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Lian WS, Wu RW, Lin YH, Chen YS, Jahr H, Wang FS. Tricarboxylic Acid Cycle Regulation of Metabolic Program, Redox System, and Epigenetic Remodeling for Bone Health and Disease. Antioxidants (Basel) 2024; 13:470. [PMID: 38671918 PMCID: PMC11047415 DOI: 10.3390/antiox13040470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Imbalanced osteogenic cell-mediated bone gain and osteoclastic remodeling accelerates the development of osteoporosis, which is the leading risk factor of disability in the elderly. Harmonizing the metabolic actions of bone-making cells and bone resorbing cells to the mineralized matrix network is required to maintain bone mass homeostasis. The tricarboxylic acid (TCA) cycle in mitochondria is a crucial process for cellular energy production and redox homeostasis. The canonical actions of TCA cycle enzymes and intermediates are indispensable in oxidative phosphorylation and adenosine triphosphate (ATP) biosynthesis for osteogenic differentiation and osteoclast formation. Knockout mouse models identify these enzymes' roles in bone mass and microarchitecture. In the noncanonical processes, the metabolites as a co-factor or a substrate involve epigenetic modification, including histone acetyltransferases, DNA demethylases, RNA m6A demethylases, and histone demethylases, which affect genomic stability or chromatin accessibility for cell metabolism and bone formation and resorption. The genetic manipulation of these epigenetic regulators or TCA cycle intermediate supplementation compromises age, estrogen deficiency, or inflammation-induced bone mass loss and microstructure deterioration. This review sheds light on the metabolic functions of the TCA cycle in terms of bone integrity and highlights the crosstalk of the TCA cycle and redox and epigenetic pathways in skeletal tissue metabolism and the intermediates as treatment options for delaying osteoporosis.
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Affiliation(s)
- Wei-Shiung Lian
- Core Laboratory for Phenomics and Diagnostic, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan; (W.-S.L.); (Y.-S.C.)
- Center for Mitochondrial Research and Medicine, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan;
- Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan
| | - Re-Wen Wu
- Department of Orthopedic Surgery, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan;
| | - Yu-Han Lin
- Center for Mitochondrial Research and Medicine, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan;
| | - Yu-Shan Chen
- Core Laboratory for Phenomics and Diagnostic, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan; (W.-S.L.); (Y.-S.C.)
- Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan
| | - Holger Jahr
- Department of Anatomy and Cell Biology, University Hospital RWTH, 52074 Aachen, Germany;
- Department of Orthopedic Surgery, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Feng-Sheng Wang
- Core Laboratory for Phenomics and Diagnostic, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan; (W.-S.L.); (Y.-S.C.)
- Center for Mitochondrial Research and Medicine, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan;
- Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan
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2
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Li Z, Yang B, Yang Z, Xie X, Guo Z, Zhao J, Wang R, Fu H, Zhao P, Zhao X, Chen G, Li G, Wei F, Bian L. Supramolecular Hydrogel with Ultra-Rapid Cell-Mediated Network Adaptation for Enhancing Cellular Metabolic Energetics and Tissue Regeneration. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307176. [PMID: 38295393 DOI: 10.1002/adma.202307176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/27/2023] [Indexed: 02/02/2024]
Abstract
Cellular energetics plays an important role in tissue regeneration, and the enhanced metabolic activity of delivered stem cells can accelerate tissue repair and regeneration. However, conventional hydrogels with limited network cell adaptability restrict cell-cell interactions and cell metabolic activities. In this work, it is shown that a cell-adaptable hydrogel with high network dynamics enhances the glucose uptake and fatty acid β-oxidation of encapsulated human mesenchymal stem cells (hMSCs) compared with a hydrogel with low network dynamics. It is further shown that the hMSCs encapsulated in the high dynamic hydrogels exhibit increased tricarboxylic acid (TCA) cycle activity, oxidative phosphorylation (OXPHOS), and adenosine triphosphate (ATP) biosynthesis via an E-cadherin- and AMP-activated protein kinase (AMPK)-dependent mechanism. The in vivo evaluation further showed that the delivery of MSCs by the dynamic hydrogel enhanced in situ bone regeneration in an animal model. It is believed that the findings provide critical insights into the impact of stem cell-biomaterial interactions on cellular metabolic energetics and the underlying mechanisms.
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Affiliation(s)
- Zhuo Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Boguang Yang
- Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, 999077, P. R. China
| | - Zhengmeng Yang
- Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, 999077, P. R. China
| | - Xian Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Zhengnan Guo
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
| | - Jianyang Zhao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
| | - Ruinan Wang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
| | - Hao Fu
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
| | - Pengchao Zhao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
| | - Xin Zhao
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, 999077, P. R. China
| | - Guosong Chen
- Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Gang Li
- Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, 999077, P. R. China
| | - Fuxin Wei
- Department of Orthopedic Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, P. R. China
- Shenzhen Key Laboratory of Bone Tissue Repair and Translational Research, Shenzhen, 518107, P. R. China
| | - Liming Bian
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 511442, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 511442, P. R. China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 511442, P. R. China
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3
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Yu Y, Zhao F, Yue Y, Zhao Y, Zhou DX. Lysine acetylation of histone acetyltransferase adaptor protein ADA2 is a mechanism of metabolic control of chromatin modification in plants. NATURE PLANTS 2024; 10:439-452. [PMID: 38326652 DOI: 10.1038/s41477-024-01623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Histone acetylation is a predominant active chromatin mark deposited by histone acetyltransferases (HATs) that transfer the acetyl group from acetyl coenzyme A (acetyl-CoA) to lysine ε-amino groups in histones. GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5) is one of the best-characterized HATs and functions in association with several adaptor proteins such as ADA2 within multiprotein HAT complexes. ADA2-GCN5 interaction increases GCN5 binding to acetyl-CoA and stimulates its HAT activity. It remains unclear whether the HAT activity of GCN5 (which acetylates not only histones but also cellular proteins) is regulated by acetyl-CoA levels, which vary greatly in cells under different metabolic and nutrition conditions. Here we show that the ADA2 protein itself is acetylated by GCN5 in rice cells. Lysine acetylation exposes ADA2 to a specific E3 ubiquitin ligase and reduces its protein stability. In rice plants, ADA2 protein accumulation reversely parallels its lysine acetylation and acetyl-CoA levels, both of which are dynamically regulated under varying growth conditions. Stress-induced ADA2 accumulation could stimulate GCN5 HAT activity to compensate for the reduced acetyl-CoA levels for histone acetylation. These results indicate that ADA2 lysine acetylation that senses cellular acetyl-CoA variations is a mechanism to regulate HAT activity and histone acetylation homeostasis in plants under changing environments.
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Affiliation(s)
- Yue Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Feng Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, France.
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Zhu J, Xu F, Lai H, Yuan H, Li XY, Hu J, Li W, Liu L, Wang C. ACO2 deficiency increases vulnerability to Parkinson's disease via dysregulating mitochondrial function and histone acetylation-mediated transcription of autophagy genes. Commun Biol 2023; 6:1201. [PMID: 38007539 PMCID: PMC10676364 DOI: 10.1038/s42003-023-05570-y] [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: 03/20/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023] Open
Abstract
Parkinson's disease (PD) is characterized by α-synuclein aggregation in dopaminergic (DA) neurons, which are sensitive to oxidative stress. Mitochondria aconitase 2 (ACO2) is an essential enzyme in the tricarboxylic acid cycle that orchestrates mitochondrial and autophagic functions to energy metabolism. Though widely linked to diseases, its relation to PD has not been fully clarified. Here we revealed that the peripheral ACO2 activity was significantly decreased in PD patients and associated with their onset age and disease durations. The knock-in mouse and Drosophila models with the A252T variant displayed aggravated motor deficits and DA neuron degeneration after 6-OHDA and rotenone-induction, and the ACO2 knockdown or blockade cells showed features of mitochondrial and autophagic dysfunction. Moreover, the transcription of autophagy-related genes LC3 and Atg5 was significantly downregulated via inhibited histone acetylation at the H3K9 and H4K5 sites. These data provided multi-dimensional evidences supporting the essential roles of ACO2, and as a potential early biomarker to be used in clinical trials for assessing the effects of antioxidants in PD. Moreover, ameliorating energy metabolism by targeting ACO2 could be considered as a potential therapeutic strategy for PD and other neurodegenerative disorders.
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Affiliation(s)
- Junge Zhu
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Fanxi Xu
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Hong Lai
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
- Department of Neurology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Huiyao Yuan
- Department of Biochemistry and Molecular Biology, Capital Medical University; School of Basic Medicine, Beijing, 100069, China
| | - Xu-Ying Li
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Junya Hu
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Wei Li
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
- Department of Stroke Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250000, China
| | - Lei Liu
- Department of Biochemistry and Molecular Biology, Capital Medical University; School of Basic Medicine, Beijing, 100069, China.
| | - Chaodong Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China.
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5
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Hu J, Zhang Z, Hu H, Yang K, Zhu Z, Yang Q, Liang W. LRH-1 activation alleviates diabetes-induced podocyte injury by promoting GLS2-mediated glutaminolysis. Cell Prolif 2023; 56:e13479. [PMID: 37057309 PMCID: PMC10623971 DOI: 10.1111/cpr.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/25/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023] Open
Abstract
Alteration of metabolic phenotype in podocytes directly contributes to the development of albuminuria and renal injury in conditions of diabetic kidney disease (DKD). This study aimed to identify and evaluate liver receptor homologue-1 (LRH-1) as a possible therapeutic target that alleviates glutamine (Gln) metabolism disorders and mitigates podocyte injury in DKD. Metabolomic and transcriptomic analyses were performed to characterize amino acid metabolism changes in the glomeruli of diabetic mice. Next, Western blotting, immunohistochemistry assays, and immunofluorescence staining were used to detect the expression of different genes in vitro and in vivo. Furthermore, Gln and glutamate (Glu) content as well as ATP generation were examined. A decrease in LRH-1 and glutaminase 2 (GLS2) expression was detected in diabetic podocytes. Conversely, the administration of LRH-1 agonist (DLPC) upregulated the expression of GLS2 and promoted glutaminolysis, with an improvement in mitochondrial dysfunction and less apoptosis in podocytes compared to those in vehicle-treated db/db mice. Our study indicates the essential role of LRH-1 in governing the Gln metabolism of podocytes, targeting LRH-1 could restore podocytes from diabetes-induced disturbed glutaminolysis in mitochondria.
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Affiliation(s)
- Jijia Hu
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
- Nephrology and Urology Research Institute of Wuhan UniversityWuhanHubeiChina
| | - Zongwei Zhang
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
- Nephrology and Urology Research Institute of Wuhan UniversityWuhanHubeiChina
| | - Hongtu Hu
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
| | - Keju Yang
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
- The First College of Clinical Medical Science, China Three Gorges UniversityYichangHubeiChina
| | - Zijing Zhu
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
| | - Qian Yang
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
- Nephrology and Urology Research Institute of Wuhan UniversityWuhanHubeiChina
| | - Wei Liang
- Division of NephrologyRenmin Hospital of Wuhan UniversityWuhanHubeiChina
- Nephrology and Urology Research Institute of Wuhan UniversityWuhanHubeiChina
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6
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Russo M, Pileri F, Ghisletti S. Novel insights into the role of acetyl-CoA producing enzymes in epigenetic regulation. Front Endocrinol (Lausanne) 2023; 14:1272646. [PMID: 37842307 PMCID: PMC10570720 DOI: 10.3389/fendo.2023.1272646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Inflammation-dependent changes in gene expression programs in innate immune cells, such as macrophages, involve extensive reprogramming of metabolism. This reprogramming is essential for the production of metabolites required for chromatin modifications, such as acetyl-CoA, and regulate their usage and availability impacting the macrophage epigenome. One of the most transcriptionally induced proinflammatory mediator is nitric oxide (NO), which has been shown to inhibit key metabolic enzymes involved in the production of these metabolites. Recent evidence indicates that NO inhibits mitochondrial enzymes such as pyruvate dehydrogenase (PDH) in macrophages induced by inflammatory stimulus. PDH is involved in the production of acetyl-CoA, which is essential for chromatin modifications in the nucleus, such as histone acetylation. In addition, acetyl-CoA levels in inflamed macrophages are regulated by ATP citrate lyase (ACLY) and citrate transporter SLC25A1. Interestingly, acetyl-CoA producing enzymes, such as PDH and ACLY, have also been reported to be present in the nucleus and to support the local generation of cofactors such as acetyl-CoA. Here, we will discuss the mechanisms involved in the regulation of acetyl-CoA production by metabolic enzymes, their inhibition by prolonged exposure to inflammation stimuli, their involvement in dynamic inflammatory expression changes and how these emerging findings could have significant implications for the design of novel therapeutic approaches.
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Affiliation(s)
| | | | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
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7
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Pouikli A, Frezza C. Metabolic control of antitumor immunity. Science 2023; 381:1287-1288. [PMID: 37733861 DOI: 10.1126/science.adk1785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Mitochondrial metabolite reduces melanoma growth by boosting antigen presentation.
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Affiliation(s)
- Andromachi Pouikli
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Christian Frezza
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- CECAD, Institute of Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
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8
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Gnocchi D, Nikolic D, Paparella RR, Sabbà C, Mazzocca A. Cellular Adaptation Takes Advantage of Atavistic Regression Programs during Carcinogenesis. Cancers (Basel) 2023; 15:3942. [PMID: 37568758 PMCID: PMC10416974 DOI: 10.3390/cancers15153942] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Adaptation of cancer cells to extreme microenvironmental conditions (i.e., hypoxia, high acidity, and reduced nutrient availability) contributes to cancer resilience. Furthermore, neoplastic transformation can be envisioned as an extreme adaptive response to tissue damage or chronic injury. The recent Systemic-Evolutionary Theory of the Origin of Cancer (SETOC) hypothesizes that cancer cells "revert" to "primitive" characteristics either ontogenically (embryo-like) or phylogenetically (single-celled organisms). This regression may confer robustness and maintain the disordered state of the tissue, which is a hallmark of malignancy. Changes in cancer cell metabolism during adaptation may also be the consequence of altered microenvironmental conditions, often resulting in a shift toward lactic acid fermentation. However, the mechanisms underlying the robust adaptive capacity of cancer cells remain largely unknown. In recent years, cancer cells' metabolic flexibility has received increasing attention among researchers. Here, we focus on how changes in the microenvironment can affect cancer cell energy production and drug sensitivity. Indeed, changes in the cellular microenvironment may lead to a "shift" toward "atavistic" biologic features, such as the switch from oxidative phosphorylation (OXPHOS) to lactic acid fermentation, which can also sustain drug resistance. Finally, we point out new integrative metabolism-based pharmacological approaches and potential biomarkers for early detection.
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Affiliation(s)
| | | | | | | | - Antonio Mazzocca
- Interdisciplinary Department of Medicine, University of Bari School of Medicine, Piazza G. Cesare, 11, 70124 Bari, Italy; (D.G.); (D.N.); (R.R.P.); (C.S.)
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9
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Huang F, Luo X, Ou Y, Gao Z, Tang Q, Chu Z, Zhu X, He Y. Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase. Science 2023; 381:eadf8822. [PMID: 37440635 DOI: 10.1126/science.adf8822] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/19/2023] [Indexed: 07/15/2023]
Abstract
Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.
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Affiliation(s)
- Fei Huang
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Xiao Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Yang Ou
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Zhaoxu Gao
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiming Tang
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Zhenzhen Chu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Xinguang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Yuehui He
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
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10
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Xu Q, Yue Y, Liu B, Chen Z, Ma X, Wang J, Zhao Y, Zhou DX. ACL and HAT1 form a nuclear module to acetylate histone H4K5 and promote cell proliferation. Nat Commun 2023; 14:3265. [PMID: 37277331 DOI: 10.1038/s41467-023-39101-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 05/30/2023] [Indexed: 06/07/2023] Open
Abstract
Acetyl-CoA utilized by histone acetyltransferases (HAT) for chromatin modification is mainly generated by ATP-citrate lyase (ACL) from glucose sources. How ACL locally establishes acetyl-CoA production for histone acetylation remains unclear. Here we show that ACL subunit A2 (ACLA2) is present in nuclear condensates, is required for nuclear acetyl-CoA accumulation and acetylation of specific histone lysine residues, and interacts with Histone AcetylTransferase1 (HAT1) in rice. The rice HAT1 acetylates histone H4K5 and H4K16 and its activity on H4K5 requires ACLA2. Mutations of rice ACLA2 and HAT1 (HAG704) genes impair cell division in developing endosperm, result in decreases of H4K5 acetylation at largely the same genomic regions, affect the expression of similar sets of genes, and lead to cell cycle S phase stagnation in the endosperm dividing nuclei. These results indicate that the HAT1-ACLA2 module selectively promotes histone lysine acetylation in specific genomic regions and unravel a mechanism of local acetyl-CoA production which couples energy metabolism with cell division.
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Affiliation(s)
- Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Biao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhengting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Xuan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China.
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay, 91405, Orsay, France.
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11
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Hemedan AA, Schneider R, Ostaszewski M. Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses. FRONTIERS IN BIOINFORMATICS 2023; 3:1189723. [PMID: 37325771 PMCID: PMC10267406 DOI: 10.3389/fbinf.2023.1189723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Computational modeling has emerged as a critical tool in investigating the complex molecular processes involved in biological systems and diseases. In this study, we apply Boolean modeling to uncover the molecular mechanisms underlying Parkinson's disease (PD), one of the most prevalent neurodegenerative disorders. Our approach is based on the PD-map, a comprehensive molecular interaction diagram that captures the key mechanisms involved in the initiation and progression of PD. Using Boolean modeling, we aim to gain a deeper understanding of the disease dynamics, identify potential drug targets, and simulate the response to treatments. Our analysis demonstrates the effectiveness of this approach in uncovering the intricacies of PD. Our results confirm existing knowledge about the disease and provide valuable insights into the underlying mechanisms, ultimately suggesting potential targets for therapeutic intervention. Moreover, our approach allows us to parametrize the models based on omics data for further disease stratification. Our study highlights the value of computational modeling in advancing our understanding of complex biological systems and diseases, emphasizing the importance of continued research in this field. Furthermore, our findings have potential implications for the development of novel therapies for PD, which is a pressing public health concern. Overall, this study represents a significant step forward in the application of computational modeling to the investigation of neurodegenerative diseases, and underscores the power of interdisciplinary approaches in tackling challenging biomedical problems.
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Lu Y, Bu Q, Chuan M, Cui X, Zhao Y, Zhou DX. Metabolic regulation of the plant epigenome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1001-1013. [PMID: 36705504 DOI: 10.1111/tpj.16122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 05/31/2023]
Abstract
Chromatin modifications shape the epigenome and are essential for gene expression reprogramming during plant development and adaptation to the changing environment. Chromatin modification enzymes require primary metabolic intermediates such as S-adenosyl-methionine, acetyl-CoA, alpha-ketoglutarate, and NAD+ as substrates or cofactors. The availability of the metabolites depends on cellular nutrients, energy and reduction/oxidation (redox) states, and affects the activity of chromatin regulators and the epigenomic landscape. The changes in the plant epigenome and the activity of epigenetic regulators in turn control cellular metabolism through transcriptional and post-translational regulation of metabolic enzymes. The interplay between metabolism and the epigenome constitutes a basis for metabolic control of plant growth and response to environmental changes. This review summarizes recent advances regarding the metabolic control of plant chromatin regulators and epigenomes, which are involved in plant adaption to environmental stresses.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Qing Bu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoyun Cui
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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Nunes-Xavier CE, Emaldi M, Mingo J, Øyjord T, Mælandsmo GM, Fodstad Ø, Errarte P, Larrinaga G, Llarena R, López JI, Pulido R. The expression pattern of pyruvate dehydrogenase kinases predicts prognosis and correlates with immune exhaustion in clear cell renal cell carcinoma. Sci Rep 2023; 13:7339. [PMID: 37147361 PMCID: PMC10162970 DOI: 10.1038/s41598-023-34087-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
Renal cancer cells constitute a paradigm of tumor cells with a glycolytic reprogramming which drives metabolic alterations favouring cell survival and transformation. We studied the expression and activity of pyruvate dehydrogenase kinases (PDK1-4), key enzymes of the energy metabolism, in renal cancer cells. We analysed the expression, subcellular distribution and clinicopathological correlations of PDK1-4 by immunohistochemistry of tumor tissue microarray samples from a cohort of 96 clear cell renal cell carcinoma (ccRCC) patients. Gene expression analysis was performed on whole tumor tissue sections of a subset of ccRCC samples. PDK2 and PDK3 protein expression in tumor cells correlated with lower patient overall survival, whereas PDK1 protein expression correlated with higher patient survival. Gene expression analysis revealed molecular association of PDK2 and PDK3 expression with PI3K signalling pathway, as well as with T cell infiltration and exhausted CD8 T cells. Inhibition of PDK by dichloroacetate in human renal cancer cell lines resulted in lower cell viability, which was accompanied by an increase in pAKT. Together, our findings suggest a differential role for PDK enzymes in ccRCC progression, and highlight PDK as actionable metabolic proteins in relation with PI3K signalling and exhausted CD8 T cells in ccRCC.
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Affiliation(s)
- Caroline E Nunes-Xavier
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.
| | - Maite Emaldi
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Tove Øyjord
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gunhild M Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Øystein Fodstad
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Peio Errarte
- Department of Nursing, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Gorka Larrinaga
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Nursing, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Roberto Llarena
- Department of Urology, Cruces University Hospital, Barakaldo, Spain
| | - José I López
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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Capone F, Sotomayor-Flores C, Bode D, Wang R, Rodolico D, Strocchi S, Schiattarella GG. Cardiac metabolism in HFpEF: from fuel to signalling. Cardiovasc Res 2023; 118:3556-3575. [PMID: 36504368 DOI: 10.1093/cvr/cvac166] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
Heart failure (HF) is marked by distinctive changes in myocardial uptake and utilization of energy substrates. Among the different types of HF, HF with preserved ejection fraction (HFpEF) is a highly prevalent, complex, and heterogeneous condition for which metabolic derangements seem to dictate disease progression. Changes in intermediate metabolism in cardiometabolic HFpEF-among the most prevalent forms of HFpEF-have a large impact both on energy provision and on a number of signalling pathways in the heart. This dual, metabolic vs. signalling, role is played in particular by long-chain fatty acids (LCFAs) and short-chain carbon sources [namely, short-chain fatty acids (SCFAs) and ketone bodies (KBs)]. LCFAs are key fuels for the heart, but their excess can be harmful, as in the case of toxic accumulation of lipid by-products (i.e. lipotoxicity). SCFAs and KBs have been proposed as a potential major, alternative source of energy in HFpEF. At the same time, both LCFAs and short-chain carbon sources are substrate for protein post-translational modifications and other forms of direct and indirect signalling of pivotal importance in HFpEF pathogenesis. An in-depth molecular understanding of the biological functions of energy substrates and their signalling role will be instrumental in the development of novel therapeutic approaches to HFpEF. Here, we summarize the current evidence on changes in energy metabolism in HFpEF, discuss the signalling role of intermediate metabolites through, at least in part, their fate as substrates for post-translational modifications, and highlight clinical and translational challenges around metabolic therapy in HFpEF.
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Affiliation(s)
- Federico Capone
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Division of Internal Medicine, Department of Medicine, University of Padua, Padua, Italy
| | - Cristian Sotomayor-Flores
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - David Bode
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Rongling Wang
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Daniele Rodolico
- Department of Cardiovascular and Pulmonary Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Stefano Strocchi
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Gabriele G Schiattarella
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Division of Cardiology, Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
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Hubbing the Cancer Cell. Cancers (Basel) 2022; 14:cancers14235924. [PMID: 36497405 PMCID: PMC9738523 DOI: 10.3390/cancers14235924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Oncogenic transformation drives adaptive changes in a growing tumor that affect the cellular organization of cancerous cells, resulting in the loss of specialized cellular functions in the polarized compartmentalization of cells. The resulting altered metabolic and morphological patterns are used clinically as diagnostic markers. This review recapitulates the known functions of actin, microtubules and the γ-tubulin meshwork in orchestrating cell metabolism and functional cellular asymmetry.
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Abstract
The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA; New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Pladevall-Morera D, Zylicz JJ. Chromatin as a sensor of metabolic changes during early development. Front Cell Dev Biol 2022; 10:1014498. [PMID: 36299478 PMCID: PMC9588933 DOI: 10.3389/fcell.2022.1014498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular metabolism is a complex network of biochemical reactions fueling development with energy and biomass; however, it can also shape the cellular epigenome. Indeed, some intermediates of metabolic reactions exert a non-canonical function by acting as co-factors, substrates or inhibitors of chromatin modifying enzymes. Therefore, fluctuating availability of such molecules has the potential to regulate the epigenetic landscape. Thanks to this functional coupling, chromatin can act as a sensor of metabolic changes and thus impact cell fate. Growing evidence suggest that both metabolic and epigenetic reprogramming are crucial for ensuring a successful embryo development from the zygote until gastrulation. In this review, we provide an overview of the complex relationship between metabolism and epigenetics in regulating the early stages of mammalian embryo development. We report on recent breakthroughs in uncovering the non-canonical functions of metabolism especially when re-localized to the nucleus. In addition, we identify the challenges and outline future perspectives to advance the novel field of epi-metabolomics especially in the context of early development.
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Gu W, Fillebeen C, Pantopoulos K. Human IRP1 Translocates to the Nucleus in a Cell-Specific and Iron-Dependent Manner. Int J Mol Sci 2022; 23:ijms231810740. [PMID: 36142654 PMCID: PMC9502121 DOI: 10.3390/ijms231810740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Iron regulatory protein 1 (IRP1) is a bifunctional protein with mutually exclusive RNA-binding or enzymatic activities that depend on the presence of a 4Fe-4S cluster. While IRP1 is a well-established cytosolic protein, work in a Drosophila model suggested that it may also exhibit nuclear localization. Herein, we addressed whether mammalian IRP1 can likewise translocate to the nucleus. We utilized primary cells and tissues from wild type and Irp1−/− mice, as well as human cell lines and tissue biopsy sections. IRP1 subcellular localization was analyzed by Western blotting, immunofluorescence and immunohistochemistry. We did not detect presence of nuclear IRP1 in wild type mouse embryonic fibroblasts (MEFs), primary hepatocytes or whole mouse liver. However, we observed IRP1-positive nuclei in human liver but not ovary sections. Biochemical fractionation studies revealed presence of IRP1 in the nucleus of human Huh7 and HepG2 hepatoma cells, but not HeLa cervical cancer cells. Importantly, nuclear IRP1 was only evident in iron-replete cells and disappeared following pharmacological iron chelation. These data provide the first experimental evidence for nuclear IRP1 expression in mammals, which appears to be species- and cell-specific. Furthermore, they suggest that the nuclear translocation of IRP1 is mediated by an iron-dependent mechanism.
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Affiliation(s)
- Wen Gu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Carine Fillebeen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-514-340-8260 (ext. 25293)
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19
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Miyazawa H, Snaebjornsson MT, Prior N, Kafkia E, Hammarén HM, Tsuchida-Straeten N, Patil KR, Beck M, Aulehla A. Glycolytic flux-signaling controls mouse embryo mesoderm development. eLife 2022; 11:83299. [PMID: 36469462 PMCID: PMC9771359 DOI: 10.7554/elife.83299] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/06/2022] [Indexed: 12/12/2022] Open
Abstract
How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here, we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Overexpression of cytoPFKFB3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPFKFB3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.
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Affiliation(s)
- Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Nicole Prior
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Eleni Kafkia
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
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