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Zhang S, Cao L, Chang R, Zhang H, Yu J, Li C, Liu G, Yan J, Xu Z. Network Analysis of Metabolome and Transcriptome Revealed Regulation of Different Nitrogen Concentrations on Hybrid Poplar Cambium Development. Int J Mol Sci 2024; 25:1017. [PMID: 38256092 PMCID: PMC10816006 DOI: 10.3390/ijms25021017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Secondary development is a key biological characteristic of woody plants and the basis of wood formation. Exogenous nitrogen can affect the secondary growth of poplar, and some regulatory mechanisms have been found in the secondary xylem. However, the effect of nitrogen on cambium has not been reported. Herein, we investigated the effects of different nitrogen concentrations on cambium development using combined transcriptome and metabolome analysis. The results show that, compared with 1 mM NH4NO3 (M), the layers of hybrid poplar cambium cells decreased under the 0.15 mM NH4NO3 (L) and 0.3 mM NH4NO3 (LM) treatments. However, there was no difference in the layers of hybrid poplar cambium cells under the 3 mM NH4NO3 (HM) and 5 mM NH4NO3 (H) treatments. Totals of 2365, 824, 649 and 398 DEGs were identified in the M versus (vs.) L, M vs. LM, M vs. HM and M vs. H groups, respectively. Expression profile analysis of the DEGs showed that exogenous nitrogen affected the gene expression involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the starch and sucrose metabolism pathway and the ubiquitin-mediated proteolysis pathway. In M vs. L, M vs. LM, M vs. HM and M vs. H, differential metabolites were enriched in flavonoids, lignans, coumarins and saccharides. The combined analysis of the transcriptome and metabolome showed that some genes and metabolites in plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism pathways may be involved in nitrogen regulation in cambium development, whose functions need to be verified. In this study, from the point of view that nitrogen influences cambium development to regulate wood formation, the network analysis of the transcriptome and metabolomics of cambium under different nitrogen supply levels was studied for the first time, revealing the potential regulatory and metabolic mechanisms involved in this process and providing new insights into the effects of nitrogen on wood development.
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Affiliation(s)
- Shuang Zhang
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (S.Z.); (R.C.)
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.C.); (H.Z.); (J.Y.); (C.L.); (G.L.)
| | - Ruhui Chang
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (S.Z.); (R.C.)
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.C.); (H.Z.); (J.Y.); (C.L.); (G.L.)
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.C.); (H.Z.); (J.Y.); (C.L.); (G.L.)
| | - Chunming Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.C.); (H.Z.); (J.Y.); (C.L.); (G.L.)
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.C.); (H.Z.); (J.Y.); (C.L.); (G.L.)
| | - Junxin Yan
- College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China
| | - Zhiru Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (S.Z.); (R.C.)
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.C.); (H.Z.); (J.Y.); (C.L.); (G.L.)
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Chowdhury SR, Koley T, Singh M, Samath EA, Kaur P. Association of Hsp90 with p53 and Fizzy related homolog (Fzr) synchronizing Anaphase Promoting Complex (APC/C): An unexplored ally towards oncogenic pathway. Biochim Biophys Acta Rev Cancer 2023; 1878:188883. [PMID: 36972769 DOI: 10.1016/j.bbcan.2023.188883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/29/2023]
Abstract
The intricate molecular interactions leading to the oncogenic pathway are the consequence of cell cycle modification controlled by a bunch of cell cycle regulatory proteins. The tumor suppressor and cell cycle regulatory proteins work in coordination to maintain a healthy cellular environment. The integrity of this cellular protein pool is perpetuated by heat shock proteins/chaperones, which assist in proper protein folding during normal and cellular stress conditions. Among these versatile groups of chaperone proteins, Hsp90 is one of the significant ATP-dependent chaperones that aid in stabilizing many tumor suppressors and cell cycle regulator protein targets. Recently, studies have revealed that in cancerous cell lines, Hsp90 stabilizes mutant p53, 'the guardian of the genome.' Hsp90 also has a significant impact on Fzr, an essential regulator of the cell cycle having an important role in the developmental process of various organisms, including Drosophila, yeast, Caenorhabditis elegans, and plants. During cell cycle progression, p53 and Fzr coordinately regulate the Anaphase Promoting Complex (APC/C) from metaphase to anaphase transition up to cell cycle exit. APC/C mediates proper centrosome function in the dividing cell. The centrosome acts as the microtubule organizing center for the correct segregation of the sister chromatids to ensure perfect cell division. This review examines the structure of Hsp90 and its co-chaperones, which work in synergy to stabilize proteins such as p53 and Fizzy-related homolog (Fzr) to synchronize the Anaphase Promoting Complex (APC/C). Dysfunction of this process activates the oncogenic pathway leading to the development of cancer. Additionally, an overview of current drugs targeting Hsp90 at various phases of clinical trials has been included.
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Affiliation(s)
- Sanghati Roy Chowdhury
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tirthankar Koley
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | | | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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He Y, Le X, Hu G, Li Q, Chen Z. Discovery of Ureido-Based Apcin Analogues as Cdc20-specific Inhibitors against Cancer. Pharmaceuticals (Basel) 2023; 16:304. [PMID: 37259447 PMCID: PMC9964651 DOI: 10.3390/ph16020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 09/14/2024] Open
Abstract
Cdc20 is a promising drug target that plays an important role in the mid-anaphase process of cellular mitosis, and Apcin is the only reported core structure of the Cdc20-specific inhibitor. Some potent Apcin derivatives were obtained in our previous research, and a structure-activity relationship was determined. In this study, we designed and synthesized a series of ureido-based Apcin derivatives. The proliferation-inhibition experiments on four cancer-cell lines showed that ureido skeleton could promote the anti-proliferation activity of purine-substituted compounds, whereas the ureido analogues with pyrimidine substitutes showed no significant improvement in the inhibitory effect compared with the original ones. Further tests confirmed that ureido-based compounds can enhance the binding affinity to Cdc20 by increasing the levels of Cdc20 downstream proteins. Compound 27 revealed a remarkably antitumor activity pattern against Hela (IC50 = 0.06 ± 0.02 μM) and potent binding affinity to Cdc20. Moreover, compound 20 induced caspase-dependent apoptosis and cell-cycle arrest at the G2/M phase, and compound 27 induced caspase-dependent apoptosis and promoted microtubule polymerization. Finally, a molecular-docking simulation was performed for compounds 20 and 27 to predict the potential ligand-protein interactions with the active sites of the Cdc20 proteins.
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Affiliation(s)
- Yiqin He
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Xiangyang Le
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Gaoyun Hu
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Zhuo Chen
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha 410013, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
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Jaiswal N, Nandi D, Cheema PS, Nag A. The anaphase-promoting complex/cyclosome co-activator, Cdh1, is a novel target of human papillomavirus 16 E7 oncoprotein in cervical oncogenesis. Carcinogenesis 2022; 43:988-1001. [PMID: 35738876 DOI: 10.1093/carcin/bgac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/01/2022] [Accepted: 06/23/2022] [Indexed: 01/13/2023] Open
Abstract
The transforming properties of the high-risk human papillomavirus (HPV) E7 oncoprotein are indispensable for driving the virus life cycle and pathogenesis. Besides inactivation of the retinoblastoma family of tumor suppressors as part of its oncogenic endeavors, E7-mediated perturbations of eminent cell cycle regulators, checkpoint proteins and proto-oncogenes are considered to be the tricks of its transformative traits. However, many such critical interactions are still unknown. In the present study, we have identified the anaphase-promoting complex/cyclosome (APC) co-activator, Cdh1, as a novel interacting partner and a degradation target of E7. We found that HPV16 E7-induced inactivation of Cdh1 promoted abnormal accumulation of multiple Cdh1 substrates. Such a mode of deregulation possibly contributes to HPV-mediated cervical oncogenesis. Our mapping studies recognized the C-terminal zinc-finger motif of E7 to associate with Cdh1 and interfere with the timely degradation of FoxM1, a bona fide Cdh1 substrate and a potent oncogene. Importantly, the E7 mutant with impaired interaction with Cdh1 exhibited defects in its ability for overriding typical cell cycle transition and oncogenic transformation, thereby validating the functional and pathological significance of the E7-Cdh1 axis during cervical carcinoma progression. Altogether, the findings from our study discover a unique nexus between E7 and APC/C-Cdh1, thereby adding to our understanding of the mechanism of E7-induced carcinogenesis and provide a promising target for the management of cervical carcinoma.
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Affiliation(s)
- Neha Jaiswal
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Marg, New Delhi, India
| | - Deeptashree Nandi
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Marg, New Delhi, India
| | - Pradeep Singh Cheema
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Marg, New Delhi, India
| | - Alo Nag
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Marg, New Delhi, India
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Korsching E, Matschke J, Hotfilder M. Splice variants denote differences between a cancer stem cell side population of EWSR1‑ERG‑based Ewing sarcoma cells, its main population and EWSR1‑FLI‑based cells. Int J Mol Med 2022; 49:39. [PMID: 35088879 PMCID: PMC8815407 DOI: 10.3892/ijmm.2022.5094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/17/2021] [Indexed: 11/06/2022] Open
Abstract
Ewing sarcoma is a challenging cancer entity, which, besides the characteristic presence of a fusion gene, is driven by multiple alternative splicing events. So far, splice variants in Ewing sarcoma cells were mainly analyzed for EWSR1‑FLI1. The present study provided a comprehensive alternative splicing study on CADO‑ES1, an Ewing model cell line for an EWSR1‑ERG fusion gene. Based on a well‑-characterized RNA‑sequencing dataset with extensive control mechanisms across all levels of analysis, the differential spliced genes in Ewing cancer stem cells were ATP13A3 and EPB41, while the main population was defined by ACADVL, NOP58 and TSPAN3. All alternatively spliced genes were further characterized by their Gene Ontology (GO) terms and by their membership in known protein complexes. These results confirm and extend previous studies towards a systematic whole‑transcriptome analysis. A highlight is the striking segregation of GO terms associated with five basic splice events. This mechanistic insight, together with a coherent integration of all observations with prior knowledge, indicates that EWSR1‑ERG is truly a close twin to EWSR1‑FLI1, but still exhibits certain individuality. Thus, the present study provided a measure of variability in Ewing sarcoma, whose understanding is essential both for clinical procedures and basic mechanistic insight.
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Affiliation(s)
- Eberhard Korsching
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, D‑48149 Münster, Germany
| | - Julian Matschke
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, D‑48149 Münster, Germany
| | - Marc Hotfilder
- Department of Pediatric Hematology and Oncology, University Hospital Münster, D‑48149 Münster, Germany
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Badarudeen B, Anand U, Mukhopadhyay S, Manna TK. Ubiquitin signaling in the control of centriole duplication. FEBS J 2021; 289:4830-4849. [PMID: 34115927 DOI: 10.1111/febs.16069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/22/2021] [Accepted: 06/10/2021] [Indexed: 12/14/2022]
Abstract
The centrosome plays an essential role in maintaining genetic stability, ciliogenesis and cell polarisation. The core of the centrosome is made up of two centrioles that duplicate precisely once during every cell cycle to generate two centrosomes that are required for bipolar spindle assembly and chromosome segregation. Abundance of centriole proteins at optimal levels and their recruitment to the centrosome are tightly regulated in time and space in order to restrict aberrant duplication of centrioles, a phenomenon that is observed in many cancers. Recent advances have conclusively shown that dedicated ubiquitin ligase-dependent protein degradation machineries are involved in governing centriole duplication. These studies revealed intricate mechanistic insights into how the ubiquitin ligases target different centriole proteins. In certain cases, a specific ubiquitin ligase targets a number of substrate proteins that co-regulate centriole assembly, prompting the possibility that substrate-targeting occurs during formation of the sub-centriolar structures. There are also instances where a specific centriole duplication protein is targeted by several ubiquitin ligases at different stages of the cell cycle, suggesting synchronised actions. Recent evidence also indicated a direct association of E3 ubiquitin ligase with the centrioles, supporting the notion that substrate-targeting occurs in the organelle itself. In this review, we highlight these advances by underlining the mechanisms of how different ubiquitin ligase machineries control centriole duplication and discuss our views on their coordination.
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Affiliation(s)
- Binshad Badarudeen
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, India
| | - Ushma Anand
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, India
| | - Swarnendu Mukhopadhyay
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, India
| | - Tapas K Manna
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, India
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7
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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: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [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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Novel Mutations in CDC20 Are Associated with Female Infertility Due to Oocyte Maturation Abnormality and Early Embryonic Arrest. Reprod Sci 2021; 28:1930-1938. [PMID: 33683667 DOI: 10.1007/s43032-021-00524-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/01/2021] [Indexed: 10/22/2022]
Abstract
The cell division cycle 20 (CDC20) protein is a co-activator of anaphase-promoting complex/cyclosome (APC/C), required for mitotic exit and also meiotic exit, containing seven WD40 repeats in the C-terminus responsible for protein-protein interactions. Recently, a previous study has shown that biallelic mutations in CDC20 are causative for female infertility with abnormalities in oocyte maturation and embryonic development. This study is to further identify new mutations of CDC20 and the prevalence of variants in our cohort. A cohort of 50 primary infertile females with oocyte maturation abnormality and early embryonic arrest were recruited. Genomic DNA was isolated from peripheral blood samples. Mutation screening of all the coding regions of CDC20 was performed by Sanger sequencing. The pathogenicity of the identified variants on the CDC20 protein was accessed in silico. Two CDC20 variants, a nonsense mutation p.R262* and a missense mutation p.A211T, identified in one female of 50 unrelated affected individuals, accounting for a relative small proportion of this cohort (2%). In silico analysis revealed that the p.R262* would cause no production of protein or a truncated protein lacking five WD40 repeats in the C-terminus; and that p.A211T may interfere with the formation of a deep hydrophobic pocket and thus disturb the binding of CDC20 protein to the substrates of APC/C. This study identified two novel mutations in CDC20, further expanding the mutation spectrum of this gene. Our findings further confirm that biallelic mutations in CDC20 occur in a proportion of infertile females with oocyte maturation abnormality and early embryonic arrest.
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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: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [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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Maurer-Stroh S, Krutz NL, Kern PS, Gunalan V, Nguyen MN, Limviphuvadh V, Eisenhaber F, Gerberick GF. AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics 2020; 35:3020-3027. [PMID: 30657872 PMCID: PMC6736023 DOI: 10.1093/bioinformatics/btz029] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/18/2018] [Accepted: 01/14/2019] [Indexed: 12/22/2022] Open
Abstract
Motivation Due to the risk of inducing an immediate Type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens. Results We developed AllerCatPro which predicts the allergenic potential of proteins based on similarity of their 3D protein structure as well as their amino acid sequence compared with a data set of known protein allergens comprising of 4180 unique allergenic protein sequences derived from the union of the major databases Food Allergy Research and Resource Program, Comprehensive Protein Allergen Resource, WHO/International Union of Immunological Societies, UniProtKB and Allergome. We extended the hexamer hit rule by removing peptides with high probability of random occurrence measured by sequence entropy as well as requiring 3 or more hexamer hits consistent with natural linear epitope patterns in known allergens. This is complemented with a Gluten-like repeat pattern detection. We also switched from a linear sequence window similarity to a B-cell epitope-like 3D surface similarity window which became possible through extensive 3D structure modeling covering the majority (74%) of allergens. In case no structure similarity is found, the decision workflow reverts to the old linear sequence window rule. The overall accuracy of AllerCatPro is 84% compared with other current methods which range from 51 to 73%. Both the FAO/WHO rules and AllerCatPro achieve highest sensitivity but AllerCatPro provides a 37-fold increase in specificity. Availability and implementation https://allercatpro.bii.a-star.edu.sg/ Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Nora L Krutz
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Petra S Kern
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Vithiagaran Gunalan
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Minh N Nguyen
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Frank Eisenhaber
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
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11
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Ubiquitin chain-elongating enzyme UBE2S activates the RING E3 ligase APC/C for substrate priming. Nat Struct Mol Biol 2020; 27:550-560. [PMID: 32393902 PMCID: PMC7293561 DOI: 10.1038/s41594-020-0424-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [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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12
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APC/C ubiquitin ligase: Functions and mechanisms in tumorigenesis. Semin Cancer Biol 2020; 67:80-91. [PMID: 32165320 DOI: 10.1016/j.semcancer.2020.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/24/2020] [Accepted: 03/02/2020] [Indexed: 12/18/2022]
Abstract
The anaphase promoting complex/ cyclosome (APC/C), is an evolutionarily conserved protein complex essential for cellular division due to its role in regulating the mitotic transition from metaphase to anaphase. In this review, we highlight recent work that has shed light on our understanding of the role of APC/C coactivators, Cdh1 and Cdc20, in cancer initiation and development. We summarize the current state of knowledge regarding APC/C structure and function, as well as the distinct ways Cdh1 and Cdc20 are dysregulated in human cancer. We also discuss APC/C inhibitors, novel approaches for targeting the APC/C as a cancer therapy, and areas for future work.
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13
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Shoji S, Hanada K, Takahashi M, Watanabe K, Yonemochi M, Tomabechi Y, Shirouzu M. The NF-κB regulator IκBβ exhibits different molecular interactivity and phosphorylation status from IκBα in an IKK2-catalysed reaction. FEBS Lett 2020; 594:1532-1549. [PMID: 32017069 DOI: 10.1002/1873-3468.13752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/06/2020] [Accepted: 01/21/2020] [Indexed: 12/13/2022]
Abstract
Activation of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) transcription factor, a central player in immune response regulation, is based on phosphorylation of inhibitor of kappaB alpha (IκBα) by the Inhibitor of kappaB kinase (IKK) that triggers IκBα degradation. Although inhibitor of kappaB beta (IκBβ) is structurally similar to IκBα, its precise characteristics remain undefined. Herein, we report that the molecular interactivity of IκBβ with the kinase-active region of IKK subunit 2 (IKK2), as well as its phosphorylation status, differs markedly from those of IκBα. A mass spectrometry analysis revealed that IκBβ phosphorylation sites are distributed in its C-terminal region, whereas IκBα phosphorylation sites are located in the N-terminal region. Furthermore, IKK2 phosphorylation sites in IκBβ are found in a region distinct from typical degradation signals, such as phosphodegron and proline/glutamic acid/serine/threonine-rich sequence (PEST) motifs. Mutation of the IκBβ phosphorylation sites enhances its resistance to homeostatic proteasomal degradation. These findings contribute a novel concept in NF-κB/IKK signalling research.
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Affiliation(s)
- Shisako Shoji
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Kazuharu Hanada
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | | | | | | | - Yuri Tomabechi
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
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14
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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: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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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15
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Mizrak A, Morgan DO. Polyanions provide selective control of APC/C interactions with the activator subunit. Nat Commun 2019; 10:5807. [PMID: 31862931 PMCID: PMC6925294 DOI: 10.1038/s41467-019-13864-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/04/2019] [Indexed: 01/18/2023] Open
Abstract
Transient interactions between the anaphase-promoting complex/cyclosome (APC/C) and its activator subunit Cdc20 or Cdh1 generate oscillations in ubiquitylation activity necessary to maintain the order of cell cycle events. Activator binds the APC/C with high affinity and exhibits negligible dissociation kinetics in vitro, and it is not clear how the rapid turnover of APC/C-activator complexes is achieved in vivo. Here, we describe a mechanism that controls APC/C-activator interactions based on the availability of substrates. We find that APC/C-activator dissociation is stimulated by abundant cellular polyanions such as nucleic acids and polyphosphate. Polyanions also interfere with substrate ubiquitylation. However, engagement with high-affinity substrate blocks the inhibitory effects of polyanions on activator binding and APC/C activity. We propose that this mechanism amplifies the effects of substrate affinity on APC/C function, stimulating processive ubiquitylation of high-affinity substrates and suppressing ubiquitylation of low-affinity substrates.
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Affiliation(s)
- Arda Mizrak
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, CA, 94143, USA.
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16
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Interplay between Phosphatases and the Anaphase-Promoting Complex/Cyclosome in Mitosis. Cells 2019; 8:cells8080814. [PMID: 31382469 PMCID: PMC6721574 DOI: 10.3390/cells8080814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Accurate division of cells into two daughters is a process that is vital to propagation of life. Protein phosphorylation and selective degradation have emerged as two important mechanisms safeguarding the delicate choreography of mitosis. Protein phosphatases catalyze dephosphorylation of thousands of sites on proteins, steering the cells through establishment of the mitotic phase and exit from it. A large E3 ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C) becomes active during latter stages of mitosis through G1 and marks hundreds of proteins for destruction. Recent studies have revealed the complex interregulation between these two classes of enzymes. In this review, we highlight the direct and indirect mechanisms by which phosphatases and the APC/C mutually influence each other to ensure accurate spatiotemporal and orderly progression through mitosis, with a particular focus on recent insights and conceptual advances.
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17
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Willison KR. The substrate specificity of eukaryotic cytosolic chaperonin CCT. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0192. [PMID: 29735743 DOI: 10.1098/rstb.2017.0192] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The cytosolic chaperonin CCT (chaperonin containing TCP-1) is an ATP-dependent double-ring protein machine mediating the folding of members of the eukaryotic cytoskeletal protein families. The actins and tubulins are obligate substrates of CCT because they are completely dependent on CCT activity to reach their native states. Genetic and proteomic analysis of the CCT interactome in the yeast Saccharomyces cerevisiae revealed a CCT network of approximately 300 genes and proteins involved in many fundamental biological processes. We classified network members into sets such as substrates, CCT cofactors and CCT-mediated assembly processes. Many members of the 7-bladed propeller family of proteins are commonly found tightly bound to CCT isolated from human and plant cells and yeasts. The anaphase promoting complex (APC/C) cofactor propellers, Cdh1p and Cdc20p, are also obligate substrates since they both require CCT for folding and functional activation. In vitro translation analysis in prokaryotic and eukaryotic cell extracts of a set of yeast propellers demonstrates their highly differential interactions with CCT and GroEL (another chaperonin). Individual propeller proteins have idiosyncratic interaction modes with CCT because they emerged independently with neo-functions many times throughout eukaryotic evolution. We present a toy model in which cytoskeletal protein biogenesis and folding flux through CCT couples cell growth and size control to time dependent cell cycle mechanisms.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Keith R Willison
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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18
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Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans. Protein J 2019; 38:58-75. [PMID: 30511317 DOI: 10.1007/s10930-018-9804-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc. In this article insilico analysis of the WDR proteins in the budding yeast Saccharomyces cerevisiae was performed. By WDSP software 83 proteins in S. cerevisiae were identified with at least one WD40 motif. WD40 proteins with 6 or more WD40 motifs were considered for further studies. The WD40 proteins in yeast which are involved in various biological processes show distribution on all chromosomes (16 chromosomes in yeast) except chromosome 1. Besides the WD40 domain some of these proteins also contain other protein domains which might be responsible for the diversity in the functions of WD40 proteins in the budding yeast. These proteins in budding yeast were analysed by DAVID and Blast2Go software for functional and domains categorization. Candida albicans, an opportunistic fungal pathogen also have orthologs of these WD40 proteins with possible similar functions. This is the first time genome wide analysis of WD40 proteins in lower eukaryote i.e. budding yeast. This data may be useful in further study of the functional diversity of yeast proteomes.
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19
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Hao C, Yin J, Sun M, Wang Q, Liang J, Bian Z, Liu H, Xu J. The meiosis‐specific APC activator
FgAMA1
is dispensable for meiosis but important for ascosporogenesis in
Fusarium graminearum. Mol Microbiol 2019; 111:1245-1262. [DOI: 10.1111/mmi.14219] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 01/21/2023]
Affiliation(s)
- Chaofeng Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
| | - Jinrong Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
| | - Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
| | - Jie Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
| | - Zhuyun Bian
- Department of Botany and Plant Pathology Purdue University West Lafayette IN 47907USA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
| | - Jin‐Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU‐Purdue Joint Research Center, College of Plant Protection Northwest A&F University Yangling Shaanxi 712100China
- Department of Botany and Plant Pathology Purdue University West Lafayette IN 47907USA
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20
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Abstract
The separation of sister chromatids at anaphase, which is regulated by an E3 ubiquitin ligase called the anaphase-promoting complex/cyclosome (APC/C), is arguably the most important irrevocable event during the cell cycle. The APC/C and cyclin-dependent kinase 1 (Cdk1) are just two of the many significant cell cycle regulators and exert control through ubiquitylation and phosphorylation, respectively. The temporal and spatial regulation of the APC/C is achieved by multiple mechanisms, including phosphorylation, interaction with the structurally related co-activators Cdc20 and Cdh1, loading of distinct E2 ubiquitin-conjugating enzymes, binding with inhibitors and differential affinities for various substrates. Since the discovery of APC/C 25 years ago, intensive studies have uncovered many aspects of APC/C regulation, but we are still far from a full understanding of this important cellular machinery. Recent high-resolution cryogenic electron microscopy analysis and reconstitution of the APC/C have greatly advanced our understanding of molecular mechanisms underpinning the enzymatic properties of APC/C. In this review, we will examine the historical background and current understanding of APC/C regulation.
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Affiliation(s)
- Hiroyuki Yamano
- Cell Cycle Control Group, UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
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21
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Rusnac DV, Lin HC, Canzani D, Tien KX, Hinds TR, Tsue AF, Bush MF, Yen HCS, Zheng N. Recognition of the Diglycine C-End Degron by CRL2 KLHDC2 Ubiquitin Ligase. Mol Cell 2018; 72:813-822.e4. [PMID: 30526872 PMCID: PMC6294321 DOI: 10.1016/j.molcel.2018.10.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/07/2018] [Accepted: 10/15/2018] [Indexed: 01/07/2023]
Abstract
Aberrant proteins can be deleterious to cells and are cleared by the ubiquitin-proteasome system. A group of C-end degrons that are recognized by specific cullin-RING ubiquitin E3 ligases (CRLs) has recently been identified in some of these abnormal polypeptides. Here, we report three crystal structures of a CRL2 substrate receptor, KLHDC2, in complex with the diglycine-ending C-end degrons of two early-terminated selenoproteins and the N-terminal proteolytic fragment of USP1. The E3 recognizes the degron peptides in a similarly coiled conformation and cradles their C-terminal diglycine with a deep surface pocket. By hydrogen bonding with multiple backbone carbonyls of the peptides, KLHDC2 further locks in the otherwise degenerate degrons with a compact interface and unexpected high affinities. Our results reveal the structural mechanism by which KLHDC2 recognizes the simplest C-end degron and suggest a functional necessity of the E3 to tightly maintain the low abundance of its select substrates.
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Affiliation(s)
- Domniţa-Valeria Rusnac
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Daniele Canzani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Karena X Tien
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Thomas R Hinds
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ashley F Tsue
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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22
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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: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [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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23
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APC/C FZR-1 Controls SAS-5 Levels To Regulate Centrosome Duplication in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2017; 7:3937-3946. [PMID: 29030390 PMCID: PMC5714490 DOI: 10.1534/g3.117.300260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As the primary microtubule-organizing center, centrosomes play a key role in establishing mitotic bipolar spindles that secure correct transmission of genomic content. For the fidelity of cell division, centrosome number must be strictly controlled by duplicating only once per cell cycle. Proper levels of centrosome proteins are shown to be critical for normal centrosome number and function. Overexpressing core centrosome factors leads to extra centrosomes, while depleting these factors results in centrosome duplication failure. In this regard, protein turnover by the ubiquitin-proteasome system provides a vital mechanism for the regulation of centrosome protein levels. Here, we report that FZR-1, the Caenorhabditis elegans homolog of Cdh1/Hct1/Fzr, a coactivator of the anaphase promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase, functions as a negative regulator of centrosome duplication in the C. elegans embryo. During mitotic cell division in the early embryo, FZR-1 is associated with centrosomes and enriched at nuclei. Loss of fzr-1 function restores centrosome duplication and embryonic viability to the hypomorphic zyg-1(it25) mutant, in part, through elevated levels of SAS-5 at centrosomes. Our data suggest that the APC/CFZR-1 regulates SAS-5 levels by directly recognizing the conserved KEN-box motif, contributing to proper centrosome duplication. Together, our work shows that FZR-1 plays a conserved role in regulating centrosome duplication in C. elegans.
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24
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Taming the Beast: Control of APC/C Cdc20-Dependent Destruction. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:111-121. [PMID: 29133301 DOI: 10.1101/sqb.2017.82.033712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a large multisubunit ubiquitin ligase that triggers the metaphase-to-anaphase transition in the cell cycle by targeting the substrates cyclin B and securin for destruction. APC/C activity toward these two key substrates requires the coactivator Cdc20. To ensure that cells enter mitosis and partition their duplicated genome with high accuracy, APC/CCdc20 activity must be tightly controlled. Here, we discuss the mechanisms that regulate APC/CCdc20 activity both before and during mitosis. We focus our discussion primarily on the chromosomal pathways that both accelerate and delay APC/C activation by targeting Cdc20 to opposing fates. The findings discussed provide an overview of how cells control the activation of this major cell cycle regulator to ensure both accurate and timely cell division.
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25
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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: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [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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26
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Kim SJ, Hyeong Lee T, Hee Nam S, Kim JH, Oh S, Sook Cho Y, Sup Lee M, Choi S, Lee PCW. Association of Uba6-Specific-E2 (USE1) With Lung Tumorigenesis. J Natl Cancer Inst 2017; 109:1-11. [PMID: 28376205 DOI: 10.1093/jnci/djw224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022] Open
Abstract
Background The UBA6-specific E2 conjugating enzyme 1 (USE1) ubiquitin enzyme cascade is a poorly characterized arm of the ubiquitin-proteasome system. We investigated whether the UBA6-USE1 enzyme cascade plays a role in lung cancer tumorigenesis. Methods USE1 expression was assessed in tumor-normal paired samples from 106 lung cancer patients by immunoblot. USE1 was stably overexpressed and knocked down in lung cancer cell lines to evaluate cell proliferation, colony formation, and invasion. Xenograft models were used to determine the effects of USE1 on tumor growth (n = 7). Proteomics analysis was used to identify proteins interacting with USE1. The USE1 gene was sequenced in lung cancer patients, and missense mutations of USE1 were generated to evaluate its function. All statistical tests were two-sided. Results USE1 proteins were frequently overexpressed in lung cancer patients (92.5%) Stable overexpression of USE1 increased cell proliferation ( P = .002), migration ( P < .001), and invasion ( P < .001), whereas knockdown of USE1 reduced cell proliferation ( P < .001), migration ( P = .003), and invasion in lung cancer cells and xenograft models ( P < .001). USE1 was found to have a conserved D-box domain, and the level of the protein was regulated by the anaphase-promoting complex. Several missense mutations in USE1 identified in patients prolong the stability of the protein. Conclusions USE1 proteins are frequently overexpressed in lung cancer, and missense mutations in USE1 prolong the half-life of the protein, promoting tumor formation. Our findings reveal novel roles for USE1 in lung cancer and the possible use of USE1 as a novel biomarker and therapeutic target for lung cancer treatment.
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Affiliation(s)
- Seong-Jin Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Tae Hyeong Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Sang Hee Nam
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Ji-Hong Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Sangho Oh
- Korean BioInformation Center (KOBIC), Daejeon, Korea
| | - Yeon Sook Cho
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Myeong Sup Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Sehoon Choi
- Department of Thoracic and Cardiovascular Surgery, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
| | - Peter C W Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center, Seoul, Korea
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27
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Cdc20: At the Crossroads between Chromosome Segregation and Mitotic Exit. Trends Biochem Sci 2017; 42:193-205. [PMID: 28202332 DOI: 10.1016/j.tibs.2016.12.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/13/2016] [Accepted: 12/06/2016] [Indexed: 11/21/2022]
Abstract
Cell-division cycle protein 20 homologue (Cdc20) has important functions in chromosome segregation and mitotic exit. Cdc20 is the target of the spindle assembly checkpoint (SAC) and a key cofactor of the anaphase-promoting complex or cyclosome (APC/C) E3 ubiquitin ligase, thus regulating APC/C ubiquitin activity on specific substrates for their subsequent degradation by the proteasome. Here we discuss the roles of Cdc20 in SAC signalling and mitotic exit, describe how the integration of traditional approaches with emerging technologies has revealed new details of Cdc20 functions, comment about the potential of Cdc20 as a therapeutic target for the treatment of human malignancies, and discuss recent advances and controversies in the mechanistic understanding of the control of chromosome segregation during cell division.
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28
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Wang R, Burton JL, Solomon MJ. Transcriptional and post-transcriptional regulation of Cdc20 during the spindle assembly checkpoint in S. cerevisiae. Cell Signal 2017; 33:41-48. [PMID: 28189585 DOI: 10.1016/j.cellsig.2017.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/21/2017] [Accepted: 02/06/2017] [Indexed: 01/26/2023]
Abstract
The anaphase-promoting complex (APC) is a ubiquitin ligase responsible for promoting the degradation of many cell cycle regulators. One of the activators and substrate-binding proteins for the APC is Cdc20. It has been shown previously that Cdc20 can promote its own degradation by the APC in normal cycling cells mainly through a cis-degradation mode (i.e. via an intramolecular mechanism). However, how Cdc20 is degraded during the spindle assembly checkpoint (SAC) is still not fully clear. In this study, we used a dual-Cdc20 system to investigate this issue and found that the cis-degradation mode is also the major pathway responsible for Cdc20 degradation during the SAC. In addition, we found that there is an inverse relationship between APCCdc20 activity and the transcriptional activity of the CDC20 promoter, which likely occurs through feedback regulation by APCCdc20 substrates, such as the cyclins Clb2 and Clb5. These findings contribute to our understanding of how the inhibition of APCCdc20 activity and enhanced Cdc20 degradation are required for proper spindle checkpoint arrest.
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Affiliation(s)
- Ruiwen Wang
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province 350108, China.
| | - Janet L Burton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Mark J Solomon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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29
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Wan L, Chen M, Cao J, Dai X, Yin Q, Zhang J, Song SJ, Lu Y, Liu J, Inuzuka H, Katon JM, Berry K, Fung J, Ng C, Liu P, Song MS, Xue L, Bronson RT, Kirschner MW, Cui R, Pandolfi PP, Wei W. The APC/C E3 Ligase Complex Activator FZR1 Restricts BRAF Oncogenic Function. Cancer Discov 2017; 7:424-441. [PMID: 28174173 DOI: 10.1158/2159-8290.cd-16-0647] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/14/2022]
Abstract
BRAF drives tumorigenesis by coordinating the activation of the RAS/RAF/MEK/ERK oncogenic signaling cascade. However, upstream pathways governing BRAF kinase activity and protein stability remain undefined. Here, we report that in primary cells with active APCFZR1, APCFZR1 earmarks BRAF for ubiquitination-mediated proteolysis, whereas in cancer cells with APC-free FZR1, FZR1 suppresses BRAF through disrupting BRAF dimerization. Moreover, we identified FZR1 as a direct target of ERK and CYCLIN D1/CDK4 kinases. Phosphorylation of FZR1 inhibits APCFZR1, leading to elevation of a cohort of oncogenic APCFZR1 substrates to facilitate melanomagenesis. Importantly, CDK4 and/or BRAF/MEK inhibitors restore APCFZR1 E3 ligase activity, which might be critical for their clinical effects. Furthermore, FZR1 depletion cooperates with AKT hyperactivation to transform primary melanocytes, whereas genetic ablation of Fzr1 synergizes with Pten loss, leading to aberrant coactivation of BRAF/ERK and AKT signaling in mice. Our findings therefore reveal a reciprocal suppression mechanism between FZR1 and BRAF in controlling tumorigenesis.Significance: FZR1 inhibits BRAF oncogenic functions via both APC-dependent proteolysis and APC-independent disruption of BRAF dimers, whereas hyperactivated ERK and CDK4 reciprocally suppress APCFZR1 E3 ligase activity. Aberrancies in this newly defined signaling network might account for BRAF hyperactivation in human cancers, suggesting that targeting CYCLIN D1/CDK4, alone or in combination with BRAF/MEK inhibition, can be an effective anti-melanoma therapy. Cancer Discov; 7(4); 424-41. ©2017 AACR.See related commentary by Zhang and Bollag, p. 356This article is highlighted in the In This Issue feature, p. 339.
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Affiliation(s)
- Lixin Wan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts. .,Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ming Chen
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Juxiang Cao
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts.
| | - Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Qing Yin
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Su-Jung Song
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Life Science, FIST, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jesse M Katon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kelsey Berry
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Fung
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Christopher Ng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Pengda Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Min Sup Song
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lian Xue
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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30
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Neuert H, Yuva-Aydemir Y, Silies M, Klämbt C. Different modes of APC/C activation control growth and neuron-glia interaction in the developing Drosophila eye. Development 2017; 144:4673-4683. [DOI: 10.1242/dev.152694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 10/23/2017] [Indexed: 12/30/2022]
Abstract
The development of the nervous system requires tight control of cell division, fate specification and migration. The anaphase promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that affects different steps of cell cycle progression, as well as having postmitotic functions in nervous system development. It can therefore link different developmental stages in one tissue. The two adaptor proteins Fizzy/Cdc20 and Fizzy-Related/Cdh1 confer APC/C substrate specificity. Here we show that two distinct modes of APC/C function act during Drosophila eye development. Fizzy/Cdc20 controls the early growth of the eye disc anlage and the concomitant entry of glial cells onto the disc. In contrast, fzr/cdh1 acts during neuronal patterning and photoreceptor axon growth, and subsequently affects neuron-glia interaction. To further address the postmitotic role of Fzr/Cdh1 in controlling neuron-glia interaction, we identified a series of novel APC/C candidate substrates. Four of our candidate genes are required for fzr/cdh1 dependent neuron-glia interaction, including the dynein light chain Dlc90F. Taken together, our data show how different modes of APC/C activation can couple early growth and neuron-glia interaction during eye disc development.
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Affiliation(s)
- Helen Neuert
- Institut für Neurobiologie, Universität Münster, Badestr. 9, 48149 Münster, Germany
- Present address: Department of Cellular and Physiological Sciences, Life Sciences Centre, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Yeliz Yuva-Aydemir
- Institut für Neurobiologie, Universität Münster, Badestr. 9, 48149 Münster, Germany
- Present address: Department of Neurology, UMASS Medical School, Worcester, MA 01605, USA
| | - Marion Silies
- Institut für Neurobiologie, Universität Münster, Badestr. 9, 48149 Münster, Germany
- European Neuroscience Institute, University Medical Center Goettingen, Grisebachstr. 5, 37077 Göttingen, Germany
| | - Christian Klämbt
- Institut für Neurobiologie, Universität Münster, Badestr. 9, 48149 Münster, Germany
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31
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Zhang M, Yao F, Luan H, Zhao W, Jing T, Zhang S, Hou L, Zou X. APC/C CDC20 and APC/C play pivotal roles in the process of embryonic development in Artemia sinica. Sci Rep 2016; 6:39047. [PMID: 27991546 PMCID: PMC5171921 DOI: 10.1038/srep39047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/17/2016] [Indexed: 11/09/2022] Open
Abstract
Anaphase Promoting Complex or Cyclosome (APC/C) is a representative E3 ubiquitin ligase, triggering the transition of metaphase to anaphase by regulating degradation and ensures the exit from mitosis. Cell division cycle 20 (CDC20) and Cell division cycle 20 related protein 1 (CDH1), as co-activators of APC/C, play significant roles in the spindle assembly checkpoint, guiding ubiquitin-mediated degradation, together with CDC23. During the embryonic development of the brine shrimp, Artemia sinica, CDC20, CDH1 and CDC23 participate in cell cycle regulation, but the specific mechanisms of their activities remain unknown. Herein, the full-length cDNAs of cdc20 and cdc23 from A. sinica were cloned. Real-time PCR analyzed the expression levels of As-cdc20 and As-cdc23. The locations of CDH1, CDC20 and CDC23 showed no tissue or organ specificity. Furthermore, western blotting showed that the levels of As-CDC20, securin, cyclin B, CDK1, CDH1, CDC14B, CDC23 and geminin proteins conformed to their complicated degradation relationships during different embryo stages. Our research revealed that As-CDC20, As-CDH1 and APC mediate the mitotic progression, downstream proteins degradation and cellular differentiation in the process of embryonic development in A. sinica.
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Affiliation(s)
- Mengchen Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Feng Yao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Hong Luan
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Wei Zhao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Ting Jing
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Shuang Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Lin Hou
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Xiangyang Zou
- Department of Biology, Dalian Medical University, Dalian 116044, China
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32
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van Twest S, Murphy VJ, Hodson C, Tan W, Swuec P, O'Rourke JJ, Heierhorst J, Crismani W, Deans AJ. Mechanism of Ubiquitination and Deubiquitination in the Fanconi Anemia Pathway. Mol Cell 2016; 65:247-259. [PMID: 27986371 DOI: 10.1016/j.molcel.2016.11.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 11/26/2022]
Abstract
Monoubiquitination and deubiquitination of FANCD2:FANCI heterodimer is central to DNA repair in a pathway that is defective in the cancer predisposition syndrome Fanconi anemia (FA). The "FA core complex" contains the RING-E3 ligase FANCL and seven other essential proteins that are mutated in various FA subtypes. Here, we purified recombinant FA core complex to reveal the function of these other proteins. The complex contains two spatially separate FANCL molecules that are dimerized by FANCB and FAAP100. FANCC and FANCE act as substrate receptors and restrict monoubiquitination to the FANCD2:FANCI heterodimer in only a DNA-bound form. FANCA and FANCG are dispensable for maximal in vitro ubiquitination. Finally, we show that the reversal of this reaction by the USP1:UAF1 deubiquitinase only occurs when DNA is disengaged. Our work reveals the mechanistic basis for temporal and spatial control of FANCD2:FANCI monoubiquitination that is critical for chemotherapy responses and prevention of Fanconi anemia.
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Affiliation(s)
- Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Winnie Tan
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St. Vincent's Health), The University of Melbourne, VIC 3010, Australia
| | - Paolo Swuec
- Architecture and Dynamics of Macromolecular Machines Laboratory, London Research Institute, South Mimms, Hertfordshire EN6 3LD, UK
| | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St. Vincent's Health), The University of Melbourne, VIC 3010, Australia
| | - Jörg Heierhorst
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St. Vincent's Health), The University of Melbourne, VIC 3010, Australia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St. Vincent's Health), The University of Melbourne, VIC 3010, Australia.
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Abstract
Chromosomal instability (CIN), the persistent inability of a cell to faithfully segregate its genome, is a feature of many cancer cells. It stands to reason that CIN enables the acquisition of multiple cancer hallmarks; however, there is a growing body of evidence suggesting that CIN impairs cellular fitness and prevents neoplastic transformation. Here, we suggest a new perspective to reconcile this apparent paradox and share an unexpected link between aneuploidy and aging that was discovered through attempts to investigate the CIN-cancer relationship. Additionally, we provide a comprehensive overview of the function and regulation of the anaphase-promoting complex, an E3 ubiquitin ligase that mediates high-fidelity chromosome segregation, and describe the mechanisms that lead to whole-chromosome gain or loss. With this review, we aim to expand our understanding of the role of CIN in cancer and aging with the long-term objective of harnessing this information for the advancement of patient care.
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Affiliation(s)
| | - Jan M van Deursen
- Department of Biochemistry and Molecular Biology
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905;
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34
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Targeting of Fzr/Cdh1 for timely activation of the APC/C at the centrosome during mitotic exit. Nat Commun 2016; 7:12607. [PMID: 27558644 PMCID: PMC5007356 DOI: 10.1038/ncomms12607] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 07/16/2016] [Indexed: 01/06/2023] Open
Abstract
A multi-subunit ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C), regulates critical cellular processes including the cell cycle. To accomplish its diverse functions, APC/C activity must be precisely regulated in time and space. The interphase APC/C activator Fizzy-related (Fzr or Cdh1) is localized at centrosomes in animal cells. However, neither the mechanism of its localization nor its importance is clear. Here we identify the centrosome component Spd2 as a major partner of Fzr in Drosophila. The localization of Fzr to the centriole during interphase depends on direct interaction with Spd2. By generating Spd2 mutants unable to bind Fzr, we show that centrosomal localization of Fzr is essential for optimal APC/C activation towards its centrosomal substrate Aurora A. Finally, we show that Spd2 is also a novel APC/CFzr substrate. Our study is the first to demonstrate the critical importance of distinct subcellular pools of APC/C activators in the spatiotemporal control of APC/C activity. The activity of the anaphase-promoting complex/cyclosome (APC/C) needs to be regulated in time and space to perform different functions. Here the authors show that Spd2 localizes the APC/C activator Fzr at the centrosomes to promote optimal APC/C activity towards its centrosomal substrate Aurora A.
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35
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Ondracka A, Robbins JA, Cross FR. An APC/C-Cdh1 Biosensor Reveals the Dynamics of Cdh1 Inactivation at the G1/S Transition. PLoS One 2016; 11:e0159166. [PMID: 27410035 PMCID: PMC4943722 DOI: 10.1371/journal.pone.0159166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/28/2016] [Indexed: 12/31/2022] Open
Abstract
B-type cyclin-dependent kinase activity must be turned off for mitotic exit and G1 stabilization. B-type cyclin degradation is mediated by the anaphase-promoting complex/cyclosome (APC/C); during and after mitotic exit, APC/C is dependent on Cdh1. Cdh1 is in turn phosphorylated and inactivated by cyclin-CDK at the Start transition of the new cell cycle. We developed a biosensor to assess the cell cycle dynamics of APC/C-Cdh1. Nuclear exit of the G1 transcriptional repressor Whi5 is a known marker of Start; APC/C-Cdh1 is inactivated 12 min after Whi5 nuclear exit with little measurable cell-to-cell timing variability. Multiple phosphorylation sites on Cdh1 act in a redundant manner to repress its activity. Reducing the number of phosphorylation sites on Cdh1 can to some extent be tolerated for cell viability, but it increases variability in timing of APC/C-Cdh1 inactivation. Mutants with minimal subsets of phosphorylation sites required for viability exhibit striking stochasticity in multiple responses including budding, nuclear division, and APC/C-Cdh1 activity itself. Multiple cyclin-CDK complexes, as well as the stoichiometric inhibitor Acm1, contribute to APC/C-Cdh1 inactivation; this redundant control is likely to promote rapid and reliable APC/C-Cdh1 inactivation immediately following the Start transition.
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Affiliation(s)
- Andrej Ondracka
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10065, United States of America
| | - Jonathan A. Robbins
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10065, United States of America
| | - Frederick R. Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10065, United States of America
- * E-mail:
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36
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Höckner S, Neumann-Arnold L, Seufert W. Dual control by Cdk1 phosphorylation of the budding yeast APC/C ubiquitin ligase activator Cdh1. Mol Biol Cell 2016; 27:2198-212. [PMID: 27226481 PMCID: PMC4945139 DOI: 10.1091/mbc.e15-11-0787] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/18/2016] [Indexed: 12/15/2022] Open
Abstract
The antagonism between cyclin-dependent kinases (Cdks) and the ubiquitin ligase APC/C-Cdh1 is central to eukaryotic cell cycle control. APC/C-Cdh1 targets cyclin B and other regulatory proteins for degradation, whereas Cdks disable APC/C-Cdh1 through phosphorylation of the Cdh1 activator protein at multiple sites. Budding yeast Cdh1 carries nine Cdk phosphorylation sites in its N-terminal regulatory domain, most or all of which contribute to inhibition. However, the precise role of individual sites has remained unclear. Here, we report that the Cdk phosphorylation sites of yeast Cdh1 are organized into autonomous subgroups and act through separate mechanisms. Cdk sites 1-3 had no direct effect on the APC/C binding of Cdh1 but inactivated a bipartite nuclear localization sequence (NLS) and thereby controlled the partitioning of Cdh1 between cytoplasm and nucleus. In contrast, Cdk sites 4-9 did not influence the cell cycle-regulated localization of Cdh1 but prevented its binding to the APC/C. Cdk sites 4-9 reside near two recently identified APC/C interaction motifs in a pattern conserved with the human Cdh1 orthologue. Thus a Cdk-inhibited NLS goes along with Cdk-inhibited APC/C binding sites in yeast Cdh1 to relay the negative control by Cdk1 phosphorylation of the ubiquitin ligase APC/C-Cdh1.
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Affiliation(s)
- Sebastian Höckner
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Lea Neumann-Arnold
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Wolfgang Seufert
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
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37
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Qin L, Guimarães DSPSF, Melesse M, Hall MC. Substrate Recognition by the Cdh1 Destruction Box Receptor Is a General Requirement for APC/CCdh1-mediated Proteolysis. J Biol Chem 2016; 291:15564-74. [PMID: 27226622 DOI: 10.1074/jbc.m116.731190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 11/06/2022] Open
Abstract
The anaphase-promoting complex, or cyclosome (APC/C), is a ubiquitin ligase that selectively targets proteins for degradation in mitosis and the G1 phase and is an important component of the eukaryotic cell cycle control system. How the APC/C specifically recognizes its substrates is not fully understood. Although well characterized degron motifs such as the destruction box (D-box) and KEN-box are commonly found in APC/C substrates, many substrates apparently lack these motifs. A variety of alternative APC/C degrons have been reported, suggesting either that multiple modes of substrate recognition are possible or that our definitions of degron structure are incomplete. We used an in vivo yeast assay to compare the G1 degradation rate of 15 known substrates of the APC/C co-activator Cdh1 under normal conditions and conditions that impair binding of D-box, KEN-box, and the recently identified ABBA motif degrons to Cdh1. The D-box receptor was required for efficient proteolysis of all Cdh1 substrates, despite the absence of canonical D-boxes in many. In contrast, the KEN-box receptor was only required for normal proteolysis of a subset of substrates and the ABBA motif receptor for a single substrate in our system. Our results suggest that binding to the D-box receptor may be a shared requirement for recognition and processing of all Cdh1 substrates.
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Affiliation(s)
- Liang Qin
- From the Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | | | - Michael Melesse
- From the Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | - Mark C Hall
- From the Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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38
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Abstract
Chromosome segregation and mitotic exit are initiated by the 1.2-MDa ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome) and its coactivator CDC20 (cell division cycle 20). To avoid chromosome missegregation, APC/C(CDC20) activation is tightly controlled. CDC20 only associates with APC/C in mitosis when APC/C has become phosphorylated and is further inhibited by a mitotic checkpoint complex until all chromosomes are bioriented on the spindle. APC/C contains 14 different types of subunits, most of which are phosphorylated in mitosis on multiple sites. However, it is unknown which of these phospho-sites enable APC/C(CDC20) activation and by which mechanism. Here we have identified 68 evolutionarily conserved mitotic phospho-sites on human APC/C bound to CDC20 and have used the biGBac technique to generate 47 APC/C mutants in which either all 68 sites or subsets of them were replaced by nonphosphorylatable or phospho-mimicking residues. The characterization of these complexes in substrate ubiquitination and degradation assays indicates that phosphorylation of an N-terminal loop region in APC1 is sufficient for binding and activation of APC/C by CDC20. Deletion of the N-terminal APC1 loop enables APC/C(CDC20) activation in the absence of mitotic phosphorylation or phospho-mimicking mutations. These results indicate that binding of CDC20 to APC/C is normally prevented by an autoinhibitory loop in APC1 and that its mitotic phosphorylation relieves this inhibition. The predicted location of the N-terminal APC1 loop implies that this loop controls interactions between the N-terminal domain of CDC20 and APC1 and APC8. These results reveal how APC/C phosphorylation enables CDC20 to bind and activate the APC/C in mitosis.
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39
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biGBac enables rapid gene assembly for the expression of large multisubunit protein complexes. Proc Natl Acad Sci U S A 2016; 113:E2564-9. [PMID: 27114506 DOI: 10.1073/pnas.1604935113] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Analyses of protein complexes are facilitated by methods that enable the generation of recombinant complexes via coexpression of their subunits from multigene DNA constructs. However, low experimental throughput limits the generation of such constructs in parallel. Here we describe a method that allows up to 25 cDNAs to be assembled into a single baculoviral expression vector in only two steps. This method, called biGBac, uses computationally optimized DNA linker sequences that enable the efficient assembly of linear DNA fragments, using reactions developed by Gibson for the generation of synthetic genomes. The biGBac method uses a flexible and modular "mix and match" approach and enables the generation of baculoviruses from DNA constructs at any assembly stage. Importantly, it is simple, efficient, and fast enough to allow the manual generation of many multigene expression constructs in parallel. We have used this method to generate and characterize recombinant forms of the anaphase-promoting complex/cyclosome, cohesin, and kinetochore complexes.
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40
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Control of APC/C-dependent ubiquitin chain elongation by reversible phosphorylation. Proc Natl Acad Sci U S A 2016; 113:1540-5. [PMID: 26811472 DOI: 10.1073/pnas.1522423113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most metazoan E3 ligases contain a signature RING domain that promotes the transfer of ubiquitin from the active site of E2 conjugating enzymes to lysine residues in substrates. Although these RING-E3s depend on E2 enzymes for catalysis, how they turn on their E2s at the right time and place remains poorly understood. Here we report a phosphorylation-dependent mechanism that ensures timely activation of the E2 Ube2S by its RING-E3, the anaphase-promoting complex (APC/C); while phosphorylation of a specific serine residue in the APC/C coactivator Cdc20 prevents delivery of Ube2S to the APC/C, removal of this mark by PP2A(B56) allows Ube2S to bind the APC/C and catalyze ubiquitin chain elongation. PP2A(B56) also stabilizes kinetochore-microtubule attachments to shut off the spindle checkpoint, suggesting that cells regulate the E2-E3 interplay to coordinate ubiquitination with critical events during cell division.
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41
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Malhotra S, Vinod PK, Mansfeld J, Stemmann O, Mayer TU. RETRACTED: The Anaphase-Promoting Complex/Cyclosome Is Essential for Entry into Meiotic M-Phase. Dev Cell 2016; 36:94-102. [DOI: 10.1016/j.devcel.2015.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 11/12/2015] [Accepted: 12/03/2015] [Indexed: 11/16/2022]
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42
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Cronin NB, Yang J, Zhang Z, Kulkarni K, Chang L, Yamano H, Barford D. Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain. J Mol Biol 2015; 427:3300-3315. [PMID: 26343760 PMCID: PMC4590430 DOI: 10.1016/j.jmb.2015.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/19/2015] [Accepted: 08/26/2015] [Indexed: 10/25/2022]
Abstract
Many essential biological processes are mediated by complex molecular machines comprising multiple subunits. Knowledge on the architecture of individual subunits and their positions within the overall multimeric complex is key to understanding the molecular mechanisms of macromolecular assemblies. The anaphase-promoting complex/cyclosome (APC/C) is a large multisubunit complex that regulates cell cycle progression by ubiquitinating cell cycle proteins for proteolysis by the proteasome. The holo-complex is composed of 15 different proteins that assemble to generate a complex of 20 subunits. Here, we describe the crystal structures of Apc4 and the N-terminal domain of Apc5 (Apc5(N)). Apc4 comprises a WD40 domain split by a long α-helical domain, whereas Apc5(N) has an α-helical fold. In a separate study, we had fitted these atomic models to a 3.6-Å-resolution cryo-electron microscopy map of the APC/C. We describe how, in the context of the APC/C, regions of Apc4 disordered in the crystal assume order through contacts to Apc5, whereas Apc5(N) shows small conformational changes relative to its crystal structure. We discuss the complementary approaches of high-resolution electron microscopy and protein crystallography to the structure determination of subunits of multimeric complexes.
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Affiliation(s)
- Nora B Cronin
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Jing Yang
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Ziguo Zhang
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Kiran Kulkarni
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom; Division of Biochemical Sciences, Council of Scientific and Industrial Research National Chemical Laboratory, Pune 411008, India
| | - Leifu Chang
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Hiroyuki Yamano
- Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - David Barford
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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Min M, Mevissen TET, De Luca M, Komander D, Lindon C. Efficient APC/C substrate degradation in cells undergoing mitotic exit depends on K11 ubiquitin linkages. Mol Biol Cell 2015; 26:4325-32. [PMID: 26446837 PMCID: PMC4666129 DOI: 10.1091/mbc.e15-02-0102] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/29/2015] [Indexed: 11/11/2022] Open
Abstract
The ubiquitin proteasome system (UPS) directs programmed destruction of key cellular regulators via posttranslational modification of its targets with polyubiquitin chains. These commonly contain Lys-48 (K48)-directed ubiquitin linkages, but chains containing atypical Lys-11 (K11) linkages also target substrates to the proteasome--for example, to regulate cell cycle progression. The ubiquitin ligase called the anaphase-promoting complex/cyclosome (APC/C) controls mitotic exit. In higher eukaryotes, the APC/C works with the E2 enzyme UBE2S to assemble K11 linkages in cells released from mitotic arrest, and these are proposed to constitute an improved proteolytic signal during exit from mitosis. We tested this idea by correlating quantitative measures of in vivo K11-specific ubiquitination of individual substrates, including Aurora kinases, with their degradation kinetics tracked at the single-cell level. All anaphase substrates tested by this methodology are stabilized by depletion of K11 linkages via UBE2S knockdown, even if the same substrates are significantly modified with K48-linked polyubiquitin. Specific examination of substrates depending on the APC/C coactivator Cdh1 for their degradation revealed Cdh1-dependent enrichment of K11 chains on these substrates, whereas other ubiquitin linkages on the same substrates added during mitotic exit were Cdh1-independent. Therefore we show that K11 linkages provide the APC/C with a means to regulate the rate of substrate degradation in a coactivator-specified manner.
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Affiliation(s)
- Mingwei Min
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Tycho E T Mevissen
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom
| | - Maria De Luca
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom
| | - Catherine Lindon
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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Tsunematsu T, Arakaki R, Yamada A, Ishimaru N, Kudo Y. The Non-Canonical Role of Aurora-A in DNA Replication. Front Oncol 2015; 5:187. [PMID: 26380219 PMCID: PMC4548192 DOI: 10.3389/fonc.2015.00187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/05/2015] [Indexed: 12/04/2022] Open
Abstract
Aurora-A is a well-known mitotic kinase that regulates mitotic entry, spindle formation, and chromosome maturation as a canonical role. During mitosis, Aurora-A protein is stabilized by its phosphorylation at Ser51 via blocking anaphase-promoting complex/cyclosome-mediated proteolysis. Importantly, overexpression and/or hyperactivation of Aurora-A is involved in tumorigenesis via aneuploidy and genomic instability. Recently, the novel function of Aurora-A for DNA replication has been revealed. In mammalian cells, DNA replication is strictly regulated for preventing over-replication. Pre-replication complex (pre-RC) formation is required for DNA replication as an initiation step occurring at the origin of replication. The timing of pre-RC formation depends on the protein level of geminin, which is controlled by the ubiquitin–proteasome pathway. Aurora-A phosphorylates geminin to prevent its ubiquitin-mediated proteolysis at the mitotic phase to ensure proper pre-RC formation and ensuing DNA replication. In this review, we introduce the novel non-canonical role of Aurora-A in DNA replication.
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Affiliation(s)
- Takaaki Tsunematsu
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School , Tokushima , Japan
| | - Rieko Arakaki
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School , Tokushima , Japan
| | - Akiko Yamada
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School , Tokushima , Japan
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School , Tokushima , Japan
| | - Yasusei Kudo
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School , Tokushima , Japan
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Sun P, Li S, Lu D, Williams JS, Kao TH. Pollen S-locus F-box proteins of Petunia involved in S-RNase-based self-incompatibility are themselves subject to ubiquitin-mediated degradation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:213-223. [PMID: 25990372 DOI: 10.1111/tpj.12880] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/05/2015] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
Many flowering plants show self-incompatibility, an intra-specific reproductive barrier by which pistils reject self-pollen to prevent inbreeding and accept non-self pollen to promote out-crossing. In Petunia, the polymorphic S-locus determines self/non-self recognition. The locus contains a gene encoding an S-RNase, which controls pistil specificity, and multiple S-locus F-box (SLF) genes that collectively control pollen specificity. Each SLF is a component of an SCF (Skp1/Cullin/F-box) complex that is responsible for mediating degradation of non-self S-RNase(s), with which the SLF interacts, via the ubiquitin-26S proteasome pathway. A complete set of SLFs is required to detoxify all non-self S-RNases to allow cross-compatible pollination. Here, we show that SLF1 of Petunia inflata is itself subject to degradation via the ubiquitin-26S proteasome pathway, and identify an 18 amino acid sequence in the C-terminal region of S2 -SLF1 (SLF1 of S2 haplotype) that contains a degradation motif. Seven of the 18 amino acids are conserved among all 17 SLF proteins of S2 haplotype and S3 haplotype involved in pollen specificity, suggesting that all SLF proteins are probably subject to similar degradation. Deleting the 18 amino acid sequence from S2 -SLF1 stabilized the protein but abolished its function in self-incompatibility, suggesting that dynamic cycling of SLF proteins is an integral part of their function in self-incompatibility.
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Affiliation(s)
- Penglin Sun
- Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Shu Li
- Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dihong Lu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Justin S Williams
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Teh-Hui Kao
- Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
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Zhang T, Qi ST, Huang L, Ma XS, Ouyang YC, Hou Y, Shen W, Schatten H, Sun QY. Cyclin B3 controls anaphase onset independent of spindle assembly checkpoint in meiotic oocytes. Cell Cycle 2015; 14:2648-54. [PMID: 26125114 DOI: 10.1080/15384101.2015.1064567] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyclin B3 is a relatively new member of the cyclin family whose functions are little known. We found that depletion of cyclin B3 inhibited metaphase-anaphase transition as indicated by a well-sustained MI spindle and cyclin B1 expression in meiotic oocytes after extended culture. This effect was independent of spindle assembly checkpoint activity, since both Bub3 and BubR1 signals were not observed at kinetochores in MI-arrested cells. The metaphase I arrest was not rescued by either Mad2 knockdown or cdc20 overexpression, but it was rescued by securin RNAi. We conclude that cyclin B3 controls the metaphase-anaphase transition by activating APC/C(cdc20) in meiotic oocytes, a process that does not rely on SAC activity.
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Affiliation(s)
- Teng Zhang
- a Institute of Reproductive Sciences; College of Animal Science and Technology; Qingdao Agricultural University ; Qingdao , China
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Chang L, Zhang Z, Yang J, McLaughlin SH, Barford D. Atomic structure of the APC/C and its mechanism of protein ubiquitination. Nature 2015; 522:450-454. [PMID: 26083744 PMCID: PMC4608048 DOI: 10.1038/nature14471] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/10/2015] [Indexed: 12/12/2022]
Abstract
The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the mitotic checkpoint complex and interphase early mitotic inhibitor 1 (Emi1) ensures the correct order and timing of distinct cell-cycle transitions. Here we use cryo-electron microscopy to determine atomic structures of APC/C-coactivator complexes with either Emi1 or a UbcH10-ubiquitin conjugate. These structures define the architecture of all APC/C subunits, the position of the catalytic module and explain how Emi1 mediates inhibition of the two E2s UbcH10 and Ube2S. Definition of Cdh1 interactions with the APC/C indicates how they are antagonized by Cdh1 phosphorylation. The structure of the APC/C with UbcH10-ubiquitin reveals insights into the initiating ubiquitination reaction. Our results provide a quantitative framework for the design of future experiments to investigate APC/C functions in vivo.
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MESH Headings
- Anaphase-Promoting Complex-Cyclosome/chemistry
- Anaphase-Promoting Complex-Cyclosome/metabolism
- Anaphase-Promoting Complex-Cyclosome/ultrastructure
- Antigens, CD
- Apc1 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry
- Apc1 Subunit, Anaphase-Promoting Complex-Cyclosome/metabolism
- Apc1 Subunit, Anaphase-Promoting Complex-Cyclosome/ultrastructure
- Apc10 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry
- Apc10 Subunit, Anaphase-Promoting Complex-Cyclosome/metabolism
- Apc10 Subunit, Anaphase-Promoting Complex-Cyclosome/ultrastructure
- Apc11 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry
- Apc11 Subunit, Anaphase-Promoting Complex-Cyclosome/metabolism
- Apc3 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry
- Apc3 Subunit, Anaphase-Promoting Complex-Cyclosome/metabolism
- Apc8 Subunit, Anaphase-Promoting Complex-Cyclosome/chemistry
- Apc8 Subunit, Anaphase-Promoting Complex-Cyclosome/metabolism
- Apc8 Subunit, Anaphase-Promoting Complex-Cyclosome/ultrastructure
- Cadherins/chemistry
- Cadherins/metabolism
- Cadherins/ultrastructure
- Catalytic Domain
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/ultrastructure
- Cryoelectron Microscopy
- Cytoskeletal Proteins/chemistry
- Cytoskeletal Proteins/metabolism
- F-Box Proteins/chemistry
- F-Box Proteins/metabolism
- F-Box Proteins/ultrastructure
- Humans
- Lysine/metabolism
- Models, Molecular
- Phosphorylation
- Protein Binding
- Protein Subunits/chemistry
- Protein Subunits/metabolism
- Structure-Activity Relationship
- Substrate Specificity
- Ubiquitin/chemistry
- Ubiquitin/metabolism
- Ubiquitin/ultrastructure
- Ubiquitin-Conjugating Enzymes/chemistry
- Ubiquitin-Conjugating Enzymes/metabolism
- Ubiquitin-Conjugating Enzymes/ultrastructure
- Ubiquitination
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Affiliation(s)
- Leifu Chang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stephen H McLaughlin
- 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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RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex. Proc Natl Acad Sci U S A 2015; 112:5272-9. [PMID: 25825779 DOI: 10.1073/pnas.1504161112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
For many E3 ligases, a mobile RING (Really Interesting New Gene) domain stimulates ubiquitin (Ub) transfer from a thioester-linked E2∼Ub intermediate to a lysine on a remotely bound disordered substrate. One such E3 is the gigantic, multisubunit 1.2-MDa anaphase-promoting complex/cyclosome (APC), which controls cell division by ubiquitinating cell cycle regulators to drive their timely degradation. Intrinsically disordered substrates are typically recruited via their KEN-box, D-box, and/or other motifs binding to APC and a coactivator such as CDH1. On the opposite side of the APC, the dynamic catalytic core contains the cullin-like subunit APC2 and its RING partner APC11, which collaborates with the E2 UBCH10 (UBE2C) to ubiquitinate substrates. However, how dynamic RING-E2∼Ub catalytic modules such as APC11-UBCH10∼Ub collide with distally tethered disordered substrates remains poorly understood. We report structural mechanisms of UBCH10 recruitment to APC(CDH1) and substrate ubiquitination. Unexpectedly, in addition to binding APC11's RING, UBCH10 is corecruited via interactions with APC2, which we visualized in a trapped complex representing an APC(CDH1)-UBCH10∼Ub-substrate intermediate by cryo-electron microscopy, and in isolation by X-ray crystallography. To our knowledge, this is the first structural view of APC, or any cullin-RING E3, with E2 and substrate juxtaposed, and it reveals how tripartite cullin-RING-E2 interactions establish APC's specificity for UBCH10 and harness a flexible catalytic module to drive ubiquitination of lysines within an accessible zone. We propose that multisite interactions reduce the degrees of freedom available to dynamic RING E3-E2∼Ub catalytic modules, condense the search radius for target lysines, increase the chance of active-site collision with conformationally fluctuating substrates, and enable regulation.
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Sivakumar S, Gorbsky GJ. Spatiotemporal regulation of the anaphase-promoting complex in mitosis. Nat Rev Mol Cell Biol 2015; 16:82-94. [PMID: 25604195 DOI: 10.1038/nrm3934] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The appropriate timing of events that lead to chromosome segregation during mitosis and cytokinesis is essential to prevent aneuploidy, and defects in these processes can contribute to tumorigenesis. Key mitotic regulators are controlled through ubiquitylation and proteasome-mediated degradation. The APC/C (anaphase-promoting complex; also known as the cyclosome) is an E3 ubiquitin ligase that has a crucial function in the regulation of the mitotic cell cycle, particularly at the onset of anaphase and during mitotic exit. Co-activator proteins, inhibitor proteins, protein kinases and phosphatases interact with the APC/C to temporally and spatially control its activity and thus ensure accurate timing of mitotic events.
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Affiliation(s)
- Sushama Sivakumar
- Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USA
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USA
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50
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Barford D. Understanding the structural basis for controlling chromosome division. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015; 373:20130392. [PMID: 25624511 PMCID: PMC4308986 DOI: 10.1098/rsta.2013.0392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The process of chromosome division, termed mitosis, involves a complex sequence of events that is tightly controlled to ensure that the faithful segregation of duplicated chromosomes is coordinated with each cell division cycle. The large macromolecular complex responsible for regulating this process is the anaphase-promoting complex or cyclosome (APC/C). In humans, the APC/C is assembled from 20 subunits derived from 15 different proteins. The APC/C functions to ubiquitinate cell cycle regulatory proteins, thereby targeting them for destruction by the proteasome. This review describes our research aimed at understanding the structure and mechanism of the APC/C. We have determined the crystal structures of individual subunits and subcomplexes that provide atomic models to interpret density maps of the whole complex derived from single particle cryo-electron microscopy. With this information, we are generating pseudo-atomic models of functional states of the APC/C that provide insights into its overall architecture and mechanisms of substrate recognition, catalysis and regulation by inhibitory complexes.
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Affiliation(s)
- David Barford
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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