1
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Bearne SL. Biochemical communication between filament-forming enzymes: Potential Regulatory Roles of Metabolites in Enzyme Co-assemblies with CTP Synthase. Bioessays 2024; 46:e2400063. [PMID: 38975656 DOI: 10.1002/bies.202400063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 07/09/2024]
Abstract
A host of metabolic enzymes reversibly self-assemble to form membrane-less, intracellular filaments under normal physiological conditions and in response to stress. Often, these enzymes reside at metabolic control points, suggesting that filament formation affords an additional regulatory mechanism. Examples include cytidine-5'-triphosphate (CTP) synthase (CTPS), which catalyzes the rate-limiting step for the de novo biosynthesis of CTP; inosine-5'-monophosphate dehydrogenase (IMPDH), which controls biosynthetic access to guanosine-5'-triphosphate (GTP); and ∆1-pyrroline-5-carboxylate (P5C) synthase (P5CS) that catalyzes the formation of P5C, which links the Krebs cycle, urea cycle, and proline metabolism. Intriguingly, CTPS can exist in co-assemblies with IMPDH or P5CS. Since GTP is an allosteric activator of CTPS, the association of CTPS and IMPDH filaments accords with the need to coordinate pyrimidine and purine biosynthesis. Herein, a hypothesis is presented furnishing a biochemical connection underlying co-assembly of CTPS and P5CS filaments - potent inhibition of CTPS by glutamate γ-semialdehyde, the open-chain form of P5C.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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Park PMC, Park J, Brown J, Hunkeler M, Roy Burman SS, Donovan KA, Yoon H, Nowak RP, Słabicki M, Ebert BL, Fischer ES. Polymerization of ZBTB transcription factors regulates chromatin occupancy. Mol Cell 2024; 84:2511-2524.e8. [PMID: 38996460 PMCID: PMC11305084 DOI: 10.1016/j.molcel.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/05/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024]
Abstract
BCL6, an oncogenic transcription factor (TF), forms polymers in the presence of a small-molecule molecular glue that stabilizes a complementary interface between homodimers of BCL6's broad-complex, tramtrack, and bric-à-brac (BTB) domain. The BTB domains of other proteins, including a large class of TFs, have similar architectures and symmetries, raising the possibility that additional BTB proteins self-assemble into higher-order structures. Here, we surveyed 189 human BTB proteins with a cellular fluorescent reporter assay and identified 18 ZBTB TFs that show evidence of polymerization. Through biochemical and cryoelectron microscopy (cryo-EM) studies, we demonstrate that these ZBTB TFs polymerize into filaments. We found that BTB-domain-mediated polymerization of ZBTB TFs enhances chromatin occupancy within regions containing homotypic clusters of TF binding sites, leading to repression of target genes. Our results reveal a role of higher-order structures in regulating ZBTB TFs and suggest an underappreciated role for TF polymerization in modulating gene expression.
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Affiliation(s)
- Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiho Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jared Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Shourya S Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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3
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Hugener J, Xu J, Wettstein R, Ioannidi L, Velikov D, Wollweber F, Henggeler A, Matos J, Pilhofer M. FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis. Cell 2024; 187:3303-3318.e18. [PMID: 38906101 DOI: 10.1016/j.cell.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/06/2024] [Accepted: 04/19/2024] [Indexed: 06/23/2024]
Abstract
Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly understood. Here, we visualized budding yeast cells undergoing meiosis by cryo-electron tomography (cryoET) and discovered elaborate filamentous assemblies decorating the nucleus, cytoplasm, and mitochondria. To determine filament composition, we developed a "filament identification" (FilamentID) workflow that combines multiscale cryoET/cryo-electron microscopy (cryoEM) analyses of partially lysed cells or organelles. FilamentID identified the mitochondrial filaments as being composed of the conserved aldehyde dehydrogenase Ald4ALDH2 and the nucleoplasmic/cytoplasmic filaments as consisting of acetyl-coenzyme A (CoA) synthetase Acs1ACSS2. Structural characterization further revealed the mechanism underlying polymerization and enabled us to genetically perturb filament formation. Acs1 polymerization facilitates the recovery of chronologically aged spores and, more generally, the cell cycle re-entry of starved cells. FilamentID is broadly applicable to characterize filaments of unknown identity in diverse cellular contexts.
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Affiliation(s)
- Jannik Hugener
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Jingwei Xu
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Rahel Wettstein
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Lydia Ioannidi
- Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Daniel Velikov
- Max Perutz Labs, University of Vienna, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Florian Wollweber
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Adrian Henggeler
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Joao Matos
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
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4
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Guo C, Wang Z, Liu J. Filamentation and inhibition of prokaryotic CTP synthase with ligands. MLIFE 2024; 3:240-250. [PMID: 38948148 PMCID: PMC11211670 DOI: 10.1002/mlf2.12119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 07/02/2024]
Abstract
Cytidine triphosphate synthase (CTPS) plays a pivotal role in the de novo synthesis of cytidine triphosphate (CTP), a fundamental building block for RNA and DNA that is essential for life. CTPS is capable of directly binding to all four nucleotide triphosphates: adenine triphosphate, uridine triphosphate, CTP, and guanidine triphosphate. Furthermore, CTPS can form cytoophidia in vivo and metabolic filaments in vitro, undergoing regulation at multiple levels. CTPS is considered a potential therapeutic target for combating invasions or infections by viral or prokaryotic pathogens. Utilizing cryo-electron microscopy, we determined the structure of Escherichia coli CTPS (ecCTPS) filament in complex with CTP, nicotinamide adenine dinucleotide (NADH), and the covalent inhibitor 6-diazo-5-oxo- l-norleucine (DON), achieving a resolution of 2.9 Å. We constructed a phylogenetic tree based on differences in filament-forming interfaces and designed a variant to validate our hypothesis, providing an evolutionary perspective on CTPS filament formation. Our computational analysis revealed a solvent-accessible ammonia tunnel upon DON binding. Through comparative structural analysis, we discern a distinct mode of CTP binding of ecCTPS that differs from eukaryotic counterparts. Combining biochemical assays and structural analysis, we determined and validated the synergistic inhibitory effects of CTP with NADH or adenine on CTPS. Our results expand our comprehension of the diverse regulatory aspects of CTPS and lay a foundation for the design of specific inhibitors targeting prokaryotic CTPS.
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Affiliation(s)
- Chenjun Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Zixuan Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Ji‐Long Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- Shanghai Clinical Research and Trial CenterShanghaiChina
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5
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. J Cell Biol 2024; 223:e202310139. [PMID: 38323936 PMCID: PMC10849882 DOI: 10.1083/jcb.202310139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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6
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Zhang SQ, Liu JL. Dynamic Cytoophidia during Late-Stage Drosophila Oogenesis. Int J Mol Sci 2024; 25:2575. [PMID: 38473824 DOI: 10.3390/ijms25052575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
CTP synthase (CTPS) catalyzes the final step of de novo synthesis of CTP. CTPS was first discovered to form filamentous structures termed cytoophidia in Drosophila ovarian cells. Subsequent studies have shown that cytoophidia are widely present in cells of three life domains. In the Drosophila ovary model, our previous studies mainly focused on the early and middle stages, with less involvement in the later stages. In this work, we focus on the later stages of female germline cells in Drosophila. We use live-cell imaging to capture the continuous dynamics of cytoophidia in Stages 10-12. We notice the heterogeneity of cytoophidia in the two types of germline cells (nurse cells and oocytes), manifested in significant differences in morphology, distribution, and dynamics. Surprisingly, we also find that neighboring nurse cells in the same egg chamber exhibit multiple dynamic patterns of cytoophidia over time. Although the described dynamics may be influenced by the in vitro incubation conditions, our observation provides an initial understanding of the dynamics of cytoophidia during late-stage Drosophila oogenesis.
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Affiliation(s)
- Shi-Qi Zhang
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, Shanghai Tech 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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Ghadirian N, Morgan RD, Horton NC. DNA Sequence Control of Enzyme Filamentation and Activation of the SgrAI Endonuclease. Biochemistry 2024; 63:326-338. [PMID: 38207281 DOI: 10.1021/acs.biochem.3c00313] [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: 01/13/2024]
Abstract
Enzyme polymerization (also known as filamentation) has emerged as a new layer of enzyme regulation. SgrAI is a sequence-dependent DNA endonuclease that forms polymeric filaments with enhanced DNA cleavage activity as well as altered DNA sequence specificity. To better understand this unusual regulatory mechanism, full global kinetic modeling of the reaction pathway, including the enzyme filamentation steps, has been undertaken. Prior work with the primary DNA recognition sequence cleaved by SgrAI has shown how the kinetic rate constants of each reaction step are tuned to maximize activation and DNA cleavage while minimizing the extent of DNA cleavage to the host genome. In the current work, we expand on our prior study by now including DNA cleavage of a secondary recognition sequence, to understand how the sequence of the bound DNA modulates filamentation and activation of SgrAI. The work shows that an allosteric equilibrium between low and high activity states is modulated by the sequence of bound DNA, with primary sequences more prone to activation and filament formation, while SgrAI bound to secondary recognition sequences favor the low (and nonfilamenting) state by up to 40-fold. In addition, the degree of methylation of secondary sequences in the host organism, Streptomyces griseus, is now reported for the first time and shows that as predicted, these sequences are left unprotected from the SgrAI endonuclease making sequence specificity critical in this unusual filament-forming enzyme.
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Affiliation(s)
- Niloofar Ghadirian
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Richard D Morgan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
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8
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Peterson A, Baskett C, Ratcliff WC, Burnetti A. Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Curr Biol 2024; 34:648-654.e3. [PMID: 38218181 DOI: 10.1016/j.cub.2023.12.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
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Affiliation(s)
- Autumn Peterson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Carina Baskett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
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9
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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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10
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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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11
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Weng RY, Zhang L, Liu JL. Connecting Hippo Pathway and Cytoophidia in Drosophila Posterior Follicle Cells. Int J Mol Sci 2024; 25:1453. [PMID: 38338731 PMCID: PMC10855297 DOI: 10.3390/ijms25031453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
CTP synthase (CTPS), the rate-limiting enzyme in the de novo synthesis of CTP, assembles into a filamentous structure termed the cytoophidium. The Hippo pathway regulates cell proliferation and apoptosis. The relationship of the nucleotide metabolism with the Hippo pathway is little known. Here, we study the impact of the Hippo pathway on the cytoophidium in Drosophila melanogaster posterior follicle cells (PFCs). We find that the inactivation of the Hippo pathway correlates with reduced cytoophidium length and number within PFCs. During the overexpression of CTPS, the presence of Hippo mutations also reduces the length of cytoophidia in PFCs. In addition, we observe that knocking down CTPS mitigates hpo (Hippo)-associated over-proliferation. In summary, our results suggest that there is a connection between the Hippo pathway and the nucleotide biosynthesis enzyme CTPS in PFCs.
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Affiliation(s)
- Rui-Yu Weng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (R.-Y.W.)
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (R.-Y.W.)
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (R.-Y.W.)
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12
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Deng R, Li YL, Liu JL. Cytoophidia Influence Cell Cycle and Size in Schizosaccharomyces pombe. Int J Mol Sci 2024; 25:608. [PMID: 38203781 PMCID: PMC10779087 DOI: 10.3390/ijms25010608] [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: 10/14/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
Cytidine triphosphate synthase (CTPS) forms cytoophidia in all three domains of life. Here we focus on the function of cytoophidia in cell proliferation using Schizosaccharomyces pombe as a model system. We find that converting His359 of CTPS into Ala359 leads to cytoophidium disassembly. By reducing the level of CTPS protein or specific mutation, the loss of cytoophidia prolongs the G2 phase and expands cell size. In addition, the loss-filament mutant of CTPS leads to a decrease in the expression of genes related to G2/M transition and cell growth, including histone chaperone slm9. The overexpression of slm9 alleviates the G2 phase elongation and cell size enlargement induced by CTPS loss-filament mutants. Overall, our results connect cytoophidia with cell cycle and cell size control in Schizosaccharomyces pombe.
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Affiliation(s)
- Ruolan Deng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Lan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, 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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Jentoft IMA, Bäuerlein FJB, Welp LM, Cooper BH, Petrovic A, So C, Penir SM, Politi AZ, Horokhovskyi Y, Takala I, Eckel H, Moltrecht R, Lénárt P, Cavazza T, Liepe J, Brose N, Urlaub H, Fernández-Busnadiego R, Schuh M. Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell 2023; 186:5308-5327.e25. [PMID: 37922900 DOI: 10.1016/j.cell.2023.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or intermediate filaments, their function has remained enigmatic to date. Here, we show that cytoplasmic lattices are sites where oocytes store essential proteins for early embryonic development. Using super-resolution light microscopy and cryoelectron tomography, we show that cytoplasmic lattices are composed of filaments with a high surface area, which contain PADI6 and subcortical maternal complex proteins. The lattices associate with many proteins critical for embryonic development, including proteins that control epigenetic reprogramming of the preimplantation embryo. Loss of cytoplasmic lattices by knocking out PADI6 or the subcortical maternal complex prevents the accumulation of these proteins and results in early embryonic arrest. Our work suggests that cytoplasmic lattices enrich maternally provided proteins to prevent their premature degradation and cellular activity, thereby enabling early mammalian development.
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Affiliation(s)
- Ida M A Jentoft
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Felix J B Bäuerlein
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Benjamin H Cooper
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Arsen Petrovic
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Sarah Mae Penir
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Antonio Z Politi
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Iina Takala
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Heike Eckel
- Kinderwunschzentrum Göttingen, 37081 Göttingen, Germany
| | | | - Peter Lénárt
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Tommaso Cavazza
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Nils Brose
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Rubén Fernández-Busnadiego
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Faculty of Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany.
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14
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Yoon J, Min CW, Kim J, Baek G, Kim D, Jang JW, Gupta R, Kim ST, Cho LH. Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3715. [PMID: 37960070 PMCID: PMC10650807 DOI: 10.3390/plants12213715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and osctps1-2 mutant, encoding a cytidine triphosphate synthase previously reported as the endospermless 2 (enl2) mutant in rice, harvested at 0 and 1 d after pollination (DAP) to understand the molecular mechanism of early seed development. In total, 5231 proteins were identified, of which 902 changed in abundance between 0 and 1 DAP seeds. Proteins that preferentially accumulated at 1 DAP were involved in DNA replication and pyrimidine biosynthetic pathways. Notably, an increased abundance of OsCTPS1 was observed at 1 DAP; however, no such changes were observed at the transcriptional level. We further observed that the inhibition of phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared with those in the WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. These results highlight the molecular mechanisms underlying early seed development in rice at the post-transcriptional level.
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Affiliation(s)
- Jinmi Yoon
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea;
- Department of Biological Sciences and Bioengineering, Industry-Academia Interactive R&E Center for Bioprocess Innovation, Inha University, Incheon 22212, Republic of Korea
| | - Cheol Woo Min
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
| | - Jiyoung Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Gibeom Baek
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Jeong Woo Jang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea;
| | - Sun Tae Kim
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Lae-Hyeon Cho
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
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15
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Nasalingkhan C, Sirinonthanawech N, Noree C. Robust assembly of the aldehyde dehydrogenase Ald4p in Saccharomyces cerevisiae. Biol Open 2023; 12:bio060070. [PMID: 37767855 PMCID: PMC10602002 DOI: 10.1242/bio.060070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023] Open
Abstract
As part of our studies of yeast aldehyde dehydrogenase (Ald4p) assembly, we identified a population of transformants (SWORD strain) that show more robust filament formation of GFP-tagged Ald4p (Ald4p-GFP) than that of a wild type ALD4::GFP strain. Sequencing of the ALD4 gene in the SWORD strain showed that the increased assembly was not due to changes to the ALD4 coding sequence, suggesting that a second mutation site was altering Ald4p assembly. Using short-read whole-genome sequencing, we identified spontaneous mutations in FLO9. Introduction of the SWORD allele of FLO9 into a wild-type ALD4::GFP yeast strain revealed that the changes to FLO9 were a contributor to the increased length of Ald4p-GFP filaments we observe in the SWORD strain and that this effect was not due to an increase in Ald4p protein levels. However, the expression of the FLO9 (SWORD) allele in wild-type yeast did not fully recapitulate the length control defect we observed in SWORD strains, arguing that there are additional genes contributing to the filament length phenotype. For our future work, this FLO9 from SWORD will be tested whether it could show global effect, promoting the assembly of some other filament-forming enzymes.
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Affiliation(s)
- Channarong Nasalingkhan
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
| | - Naraporn Sirinonthanawech
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
| | - Chalongrat Noree
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
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16
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Paukštytė J, López Cabezas RM, Feng Y, Tong K, Schnyder D, Elomaa E, Gregorova P, Doudin M, Särkkä M, Sarameri J, Lippi A, Vihinen H, Juutila J, Nieminen A, Törönen P, Holm L, Jokitalo E, Krisko A, Huiskonen J, Sarin LP, Hietakangas V, Picotti P, Barral Y, Saarikangas J. Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity. Mol Cell 2023; 83:3360-3376.e11. [PMID: 37699397 DOI: 10.1016/j.molcel.2023.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/18/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
Aging is associated with progressive phenotypic changes. Virtually all cellular phenotypes are produced by proteins, and their structural alterations can lead to age-related diseases. However, we still lack comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contributions to age-related phenotypes. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry (LiP-MS). The results, compiled in online ProtAge catalog, unraveled age-related functional changes in regulators of translation, protein folding, and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging, causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction, and led to lifespan extension. Altogether, this comprehensive map of protein structural changes enables identifying mechanisms of age-related phenotypes and offers opportunities for their reversal.
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Affiliation(s)
- Jurgita Paukštytė
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Rosa María López Cabezas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Ellinoora Elomaa
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Pavlina Gregorova
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Matteo Doudin
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Meeri Särkkä
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Jesse Sarameri
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helena Vihinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anni Nieminen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Törönen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Liisa Holm
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Juha Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - L Peter Sarin
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland.
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17
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558867. [PMID: 37790411 PMCID: PMC10542554 DOI: 10.1101/2023.09.21.558867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanosine triphosphate (GTP) synthesis and is controlled by feedback inhibition and allosteric regulation. IMPDH assembles into micron-scale filaments in cells, which desensitizes the enzyme to feedback inhibition by GTP and boosts nucleotide production. The vertebrate retina expresses two tissue-specific splice variants IMPDH1(546) and IMPDH1(595). IMPDH1(546) filaments adopt high and low activity conformations, while IMPDH1(595) filaments maintain high activity. In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of phosphorylation in IMPDH1 variants. The S477D mutation re-sensitized both variants to GTP inhibition, but only blocked assembly of IMPDH1(595) filaments and not IMPDH1(546) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of the high activity assembly interface, still allowing assembly of low activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, phosphorylation at S477 acts as a mechanism for downregulating retinal GTP synthesis in the dark, when nucleotide turnover is decreased. Like IMPDH1, many other metabolic enzymes dynamically assemble filamentous polymers that allosterically regulate activity. Our work suggests that posttranslational modifications may be yet another layer of regulatory control to finely tune activity by modulating filament assembly in response to changing metabolic demands.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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18
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Liu J, Zhang Y, Wang QQ, Zhou Y, Liu JL. Fat body-specific reduction of CTPS alleviates HFD-induced obesity. eLife 2023; 12:e85293. [PMID: 37695169 PMCID: PMC10495109 DOI: 10.7554/elife.85293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
Obesity induced by high-fat diet (HFD) is a multi-factorial disease including genetic, physiological, behavioral, and environmental components. Drosophila has emerged as an effective metabolic disease model. Cytidine 5'-triphosphate synthase (CTPS) is an important enzyme for the de novo synthesis of CTP, governing the cellular level of CTP and the rate of phospholipid synthesis. CTPS is known to form filamentous structures called cytoophidia, which are found in bacteria, archaea, and eukaryotes. Our study demonstrates that CTPS is crucial in regulating body weight and starvation resistance in Drosophila by functioning in the fat body. HFD-induced obesity leads to increased transcription of CTPS and elongates cytoophidia in larval adipocytes. Depleting CTPS in the fat body prevented HFD-induced obesity, including body weight gain, adipocyte expansion, and lipid accumulation, by inhibiting the PI3K-Akt-SREBP axis. Furthermore, a dominant-negative form of CTPS also prevented adipocyte expansion and downregulated lipogenic genes. These findings not only establish a functional link between CTPS and lipid homeostasis but also highlight the potential role of CTPS manipulation in the treatment of HFD-induced obesity.
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Affiliation(s)
- Jingnan Liu
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- College of Life Sciences, Shanghai Normal UniversityShanghaiChina
| | - Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qiao-Qi Wang
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Youfang Zhou
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
- Department of Physiology, Anatomy and Genetics, University of OxfordOxfordUnited Kingdom
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19
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Minet N, Boschat AC, Lane R, Laughton D, Beer P, Asnagli H, Soudais C, Bourne T, Fischer A, Martin E, Latour S. Differential roles of CTP synthetases CTPS1 and CTPS2 in cell proliferation. Life Sci Alliance 2023; 6:e202302066. [PMID: 37348953 PMCID: PMC10288033 DOI: 10.26508/lsa.202302066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
The CTP nucleotide is a key precursor of nucleic acids metabolism essential for DNA replication. De novo CTP production relies on CTP synthetases 1 and 2 (CTPS1 and CTPS2) that catalyze the conversion of UTP into CTP. CTP synthetase activity is high in proliferating cells including cancer cells; however, the respective roles of CTPS1 and CTPS2 in cell proliferation are not known. By inactivation of CTPS1 and/or CTPS2 and complementation experiments, we showed that both CTPS1 and CTPS2 are differentially required for cell proliferation. CTPS1 was more efficient in promoting proliferation than CTPS2, in association with a higher intrinsic enzymatic activity that was more resistant to inhibition by 3-deaza-uridine, an UTP analog. The contribution of CTPS2 to cell proliferation was modest when CTPS1 was expressed but essential in absence of CTPS1. Public databases analysis of more than 1,000 inactivated cancer cell lines for CTPS1 or CTPS2 confirmed that cell growth is highly dependent of CTPS1 but less or not of CTPS2. Therefore, our results demonstrate that CTPS1 is the main contributor to cell proliferation.
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Affiliation(s)
- Norbert Minet
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Imagine Institute, Paris, France
- Université de Paris, Paris, France
| | - Anne-Claire Boschat
- Université de Paris, Paris, France
- Plateforme Spectrométrie de masse, Institut Imagine, Paris, France
- Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker Enfants-Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | | | | | | | | - Claire Soudais
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Imagine Institute, Paris, France
- Université de Paris, Paris, France
| | - Tim Bourne
- Step-Pharma, Saint-Genis-Pouilly, France
| | - Alain Fischer
- Collège de France, Paris, France
- Imagine Institute, Paris, France
| | - Emmanuel Martin
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Imagine Institute, Paris, France
- Université de Paris, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Imagine Institute, Paris, France
- Université de Paris, Paris, France
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20
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Fischbach A, Johns A, Schneider KL, Hao X, Tessarz P, Nyström T. Artificial Hsp104-mediated systems for re-localizing protein aggregates. Nat Commun 2023; 14:2663. [PMID: 37160881 PMCID: PMC10169802 DOI: 10.1038/s41467-023-37706-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Spatial Protein Quality Control (sPQC) sequesters misfolded proteins into specific, organelle-associated inclusions within the cell to control their toxicity. To approach the role of sPQC in cellular fitness, neurodegenerative diseases and aging, we report on the construction of Hsp100-based systems in budding yeast cells, which can artificially target protein aggregates to non-canonical locations. We demonstrate that aggregates of mutant huntingtin (mHtt), the disease-causing agent of Huntington's disease can be artificially targeted to daughter cells as well as to eisosomes and endosomes with this approach. We find that the artificial removal of mHtt inclusions from mother cells protects them from cell death suggesting that even large mHtt inclusions may be cytotoxic, a trait that has been widely debated. In contrast, removing inclusions of endogenous age-associated misfolded proteins does not significantly affect the lifespan of mother cells. We demonstrate also that this approach is able to manipulate mHtt inclusion formation in human cells and has the potential to be useful as an alternative, complementary approach to study the role of sPQC, for example in aging and neurodegenerative disease.
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Affiliation(s)
- Arthur Fischbach
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Angela Johns
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), Cologne, Germany
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
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21
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Hvorecny KL, Kollman JM. Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments. Curr Opin Struct Biol 2023; 79:102530. [PMID: 36709625 PMCID: PMC10023394 DOI: 10.1016/j.sbi.2023.102530] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 01/28/2023]
Abstract
Recent work in structural biology is shedding light on how many of the enzymes of intermediary metabolism are self- and co-assembling into large, filamentous polymers or agglomerates to organize and regulate the complex and essential biochemical pathways in cells. Filament assembly provides an additional layer of regulation by modulating the intrinsic allostery of the enzyme protomers which tunes activity in response to a variety of environmental cues. Enzyme filaments dynamically assemble and disassemble in response to changes in metabolite levels and environmental cues, shifting metabolic flux on a more rapid timescale than transcriptional or translational reprogramming. Here we present recent examples of high-resolution structures of filaments from proteins in intermediary metabolism and we discuss how filament assembly modulates the activities of these and other proteins.
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Affiliation(s)
- Kelli L Hvorecny
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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22
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Zhang Y, Zhang B, Liu JL. STAMP: Spatio-Temporal Association Mapping of Proteins. Methods Mol Biol 2023; 2626:365-379. [PMID: 36715916 DOI: 10.1007/978-1-0716-2970-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We describe a tool, Spatio-Temporal Association Mapping of Proteins (STAMP), for identifying protein interactomes via proximity labeling. For a proof-of-principle study, we use cytidine 5'-triphosphate synthase (CTPS) as an example. CTPS, a metabolic enzyme, forms filamentous structures termed cytoophidia in various tissues. We apply STAMP to a variety of developmental stages and tissues in Drosophila including adult ovaries. Using a cell-specific GAL4 driver, we verify that TurboID can biotinylate the bait protein CTPS, making possible the identification of protein-protein interactions (PPIs) in individual cells. Using the wild-type and mutant CTPS as bait proteins, STAMP results in two distinct sets of proximate proteomes. Our results suggest that STAMP is a feasible tool to catch in vivo PPIs in situ at a defined spatiotemporal resolution.
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Affiliation(s)
- Yuanbing Zhang
- 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
| | - Bo Zhang
- 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
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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23
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Smeele PH, Vaccari T. Snapshots from within the cell: Novel trafficking and non trafficking functions of Snap29 during tissue morphogenesis. Semin Cell Dev Biol 2023; 133:42-52. [PMID: 35256275 DOI: 10.1016/j.semcdb.2022.02.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 01/27/2023]
Abstract
Membrane trafficking is a core cellular process that supports diversification of cell shapes and behaviors relevant to morphogenesis during development and in adult organisms. However, how precisely trafficking components regulate specific differentiation programs is incompletely understood. Snap29 is a multifaceted Soluble N-ethylmaleimide-sensitive factor Attachment protein Receptor, involved in a wide range of trafficking and non-trafficking processes in most cells. A body of knowledge, accrued over more than two decades since its discovery, reveals that Snap29 is essential for establishing and maintaining the operation of a number of cellular events that support cell polarity and signaling. In this review, we first summarize established functions of Snap29 and then we focus on novel ones in the context of autophagy, Golgi trafficking and vesicle fusion at the plasma membrane, as well as on non-trafficking activities of Snap29. We further describe emerging evidence regarding the compartmentalisation and regulation of Snap29. Finally, we explore how the loss of distinct functions of human Snap29 may lead to the clinical manifestations of congenital disorders such as CEDNIK syndrome and how altered SNAP29 activity may contribute to the pathogenesis of cancer, viral infection and neurodegenerative diseases.
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Affiliation(s)
- Paulien H Smeele
- Department of Biosciences, Università Degli Studi Di Milano, Milan, Italy
| | - Thomas Vaccari
- Department of Biosciences, Università Degli Studi Di Milano, Milan, Italy.
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24
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You DD, Zhou XL, Wang QQ, Liu JL. Cytoophidia safeguard binucleation of Drosophila male accessory gland cells. Exp Cell Res 2023; 422:113433. [PMID: 36423659 DOI: 10.1016/j.yexcr.2022.113433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
Although most cells are mononuclear, the nucleus can exist in the form of binucleate or even multinucleate to respond to different physiological processes. The male accessory gland of Drosophila is the organ that produces semen, and its main cells are binucleate. Here we observe that CTP synthase (CTPS) forms filamentous cytoophidia in binuclear main cells, primarily located at the cell boundary. In CTPSH355A, a point mutation that destroys the formation of cytoophidia, we find that the nucleation mode of the main cells changes, including mononucleates and vertical distribution of binucleates. Although the overexpression of CTPSH355A can restore the level of CTPS protein, it will neither form cytoophidia nor eliminate the abnormal nucleation pattern. Therefore, our data indicate that there is an unexpected functional link between the formation of cytoophidia and the maintenance of binucleation in Drosophila main cells.
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Affiliation(s)
- Dong-Dong You
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiao-Li Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qiao-Qi Wang
- 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, United Kingdom.
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25
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The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. Biochem Soc Trans 2022; 50:1703-1714. [PMID: 36398769 PMCID: PMC9788392 DOI: 10.1042/bst20220547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein-DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.
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26
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Wang QQ, You DD, Liu JL. Cytoophidia Maintain the Integrity of Drosophila Follicle Epithelium. Int J Mol Sci 2022; 23:ijms232315282. [PMID: 36499609 PMCID: PMC9740582 DOI: 10.3390/ijms232315282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
CTP synthase (CTPS) forms a filamentous structure termed the cytoophidium in all three domains of life. The female reproductive system of Drosophila is an excellent model for studying the physiological function of cytoophidia. Here, we use CTPSH355A, a point mutation that destroys the cytoophidium-forming ability of CTPS, to explore the in vivo function of cytoophidia. In CTPSH355A egg chambers, we observe the ingression and increased heterogeneity of follicle cells. In addition, we find that the cytoophidium-forming ability of CTPS, rather than the protein level, is the cause of the defects observed in CTPSH355A mutants. To sum up, our data indicate that cytoophidia play an important role in maintaining the integrity of follicle epithelium.
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Affiliation(s)
- Qiao-Qi Wang
- School of Life Science and Technology, Shanghai Technology University, Shanghai 201210, China
| | - Dong-Dong You
- School of Life Science and Technology, Shanghai Technology University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, Shanghai Technology University, Shanghai 201210, China
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
- Correspondence: or
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27
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Lin JMG, Kourtis S, Ghose R, Pardo Lorente N, Kubicek S, Sdelci S. Metabolic modulation of transcription: The role of one-carbon metabolism. Cell Chem Biol 2022; 29:S2451-9456(22)00415-9. [PMID: 36513079 DOI: 10.1016/j.chembiol.2022.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 10/05/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
While it is well known that expression levels of metabolic enzymes regulate the metabolic state of the cell, there is mounting evidence that the converse is also true, that metabolite levels themselves can modulate gene expression via epigenetic modifications and transcriptional regulation. Here we focus on the one-carbon metabolic pathway, which provides the essential building blocks of many classes of biomolecules, including purine nucleotides, thymidylate, serine, and methionine. We review the epigenetic roles of one-carbon metabolic enzymes and their associated metabolites and introduce an interactive computational resource that places enzyme essentiality in the context of metabolic pathway topology. Therefore, we briefly discuss examples of metabolic condensates and higher-order complexes of metabolic enzymes downstream of one-carbon metabolism. We speculate that they may be required to the formation of transcriptional condensates and gene expression control. Finally, we discuss new ways to exploit metabolic pathway compartmentalization to selectively target these enzymes in cancer.
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Affiliation(s)
- Jung-Ming G Lin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Vienna 1090, Austria
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Ritobrata Ghose
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Natalia Pardo Lorente
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Vienna 1090, Austria
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.
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28
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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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29
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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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30
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Gillis TD, Bearne SL. Effects of the 5'-Triphosphate Metabolites of Ribavirin, Sofosbuvir, Vidarabine, and Molnupiravir on CTP Synthase Catalysis and Filament Formation: Implications for Repurposing Antiviral Agents against SARS-CoV-2. ChemMedChem 2022; 17:e202200399. [PMID: 36184568 PMCID: PMC9538051 DOI: 10.1002/cmdc.202200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Indexed: 01/14/2023]
Abstract
Repurposing of antiviral drugs affords a rapid and effective strategy to develop therapies to counter pandemics such as COVID-19. SARS-CoV-2 replication is closely linked to the metabolism of cytosine-containing nucleotides, especially cytidine-5'-triphosphate (CTP), such that the integrity of the viral genome is highly sensitive to intracellular CTP levels. CTP synthase (CTPS) catalyzes the rate-limiting step for the de novo biosynthesis of CTP. Hence, it is of interest to know the effects of the 5'-triphosphate (TP) metabolites of repurposed antiviral agents on CTPS activity. Using E. coli CTPS as a model enzyme, we show that ribavirin-5'-TP is a weak allosteric activator of CTPS, while sofosbuvir-5'-TP and adenine-arabinofuranoside-5'-TP are both substrates. β-d-N4 -Hydroxycytidine-5'-TP is a weak competitive inhibitor relative to CTP, but induces filament formation by CTPS. Alternatively, sofosbuvir-5'-TP prevented CTP-induced filament formation. These results reveal the underlying potential for repurposed antivirals to affect the activity of a critical pyrimidine nucleotide biosynthetic enzyme.
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Affiliation(s)
- Thomas D. Gillis
- Dalhousie UniversityDepartment of Biochemistry & Molecular Biology5850 College St.Tupper Medical Building, 9JB3H 4R2HalifaxCANADA
| | - Stephen L. Bearne
- Dalhousie UniversityBiochemistry & Molecular Biology5850 College StreetTupper Medical BuildingB3H 4R2HalifaxCANADA
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31
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Fang YF, Li YL, Li XM, Liu JL. Super-Resolution Imaging Reveals Dynamic Reticular Cytoophidia. Int J Mol Sci 2022; 23:11698. [PMID: 36233000 PMCID: PMC9569780 DOI: 10.3390/ijms231911698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
CTP synthase (CTPS) can form filamentous structures termed cytoophidia in cells in all three domains of life. In order to study the mesoscale structure of cytoophidia, we perform fluorescence recovery after photobleaching (FRAP) and stimulated emission depletion (STED) microscopy in human cells. By using an EGFP dimeric tag as a tool to explore the physical properties of cytoophidia, we find that cytoophidia are dynamic and reticular. The reticular structure of CTPS cytoophidia may provide space for other components, such as IMPDH. In addition, we observe CTPS granules with tentacles.
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Affiliation(s)
- Yi-Fan Fang
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Yi-Lan Li
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xiao-Ming Li
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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32
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Liu J, Zhang Y, Zhou Y, Wang QQ, Ding K, Zhao S, Lu P, Liu JL. Cytoophidia coupling adipose architecture and metabolism. Cell Mol Life Sci 2022; 79:534. [PMID: 36180607 DOI: 10.1007/s00018-022-04567-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 01/05/2023]
Abstract
Tissue architecture determines its unique physiology and function. How these properties are intertwined has remained unclear. Here we show that the metabolic enzyme CTP synthase (CTPS) form filamentous structures termed cytoophidia along the adipocyte cortex in Drosophila adipose tissue. Loss of cytoophidia, whether due to reduced CTPS expression or a point mutation that specifically abrogates its polymerization ability, causes impaired adipocyte adhesion and defective adipose tissue architecture. Moreover, CTPS influences integrin distribution and dot-like deposition of type IV collagen (Col IV). Col IV-integrin signaling reciprocally regulates the assembly of cytoophidia in adipocytes. Our results demonstrate that a positive feedback signaling loop containing both cytoophidia and integrin adhesion complex couple tissue architecture and metabolism in Drosophila adipose tissue.
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Affiliation(s)
- Jingnan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuanbing Zhang
- 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
| | - Youfang Zhou
- 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
| | - 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
| | - 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
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Pengfei Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.
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33
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Fu X, Chen W, Pan Y, Liu C, Zhang Z, Shao S, Zhang W. CTPS cytoophidia formation affects cell cycle progression and promotes TSN‑induced apoptosis of MKN45 cells. Mol Med Rep 2022; 26:319. [PMID: 36043523 PMCID: PMC9471557 DOI: 10.3892/mmr.2022.12835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/03/2022] [Indexed: 11/06/2022] Open
Abstract
Cytidine triphosphate synthase (CTPS) forms filamentous structures termed cytoophidia in numerous types of cell. Toosendanin (TSN) is a tetracyclic triterpenoid and induces CTPS to form cytoophidia in MKN45 cells. However, the effects of CTPS cytoophidia on the proliferation and apoptosis of human gastric cancer cells remain poorly understood. In the present study, CTPS‑overexpression and R294D‑CTPS mutant vectors were generated to assess the effect of CTPS cytoophidia on the proliferation and apoptosis of gastric cancer MKN45 cells. Formation of CTPS cytoophidia significantly inhibited MKN45 cell proliferation (evaluated using EdU incorporation assay), significantly blocked the cell cycle in G1 phase (assessed using flow cytometry) and significantly decreased mRNA and protein expression levels of cyclin D1 (assessed by reverse transcription‑quantitative PCR and western blotting, respectively). Furthermore, the number of apoptotic bodies and apoptosis rate were markedly elevated and mitochondrial membrane potential was markedly decreased. Moreover, mRNA and protein expression levels of Bax increased and Bcl‑2 decreased markedly in MKN45 cells following transfection with the CTPS‑overexpression vector. The proliferation rate increased, percentage of G1/G0‑phase cells decreased and apoptosis was attenuated in cells transfected with the R294D‑CTPS mutant vector and this mutation did not lead to formation of cytoophidia. The results of the present study suggested that formation of CTPS cytoophidia inhibited proliferation and promoted apoptosis in MKN45 cells. These results may provide insights into the role of CTPS cytoophidia in cancer cell proliferation and apoptosis.
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Affiliation(s)
- Xuepeng Fu
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Wen Chen
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Yang Pan
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Chang Liu
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Zhenzhu Zhang
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Shuli Shao
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Weiwei Zhang
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
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34
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Langlois-Lemay L, D’Amours D. Moonlighting at the Poles: Non-Canonical Functions of Centrosomes. Front Cell Dev Biol 2022; 10:930355. [PMID: 35912107 PMCID: PMC9329689 DOI: 10.3389/fcell.2022.930355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Centrosomes are best known as the microtubule organizing centers (MTOCs) of eukaryotic cells. In addition to their classic role in chromosome segregation, centrosomes play diverse roles unrelated to their MTOC activity during cell proliferation and quiescence. Metazoan centrosomes and their functional doppelgängers from lower eukaryotes, the spindle pole bodies (SPBs), act as important structural platforms that orchestrate signaling events essential for cell cycle progression, cellular responses to DNA damage, sensory reception and cell homeostasis. Here, we provide a critical overview of the unconventional and often overlooked roles of centrosomes/SPBs in the life cycle of eukaryotic cells.
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Affiliation(s)
- Laurence Langlois-Lemay
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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35
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Hu HH, Lu GM, Chang CC, Li Y, Zhong J, Guo CJ, Zhou X, Yin B, Zhang T, Liu JL. Filamentation modulates allosteric regulation of PRPS. eLife 2022; 11:79552. [PMID: 35736577 PMCID: PMC9232217 DOI: 10.7554/elife.79552] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of E. coli PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation.
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Affiliation(s)
- Huan-Huan Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guang-Ming Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yilan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chen-Jun Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xian Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Boqi Yin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tianyi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Ugbogu EA, Schweizer LM, Schweizer M. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Cells 2022; 11:1909. [PMID: 35741038 PMCID: PMC9221600 DOI: 10.3390/cells11121909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.
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Affiliation(s)
- Eziuche A. Ugbogu
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Lilian M. Schweizer
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Engineering (IB3), School of Engineering &Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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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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38
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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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Ishikawa H, Tian JL, Yu JE, Marshall WF, Qin H. Biosynthesis of Linear Protein Nanoarrays Using the Flagellar Axoneme. ACS Synth Biol 2022; 11:1454-1465. [PMID: 35271249 DOI: 10.1021/acssynbio.1c00439] [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] [Indexed: 12/15/2022]
Abstract
Applications in biotechnology and synthetic biology often make use of soluble proteins, but there are many potential advantages of anchoring enzymes to a stable substrate, including stability and the possibility for substrate channeling. To avoid the necessity of protein purification and chemical immobilization, there has been growing interest in bio-assembly of protein-containing nanoparticles, exploiting the self-assembly of viral capsid proteins or other proteins that form polyhedral structures. However, these nanoparticles are limited in size, which constrains the packaging and the accessibility of the proteins. An axoneme, the insoluble protein core of the eukaryotic flagellum or cilium, is a highly ordered protein structure that can be several microns in length, orders of magnitude larger than other types of nanoparticles. We show that when proteins of interest are fused to specific axonemal proteins and expressed in living Chlamydomonas reinhardtii cells, they become incorporated into linear arrays, which have the advantages of high protein loading capacity and single-step purification with retention of biomass. The arrays can be isolated as membrane-enclosed vesicles or as exposed protein arrays. The approach is demonstrated for both a fluorescent protein and an enzyme (beta-lactamase), showing that incorporation into axonemes retains protein function in a stable, easily isolated array form.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143, United States
- NSF Center for Cellular Construction, San Francisco, California 94143, United States
| | - Jie L. Tian
- Molecular & Environmental Plant Sciences, Texas A&M University, College Station, Texas 77845, United States
| | - Jefer E. Yu
- Department of Biology, Texas A&M University, College Station, Texas 77845, United States
| | - Wallace F. Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143, United States
- NSF Center for Cellular Construction, San Francisco, California 94143, United States
| | - Hongmin Qin
- Department of Biology, Texas A&M University, College Station, Texas 77845, United States
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Huang P, Chen S, Chiang W, Ho M, Wu K. Structural basis for the helical filament formation of
Escherichia coli
glutamine synthetase. Protein Sci 2022; 31:e4304. [PMID: 35481643 PMCID: PMC8996467 DOI: 10.1002/pro.4304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023]
Abstract
Escherichia coli glutamine synthetase (EcGS) spontaneously forms a dodecamer that catalytically converts glutamate to glutamine. EcGS stacks with other dodecamers to create a filament-like polymer visible under transmission electron microscopy. Filamentous EcGS is induced by environmental metal ions. We used cryo-electron microscopy (cryo-EM) to decipher the structure of metal ion (nickel)-induced EcGS helical filament at a sub-3Å resolution. EcGS filament formation involves stacking of native dodecamers by chelating nickel ions to residues His5 and His13 in the first N-terminal helix (H1). His5 and His13 from paired parallel H1 helices provide salt bridges and hydrogen bonds to tightly stack two dodecamers. One subunit of the EcGS filament hosts two nickel ions, whereas the dodecameric interface and the ATP/Mg-binding site both host a nickel ion each. We reveal that upon adding glutamate or ATP for catalytic reactions, nickel-induced EcGS filament reverts to individual dodecamers. Such tunable filament formation is often associated with stress responses. Our results provide detailed structural information on the mechanism underlying reversible and tunable EcGS filament formation.
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Affiliation(s)
- Pei‐Chi Huang
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan Normal University Taipei Taiwan
| | - Shao‐Kang Chen
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Wei‐Hung Chiang
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Meng‐Ru Ho
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Kuen‐Phon Wu
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
- Institute of Biochemical Science College of Life Science, National Taiwan University Taipei Taiwan
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41
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Cañonero L, Pautasso C, Galello F, Sigaut L, Pietrasanta L, Arroyo J, Bermúdez-Moretti M, Portela P, Rossi S. Heat stress regulates the expression of TPK1 gene at transcriptional and post-transcriptional levels in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119209. [PMID: 34999138 DOI: 10.1016/j.bbamcr.2021.119209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 12/11/2022]
Abstract
In Saccharomyces cerevisiae cAMP regulates different cellular processes through PKA. The specificity of the response of the cAMP-PKA pathway is highly regulated. Here we address the mechanism through which the cAMP-PKA pathway mediates its response to heat shock and thermal adaptation in yeast. PKA holoenzyme is composed of a regulatory subunit dimer (Bcy1) and two catalytic subunits (Tpk1, Tpk2, or Tpk3). PKA subunits are differentially expressed under certain growth conditions. Here we demonstrate the increased abundance and half-life of TPK1 mRNA and the assembly of this mRNA in cytoplasmic foci during heat shock at 37 °C. The resistance of the foci to cycloheximide-induced disassembly along with the polysome profiling analysis suggest that TPK1 mRNA is impaired for entry into translation. TPK1 expression was also evaluated during a recurrent heat shock and thermal adaptation. Tpk1 protein level is significantly increased during the recovery periods. The crosstalk of cAMP-PKA pathway and CWI signalling was also studied. Wsc3 sensor and some components of the CWI pathway are necessary for the TPK1 expression upon heat shock. The assembly in foci upon thermal stress depends on Wsc3. Tpk1 expression is lower in a wsc3∆ mutant than in WT strain during thermal adaptation and thus the PKA levels are also lower. An increase in Tpk1 abundance in the PKA holoenzyme in response to heat shock is presented, suggesting that a recurrent stress enhanced the fitness for the coming favourable conditions. Therefore, the regulation of TPK1 expression by thermal stress contributes to the specificity of cAMP-PKA signalling.
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Affiliation(s)
- Luciana Cañonero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Constanza Pautasso
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Fiorella Galello
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Lorena Sigaut
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Física, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA), Buenos Aires, Argentina
| | - Lia Pietrasanta
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Física, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Física de Buenos Aires (IFIBA), Buenos Aires, Argentina
| | - Javier Arroyo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Mariana Bermúdez-Moretti
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
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42
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Connecting Ras and CTP synthase in Drosophila. Exp Cell Res 2022; 416:113155. [DOI: 10.1016/j.yexcr.2022.113155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/04/2022]
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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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44
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Krämer M, Dörfer E, Hickl D, Bellin L, Scherer V, Möhlmann T. Cytidine Triphosphate Synthase Four From Arabidopsis thaliana Attenuates Drought Stress Effects. FRONTIERS IN PLANT SCIENCE 2022; 13:842156. [PMID: 35360303 PMCID: PMC8960734 DOI: 10.3389/fpls.2022.842156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Cytidine triphosphate synthase (CTPS) catalyzes the final step in pyrimidine de novo synthesis. In Arabidopsis, this protein family consists of five members (CTPS1-5), and all of them localize to the cytosol. Specifically, CTPS4 showed a massive upregulation of transcript levels during abiotic stress, in line with increased staining of CTPS4 promoter:GUS lines in hypocotyl, root and to lesser extend leaf tissues. In a setup to study progressive drought stress, CTPS4 knockout mutants accumulated less fresh and dry weight at days 5-7 and showed impaired ability to recover from this stress after 3 days of rewatering. Surprisingly, a thorough physiological characterization of corresponding plants only revealed alterations in assimilation and accumulation of soluble sugars including those related to drought stress in the mutant. Bimolecular fluorescence complementation (BiFC) studies indicated the interaction of CTPS4 with other isoforms, possibly affecting cytoophidia (filaments formed by CTPS formation. Although the function of these structures has not been thoroughly investigated in plants, altered enzyme activity and effects on cell structure are reported in other organisms. CTPS activity is required for cell cycle progression and growth. Furthermore, drought can lead to the accumulation of reactive oxygen species (ROS) and by this, to DNA damage. We hypothesize that effects on the cell cycle or DNA repair might be relevant for the observed impaired reduced drought stress tolerance of CTPS4 mutants.
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45
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Ajazi A, Choudhary R, Tronci L, Bachi A, Bruhn C. CTP sensing and Mec1ATR-Rad53CHK1/CHK2 mediate a two-layered response to inhibition of glutamine metabolism. PLoS Genet 2022; 18:e1010101. [PMID: 35239666 PMCID: PMC8923462 DOI: 10.1371/journal.pgen.1010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/15/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
Glutamine analogs are potent suppressors of general glutamine metabolism with anti-cancer activity. 6-diazo-5-oxo-L-norleucine (DON) is an orally available glutamine analog which has been recently improved by structural modification for cancer treatment. Here, we explored the chemogenomic landscape of DON sensitivity using budding yeast as model organism. We identify evolutionarily conserved proteins that mediate cell resistance to glutamine analogs, namely Ura8CTPS1/2, Hpt1HPRT1, Mec1ATR, Rad53CHK1/CHK2 and Rtg1. We describe a function of Ura8 as inducible CTP synthase responding to inhibition of glutamine metabolism and propose a model for its regulation by CTP levels and Nrd1-dependent transcription termination at a cryptic unstable transcript. Disruption of the inducible CTP synthase under DON exposure hyper-activates the Mec1-Rad53 DNA damage response (DDR) pathway, which prevents chromosome breakage. Simultaneous inhibition of CTP synthase and Mec1 kinase synergistically sensitizes cells to DON, whereas CTP synthase over-expression hampers DDR mutant sensitivity. Using genome-wide suppressor screening, we identify factors promoting DON-induced CTP depletion (TORC1, glutamine transporter) and DNA breakage in DDR mutants. Together, our results identify CTP regulation and the Mec1-Rad53 DDR axis as key glutamine analog response pathways, and provide a rationale for the combined targeting of glutamine and CTP metabolism in DDR-deficient cancers. Cancer cell proliferation is supported by high metabolic activity. Targeting metabolic pathways is therefore a strategy to suppress cancer cell growth and survival. Glutamine is a key metabolite that supports a plethora of anabolic, growth-promoting reactions in the cell. Therefore, the use of small molecules that block glutamine-dependent reactions has been extensively investigated in cancer therapy. Knowledge about the pathways that influence sensitivity towards glutamine metabolism inhibitors would help to tailor the use of such glutamine-targeting therapies. In this study, we use budding yeast as model system to identify the pathways that mediate or restrict the toxicity of a representative inhibitor of glutamine metabolism, the glutamine analog 6-diazo-5-oxo-L-norleucine (DON). We describe a response mechanism mediated by an inducible CTP synthase that promotes nucleotide homeostasis during DON exposure to prevent DNA breaks. Moreover, we show that combined inhibition of the inducible CTP synthase and DNA damage response enhances DON toxicity, pointing out a potential therapeutic application in cancers with defective DNA damage response.
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Affiliation(s)
- Arta Ajazi
- The FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
- * E-mail: (AA); (CB)
| | | | - Laura Tronci
- The FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
- IRCCS San Raffaele Scientific Institute, Molecular Basis of Cystic Kidney Diseases, Division of Genetics and Cell Biology, Milan, Italy
| | - Angela Bachi
- The FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Christopher Bruhn
- The FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
- * E-mail: (AA); (CB)
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Yoon SY, Jang E, Ko N, Kim M, Kim SY, Moon Y, Nam JS, Lee S, Jun Y. A Genome-Wide Screen Reveals That Endocytic Genes Are Important for Pma1p Asymmetry during Cell Division in Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms23042364. [PMID: 35216480 PMCID: PMC8874555 DOI: 10.3390/ijms23042364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
An asymmetry in cytosolic pH between mother and daughter cells was reported to underlie cellular aging in the budding yeast Saccharomyces cerevisiae; however, the underlying mechanism remains unknown. Preferential accumulation of Pma1p, which pumps cytoplasmic protons out of cells, at the plasma membrane of mother cells, but not of their newly-formed daughter cells, is believed to be responsible for the pH increase in mother cells by reducing the level of cytoplasmic protons. This, in turn, decreases the acidity of vacuoles, which is well correlated with aging of yeast cells. In this study, to identify genes that regulate the preferential accumulation of Pma1p in mother cells, we performed a genome-wide screen using a collection of single gene deletion yeast strains. A subset of genes involved in the endocytic pathway, such as VPS8, VPS9, and VPS21, was important for Pma1p accumulation. Unexpectedly, however, there was little correlation between deletion of each of these genes and the replicative lifespan of yeast, suggesting that Pma1p accumulation in mother cells is not the key determinant that underlies aging of mother cells.
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Affiliation(s)
- So-Young Yoon
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
| | - Eunhong Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
| | - Naho Ko
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
| | - Minseok Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
| | - Su Yoon Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
| | - Yeojin Moon
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
| | - Jeong-Seok Nam
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
| | - Sunjae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
| | - Youngsoo Jun
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; (S.-Y.Y.); (E.J.); (N.K.); (M.K.); (S.Y.K.); (Y.M.); (J.-S.N.); (S.L.)
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea
- Correspondence: ; Tel.: +82-62-715-2510
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Miura N. Condensate Formation by Metabolic Enzymes in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10020232. [PMID: 35208686 PMCID: PMC8876316 DOI: 10.3390/microorganisms10020232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
Condensate formation by a group of metabolic enzymes in the cell is an efficient way of regulating cell metabolism through the formation of “membrane-less organelles.” Because of the use of green fluorescent protein (GFP) for investigating protein localization, various enzymes were found to form condensates or filaments in living Saccharomyces cerevisiae, mammalian cells, and in other organisms, thereby regulating cell metabolism in the certain status of the cells. Among different environmental stresses, hypoxia triggers the spatial reorganization of many proteins, including more than 20 metabolic enzymes, to form numerous condensates, including “Glycolytic body (G-body)” and “Purinosome.” These individual condensates are collectively named “Metabolic Enzymes Transiently Assembling (META) body”. This review overviews condensate or filament formation by metabolic enzymes in S. cerevisiae, focusing on the META body, and recent reports in elucidating regulatory machinery of META body formation.
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Affiliation(s)
- Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
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48
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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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49
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Hansen JM, Horowitz A, Lynch EM, Farrell DP, Quispe J, DiMaio F, Kollman JM. Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation. eLife 2021; 10:73368. [PMID: 34734801 PMCID: PMC8641951 DOI: 10.7554/elife.73368] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize in vitro polymerization and investigate in vivo consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or pH-insensitive mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.
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Affiliation(s)
- Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, United States.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, United States
| | - Avital Horowitz
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Daniel P Farrell
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, United States
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50
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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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