1
|
Huang PJ, Lin YL, Chen CH, Lin HY, Fang SC. A chloroplast sulphate transporter modulates glutathione-mediated redox cycling to regulate cell division. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39189939 DOI: 10.1111/pce.15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024]
Abstract
Glutathione redox cycling is important for cell cycle regulation, but its mechanisms are not well understood. We previously identified a small-sized mutant, suppressor of mat3 15-1 (smt15-1) that has elevated cellular glutathione. Here, we demonstrated that SMT15 is a chloroplast sulphate transporter. Reducing expression of γ-GLUTAMYLCYSTEINE SYNTHETASE, encoding the rate-limiting enzyme required for glutathione biosynthesis, corrected the size defect of smt15-1 cells. Overexpressing GLUTATHIONE SYNTHETASE (GSH2) recapitulated the small-size phenotype of smt15-1 mutant, confirming the role of glutathione in cell division. Hence, SMT15 may regulate chloroplast sulphate concentration to modulate cellular glutathione levels. In wild-type cells, glutathione and/or thiol-containing molecules (GSH/thiol) accumulated in the cytosol at the G1 phase and decreased as cells entered the S/M phase. While the cytosolic GSH/thiol levels in the small-sized mutants, smt15-1 and GSH2 overexpressors, mirrored those of wild-type cells (accumulating during G1 and declining at early S/M phase), GSH/thiol was specifically accumulated in the basal bodies at early S/M phase in the small-sized mutants. Therefore, we propose that GSH/thiol-mediated redox signalling in the basal bodies may regulate mitotic division number in Chlamydomonas reinhardtii. Our findings suggest a new mechanism by which glutathione regulates the multiple fission cell cycle in C. reinhardtii.
Collapse
Affiliation(s)
- Pin-Jui Huang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Ling Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
2
|
Holland JG, Prior KF, O'Donnell AJ, Reece SE. Testing the evolutionary drivers of malaria parasite rhythms and their consequences for host-parasite interactions. Evol Appl 2024; 17:e13752. [PMID: 39006006 PMCID: PMC11246599 DOI: 10.1111/eva.13752] [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: 08/14/2023] [Revised: 06/05/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Undertaking certain activities at the time of day that maximises fitness is assumed to explain the evolution of circadian clocks. Organisms often use daily environmental cues such as light and food availability to set the timing of their clocks. These cues may be the environmental rhythms that ultimately determine fitness, act as proxies for the timing of less tractable ultimate drivers, or are used simply to maintain internal synchrony. While many pathogens/parasites undertake rhythmic activities, both the proximate and ultimate drivers of their rhythms are poorly understood. Explaining the roles of rhythms in infections offers avenues for novel interventions to interfere with parasite fitness and reduce the severity and spread of disease. Here, we perturb several rhythms in the hosts of malaria parasites to investigate why parasites align their rhythmic replication to the host's feeding-fasting rhythm. We manipulated host rhythms governed by light, food or both, and assessed the fitness implications for parasites, and the consequences for hosts, to test which host rhythms represent ultimate drivers of the parasite's rhythm. We found that alignment with the host's light-driven rhythms did not affect parasite fitness metrics. In contrast, aligning with the timing of feeding-fasting rhythms may be beneficial for the parasite, but only when the host possess a functional canonical circadian clock. Because parasites in clock-disrupted hosts align with the host's feeding-fasting rhythms and yet derive no apparent benefit, our results suggest cue(s) from host food act as a proxy rather than being a key selective driver of the parasite's rhythm. Alternatively, parasite rhythmicity may only be beneficial because it promotes synchrony between parasite cells and/or allows parasites to align to the biting rhythms of vectors. Our results also suggest that interventions can disrupt parasite rhythms by targeting the proxies or the selective factors driving them without impacting host health.
Collapse
Affiliation(s)
- Jacob G. Holland
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | | | | | - Sarah E. Reece
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
- Institute of Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
| |
Collapse
|
3
|
Xu Z, He D, Huang L, Deng K, Jiang W, Qin J, Zheng Z, Zheng T, Li S. Metabolic reprogramming-driven homologous recombination and TCA cycle dysregulation contribute to poor prognoses in lung adenocarcinoma. J Cell Mol Med 2024; 28:e18406. [PMID: 38822457 PMCID: PMC11142899 DOI: 10.1111/jcmm.18406] [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: 01/24/2024] [Revised: 04/04/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024] Open
Abstract
Increasing evidence has shown that homologous recombination (HR) and metabolic reprogramming are essential for cellular homeostasis. These two processes are independent as well as closely intertwined. Nevertheless, they have rarely been reported in lung adenocarcinoma (LUAD). We analysed the genomic, immune microenvironment and metabolic microenvironment features under different HR activity states. Using cell cycle, EDU and cell invasion assays, we determined the impacts of si-SHFM1 on the LUAD cell cycle, proliferation and invasion. The levels of isocitrate dehydrogenase (IDH) and α-ketoglutarate dehydrogenase (α-KGDH) were determined by ELISA in the NC and si-SHFM1 groups of A549 cells. Finally, cell samples were used to extract metabolites for HPIC-MS/MS to analyse central carbon metabolism. We found that high HR activity was associated with a poor prognosis in LUAD, and HR was an independent prognostic factor for TCGA-LUAD patients. Moreover, LUAD samples with a high HR activity presented low immune infiltration levels, a high degree of genomic instability, a good response status to immune checkpoint blockade therapy and a high degree of drug sensitivity. The si-SHFM1 group presented a significantly higher proportion of cells in the G0/G1 phase, lower levels of DNA replication, and significantly lower levels of cell migration and both TCA enzymes. Our current results indicated that there is a strong correlation between HR and the TCA cycle in LUAD. The TCA cycle can promote SHFM1-mediated HR in LUAD, raising their activities, which can finally result in a poor prognosis and impair immunotherapeutic efficacy.
Collapse
Affiliation(s)
- Zhanyu Xu
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Dongming He
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Liuliu Huang
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Kun Deng
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Wei Jiang
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Junqi Qin
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Zhiwen Zheng
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Tiaozhan Zheng
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Shikang Li
- Department of Thoracic and Cardiovascular SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| |
Collapse
|
4
|
Han JDJ. The ticking of aging clocks. Trends Endocrinol Metab 2024; 35:11-22. [PMID: 37880054 DOI: 10.1016/j.tem.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Computational models that measure biological age and aging rate regardless of chronological age are called aging clocks. The underlying counting mechanisms of the intrinsic timers of these clocks are still unclear. Molecular mediators and determinants of aging rate point to the key roles of DNA damage, epigenetic drift, and inflammation. Persistent DNA damage leads to cellular senescence and the senescence-associated secretory phenotype (SASP), which induces cytotoxic immune cell infiltration; this further induces DNA damage through reactive oxygen and nitrogen species (RONS). I discuss the possibility that DNA damage (or the response to it, including epigenetic changes) is the fundamental counting unit of cell cycles and cellular senescence, that ultimately accounts for cell composition changes and functional decline in tissues, as well as the key intervention points.
Collapse
Affiliation(s)
- Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; International Center for Aging and Cancer (ICAC), The First Affiliated Hospital, Hainan Medical University, Haikou, China.
| |
Collapse
|
5
|
Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
Collapse
Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| |
Collapse
|
6
|
Soultanas P, Janniere L. The metabolic control of DNA replication: mechanism and function. Open Biol 2023; 13:230220. [PMID: 37582405 PMCID: PMC10427196 DOI: 10.1098/rsob.230220] [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: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Metabolism and DNA replication are the two most fundamental biological functions in life. The catabolic branch of metabolism breaks down nutrients to produce energy and precursors used by the anabolic branch of metabolism to synthesize macromolecules. DNA replication consumes energy and precursors for faithfully copying genomes, propagating the genetic material from generation to generation. We have exquisite understanding of the mechanisms that underpin and regulate these two biological functions. However, the molecular mechanism coordinating replication to metabolism and its biological function remains mostly unknown. Understanding how and why living organisms respond to fluctuating nutritional stimuli through cell-cycle dynamic changes and reproducibly and distinctly temporalize DNA synthesis in a wide-range of growth conditions is important, with wider implications across all domains of life. After summarizing the seminal studies that founded the concept of the metabolic control of replication, we review data linking metabolism to replication from bacteria to humans. Molecular insights underpinning these links are then presented to propose that the metabolic control of replication uses signalling systems gearing metabolome homeostasis to orchestrate replication temporalization. The remarkable replication phenotypes found in mutants of this control highlight its importance in replication regulation and potentially genetic stability and tumorigenesis.
Collapse
Affiliation(s)
- Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| |
Collapse
|
7
|
Leite AC, Costa V, Pereira C. Mitochondria and the cell cycle in budding yeast. Int J Biochem Cell Biol 2023; 161:106444. [PMID: 37419443 DOI: 10.1016/j.biocel.2023.106444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
As centers for energy production and essential biosynthetic activities, mitochondria are vital for cell growth and proliferation. Accumulating evidence suggests an integrated regulation of these organelles and the nuclear cell cycle in distinct organisms. In budding yeast, a well-established example of this coregulation is the coordinated movement and positional control of mitochondria during the different phases of the cell cycle. The molecular determinants involved in the inheritance of the fittest mitochondria by the bud also seem to be cell cycle-regulated. In turn, loss of mtDNA or defects in mitochondrial structure or inheritance often lead to a cell cycle delay or arrest, indicating that mitochondrial function can also regulate cell cycle progression, possibly through the activation of cell cycle checkpoints. The up-regulation of mitochondrial respiration at G2/M, presumably to fulfil energetic requirements for progression at this phase, also supports a mitochondria-cell cycle interplay. Cell cycle-linked mitochondrial regulation is accomplished at the transcription level and through post-translational modifications, predominantly protein phosphorylation. Here, we address mitochondria-cell cycle interactions in the yeast Saccharomyces cerevisiae and discuss future challenges in the field.
Collapse
Affiliation(s)
- Ana Cláudia Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Vítor Costa
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Clara Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
| |
Collapse
|
8
|
Darshi M, Tumova J, Saliba A, Kim J, Baek J, Pennathur S, Sharma K. Crabtree effect in kidney proximal tubule cells via late-stage glycolytic intermediates. iScience 2023; 26:106462. [PMID: 37091239 PMCID: PMC10119590 DOI: 10.1016/j.isci.2023.106462] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
The Crabtree effect is defined as a rapid glucose-induced repression of mitochondrial oxidative metabolism and has been described in yeasts and tumor cells. Using plate-based respirometry, we identified the Crabtree effect in normal (non-tumor) kidney proximal tubule epithelial cells (PTEC) but not in other kidney cells (podocytes or mesangial cells) or mammalian cells (C2C12 myoblasts). Glucose-induced repression of respiration was prevented by reducing glycolysis at the proximal step with 2-deoxyglucose and partially reversed by pyruvate. The late-stage glycolytic intermediates glyceraldehyde 3-phosphate, 3-phosphoglycerate, and phosphoenolpyruvate, but not the early-stage glycolytic intermediates or lactate, inhibited respiration in permeabilized PTEC and kidney cortex mitochondria, mimicking the Crabtree effect. Studies in diabetic mice indicated a pattern of increased late-stage glycolytic intermediates consistent with a similar pattern occurring in vivo. Our results show the unique presence of the Crabtree effect in kidney PTEC and identify the major mediators of this effect.
Collapse
Affiliation(s)
- Manjula Darshi
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jana Tumova
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Pathophysiology, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Afaf Saliba
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jiwan Kim
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Judy Baek
- Department of Internal Medicine-Nephrology and Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Subramaniam Pennathur
- Department of Internal Medicine-Nephrology and Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kumar Sharma
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| |
Collapse
|
9
|
de Obeso Fernández Del Valle A, Scheckhuber CQ, Chavaro-Pérez DA, Ortega-Barragán E, Maciver SK. mRNA Sequencing Reveals Upregulation of Glutathione S-Transferase Genes during Acanthamoeba Encystation. Microorganisms 2023; 11:992. [PMID: 37110414 PMCID: PMC10142586 DOI: 10.3390/microorganisms11040992] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Some members of the genus Acanthamoeba are facultative pathogens typically with a biphasic lifestyle: trophozoites and cysts. Acanthamoeba is capable of infecting the cornea, resulting in Acanthamoeba keratitis. The cyst is one of the key components for the persistence of infection. Gene expression during Acanthamoeba encystation showed an upregulation of glutathione S-transferase (GST) genes and other closely related proteins. mRNA sequencing showed GST, and five genes with similar sequences were upregulated after 24 h of inducing encystation. GST overexpression was verified with qPCR using the HPRT and the cyst-specific protein 21 genes as controls. The GST inhibitor ethacrynic acid was found to decrease cell viability by 70%. These results indicate a role of GST in successful encystation, possibly by maintaining redox balance. GST and associated processes could be targets for potential treatments alongside regular therapies to reduce relapses of Acanthamoeba infection.
Collapse
Affiliation(s)
- Alvaro de Obeso Fernández Del Valle
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Nuevo León, Mexico
| | - Christian Quintus Scheckhuber
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Nuevo León, Mexico
| | - David Armando Chavaro-Pérez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Nuevo León, Mexico
| | - Erandi Ortega-Barragán
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Nuevo León, Mexico
| | - Sutherland K Maciver
- Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, Scotland, UK
| |
Collapse
|
10
|
Camponeschi I, Montanari A, Mazzoni C, Bianchi MM. Light Stress in Yeasts: Signaling and Responses in Creatures of the Night. Int J Mol Sci 2023; 24:ijms24086929. [PMID: 37108091 PMCID: PMC10139380 DOI: 10.3390/ijms24086929] [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: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Living organisms on the surface biosphere are periodically yet consistently exposed to light. The adaptive or protective evolution caused by this source of energy has led to the biological systems present in a large variety of organisms, including fungi. Among fungi, yeasts have developed essential protective responses against the deleterious effects of light. Stress generated by light exposure is propagated through the synthesis of hydrogen peroxide and mediated by regulatory factors that are also involved in the response to other stressors. These have included Msn2/4, Crz1, Yap1, and Mga2, thus suggesting that light stress is a common factor in the yeast environmental response.
Collapse
Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Cristina Mazzoni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Michele Maria Bianchi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| |
Collapse
|
11
|
Leite AC, Barbedo M, Costa V, Pereira C. The APC/C Activator Cdh1p Plays a Role in Mitochondrial Metabolic Remodelling in Yeast. Int J Mol Sci 2023; 24:ijms24044111. [PMID: 36835555 PMCID: PMC9967508 DOI: 10.3390/ijms24044111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Cdh1p is one of the two substrate adaptor proteins of the anaphase promoting complex/cyclosome (APC/C), a ubiquitin ligase that regulates proteolysis during cell cycle. In this work, using a proteomic approach, we found 135 mitochondrial proteins whose abundance was significantly altered in the cdh1Δ mutant, with 43 up-regulated proteins and 92 down-regulated proteins. The group of significantly up-regulated proteins included subunits of the mitochondrial respiratory chain, enzymes from the tricarboxylic acid cycle and regulators of mitochondrial organization, suggesting a metabolic remodelling towards an increase in mitochondrial respiration. In accordance, mitochondrial oxygen consumption and Cytochrome c oxidase activity increased in Cdh1p-deficient cells. These effects seem to be mediated by the transcriptional activator Yap1p, a major regulator of the yeast oxidative stress response. YAP1 deletion suppressed the increased Cyc1p levels and mitochondrial respiration in cdh1Δ cells. In agreement, Yap1p is transcriptionally more active in cdh1Δ cells and responsible for the higher oxidative stress tolerance of cdh1Δ mutant cells. Overall, our results unveil a new role for APC/C-Cdh1p in the regulation of the mitochondrial metabolic remodelling through Yap1p activity.
Collapse
Affiliation(s)
- Ana Cláudia Leite
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Maria Barbedo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Vítor Costa
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Clara Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-220408800
| |
Collapse
|
12
|
Takhaveev V, Özsezen S, Smith EN, Zylstra A, Chaillet ML, Chen H, Papagiannakis A, Milias-Argeitis A, Heinemann M. Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle. Nat Metab 2023; 5:294-313. [PMID: 36849832 PMCID: PMC9970877 DOI: 10.1038/s42255-023-00741-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Many cell biological and biochemical mechanisms controlling the fundamental process of eukaryotic cell division have been identified; however, the temporal dynamics of biosynthetic processes during the cell division cycle are still elusive. Here, we show that key biosynthetic processes are temporally segregated along the cell cycle. Using budding yeast as a model and single-cell methods to dynamically measure metabolic activity, we observe two peaks in protein synthesis, in the G1 and S/G2/M phase, whereas lipid and polysaccharide synthesis peaks only once, during the S/G2/M phase. Integrating the inferred biosynthetic rates into a thermodynamic-stoichiometric metabolic model, we find that this temporal segregation in biosynthetic processes causes flux changes in primary metabolism, with an acceleration of glucose-uptake flux in G1 and phase-shifted oscillations of oxygen and carbon dioxide exchanges. Through experimental validation of the model predictions, we demonstrate that primary metabolism oscillates with cell-cycle periodicity to satisfy the changing demands of biosynthetic processes exhibiting unexpected dynamics during the cell cycle.
Collapse
Affiliation(s)
- Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Serdar Özsezen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, The Netherlands
| | - Edward N Smith
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andre Zylstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marten L Chaillet
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Haoqi Chen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biology and Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
13
|
Rödl S, den Brave F, Räschle M, Kizmaz B, Lenhard S, Groh C, Becker H, Zimmermann J, Morgan B, Richling E, Becker T, Herrmann JM. The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import. Life Sci Alliance 2022; 6:6/1/e202201526. [PMID: 36253107 PMCID: PMC9579816 DOI: 10.26508/lsa.202201526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022] Open
Abstract
Mitochondria play a key role in cellular energy metabolism. Transitions between glycolytic and respiratory conditions induce considerable adaptations of the cellular proteome. These metabolism-dependent changes are particularly pronounced for the protein composition of mitochondria. Here, we show that the yeast cytosolic ubiquitin conjugase Ubc8 plays a crucial role in the remodeling process when cells transition from respiratory to fermentative conditions. Ubc8 is a conserved and well-studied component of the catabolite control system that is known to regulate the stability of gluconeogenic enzymes. Unexpectedly, we found that Ubc8 also promotes the assembly of the translocase of the outer membrane of mitochondria (TOM) and increases the levels of its cytosol-exposed receptor subunit Tom22. Ubc8 deficiency results in compromised protein import into mitochondria and reduced steady-state levels of mitochondrial proteins. Our observations show that Ubc8, which is controlled by the prevailing metabolic conditions, promotes the switch from glucose synthesis to glucose usage in the cytosol and induces the biogenesis of the mitochondrial TOM machinery to improve mitochondrial protein import during phases of metabolic transition.
Collapse
Affiliation(s)
- Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Hanna Becker
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jannik Zimmermann
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Bruce Morgan
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Elke Richling
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | | |
Collapse
|
14
|
Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data. mSystems 2022; 7:e0134721. [PMID: 35695574 PMCID: PMC9239220 DOI: 10.1128/msystems.01347-21] [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] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae undergoes robust oscillations to regulate its physiology for adaptation and survival under nutrient-limited conditions. Environmental cues can induce rhythmic metabolic alterations in order to facilitate the coordination of dynamic metabolic behaviors. Of such metabolic processes, the yeast metabolic cycle enables adaptation of the cells to varying nutritional status through oscillations in gene expression and metabolite production levels. In this process, yeast metabolism is altered between diverse cellular states based on changing oxygen consumption levels: quiescent (reductive charging [RC]), growth (oxidative [OX]), and proliferation (reductive building [RB]) phases. We characterized metabolic alterations during the yeast metabolic cycle using a variety of approaches. Gene expression levels are widely used for condition-specific metabolic simulations, whereas the use of epigenetic information in metabolic modeling is still limited despite the clear relationship between epigenetics and metabolism. This prompted us to investigate the contribution of epigenomic information to metabolic predictions for progression of the yeast metabolic cycle. In this regard, we determined altered pathways through the prediction of regulated reactions and corresponding model genes relying on differential chromatin accessibility levels. The predicted metabolic alterations were confirmed via data analysis and literature. We subsequently utilized RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data sets in the contextualization of the yeast model. The use of ATAC-seq data considerably enhanced the predictive capability of the model. To the best of our knowledge, this is the first attempt to use genome-wide chromatin accessibility data in metabolic modeling. The preliminary results showed that epigenomic data sets can pave the way for more accurate metabolic simulations. IMPORTANCE Dynamic chromatin organization mediates the emergence of condition-specific phenotypes in eukaryotic organisms. Saccharomyces cerevisiae can alter its metabolic profile via regulation of genome accessibility and robust transcriptional oscillations under nutrient-limited conditions. Thus, both epigenetic information and transcriptomic information are crucial in the understanding of condition-specific metabolic behavior in this organism. Based on genome-wide alterations in chromatin accessibility and transcription, we investigated the yeast metabolic cycle, which is a remarkable example of coordinated and dynamic yeast behavior. In this regard, we assessed the use of ATAC-seq and RNA-seq data sets in condition-specific metabolic modeling. To our knowledge, this is the first attempt to use chromatin accessibility data in the reconstruction of context-specific metabolic models, despite the extensive use of transcriptomic data. As a result of comparative analyses, we propose that the incorporation of epigenetic information is a promising approach in the accurate prediction of metabolic dynamics.
Collapse
|
15
|
Li L, Wang J, Yang Z, Zhao Y, Jiang H, Jiang L, Hou W, Ye R, He Q, Kupiec M, Luke B, Cao Q, Qi Z, Li Z, Lou H. Metabolic remodeling maintains a reducing environment for rapid activation of the yeast DNA replication checkpoint. EMBO J 2022; 41:e108290. [PMID: 35028974 PMCID: PMC8844976 DOI: 10.15252/embj.2021108290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022] Open
Abstract
Nucleotide metabolism fuels normal DNA replication and is also primarily targeted by the DNA replication checkpoint when replication stalls. To reveal a comprehensive interconnection between genome maintenance and metabolism, we analyzed the metabolomic changes upon replication stress in the budding yeast S. cerevisiae. We found that upon treatment of cells with hydroxyurea, glucose is rapidly diverted to the oxidative pentose phosphate pathway (PPP). This effect is mediated by the AMP-dependent kinase, SNF1, which phosphorylates the transcription factor Mig1, thereby relieving repression of the gene encoding the rate-limiting enzyme of the PPP. Surprisingly, NADPH produced by the PPP is required for efficient recruitment of replication protein A (RPA) to single-stranded DNA, providing the signal for the activation of the Mec1/ATR-Rad53/CHK1 checkpoint signaling kinase cascade. Thus, SNF1, best known as a central energy controller, determines a fast mode of replication checkpoint activation through a redox mechanism. These findings establish that SNF1 provides a hub with direct links to cellular metabolism, redox, and surveillance of DNA replication in eukaryotes.
Collapse
Affiliation(s)
- Lili Li
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jie Wang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zijia Yang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yiling Zhao
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Hui Jiang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Luguang Jiang
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Maize Improvement Center of ChinaCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wenya Hou
- Shenzhen University General HospitalGuangdong Key Laboratory for Genome Stability and Disease PreventionShenzhen University School of MedicineShenzhenChina
| | - Risheng Ye
- Department of Medical EducationTexas Tech University Health Sciences Center Paul L. Foster School of MedicineEl PasoTXUSA
| | - Qun He
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer ResearchTel Aviv UniversityRamat AvivIsrael
| | - Brian Luke
- Institute of Molecular Biology (IMB)MainzGermany,Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversitätMainzGermany
| | - Qinhong Cao
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhi Qi
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Zhen Li
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Huiqiang Lou
- South China HospitalHealth Science CenterGuangdong Key Laboratory of Genome Instability and Disease PreventionShenzhen University School of MedicineShenzhenChina
| |
Collapse
|
16
|
Liu J, Peng Y, Wei W. Cell cycle on the crossroad of tumorigenesis and cancer therapy. Trends Cell Biol 2022; 32:30-44. [PMID: 34304958 PMCID: PMC8688170 DOI: 10.1016/j.tcb.2021.07.001] [Citation(s) in RCA: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Aberrancy in cell cycle progression is one of the fundamental mechanisms underlying tumorigenesis, making regulators of the cell cycle machinery rational anticancer therapeutic targets. A growing body of evidence indicates that the cell cycle regulatory pathway integrates into other hallmarks of cancer, including metabolism remodeling and immune escape. Thus, therapies against cell cycle machinery components can not only repress the division of cancer cells, but also reverse cancer metabolism and restore cancer immune surveillance. Besides the ongoing effects on the development of small molecule inhibitors (SMIs) of the cell cycle machinery, proteolysis targeting chimeras (PROTACs) have recently been used to target these oncogenic proteins related to cell cycle progression. Here, we discuss the rationale of cell cycle targeting therapies, particularly PROTACs, to more efficiently retard tumorigenesis.
Collapse
Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| |
Collapse
|
17
|
Musiol R, Malecki P, Pacholczyk M, Mularski J. Terpyridines as promising antitumor agents: an overview of their discovery and development. Expert Opin Drug Discov 2021; 17:259-271. [PMID: 34928186 DOI: 10.1080/17460441.2022.2017877] [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] [Indexed: 02/04/2023]
Abstract
INTRODUCTION The fused aromatic system of terpyridines makes them good, innocent ligands for various metals. The resulting complexes have been extensively studied for both their biological activity and physico-chemical properties. However, although free ligands also have an interesting biological activity, their share in recent research is considerably limited. AREAS COVERED This review covers the literature on the anticancer activity of terpyridines with special attention being paid to their use as free ligands. Whenever possible, the mechanism of action has been discussed, thereby providing evidence of the substantial differences between sole ligands or less stable complexes and those that have heavier elements. EXPERT OPINION The existing literature indicates that there is a specific attitude for investigating terpyridines and their transition metal complexes. While the latter have been well explored and recognized in the scientific community, the free terpyridines are considered to be useful solely due to their complexing ability. At the same time, terpyridines could have similar or even higher anticancer potency than their complexes. Moreover, a mechanistic analysis of the stability and intracellular activity would provide information that would be useful for designing new drugs.
Collapse
Affiliation(s)
- Robert Musiol
- Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 7, Katowice, Poland
| | | | - Marcin Pacholczyk
- Department of Systems Biology and Engineering, Silesian University of Technology, Akademicka 16, Gliwice, Poland
| | - Jacek Mularski
- Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 7, Katowice, Poland
| |
Collapse
|
18
|
Brown MR, Sen SK, Mazzone A, Her TK, Xiong Y, Lee JH, Javeed N, Colwell CS, Rakshit K, LeBrasseur NK, Gaspar-Maia A, Ordog T, Matveyenko AV. Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β cell function. SCIENCE ADVANCES 2021; 7:eabg6856. [PMID: 34910509 PMCID: PMC8673777 DOI: 10.1126/sciadv.abg6856] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 10/28/2021] [Indexed: 05/30/2023]
Abstract
Circadian rhythm disruption (CD) is associated with impaired glucose homeostasis and type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates metabolic dysfunction. Here, we used an approach encompassing analysis of behavioral, physiological, transcriptomic, and epigenomic effects of CD and consequences of restoring fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β cell function and loss of circadian transcriptional and epigenetic identity. In contrast, restoration of fasting/feeding cycle prevented CD-mediated dysfunction by reestablishing circadian regulation of glucose tolerance, β cell function, transcriptional profile, and reestablishment of proline and acidic amino acid–rich basic leucine zipper (PAR bZIP) transcription factor DBP expression/activity. This study provides mechanistic insights into circadian regulation of β cell function and corresponding beneficial effects of tRF in prevention of T2DM.
Collapse
Affiliation(s)
- Matthew R. Brown
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Satish K. Sen
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Amelia Mazzone
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tracy K. Her
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Yuning Xiong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Jeong-Heon Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Naureen Javeed
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Christopher S. Colwell
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kuntol Rakshit
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Nathan K. LeBrasseur
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Alexandre Gaspar-Maia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Aleksey V. Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| |
Collapse
|
19
|
Prathom K, Young TR. Universality of stable multi-cluster periodic solutions in a population model of the cell cycle with negative feedback. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:455-522. [PMID: 34490835 DOI: 10.1080/17513758.2021.1971781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
We study a population model where cells in one part of the cell cycle may affect the progress of cells in another part. If the influence, or feedback, from one part to another is negative, simulations of the model almost always result in multiple temporal clusters formed by groups of cells. We study regions in parameter space where periodic 'k-cyclic' solutions are stable. The regions of stability coincide with sub-triangles on which certain events occur in a fixed order. For boundary sub-triangles with order 'rs1', we prove that the k-cyclic periodic solution is asymptotically stable if the index of the sub-triangle is relatively prime with respect to the number of clusters k and neutrally stable otherwise. For negative linear feedback, we prove that the interior of the parameter set is covered by stable sub-triangles, i.e. a stable k-cyclic solution always exists for some k. We observe numerically that the result also holds for many forms of nonlinear feedback, but may break down in extreme cases.
Collapse
|
20
|
Levine DC, Ramsey KM, Bass J. Circadian NAD(P)(H) cycles in cell metabolism. Semin Cell Dev Biol 2021; 126:15-26. [PMID: 34281771 DOI: 10.1016/j.semcdb.2021.07.008] [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: 03/31/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Intrinsic circadian clocks are present in all forms of photosensitive life, enabling daily anticipation of the light/dark cycle and separation of energy storage and utilization cycles on a 24-h timescale. The core mechanism underlying circadian rhythmicity involves a cell-autonomous transcription/translation feedback loop that in turn drives rhythmic organismal physiology. In mammals, genetic studies have established that the core clock plays an essential role in maintaining metabolic health through actions within both brain pacemaker neurons and peripheral tissues and that disruption of the clock contributes to disease. Peripheral clocks, in turn, can be entrained by metabolic cues. In this review, we focus on the role of the nucleotide NAD(P)(H) and NAD+-dependent sirtuin deacetylases as integrators of circadian and metabolic cycles, as well as the implications for this interrelationship in healthful aging.
Collapse
Affiliation(s)
- Daniel C Levine
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn M Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
21
|
|
22
|
Peroxiredoxins couple metabolism and cell division in an ultradian cycle. Nat Chem Biol 2021; 17:477-484. [PMID: 33574615 DOI: 10.1038/s41589-020-00728-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Redox cycles have been reported in ultradian, circadian and cell cycle-synchronized systems. Redox cycles persist in the absence of transcription and cyclin-CDK activity, indicating that cells harbor multiple coupled oscillators. Nonetheless, the causal relationships and molecular mechanisms by which redox cycles are embedded within ultradian, circadian or cell division cycles remain largely elusive. Yeast harbor an ultradian oscillator, the yeast metabolic cycle (YMC), which comprises metabolic/redox cycles, transcriptional cycles and synchronized cell division. Here, we reveal the existence of robust cycling of H2O2 and peroxiredoxin oxidation during the YMC and show that peroxiredoxin inactivation disrupts metabolic cycling and abolishes coupling with cell division. We find that thiol-disulfide oxidants and reductants predictably modulate the switching between different YMC metabolic states, which in turn predictably perturbs cell cycle entry and exit. We propose that oscillatory H2O2-dependent protein thiol oxidation is a key regulator of metabolic cycling and its coordination with cell division.
Collapse
|
23
|
Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE. New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics 2021; 217:6117222. [PMID: 33681970 DOI: 10.1093/genetics/iyab007] [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: 03/15/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
Collapse
Affiliation(s)
- Manon Quiquand
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nan Qiao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chunyu Zhao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Matthew Slattery
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jackie J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
24
|
Bruhn C, Ajazi A, Ferrari E, Lanz MC, Batrin R, Choudhary R, Walvekar A, Laxman S, Longhese MP, Fabre E, Smolka MB, Foiani M. The Rad53 CHK1/CHK2-Spt21 NPAT and Tel1 ATM axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nat Commun 2020; 11:4154. [PMID: 32814778 PMCID: PMC7438486 DOI: 10.1038/s41467-020-17961-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
The DNA damage response (DDR) coordinates DNA metabolism with nuclear and non-nuclear processes. The DDR kinase Rad53CHK1/CHK2 controls histone degradation to assist DNA repair. However, Rad53 deficiency causes histone-dependent growth defects in the absence of DNA damage, pointing out unknown physiological functions of the Rad53-histone axis. Here we show that histone dosage control by Rad53 ensures metabolic homeostasis. Under physiological conditions, Rad53 regulates histone levels through inhibitory phosphorylation of the transcription factor Spt21NPAT on Ser276. Rad53-Spt21 mutants display severe glucose dependence, caused by excess histones through two separable mechanisms: dampening of acetyl-coenzyme A-dependent carbon metabolism through histone hyper-acetylation, and Sirtuin-mediated silencing of starvation-induced subtelomeric domains. We further demonstrate that repression of subtelomere silencing by physiological Tel1ATM and Rpd3HDAC activities coveys tolerance to glucose restriction. Our findings identify DDR mutations, histone imbalances and aberrant subtelomeric chromatin as interconnected causes of glucose dependence, implying that DDR kinases coordinate metabolism and epigenetic changes.
Collapse
Affiliation(s)
- Christopher Bruhn
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
| | - Arta Ajazi
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Elisa Ferrari
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Ramveer Choudhary
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Adhish Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Edificio U3, Piazza della Scienza 2, 20126, Milan, Italy
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Marcus Bustamente Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marco Foiani
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
- Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy.
| |
Collapse
|
25
|
Cell-cycle-dependent phosphorylation of RRM1 ensures efficient DNA replication and regulates cancer vulnerability to ATR inhibition. Oncogene 2020; 39:5721-5733. [PMID: 32712628 DOI: 10.1038/s41388-020-01403-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 11/08/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate-limiting step of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs) building blocks for DNA synthesis, and is a well-recognized target for cancer therapy. RNR is a heterotetramer consisting of two large RRM1 subunits and two small RRM2 subunits. RNR activity is greatly stimulated by transcriptional activation of RRM2 during S/G2 phase to ensure adequate dNTP supply for DNA replication. However, little is known about the cell-cycle-dependent regulation of RNR activity through RRM1. Here, we report that RRM1 is phosphorylated at Ser 559 by CDK2/cyclin A during S/G2 phase. And this S559 phosphorylation of RRM1enhances RNR enzymatic activity and is required for maintaining sufficient dNTPs during normal DNA replication. Defective RRM1 S559 phosphorylation causes DNA replication stress, double-strand break, and genomic instability. Moreover, combined targeting of RRM1 S559 phosphorylation and ATR triggers lethal replication stress and profound antitumor effects. Thus, this posttranslational phosphorylation of RRM1 provides an alternative mechanism to finely regulating RNR and therapeutic opportunities for cancer treatment.
Collapse
|
26
|
Liu J, Peng Y, Shi L, Wan L, Inuzuka H, Long J, Guo J, Zhang J, Yuan M, Zhang S, Wang X, Gao J, Dai X, Furumoto S, Jia L, Pandolfi PP, Asara JM, Kaelin WG, Liu J, Wei W. Skp2 dictates cell cycle-dependent metabolic oscillation between glycolysis and TCA cycle. Cell Res 2020; 31:80-93. [PMID: 32669607 DOI: 10.1038/s41422-020-0372-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Whether glucose is predominantly metabolized via oxidative phosphorylation or glycolysis differs between quiescent versus proliferating cells, including tumor cells. However, how glucose metabolism is coordinated with cell cycle in mammalian cells remains elusive. Here, we report that mammalian cells predominantly utilize the tricarboxylic acid (TCA) cycle in G1 phase, but prefer glycolysis in S phase. Mechanistically, coupling cell cycle with metabolism is largely achieved by timely destruction of IDH1/2, key TCA cycle enzymes, in a Skp2-dependent manner. As such, depleting SKP2 abolishes cell cycle-dependent fluctuation of IDH1 protein abundance, leading to reduced glycolysis in S phase. Furthermore, elevated Skp2 abundance in prostate cancer cells destabilizes IDH1 to favor glycolysis and subsequent tumorigenesis. Therefore, our study reveals a mechanistic link between two cancer hallmarks, aberrant cell cycle and addiction to glycolysis, and provides the underlying mechanism for the coupling of metabolic fluctuation with periodic cell cycle in mammalian cells.
Collapse
Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.,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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Yunhua Peng
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Le Shi
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Lixin Wan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.,Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jiangang Long
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.,Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.,Medical Research Institute, School of Medicine, Wuhan University, Wuhan, Hubei, 430071, China
| | - Min Yuan
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Shuangxi Zhang
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Xun Wang
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.,Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jing Gao
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Shozo Furumoto
- Division of Radiopharmaceutical Chemistry, Cyclotron and Radioisotope Center, Tohoku University, Sendai, 980-8578, Japan
| | - Lijun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Pier Paolo Pandolfi
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - John M Asara
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - William G Kaelin
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jiankang Liu
- 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 Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| |
Collapse
|
27
|
Caldez MJ, Bjorklund M, Kaldis P. Cell cycle regulation in NAFLD: when imbalanced metabolism limits cell division. Hepatol Int 2020; 14:463-474. [PMID: 32578019 PMCID: PMC7366567 DOI: 10.1007/s12072-020-10066-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022]
Abstract
Cell division is essential for organismal growth and tissue homeostasis. It is exceptionally significant in tissues chronically exposed to intrinsic and external damage, like the liver. After decades of studying the regulation of cell cycle by extracellular signals, there are still gaps in our knowledge on how these two interact with metabolic pathways in vivo. Studying the cross-talk of these pathways has direct clinical implications as defects in cell division, signaling pathways, and metabolic homeostasis are frequently observed in liver diseases. In this review, we will focus on recent reports which describe various functions of cell cycle regulators in hepatic homeostasis. We will describe the interplay between the cell cycle and metabolism during liver regeneration after acute and chronic damage. We will focus our attention on non-alcoholic fatty liver disease, especially non-alcoholic steatohepatitis. The global incidence of non-alcoholic fatty liver disease is increasing exponentially. Therefore, understanding the interplay between cell cycle regulators and metabolism may lead to the discovery of novel therapeutic targets amenable to intervention.
Collapse
Affiliation(s)
- Matias J Caldez
- WPI Immunology Frontiers Research Centre, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Mikael Bjorklund
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute and 2nd Affiliated Hospital, Zhejiang University School of Medicine, 718 East Haizhou Rd., Haining, 314400, Zhejiang, People's Republic of China
| | - Philipp Kaldis
- Department of Clinical Sciences, Clinical Research Centre (CRC), Lund University, Box 50332, 202 13, Malmö, Sweden.
| |
Collapse
|
28
|
Morrison AJ. Chromatin-remodeling links metabolic signaling to gene expression. Mol Metab 2020; 38:100973. [PMID: 32251664 PMCID: PMC7300377 DOI: 10.1016/j.molmet.2020.100973] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND ATP-dependent chromatin remodelers are evolutionarily conserved complexes that alter nucleosome positioning to influence many DNA-templated processes, such as replication, repair, and transcription. In particular, chromatin remodeling can dynamically regulate gene expression by altering accessibility of chromatin to transcription factors. SCOPE OF REVIEW This review provides an overview of the importance of chromatin remodelers in the regulation of metabolic gene expression. Particular emphasis is placed on the INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers in both yeast and mammals. This review details discoveries from the initial identification of chromatin remodelers in Saccharomyces cerevisiae to recent discoveries in the metabolic requirements of developing embryonic tissues in mammals. MAJOR CONCLUSIONS INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers regulate the expression of energy metabolism pathways in S. cerevisiae and mammals in response to diverse nutrient environments. In particular, the INO80 complex organizes the temporal expression of gene expression in the metabolically synchronized S. cerevisiae system. INO80-mediated chromatin remodeling is also needed to constrain cell division during metabolically favorable conditions. Conversely, the BAF/PBAF remodeler regulates tissue-specific glycolytic metabolism and is disrupted in cancers that are dependent on glycolysis for proliferation. The role of chromatin remodeling in metabolic gene expression is downstream of the metabolic signaling pathways, such as the TOR pathway, a critical regulator of metabolic homeostasis. Furthermore, the INO80 and BAF/PBAF chromatin remodelers have both been shown to regulate heart development, the tissues of which have unique requirements for energy metabolism during development. Collectively, these results demonstrate that chromatin remodelers communicate metabolic status to chromatin and are a central component of homeostasis pathways that optimize cell fitness, organismal development, and prevent disease.
Collapse
Affiliation(s)
- Ashby J Morrison
- Department of Biology, Stanford University, Stanford CA 94305, USA.
| |
Collapse
|
29
|
Hartl J, Kiefer P, Kaczmarczyk A, Mittelviefhaus M, Meyer F, Vonderach T, Hattendorf B, Jenal U, Vorholt JA. Untargeted metabolomics links glutathione to bacterial cell cycle progression. Nat Metab 2020; 2:153-166. [PMID: 32090198 PMCID: PMC7035108 DOI: 10.1038/s42255-019-0166-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
Abstract
Cell cycle progression requires the coordination of cell growth, chromosome replication, and division. Consequently, a functional cell cycle must be coupled with metabolism. However, direct measurements of metabolome dynamics remained scarce, in particular in bacteria. Here, we describe an untargeted metabolomics approach with synchronized Caulobacter crescentus cells to monitor the relative abundance changes of ~400 putative metabolites as a function of the cell cycle. While the majority of metabolite pools remains homeostatic, ~14% respond to cell cycle progression. In particular, sulfur metabolism is redirected during the G1-S transition, and glutathione levels periodically change over the cell cycle with a peak in late S phase. A lack of glutathione perturbs cell size by uncoupling cell growth and division through dysregulation of KefB, a K+/H+ antiporter. Overall, we here describe the impact of the C. crescentus cell cycle progression on metabolism, and in turn relate glutathione and potassium homeostasis to timely cell division.
Collapse
Affiliation(s)
- Johannes Hartl
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland.
| | - Patrick Kiefer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | | | | | - Fabian Meyer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | - Thomas Vonderach
- ETH Zurich, Laboratory of Inorganic Chemistry, Zurich, Switzerland
| | - Bodo Hattendorf
- ETH Zurich, Laboratory of Inorganic Chemistry, Zurich, Switzerland
| | - Urs Jenal
- Biozentrum of the University of Basel, Basel, Switzerland
| | | |
Collapse
|
30
|
Abstract
During sleep, animals do not eat, reproduce or forage. Sleeping animals are vulnerable to predation. Yet, the persistence of sleep despite evolutionary pressures, and the deleterious effects of sleep deprivation, indicate that sleep serves a function or functions that cannot easily be bypassed. Recent research demonstrates sleep to be phylogenetically far more pervasive than previously appreciated; it is possible that the very first animals slept. Here, we give an overview of sleep across various species, with the aim of determining its original purpose. Sleep exists in animals without cephalized nervous systems and can be influenced by non-neuronal signals, including those associated with metabolic rhythms. Together, these observations support the notion that sleep serves metabolic functions in neural and non-neural tissues.
Collapse
Affiliation(s)
- Ron C Anafi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center for Sleep and Circadian Neurobiology and the Program for Chronobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew S Kayser
- Center for Sleep and Circadian Neurobiology and the Program for Chronobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Psychiatry and Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David M Raizen
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Center for Sleep and Circadian Neurobiology and the Program for Chronobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
31
|
Ter Beek J, Parkash V, Bylund GO, Osterman P, Sauer-Eriksson AE, Johansson E. Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ϵ. Nucleic Acids Res 2019; 47:5712-5722. [PMID: 30968138 PMCID: PMC6582351 DOI: 10.1093/nar/gkz248] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 03/10/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
DNA polymerase ϵ (Pol ϵ), the major leading-strand DNA polymerase in eukaryotes, has a catalytic subunit (Pol2) and three non-catalytic subunits. The N-terminal half of Pol2 (Pol2CORE) exhibits both polymerase and exonuclease activity. It has been suggested that both the non-catalytic C-terminal domain of Pol2 (with the two cysteine motifs CysA and CysB) and Pol2CORE (with the CysX cysteine motif) are likely to coordinate an Fe–S cluster. Here, we present two new crystal structures of Pol2CORE with an Fe–S cluster bound to the CysX motif, supported by an anomalous signal at that position. Furthermore we show that purified four-subunit Pol ϵ, Pol ϵ CysAMUT (C2111S/C2133S), and Pol ϵ CysBMUT (C2167S/C2181S) all have an Fe–S cluster that is not present in Pol ϵ CysXMUT (C665S/C668S). Pol ϵ CysAMUT and Pol ϵ CysBMUT behave similarly to wild-type Pol ϵ in in vitro assays, but Pol ϵ CysXMUT has severely compromised DNA polymerase activity that is not the result of an excessive exonuclease activity. Tetrad analyses show that haploid yeast strains carrying CysXMUT are inviable. In conclusion, Pol ϵ has a single Fe–S cluster bound at the base of the P-domain, and this Fe–S cluster is essential for cell viability and polymerase activity.
Collapse
Affiliation(s)
- Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| | - Vimal Parkash
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| | - Göran O Bylund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| | - Pia Osterman
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| | | | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| |
Collapse
|
32
|
INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division. Cell Rep 2019; 22:611-623. [PMID: 29346761 PMCID: PMC5949282 DOI: 10.1016/j.celrep.2017.12.079] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states.
Collapse
|
33
|
Miyagishima SY, Era A, Hasunuma T, Matsuda M, Hirooka S, Sumiya N, Kondo A, Fujiwara T. Day/Night Separation of Oxygenic Energy Metabolism and Nuclear DNA Replication in the Unicellular Red Alga Cyanidioschyzon merolae. mBio 2019; 10:e00833-19. [PMID: 31266864 PMCID: PMC6606799 DOI: 10.1128/mbio.00833-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
The transition from G1 to S phase and subsequent nuclear DNA replication in the cells of many species of eukaryotic algae occur predominantly during the evening and night in the absence of photosynthesis; however, little is known about how day/night changes in energy metabolism and cell cycle progression are coordinated and about the advantage conferred by the restriction of S phase to the night. Using a synchronous culture of the unicellular red alga Cyanidioschyzon merolae, we found that the levels of photosynthetic and respiratory activities peak during the morning and then decrease toward the evening and night, whereas the pathways for anaerobic consumption of pyruvate, produced by glycolysis, are upregulated during the evening and night as reported recently in the green alga Chlamydomonas reinhardtii Inhibition of photosynthesis by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) largely reduced respiratory activity and the amplitude of the day/night rhythm of respiration, suggesting that the respiratory rhythm depends largely on photosynthetic activity. Even when the timing of G1/S-phase transition was uncoupled from the day/night rhythm by depletion of retinoblastoma-related (RBR) protein, the same patterns of photosynthesis and respiration were observed, suggesting that cell cycle progression and energy metabolism are regulated independently. Progression of the S phase under conditions of photosynthesis elevated the frequency of nuclear DNA double-strand breaks (DSB). These results suggest that the temporal separation of oxygenic energy metabolism, which causes oxidative stress, from nuclear DNA replication reduces the risk of DSB during cell proliferation in C. merolaeIMPORTANCE Eukaryotes acquired chloroplasts through an endosymbiotic event in which a cyanobacterium or a unicellular eukaryotic alga was integrated into a previously nonphotosynthetic eukaryotic cell. Photosynthesis by chloroplasts enabled algae to expand their habitats and led to further evolution of land plants. However, photosynthesis causes greater oxidative stress than mitochondrion-based respiration. In seed plants, cell division is restricted to nonphotosynthetic meristematic tissues and populations of photosynthetic cells expand without cell division. Thus, seemingly, photosynthesis is spatially sequestrated from cell proliferation. In contrast, eukaryotic algae possess photosynthetic chloroplasts throughout their life cycle. Here we show that oxygenic energy conversion (daytime) and nuclear DNA replication (night time) are temporally sequestrated in C. merolae This sequestration enables "safe" proliferation of cells and allows coexistence of chloroplasts and the eukaryotic host cell, as shown in yeast, where mitochondrial respiration and nuclear DNA replication are temporally sequestrated to reduce the mutation rate.
Collapse
Affiliation(s)
- Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Atsuko Era
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Nada, Kobe, Japan
- Engineering Biology Research Center, Kobe University, Nada, Kobe, Japan
| | - Mami Matsuda
- Engineering Biology Research Center, Kobe University, Nada, Kobe, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Nobuko Sumiya
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Nada, Kobe, Japan
- Engineering Biology Research Center, Kobe University, Nada, Kobe, Japan
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| |
Collapse
|
34
|
Gupta R, Walvekar AS, Liang S, Rashida Z, Shah P, Laxman S. A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis. eLife 2019; 8:e44795. [PMID: 31259691 PMCID: PMC6688859 DOI: 10.7554/elife.44795] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/30/2019] [Indexed: 12/21/2022] Open
Abstract
Cells must appropriately sense and integrate multiple metabolic resources to commit to proliferation. Here, we report that S. cerevisiae cells regulate carbon and nitrogen metabolic homeostasis through tRNA U34-thiolation. Despite amino acid sufficiency, tRNA-thiolation deficient cells appear amino acid starved. In these cells, carbon flux towards nucleotide synthesis decreases, and trehalose synthesis increases, resulting in a starvation-like metabolic signature. Thiolation mutants have only minor translation defects. However, in these cells phosphate homeostasis genes are strongly down-regulated, resulting in an effectively phosphate-limited state. Reduced phosphate enforces a metabolic switch, where glucose-6-phosphate is routed towards storage carbohydrates. Notably, trehalose synthesis, which releases phosphate and thereby restores phosphate availability, is central to this metabolic rewiring. Thus, cells use thiolated tRNAs to perceive amino acid sufficiency, balance carbon and amino acid metabolic flux and grow optimally, by controlling phosphate availability. These results further biochemically explain how phosphate availability determines a switch to a 'starvation-state'.
Collapse
Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Adhish S Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Shun Liang
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Premal Shah
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| |
Collapse
|
35
|
Westwood ML, O'Donnell AJ, de Bekker C, Lively CM, Zuk M, Reece SE. The evolutionary ecology of circadian rhythms in infection. Nat Ecol Evol 2019; 3:552-560. [PMID: 30886375 PMCID: PMC7614806 DOI: 10.1038/s41559-019-0831-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/30/2019] [Indexed: 01/05/2023]
Abstract
Biological rhythms coordinate organisms' activities with daily rhythms in the environment. For parasites, this includes rhythms in both the external abiotic environment and the within-host biotic environment. Hosts exhibit rhythms in behaviours and physiologies, including immune responses, and parasites exhibit rhythms in traits underpinning virulence and transmission. Yet, the evolutionary and ecological drivers of rhythms in traits underpinning host defence and parasite offence are largely unknown. Here, we explore how hosts use rhythms to defend against infection, why parasites have rhythms and whether parasites can manipulate host clocks to their own ends. Harnessing host rhythms or disrupting parasite rhythms could be exploited for clinical benefit; we propose an interdisciplinary effort to drive this emerging field forward.
Collapse
Affiliation(s)
- Mary L Westwood
- Institute of Evolutionary Biology and Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Aidan J O'Donnell
- Institute of Evolutionary Biology and Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Curtis M Lively
- Department of Biology, Indiana University, Bloomington, IL, USA
| | - Marlene Zuk
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
| | - Sarah E Reece
- Institute of Evolutionary Biology and Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
36
|
Nouri H, Monnier AF, Fossum-Raunehaug S, Maciag-Dorszynska M, Cabin-Flaman A, Képès F, Wegrzyn G, Szalewska-Palasz A, Norris V, Skarstad K, Janniere L. Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis. DNA Res 2019; 25:641-653. [PMID: 30256918 PMCID: PMC6289782 DOI: 10.1093/dnares/dsy031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/17/2018] [Indexed: 12/27/2022] Open
Abstract
DNA replication is coupled to growth by an unknown mechanism. Here, we investigated this coupling by analyzing growth and replication in 15 mutants of central carbon metabolism (CCM) cultivated in three rich media. In about one-fourth of the condition tested, defects in replication resulting from changes in initiation or elongation were detected. This uncovered 11 CCM genes important for replication and showed that some of these genes have an effect in one, two or three media. Additional results presented here and elsewhere (Jannière, L., Canceill, D., Suski, C., et al. (2007), PLoS One, 2, e447.) showed that, in the LB medium, the CCM genes important for DNA elongation (gapA and ackA) are genetically linked to the lagging strand polymerase DnaE while those important for initiation (pgk and pykA) are genetically linked to the replication enzymes DnaC (helicase), DnaG (primase) and DnaE. Our work thus shows that the coupling between growth and replication involves multiple, medium-dependent links between CCM and replication. They also suggest that changes in CCM may affect initiation by altering the functional recruitment of DnaC, DnaG and DnaE at the chromosomal origin, and may affect elongation by altering the activity of DnaE at the replication fork. The underlying mechanism is discussed.
Collapse
Affiliation(s)
- Hamid Nouri
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France.,MICALIS, INRA, Jouy en Josas, France
| | | | | | | | | | - François Képès
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Vic Norris
- Laboratoire MERCI, AMMIS, Faculté des Sciences, Mont-Saint-Aignan, France
| | - Kirsten Skarstad
- Department of Cell Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Laurent Janniere
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France.,MICALIS, INRA, Jouy en Josas, France
| |
Collapse
|
37
|
Bokhari B, Sharma S. Stress Marks on the Genome: Use or Lose? Int J Mol Sci 2019; 20:ijms20020364. [PMID: 30654540 PMCID: PMC6358951 DOI: 10.3390/ijms20020364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/31/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Oxidative stress and the resulting damage to DNA are inevitable consequence of endogenous physiological processes further amplified by cellular responses to environmental exposures. If left unrepaired, oxidative DNA lesions can block essential processes such as transcription and replication or can induce mutations. Emerging data also indicate that oxidative base modifications such as 8-oxoG in gene promoters may serve as epigenetic marks, and/or provide a platform for coordination of the initial steps of DNA repair and the assembly of the transcriptional machinery to launch adequate gene expression alterations. Here, we briefly review the current understanding of oxidative lesions in genome stability maintenance and regulation of basal and inducible transcription.
Collapse
Affiliation(s)
- Bayan Bokhari
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA.
- Department of Biochemistry, Faculty of Applied Medical Science, Umm Al- Qura University, Makkah 21421, Saudi Arabia.
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA.
- National Human Genome Center, College of Medicine, Howard University, 2041 Georgia Avenue, NW, Washington, DC 20060, USA.
| |
Collapse
|
38
|
Abstract
The epidemic of Type 2 diabetes mellitus necessitates development of novel therapeutic and preventative strategies to attenuate expansion of this debilitating disease. Evidence links the circadian system to various aspects of diabetes pathophysiology and treatment. The aim of this review will be to outline the rationale for therapeutic targeting of the circadian system in the treatment and prevention of Type 2 diabetes mellitus and consequent metabolic comorbidities.
Collapse
Affiliation(s)
- Naureen Javeed
- Department of Physiology and Biomedical Engineering, Mayo Clinic , Rochester, Minnesota
| | - Aleksey V Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic , Rochester, Minnesota.,Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Mayo Clinic School of Medicine, Mayo Clinic , Rochester, Minnesota
| |
Collapse
|
39
|
Cimini S, Gualtieri C, Macovei A, Balestrazzi A, De Gara L, Locato V. Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:989. [PMID: 31428113 PMCID: PMC6688120 DOI: 10.3389/fpls.2019.00989] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/15/2019] [Indexed: 05/05/2023]
Abstract
Plants are continuously faced with complex environmental conditions which can affect the oxidative metabolism and photosynthetic efficiency, thus leading to the over-production of reactive oxygen species (ROS). Over a certain threshold, ROS can damage DNA. DNA damage, unless repaired, can affect genome stability, thus interfering with cell survival and severely reducing crop productivity. A complex network of pathways involved in DNA damage response (DDR) needs to be activated in order to maintain genome integrity. The expression of specific genes belonging to these pathways can be used as indicators of oxidative DNA damage and effective DNA repair in plants subjected to stress conditions. Managing ROS levels by modulating their production and scavenging systems shifts the role of these compounds from toxic molecules to key messengers involved in plant tolerance acquisition. Oxidative and anti-oxidative signals normally move among the different cell compartments, including the nucleus, cytosol, and organelles. Nuclei are dynamically equipped with different redox systems, such as glutathione (GSH), thiol reductases, and redox regulated transcription factors (TFs). The nuclear redox network participates in the regulation of the DNA metabolism, in terms of transcriptional events, replication, and repair mechanisms. This mainly occurs through redox-dependent regulatory mechanisms comprising redox buffering and post-translational modifications, such as the thiol-disulphide switch, glutathionylation, and S-nitrosylation. The regulatory role of microRNAs (miRNAs) is also emerging for the maintenance of genome stability and the modulation of antioxidative machinery under adverse environmental conditions. In fact, redox systems and DDR pathways can be controlled at a post-transcriptional level by miRNAs. This review reports on the interconnections between the DDR pathways and redox balancing systems. It presents a new dynamic picture by taking into account the shared regulatory mechanism mediated by miRNAs in plant defense responses to stress.
Collapse
Affiliation(s)
- Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Carla Gualtieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
- *Correspondence: Vittoria Locato,
| |
Collapse
|
40
|
Causton HC. Metabolic rhythms: A framework for coordinating cellular function. Eur J Neurosci 2018; 51:1-12. [PMID: 30548718 DOI: 10.1111/ejn.14296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]
Abstract
Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.
Collapse
Affiliation(s)
- Helen C Causton
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, New York
| |
Collapse
|
41
|
Miyazawa H, Aulehla A. Revisiting the role of metabolism during development. Development 2018; 145:145/19/dev131110. [DOI: 10.1242/dev.131110] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
ABSTRACT
An emerging view emphasizes that metabolism is highly regulated in both time and space. In addition, it is increasingly being recognized that metabolic pathways are tightly connected to specific biological processes such as cell signaling, proliferation and differentiation. As we obtain a better view of this spatiotemporal regulation of metabolism, and of the molecular mechanisms that connect metabolism and signaling, we can now move from largely correlative to more functional studies. It is, therefore, a particularly promising time to revisit how metabolism can affect multiple aspects of animal development. In this Review, we discuss how metabolism is mechanistically linked to cellular and developmental programs through both its bioenergetic and metabolic signaling functions. We highlight how metabolism is regulated across various spatial and temporal scales, and discuss how this regulation can influence cellular processes such as cell signaling, gene expression, and epigenetic and post-translational modifications during embryonic development.
Collapse
Affiliation(s)
- Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| |
Collapse
|
42
|
Tamberg N, Tahk S, Koit S, Kristjuhan K, Kasvandik S, Kristjuhan A, Ilves I. Keap1-MCM3 interaction is a potential coordinator of molecular machineries of antioxidant response and genomic DNA replication in metazoa. Sci Rep 2018; 8:12136. [PMID: 30108253 PMCID: PMC6092318 DOI: 10.1038/s41598-018-30562-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/02/2018] [Indexed: 01/19/2023] Open
Abstract
Coordination of DNA replication and cellular redox homeostasis mechanisms is essential for the sustained genome stability due to the sensitivity of replicating DNA to oxidation. However, substantial gaps remain in our knowledge of underlying molecular pathways. In this study, we characterise the interaction of Keap1, a central antioxidant response regulator in Metazoa, with the replicative helicase subunit protein MCM3. Our analysis suggests that structural determinants of the interaction of Keap1 with its critical downstream target - Nrf2 master transactivator of oxidative stress response genes – may have evolved in evolution to mimic the conserved helix-2-insert motif of MCM3. We show that this has led to a competition between MCM3 and Nrf2 proteins for Keap1 binding, and likely recruited MCM3 for the competitive binding dependent modulation of Keap1 controlled Nrf2 activities. We hypothesise that such mechanism could help to adjust the Keap1-Nrf2 antioxidant response pathway according to the proliferative and replicative status of the cell, with possible reciprocal implications also for the regulation of cellular functions of MCM3. Altogether this suggests about important role of Keap1-MCM3 interaction in the cross-talk between replisome and redox homeostasis machineries in metazoan cells.
Collapse
Affiliation(s)
- Nele Tamberg
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Siret Tahk
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Sandra Koit
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Kersti Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Arnold Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Ivar Ilves
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia.
| |
Collapse
|
43
|
Ocaña MC, Martínez-Poveda B, Quesada AR, Medina MÁ. Metabolism within the tumor microenvironment and its implication on cancer progression: An ongoing therapeutic target. Med Res Rev 2018; 39:70-113. [DOI: 10.1002/med.21511] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Ma Carmen Ocaña
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Andalucía Tech; Universidad de Málaga; Málaga Spain
| | - Beatriz Martínez-Poveda
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Andalucía Tech; Universidad de Málaga; Málaga Spain
| | - Ana R. Quesada
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Andalucía Tech; Universidad de Málaga; Málaga Spain
- CIBER de Enfermedades Raras (CIBERER); Málaga Spain
| | - Miguel Ángel Medina
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Andalucía Tech; Universidad de Málaga; Málaga Spain
- CIBER de Enfermedades Raras (CIBERER); Málaga Spain
| |
Collapse
|
44
|
Somyajit K, Gupta R, Sedlackova H, Neelsen KJ, Ochs F, Rask MB, Choudhary C, Lukas J. Redox-sensitive alteration of replisome architecture safeguards genome integrity. Science 2018; 358:797-802. [PMID: 29123070 DOI: 10.1126/science.aao3172] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/26/2017] [Indexed: 01/02/2023]
Abstract
DNA replication requires coordination between replication fork progression and deoxynucleotide triphosphate (dNTP)-generating metabolic pathways. We find that perturbation of ribonucleotide reductase (RNR) in humans elevates reactive oxygen species (ROS) that are detected by peroxiredoxin 2 (PRDX2). In the oligomeric state, PRDX2 forms a replisome-associated ROS sensor, which binds the fork accelerator TIMELESS when exposed to low levels of ROS. Elevated ROS levels generated by RNR attenuation disrupt oligomerized PRDX2 to smaller subunits, whose dissociation from chromatin enforces the displacement of TIMELESS from the replisome. This process instantly slows replication fork progression, which mitigates pathological consequences of replication stress. Thus, redox signaling couples fluctuations of dNTP biogenesis with replisome activity to reduce stress during genome duplication. We propose that cancer cells exploit this pathway to increase their adaptability to adverse metabolic conditions.
Collapse
Affiliation(s)
- Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Rajat Gupta
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Hana Sedlackova
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Kai John Neelsen
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Fena Ochs
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
| |
Collapse
|
45
|
Medeiros TC, Thomas RL, Ghillebert R, Graef M. Autophagy balances mtDNA synthesis and degradation by DNA polymerase POLG during starvation. J Cell Biol 2018. [PMID: 29519802 PMCID: PMC5940314 DOI: 10.1083/jcb.201801168] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Medeiros et al. show that mtDNA polymerase POLG controls mtDNA copy number in the context of autophagy-mediated metabolic homeostasis. After prolonged starvation, the mtDNA degradative activity of POLG is activated to adjust the increasing mtDNA copy number in WT cells, whereas in autophagy-deficient cells, POLG’s continued degradative activity causes mtDNA instability and respiratory dysfunction as a result of nucleotide insufficiency. Mitochondria contain tens to thousands of copies of their own genome (mitochondrial DNA [mtDNA]), creating genetic redundancy capable of buffering mutations in mitochondrial genes essential for cellular function. However, the mechanisms regulating mtDNA copy number have been elusive. Here we found that DNA synthesis and degradation by mtDNA polymerase γ (POLG) dynamically controlled mtDNA copy number in starving yeast cells dependent on metabolic homeostasis provided by autophagy. Specifically, the continuous mtDNA synthesis by POLG in starving wild-type cells was inhibited by nucleotide insufficiency and elevated mitochondria-derived reactive oxygen species in the presence of autophagy dysfunction. Moreover, after prolonged starvation, 3′–5′ exonuclease–dependent mtDNA degradation by POLG adjusted the initially increasing mtDNA copy number in wild-type cells, but caused quantitative mtDNA instability and irreversible respiratory dysfunction in autophagy-deficient cells as a result of nucleotide limitations. In summary, our study reveals that mitochondria rely on the homeostatic functions of autophagy to balance synthetic and degradative modes of POLG, which control copy number dynamics and stability of the mitochondrial genome.
Collapse
Affiliation(s)
| | - Ryan Lee Thomas
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Martin Graef
- Max Planck Institute for Biology of Ageing, Cologne, Germany .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| |
Collapse
|
46
|
Werling D. WITHDRAWN: Non-infectious stressors and innate immune response. Res Vet Sci 2018:S0034-5288(17)30980-3. [PMID: 29373122 DOI: 10.1016/j.rvsc.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/01/2018] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
This article has been withdrawn at the request of the author(s). The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, United Kingdom.
| |
Collapse
|
47
|
Scheffler K, Rachek L, You P, Rowe AD, Wang W, Kuśnierczyk A, Kittelsen L, Bjørås M, Eide L. 8-oxoguanine DNA glycosylase (Ogg1) controls hepatic gluconeogenesis. DNA Repair (Amst) 2017; 61:56-62. [PMID: 29207315 DOI: 10.1016/j.dnarep.2017.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022]
Abstract
Mitochondrial DNA (mtDNA) resides in close proximity to metabolic reactions, and is maintained by the 8-oxoguanine DNA glycosylase (Ogg1) and other members of the base excision repair pathway. Here, we tested the hypothesis that changes in liver metabolism as under fasting/feeding conditions would be sensed by liver mtDNA, and that Ogg1 deficient mice might unravel a metabolic phenotype. Wild type (WT) and ogg1-/- mice were either fed ad libitum or subjected to fasting for 24h, and the corresponding effects on liver gene expression, DNA damage, as well as serum values were analyzed. Ogg1 deficient mice fed ad libitum exhibited hyperglycemia, elevated insulin levels and higher liver glycogen content as well as increased accumulation of 8oxoG in mtDNA compared to age- and gender matched WT mice. Interestingly, these phenotypes were absent in ogg1-/- mice during fasting. Gene expression and functional analyses suggest that the diabetogenic phenotype in the ogg1-/- mice is due to a failure to suppress gluconeogensis in the fed state. The ogg1-/- mice exhibited reduced mitochondrial electron transport chain (ETC) capacity and a combined low activity of the pyruvate dehydrogenase (PDH), alluding to inefficient channeling of glycolytic products into the citric acid cycle. Our data demonstrate a physiological role of base excision repair that goes beyond DNA maintenance, and implies that DNA repair is involved in regulating metabolism.
Collapse
Affiliation(s)
- Katja Scheffler
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Lyudmila Rachek
- University of South Alabama, Mobile, AL, United States of America
| | - Panpan You
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Newborn Screening, Oslo University Hospital, Norway
| | - Wei Wang
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lene Kittelsen
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway
| | - Magnar Bjørås
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway.
| |
Collapse
|
48
|
Abstract
The canonical Wnt/β-catenin signaling pathway, an important modulator of progenitor cell proliferation and differentiation, is highly regulated for the maintenance of critical biological homeostasis. Decades of studies in cancer genetics and genomics have demonstrated that multiple genes encoding key proteins in this signaling pathway serve as targets for recurrent mutational alterations. Among these proteins, β-catenin and adenomatosis polyposis coli (APC) are two key nodes. β-catenin contributes in transporting extracellular signals for nuclear programming. Mutations of the CTNNB1 gene that encodes β-catenin occur in a wide spectrum of cancers. These mutations alter the spatial characteristics of the β-catenin protein, leading to drastic reprogramming of the nuclear transcriptional network. Among the outcomes of this reprogramming are increased cell proliferation, enhanced immunosuppression, and disruption of metabolic regulation. Herein we review the current understanding of CTNNB1 mutations, their roles in tumorigenesis and discuss their possible therapeutic implications for cancer.
Collapse
|
49
|
Ahn E, Kumar P, Mukha D, Tzur A, Shlomi T. Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle. Mol Syst Biol 2017; 13:953. [PMID: 29109155 PMCID: PMC5731346 DOI: 10.15252/msb.20177763] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Cellular metabolic demands change throughout the cell cycle. Nevertheless, a characterization of how metabolic fluxes adapt to the changing demands throughout the cell cycle is lacking. Here, we developed a temporal‐fluxomics approach to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle. This is achieved by combining pulse‐chase LC‐MS‐based isotope tracing in synchronized cell populations with computational deconvolution and metabolic flux modeling. We find that TCA cycle fluxes are rewired as cells progress through the cell cycle with complementary oscillations of glucose versus glutamine‐derived fluxes: Oxidation of glucose‐derived flux peaks in late G1 phase, while oxidative and reductive glutamine metabolism dominates S phase. These complementary flux oscillations maintain a constant production rate of reducing equivalents and oxidative phosphorylation flux throughout the cell cycle. The shift from glucose to glutamine oxidation in S phase plays an important role in cell cycle progression and cell proliferation.
Collapse
Affiliation(s)
- Eunyong Ahn
- Department of Computer Science, Technion, Haifa, Israel
| | | | | | - Amit Tzur
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Tomer Shlomi
- Department of Computer Science, Technion, Haifa, Israel .,Department of Biology, Technion, Haifa, Israel.,Lokey Center for Life Science and Engineering, Technion, Haifa, Israel
| |
Collapse
|
50
|
Weger M, Diotel N, Dorsemans AC, Dickmeis T, Weger BD. Stem cells and the circadian clock. Dev Biol 2017; 431:111-123. [DOI: 10.1016/j.ydbio.2017.09.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/11/2017] [Accepted: 09/08/2017] [Indexed: 12/20/2022]
|