1
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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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2
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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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3
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Yoon J, Cho L, Kim S, Tun W, Peng X, Pasriga R, Moon S, Hong W, Ji H, Jung K, Jeon J, An G. CTP synthase is essential for early endosperm development by regulating nuclei spacing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2177-2191. [PMID: 34058048 PMCID: PMC8541778 DOI: 10.1111/pbi.13644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Lae‐Hyeon Cho
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Sung‐Ryul Kim
- Gene Identification and Validation GroupGenetic Design and Validation UnitInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Win Tun
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Xin Peng
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Sunok Moon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Woo‐Jong Hong
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Hyeonso Ji
- National Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Ki‐Hong Jung
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Jong‐Seong Jeon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
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4
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Jia F, Chi C, Han M. Regulation of Nucleotide Metabolism and Germline Proliferation in Response to Nucleotide Imbalance and Genotoxic Stresses by EndoU Nuclease. Cell Rep 2021; 30:1848-1861.e5. [PMID: 32049015 PMCID: PMC7050212 DOI: 10.1016/j.celrep.2020.01.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/06/2019] [Accepted: 01/15/2020] [Indexed: 12/23/2022] Open
Abstract
Nucleotide deprivation and imbalance present detrimental conditions for animals and are thus expected to trigger cellular responses that direct protective changes in metabolic, developmental, and behavioral programs, albeit such mechanisms are vastly underexplored. Following our previous finding that Caenorhabditis elegans shut down germ cell proliferation in response to pyrimidine deprivation, we find in this study that endonuclease ENDU-2 regulates nucleotide metabolism and germ cell proliferation in response to nucleotide imbalance and other genotoxic stress, and that it affects mitotic chromosomal segregation in the intestine and lifespan. ENDU-2 expression is induced by nucleotide imbalance and genotoxic stress, and ENDU-2 exerts its function in the intestine, mostly by inhibiting the phosphorylation of CTPS-1 through repressing the PKA pathway and histone deacetylase HDA-1. Human EndoU also affects the response to genotoxic drugs. Our work reveals an unknown role of ENDU-2 in regulating nucleotide metabolism and animals' response to genotoxic stress, which may link EndoU function to cancer treatment.
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Affiliation(s)
- Fan Jia
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Colorado at Boulder, Boulder, CO 80309-0347, USA.
| | - Congwu Chi
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Colorado at Boulder, Boulder, CO 80309-0347, USA
| | - Min Han
- Department of Molecular, Cellular, and Developmental Biology (MCDB), University of Colorado at Boulder, Boulder, CO 80309-0347, USA
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5
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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: 8] [Impact Index Per Article: 2.0] [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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6
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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7
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Boschat AC, Minet N, Martin E, Barouki R, Latour S, Sanquer S. CTP synthetase activity assay by liquid chromatography tandem mass spectrometry in the multiple reaction monitoring mode. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:885-893. [PMID: 31524312 DOI: 10.1002/jms.4442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Cytidine 5'-triphosphate synthetase (CTPS) is known to be a central enzyme in the de novo synthesis of CTP. We have recently demonstrated that a deficiency in CTPS1 is associated with an impaired capacity of activated lymphocytes to proliferate leading to a combined immunodeficiency disease. In order to better document its role in immunomodulation, we developed a method for measuring CTPS activity in human lymphocytes. Using liquid chromatography-mass spectrometry, we quantified CTPS activity by measuring CTP in cell lysates. A stable isotope analog of CTP served as internal standard. We characterized the kinetic parameters Vmax and Km of CTPS and verified that an inhibition of the enzyme activity was induced after 3-deazauridine (3DAU) treatment, a known inhibitor of CTPS. We then determined CTPS activity in healthy volunteers, in a family whose child displayed a homozygous mutation in CTPS1 gene and in patients who had developed or not a chronic lung allograft dysfunction (CLAD) after lung transplantation. Linearity of the CTP determination was observed up to 451 μmol/L, with accuracy in the 15% tolerance range. Michaelis-Menten kinetics for lysates of resting cells were Km =280±310 μmol/L for UTP, Vmax =83±20 pmol/min and, for lysates of activated PBMCs, Km =230±280 μmol/L for UTP, Vmax =379±90 pmol/min. Treatment by 3DAU and homozygous mutation in CTPS1 gene abolished the induction of CTPS activity associated with cell stimulation, and CTPS activity was significantly reduced in the patients who developed CLAD. We conclude that this test is suitable to reveal the involvement of CTPS alteration in immunodeficiency.
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Affiliation(s)
- Anne-Claire Boschat
- Plateforme de métabolomique, Institut Imagine, Université Paris Descartes, Paris, France
- INSERM UMR-S 1124, Centre Universitaire des Saints-Pères Université Paris Descartes, Paris, France
| | - Norbert Minet
- Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris, France
- INSERM UMR 1163, Université Paris Descartes, Institut Imagine, Paris, France
| | - Emmanuel Martin
- Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris, France
- INSERM UMR 1163, Université Paris Descartes, Institut Imagine, Paris, France
| | - Robert Barouki
- INSERM UMR-S 1124, Centre Universitaire des Saints-Pères Université Paris Descartes, Paris, France
- Plateforme de spectrométrie de masse, AP-HP.Centre, Hôpital Universitaire Necker-enfants malades, Paris, France
- Service de Biochimie Métabolomique et Protéomique, AP-HP.Centre, Hôpital Universitaire Necker-Enfants malades, Paris, France
| | - Sylvain Latour
- Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris, France
- INSERM UMR 1163, Université Paris Descartes, Institut Imagine, Paris, France
| | - Sylvia Sanquer
- INSERM UMR-S 1124, Centre Universitaire des Saints-Pères Université Paris Descartes, Paris, France
- Service de Biochimie Métabolomique et Protéomique, AP-HP.Centre, Hôpital Universitaire Necker-Enfants malades, Paris, France
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8
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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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9
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Sun Z, Liu JL. mTOR-S6K1 pathway mediates cytoophidium assembly. J Genet Genomics 2019; 46:65-74. [PMID: 30857853 PMCID: PMC6459811 DOI: 10.1016/j.jgg.2018.11.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/21/2018] [Accepted: 11/30/2018] [Indexed: 01/17/2023]
Abstract
CTP synthase (CTPS), the rate-limiting enzyme in de novo CTP biosynthesis, has been demonstrated to assemble into evolutionarily conserved filamentous structures, termed cytoophidia, in Drosophila, bacteria, yeast and mammalian cells. However, the regulation and function of the cytoophidium remain elusive. Here, we provide evidence that the mechanistic target of rapamycin (mTOR) pathway controls cytoophidium assembly in mammalian and Drosophila cells. In mammalian cells, we find that inhibition of mTOR pathway attenuates cytoophidium formation. Moreover, CTPS cytoophidium assembly appears to be dependent on the mTOR complex 1 (mTORC1) mainly. In addition, knockdown of the mTORC1 downstream target S6K1 can inhibit cytoophidium formation, while overexpression of the constitutively active S6K1 reverses mTOR knockdown-induced cytoophidium disassembly. Finally, reducing mTOR protein expression results in a decrease of the length of cytoophidium in Drosophila follicle cells. Therefore, our study connects CTPS cytoophidium formation with the mTOR signaling pathway.
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Affiliation(s)
- Zhe Sun
- 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.
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10
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Zhao Y, Yan L, Peng L, Huang X, Zhang G, Chen B, Ren J, Zhou Y, Yang L, Peng L, Jin X, Wang Y. Oleoylethanolamide alleviates macrophage formation via AMPK/PPARα/STAT3 pathway. Pharmacol Rep 2018; 70:1185-1194. [DOI: 10.1016/j.pharep.2018.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 06/08/2018] [Accepted: 06/22/2018] [Indexed: 01/22/2023]
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11
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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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12
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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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13
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Lynch EM, Hicks DR, Shepherd M, Endrizzi JA, Maker A, Hansen JM, Barry RM, Gitai Z, Baldwin EP, Kollman JM. Human CTP synthase filament structure reveals the active enzyme conformation. Nat Struct Mol Biol 2017; 24:507-514. [PMID: 28459447 PMCID: PMC5472220 DOI: 10.1038/nsmb.3407] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/06/2017] [Indexed: 12/11/2022]
Abstract
The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we show that for human CTPS, polymerization increases catalytic activity. The cryo-EM structures of bacterial and human CTPS filaments differ considerably in overall architecture and in the conformation of the CTPS protomer, explaining the divergent consequences of polymerization on activity. The structure of human CTPS filament, the first structure of the full-length human enzyme, reveals a novel active conformation. The filament structures elucidate allosteric mechanisms of assembly and regulation that rely on a conserved conformational equilibrium. The findings may provide a mechanism for increasing human CTPS activity in response to metabolic state and challenge the assumption that metabolic filaments are generally storage forms of inactive enzymes. Allosteric regulation of CTPS polymerization by ligands likely represents a fundamental mechanism underlying assembly of other metabolic filaments.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
| | - Matthew Shepherd
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - James A Endrizzi
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
| | - Allison Maker
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, Washington, USA
| | - Rachael M Barry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Enoch P Baldwin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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14
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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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15
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Pai LM, Wang PY, Lin WC, Chakraborty A, Yeh CT, Lin YH. Ubiquitination and filamentous structure of cytidine triphosphate synthase. Fly (Austin) 2016; 10:108-14. [PMID: 27116391 PMCID: PMC4970526 DOI: 10.1080/19336934.2016.1182268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Living organisms respond to nutrient availability by regulating the activity of metabolic enzymes. Therefore, the reversible post-translational modification of an enzyme is a common regulatory mechanism for energy conservation. Recently, cytidine-5'-triphosphate (CTP) synthase was discovered to form a filamentous structure that is evolutionarily conserved from flies to humans. Interestingly, induction of the formation of CTP synthase filament is responsive to starvation or glutamine depletion. However, the biological roles of this structure remain elusive. We have recently shown that ubiquitination regulates CTP synthase activity by promoting filament formation in Drosophila ovaries during endocycles. Intriguingly, although the ubiquitination process was required for filament formation induced by glutamine depletion, CTP synthase ubiquitination was found to be inversely correlated with filament formation in Drosophila and human cell lines. In this article, we discuss the putative dual roles of ubiquitination, as well as its physiological implications, in the regulation of CTP synthase structure.
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Affiliation(s)
- Li-Mei Pai
- a Department of Biochemistry , Chang Gung University , Taoyuan City , Taiwan.,b Molecular Medicine Research Center, Chang Gung University , Taoyuan City , Taiwan.,c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan.,d Liver Research Center, Chang Gung Memorial Hospital , Taoyuan City , Taiwan
| | - Pei-Yu Wang
- a Department of Biochemistry , Chang Gung University , Taoyuan City , Taiwan.,b Molecular Medicine Research Center, Chang Gung University , Taoyuan City , Taiwan
| | - Wei-Cheng Lin
- b Molecular Medicine Research Center, Chang Gung University , Taoyuan City , Taiwan
| | - Archan Chakraborty
- c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan
| | - Chau-Ting Yeh
- c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan.,d Liver Research Center, Chang Gung Memorial Hospital , Taoyuan City , Taiwan
| | - Yu-Hung Lin
- c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan
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16
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Aughey GN, Grice SJ, Shen QJ, Xu Y, Chang CC, Azzam G, Wang PY, Freeman-Mills L, Pai LM, Sung LY, Yan J, Liu JL. Nucleotide synthesis is regulated by cytoophidium formation during neurodevelopment and adaptive metabolism. Biol Open 2014; 3:1045-56. [PMID: 25326513 PMCID: PMC4232762 DOI: 10.1242/bio.201410165] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The essential metabolic enzyme CTP synthase (CTPsyn) can be compartmentalised to form an evolutionarily-conserved intracellular structure termed the cytoophidium. Recently, it has been demonstrated that the enzymatic activity of CTPsyn is attenuated by incorporation into cytoophidia in bacteria and yeast cells. Here we demonstrate that CTPsyn is regulated in a similar manner in Drosophila tissues in vivo. We show that cytoophidium formation occurs during nutrient deprivation in cultured cells, as well as in quiescent and starved neuroblasts of the Drosophila larval central nervous system. We also show that cytoophidia formation is reversible during neurogenesis, indicating that filament formation regulates pyrimidine synthesis in a normal developmental context. Furthermore, our global metabolic profiling demonstrates that CTPsyn overexpression does not significantly alter CTPsyn-related enzymatic activity, suggesting that cytoophidium formation facilitates metabolic stabilisation. In addition, we show that overexpression of CTPsyn only results in moderate increase of CTP pool in human stable cell lines. Together, our study provides experimental evidence, and a mathematical model, for the hypothesis that inactive CTPsyn is incorporated into cytoophidia.
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Affiliation(s)
- Gabriel N Aughey
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stuart J Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Qing-Ji Shen
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Yichi Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chia-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Ghows Azzam
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Pei-Yu Wang
- Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan, Republic of China Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China
| | - Luke Freeman-Mills
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Li-Mei Pai
- Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan, Republic of China Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
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17
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Strochlic TI, Stavrides KP, Thomas SV, Nicolas E, O'Reilly AM, Peterson JR. Ack kinase regulates CTP synthase filaments during Drosophila oogenesis. EMBO Rep 2014; 15:1184-91. [PMID: 25223282 DOI: 10.15252/embr.201438688] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The enzyme CTP synthase (CTPS) dynamically assembles into macromolecular filaments in bacteria, yeast, Drosophila, and mammalian cells, but the role of this morphological reorganization in regulating CTPS activity is controversial. During Drosophila oogenesis, CTPS filaments are transiently apparent in ovarian germline cells during a period of intense genomic endoreplication and stockpiling of ribosomal RNA. Here, we demonstrate that CTPS filaments are catalytically active and that their assembly is regulated by the non-receptor tyrosine kinase DAck, the Drosophila homologue of mammalian Ack1 (activated cdc42-associated kinase 1), which we find also localizes to CTPS filaments. Egg chambers from flies deficient in DAck or lacking DAck catalytic activity exhibit disrupted CTPS filament architecture and morphological defects that correlate with reduced fertility. Furthermore, ovaries from these flies exhibit reduced levels of total RNA, suggesting that DAck may regulate CTP synthase activity. These findings highlight an unexpected function for DAck and provide insight into a novel pathway for the developmental control of an essential metabolic pathway governing nucleotide biosynthesis.
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Affiliation(s)
- Todd I Strochlic
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kevin P Stavrides
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sam V Thomas
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Alana M O'Reilly
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA, USA
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18
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Noree C, Monfort E, Shiau AK, Wilhelm JE. Common regulatory control of CTP synthase enzyme activity and filament formation. Mol Biol Cell 2014; 25:2282-90. [PMID: 24920825 PMCID: PMC4116302 DOI: 10.1091/mbc.e14-04-0912] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTP synthase is one of many enzymes that form novel intracellular filaments/structures. A
structure–function approach is used to show that the same regulatory sites that control CTP
synthase enzyme activity also control filament formation. Close coupling of assembly to enzyme
regulation is proposed to be a general feature of these structures. The ability of enzymes to assemble into visible supramolecular complexes is a widespread
phenomenon. Such complexes have been hypothesized to play a number of roles; however, little is
known about how the regulation of enzyme activity is coupled to the assembly/disassembly of these
cellular structures. CTP synthase is an ideal model system for addressing this question because its
activity is regulated via multiple mechanisms and its filament-forming ability is evolutionarily
conserved. Our structure–function studies of CTP synthase in Saccharomyces
cerevisiae reveal that destabilization of the active tetrameric form of the enzyme
increases filament formation, suggesting that the filaments comprise inactive CTP synthase dimers.
Furthermore, the sites responsible for feedback inhibition and allosteric activation control
filament length, implying that multiple regions of the enzyme can influence filament structure. In
contrast, blocking catalysis without disrupting the regulatory sites of the enzyme does not affect
filament formation or length. Together our results argue that the regulatory sites that control CTP
synthase function, but not enzymatic activity per se, are critical for controlling filament
assembly. We predict that the ability of enzymes to form supramolecular structures in general is
closely coupled to the mechanisms that regulate their activity.
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Affiliation(s)
- Chalongrat Noree
- Section on Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Elena Monfort
- Section on Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Andrew K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093
| | - James E Wilhelm
- Section on Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
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19
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Deranieh RM, He Q, Caruso JA, Greenberg ML. Phosphorylation regulates myo-inositol-3-phosphate synthase: a novel regulatory mechanism of inositol biosynthesis. J Biol Chem 2013; 288:26822-33. [PMID: 23902760 DOI: 10.1074/jbc.m113.479121] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
myo-Inositol-3-phosphate synthase (MIPS) plays a crucial role in inositol homeostasis. Transcription of the coding gene INO1 is highly regulated. However, regulation of the enzyme is not well defined. We previously showed that MIPS is indirectly inhibited by valproate, suggesting that the enzyme is post-translationally regulated. Using (32)Pi labeling and phosphoamino acid analysis, we show that yeast MIPS is a phosphoprotein. Mass spectrometry analysis identified five phosphosites, three of which are conserved in the human MIPS. Analysis of phosphorylation-deficient and phosphomimetic site mutants indicated that the three conserved sites in yeast (Ser-184, Ser-296, and Ser-374) and humans (Ser-177, Ser-279, and Ser-357) affect MIPS activity. Both S296A and S296D yeast mutants and S177A and S177D human mutants exhibited decreased enzymatic activity, suggesting that a serine residue is critical at that location. The phosphomimetic mutations S184D (human S279D) and S374D (human S357D) but not the phosphodeficient mutations decreased activity, suggesting that phosphorylation of these two sites is inhibitory. The double mutation S184A/S374A caused an increase in MIPS activity, conferred a growth advantage, and partially rescued sensitivity to valproate. Our findings identify a novel mechanism of regulation of inositol synthesis by phosphorylation of MIPS.
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20
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Natter K, Kohlwein SD. Yeast and cancer cells - common principles in lipid metabolism. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1831:314-26. [PMID: 22989772 PMCID: PMC3549488 DOI: 10.1016/j.bbalip.2012.09.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 09/07/2012] [Accepted: 09/08/2012] [Indexed: 12/15/2022]
Abstract
One of the paradigms in cancer pathogenesis is the requirement of a cell to undergo transformation from respiration to aerobic glycolysis - the Warburg effect - to become malignant. The demands of a rapidly proliferating cell for carbon metabolites for the synthesis of biomass, energy and redox equivalents, are fundamentally different from the requirements of a differentiated, quiescent cell, but it remains open whether this metabolic switch is a cause or a consequence of malignant transformation. One of the major requirements is the synthesis of lipids for membrane formation to allow for cell proliferation, cell cycle progression and cytokinesis. Enzymes involved in lipid metabolism were indeed found to play a major role in cancer cell proliferation, and most of these enzymes are conserved in the yeast, Saccharomyces cerevisiae. Most notably, cancer cell physiology and metabolic fluxes are very similar to those in the fermenting and rapidly proliferating yeast. Both types of cells display highly active pathways for the synthesis of fatty acids and their incorporation into complex lipids, and imbalances in synthesis or turnover of lipids affect growth and viability of both yeast and cancer cells. Thus, understanding lipid metabolism in S. cerevisiae during cell cycle progression and cell proliferation may complement recent efforts to understand the importance and fundamental regulatory mechanisms of these pathways in cancer.
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Affiliation(s)
- Klaus Natter
- University of Graz, Institute of Molecular Biosciences, Lipidomics Research Center Graz, Humboldtstrasse 50/II, 8010 Graz,
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21
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Lauritsen I, Willemoës M, Jensen KF, Johansson E, Harris P. Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:201-8. [PMID: 21301086 PMCID: PMC3034608 DOI: 10.1107/s1744309110052334] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 12/13/2010] [Indexed: 11/10/2022]
Abstract
CTP synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. Active CTP synthase is a tetrameric enzyme composed of a dimer of dimers. The tetramer is favoured in the presence of the substrate nucleotides ATP and UTP; when saturated with nucleotide, the tetramer completely dominates the oligomeric state of the enzyme. Furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. The crystal structure of a dimeric form of CTP synthase from Sulfolobus solfataricus has been determined at 2.5 Å resolution. A comparison of the dimeric interface with the intermolecular interfaces in the tetrameric structures of Thermus thermophilus CTP synthase and Escherichia coli CTP synthase shows that the dimeric interfaces are almost identical in the three systems. Residues that are involved in the tetramerization of S. solfataricus CTP synthase according to a structural alignment with the E. coli enzyme all have large thermal parameters in the dimeric form. Furthermore, they are seen to undergo substantial movement upon tetramerization.
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Affiliation(s)
- Iben Lauritsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Martin Willemoës
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kaj Frank Jensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Eva Johansson
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, DK-2800 Kgs. Lyngby, Denmark
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22
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Kassel KM, Au DR, Higgins MJ, Hines M, Graves LM. Regulation of human cytidine triphosphate synthetase 2 by phosphorylation. J Biol Chem 2010; 285:33727-36. [PMID: 20739275 DOI: 10.1074/jbc.m110.178566] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytidine triphosphate synthetase (CTPS) is the rate-limiting enzyme in de novo CTP synthesis and is required for the formation of RNA, DNA, and phospholipids. This study determined the kinetic properties of the individual human CTPS isozymes (hCTPS1 and hCTPS2) and regulation through substrate concentration, oligomerization, and phosphorylation. Kinetic analysis demonstrated that both hCTPS1 and hCTPS2 were maximally active at physiological concentrations of ATP, GTP, and glutamine, whereas the K(m) and IC(50) values for the substrate UTP and the product CTP, respectively, were close to their physiological concentrations, indicating that the intracellular concentrations of UTP and CTP may precisely regulate hCTPS activity. Low serum treatment increased hCTPS2 phosphorylation, and five probable phosphorylation sites were identified in the hCTPS2 C-terminal domain. Metabolic labeling of hCTPS2 with [(32)P]H(3)PO(4) demonstrated that Ser(568) and Ser(571) were two major phosphorylation sites, and additional studies demonstrated that Ser(568) was phosphorylated by casein kinase 1 both in vitro and in vivo. Interestingly, mutation of Ser(568) (S568A) but not Ser(571) significantly increased hCTPS2 activity, demonstrating that Ser(568) is a major inhibitory phosphorylation site. The S568A mutation had a greater effect on the glutamine than ammonia-dependent activity, indicating that phosphorylation of this site may influence the glutaminase domain of hCTPS2. Deletion of the C-terminal regulatory domain of hCTPS1 also greatly increased the V(max) of this enzyme. In summary, this is the first study to characterize the kinetic properties of hCTPS1 and hCTPS2 and to identify Ser(568) as a major site of CTPS2 regulation by phosphorylation.
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Affiliation(s)
- Karen M Kassel
- Department of Pharmacology, University of North Carolina at Chapel Hill, North Carolina 27599, USA
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23
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Roy AC, Lunn FA, Bearne SL. Inhibition of CTP synthase from Escherichia coli by xanthines and uric acids. Bioorg Med Chem Lett 2009; 20:141-4. [PMID: 20004571 DOI: 10.1016/j.bmcl.2009.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 11/05/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
CTP synthase (CTPS) catalyzes the conversion of UTP to CTP and is a recognized target for the development of anticancer, antiviral, and antiprotozoal agents. Xanthine and related compounds inhibit CTPS activity (IC(50)=0.16-0.58mM). The presence of an 8-oxo function (i.e., uric acids) enhances inhibition (IC(50)=0.060-0.121mM). An intact purine ring with anionic character favors inhibition. In general, methylation of the purine does not significantly affect inhibition.
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Affiliation(s)
- Alexander C Roy
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
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24
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Taylor SD, Lunn FA, Bearne SL. Ground state, intermediate, and multivalent nucleotide analogue inhibitors of cytidine 5'-triphosphate synthase. ChemMedChem 2009; 3:1853-7. [PMID: 18988211 DOI: 10.1002/cmdc.200800236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L3G1, Canada.
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25
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Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly(142) is critical for tetramerization of CTP synthase from Escherichia coli. Biochem J 2008; 412:113-21. [PMID: 18260824 DOI: 10.1042/bj20071163] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CTPS (cytidine 5'-triphosphate synthase) catalyses the ATP-dependent formation of CTP from UTP using either ammonia or L-glutamine as the nitrogen source. Binding of the substrates ATP and UTP, or the product CTP, promotes oligomerization of CTPS from inactive dimers to active tetramers. In the present study, site-directed mutagenesis was used to replace the fully conserved glycine residues 142 and 143 within the UTP-binding site and 146 within the CTP-binding site of Escherchia coli CTPS. CD spectral analyses of wild-type CTPS and the glycine mutants showed a slight reduction of approximately 15% in alpha-helical content for G142A and G143A relative to G146A and wild-type CTPS, suggesting some local alterations in structure. Relative to wild-type CTPS, the values of k(cat)/K(m) for ammonia-dependent and glutamine-dependent CTP formation catalysed by G143A were reduced 22- and 16-fold respectively, whereas the corresponding values for G146A were reduced only 1.4- and 1.8-fold respectively. The glutaminase activity (k(cat)) of G146A was similar to that exhibited by the wild-type enzyme, whereas that of G143A was reduced 7.5-fold. G146A exhibited substrate inhibition at high concentrations of ammonia and a partial uncoupling of glutamine hydrolysis from CTP production. Although the apparent affinity (1/[S](0.5)) of G143A and G146A for UTP was reduced approximately 4-fold, G146A exhibited increased co-operativity with respect to UTP. Thus mutations in the CTP-binding site can affect UTP-dependent activity. Surprisingly, G142A was inactive with both ammonia and glutamine as substrates. Gel-filtration HPLC experiments revealed that both G143A and G146A were able to form active tetramers in the presence of ATP and UTP; however, nucleotide-dependent tetramerization of G142A was significantly impaired. Our observations highlight the sensitivity of the structure of CTPS to mutations in the UTP- and CTP-binding sites, with Gly(142) being critical for nucleotide-dependent oligomerization of CTPS to active tetramers. This 'structural sensitivity' may limit the number and/or types of mutations that could be selected for during the development of resistance to cytotoxic pyrimidine nucleotide analogues.
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26
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Chang YF, Carman GM. CTP synthetase and its role in phospholipid synthesis in the yeast Saccharomyces cerevisiae. Prog Lipid Res 2008; 47:333-9. [PMID: 18439916 DOI: 10.1016/j.plipres.2008.03.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CTP synthetase is a cytosolic-associated glutamine amidotransferase enzyme that catalyzes the ATP-dependent transfer of the amide nitrogen from glutamine to the C-4 position of UTP to form CTP. In the yeast Saccharomyces cerevisiae, the reaction product CTP is an essential precursor of all membrane phospholipids that are synthesized via the Kennedy (CDP-choline and CDP-ethanolamine branches) and CDP-diacylglycerol pathways. The URA7 and URA8 genes encode CTP synthetase in S. cerevisiae, and the URA7 gene is responsible for the majority of CTP synthesized in vivo. The CTP synthetase enzymes are allosterically regulated by CTP product inhibition. Mutations that alleviate this regulation result in an elevated cellular level of CTP and an increase in phospholipid synthesis via the Kennedy pathway. The URA7-encoded enzyme is phosphorylated by protein kinases A and C, and these phosphorylations stimulate CTP synthetase activity and increase cellular CTP levels and the utilization of the Kennedy pathway. The CTPS1 and CTPS2 genes that encode human CTP synthetase enzymes are functionally expressed in S. cerevisiae, and rescue the lethal phenotype of the ura7Deltaura8Delta double mutant that lacks CTP synthetase activity. The expression in yeast has revealed that the human CTPS1-encoded enzyme is also phosphorylated and regulated by protein kinases A and C.
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Affiliation(s)
- Yu-Fang Chang
- Department of Food Science, Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, United States
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27
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Lunn FA, MacDonnell JE, Bearne SL. Structural requirements for the activation of Escherichia coli CTP synthase by the allosteric effector GTP are stringent, but requirements for inhibition are lax. J Biol Chem 2007; 283:2010-20. [PMID: 18003612 DOI: 10.1074/jbc.m707803200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cytidine 5'-triphosphate synthase catalyzes the ATP-dependent formation of CTP from UTP using either NH(3) or l-glutamine (Gln) as the source of nitrogen. GTP acts as an allosteric effector promoting Gln hydrolysis but inhibiting Gln-dependent CTP formation at concentrations of >0.15 mM and NH(3)-dependent CTP formation at all concentrations. A structure-activity study using a variety of GTP and guanosine analogues revealed that only a few GTP analogues were capable of activating Gln-dependent CTP formation to varying degrees: GTP approximately 6-thio-GTP > ITP approximately guanosine 5'-tetraphosphate > O(6)-methyl-GTP > 2'-deoxy-GTP. No activation was observed with guanosine, GMP, GDP, 2',3'-dideoxy-GTP, acycloguanosine, and acycloguanosine monophosphate, indicating that the 5'-triphosphate, 2'-OH, and 3'-OH are required for full activation. The 2-NH(2) group plays an important role in binding recognition, whereas substituents at the 6-position play an important role in activation. The presence of a 6-NH(2) group obviates activation, consistent with the inability of ATP to substitute for GTP. Nucleotide and nucleoside analogues of GTP and guanosine, respectively, all inhibited NH(3)- and Gln-dependent CTP formation (often in a cooperative manner) to a similar extent (IC(50) approximately 0.2-0.5 mM). This inhibition appeared to be due solely to the purine base and was relatively insensitive to the identity of the purine with the exception of inosine, ITP, and adenosine (IC(50) approximately 4-12 mM). 8-Oxoguanosine was the best inhibitor identified (IC(50) = 80 microM). Our findings suggest that modifying 2-aminopurine or 2-aminopurine riboside may serve as an effective strategy for developing cytidine 5'-triphosphate synthase inhibitors.
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Affiliation(s)
- Faylene A Lunn
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
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