1
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McCormick LE, Suarez C, Herring LE, Cannon KS, Kovar DR, Brown NG, Gupton SL. Multi-monoubiquitylation controls VASP-mediated actin dynamics. J Cell Sci 2024; 137:jcs261527. [PMID: 38277158 PMCID: PMC10917064 DOI: 10.1242/jcs.261527] [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: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024] Open
Abstract
The actin cytoskeleton performs multiple cellular functions, and as such, actin polymerization must be tightly regulated. We previously demonstrated that reversible, non-degradative ubiquitylation regulates the function of the actin polymerase VASP in developing neurons. However, the underlying mechanism of how ubiquitylation impacts VASP activity was unknown. Here, we show that mimicking multi-monoubiquitylation of VASP at K240 and K286 negatively regulates VASP interactions with actin. Using in vitro biochemical assays, we demonstrate the reduced ability of multi-monoubiquitylated VASP to bind, bundle, and elongate actin filaments. However, multi-monoubiquitylated VASP maintained the ability to bind and protect barbed ends from capping protein. Finally, we demonstrate the electroporation of recombinant multi-monoubiquitylated VASP protein altered cell spreading morphology. Collectively, these results suggest a mechanism in which ubiquitylation controls VASP-mediated actin dynamics.
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Affiliation(s)
- Laura E. McCormick
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cristian Suarez
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Laura E. Herring
- Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin S. Cannon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R. Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas G. Brown
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie L. Gupton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn KM, Zhang W, Zhong ED, Haselbach D, Brown NG. Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). Nat Struct Mol Biol 2023; 30:1663-1674. [PMID: 37735619 PMCID: PMC10643132 DOI: 10.1038/s41594-023-01105-5] [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: 12/20/2022] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2 MDa E3 ubiquitin ligase, known as the anaphase-promoting complex/cyclosome (APC/C), and its E2 co-enzymes (UBE2C/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal.
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Affiliation(s)
- Tatyana Bodrug
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kaeli A Welsh
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Ethan Paulаkonis
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Raquel C Martinez-Chacin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Bei Liu
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- College of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
| | - Nicholas Pinkin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas Bonacci
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Liying Cui
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Pengning Xu
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Sascha Josef Amann
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Joshua P Steimel
- School of Engineering, California Polytechnic State University Humboldt, Arcata, CA, USA
| | - Klaus M Hahn
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Ellen D Zhong
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - David Haselbach
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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3
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Yan D, He Q, Pei L, Yang M, Huang L, Kong J, He W, Liu H, Xu S, Qin H, Lin T, Huang J. The APC/C E3 ligase subunit ANAPC11 mediates FOXO3 protein degradation to promote cell proliferation and lymph node metastasis in urothelial bladder cancer. Cell Death Dis 2023; 14:516. [PMID: 37573356 PMCID: PMC10423259 DOI: 10.1038/s41419-023-06000-x] [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: 02/01/2023] [Revised: 06/18/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
Urothelial bladder cancer (UBC) is one of the most prevalent malignancies worldwide, with striking tumor heterogeneity. Elucidating the molecular mechanisms that can be exploited for the treatment of aggressive UBC is a particularly relevant goal. Protein ubiquitination is a critical post-translational modification (PTM) that mediates the degradation of target protein via the proteasome. However, the roles of aberrant protein ubiquitination in UBC development and the underlying mechanisms by which it drives tumor progression remain unclear. In this study, taking advantage of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) 9 technology, we identified the ubiquitin E3 ligase ANAPC11, a critical subunit of the anaphase-promoting complex/cyclosome (APC/C), as a potential oncogenic molecule in UBC cells. Our clinical analysis showed that elevated expression of ANAPC11 was significantly correlated with high T stage, positive lymph node (LN) metastasis, and poor outcomes in UBC patients. By employing a series of in vitro experiments, we demonstrated that ANAPC11 enhanced the proliferation and invasiveness of UBC cells, while knockout of ANAPC11 inhibited the growth and LN metastasis of UBC cells in vivo. By conducting immunoprecipitation coupled with mass spectrometry, we confirmed that ANAPC11 increased the ubiquitination level of the Forkhead transcription factor FOXO3. The resulting decrease in FOXO3 protein stability led to the downregulation of the cell cycle regulator p21 and decreased expression of GULP1, a downstream effector of androgen receptor signaling. Taken together, these findings indicated that ANAPC11 plays an oncogenic role in UBC by modulating FOXO3 protein degradation. The ANAPC11-FOXO3 regulatory axis might serve as a novel therapeutic target for UBC.
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Affiliation(s)
- Dong Yan
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qingqing He
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lu Pei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meihua Yang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lifang Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianqiu Kong
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wang He
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hao Liu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shizhong Xu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haide Qin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Tianxin Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Jian Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
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4
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McCormick LE, Suarez C, Herring LE, Cannon KS, Kovar DR, Brown NG, Gupton SL. Multi-monoubiquitination controls VASP-mediated actin dynamics. bioRxiv 2023:2023.07.16.549237. [PMID: 37503134 PMCID: PMC10370145 DOI: 10.1101/2023.07.16.549237] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The actin cytoskeleton performs multiple cellular functions, and as such, actin polymerization must be tightly regulated. We previously demonstrated that reversible, non-degradative ubiquitination regulates the function of the actin polymerase VASP in developing neurons. However, the underlying mechanism of how ubiquitination impacts VASP activity was unknown. Here we show that mimicking multi-monoubiquitination of VASP at K240 and K286 negatively regulates VASP interactions with actin. Using in vitro biochemical assays, we demonstrate the reduced ability of multi-monoubiquitinated VASP to bind, bundle, and elongate actin filaments. However, multi-monoubiquitinated VASP maintained the ability to bind and protect barbed ends from capping protein. Lastly, we demonstrate the introduction of recombinant multi-monoubiquitinated VASP protein altered cell spreading morphology. Collectively, these results suggest a mechanism in which ubiquitination controls VASP-mediated actin dynamics.
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Affiliation(s)
- Laura E McCormick
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Cristian Suarez
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Laura E Herring
- Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kevin S Cannon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephanie L Gupton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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5
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Liu W, Wang Y, Bozi LHM, Fischer PD, Jedrychowski MP, Xiao H, Wu T, Darabedian N, He X, Mills EL, Burger N, Shin S, Reddy A, Sprenger HG, Tran N, Winther S, Hinshaw SM, Shen J, Seo HS, Song K, Xu AZ, Sebastian L, Zhao JJ, Dhe-Paganon S, Che J, Gygi SP, Arthanari H, Chouchani ET. Lactate regulates cell cycle by remodelling the anaphase promoting complex. Nature 2023; 616:790-797. [PMID: 36921622 DOI: 10.1038/s41586-023-05939-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [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: 11/21/2021] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Lactate is abundant in rapidly dividing cells owing to the requirement for elevated glucose catabolism to support proliferation1-6. However, it is not known whether accumulated lactate affects the proliferative state. Here we use a systematic approach to determine lactate-dependent regulation of proteins across the human proteome. From these data, we identify a mechanism of cell cycle regulation whereby accumulated lactate remodels the anaphase promoting complex (APC/C). Remodelling of APC/C in this way is caused by direct inhibition of the SUMO protease SENP1 by lactate. We find that accumulated lactate binds and inhibits SENP1 by forming a complex with zinc in the SENP1 active site. SENP1 inhibition by lactate stabilizes SUMOylation of two residues on APC4, which drives UBE2C binding to APC/C. This direct regulation of APC/C by lactate stimulates timed degradation of cell cycle proteins, and efficient mitotic exit in proliferative human cells. This mechanism is initiated upon mitotic entry when lactate abundance reaches its apex. In this way, accumulation of lactate communicates the consequences of a nutrient-replete growth phase to stimulate timed opening of APC/C, cell division and proliferation. Conversely, persistent accumulation of lactate drives aberrant APC/C remodelling and can overcome anti-mitotic pharmacology via mitotic slippage. In sum, we define a biochemical mechanism through which lactate directly regulates protein function to control the cell cycle and proliferation.
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Affiliation(s)
- Weihai Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Musculoskeletal Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yun Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Luiz H M Bozi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Patrick D Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Mark P Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Tao Wu
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Narek Darabedian
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xiadi He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Evanna L Mills
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nils Burger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Sanghee Shin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Anita Reddy
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Hans-Georg Sprenger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nhien Tran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Sally Winther
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Stephen M Hinshaw
- Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jingnan Shen
- Department of Musculoskeletal Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Z Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luke Sebastian
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jean J Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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6
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Peter JJ, Magnussen HM, DaRosa PA, Millrine D, Matthews SP, Lamoliatte F, Sundaramoorthy R, Kopito RR, Kulathu Y. A non-canonical scaffold-type E3 ligase complex mediates protein UFMylation. EMBO J 2022; 41:e111015. [PMID: 36121123 DOI: 10.15252/embj.2022111015] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/24/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Protein UFMylation, i.e., post-translational modification with ubiquitin-fold modifier 1 (UFM1), is essential for cellular and endoplasmic reticulum homeostasis. Despite its biological importance, we have a poor understanding of how UFM1 is conjugated onto substrates. Here, we use a rebuilding approach to define the minimal requirements of protein UFMylation. We find that the reported cognate E3 ligase UFL1 is inactive on its own and instead requires the adaptor protein UFBP1 to form an active E3 ligase complex. Structure predictions suggest the UFL1/UFBP1 complex to be made up of winged helix (WH) domain repeats. We show that UFL1/UFBP1 utilizes a scaffold-type E3 ligase mechanism that activates the UFM1-conjugating E2 enzyme, UFC1, for aminolysis. Further, we characterize a second adaptor protein CDK5RAP3 that binds to and forms an integral part of the ligase complex. Unexpectedly, we find that CDK5RAP3 inhibits UFL1/UFBP1 ligase activity in vitro. Results from reconstituting ribosome UFMylation suggest that CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26. In summary, our reconstitution approach reveals the biochemical basis of UFMylation and regulatory principles of this atypical E3 ligase complex.
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Affiliation(s)
- Joshua J Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Stephen P Matthews
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
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7
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Wang J, Zhang M, Liu S, He Z, Wang R, Liang M, An Y, Jiang C, Song C, Ning Z, Yin F, Huang H, Li Z, Ye Y. Targeting UBE2C for degradation by bioPROTACs based on bacterial E3 ligase. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Bolhuis DL, Martinez‐Chacin RC, Welsh KA, Bodrug T, Cui L, Emanuele MJ, Brown NG. Examining the mechanistic relationship of
APC
/
C
CDH1
and its interphase inhibitor
EMI1. Protein Sci 2022; 31:e4324. [DOI: 10.1002/pro.4324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/22/2022] [Accepted: 04/06/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Derek L. Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
| | - Raquel C. Martinez‐Chacin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
| | - Kaeli A. Welsh
- Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
| | - Tatyana Bodrug
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
| | - Liying Cui
- Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
| | - Michael J. Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
| | - Nicholas G. Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill North Carolina USA
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9
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Kolla S, Ye M, Mark KG, Rapé M. Assembly and function of branched ubiquitin chains. Trends Biochem Sci 2022. [DOI: 10.1016/j.tibs.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
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10
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Ferguson CJ, Urso O, Bodrug T, Gassaway BM, Watson ER, Prabu JR, Lara-Gonzalez P, Martinez-Chacin RC, Wu DY, Brigatti KW, Puffenberger EG, Taylor CM, Haas-Givler B, Jinks RN, Strauss KA, Desai A, Gabel HW, Gygi SP, Schulman BA, Brown NG, Bonni A. APC7 mediates ubiquitin signaling in constitutive heterochromatin in the developing mammalian brain. Mol Cell 2022; 82:90-105.e13. [PMID: 34942119 PMCID: PMC8741739 DOI: 10.1016/j.molcel.2021.11.031] [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: 12/08/2020] [Revised: 10/14/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
Neurodevelopmental cognitive disorders provide insights into mechanisms of human brain development. Here, we report an intellectual disability syndrome caused by the loss of APC7, a core component of the E3 ubiquitin ligase anaphase promoting complex (APC). In mechanistic studies, we uncover a critical role for APC7 during the recruitment and ubiquitination of APC substrates. In proteomics analyses of the brain from mice harboring the patient-specific APC7 mutation, we identify the chromatin-associated protein Ki-67 as an APC7-dependent substrate of the APC in neurons. Conditional knockout of the APC coactivator protein Cdh1, but not Cdc20, leads to the accumulation of Ki-67 protein in neurons in vivo, suggesting that APC7 is required for the function of Cdh1-APC in the brain. Deregulated neuronal Ki-67 upon APC7 loss localizes predominantly to constitutive heterochromatin. Our findings define an essential function for APC7 and Cdh1-APC in neuronal heterochromatin regulation, with implications for understanding human brain development and disease.
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Affiliation(s)
- Cole J Ferguson
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Neuropathology Division, Physician-Scientist Training Program, Washington University, St. Louis, MO 63110, USA
| | - Olivia Urso
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA
| | - Tatyana Bodrug
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | - Pablo Lara-Gonzalez
- Department of Cellular and Molecular Medicine, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Raquel C Martinez-Chacin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA
| | | | | | - Cora M Taylor
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA 17837, USA
| | - Barbara Haas-Givler
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA 17837, USA
| | - Robert N Jinks
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17603, USA
| | | | - Arshad Desai
- Department of Cellular and Molecular Medicine, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University, Boston, MA 02138, USA
| | | | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA.
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11
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Welsh KA, Bolhuis DL, Nederstigt AE, Boyer J, Temple BRS, Bonacci T, Gu L, Ordureau A, Harper JW, Steimel JP, Zhang Q, Emanuele MJ, Harrison JS, Brown NG. Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes. EMBO J 2021; 41:e108823. [PMID: 34942047 PMCID: PMC8804933 DOI: 10.15252/embj.2021108823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/26/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 02/05/2023] Open
Abstract
Polyubiquitination by E2 and E3 enzymes is crucial to cell cycle control, epigenetic regulation, and development. The hallmark of the E2 family is the ubiquitin (Ub)-conjugating (UBC) domain that forms a dynamic thioester conjugate with ubiquitin (E2~Ub). Numerous studies have focused on E2 surfaces, such as the N-terminal and crossover helices, that directly interact with an E3 or the conjugated ubiquitin to stabilize the active, "closed" state of the E2~Ub. However, it remains unclear how other E2 surfaces regulate ubiquitin transfer. Here, we demonstrate the helix-turn-helix (HTH) motif of the UBC tunes the intrinsic polyubiquitination activity through distinct functions in different E2s. Interestingly, the E2HTH motif is repurposed in UBE2S and UBE2R2 to interact with the conjugated or acceptor ubiquitin, respectively, modulating ubiquitin transfer. Furthermore, we propose that Anaphase-Promoting Complex/Cyclosome binding to the UBE2SHTH reduces the conformational space of the flexible E2~Ub, demonstrating an atypical E3-dependent activation mechanism. Altogether, we postulate the E2HTH motif evolved to provide new functionalities that can be harnessed by E3s and permits additional regulation to facilitate specific E2-E3-mediated polyubiquitination.
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Affiliation(s)
- Kaeli A Welsh
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Joshua Boyer
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brenda R S Temple
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,R L Juliano Structural Bioinformatics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Bonacci
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Li Gu
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, CA, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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12
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Sultanova E, Gazalieva A, Makarov E, Belov R, Evtugyn V, Burilov V, Solovieva S, Antipin I. Novel aminocalixarene-modified polydiacetylene vesicles: Synthesis and naked-eye detection of ATP. Colloids Surf A Physicochem Eng Asp 2021; 630:127642. [DOI: 10.1016/j.colsurfa.2021.127642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Henneberg LT, Schulman BA. Decoding the messaging of the ubiquitin system using chemical and protein probes. Cell Chem Biol 2021; 28:889-902. [PMID: 33831368 PMCID: PMC7611516 DOI: 10.1016/j.chembiol.2021.03.009] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modification of proteins by ubiquitin is required for nearly all aspects of eukaryotic cell function. The numerous targets of ubiquitylation, and variety of ubiquitin modifications, are often likened to a code, where the ultimate messages are diverse responses to target ubiquitylation. E1, E2, and E3 multiprotein enzymatic assemblies modify specific targets and thus function as messengers. Recent advances in chemical and protein tools have revolutionized our ability to explore the ubiquitin system, through enabling new high-throughput screening methods, matching ubiquitylation enzymes with their cellular targets, revealing intricate allosteric mechanisms regulating ubiquitylating enzymes, facilitating structural revelation of transient assemblies determined by multivalent interactions, and providing new paradigms for inhibiting and redirecting ubiquitylation in vivo as new therapeutics. Here we discuss the development of methods that control, disrupt, and extract the flow of information across the ubiquitin system and have enabled elucidation of the underlying molecular and cellular biology.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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14
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Koliopoulos MG, Alfieri C. Cell cycle regulation by complex nanomachines. FEBS J 2021; 289:5100-5120. [PMID: 34143558 DOI: 10.1111/febs.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The cell cycle is the essential biological process where one cell replicates its genome and segregates the resulting two copies into the daughter cells during mitosis. Several aspects of this process have fascinated humans since the nineteenth century. Today, the cell cycle is exhaustively investigated because of its profound connections with human diseases and cancer. At the heart of the molecular network controlling the cell cycle, we find the cyclin-dependent kinases (CDKs) acting as an oscillator to impose an orderly and highly regulated progression through the different cell cycle phases. This oscillator integrates both internal and external signals via a multitude of signalling pathways involving posttranslational modifications including phosphorylation, protein ubiquitination and mechanisms of transcriptional regulation. These tasks are specifically performed by multi-subunit complexes, which are intensively studied both biochemically and structurally with the aim to unveil mechanistic insights into their molecular function. The scope of this review is to summarise the structural biology of the cell cycle machinery, with specific focus on the core cell cycle machinery involving the CDK-cyclin oscillator. We highlight the contribution of cryo-electron microscopy, which has started to revolutionise our understanding of the molecular function and dynamics of the key players of the cell cycle.
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Affiliation(s)
- Marios G Koliopoulos
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
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15
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Bodrug T, Welsh KA, Hinkle M, Emanuele MJ, Brown NG. Intricate Regulatory Mechanisms of the Anaphase-Promoting Complex/Cyclosome and Its Role in Chromatin Regulation. Front Cell Dev Biol 2021; 9:687515. [PMID: 34109183 PMCID: PMC8182066 DOI: 10.3389/fcell.2021.687515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 02/04/2023] Open
Abstract
The ubiquitin (Ub)-proteasome system is vital to nearly every biological process in eukaryotes. Specifically, the conjugation of Ub to target proteins by Ub ligases, such as the Anaphase-Promoting Complex/Cyclosome (APC/C), is paramount for cell cycle transitions as it leads to the irreversible destruction of cell cycle regulators by the proteasome. Through this activity, the RING Ub ligase APC/C governs mitosis, G1, and numerous aspects of neurobiology. Pioneering cryo-EM, biochemical reconstitution, and cell-based studies have illuminated many aspects of the conformational dynamics of this large, multi-subunit complex and the sophisticated regulation of APC/C function. More recent studies have revealed new mechanisms that selectively dictate APC/C activity and explore additional pathways that are controlled by APC/C-mediated ubiquitination, including an intimate relationship with chromatin regulation. These tasks go beyond the traditional cell cycle role historically ascribed to the APC/C. Here, we review these novel findings, examine the mechanistic implications of APC/C regulation, and discuss the role of the APC/C in previously unappreciated signaling pathways.
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Affiliation(s)
- Tatyana Bodrug
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kaeli A Welsh
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Megan Hinkle
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Michael J Emanuele
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Nicholas G Brown
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
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16
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Abstract
Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. In this review, we give an overview of both commonly used and recently developed biochemical methodologies for covalent stabilization of macromolecular complexes enabling structural investigation via crystallography, nuclear magnetic resonance, and cryo-electron microscopy. We divided the strategies into nonenzymatic- and enzymatic-driven cross-linking and further categorized them in either naturally occurring or engineered covalent linkage. This review offers a compilation of recent advances in diverse scientific fields where the structural characterization of macromolecular complexes was achieved by the aid of intermolecular covalent linkage.
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Affiliation(s)
- Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
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17
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Yatskevich S, Kroonen JS, Alfieri C, Tischer T, Howes AC, Clijsters L, Yang J, Zhang Z, Yan K, Vertegaal ACO, Barford D. Molecular mechanisms of APC/C release from spindle assembly checkpoint inhibition by APC/C SUMOylation. Cell Rep 2021; 34:108929. [PMID: 33789095 PMCID: PMC8028313 DOI: 10.1016/j.celrep.2021.108929] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that controls cell cycle transitions. Its regulation by the spindle assembly checkpoint (SAC) is coordinated with the attachment of sister chromatids to the mitotic spindle. APC/C SUMOylation on APC4 ensures timely anaphase onset and chromosome segregation. To understand the structural and functional consequences of APC/C SUMOylation, we reconstituted SUMOylated APC/C for electron cryo-microscopy and biochemical analyses. SUMOylation of the APC/C causes a substantial rearrangement of the WHB domain of APC/C's cullin subunit (APC2WHB). Although APC/CCdc20 SUMOylation results in a modest impact on normal APC/CCdc20 activity, repositioning APC2WHB reduces the affinity of APC/CCdc20 for the mitotic checkpoint complex (MCC), the effector of the SAC. This attenuates MCC-mediated suppression of APC/CCdc20 activity, allowing for more efficient ubiquitination of APC/CCdc20 substrates in the presence of the MCC. Thus, SUMOylation stimulates the reactivation of APC/CCdc20 when the SAC is silenced, contributing to timely anaphase onset.
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Affiliation(s)
- Stanislau Yatskevich
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jessie S Kroonen
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Claudio Alfieri
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas Tischer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anna C Howes
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Linda Clijsters
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kaige Yan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - David Barford
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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18
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Witus SR, Burrell AL, Farrell DP, Kang J, Wang M, Hansen JM, Pravat A, Tuttle LM, Stewart MD, Brzovic PS, Chatterjee C, Zhao W, DiMaio F, Kollman JM, Klevit RE. BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1. Nat Struct Mol Biol 2021; 28:268-277. [PMID: 33589814 PMCID: PMC8007219 DOI: 10.1038/s41594-020-00556-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 08/28/2020] [Accepted: 12/23/2020] [Indexed: 01/31/2023]
Abstract
Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system. The structure reveals that a novel BARD1-histone interface couples to a repositioning of UbcH5c compared to the structurally similar PRC1 E3 ligase Ring1b/Bmi1 that ubiquitylates H2A Lys119 in nucleosomes. This interface is sensitive to both H3 Lys79 methylation status and mutations found in individuals with cancer. Furthermore, NMR reveals an unexpected mode of E3-mediated substrate regulation through modulation of dynamics in the C-terminal tail of H2A. Our findings provide insight into how E3 ligases preferentially target nearby lysine residues in nucleosomes by a steric occlusion and distancing mechanism.
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Affiliation(s)
- Samuel R Witus
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Daniel P Farrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jianming Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Meiling Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Pravat
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Lisa M Tuttle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mikaela D Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biology, Texas Christian University, Fort Worth, TX, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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19
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Franks JL, Martinez-Chacin RC, Wang X, Tiedemann RL, Bonacci T, Choudhury R, Bolhuis DL, Enrico TP, Mouery RD, Damrauer JS, Yan F, Harrison JS, Major MB, Hoadley KA, Suzuki A, Rothbart SB, Brown NG, Emanuele MJ. In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators. PLoS Biol 2020; 18:e3000975. [PMID: 33306668 DOI: 10.1371/journal.pbio.3000975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 12/23/2020] [Accepted: 11/05/2020] [Indexed: 01/07/2023] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and critical regulator of cell cycle progression. Despite its vital role, it has remained challenging to globally map APC/C substrates. By combining orthogonal features of known substrates, we predicted APC/C substrates in silico. This analysis identified many known substrates and suggested numerous candidates. Unexpectedly, chromatin regulatory proteins are enriched among putative substrates, and we show experimentally that several chromatin proteins bind APC/C, oscillate during the cell cycle, and are degraded following APC/C activation, consistent with being direct APC/C substrates. Additional analysis revealed detailed mechanisms of ubiquitylation for UHRF1, a key chromatin regulator involved in histone ubiquitylation and DNA methylation maintenance. Disrupting UHRF1 degradation at mitotic exit accelerates G1-phase cell cycle progression and perturbs global DNA methylation patterning in the genome. We conclude that APC/C coordinates crosstalk between cell cycle and chromatin regulatory proteins. This has potential consequences in normal cell physiology, where the chromatin environment changes depending on proliferative state, as well as in disease.
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20
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Baek K, Scott DC, Schulman BA. NEDD8 and ubiquitin ligation by cullin-RING E3 ligases. Curr Opin Struct Biol 2020; 67:101-109. [PMID: 33160249 DOI: 10.1016/j.sbi.2020.10.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 01/31/2023]
Abstract
RING E3s comprise the largest family of ubiquitin (UB) and ubiquitin-like protein (UBL) ligases. RING E3s typically promote UB or UBL transfer from the active site of an associated E2 enzyme to a distally-recruited substrate. Many RING E3s - including the cullin-RING ligase family - are multifunctional, interacting with various E2s (or other E3s) to target distinct proteins, transfer different UBLs, or to initially modify substrates with UB or subsequently elongate UB chains. Here we consider recent structures of cullin-RING ligases, and their partner E2 enzymes, representing ligation reactions. The studies collectively reveal multimodal mechanisms - interactions between ancillary E2 or E3 domains, post-translational modifications, or auxiliary binding partners - directing cullin-RING E3-E2 enzyme active sites to modify their specific targets.
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Affiliation(s)
- Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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21
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Lips C, Ritterhoff T, Weber A, Janowska MK, Mustroph M, Sommer T, Klevit RE. Who with whom: functional coordination of E2 enzymes by RING E3 ligases during poly-ubiquitylation. EMBO J 2020; 39:e104863. [PMID: 33015833 PMCID: PMC7667886 DOI: 10.15252/embj.2020104863] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 11/09/2022] Open
Abstract
Protein modification with poly-ubiquitin chains is a crucial process involved in a myriad of cellular pathways. Chain synthesis requires two steps: substrate modification with ubiquitin (priming) followed by repetitive ubiquitin-to-ubiquitin attachment (elongation). RING-type E3 ligases catalyze both reactions in collaboration with specific priming and elongating E2 enzymes. We provide kinetic insight into poly-ubiquitylation during protein quality control by showing that priming is the rate-determining step in protein degradation as directed by the yeast ERAD RING E3 ligases, Hrd1 and Doa10. Doa10 cooperates with the dedicated priming E2, Ubc6, while both E3s use Ubc7 for elongation. Here, we provide direct evidence that Hrd1 uses Ubc7 also for priming. We found that Ubc6 has an unusually high basal activity that does not require strong stimulation from an E3. Doa10 exploits this property to pair with Ubc6 over Ubc7 during priming. Our work not only illuminates the mechanisms of specific E2/E3 interplay in ERAD, but also offers a basis to understand how RING E3s may have properties that are tailored to pair with their preferred E2s.
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Affiliation(s)
- Christian Lips
- Max Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany
| | - Tobias Ritterhoff
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, USA
| | - Annika Weber
- Max Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany
| | - Maria K Janowska
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, USA
| | - Mandy Mustroph
- Max Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany
| | - Thomas Sommer
- Max Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.,Lady Davies Guest Professor, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rachel E Klevit
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, USA
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22
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LeBlanc N, Mallette E, Zhang W. Targeted modulation of E3 ligases using engineered ubiquitin variants. FEBS J 2020; 288:2143-2165. [PMID: 32867007 DOI: 10.1111/febs.15536] [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: 05/15/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitination plays an essential role in signal transduction to regulate most if not all cellular processes. Among the enzymes that are involved in the ubiquitin (Ub) signaling cascade, tremendous efforts have been focused on elucidating the roles of E3 Ub ligases as they determine the complexity and specificity of ubiquitination. Not surprisingly, the malfunction of E3 ligases is directly implicated in many human diseases, including cancer. Therefore, there is an urgent need to develop potent and specific molecules to modulate E3 ligase activity as intracellular probes for target validation and as pharmacological agents in preclinical research. Unfortunately, the progress has been hampered by the dynamic regulation mechanisms for different types of E3 ligases. Here, we summarize the progress of using protein engineering to develop Ub variant (UbV) inhibitors for all major families of E3 ligases and UbV activators for homologous with E6-associated protein C terminus E3s and homodimeric RING E3s. We believe that this provides a general strategy and a valuable toolkit for the research community to inhibit or activate E3 ligases and these synthetic molecules have important implications in exploring protein degradation for drug discovery.
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Affiliation(s)
- Nicole LeBlanc
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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23
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VanGenderen C, Harkness TAA, Arnason TG. The role of Anaphase Promoting Complex activation, inhibition and substrates in cancer development and progression. Aging (Albany NY) 2020; 12:15818-15855. [PMID: 32805721 PMCID: PMC7467358 DOI: 10.18632/aging.103792] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
The Anaphase Promoting Complex (APC), a multi-subunit ubiquitin ligase, facilitates mitotic and G1 progression, and is now recognized to play a role in maintaining genomic stability. Many APC substrates have been observed overexpressed in multiple cancer types, such as CDC20, the Aurora A and B kinases, and Forkhead box M1 (FOXM1), suggesting APC activity is important for cell health. We performed BioGRID analyses of the APC coactivators CDC20 and CDH1, which revealed that at least 69 proteins serve as APC substrates, with 60 of them identified as playing a role in tumor promotion and 9 involved in tumor suppression. While these substrates and their association with malignancies have been studied in isolation, the possibility exists that generalized APC dysfunction could result in the inappropriate stabilization of multiple APC targets, thereby changing tumor behavior and treatment responsiveness. It is also possible that the APC itself plays a crucial role in tumorigenesis through its regulation of mitotic progression. In this review the connections between APC activity and dysregulation will be discussed with regards to cell cycle dysfunction and chromosome instability in cancer, along with the individual roles that the accumulation of various APC substrates may play in cancer progression.
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Affiliation(s)
- Cordell VanGenderen
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Troy Anthony Alan Harkness
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Terra Gayle Arnason
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.,Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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24
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Alfieri C, Tischer T, Barford D. A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase. EMBO Rep 2020; 21:e49831. [PMID: 32307883 PMCID: PMC7271329 DOI: 10.15252/embr.201949831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 12/08/2019] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 11/09/2022] Open
Abstract
The anaphase-promoting complex (APC/C) is the key E3 ubiquitin ligase which directs mitotic progression and exit by catalysing the sequential ubiquitination of specific substrates. The activity of the APC/C in mitosis is restrained by the spindle assembly checkpoint (SAC), which coordinates chromosome segregation with the assembly of the mitotic spindle. The SAC effector is the mitotic checkpoint complex (MCC), which binds and inhibits the APC/C. It is incompletely understood how the APC/C switches substrate specificity in a cell cycle-specific manner. For instance, it is unclear how in prometaphase, when APC/C activity towards cyclin B and securin is repressed by the MCC, the kinase Nek2A is ubiquitinated. Here, we combine biochemical and structural analysis with functional studies in cells to show that Nek2A is a conformational-specific binder of the APC/C-MCC complex (APC/CMCC ) and that, in contrast to cyclin A, Nek2A can be ubiquitinated efficiently by the APC/C in conjunction with both the E2 enzymes UbcH10 and UbcH5. We propose that these special features of Nek2A allow its prometaphase-specific ubiquitination.
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Affiliation(s)
- Claudio Alfieri
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Institute of Cancer ResearchLondonUK
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25
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Martinez-Chacin RC, Bodrug T, Bolhuis DL, Kedziora KM, Bonacci T, Ordureau A, Gibbs ME, Weissmann F, Qiao R, Grant GD, Cook JG, Peters JM, Wade Harper J, Emanuele MJ, Brown NG. Ubiquitin chain-elongating enzyme UBE2S activates the RING E3 ligase APC/C for substrate priming. Nat Struct Mol Biol 2020; 27:550-60. [PMID: 32393902 DOI: 10.1038/s41594-020-0424-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/25/2020] [Indexed: 01/19/2023]
Abstract
The interplay between E2 and E3 enzymes regulates the polyubiquitination of substrates in eukaryotes. Among the several RING-domain E3 ligases in humans, many utilize two distinct E2s for polyubiquitination. For example, the cell cycle regulatory E3, human Anaphase-Promoting Complex/Cyclosome (APC/C), relies on UBE2C to prime substrates with ubiquitin (Ub) and UBE2S to extend polyubiquitin chains. However, the potential coordination between these steps in ubiquitin chain formation remains undefined. While numerous studies have unveiled how RING E3s stimulate individual E2s for Ub transfer, here we change perspective to describe a case where the chain-elongating E2 UBE2S feeds back and directly stimulates the E3 APC/C to promote substrate priming and subsequent multiubiquitination by UBE2C. Our work reveals an unexpected paradigm for the mechanisms of RING E3-dependent ubiquitination and for the diverse and complex interrelationship between components of the ubiquitination cascade.
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26
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Sonn-Segev A, Belacic K, Bodrug T, Young G, VanderLinden RT, Schulman BA, Schimpf J, Friedrich T, Dip PV, Schwartz TU, Bauer B, Peters JM, Struwe WB, Benesch JLP, Brown NG, Haselbach D, Kukura P. Quantifying the heterogeneity of macromolecular machines by mass photometry. Nat Commun 2020; 11:1772. [PMID: 32286308 DOI: 10.1038/s41467-020-15642-w] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Sample purity is central to in vitro studies of protein function and regulation, and to the efficiency and success of structural studies using techniques such as x-ray crystallography and cryo-electron microscopy (cryo-EM). Here, we show that mass photometry (MP) can accurately characterize the heterogeneity of a sample using minimal material with high resolution within a matter of minutes. To benchmark our approach, we use negative stain electron microscopy (nsEM), a popular method for EM sample screening. We include typical workflows developed for structure determination that involve multi-step purification of a multi-subunit ubiquitin ligase and chemical cross-linking steps. When assessing the integrity and stability of large molecular complexes such as the proteasome, we detect and quantify assemblies invisible to nsEM. Our results illustrate the unique advantages of MP over current methods for rapid sample characterization, prioritization and workflow optimization. Mass photometry is a label-free optical approach capable of detecting, imaging and accurately measuring the mass of single biomolecules in solution. Here, the authors demonstrate the potential of mass photometry for quantitatively characterizing sample heterogeneity of purified protein complexes with implications for structural studies specifically and in vitro studies more generally.
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27
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Barford D. Structural interconversions of the anaphase-promoting complex/cyclosome (APC/C) regulate cell cycle transitions. Curr Opin Struct Biol 2020; 61:86-97. [PMID: 31864160 DOI: 10.1016/j.sbi.2019.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 10/09/2019] [Accepted: 11/19/2019] [Indexed: 01/14/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a large multi-subunit complex that functions as a RING domain E3 ubiquitin ligase to regulate transitions through the cell cycle, achieved by controlling the defined ubiquitin-dependent degradation of specific cell cycle regulators. APC/C activity and substrate selection are controlled at various levels to ensure that specific cell cycle events occur in the correct order and time. Structural and mechanistic studies over the past two decades have complemented functional studies to provide comprehensive insights that explain APC/C molecular mechanisms. This review discusses how modifications of the core APC/C are responsible for the APC/C's interconversion between different structural and functional states that govern its capacity to control transitions between specific cell cycle phases. A unifying theme is that these structural interconversions involve competition between short linear sequence motifs (SLIMs), shared between substrates, coactivators, inhibitors and E2s, for their common binding sites on the APC/C.
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Affiliation(s)
- David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom.
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28
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Abstract
The stalling of ribosomes during protein synthesis results in the production of truncated polypeptides that can have deleterious effects on cells and therefore must be eliminated. In eukaryotes, this function is carried out by a dedicated surveillance mechanism known as ribosome-associated protein quality control (RQC). The E3 ubiquitin ligase Ltn1 (listerin in mammals) plays a key part in RQC by targeting the aberrant nascent polypeptides for proteasomal degradation. Consistent with having an important protein quality control function, mutations in listerin cause neurodegeneration in mice. Ltn1/listerin is part of the multisubunit RQC complex, and recent findings have revealed that the Rqc2 subunit of this complex catalyses the formation of carboxy-terminal alanine and threonine tails (CAT tails), which are extensions of nascent chains known to either facilitate substrate ubiquitylation and targeting for degradation or induce protein aggregation. RQC, originally described for quality control on ribosomes translating cytosolic proteins, is now known to also have a role on the surfaces of the endoplasmic reticulum and mitochondria. This Review describes our current knowledge on RQC mechanisms, highlighting key features of Ltn1/listerin action that provide a paradigm for understanding how E3 ligases operate in protein quality control in general, and discusses how defects in this pathway may compromise cellular function and lead to disease.
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Affiliation(s)
- Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA.
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29
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Oh E, Mark KG, Mocciaro A, Watson ER, Prabu JR, Cha DD, Kampmann M, Gamarra N, Zhou CY, Rape M. Gene expression and cell identity controlled by anaphase-promoting complex. Nature 2020; 579:136-140. [PMID: 32076268 PMCID: PMC7402266 DOI: 10.1038/s41586-020-2034-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [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: 11/09/2018] [Accepted: 01/01/2020] [Indexed: 01/08/2023]
Abstract
Metazoan development requires robust proliferation of progenitor cells, whose identities are established by tightly controlled transcriptional networks 1. As gene expression is globally inhibited during mitosis, the transcriptional programs defining cell identity must be restarted in each cell cycle 2-5, yet how this is accomplished is poorly understood. Here, we identified a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active interphase promoters 6,7, recruit the anaphase-promoting complex (APC/C) to specific transcription start sites (TSS) during mitosis. This allows APC/C to decorate histones with K11/K48-branched ubiquitin chains that recruit p97/VCP and the proteasome and ensure rapid expression of pluripotency genes in the next cell cycle. Mitotic exit and transcription re-initiation are thus controlled by the same regulator, APC/C, which provides a robust mechanism to maintain cell identity through cell division.
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Affiliation(s)
- Eugene Oh
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Kevin G Mark
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Annamaria Mocciaro
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Berkeley Lights, Emeryville, CA, USA
| | - Edmond R Watson
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Denny D Cha
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
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30
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Burilov VA, Mironova DA, Grygoriev IA, Valiyakhmetova AM, Solovieva SE, Antipin IS. Synthesis of Water-Soluble Polyammonium Thiacalix[4]arene Derivative and Its Interaction with Calf Thymus DNA. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220010156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Bansal S, Tiwari S. Mechanisms for the temporal regulation of substrate ubiquitination by the anaphase-promoting complex/cyclosome. Cell Div 2019; 14:14. [PMID: 31889987 PMCID: PMC6927175 DOI: 10.1186/s13008-019-0057-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 07/02/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit, multifunctional ubiquitin ligase that controls the temporal degradation of numerous cell cycle regulatory proteins to direct the unidirectional cell cycle phases. Several different mechanisms contribute to ensure the correct order of substrate modification by the APC/C complex. Recent advances in biochemical, biophysical and structural studies of APC/C have provided a deep mechanistic insight into the working of this complex ubiquitin ligase. This complex displays remarkable conformational flexibility in response to various binding partners and post-translational modifications, which together regulate substrate selection and catalysis of APC/C. Apart from this, various features and modifications of the substrates also influence their recognition and affinity to APC/C complex. Ultimately, temporal degradation of substrates depends on the kind of ubiquitin modification received, the processivity of APC/C, and other extrinsic mechanisms. This review discusses our current understanding of various intrinsic and extrinsic mechanisms responsible for ‘substrate ordering’ by the APC/C complex.
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Affiliation(s)
- Shivangee Bansal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Swati Tiwari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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32
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Walters KJ. Ubiquitin in disguise unveils a cryptic binding site in 1.2-MDa anaphase-promoting complex/cyclosome. Proc Natl Acad Sci U S A 2019; 116:17142-4. [PMID: 31371495 DOI: 10.1073/pnas.1911388116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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33
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Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andrés-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guérillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thomä NH. Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation. Mol Cell 2019; 75:483-497.e9. [PMID: 31253574 PMCID: PMC6695476 DOI: 10.1016/j.molcel.2019.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/30/2019] [Accepted: 05/31/2019] [Indexed: 01/03/2023]
Abstract
In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions.
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Affiliation(s)
- Julius Rabl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Wassim Abdulrahman
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Amparo Andrés-Pons
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Martijn S Luijsterburg
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Adel F M Ibrahim
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Emma Branigan
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Aimee H Marceau
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Claire Guérillon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | - Haico van Attikum
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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34
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Watson ER, Grace CRR, Zhang W, Miller DJ, Davidson IF, Prabu JR, Yu S, Bolhuis DL, Kulko ET, Vollrath R, Haselbach D, Stark H, Peters JM, Brown NG, Sidhu SS, Schulman BA. Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc Natl Acad Sci U S A 2019; 116:17280-9. [PMID: 31350353 DOI: 10.1073/pnas.1902889116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.
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35
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Abstract
Protein ubiquitination impacts virtually every biochemical pathway in eukaryotic cells. The fate of a ubiquitinated protein is largely dictated by the type of ubiquitin modification with which it is decorated, including a large variety of polymeric chains. As a result, there have been intense efforts over the last two decades to dissect the molecular details underlying the synthesis of ubiquitin chains by ubiquitin-conjugating (E2) enzymes and ubiquitin ligases (E3s). In this review, we highlight these advances. We discuss the evidence in support of the alternative models of transferring one ubiquitin at a time to a growing substrate-linked chain (sequential addition model) versus transferring a pre-assembled ubiquitin chain (en bloc model) to a substrate. Against this backdrop, we outline emerging principles of chain assembly: multisite interactions, distinct mechanisms of chain initiation and elongation, optimal positioning of ubiquitin molecules that are ultimately conjugated to each other, and substrate-assisted catalysis. Understanding the enzymatic logic of ubiquitin chain assembly has important biomedical implications, as the misregulation of many E2s and E3s and associated perturbations in ubiquitin chain formation contribute to human disease. The resurgent interest in bifunctional small molecules targeting pathogenic proteins to specific E3s for polyubiquitination and subsequent degradation provides an additional incentive to define the mechanisms responsible for efficient and specific chain synthesis and harness them for therapeutic benefit.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, United States
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36
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Donato L, Scimone C, Nicocia G, D'Angelo R, Sidoti A. Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. Cell Cycle 2018; 18:84-104. [PMID: 30569795 DOI: 10.1080/15384101.2018.1558873] [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] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is a very heterogeneous inherited ocular disorder group characterized by progressive retinal disruption. Retinal pigment epithelium (RPE) degeneration, due to oxidative stress which arrests the metabolic support to photoreceptors, represents one of the principal causes of RP. Here, the role of oxidative stress in RP onset and progression was analyzed by a comparative whole transcriptome analysis of human RPE cells, treated with 100 µg/ml of oxLDL and untreated, at different time points. Experiment was thrice repeated and performed on Ion ProtonTM sequencing system. Data analysis, including low quality reads trimming and gene expression quantification, was realized by CLC Genomics Workbench software. The whole analysis highlighted 14 clustered "macro-pathways" and many sub-pathways, classified by selection of 5271 genes showing the highest alteration of expression. Among them, 23 genes were already known to be RP causative ones (15 over-expressed and 8 down-expressed), and their enrichment and intersection analyses highlighted new 77 candidate related genes (49 over-expressed and 28 down-expressed). A final filtering analysis then highlighted 29 proposed candidate genes. This data suggests that many new genes, not yet associated with RP, could influence its etiopathogenesis.
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Affiliation(s)
- Luigi Donato
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Concetta Scimone
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Giacomo Nicocia
- c Department of Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Rosalia D'Angelo
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Antonina Sidoti
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
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37
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DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, Kuhlman B, Klevit RE. A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation. Mol Cell 2018; 72:753-765.e6. [PMID: 30392931 DOI: 10.1016/j.molcel.2018.09.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 03/23/2018] [Revised: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 12/27/2022]
Abstract
DNA methylation patterns regulate gene expression programs and are maintained through a highly coordinated process orchestrated by the RING E3 ubiquitin ligase UHRF1. UHRF1 controls DNA methylation inheritance by reading epigenetic modifications to histones and DNA to activate histone H3 ubiquitylation. Here, we find that all five domains of UHRF1, including the previously uncharacterized ubiquitin-like domain (UBL), cooperate for hemi-methylated DNA-dependent H3 ubiquitin ligation. Our structural and biochemical studies, including mutations found in cancer genomes, reveal a bifunctional requirement for the UBL in histone modification: (1) the UBL makes an essential interaction with the backside of the E2 and (2) the UBL coordinates with other UHRF1 domains that recognize epigenetic marks on DNA and histone H3 to direct ubiquitin to H3. Finally, we show UBLs from other E3s also have a conserved interaction with the E2, Ube2D, highlighting a potential prevalence of interactions between UBLs and E2s.
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Affiliation(s)
- Paul A DaRosa
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27499, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Peter Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27499, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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38
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Watson ER, Brown NG, Peters JM, Stark H, Schulman BA. Posing the APC/C E3 Ubiquitin Ligase to Orchestrate Cell Division. Trends Cell Biol 2018; 29:117-134. [PMID: 30482618 DOI: 10.1016/j.tcb.2018.09.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 08/07/2018] [Revised: 09/23/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023]
Abstract
The anaphase promoting complex/cyclosome (APC/C) E3 ligase controls mitosis and nonmitotic pathways through interactions with proteins that coordinate ubiquitylation. Since the discovery that the catalytic subunits of APC/C are conformationally dynamic cullin and RING proteins, many unexpected and intricate regulatory mechanisms have emerged. Here, we review structural knowledge of this regulation, focusing on: (i) coactivators, E2 ubiquitin (Ub)-conjugating enzymes, and inhibitors engage or influence multiple sites on APC/C including the cullin-RING catalytic core; and (ii) the outcomes of these interactions rely on mobility of coactivators and cullin-RING domains, which permits distinct conformations specifying different functions. Thus, APC/C is not simply an interaction hub, but is instead a dynamic, multifunctional molecular machine whose structure is remodeled by binding partners to achieve temporal ubiquitylation regulating cell division.
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Affiliation(s)
- Edmond R Watson
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Campus Vienna Biocenter (VBC) 1, 1030 Vienna, Austria
| | - Holger Stark
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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39
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Bonacci T, Suzuki A, Grant GD, Stanley N, Cook JG, Brown NG, Emanuele MJ. Cezanne/OTUD7B is a cell cycle-regulated deubiquitinase that antagonizes the degradation of APC/C substrates. EMBO J 2018; 37:embj.201798701. [PMID: 29973362 DOI: 10.15252/embj.201798701] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 12/14/2017] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and key regulator of cell cycle progression. Since APC/C promotes the degradation of mitotic cyclins, it controls cell cycle-dependent oscillations in cyclin-dependent kinase (CDK) activity. Both CDKs and APC/C control a large number of substrates and are regulated by analogous mechanisms, including cofactor-dependent activation. However, whereas substrate dephosphorylation is known to counteract CDK, it remains largely unknown whether deubiquitinating enzymes (DUBs) antagonize APC/C substrate ubiquitination during mitosis. Here, we demonstrate that Cezanne/OTUD7B is a cell cycle-regulated DUB that opposes the ubiquitination of APC/C targets. Cezanne is remarkably specific for K11-linked ubiquitin chains, which are formed by APC/C in mitosis. Accordingly, Cezanne binds established APC/C substrates and reverses their APC/C-mediated ubiquitination. Cezanne depletion accelerates APC/C substrate degradation and causes errors in mitotic progression and formation of micronuclei. These data highlight the importance of tempered APC/C substrate destruction in maintaining chromosome stability. Furthermore, Cezanne is recurrently amplified and overexpressed in numerous malignancies, suggesting a potential role in genome maintenance and cancer cell proliferation.
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Affiliation(s)
- Thomas Bonacci
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aussie Suzuki
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gavin D Grant
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette G Cook
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA .,Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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40
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Abstract
The Anaphase Promoting Complex/Cyclosome (APC/C) is a ubiquitin E3 ligase that functions as the gatekeeper to mitotic exit. APC/C activity is controlled by an interplay of multiple pathways during mitosis, including the spindle assembly checkpoint (SAC), that are not yet fully understood. Here, we show that sumoylation of the APC4 subunit of the APC/C peaks during mitosis and is critical for timely APC/C activation and anaphase onset. We have also identified a functionally important SUMO interacting motif in the cullin-homology domain of APC2 located near the APC4 sumoylation sites and APC/C catalytic core. Our findings provide evidence of an important regulatory role for SUMO modification and binding in affecting APC/C activation and mitotic exit.
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Affiliation(s)
- Christine C Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, United States
| | - Bing Li
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hongtao Yu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, United States
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41
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Streich FC, Lima CD. Strategies to Trap Enzyme-Substrate Complexes that Mimic Michaelis Intermediates During E3-Mediated Ubiquitin-Like Protein Ligation. Methods Mol Biol 2018; 1844:169-196. [PMID: 30242710 DOI: 10.1007/978-1-4939-8706-1_12] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Most cellular functions rely on pathways that catalyze posttranslational modification of cellular proteins by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. Like other posttranslational modifications that require distinct writers, readers, and erasers during signaling, Ub/Ubl pathways employ distinct enzymes that catalyze Ub/Ubl attachment, Ub/Ubl recognition, and Ub/Ubl removal. Ubl protein conjugation typically relies on parallel but distinct enzymatic cascades catalyzed by an E1-activating enzyme, an E2 carrier protein, and an E3 ubiquitin-like protein ligase. One major class of E3, with ca. 600 members, harbors RING or the RING-like SP-RING or Ubox domains. These RING/RING-like domains bind and activate the E2-Ubl thioester by stabilizing a conformation that is optimal for nucleophilic attack by the side chain residue (typically lysine) on the substrate. These RING/RING-like domains typically function together with other domains or protein complexes that often serve to recruit particular substrates. How these RING/RING-like E3 domains function to activate the E2-Ubl thioester while engaged with substrate remains poorly understood. We describe a strategy to generate and purify a unique E2Ubc9-UblSUMO thioester mimetic that can be cross-linked to the SubstratePCNA at Lys164, a conjugation site that is only observed in the presence of E3Siz1. We describe two techniques to cross-link the E2Ubc9-UblSUMO thioester mimetic active site to the site of modification on PCNA and the subsequent purification of these complexes. Finally, we describe the reconstitution and purification of the E2Ubc9-UblSUMO-PCNA complex with the E3Siz1 and purification that enabled its crystallization and structure determination. We think this technique can be extended to other E2-Ubl-substrate/E3 complexes to better probe the function and specificity of RING-based E3 Ubl ligases.
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Affiliation(s)
- Frederick C Streich
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, USA.
- Howard Hughes Medical Institute, 1275 York Ave, New York, NY, USA.
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42
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Karg E, Smets M, Ryan J, Forné I, Qin W, Mulholland CB, Kalideris G, Imhof A, Bultmann S, Leonhardt H. Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells. J Mol Biol 2017; 429:3814-24. [DOI: 10.1016/j.jmb.2017.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/26/2017] [Accepted: 10/12/2017] [Indexed: 12/30/2022]
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43
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Alfieri C, Zhang S, Barford D. Visualizing the complex functions and mechanisms of the anaphase promoting complex/cyclosome (APC/C). Open Biol 2017; 7:170204. [PMID: 29167309 PMCID: PMC5717348 DOI: 10.1098/rsob.170204] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [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: 08/30/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
The anaphase promoting complex or cyclosome (APC/C) is a large multi-subunit E3 ubiquitin ligase that orchestrates cell cycle progression by mediating the degradation of important cell cycle regulators. During the two decades since its discovery, much has been learnt concerning its role in recognizing and ubiquitinating specific proteins in a cell-cycle-dependent manner, the mechanisms governing substrate specificity, the catalytic process of assembling polyubiquitin chains on its target proteins, and its regulation by phosphorylation and the spindle assembly checkpoint. The past few years have witnessed significant progress in understanding the quantitative mechanisms underlying these varied APC/C functions. This review integrates the overall functions and properties of the APC/C with mechanistic insights gained from recent cryo-electron microscopy (cryo-EM) studies of reconstituted human APC/C complexes.
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Affiliation(s)
- Claudio Alfieri
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Suyang Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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44
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Abstract
Ubiquitylation is essential for signal transduction as well as cell division and differentiation in all eukaryotes. Substrate modifications range from a single ubiquitin molecule to complex polymeric chains, with different types of ubiquitylation often eliciting distinct outcomes. The recent identification of novel chain topologies has improved our understanding of how ubiquitylation establishes precise communication within cells. Here, we discuss how the increasing complexity of ubiquitylation is employed to ensure robust and faithful signal transduction in eukaryotic cells.
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45
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Paiva SL, da Silva SR, de Araujo ED, Gunning PT. Regulating the Master Regulator: Controlling Ubiquitination by Thinking Outside the Active Site. J Med Chem 2017; 61:405-421. [DOI: 10.1021/acs.jmedchem.6b01346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Stacey-Lynn Paiva
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Sara R. da Silva
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Elvin D. de Araujo
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Patrick T. Gunning
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
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46
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Abstract
Ubiquitin-like proteins (Ubl's) are conjugated to target proteins or lipids to regulate their activity, stability, subcellular localization, or macromolecular interactions. Similar to ubiquitin, conjugation is achieved through a cascade of activities that are catalyzed by E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. In this review, we will summarize structural and mechanistic details of enzymes and protein cofactors that participate in Ubl conjugation cascades. Precisely, we will focus on conjugation machinery in the SUMO, NEDD8, ATG8, ATG12, URM1, UFM1, FAT10, and ISG15 pathways while referring to the ubiquitin pathway to highlight common or contrasting themes. We will also review various strategies used to trap intermediates during Ubl activation and conjugation.
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Affiliation(s)
- Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States.,Howard Hughes Medical Institute, Sloan Kettering Institute , New York, New York 10021, United States
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47
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Abstract
In eukaryotic cell division, the Spindle Assembly Checkpoint (SAC) plays a key regulatory role by monitoring the status of chromosome-microtubule attachments and allowing chromosome segregation only after all chromosomes are properly attached to spindle microtubules. While the identities of SAC components have been known, in some cases, for over two decades, the molecular mechanisms of the SAC have remained mostly mysterious until very recently. In the past few years, advances in biochemical reconstitution, structural biology, and bioinformatics have fueled an explosion in the molecular understanding of the SAC. This chapter seeks to synthesize these recent advances and place them in a biological context, in order to explain the mechanisms of SAC activation and silencing at a molecular level.
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Affiliation(s)
- Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA.
- Departments of Cellular & Molecular Medicine and Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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48
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Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA. Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell 2016; 165:1440-1453. [PMID: 27259151 DOI: 10.1016/j.cell.2016.05.037] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/16/2016] [Accepted: 05/09/2016] [Indexed: 11/25/2022]
Abstract
Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.
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Affiliation(s)
- Nicholas G Brown
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan VanderLinden
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA
| | - Edmond R Watson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kuen-Phon Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Shanshan Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Y Mercredi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Renping Qiao
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Prakash Dube
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael R Brunner
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Haselbach
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marc A Jarvis
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Masaya Yamaguchi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Yanishevski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Georg Petzold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
| | - Holger Stark
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA.
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49
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Gorelik M, Sidhu SS. Specific targeting of the deubiquitinase and E3 ligase families with engineered ubiquitin variants. Bioeng Transl Med 2016; 2:31-42. [PMID: 28580429 PMCID: PMC5434665 DOI: 10.1002/btm2.10044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 07/26/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin proteasome system (UPS) has garnered much attention due to its potential for the development of therapeutics. Following a successful clinical application of general proteasome inhibitors much effort has been devoted to targeting individual UPS components including E3 enzymes and deubiquitinases that control specificity of ubiquitination. Our group has developed a novel approach for targeting the UPS proteins using engineered ubiquitin variants (Ubvs). These drug‐like proteins can serve as valuable tools to study biological function of UPS components and assist in the development of small molecules for clinical use. In this review, we summarize studies of Ubvs targeting members of three major families, including deubiquitinases, HECT E3 ligases, and CRL E3 ligases. In particular, we focus on Ubv binding mechanisms, structural studies, and effects on enzyme function. Furthermore, new insights gained from the Ubvs are discussed in the context of small molecule studies.
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Affiliation(s)
- Maryna Gorelik
- Banting and Best Dept. of Medical Research and the Dept. of Molecular Genetics Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON Canada M5S 3E1
| | - Sachdev S Sidhu
- Banting and Best Dept. of Medical Research and the Dept. of Molecular Genetics Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON Canada M5S 3E1
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50
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Abstract
Post-translational modification (PTM) of proteins by ubiquitination is an essential cellular regulatory process. Such regulation drives the cell cycle and cell division, signalling and secretory pathways, DNA replication and repair processes and protein quality control and degradation pathways. A huge range of ubiquitin signals can be generated depending on the specificity and catalytic activity of the enzymes required for attachment of ubiquitin to a given target. As a consequence of its importance to eukaryotic life, dysfunction in the ubiquitin system leads to many disease states, including cancers and neurodegeneration. This review takes a retrospective look at our progress in understanding the molecular mechanisms that govern the specificity of ubiquitin conjugation.
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