppressed lung tumorigenesis and extended murine life span. Using cultured lung cancer cells, we showed that SAG knockdown suppressed growth and survival, inactivated both NF-κB and mTOR pathways, and resulted in accumulation of tumor suppressor substrates, including p21, p27, NOXA, and BIM. Importantly, growth suppression by SAG knockdown was partially rescued by simultaneous knockdown of p21 or the mTOR inhibitor DEPTOR. Treatment with MLN4924, a small molecule inhibitor of CRL E3s, also inhibited the formation of KrasG12D-induced lung tumors through a similar mechanism involving inactivation of NF-κB and mTOR and accumulation of tumor suppressor substrates. Together, our results demonstrate that Sag is a Kras-cooperating oncogene that promotes lung tumorigenesis and suggest that targeting SAG-CRL E3 ligases may be an effective therapeutic approach for Kras-driven lung cancers.
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Affiliation(s)
- Hua Li
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Mingjia Tan
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Lijun Jia
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Dongping Wei
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yongchao Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Guoan Chen
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jie Xu
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Lili Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Dafydd Thomas
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - David G. Beer
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yi Sun
- Division of Radiation and Cancer Biology, Department of Radiation Oncology,
Thoracic Surgery, Department of Surgery,
Department of Biostatistics, and
Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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45
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Abstract
The RING-in-between-RING (RBR) E3s are a curious family of ubiquitin E3-ligases, whose mechanism of action is unusual in several ways. Their activities are auto-inhibited, causing a requirement for activation by protein-protein interactions or posttranslational modifications. They catalyse ubiquitin conjugation by a concerted RING/HECT-like mechanism in which the RING1 domain facilitates E2-discharge to directly form a thioester intermediate with a cysteine in RING2. This short-lived, HECT-like intermediate then modifies the target. Uniquely, the RBR ligase HOIP makes use of this mechanism to target the ubiquitin amino-terminus, by presenting the target ubiquitin for modification using its distinctive LDD region.
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Affiliation(s)
- Judith J Smit
- Division of Biochemistry and Cancer Genomics Centre, The Netherlands Cancer InstituteAmsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Centre, The Netherlands Cancer InstituteAmsterdam, The Netherlands
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46
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Abstract
Cell division is controlled by a highly regulated program to accurately duplicate and segregate chromosomes. An important feature of the cell cycle regulatory program is that key cell cycle proteins are present and active during specific cell cycle stages but are later removed or inhibited to maintain appropriate timing. The ubiquitin-proteasome system has emerged as an important mechanism to target cell cycle proteins for degradation at critical junctures during cell division. Two key E3 ubiquitin ligase complexes that target key cell cycle proteins are the Skp1-Cul1-F-box protein complex and the anaphase-promoting complex/cyclosome. This chapter focuses on the role of these E3 ubiquitin ligases and how ubiquitin-dependent degradation of central cell cycle regulatory proteins advances the cell cycle.
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Affiliation(s)
- Deanna M Koepp
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA,
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47
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Severo MS, Choy A, Stephens KD, Sakhon OS, Chen G, Chung DWD, Le Roch KG, Blaha G, Pedra JHF. The E3 ubiquitin ligase XIAP restricts Anaplasma phagocytophilum colonization of Ixodes scapularis ticks. J Infect Dis 2013; 208:1830-40. [PMID: 23901084 DOI: 10.1093/infdis/jit380] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ubiquitination is a posttranslational modification that regulates protein degradation and signaling in eukaryotes. Although it is acknowledged that pathogens exploit ubiquitination to infect mammalian cells, it remains unknown how microbes interact with the ubiquitination machinery in medically relevant arthropods. Here, we show that the ubiquitination machinery is present in the tick Ixodes scapularis and demonstrate that the E3 ubiquitin ligase named x-linked inhibitor of apoptosis protein (XIAP) restricts bacterial colonization of this arthropod vector. We provide evidence that xiap silencing significantly increases tick colonization by the bacterium Anaplasma phagocytophilum, the causative agent of human granulocytic anaplasmosis. We also demonstrate that (i) XIAP polyubiquitination is dependent on the really interesting new gene (RING) catalytic domain, (ii) XIAP polyubiquitination occurs via lysine (K)-63 but not K-48 residues, and (iii) XIAP-dependent K-63 polyubiquitination requires zinc for catalysis. Taken together, our data define a role for ubiquitination during bacterial colonization of disease vectors.
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Affiliation(s)
- Maiara S Severo
- Center for Disease Vector Research and Department of Entomology
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48
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Sarkari F, Wheaton K, La Delfa A, Mohamed M, Shaikh F, Khatun R, Arrowsmith CH, Frappier L, Saridakis V, Sheng Y. Ubiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1. J Biol Chem 2013; 288:16975-16985. [PMID: 23603909 DOI: 10.1074/jbc.m113.469262] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme found in all eukaryotes that catalyzes the removal of ubiquitin from specific target proteins. Here, we report that UbE2E1, an E2 ubiquitin conjugation enzyme with a unique N-terminal extension, is a novel USP7-interacting protein. USP7 forms a complex with UbE2E1 in vitro and in vivo through the ASTS USP7 binding motif within its N-terminal extension in an identical manner with other known USP7 binding proteins. We show that USP7 attenuates UbE2E1-mediated ubiquitination, an effect that requires the N-terminal ASTS sequence of UbE2E1 as well as the catalytic activity of USP7. Additionally, USP7 is critical in maintaining the steady state levels of UbE2E1 in cells. This study reveals a new cellular mechanism that couples the opposing activities of the ubiquitination machinery and a deubiquitinating enzyme to maintain and modulate the dynamic balance of the ubiquitin-proteasome system.
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Affiliation(s)
- Feroz Sarkari
- Department of Biology, York University, Toronto, Ontario M3J 1P3
| | - Keith Wheaton
- Department of Biology, York University, Toronto, Ontario M3J 1P3
| | - Anthony La Delfa
- Department of Biology, York University, Toronto, Ontario M3J 1P3
| | - Majda Mohamed
- Department of Biology, York University, Toronto, Ontario M3J 1P3
| | - Faryal Shaikh
- Department of Biology, York University, Toronto, Ontario M3J 1P3
| | - Rahima Khatun
- Department of Biology, York University, Toronto, Ontario M3J 1P3
| | - Cheryl H Arrowsmith
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, Toronto, Ontario M5G 1L7
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Vivian Saridakis
- Department of Biology, York University, Toronto, Ontario M3J 1P3.
| | - Yi Sheng
- Department of Biology, York University, Toronto, Ontario M3J 1P3.
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Abstract
The SCF (SKP1 (S-phase-kinase-associated protein 1), Cullin-1, F-box protein) E3 ubiquitin ligases, the founding member of Cullin-RING ligases (CRLs), are the largest family of E3 ubiquitin ligases in mammals. Each individual SCF E3 ligase consists of one adaptor protein SKP1, one scaffold protein cullin-1 (the first family member of the eight cullins), one F-box protein out of 69 family members, and one out of two RING (Really Interesting New Gene) family proteins RBX1/ROC1 or RBX2/ROC2/SAG/RNF7. Various combinations of these four components construct a large number of SCF E3s that promote the degradation of many key regulatory proteins in cell-context, temporally, and spatially dependent manners, thus controlling precisely numerous important cellular processes, including cell cycle progression, apoptosis, gene transcription, signal transduction, DNA replication, maintenance of genome integrity, and tumorigenesis. To understand how the SCF E3 ligases regulate these cellular processes and embryonic development under in vivo physiological conditions, a number of mouse models with transgenic (Tg) expression or targeted deletion of components of SCF have been established and characterized. In this review, we will provide a brief introduction to the ubiquitin-proteasome system (UPS) and the SCF E3 ubiquitin ligases, followed by a comprehensive overview on the existing Tg and knockout (KO) mouse models of the SCF E3s, and discuss the role of each component in mouse embryogenesis, cell proliferation, apoptosis, carcinogenesis, as well as other pathogenic processes associated with human diseases. We will end with a brief discussion on the future directions of this research area and the potential applications of the knowledge gained to more effective therapeutic interventions of human diseases.
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Affiliation(s)
- Weihua Zhou
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
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Xie CM, Wei W, Sun Y. Role of SKP1-CUL1-F-box-protein (SCF) E3 ubiquitin ligases in skin cancer. J Genet Genomics 2013; 40:97-106. [PMID: 23522382 DOI: 10.1016/j.jgg.2013.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 01/30/2013] [Accepted: 02/04/2013] [Indexed: 11/25/2022]
Abstract
Many biological processes such as cell proliferation, differentiation, and cell death depend precisely on the timely synthesis and degradation of key regulatory proteins. While protein synthesis can be regulated at multiple levels, protein degradation is mainly controlled by the ubiquitin-proteasome system (UPS), which consists of two distinct steps: (1) ubiquitylation of targeted protein by E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme and E3 ubiquitin ligase, and (2) subsequent degradation by the 26S proteasome. Among all E3 ubiquitin ligases, the SCF (SKP1-CUL1-F-box protein) E3 ligases are the largest family and are responsible for the turnover of many key regulatory proteins. Aberrant regulation of SCF E3 ligases is associated with various human diseases, such as cancers, including skin cancer. In this review, we provide a comprehensive overview of all currently published data to define a promoting role of SCF E3 ligases in the development of skin cancer. The future directions in this area of research are also discussed with an ultimate goal to develop small molecule inhibitors of SCF E3 ligases as a novel approach for the treatment of human skin cancer. Furthermore, altered components or substrates of SCF E3 ligases may also be developed as the biomarkers for early diagnosis or predicting prognosis.
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Affiliation(s)
- Chuan-Ming Xie
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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