1
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Peng M, Keppeke GD, Tsai LK, Chang CC, Liu JL, Sung LY. The IMPDH cytoophidium couples metabolism and fetal development in mice. Cell Mol Life Sci 2024; 81:210. [PMID: 38717553 PMCID: PMC11078715 DOI: 10.1007/s00018-024-05233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
The cytoophidium is an evolutionarily conserved subcellular structure formed by filamentous polymers of metabolic enzymes. In vertebrates, inosine monophosphate dehydrogenase (IMPDH), which catalyses the rate-limiting step in guanosine triphosphate (GTP) biosynthesis, is one of the best-known cytoophidium-forming enzymes. Formation of the cytoophidium has been proposed to alleviate the inhibition of IMPDH, thereby facilitating GTP production to support the rapid proliferation of certain cell types such as lymphocytes, cancer cells and pluripotent stem cells (PSCs). However, past studies lacked appropriate models to elucidate the significance of IMPDH cytoophidium under normal physiological conditions. In this study, we demonstrate that the presence of IMPDH cytoophidium in mouse PSCs correlates with their metabolic status rather than pluripotency. By introducing IMPDH2 Y12C point mutation through genome editing, we established mouse embryonic stem cell (ESC) lines incapable of forming IMPDH polymers and the cytoophidium. Our data indicate an important role of IMPDH cytoophidium in sustaining a positive feedback loop that couples nucleotide biosynthesis with upstream metabolic pathways. Additionally, we find that IMPDH2 Y12C mutation leads to decreased cell proliferation and increased DNA damage in teratomas, as well as impaired embryo development following blastocoel injection. Further analysis shows that IMPDH cytoophidium assembly in mouse embryonic development begins after implantation and gradually increases throughout fetal development. These findings provide insights into the regulation of IMPDH polymerisation in embryogenesis and its significance in coordinating cell metabolism and development.
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Affiliation(s)
- Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Gerson D Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
| | - Li-Kuang Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Chia-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
- Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan.
- Center for Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
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2
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Chang J, Yuan W, Gao C, Zhang B, Liu JL, Chen G, Tan YW. Single-Molecule Fluorescence Imaging Reveals Coassembly of CTPS and P5CS. J Phys Chem B 2024; 128:949-959. [PMID: 38236746 DOI: 10.1021/acs.jpcb.3c06498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The cellular compartmentation induced by self-assembly of natural proteins has recently attracted widespread attention due to its structural-functional significance. Among them, as a highly conserved metabolic enzyme and one of the potential targets for cancers and parasitic diseases in drug development, CTP synthase (CTPS) has also been reported to self-assemble into filamentous structures termed cytoophidia. To elucidate the dynamical mechanism of cytoophidium filamentation, we utilize single-molecule fluorescence imaging to observe the real-time self-assembly dynamics of CTPS and the coordinated assembly between CTPS and its interaction partner, Δ1-pyrroline-5-carboxylate synthase (P5CS). Significant differences exist in the direction of growth and extension when the two proteins self-assemble. The oligomer state distribution analysis of the CTPS minimum structural subunit under different conditions and the stoichiometry statistics of binding CTPS and P5CS by single-molecule fluorescence photobleach counting further confirm that the CTPS cytoophidia are mainly stacked with tetramers. CTPS can act as the nucleation core to induce the subsequent growth of the P5CS filaments. Our work not only provide evidence from the molecular level for the self-assembly and coordinated assembly (coassembly) of CTPS with its interaction partner P5CS in vitro but also offer new experimental perspectives for the dynamics research of coordinated regulation between other protein polymers.
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Affiliation(s)
- Jian Chang
- State Key Laboratory of Surface Physics, Shanghai Key Laboratory of Metasurfaces for Light Manipulation, Department of Physics, Fudan University, Shanghai 200433, China
| | - Weijie Yuan
- State Key Laboratory of Surface Physics, Shanghai Key Laboratory of Metasurfaces for Light Manipulation, Department of Physics, Fudan University, Shanghai 200433, China
| | - Chendi Gao
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Bo Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Shanghai Key Laboratory of Metasurfaces for Light Manipulation, Department of Physics, Fudan University, Shanghai 200433, China
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3
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Yin Y, Yu H, Wang X, Hu Q, Liu Z, Luo D, Yang X. Cytoophidia: a conserved yet promising mode of enzyme regulation in nucleotide metabolism. Mol Biol Rep 2024; 51:245. [PMID: 38300325 DOI: 10.1007/s11033-024-09208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Nucleotide biosynthesis encompasses both de novo and salvage synthesis pathways, each characterized by significant material and procedural distinctions. Despite these differences, cells with elevated nucleotide demands exhibit a preference for the more intricate de novo synthesis pathway, intricately linked to modes of enzyme regulation. In this study, we primarily scrutinize the biological importance of a conserved yet promising mode of enzyme regulation in nucleotide metabolism-cytoophidia. Cytoophidia, comprising cytidine triphosphate synthase or inosine monophosphate dehydrogenase, is explored across diverse biological models, including yeasts, Drosophila, mice, and human cancer cell lines. Additionally, we delineate potential biomedical applications of cytoophidia. As our understanding of cytoophidia deepens, the roles of enzyme compartmentalization and polymerization in various biochemical processes will unveil, promising profound impacts on both research and the treatment of metabolism-related diseases.
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Affiliation(s)
- Yue Yin
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Huanhuan Yu
- First School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Xinyi Wang
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiaohao Hu
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Zhuoqi Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Daya Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
| | - Xiaohong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
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4
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Andreadis C, Li T, Liu JL. Ubiquitination regulates cytoophidium assembly in Schizosaccharomyces pombe. Exp Cell Res 2022; 420:113337. [PMID: 36087798 DOI: 10.1016/j.yexcr.2022.113337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/30/2022]
Abstract
CTP synthase (CTPS), a metabolic enzyme responsible for the de novo synthesis of CTP, can form filamentous structures termed cytoophidia, which are evolutionarily conserved from bacteria to humans. Here we used Schizosaccharomyces pombe to study the cytoophidium assembly regulation by ubiquitination. We tested the CTP synthase's capacity to be post-translationally modified by ubiquitin or be affected by the ubiquitination state of the cell and showed that ubiquitination is important for the maintenance of the CTPS filamentous structure in fission yeast. We have identified proteins which are in complex with CTPS, including specific ubiquitination regulators which significantly affect CTPS filamentation, and mapped probable ubiquitination targets on CTPS. Furthermore, we discovered that a cohort of deubiquitinating enzymes is important for the regulation of cytoophidium's filamentous morphology. Our study provides a framework for the analysis of the effects that ubiquitination and deubiquitination have on the formation of cytoophidia.
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Affiliation(s)
- Christos Andreadis
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Tianhao Li
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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5
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Darekar S, Laín S. Asymmetric inheritance of cytoophidia could contribute to determine cell fate and plasticity: The onset of alternative differentiation patterns in daughter cells may rely on the acquisition of either CTPS or IMPDH cytoophidia: The onset of alternative differentiation patterns in daughter cells may rely on the acquisition of either CTPS or IMPDH cytoophidia. Bioessays 2022; 44:e2200128. [PMID: 36209393 DOI: 10.1002/bies.202200128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 12/20/2022]
Abstract
Two enzymes involved in the synthesis of pyrimidine and purine nucleotides, CTP synthase (CTPS) and IMP dehydrogenase (IMPDH), can assemble into a single or very few large filaments called rods and rings (RR) or cytoophidia. Most recently, asymmetric cytoplasmic distribution of organelles during cell division has been described as a decisive event in hematopoietic stem cell fate. We propose that cytoophidia, which could be considered as membrane-less organelles, may also be distributed asymmetrically during mammalian cell division as previously described for Schizosaccharomyces pombe. Furthermore, because each type of nucleotide intervenes in distinct processes (e.g., membrane synthesis, glycosylation, and G protein-signaling), alterations in the rate of synthesis of specific nucleotide types could influence cell differentiation in multiple ways. Therefore, we hypothesize that whether a daughter cell inherits or not CTPS or IMPDH filaments determines its fate and that this asymmetric inheritance, together with the dynamic nature of these structures enables plasticity in a cell population.
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Affiliation(s)
- Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
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6
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Chang CC, Peng M, Zhong J, Zhang Z, Keppeke GD, Sung LY, Liu JL. Molecular crowding facilitates bundling of IMPDH polymers and cytoophidium formation. Cell Mol Life Sci 2022; 79:420. [PMID: 35833994 PMCID: PMC11072341 DOI: 10.1007/s00018-022-04448-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
The cytoophidium is a unique type of membraneless compartment comprising of filamentous protein polymers. Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step of de novo GTP biosynthesis and plays critical roles in active cell metabolism. However, the molecular regulation of cytoophidium formation is poorly understood. Here we show that human IMPDH2 polymers bundle up to form cytoophidium-like aggregates in vitro when macromolecular crowders are present. The self-association of IMPDH polymers is suggested to rely on electrostatic interactions. In cells, the increase of molecular crowding with hyperosmotic medium induces cytoophidia, while the decrease of that by the inhibition of RNA synthesis perturbs cytoophidium assembly. In addition to IMPDH, CTPS and PRPS cytoophidium could be also induced by hyperosmolality, suggesting a universal phenomenon of cytoophidium-forming proteins. Finally, our results indicate that the cytoophidium can prolong the half-life of IMPDH, which is proposed to be one of conserved functions of this subcellular compartment.
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Affiliation(s)
- Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Gerson Dierley Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, 04023-062, Brazil
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.
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7
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Wu Z, Liu JL. CTP synthase does not form cytoophidia in Drosophila interfollicular stalks. Exp Cell Res 2022; 418:113250. [PMID: 35691380 DOI: 10.1016/j.yexcr.2022.113250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022]
Abstract
CTP synthase (CTPS) catalyzes the final step of de novo synthesis of the nucleotide CTP. In 2010, CTPS has been found to form filamentous structures termed cytoophidia in Drosophila follicle cells and germline cells. Subsequently, cytoophidia have been reported in many species across three domains of life: bacteria, eukaryotes and archaea. Forming cytoophidia appears to be a highly conserved and ancient property of CTPS. To our surprise, here we find that polar cells and stalk cells, two specialized types of cells composing Drosophila interfollicular stalks, do not possess obvious cytoophidia. We show that Myc level is low in these two types of cells. Treatment with a glutamine analog, 6-diazo-5-oxo-l-norleucine (DON), increases cytoophidium assembly in main follicle cells, but not in polar cells or stalk cells. Moreover, overexpressing Myc induces cytoophidium formation in stalk cells. When CTPS is overexpressed, cytoophidia can be observed both in stalk cells and polar cells. Our findings provide an interesting paradigm for the in vivo study of cytoophidium assembly and disassembly among different populations of follicle cells.
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Affiliation(s)
- Zheng Wu
- School of Life Science and Technology, ShanghaiTech University, 230 Haike Road, 201210, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, 230 Haike Road, 201210, Shanghai, China; Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, United Kingdom.
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8
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GTP-Dependent Regulation of CTP Synthase: Evolving Insights into Allosteric Activation and NH3 Translocation. Biomolecules 2022; 12:biom12050647. [PMID: 35625575 PMCID: PMC9138612 DOI: 10.3390/biom12050647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
Cytidine-5′-triphosphate (CTP) synthase (CTPS) is the class I glutamine-dependent amidotransferase (GAT) that catalyzes the last step in the de novo biosynthesis of CTP. Glutamine hydrolysis is catalyzed in the GAT domain and the liberated ammonia is transferred via an intramolecular tunnel to the synthase domain where the ATP-dependent amination of UTP occurs to form CTP. CTPS is unique among the glutamine-dependent amidotransferases, requiring an allosteric effector (GTP) to activate the GAT domain for efficient glutamine hydrolysis. Recently, the first cryo-electron microscopy structure of Drosophila CTPS was solved with bound ATP, UTP, and, notably, GTP, as well as the covalent adduct with 6-diazo-5-oxo-l-norleucine. This structural information, along with the numerous site-directed mutagenesis, kinetics, and structural studies conducted over the past 50 years, provide more detailed insights into the elaborate conformational changes that accompany GTP binding at the GAT domain and their contribution to catalysis. Interactions between GTP and the L2 loop, the L4 loop from an adjacent protomer, the L11 lid, and the L13 loop (or unique flexible “wing” region), induce conformational changes that promote the hydrolysis of glutamine at the GAT domain; however, direct experimental evidence on the specific mechanism by which these conformational changes facilitate catalysis at the GAT domain is still lacking. Significantly, the conformational changes induced by GTP binding also affect the assembly and maintenance of the NH3 tunnel. Hence, in addition to promoting glutamine hydrolysis, the allosteric effector plays an important role in coordinating the reactions catalyzed by the GAT and synthase domains of CTPS.
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9
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Sun Z, Zhang Z, Wang QQ, Liu JL. Combined Inactivation of CTPS1 and ATR Is Synthetically Lethal to MYC-Overexpressing Cancer Cells. Cancer Res 2022; 82:1013-1024. [PMID: 35022212 PMCID: PMC9359733 DOI: 10.1158/0008-5472.can-21-1707] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/30/2021] [Accepted: 12/28/2021] [Indexed: 01/07/2023]
Abstract
The "undruggable" oncogene MYC supports cancer cell proliferation and survival through parallel induction of multiple anabolic processes. Here we find that inhibiting CTP synthase (CTPS) selectively decreases cell viability and induces DNA replication stress in MYC-overexpressing cells. MYC-driven rRNA synthesis caused the selective DNA replication stress upon CTPS inhibition. Combined inhibition of CTPS and ataxia telangiectasia and Rad3-related protein (ATR) is synthetically lethal in MYC-overexpressing cells, promoting cell death in vitro and decreasing tumor growth in vivo. Unexpectedly, interfering with CTPS1 but not CTPS2 is required to induce replication stress in MYC-deregulated cancer cells and consequent cell death in the presence of an ATR inhibitor. These results highlight a specific and key role of CTPS1 in MYC-driven cancer, suggesting that selectively inhibiting CTPS1 in combination with ATR could be a promising strategy to combat disease progression. SIGNIFICANCE Inhibition of CTPS in MYC-overexpressing cells blocks pyrimidine synthesis while maintaining ribosome synthesis activity to create an anabolic imbalance that induces replication stress, providing a new approach to selectively target MYC-driven cancer. See related commentary by Chabanon and Postel-Vinay, p. 969.
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Affiliation(s)
- Zhe Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qiao-Qi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Corresponding Author: Ji-Long Liu, School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China. Phone: 8618-2176-28315; E-mail:
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10
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Thangadurai S, Bajgiran M, Manickam S, Mohana-Kumaran N, Azzam G. CTP synthase: the hissing of the cellular serpent. Histochem Cell Biol 2022; 158:517-534. [PMID: 35881195 PMCID: PMC9314535 DOI: 10.1007/s00418-022-02133-w] [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] [Accepted: 06/26/2022] [Indexed: 12/24/2022]
Abstract
CTP biosynthesis is carried out by two pathways: salvage and de novo. CTPsyn catalyzes the latter. The study of CTPsyn activity in mammalian cells began in the 1970s, and various fascinating discoveries were made regarding the role of CTPsyn in cancer and development. However, its ability to fit into a cellular serpent-like structure, termed 'cytoophidia,' was only discovered a decade ago by three independent groups of scientists. Although the self-assembly of CTPsyn into a filamentous structure is evolutionarily conserved, the enzyme activity upon this self-assembly varies in different species. CTPsyn is required for cellular development and homeostasis. Changes in the expression of CTPsyn cause developmental changes in Drosophila melanogaster. A high level of CTPsyn activity and formation of cytoophidia are often observed in rapidly proliferating cells such as in stem and cancer cells. Meanwhile, the deficiency of CTPsyn causes severe immunodeficiency leading to immunocompromised diseases caused by bacteria, viruses, and parasites, making CTPsyn an attractive therapeutic target. Here, we provide an overview of the role of CTPsyn in cellular and disease perspectives along with its potential as a drug target.
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Affiliation(s)
- Shallinie Thangadurai
- grid.11875.3a0000 0001 2294 3534School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Morteza Bajgiran
- grid.11875.3a0000 0001 2294 3534School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Sharvin Manickam
- grid.11875.3a0000 0001 2294 3534School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Nethia Mohana-Kumaran
- grid.11875.3a0000 0001 2294 3534School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Ghows Azzam
- grid.11875.3a0000 0001 2294 3534School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia ,grid.454125.3Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000 Kajang, Selangor Malaysia
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11
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Drosophila intestinal homeostasis requires CTP synthase. Exp Cell Res 2021; 408:112838. [PMID: 34560103 DOI: 10.1016/j.yexcr.2021.112838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022]
Abstract
CTP synthase (CTPS) senses all four nucleotides and forms filamentous structures termed cytoophidia in all three domains of life. How CTPS and cytoophidia function in a developmental context, however, remains underexplored. We report that CTPS forms cytoophidia in a subset of cells in the Drosophila midgut. We found that cytoophidia exist in intestinal stem cells (ISC) and enteroblasts in similar proportions. Both refeeding after starvation and feeding with dextran sulfate sodium (DSS) induce ISC proliferation and elongate cytoophidia. Knockdown of CTPS inhibits ISC proliferation. Remarkably, disruption of CTPS cytoophidia inhibits DSS-induced ISC proliferation. Taken together, these data suggest that both the expression level and the filament-form property of CTPS are crucial for intestinal homeostasis in Drosophila.
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12
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Zhang S, Feng HC, Liu JL. ASNS disruption shortens CTPS cytoophidia in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6080684. [PMID: 33561249 PMCID: PMC8022725 DOI: 10.1093/g3journal/jkaa060] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 12/09/2020] [Indexed: 02/07/2023]
Abstract
Asparagine synthetase (ASNS) and CTP synthase (CTPS) are two metabolic enzymes that catalyze the biosynthesis of asparagine and CTP, respectively. Both CTPS and ASNS have been identified to form cytoophidia in Saccharomyces cerevisiae. Glutamine is a common substrate for both these enzymes, and they play an important role in glutamine homeostasis. Here, we find that the ASNS cytoophidia are shorter than the CTPS cytoophidia, and that disruption of ASNS shortens the length of CTPS cytoophidia. However, the deletion of CTPS has no effect on the formation and length of ASNS cytoophidia, or on the ASNS protein level. We also find that Asn1 overexpression induces the formation of a multi-dot structure in diauxic phase which suggests that the increased protein level may trigger cytoophidia formation. Collectively, our results reveal a connection between ASNS cytoophidia and CTPS cytoophidia.
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Affiliation(s)
- Shanshan Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Han-Chao Feng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
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13
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Chang CC, Keppeke GD, Antos CL, Peng M, Andrade LEC, Sung LY, Liu JL. CTPS forms the cytoophidium in zebrafish. Exp Cell Res 2021; 405:112684. [PMID: 34129847 DOI: 10.1016/j.yexcr.2021.112684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/26/2022]
Abstract
Cytidine triphosphate synthase (CTPS) catalyzes the rate-limiting step of de novo CTP biosynthesis. An intracellular structure of CTPS, the cytoophidium, has been found in many organisms including prokaryotes and eukaryotes. Formation of the cytoophidium has been suggested to regulate the activity and stability of CTPS and may participate in certain physiological events. Herein, we demonstrate that both CTPS1a and CTPS1b in zebrafish are able to form the cytoophidium in cultured cells. A point mutation, H355A, abrogates cytoophidium assembly of zebrafish CTPS1a and CTPS1b. In addition, we show the presence of CTPS cytoophidia in multiple tissues of larval and adult fish under normal conditions, while treatment with a CTPS inhibitor 6-diazo-5-oxo-l-norleucine (DON) can induce more cytoophidia in some tissues. Our findings reveal that forming the CTPS cytoophidium is a natural phenomenon of zebrafish and provide valuable information for future research on the physiological importance of this intracellular structure in vertebrates.
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Affiliation(s)
- Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Gerson Dierley Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP 04023-062, Brazil
| | - Christopher L Antos
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Luis Eduardo Coelho Andrade
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP 04023-062, Brazil
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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14
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Simonet JC, Burrell AL, Kollman JM, Peterson JR. Freedom of assembly: metabolic enzymes come together. Mol Biol Cell 2021; 31:1201-1205. [PMID: 32463766 PMCID: PMC7353150 DOI: 10.1091/mbc.e18-10-0675] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many different enzymes in intermediate metabolism dynamically assemble filamentous polymers in cells, often in response to changes in physiological conditions. Most of the enzyme filaments known to date have only been observed in cells, but in a handful of cases structural and biochemical studies have revealed the mechanisms and consequences of assembly. In general, enzyme polymerization functions as a mechanism to allosterically tune enzyme kinetics, and it may play a physiological role in integrating metabolic signaling. Here, we highlight some principles of metabolic filaments by focusing on two well-studied examples in nucleotide biosynthesis pathways—inosine-5’-monophosphate (IMP) dehydrogenase and cytosine triphosphate (CTP) synthase.
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Affiliation(s)
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
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15
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Keppeke GD, Chang CC, Antos CL, Peng M, Sung LY, Andrade LEC, Liu JL. IMPDH forms the cytoophidium in zebrafish. Dev Biol 2021; 478:89-101. [PMID: 34048735 DOI: 10.1016/j.ydbio.2021.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in de novo guanine nucleotide biosynthesis. Its activity is negatively regulated by the binding of GTP. IMPDH can form a membraneless subcellular structure termed the cytoophidium in response to certain changes in the metabolic status of the cell. The polymeric form of IMPDH, which is the subunit of the cytoophidium, has been shown to be more resistant to the inhibition by GTP at physiological concentrations, implying a functional correlation between cytoophidium formation and the upregulation of GTP biosynthesis. Herein we demonstrate that zebrafish IMPDH1b and IMPDH2 isoforms can assemble abundant cytoophidium in most of cultured cells under stimuli, while zebrafish IMPDH1a shows distinctive properties of forming the cytoophidium in different cell types. Point mutations that disrupt cytoophidium structure in mammalian models also prevent the aggregation of zebrafish IMPDHs. In addition, we discover the presence of the IMPDH cytoophidium in various tissues of larval and adult fish under normal growth conditions. Our results reveal that polymerization and cytoophidium assembly of IMPDH can be a regulatory machinery conserved among vertebrates, and with specific physiological purposes.
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Affiliation(s)
- Gerson Dierley Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, 04023-062, Brazil
| | - Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Christopher L Antos
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Luis Eduardo Coelho Andrade
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, 04023-062, Brazil
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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16
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Peng M, Chang CC, Liu JL, Sung LY. CTPS and IMPDH form cytoophidia in developmental thymocytes. Exp Cell Res 2021; 405:112662. [PMID: 34022203 DOI: 10.1016/j.yexcr.2021.112662] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
The cytoophidium, a filamentous structure formed by metabolic enzymes, has emerged as a novel regulatory machinery for certain proteins. The rate-limiting enzymes of de novo CTP and GTP synthesis, cytidine triphosphate synthase (CTPS) and inosine monophosphate dehydrogenase (IMPDH), are the most characterized cytoophidium-forming enzymes in mammalian models. Although the assembly of CTPS cytoophidia has been demonstrated in various organisms including multiple human cancers, a systemic survey for the presence of CTPS cytoophidia in mammalian tissues in normal physiological conditions has not yet been reported. Herein, we examine major organs of adult mouse and observe that CTPS cytoophidia are displayed by a specific thymocyte population ranging between DN3 to early DP stages. Most of these cytoophidium-presenting cells have both CTPS and IMPDH cytoophidia and undergo rapid cell proliferation. In addition, we show that cytoophidium formation is associated with active glycolytic metabolism as the cytoophidium-presenting cells exhibit higher levels of c-Myc, phospho-Akt and PFK. Inhibition of glycolysis with 2DG, however, disrupts most of cytoophidium structures and impairs cell proliferation. Our findings not only indicate that the regulation of CTPS and IMPDH cytoophidia are correlated with the metabolic switch triggered by pre-TCR signaling, but also suggest physiological roles of the cytoophidium in thymocyte development.
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Affiliation(s)
- Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan; Animal Resource Center, National Taiwan University, Taipei, 106, Taiwan.
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17
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Histone transcription regulator Slm9 is required for cytoophidium biogenesis. Exp Cell Res 2021; 403:112582. [PMID: 33812868 DOI: 10.1016/j.yexcr.2021.112582] [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: 11/20/2020] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 11/23/2022]
Abstract
The cytoophidium, a subcellular structure composed of CTP synthase, can be observed during the division of Schizosaccharomyces pombe. Cytoophidium formation changes periodically with the cell cycle of yeast cells. Here, we find that histone chaperone Slm9 is required for the integrity of cytoophidia in fission yeast. When the slm9 gene is knocked out, we observe that morphological characteristics, the abundance of cytoophidia and the division of the yeast cells are significantly affected. Fragmented cytoophidia occur in slm9 mutant cells, a phenomenon rarely observed in wild-type cells. Our study reveals a potential link between a chromosomal regulatory factor and cytoophidium biogenesis.
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18
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Wang QQ, Zhao PA, Tastan ÖY, Liu JL. Polarised maintenance of cytoophidia in Drosophila follicle epithelia. Exp Cell Res 2021; 402:112564. [PMID: 33737069 DOI: 10.1016/j.yexcr.2021.112564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 12/20/2022]
Abstract
The metabolic enzyme CTP synthase (CTPS) can form filamentous structures named cytoophidia in numerous types of cells, including follicle cells. However, the regulation of cytoophidium assembly remains elusive. The apicobasal polarity, a defining characteristic of Drosophila follicle epithelium, is established and regulated by a variety of membrane domains. Here we show that CTPS can form cytoophidia in Drosophila epithelial follicle cells. Cytoophidia localise to the basolateral side of follicle cells. If apical polarity regulators are knocked down, cytoophidia become unstable and distribute abnormally. Knockdown of basolateral polarity regulators has no significant effect on cytoophidia, even though the polarity is disturbed. Our results indicate that cytoophidia are maintained via polarised distribution on the basolateral side of Drosophila follicle epithelia, which is primarily achieved through the apical polarity regulators.
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Affiliation(s)
- Qiao-Qi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peiyao A Zhao
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Ömür Y Tastan
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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19
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Ma K, Li N, Yan X, Zhu Y, Zhang C. Energy deficiency caused by CTPS downregulation in decidua may contribute to pre-eclampsia by impairing decidualization. J Cell Physiol 2021; 236:6520-6533. [PMID: 33576499 DOI: 10.1002/jcp.30326] [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: 08/23/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 11/10/2022]
Abstract
Pre-eclampsia (PE) is a pregnancy-related disorder that occurs after 20 weeks of gestation. It seriously affects the health of maternity and the fetus. However, the pathogenesis of PE is still unknown. Decidualization deficiency is considered a contributing factor to the development of PE. CTP synthetase (CTPS) which is the rate-limiting enzyme in the CTP de novo biosynthesis, is essential for nucleic acid synthesis and cellular energy metabolism, and often appears as cytoophidium in many cell types. Here, we found that the expression of CTPS was significantly downregulated in decidual tissues of patients with severe PE compared with healthy pregnant women. During in vitro decidualization, changes in CTPS were accompanied by opposite fluctuation of the AMPK signaling pathway. Moreover, the downregulation of CTPS by glutamine analogs or CTPS small interfering RNA inhibited the decidualization process and the AMPK signaling pathway. Investigating the underlying mechanism of action by co-immunoprecipitation coupled with mass spectrometry showed that CTPS interacted with ATP synthase (ATPS) and maintained the content of ATP on Day 3 of decidualization. However, when combined with mitochondrial stress protein STRESS-70 instead of ATPS, the concentration of ATP on Day 6 of induction was reduced. Corresponding to this, CTPS was mainly distributes in the cytoplasm on Day 3 of induction, while it appeared both in the cytoplasm and the nucleus on Day 6 in decidualized cells, which was similar to that in cells before induction. In summary, we believe that CTPS plays an important role in decidualization by participating in energy metabolism. Abnormal expression of CTPS in decidualization would lead to abnormal decidualization and consequently result in the occurrence of PE.
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Affiliation(s)
- Ke Ma
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Na Li
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xingyu Yan
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yunqing Zhu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Cong Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
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20
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Li YL, Liu JL. Hypoosmolality impedes cytoophidium integrity during nitrogen starvation. Yeast 2021; 38:276-289. [PMID: 33294993 DOI: 10.1002/yea.3542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/18/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
CTP synthase (CTPS) cytoophidia have been found in many species over domains of life in the past 10 years, implying the evolutionary conservation of these structures. However, there are differences in cytoophidia between species. The difference in CTPS cytoophidium properties between budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) inspires this research. We study the effects of culture environment on cytoophidia in S. cerevisiae by switching to the optimal medium for S. pombe. S. cerevisiae CTPS cytoophidium fragmentation and pseudohyphae formation are observed after treatment with S. pombe medium YES instead of S. cerevisiae medium YPD. By modifying the level of each ingredient of the media, we find that hypoosmolality impedes cytoophidium integrity during nitrogen starvation. Our study demonstrates the relationship between cytoophidium integrity and environmental stress, supporting the role of cytoophidia in stress resistance.
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Affiliation(s)
- Yi-Lan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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21
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Mollick T, Laín S. Modulating pyrimidine ribonucleotide levels for the treatment of cancer. Cancer Metab 2020; 8:12. [PMID: 33020720 PMCID: PMC7285601 DOI: 10.1186/s40170-020-00218-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/14/2020] [Indexed: 12/25/2022] Open
Abstract
By providing the necessary building blocks for nucleic acids and precursors for cell membrane synthesis, pyrimidine ribonucleotides are essential for cell growth and proliferation. Therefore, depleting pyrimidine ribonucleotide pools has long been considered as a strategy to reduce cancer cell growth. Here, we review the pharmacological approaches that have been employed to modulate pyrimidine ribonucleotide synthesis and degradation routes and discuss their potential use in cancer therapy. New developments in the treatment of myeloid malignancies with inhibitors of pyrimidine ribonucleotide synthesis justify revisiting the literature as well as discussing whether targeting this metabolic pathway can be effective and sufficiently selective for cancer cells to warrant an acceptable therapeutic index in patients.
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Affiliation(s)
- Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65, Solna, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23, SE-171 65, Solna, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65, Solna, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23, SE-171 65, Solna, Stockholm, Sweden
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22
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Simonet JC, Foster MJ, Lynch EM, Kollman JM, Nicholas E, O'Reilly AM, Peterson JR. CTP synthase polymerization in germline cells of the developing Drosophila egg supports egg production. Biol Open 2020; 9:bio050328. [PMID: 32580972 PMCID: PMC7390647 DOI: 10.1242/bio.050328] [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: 12/20/2019] [Accepted: 06/16/2020] [Indexed: 01/19/2023] Open
Abstract
Polymerization of metabolic enzymes into micron-scale assemblies is an emerging mechanism for regulating their activity. CTP synthase (CTPS) is an essential enzyme in the biosynthesis of the nucleotide CTP and undergoes regulated and reversible assembly into large filamentous structures in organisms from bacteria to humans. The purpose of these assemblies is unclear. A major challenge to addressing this question has been the inability to abolish assembly without eliminating CTPS protein. Here we demonstrate that a recently reported point mutant in CTPS, Histidine 355A (H355A), prevents CTPS filament assembly in vivo and dominantly inhibits the assembly of endogenous wild-type CTPS in the Drosophila ovary. Expressing this mutant in ovarian germline cells, we show that disruption of CTPS assembly in early stage egg chambers reduces egg production. This effect is exacerbated in flies fed the glutamine antagonist 6-diazo-5-oxo-L-norleucine, which inhibits de novo CTP synthesis. These findings introduce a general approach to blocking the assembly of polymerizing enzymes without eliminating their catalytic activity and demonstrate a role for CTPS assembly in supporting egg production, particularly under conditions of limited glutamine metabolism.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jacqueline C Simonet
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Maya J Foster
- Immersion Science Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Emmanuelle Nicholas
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Alana M O'Reilly
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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23
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Zhang Y, Liu J, Liu JL. The atlas of cytoophidia in Drosophila larvae. J Genet Genomics 2020; 47:321-331. [PMID: 32912804 DOI: 10.1016/j.jgg.2020.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/07/2020] [Accepted: 06/21/2020] [Indexed: 02/08/2023]
Abstract
In 2010, cytidine 5'-triphosphate synthase (CTPS) was reported to form the filamentous or serpentine structure in Drosophila, which we termed the cytoophidium. In the last decade, CTPS filaments/cytoophidia have been found in bacteria, budding yeast, human cells, mice, fission yeast, plants, and archaea, indicating that this mechanism is highly conserved in evolution. In addition to CTPS, other metabolic enzymes have been identified to have the characteristics of forming cytoophidia or similar advanced structures, demonstrating that this is a basic strategy of cells. Nevertheless, our understanding of the physiological function of the cytoophidium remains incomplete and elusive. Here, we took the larva of Drosophila melanogaster as a model to systematically describe the localization and distribution of cytoophidia in different tissues during larval development. We found that the distribution pattern of CTPS cytoophidia is dynamic and heterogenic in larval tissues. Our study provides a road map for further understanding of the function and regulatory mechanism of cytoophidia.
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Affiliation(s)
- Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jingnan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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24
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Lynch EM, Kollman JM, Webb BA. Filament formation by metabolic enzymes-A new twist on regulation. Curr Opin Cell Biol 2020; 66:28-33. [PMID: 32417394 DOI: 10.1016/j.ceb.2020.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/18/2023]
Abstract
Compartmentalization of metabolic enzymes through protein-protein interactions is an emerging mechanism for localizing and regulating metabolic activity. Self-assembly into linear filaments is a common strategy for cellular compartmentalization of enzymes. Polymerization is often driven by changes in the metabolic state of the cell, suggesting that it is a strategy for shifting metabolic flux in response to cellular demand. Although polymerization of metabolic enzymes is widespread, observed from bacteria to humans, we are just beginning to appreciate their role in regulating cellular metabolism. In most cases, one functional role of metabolic enzyme filaments is allosteric control of enzyme activity. Here, we highlight recent findings, providing insight into the structural and functional significance of filamentation of metabolic enzymes in cells.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, USA
| | | | - Bradley A Webb
- Department of Biochemistry, West Virginia University, USA.
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25
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Chakraborty A, Lin WC, Lin YT, Huang KJ, Wang PY, Chang IYF, Wang HI, Ma KT, Wang CY, Huang XR, Lee YH, Chen BC, Hsieh YJ, Chien KY, Lin TY, Liu JL, Sung LY, Yu JS, Chang YS, Pai LM. SNAP29 mediates the assembly of histidine-induced CTP synthase filaments in proximity to the cytokeratin network. J Cell Sci 2020; 133:jcs240200. [PMID: 32184263 DOI: 10.1242/jcs.240200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
Under metabolic stress, cellular components can assemble into distinct membraneless organelles for adaptation. One such example is cytidine 5'-triphosphate synthase (CTPS, for which there are CTPS1 and CTPS2 forms in mammals), which forms filamentous structures under glutamine deprivation. We have previously demonstrated that histidine (His)-mediated methylation regulates the formation of CTPS filaments to suppress enzymatic activity and preserve the CTPS protein under glutamine deprivation, which promotes cancer cell growth after stress alleviation. However, it remains unclear where and how these enigmatic structures are assembled. Using CTPS-APEX2-mediated in vivo proximity labeling, we found that synaptosome-associated protein 29 (SNAP29) regulates the spatiotemporal filament assembly of CTPS along the cytokeratin network in a keratin 8 (KRT8)-dependent manner. Knockdown of SNAP29 interfered with assembly and relaxed the filament-induced suppression of CTPS enzymatic activity. Furthermore, APEX2 proximity labeling of keratin 18 (KRT18) revealed a spatiotemporal association of SNAP29 with cytokeratin in response to stress. Super-resolution imaging suggests that during CTPS filament formation, SNAP29 interacts with CTPS along the cytokeratin network. This study links the cytokeratin network to the regulation of metabolism by compartmentalization of metabolic enzymes during nutrient deprivation.
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Affiliation(s)
- Archan Chakraborty
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Wei-Cheng Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yu-Tsun Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kuang-Jing Huang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Pei-Yu Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 33302, Taiwan
| | - Hsiang-Iu Wang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kung-Ting Ma
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chun-Yen Wang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Xuan-Rong Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yen-Hsien Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ya-Ju Hsieh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kun-Yi Chien
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Clinical Proteomics Core laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Tzu-Yang Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Li-Ying Sung
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Li-Mei Pai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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26
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Zhou S, Xiang H, Liu JL. CTP synthase forms cytoophidia in archaea. J Genet Genomics 2020; 47:213-223. [DOI: 10.1016/j.jgg.2020.03.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022]
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27
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Zhang B, Tastan ÖY, Zhou X, Guo CJ, Liu X, Thind A, Hu HH, Zhao S, Liu JL. The proline synthesis enzyme P5CS forms cytoophidia in Drosophila. J Genet Genomics 2020; 47:131-143. [PMID: 32317150 DOI: 10.1016/j.jgg.2020.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/25/2020] [Accepted: 02/29/2020] [Indexed: 01/26/2023]
Abstract
Compartmentation of enzymes via filamentation has arisen as a mechanism for the regulation of metabolism. In 2010, three groups independently reported that CTP synthase (CTPS) can assemble into a filamentous structure termed the cytoophidium. In searching for CTPS-interacting proteins, here we perform a yeast two-hybrid screening of Drosophila proteins and identify a putative CTPS-interacting protein, △1-pyrroline-5-carboxylate synthase (P5CS). Using the Drosophila follicle cell as the in vivo model, we confirm that P5CS forms cytoophidia, which are associated with CTPS cytoophidia. Overexpression of P5CS increases the length of CTPS cytoophidia. Conversely, filamentation of CTPS affects the morphology of P5CS cytoophidia. Finally, in vitro analyses confirm the filament-forming property of P5CS. Our work links CTPS with P5CS, two enzymes involved in the rate-limiting steps in pyrimidine and proline biosynthesis, respectively.
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Affiliation(s)
- Bo Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ömür Y Tastan
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Xian Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chen-Jun Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xuyang Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Aaron Thind
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Huan-Huan Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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28
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Zhou X, Guo CJ, Hu HH, Zhong J, Sun Q, Liu D, Zhou S, Chang CC, Liu JL. Drosophila CTP synthase can form distinct substrate- and product-bound filaments. J Genet Genomics 2019; 46:537-545. [PMID: 31902586 DOI: 10.1016/j.jgg.2019.11.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 01/26/2023]
Abstract
Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells. However, recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells. In this study, using negative staining and cryo-electron microscopy, we demonstrate that Drosophila CTPS, whether in substrate-bound or product-bound form, can form filaments. Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species. We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation.
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Affiliation(s)
- Xian Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chen-Jun Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Huan-Huan Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianqian Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Dandan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Shuang Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chia Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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29
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Lin WC, Chakraborty A, Huang SC, Wang PY, Hsieh YJ, Chien KY, Lee YH, Chang CC, Tang HY, Lin YT, Tung CS, Luo JD, Chen TW, Lin TY, Cheng ML, Chen YT, Yeh CT, Liu JL, Sung LY, Shiao MS, Yu JS, Chang YS, Pai LM. Histidine-Dependent Protein Methylation Is Required for Compartmentalization of CTP Synthase. Cell Rep 2019; 24:2733-2745.e7. [PMID: 30184506 DOI: 10.1016/j.celrep.2018.08.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/11/2018] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
CTP synthase (CTPS) forms compartmentalized filaments in response to substrate availability and environmental nutrient status. However, the physiological role of filaments and mechanisms for filament assembly are not well understood. Here, we provide evidence that CTPS forms filaments in response to histidine influx during glutamine starvation. Tetramer conformation-based filament formation restricts CTPS enzymatic activity during nutrient deprivation. CTPS protein levels remain stable in the presence of histidine during nutrient deprivation, followed by rapid cell growth after stress relief. We demonstrate that filament formation is controlled by methylation and that histidine promotes re-methylation of homocysteine by donating one-carbon intermediates to the cytosolic folate cycle. Furthermore, we find that starvation stress and glutamine deficiency activate the GCN2/ATF4/MTHFD2 axis, which coordinates CTPS filament formation. CTPS filament formation induced by histidine-mediated methylation may be a strategy used by cancer cells to maintain homeostasis and ensure a growth advantage in adverse environments.
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Affiliation(s)
- Wei-Cheng Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Archan Chakraborty
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Shih-Chia Huang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Pei-Yu Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ya-Ju Hsieh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kun-Yi Chien
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yen-Hsien Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chia-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hsiang-Yu Tang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Healthy Aging Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yu-Tsun Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chang-Shung Tung
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ji-Dung Luo
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; Departments of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Tzu-Yang Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Mei-Ling Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Healthy Aging Research Center, Chang Gung University, Taoyuan 33302, Taiwan; Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chau-Ting Yeh
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Li-Ying Sung
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Ming-Shi Shiao
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Healthy Aging Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Li-Mei Pai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan; Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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30
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MicroRNA regulation of CTP synthase and cytoophidium in Drosophila melanogaster. Exp Cell Res 2019; 385:111688. [PMID: 31678212 DOI: 10.1016/j.yexcr.2019.111688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 11/21/2022]
Abstract
CTPsyn is a crucial metabolic enzyme which synthesizes CTP nucleotides. It has the extraordinary ability to compartmentalize into filaments termed cytoophidia. Though the structure is evolutionarily conserved across kingdoms, the mechanisms behind their formation remain unknown. MicroRNAs (miRNAs) are short single-stranded RNA capable of directing mRNA silencing and degradation. D. melanogaster has a high total gene count to miRNA gene number ratio, alluding to the possibility that CTPsyn too may come under their regulation. A thorough miRNA overexpression involving 123 miRNAs was conducted, followed by CTPsyn-specific staining upon cytoophidia-rich egg chambers. This revealed a small group of candidates which confer either a lengthening or truncating effect on cytoophidia, suggesting they may play a role in regulating CTPsyn. MiR-975 and miR-1014 are both cytoophidia-elongating, whereas miR-190 and miR-932 are cytoophidia-shortening. Though target prediction shows that miR-975 and miR-932 do indeed have binding sites on CTPsyn mRNA, in vitro assays instead revealed a low probability of this being true, instead indicating that the effects asserted by overexpressed miRNAs indirectly reach CTPsyn and its cytoophidia through the actions of middling elements. In silico target prediction and qPCR quantification indicated that, at least for miR-932 and miR-1014, these undetermined elements may be players in fat metabolism. This is the first study to thoroughly investigate miRNAs in connection to CTPsyn expression and activity in any species. The findings presented could serve as a basis for further queries into not only the fundamental aspects of the enzyme's regulation, but may uncover new facets of closely related pathways as well.
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31
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Zhang J, Liu JL. Temperature-sensitive cytoophidium assembly in Schizosaccharomyces pombe. J Genet Genomics 2019; 46:423-432. [PMID: 31611173 PMCID: PMC6868507 DOI: 10.1016/j.jgg.2019.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
The metabolic enzyme CTP synthase (CTPS) is able to compartmentalize into filaments, termed cytoophidia, in a variety of organisms including bacteria, budding yeast, fission yeast, fruit flies and mammals. A previous study in budding yeast shows that the filament-forming process of CTPS is not sensitive to temperature shift. Here we study CTPS filamentation in the fission yeast Schizosaccharomyces pombe. To our surprise, we find that both the length and the occurrence of cytoophidia in S. pombe decrease upon cold shock or heat shock. The temperature-dependent changes of cytoophidia are fast and reversible. Taking advantage of yeast genetics, we demonstrate that heat-shock proteins are required for cytoophidium assembly in S. pombe. Temperature sensitivity of cytoophidia makes S. pombe an attractive model system for future investigations of this novel membraneless organelle.
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Affiliation(s)
- Jing Zhang
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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32
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Andreadis C, Hulme L, Wensley K, Liu JL. The TOR pathway modulates cytoophidium formation in Schizosaccharomyces pombe. J Biol Chem 2019; 294:14686-14703. [PMID: 31431504 PMCID: PMC6779450 DOI: 10.1074/jbc.ra119.009913] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/09/2019] [Indexed: 12/30/2022] Open
Abstract
CTP synthase (CTPS) has been demonstrated to form evolutionarily-conserved filamentous structures termed cytoophidia whose exact cellular functions remain unclear, but they may play a role in intracellular compartmentalization. We have previously shown that the mammalian target of rapamycin complex 1 (mTORC1)-S6K1 pathway mediates cytoophidium assembly in mammalian cells. Here, using the fission yeast Schizosaccharomyces pombe as a model of a unicellular eukaryote, we demonstrate that the target of rapamycin (TOR)-signaling pathway regulates cytoophidium formation (from the S. pombe CTPS ortholog Cts1) also in S. pombe Conducting a systematic analysis of all viable single TOR subunit-knockout mutants and of several major downstream effector proteins, we found that Cts1 cytoophidia are significantly shortened and often dissociate when TOR is defective. We also found that the activities of the downstream effector kinases of the TORC1 pathway, Sck1, Sck2, and Psk1 S6, as well as of the S6K/AGC kinase Gad8, the major downstream effector kinase of the TORC2 pathway, are necessary for proper cytoophidium filament formation. Interestingly, we observed that the Crf1 transcriptional corepressor for ribosomal genes is a strong effector of Cts1 filamentation. Our findings connect TOR signaling, a major pathway required for cell growth, with the compartmentalization of the essential nucleotide synthesis enzyme CTPS, and we uncover differences in the regulation of its filamentation among higher multicellular and unicellular eukaryotic systems.
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Affiliation(s)
- Christos Andreadis
- School of Life Sciences and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Lydia Hulme
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Katherine Wensley
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ji-Long Liu
- School of Life Sciences and Technology, ShanghaiTech University, 201210 Shanghai, China .,MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
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33
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Lee WH, Oh JY, Maeng PJ. The NADP +-dependent glutamate dehydrogenase Gdh1 is subjected to glucose starvation-induced reversible aggregation that affects stress resistance in yeast. J Microbiol 2019; 57:884-892. [PMID: 31376105 DOI: 10.1007/s12275-019-9065-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 11/28/2022]
Abstract
The yeast Saccharomyces cerevisiae has two isoforms of NADP+-dependent glutamate dehydrogenase (Gdh1 and Gdh3) that catalyze the synthesis of glutamate from α-ketoglutarate and NH4+. In the present study, we confirmed that Gdh3, but not Gdh1, mainly contributes to the oxidative stress resistance of stationary-phase cells and found evidence suggesting that the insignificance of Gdh1 to stress resistance is possibly resulted from conditional and reversible aggregation of Gdh1 into punctuate foci initiated in parallel with post-diauxic growth. Altered localization to the mitochondria or peroxisomes prevented Gdh1, which was originally localized in the cytoplasm, from stationary phase-specific aggregation, suggesting that some cytosolic factors are involved in the process of Gdh1 aggregation. Glucose starvation triggered the transition of the soluble form of Gdh1 into the insoluble aggregate form, which could be redissolved by replenishing glucose, without any requirement for protein synthesis. Mutational analysis showed that the N-terminal proximal region of Gdh1 (NTP1, aa 21-26, TLFEQH) is essential for glucose starvation-induced aggregation. We also found that the substitution of NTP1 with the corresponding region of Gdh3 (NTP3) significantly increased the contribution of the mutant Gdh1 to the stress resistance of stationary-phase cells. Thus, this suggests that NTP1 is responsible for the negligible role of Gdh1 in maintaining the oxidative stress resistance of stationary-phase cells and the stationary phase-specific stresssensitive phenotype of the mutants lacking Gdh3.
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Affiliation(s)
- Woo Hyun Lee
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ju Yeong Oh
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Pil Jae Maeng
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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34
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Hayward D, Kouznetsova VL, Pierson HE, Hasan NM, Guzman ER, Tsigelny IF, Lutsenko S. ANKRD9 is a metabolically-controlled regulator of IMPDH2 abundance and macro-assembly. J Biol Chem 2019; 294:14454-14466. [PMID: 31337707 DOI: 10.1074/jbc.ra119.008231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/10/2019] [Indexed: 12/17/2022] Open
Abstract
Members of a large family of Ankyrin Repeat Domain (ANKRD) proteins regulate numerous cellular processes by binding to specific protein targets and modulating their activity, stability, and other properties. The same ANKRD protein may interact with different targets and regulate distinct cellular pathways. The mechanisms responsible for switches in the ANKRDs' behavior are often unknown. We show that cells' metabolic state can markedly alter interactions of an ANKRD protein with its target and the functional outcomes of this interaction. ANKRD9 facilitates degradation of inosine monophosphate dehydrogenase 2 (IMPDH2), the rate-limiting enzyme in GTP biosynthesis. Under basal conditions ANKRD9 is largely segregated from the cytosolic IMPDH2 in vesicle-like structures. Upon nutrient limitation, ANKRD9 loses its vesicular pattern and assembles with IMPDH2 into rodlike filaments, in which IMPDH2 is stable. Inhibition of IMPDH2 activity with ribavirin favors ANKRD9 binding to IMPDH2 rods. The formation of ANKRD9/IMPDH2 rods is reversed by guanosine, which restores ANKRD9 associations with the vesicle-like structures. The conserved Cys109Cys110 motif in ANKRD9 is required for the vesicle-to-rods transition as well as binding and regulation of IMPDH2. Oppositely to overexpression, ANKRD9 knockdown increases IMPDH2 levels and prevents formation of IMPDH2 rods upon nutrient limitation. Taken together, the results suggest that a guanosine-dependent metabolic switch determines the mode of ANKRD9 action toward IMPDH2.
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Affiliation(s)
- Dawn Hayward
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Valentina L Kouznetsova
- The Moores Cancer Center, University of California San Diego, La Jolla, California 92093.,San Diego Supercomputer Center University of California San Diego, La Jolla, California 92093
| | - Hannah E Pierson
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Nesrin M Hasan
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Estefany R Guzman
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Igor F Tsigelny
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.,San Diego Supercomputer Center University of California San Diego, La Jolla, California 92093.,Department of Neurosciences, University of California San Diego, La Jolla, California 92093
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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35
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Wu Z, Liu JL. Cytoophidia respond to nutrient stress in Drosophila. Exp Cell Res 2019; 376:159-167. [PMID: 30768932 PMCID: PMC6403103 DOI: 10.1016/j.yexcr.2019.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/13/2019] [Accepted: 02/09/2019] [Indexed: 01/08/2023]
Abstract
CTP synthase (CTPsyn) is a metabolic enzyme essential for the de novo synthesis of CTP the nucleotide. CTPsyn can be compartmented into filamentous structures named cytoophidia. Cytoophidia are conserved in a wide range of species and are highly abundant in Drosophila ovaries. Here we report that cytoophidia elongate upon nutrient deprivation, CTPsyn overexpression or heat shock in Drosophila ovaries. We also show that the curvature of cytoophidia changes during apoptosis. Moreover, cytoophidia can be transported from nurse cells to the oocyte via ring canals. Our study demonstrates that cytoophidia can respond to stress and are very dynamic in Drosophila ovaries.
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Affiliation(s)
- Zheng Wu
- School of Life Science and Technology, ShanghaiTech University, 230 Haike Road, 201210 Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, 230 Haike Road, 201210 Shanghai, China; MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, United Kingdom.
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36
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Calise SJ, Abboud G, Kasahara H, Morel L, Chan EKL. Immune Response-Dependent Assembly of IMP Dehydrogenase Filaments. Front Immunol 2018; 9:2789. [PMID: 30555474 PMCID: PMC6283036 DOI: 10.3389/fimmu.2018.02789] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to xanthosine monophosphate, the rate-limiting step in de novo guanosine monophosphate (GMP) synthesis. In cultured cells, IMPDH polymerizes into micron-scale filamentous structures when GMP synthesis is inhibited by depletion of purine precursors or by various drugs, including mycophenolic acid, ribavirin, and methotrexate. IMPDH filaments also spontaneously form in undifferentiated mouse embryonic stem cells and induced pluripotent stem cells, hinting they might function in various highly proliferative cell types. Therefore, we investigated IMPDH filament formation in human and murine T cells, which rely heavily on de novo guanine nucleotide synthesis to rapidly proliferate in response to antigenic challenge. We discovered extensive in vivo IMPDH filament formation in mature T cells, B cells, and other proliferating splenocytes of normal, adult B6 mice. Both cortical and medullary thymocytes in young and old mice also showed considerable assembly of IMPDH filaments. We then stimulated primary human peripheral blood mononuclear cells ex vivo with T cell mitogens phytohemagglutinin (PHA), concanavalin A (ConA), or antibodies to CD3 and CD28 for 72 h. We detected IMPDH filaments in 40–60% of T cells after activation compared to 0–10% of unstimulated T cells. Staining of activated T cells for the proliferation marker Ki-67 also showed an association between IMPDH filament formation and proliferation. Additionally, we transferred ovalbumin-specific CD4+ T cells from B6.OT-II mice into B6.Ly5a recipient mice, challenged these mice with ovalbumin, and harvested spleens 6 days later. In these spleens, we identified abundant IMPDH filaments in transferred T cells by immunofluorescence, indicating that IMPDH also polymerizes during in vivo antigen-specific T cell activation. Overall, our data indicate that IMPDH filament formation is a novel aspect of T cell activation and proliferation, and that filaments might be useful morphological markers for T cell activation. The data also suggest that in vivo IMPDH filament formation could be occurring in a variety of proliferating cell types throughout the body. We propose that T cell activation will be a valuable model for future experiments probing the molecular mechanisms that drive IMPDH polymerization, as well as how IMPDH filament formation affects cell function.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Georges Abboud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
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37
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Zhang S, Ding K, Shen QJ, Zhao S, Liu JL. Filamentation of asparagine synthetase in Saccharomyces cerevisiae. PLoS Genet 2018; 14:e1007737. [PMID: 30365499 PMCID: PMC6221361 DOI: 10.1371/journal.pgen.1007737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 11/07/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022] Open
Abstract
Asparagine synthetase (ASNS) and CTP synthase (CTPS) are two metabolic enzymes crucial for glutamine homeostasis. A genome-wide screening in Saccharomyces cerevisiae reveal that both ASNS and CTPS form filamentous structures termed cytoophidia. Although CTPS cytoophidia were well documented in recent years, the filamentation of ASNS is less studied. Using the budding yeast as a model system, here we confirm that two ASNS proteins, Asn1 and Asn2, are capable of forming cytoophidia in diauxic and stationary phases. We find that glucose deprivation induces ASNS filament formation. Although ASNS and CTPS form distinct cytoophidia with different lengths, both structures locate adjacently to each other in most cells. Moreover, we demonstrate that the Asn1 cytoophidia colocalize with the Asn2 cytoophidia, while Asn2 filament assembly is largely dependent on Asn1. In addition, we are able to alter Asn1 filamentation by mutagenizing key sites on the dimer interface. Finally, we show that ASN1D330V promotes filamentation. The ASN1D330V mutation impedes cell growth in an ASN2 knockout background, while growing normally in an ASN2 wild-type background. Together, this study reveals a connection between ASNS and CTPS cytoophidia and the differential filament-forming capability between two ASNS paralogs. Asparagine synthetase (ASNS) is an essential enzyme for biosynthesis of asparagine. We have recently shown that ASNS, similar to CTP synthase (CTPS), can assemble into snake-shaped structures termed cytoophidia. In this study, we reveal that the ASNS cytoophidium stays close with the CTPS cytoophidium in most cells. Two ASNS proteins, Asn1 and Asn2, localize in the same structure. The Asn1 protein is important for the formation of the Asn2 filaments. Mutant cells with branching Asn1 cytoophidia grow slower than wild-type cells. Our findings provide a better understanding of the ASNS cytoophidium as well as its relationship with the CTPS cytoophidium.
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Affiliation(s)
- Shanshan Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, China
| | - Kang Ding
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Qing-Ji Shen
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: ,
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McCluskey GD, Bearne SL. Anfractuous assemblies of IMP dehydrogenase and CTP synthase: new twists on regulation? FEBS J 2018; 285:3724-3728. [PMID: 30285320 DOI: 10.1111/febs.14658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022]
Abstract
CTP synthase (CTPS) and IMP dehydrogenase (IMPDH) catalyse the rate-limiting steps of de novo CTP and guanosine nucleotide biosynthesis, respectively, and form filament assemblies in response to inhibitors. A recent study explores the morphology and dynamics of these assemblies using fluorescence and super-resolution confocal microscopy with cell lines expressing CTPS1 and IMPDH2 fusion proteins. The formation and dismantling of mixed assemblies depends on nucleotide levels, suggesting a co-regulation function.
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Affiliation(s)
- Gregory D McCluskey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Stephen L Bearne
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Department of Chemistry, Dalhousie University, Halifax, Canada
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Chang CC, Keppeke GD, Sung LY, Liu JL. Interfilament interaction between IMPDH and CTPS cytoophidia. FEBS J 2018; 285:3753-3768. [PMID: 30085408 PMCID: PMC6220823 DOI: 10.1111/febs.14624] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 07/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) and cytidine triphosphate synthase (CTPS) are two metabolic enzymes that perform rate‐limiting steps in the de novo synthesis of purine and pyrimidine nucleotides, respectively. It has been shown that IMPDH and CTPS can comprise a filamentous macrostructure termed the cytoophidium, which may play a role in regulation of their catalytic activity. Although these two proteins may colocalise in the same cytoophidium, how they associate with one another is still elusive. As reported herein, we established a model HeLa cell line coexpressing OFP‐tagged IMPDH2 and GFP‐tagged CTPS1 and recorded the assembly, disassembly and movement of the cytoophidium in live cells. Moreover, by using super‐resolution confocal imaging, we demonstrate how IMPDH‐ and CTPS‐based filaments are aligned or intertwined in the mixed cytoophidium. Collectively, our findings provide a panorama of cytoophidium dynamics and suggest that IMPDH and CTPS cytoophidia may coordinate by interfilament interaction.
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Affiliation(s)
- Chia-Chun Chang
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Gerson D Keppeke
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK.,School of Life Science and Technology, ShanghaiTech University, China
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40
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McCluskey GD, Bearne SL. "Pinching" the ammonia tunnel of CTP synthase unveils coordinated catalytic and allosteric-dependent control of ammonia passage. Biochim Biophys Acta Gen Subj 2018; 1862:2714-2727. [PMID: 30251661 DOI: 10.1016/j.bbagen.2018.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/20/2018] [Accepted: 08/06/2018] [Indexed: 01/10/2023]
Abstract
Molecular gates within enzymes often play important roles in synchronizing catalytic events. We explored the role of a gate in cytidine-5'-triphosphate synthase (CTPS) from Escherichia coli. This glutamine amidotransferase catalyzes the biosynthesis of CTP from UTP using either l-glutamine or exogenous NH3 as a substrate. Glutamine is hydrolyzed in the glutaminase domain, with GTP acting as a positive allosteric effector, and the nascent NH3 passes through a gate located at the end of a ~25-Å tunnel before entering the synthase domain where CTP is generated. Substitution of the gate residue Val 60 by Ala, Cys, Asp, Trp, or Phe using site-directed mutagenesis and subsequent kinetic analyses revealed that V60-substitution impacts glutaminase activity, nucleotide binding, salt-dependent inhibition, and inter-domain NH3 transport. Surprisingly, the increase in steric bulk present in V60F perturbed the local structure consistent with "pinching" the tunnel, thereby revealing processes that synchronize the transfer of NH3 from the glutaminase domain to the synthase domain. V60F had a slightly reduced coupling efficiency at maximal glutaminase activity that was ameliorated by slowing down the glutamine hydrolysis reaction, consistent with a "bottleneck" effect. The inability of V60F to use exogenous NH3 was overcome in the presence of GTP, and more so if CTPS was covalently modified by 6-diazo-5-oxo-l-norleucine. Use of NH2OH by V60F as an alternative bulkier substrate occurred most efficiently when it was concomitant with the glutaminase reaction. Thus, the glutaminase activity and GTP-dependent activation act in concert to open the NH3 gate of CTPS to mediate inter-domain NH3 transport.
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Affiliation(s)
- Gregory D McCluskey
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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41
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Schiavon CR, Griffin ME, Pirozzi M, Parashuraman R, Zhou W, Jinnah HA, Reines D, Kahn RA. Compositional complexity of rods and rings. Mol Biol Cell 2018; 29:2303-2316. [PMID: 30024290 PMCID: PMC6249804 DOI: 10.1091/mbc.e18-05-0274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Maxwell E Griffin
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Marinella Pirozzi
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Raman Parashuraman
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - H A Jinnah
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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42
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Keppeke GD, Chang CC, Peng M, Chen LY, Lin WC, Pai LM, Andrade LEC, Sung LY, Liu JL. IMP/GTP balance modulates cytoophidium assembly and IMPDH activity. Cell Div 2018; 13:5. [PMID: 29946345 PMCID: PMC6004095 DOI: 10.1186/s13008-018-0038-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/06/2018] [Indexed: 02/07/2023] Open
Abstract
Background Inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme in de novo GTP biosynthesis, plays an important role in cell metabolism and proliferation. It has been demonstrated that IMPDH can aggregate into a macrostructure, termed the cytoophidium, in mammalian cells under a variety of conditions. However, the regulation and function of the cytoophidium are still elusive. Results In this study, we report that spontaneous filamentation of IMPDH is correlated with rapid cell proliferation. Intracellular IMP accumulation promoted cytoophidium assembly, whereas elevated GTP level triggered disassociation of aggregates. By using IMPDH2 CBS domain mutant cell models, which are unable to form the cytoophidium, we have determined that the cytoophidium is of the utmost importance for maintaining the GTP pool and normal cell proliferation in the condition that higher IMPDH activity is required. Conclusions Together, our results suggest a novel mechanism whereby cytoophidium assembly upregulates IMPDH activity and mediates guanine nucleotide homeostasis. Electronic supplementary material The online version of this article (10.1186/s13008-018-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerson Dierley Keppeke
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK
| | - Chia Chun Chang
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK.,2Institute of Biotechnology, National Taiwan University, Taipei, 106 Taiwan, ROC
| | - Min Peng
- 2Institute of Biotechnology, National Taiwan University, Taipei, 106 Taiwan, ROC
| | - Li-Yu Chen
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK
| | - Wei-Cheng Lin
- 3Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC
| | - Li-Mei Pai
- 3Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC.,4Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC.,5Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC
| | - Luis Eduardo Coelho Andrade
- 6Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP 04023-062 Brazil
| | - Li-Ying Sung
- 2Institute of Biotechnology, National Taiwan University, Taipei, 106 Taiwan, ROC.,7Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan, ROC
| | - Ji-Long Liu
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK.,8School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
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43
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Narvaez-Ortiz HY, Lopez AJ, Gupta N, Zimmermann BH. A CTP Synthase Undergoing Stage-Specific Spatial Expression Is Essential for the Survival of the Intracellular Parasite Toxoplasma gondii. Front Cell Infect Microbiol 2018; 8:83. [PMID: 29623259 PMCID: PMC5874296 DOI: 10.3389/fcimb.2018.00083] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/28/2018] [Indexed: 01/17/2023] Open
Abstract
Cytidine triphosphate synthase catalyzes the synthesis of cytidine 5′-triphosphate (CTP) from uridine 5′-triphosphate (UTP), the final step in the production of cytidine nucleotides. CTP synthases also form filamentous structures of different morphologies known as cytoophidia, whose functions in most organisms are unknown. Here, we identified and characterized a novel CTP synthase (TgCTPS) from Toxoplasma gondii. We show that TgCTPS is capable of substituting for its counterparts in the otherwise lethal double mutant (ura7Δ ura8Δ) of Saccharomyces cerevisiae. Equally, recombinant TgCTPS purified from Escherichia coli encodes for a functional protein in enzyme assays. The epitope-tagged TgCTPS under the control of its endogenous promoter displays a punctate cytosolic distribution, which undergoes spatial reorganization to form foci or filament-like structures when the parasite switches from a nutrient-replete (intracellular) to a nutrient-scarce (extracellular) condition. An analogous phenotype is observed upon nutrient stress or after treatment with a glutamine analog, 6-diazo-5-oxo-L-norleucine (DON). The exposure of parasites to DON disrupts the lytic cycle, and the TgCTPS is refractory to a genetic deletion, suggesting an essential requirement of this enzyme for T. gondii. Not least, this study, together with previous studies, supports that CTP synthase can serve as a potent drug target, because the parasite, unlike human host cells, cannot compensate for the lack of CTP synthase activity.
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Affiliation(s)
| | - Andrea J Lopez
- Departamento de Ciencias Biologicas, Universidad de los Andes, Bogota, Colombia
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
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44
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CTP synthase forms the cytoophidium in human hepatocellular carcinoma. Exp Cell Res 2017; 361:292-299. [DOI: 10.1016/j.yexcr.2017.10.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/16/2022]
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Abstract
The organization of metabolic multienzyme complexes has been hypothesized to benefit metabolic processes and provide a coordinated way for the cell to regulate metabolism. Historically, their existence has been supported by various in vitro techniques. However, it is only recently that the existence of metabolic complexes inside living cells has come to light to corroborate this long-standing hypothesis. Indeed, subcellular compartmentalization of metabolic enzymes appears to be widespread and highly regulated. On the other hand, it is still challenging to demonstrate the functional significance of these enzyme complexes in the context of the cellular milieu. In this review, we discuss the current understanding of metabolic enzyme complexes by primarily focusing on central carbon metabolism and closely associated metabolic pathways in a variety of organisms, as well as their regulation and functional contributions to cells.
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Affiliation(s)
- Danielle L Schmitt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC) , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Songon An
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC) , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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46
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Huang Y, Wang JJ, Ghosh S, Liu JL. Critical roles of CTP synthase N-terminal in cytoophidium assembly. Exp Cell Res 2017; 354:122-133. [PMID: 28342900 PMCID: PMC5405848 DOI: 10.1016/j.yexcr.2017.03.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/18/2017] [Accepted: 03/20/2017] [Indexed: 01/27/2023]
Abstract
Several metabolic enzymes assemble into distinct intracellular structures in prokaryotes and eukaryotes suggesting an important functional role in cell physiology. The CTP-generating enzyme CTP synthase forms long filamentous structures termed cytoophidia in bacteria, yeast, fruit flies and human cells independent of its catalytic activity. However, the amino acid determinants for protein-protein interaction necessary for polymerisation remained unknown. In this study, we systematically analysed the role of the conserved N-terminal of Drosophila CTP synthase in cytoophidium assembly. Our mutational analyses identified three key amino acid residues within this region that play an instructive role in organisation of CTP synthase into a filamentous structure. Co-transfection assays demonstrated formation of heteromeric CTP synthase filaments which is disrupted by protein carrying a mutated N-terminal alanine residue thus revealing a dominant-negative activity. Interestingly, the dominant-negative activity is supressed by the CTP synthase inhibitor DON. Furthermore, we found that the amino acids at the corresponding position in the human protein exhibit similar properties suggesting conservation of their function through evolution. Our data suggest that cytoophidium assembly is a multi-step process involving N-terminal-dependent sequential interactions between correctly folded structural units and provide insights into the assembly of these enigmatic structures. CTP synthase mutational analyses reveal N-terminal amino acids that regulate filament self-assembly. Amino acid 20 of CTP synthase plays key role in protein interactions necessary for polymerisation. The dominant-negative activity is supressed by CTP synthase inhibitor DON. The functional properties of the amino acids are conserved in Drosophila and human CTP synthases.
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Affiliation(s)
- Yong Huang
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom; Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Sanjay Ghosh
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom.
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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Chitrakar I, Kim-Holzapfel DM, Zhou W, French JB. Higher order structures in purine and pyrimidine metabolism. J Struct Biol 2017; 197:354-364. [PMID: 28115257 DOI: 10.1016/j.jsb.2017.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
The recent discovery of several forms of higher order protein structures in cells has shifted the paradigm of how we think about protein organization and metabolic regulation. These dynamic and controllable protein assemblies, which are composed of dozens or hundreds of copies of an enzyme or related enzymes, have emerged as important players in myriad cellular processes. We are only beginning to appreciate the breadth of function of these types of macromolecular assemblies. These higher order structures, which can be assembled in response to varied cellular stimuli including changing metabolite concentrations or signaling cascades, give the cell the capacity to modulate levels of biomolecules both temporally and spatially. This provides an added level of control with distinct kinetics and unique features that can be harnessed as a subtle, yet powerful regulatory mechanism. Due, in large part, to advances in structural methods, such as crystallography and cryo-electron microscopy, and the advent of super-resolution microscopy techniques, a rapidly increasing number of these higher order structures are being identified and characterized. In this review, we detail what is known about the structure, function and control mechanisms of these mesoscale protein assemblies, with a particular focus on those involved in purine and pyrimidine metabolism. These structures have important implications both for our understanding of fundamental cellular processes and as fertile ground for new targets for drug discovery and development.
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Affiliation(s)
- Iva Chitrakar
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Deborah M Kim-Holzapfel
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Weijie Zhou
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States
| | - Jarrod B French
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States.
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48
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Anti-rods/rings autoantibody seropositivity does not affect response to telaprevir treatment for chronic hepatitis C infection. AUTOIMMUNITY HIGHLIGHTS 2016; 7:15. [PMID: 27844412 PMCID: PMC5108729 DOI: 10.1007/s13317-016-0087-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022]
Abstract
PURPOSE Autoantibodies to intracellular 'rods and rings' structures (anti-rods/rings or anti-RR) are strongly associated with hepatitis C (HCV) patients treated with interferon-α/ribavirin (IFN/RBV) and are linked with non-responsiveness to IFN/RBV or relapse, especially in Italian patients. This is the first study to determine whether there is any correlation of anti-RR with non-responsiveness to IFN/RBV treatment in patients also treated with telaprevir (TPV), one of several new therapies for chronic HCV recently implemented. METHODS From 2013 to 2014, 52 HCV-infected patients were treated with IFN/RBV and TPV at five Italian clinics. Patient sera were collected and analyzed by indirect immunofluorescence for the presence of anti-RR antibodies. Patients were classified as anti-RR positive or anti-RR negative, and then various biological and clinical variables were analyzed to compare the two groups, including gender, age, HCV genotype, previous IFN/RBV treatment, and IFN/RBV/TPV treatment outcome. RESULTS Of these 52 HCV patients treated with IFN/RBV/TPV, 10/32 (31%) who previously received IFN/RBV were anti-RR positive, compared to 0 of 20 treatment-naïve patients. Anti-RR-positive patients relapsed more than anti-RR-negative patients (3/10, 30% vs. 2/42, 5%; p < 0.05). However, zero anti-RR-positive patients were non-responsive, and frequencies of sustained virological response were similar (anti-RR positive: 7/10, 70% vs. anti-RR negative: 33/42, 79%). CONCLUSIONS Overall, the data suggest that anti-RR seropositivity is not associated with resistance to TPV treatment in this patient cohort, but monitoring anti-RR-positive patients for relapse within the first 6 months after treatment may be useful.
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49
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Liu JL. The Cytoophidium and Its Kind: Filamentation and Compartmentation of Metabolic Enzymes. Annu Rev Cell Dev Biol 2016; 32:349-372. [DOI: 10.1146/annurev-cellbio-111315-124907] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China;
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50
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Calise SJ, Purich DL, Nguyen T, Saleem DA, Krueger C, Yin JD, Chan EKL. 'Rod and ring' formation from IMP dehydrogenase is regulated through the one-carbon metabolic pathway. J Cell Sci 2016; 129:3042-52. [PMID: 27343244 DOI: 10.1242/jcs.183400] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/21/2016] [Indexed: 12/29/2022] Open
Abstract
'Rods and rings' (RRs) are conserved, non-membrane-bound intracellular polymeric structures composed, in part, of inosine monophosphate dehydrogenase (IMPDH), a key enzyme leading to GMP and GTP biosynthesis. RR formation is induced by IMPDH inhibitors as well as glutamine deprivation. They also form upon treatment of cells with glutamine synthetase inhibitors. We now report that depriving cells of serine and glycine promotes RR formation, and we have traced these effects to dihydrofolate reductase (DHFR) and serine hydroxymethyltransferase-2 (SHMT2), pivotal enzymes in one-carbon metabolism and nucleotide biosynthesis. RR assembly is likewise induced upon DHFR inhibition by methotrexate or aminopterin as well as siRNA-mediated knockdown of DHFR or SHMT2. Because RR assembly occurs when guanine nucleotide biosynthesis is inhibited, and because RRs rapidly disassemble after the addition of guanine nucleotide precursors, RR formation might be an adaptive homeostatic mechanism, allowing IMPDH to sense changes in the one-carbon folate pathway.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Daniel L Purich
- Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610-0245, USA
| | - Thuy Nguyen
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Dania A Saleem
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Claire Krueger
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Joyce D Yin
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
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