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Wang Y, Liu M, Wang S, Mai X, Wang X, Teng F, Lyu T, Su MY, Stjepanovic G. Mechanism of D-type cyclin recognition by the AMBRA1 E3 ligase receptor. SCIENCE ADVANCES 2025; 11:eadu8708. [PMID: 40408472 PMCID: PMC12101500 DOI: 10.1126/sciadv.adu8708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 04/18/2025] [Indexed: 05/25/2025]
Abstract
AMBRA1 is a tumor suppressor protein that functions as a substrate receptor in the ubiquitin conjugation system and regulates the stability of D-type cyclins and cell proliferation. Here, we present the cryo-EM structure of cyclin D1-bound AMBRA1-DDB1 complex at 3.55-Å resolution. The structure reveals a substrate interaction surface on the AMBRA1 WD40 domain that specifically binds to the C-terminal region of D-type cyclins. This interaction is dependent on the phosphorylation of Thr286 residue in the C-terminal phosphodegron site of D-type cyclins. The phosphodegron motif folds into a turn-like conformation, followed by a 310 helix that promotes its assembly with AMBRA1. In addition, we show that AMBRA1 mutants, which are defective in cyclin D1 binding, lead to cyclin D1 accumulation and DNA damage. Understanding the AMBRA1-D-type cyclin structure enhances the knowledge of the molecular mechanisms that govern the cell cycle control and may lead to potential therapeutic approaches for cancers linked to abnormal cyclin D activity.
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Affiliation(s)
- Yang Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ming Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Shan Wang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xinyi Mai
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Xi Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Fei Teng
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tianrui Lyu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ming-Yuan Su
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Goran Stjepanovic
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
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Roy S, Saha G, Ghosh MK. UPS and Kinases-Gatekeepers of the G1/S Transition. Biofactors 2025; 51:e70020. [PMID: 40305374 DOI: 10.1002/biof.70020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 04/08/2025] [Accepted: 04/16/2025] [Indexed: 05/02/2025]
Abstract
The G1/S transition is a highly regulated and pivotal checkpoint in the cell cycle, where the cell decides whether to commit to DNA replication and subsequent division or enter a non-dividing state. This checkpoint serves as a critical control point for preventing uncontrolled cell proliferation and maintaining genomic stability. The major driving force underlying the G1/S transition is the sequential activation of Cyclin-dependent kinases (CDKs), which is regulated by the coordinated binding of Cyclin partners, as well as the phosphorylation and ubiquitin-mediated degradation of both Cyclin partners and Cyclin-dependent kinase inhibitors (CKIs). Various E3 ligase families govern the timely degradation of these regulatory proteins, with their activity intricately controlled by phosphorylation events. This coordination enables the cells to efficiently translate the environmental cues and molecular signaling inputs to determine their fate. We explore the evolution of three distinct models describing the G1/S transition, highlighting how the traditional linear model is being challenged by recent paradigm shifts and conflicting findings. These advances reveal emerging complexity and unresolved questions in the field, particularly regarding how the latest insights into coordinated phosphorylation and ubiquitination-dependent degradation integrate into contemporary models of the G1/S transition.
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Affiliation(s)
- Srija Roy
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Gouranga Saha
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, West Bengal, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
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3
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Sampath R, Vaeth K, Mikalayeva V, Skeberdis VA, Prekeris R, Han KJ. Rab40 GTPases regulate AMBRA1-mediated transcription and cell migration. J Cell Sci 2025; 138:jcs263707. [PMID: 40110710 PMCID: PMC12045048 DOI: 10.1242/jcs.263707] [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: 11/06/2024] [Accepted: 02/03/2025] [Indexed: 03/22/2025] Open
Abstract
The Rab40 subfamily of proteins consists of unique small monomeric GTPases that form CRL5-based ubiquitin E3 ligase complexes and regulate ubiquitylation of specific target proteins. Recent studies have shown that Rab40 proteins play an important role in regulating cell migration, but the underlying mechanisms of how the Rab40-CRL5 complex functions are still not fully understood. In this study, we identified AMBRA1 as a novel binding partner of Rab40 GTPases and show that this interaction mediates a bidirectional crosstalk between the CRL4 and CRL5 E3 ligases. Importantly, we found that Rab40-CRL5 ubiquitylates AMBRA1, which does not result in AMBRA1 degradation but, instead, appears to induce AMBRA1-dependent regulation of gene transcription. The global transcriptional profiles identified by RNA sequencing showed that AMBRA1 regulates transcription of genes related to cell adhesion and migration. Additionally, we show that AMBRA1-dependent transcription regulation does not require the enzymatic activity of AMBRA1-CRL4, and that Rab40-induced AMBRA1 ubiquitylation leads to dissociation of the AMBRA1-CRL4 complex. Taken together, our findings reveal a novel function of the Rab40-CRL5 complex as an important regulator of AMBRA1-dependent transcription of genes involved in cell migration.
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Affiliation(s)
- Revathi Sampath
- The Laboratory of Cell Culture, Lithuanian University of Health Sciences, Kaunas, 50103, Lithuania
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Katherine Vaeth
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Valeryia Mikalayeva
- The Laboratory of Cell Culture, Lithuanian University of Health Sciences, Kaunas, 50103, Lithuania
| | | | - Rytis Prekeris
- The Laboratory of Cell Culture, Lithuanian University of Health Sciences, Kaunas, 50103, Lithuania
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ke-Jun Han
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Sampath R, Vaeth K, Mikalayeva V, Skeberdis VA, Prekeris R, Han KJ. Rab40 GTPases regulate AMBRA1-mediated transcription and cell migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.07.622540. [PMID: 39574679 PMCID: PMC11580987 DOI: 10.1101/2024.11.07.622540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2024]
Abstract
The Rab40 subfamily are unique small monomeric GTPases that form CRL5-based ubiquitin E3 ligase complex and regulate ubiquitylation of specific target proteins. Recent studies have shown that Rab40s play an important role in regulating cell migration, but the underlying mechanisms of Rab40/CRL5 complex function are still not fully understood. In this study we identified AMBRA1 as a novel binding partner of Rab40 GTPases and showed that this interaction mediates a bi-directional crosstalk between CRL4 and CRL5 E3 ligases. Importantly, we found that Rab40/CRL5 ubiquitylates AMBRA1, which does not result in AMBRA1 degradation, but instead it seems to induce AMBRA1-dependent regulation of gene transcription. The global transcriptional profiles identified by RNA-seq showed that AMBRA1 regulates transcription of genes related to cell adhesion and migration. Additionally, we have shown that AMBRA1-dependent transcription regulation does not require the enzymatic activity of AMBRA1/CRL4, and that Rab40-induced AMBRA1 ubiquitylation leads to dissociation of AMBRA1/CRL4 complex. Taken together, our findings reveal a novel function of Rab40/CRL5 complex as an important regulator for AMBRA1-dependent transcription of genes involved in cell migration.
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Affiliation(s)
- Revathi Sampath
- Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Katherine Vaeth
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | | | | | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ke-Jun Han
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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Saleban M, Harris EL, Poulter JA. D-Type Cyclins in Development and Disease. Genes (Basel) 2023; 14:1445. [PMID: 37510349 PMCID: PMC10378862 DOI: 10.3390/genes14071445] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
D-type cyclins encode G1/S cell cycle checkpoint proteins, which play a crucial role in defining cell cycle exit and progression. Precise control of cell cycle exit is vital during embryonic development, with defects in the pathways regulating intracellular D-type cyclins resulting in abnormal initiation of stem cell differentiation in a variety of different organ systems. Furthermore, stabilisation of D-type cyclins is observed in a wide range of disorders characterized by cellular over-proliferation, including cancers and overgrowth disorders. In this review, we will summarize and compare the roles played by each D-type cyclin during development and provide examples of how their intracellular dysregulation can be an underlying cause of disease.
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Affiliation(s)
- Mostafa Saleban
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
| | - Erica L Harris
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
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Simoneschi D. Uncovering the degrader of D-type cyclins. Science 2022; 378:845. [DOI: 10.1126/science.adf4868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AMBRA1 is identified as the long-sought, major controller of D-type cyclins
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Affiliation(s)
- Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, Grossman School of Medicine, New York University, New York, NY, USA
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Qin YQ, Liu SY, Lv ML, Sun WL. Ambra1 in cancer: implications for clinical oncology. Apoptosis 2022; 27:720-729. [PMID: 35994214 DOI: 10.1007/s10495-022-01762-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
Activating molecule in Beclin-1-regulated autophagy protein 1 (Ambra1) is well known to mediate the autophagy process and promote the formation of autophagosomes. In addition, Ambra1 is involved in the execution of apoptosis. A growing number of studies have revealed that this protein modifies the sensitivity of cancer cells to anticancer drugs by controlling the balance between autophagy and apoptosis. In addition, Ambra1 is a key factor in regulating the cell cycle, proliferation, invasion and migration. Therefore, it plays a key role in tumorigenesis and progression. Moreover, Ambra1 is highly expressed in a variety of cancers and is closely related to the prognosis of patients. Thus, it appears that Ambra1 has multiple roles in tumorigenesis and progression, which may have implications for clinical oncology. The present review focuses on recent advances in the study of Ambra1, especially the role of the protein in tumorigenesis, progression and effects on anticancer drug sensitivity.
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Affiliation(s)
- Yan-Qiu Qin
- Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, No. 166 Daxuedong Road, Nanning, 530007, Guangxi, People's Republic of China
| | - Si-Yu Liu
- Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, No. 166 Daxuedong Road, Nanning, 530007, Guangxi, People's Republic of China
| | - Mei-Ling Lv
- Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, No. 166 Daxuedong Road, Nanning, 530007, Guangxi, People's Republic of China
| | - Wei-Liang Sun
- Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, No. 166 Daxuedong Road, Nanning, 530007, Guangxi, People's Republic of China.
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Witkiewicz AK, Kumarasamy V, Sanidas I, Knudsen ES. Cancer cell cycle dystopia: heterogeneity, plasticity, and therapy. Trends Cancer 2022; 8:711-725. [PMID: 35599231 PMCID: PMC9388619 DOI: 10.1016/j.trecan.2022.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/20/2022]
Abstract
The mammalian cell cycle has been extensively studied regarding cancer etiology, progression, and therapeutic intervention. The canonical cell cycle framework is supported by a plethora of data pointing to a relatively simple linear pathway in which mitogenic signals are integrated in a stepwise fashion to allow progression through G1/S with coordinate actions of cyclin-dependent kinases (CDK)4/6 and CDK2 on the RB tumor suppressor. Recent work on adaptive mechanisms and intrinsic heterogeneous dependencies indicates that G1/S control of the cell cycle is a variable signaling pathway rather than an invariant engine that drives cell division. These alterations can limit the effectiveness of pharmaceutical agents but provide new avenues for therapeutic interventions. These findings support a dystopian view of the cell cycle in cancer where the canonical utopian cell cycle is often not observed. However, recognizing the extent of cell cycle heterogeneity likely creates new opportunities for precision therapeutic approaches specifically targeting these states.
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Affiliation(s)
- Agnieszka K Witkiewicz
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA.
| | - Vishnu Kumarasamy
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Ioannis Sanidas
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Erik S Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA.
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