51
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Zhang J, Liu JL. Temperature-sensitive cytoophidium assembly in Schizosaccharomyces pombe. J Genet Genomics 2019; 46:423-432. [PMID: 31611173 PMCID: PMC6868507 DOI: 10.1016/j.jgg.2019.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
The metabolic enzyme CTP synthase (CTPS) is able to compartmentalize into filaments, termed cytoophidia, in a variety of organisms including bacteria, budding yeast, fission yeast, fruit flies and mammals. A previous study in budding yeast shows that the filament-forming process of CTPS is not sensitive to temperature shift. Here we study CTPS filamentation in the fission yeast Schizosaccharomyces pombe. To our surprise, we find that both the length and the occurrence of cytoophidia in S. pombe decrease upon cold shock or heat shock. The temperature-dependent changes of cytoophidia are fast and reversible. Taking advantage of yeast genetics, we demonstrate that heat-shock proteins are required for cytoophidium assembly in S. pombe. Temperature sensitivity of cytoophidia makes S. pombe an attractive model system for future investigations of this novel membraneless organelle.
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Affiliation(s)
- Jing Zhang
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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52
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Noree C, Begovich K, Samilo D, Broyer R, Monfort E, Wilhelm JE. A quantitative screen for metabolic enzyme structures reveals patterns of assembly across the yeast metabolic network. Mol Biol Cell 2019; 30:2721-2736. [PMID: 31483745 PMCID: PMC6761767 DOI: 10.1091/mbc.e19-04-0224] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Despite the proliferation of proteins that can form filaments or phase-separated condensates, it remains unclear how this behavior is distributed over biological networks. We have found that 60 of the 440 yeast metabolic enzymes robustly form structures, including 10 that assemble within mitochondria. Additionally, the ability to assemble is enriched at branch points on several metabolic pathways. The assembly of enzymes at the first branch point in de novo purine biosynthesis is coordinated, hierarchical, and based on their position within the pathway, while the enzymes at the second branch point are recruited to RNA stress granules. Consistent with distinct classes of structures being deployed at different control points in a pathway, we find that the first enzyme in the pathway, PRPP synthetase, forms evolutionarily conserved filaments that are sequestered in the nucleus in higher eukaryotes. These findings provide a roadmap for identifying additional conserved features of metabolic regulation by condensates/filaments.
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Affiliation(s)
- Chalongrat Noree
- Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543.,Institute of Molecular Biosciences, Mahidol University, Phuttamonthon, Nakhon Pathom 73170, Thailand
| | - Kyle Begovich
- Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Dane Samilo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Risa Broyer
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elena Monfort
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - James E Wilhelm
- Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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53
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Lee WH, Oh JY, Maeng PJ. The NADP +-dependent glutamate dehydrogenase Gdh1 is subjected to glucose starvation-induced reversible aggregation that affects stress resistance in yeast. J Microbiol 2019; 57:884-892. [PMID: 31376105 DOI: 10.1007/s12275-019-9065-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 11/28/2022]
Abstract
The yeast Saccharomyces cerevisiae has two isoforms of NADP+-dependent glutamate dehydrogenase (Gdh1 and Gdh3) that catalyze the synthesis of glutamate from α-ketoglutarate and NH4+. In the present study, we confirmed that Gdh3, but not Gdh1, mainly contributes to the oxidative stress resistance of stationary-phase cells and found evidence suggesting that the insignificance of Gdh1 to stress resistance is possibly resulted from conditional and reversible aggregation of Gdh1 into punctuate foci initiated in parallel with post-diauxic growth. Altered localization to the mitochondria or peroxisomes prevented Gdh1, which was originally localized in the cytoplasm, from stationary phase-specific aggregation, suggesting that some cytosolic factors are involved in the process of Gdh1 aggregation. Glucose starvation triggered the transition of the soluble form of Gdh1 into the insoluble aggregate form, which could be redissolved by replenishing glucose, without any requirement for protein synthesis. Mutational analysis showed that the N-terminal proximal region of Gdh1 (NTP1, aa 21-26, TLFEQH) is essential for glucose starvation-induced aggregation. We also found that the substitution of NTP1 with the corresponding region of Gdh3 (NTP3) significantly increased the contribution of the mutant Gdh1 to the stress resistance of stationary-phase cells. Thus, this suggests that NTP1 is responsible for the negligible role of Gdh1 in maintaining the oxidative stress resistance of stationary-phase cells and the stationary phase-specific stresssensitive phenotype of the mutants lacking Gdh3.
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Affiliation(s)
- Woo Hyun Lee
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ju Yeong Oh
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Pil Jae Maeng
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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54
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Kokina A, Ozolina Z, Liepins J. Purine auxotrophy: Possible applications beyond genetic marker. Yeast 2019; 36:649-656. [PMID: 31334866 DOI: 10.1002/yea.3434] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/09/2023] Open
Abstract
Exploring new drug candidates or drug targets against many illnesses is necessary as "traditional" treatments lose their effectivity. Cancer and sicknesses caused by protozoan parasites are among these diseases. Cell purine metabolism is an important drug target. Theoretically, inhibiting purine metabolism could stop the proliferation of unwanted cells. Purine metabolism is similar across all eukaryotes. However, some medically important organisms or cell lines rely on their host purine metabolism. Protozoans causing malaria, leishmaniasis, or toxoplasmosis are purine auxotrophs. Some cancer forms have also lost the ability to synthesize purines de novo. Budding yeast can serve as an effective model for eukaryotic purine metabolism, and thus, purine auxotrophic strains could be an important tool. In this review, we present the common principles of purine metabolism in eukaryotes, effects of purine starvation in eukaryotic cells, and purine-starved Saccharomyces cerevisiae as a model for purine depletion-elicited metabolic states with applications in evolution studies and pharmacology. Purine auxotrophic yeast strains behave differently when growing in media with sufficient supplementation with adenine or in media depleted of adenine (starvation). In the latter, they undergo cell cycle arrest at G1/G0 and become stress resistant. Importantly, similar effects have also been observed among parasitic protozoans or cancer cells. We consider that studies on metabolic changes caused by purine auxotrophy could reveal new options for parasite or cancer therapy. Further, knowledge on phenotypic changes will improve the use of auxotrophic strains in high-throughput screening for primary drug candidates.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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55
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Li S, Yang Z, Zhang H, Peng M, Ma H. Potential role of ALDH3A2 on the lipid and glucose metabolism regulated by (-)-hydroxycitric acid in chicken embryos. Anim Sci J 2019; 90:961-976. [PMID: 31132807 DOI: 10.1111/asj.13225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/10/2019] [Accepted: 04/18/2019] [Indexed: 01/29/2023]
Abstract
This study aimed to investigate the effect of (-)-hydroxycitric acid ((-)-HCA) on lipid and glucose metabolism, and further analyzed these actions whether associated with modulation of aldehyde dehydrogenase 3 family member A2 (ALDH3A2) expression in chicken embryos. Results showed that (-)-HCA decreased triglyceride content and lipid droplet counts, while these effects induced by (-)-HCA were reversed in chicken embryos pre-transfected with sh4-ALDH3A2. (-)-HCA decreased malic enzyme, acetyl-CoA carboxylase, fatty acid synthase, and sterol regulatory element binding protein-1c mRNA level, while increased carnitine palmitoyl transferase 1A (CPT1A) and peroxisome proliferators-activated receptor α (PPARα) mRNA level; and the action of (-)-HCA on lipid metabolism factors had completely eliminated in embryos pre-transfected with sh4-ALDH3A2. Chicken embryos pre-transfected with sh4-ALDH3A2 had eliminated the increasing of serum glucose and hepatic glycogen content induced by (-)-HCA. (-)-HCA decreased phosphofructokinase-1 and increased G6P, fructose-1,6-bisphosphatase, phosphoenolpyruvate carboxykinase (PEPCK), and pyruvate carboxylase mRNA level in chicken embryos. Similarly, the effect of (-)-HCA on these key enzyme mRNA level was reversed in embryos pre-transfected with sh4-ALDH3A2. Furthermore, (-)-HCA increased PPAR-γ-coactivator-1α (PGC-1α), PPARα, hepatic nuclear factor-4A, PEPCK, and CPT1A protein level, and these actions of (-)-HCA disappeared in embryos pre-transfected with sh4-ALDH3A2. These results indicated that (-)-HCA reduced fat accumulation and accelerated gluconeogenesis via activation of PGC-1α signaling pathway, and these effects of (-)-HCA might associate with the increasing of ALDH3A2 expression level in chicken embryos.
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Affiliation(s)
- Shengnan Li
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhongmiao Yang
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Huihui Zhang
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mengling Peng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Haitian Ma
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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56
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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57
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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58
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Laurinyecz B, Vedelek V, Kovács AL, Szilasi K, Lipinszki Z, Slezák C, Darula Z, Juhász G, Sinka R. Sperm-Leucylaminopeptidases are required for male fertility as structural components of mitochondrial paracrystalline material in Drosophila melanogaster sperm. PLoS Genet 2019; 15:e1007987. [PMID: 30802236 PMCID: PMC6388916 DOI: 10.1371/journal.pgen.1007987] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/26/2019] [Indexed: 01/30/2023] Open
Abstract
Drosophila melanogaster sperm reach an extraordinary long size, 1.8 mm, by the end of spermatogenesis. The mitochondrial derivatives run along the entire flagellum and provide structural rigidity for flagellar movement, but its precise function and organization is incompletely understood. The two mitochondrial derivatives differentiate and by the end of spermatogenesis the minor one reduces its size and the major one accumulates paracrystalline material inside it. The molecular constituents and precise function of the paracrystalline material have not yet been revealed. Here we purified the paracrystalline material from mature sperm and identified by mass spectrometry Sperm-Leucylaminopeptidase (S-Lap) family members as important constituents of it. To study the function of S-Lap proteins we show the characterization of classical mutants and RNAi lines affecting of the S-Lap genes and the analysis of their mutant phenotypes. We show that the male sterile phenotype of the S-Lap mutants is caused by defects in paracrystalline material accumulation and abnormal structure of the elongated major mitochondrial derivatives. Our work shows that S-Lap proteins localize and accumulate in the paracrystalline material of the major mitochondrial derivative. Therefore, we propose that S-Lap proteins are important constituents of the paracrystalline material of Drosophila melanogaster sperm.
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Affiliation(s)
| | - Viktor Vedelek
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Attila L. Kovács
- Department of Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - Kinga Szilasi
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Zoltán Lipinszki
- Institute of Biochemistry and MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Csilla Slezák
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Zsuzsanna Darula
- Laboratory of Proteomics Research, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gábor Juhász
- Department of Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - Rita Sinka
- Department of Genetics, University of Szeged, Szeged, Hungary
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59
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Noree C, Sirinonthanawech N, Wilhelm JE. Saccharomyces cerevisiae ASN1 and ASN2 are asparagine synthetase paralogs that have diverged in their ability to polymerize in response to nutrient stress. Sci Rep 2019; 9:278. [PMID: 30670751 PMCID: PMC6342913 DOI: 10.1038/s41598-018-36719-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/26/2018] [Indexed: 11/10/2022] Open
Abstract
Recent work has found that many metabolic enzymes have the ability to polymerize in response to metabolic changes or environmental stress. This ability to polymerize is well conserved for the few metabolic enzyme paralogs that have been studied in yeast. Here we describe the first set of paralogs, Asn1p and Asn2p, that have differential assembly behavior. Asn1p and Asn2p both co-assemble into filaments in response to nutrient limitation. However, the ability of Asn2p to form filaments is strictly dependent on the presence of Asn1p. Using mutations that block enzyme activity but have differential effects on Asn1p polymerization, we have found that Asn1p polymers are unlikely to have acquired a moonlighting function. Together these results provide a novel system for understanding the regulation and evolution of metabolic enzyme polymerization.
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Affiliation(s)
- Chalongrat Noree
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
| | - Naraporn Sirinonthanawech
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand
| | - James E Wilhelm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive (MC 0347), La Jolla, CA, 92093-0347, USA.
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60
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Fernández-Justel D, Núñez R, Martín-Benito J, Jimeno D, González-López A, Soriano EM, Revuelta JL, Buey RM. A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity. J Mol Biol 2019; 431:956-969. [PMID: 30664871 DOI: 10.1016/j.jmb.2019.01.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/29/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo GTP biosynthetic pathway and plays essential roles in cell proliferation. As a clinical target, IMPDH has been studied for decades, but it has only been within the last years that we are starting to understand the complexity of the mechanisms of its physiological regulation. Here, we report structural and functional insights into how adenine and guanine nucleotides control a conformational switch that modulates the assembly of the two human IMPDH enzymes into cytoophidia and allosterically regulates their catalytic activity. In vitro reconstituted micron-length cytoophidia-like structures show catalytic activity comparable to unassembled IMPDH but, in turn, are more resistant to GTP/GDP allosteric inhibition. Therefore, IMPDH cytoophidia formation facilitates the accumulation of high levels of guanine nucleotides when the cell requires it. Finally, we demonstrate that most of the IMPDH retinopathy-associated mutations abrogate GTP/GDP-induced allosteric inhibition and alter cytoophidia dynamics.
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Affiliation(s)
- David Fernández-Justel
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Rafael Núñez
- Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jaime Martín-Benito
- Centro Nacional de Biotecnología (CNB), Spanish National Research Council (CSIC), Darwin 3, 28039 Madrid, Spain
| | - David Jimeno
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Adrián González-López
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Eva María Soriano
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Rubén M Buey
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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61
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Noree C, Monfort E, Shotelersuk V. Human asparagine synthetase associates with the mitotic spindle. Biol Open 2018; 7:bio.038307. [PMID: 30464009 PMCID: PMC6310878 DOI: 10.1242/bio.038307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cancer cells are characterized by extensive reprogramming of metabolic pathways in order to promote cell division and survival. However, the growth promotion effects of metabolic reprogramming can be due to moonlighting functions of metabolic enzymes as well as the redirection of flux through particular pathways. To identify metabolic enzymes that might have potential moonlighting functions in oncogenesis, we have examined recent screens of the yeast GFP strain collection for metabolic enzymes that have been implicated in cancer metabolism with an unusual subcellular localization. Asparagine synthetase forms filaments in yeast in response to nutrient limitation and is part of a pathway that is a chemotherapy target in acute lymphoblastic leukemia. Interestingly, while yeast asparagine synthetase forms cytoplasmic filaments in response to nutrient stress, human asparagine synthetase is associated with the centrosomes and mitotic spindles. This localization is disrupted by both nocodazole and asparaginase treatments. This failure to localize occurs even though asparagine synthetase is highly upregulated in response to asparaginase treatment. Together, these results argue that human asparagine synthetase undergoes regulated recruitment to the mitotic spindles and that it may have acquired a second role in mitosis similar to other metabolic enzymes that contribute to metabolic reprogramming in cancer cells. Summary: While yeast Asn1p/ASN2p forms cytoplasmic filaments in response to nutrient limitation, hASNS is associated with centrosomes and mitotic spindles in actively dividing cells, suggesting its additional role in cell division.
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Affiliation(s)
- Chalongrat Noree
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170, Thailand
| | - Elena Monfort
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive (MC 0347), La Jolla, CA 92093-0347, USA
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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62
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Prouteau M, Loewith R. Regulation of Cellular Metabolism through Phase Separation of Enzymes. Biomolecules 2018; 8:biom8040160. [PMID: 30513998 PMCID: PMC6316564 DOI: 10.3390/biom8040160] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/21/2023] Open
Abstract
Metabolism is the sum of the life-giving chemical processes that occur within a cell. Proper regulation of these processes is essential for all organisms to thrive and prosper. When external factors are too extreme, or if internal regulation is corrupted through genetic or epigenetic changes, metabolic homeostasis is no longer achievable and diseases such as metabolic syndrome or cancer, aging, and, ultimately, death ensue. Metabolic reactions are catalyzed by proteins, and the in vitro kinetic properties of these enzymes have been studied by biochemists for many decades. These efforts led to the appreciation that enzyme activities can be acutely regulated and that this regulation is critical to metabolic homeostasis. Regulation can be mediated through allosteric interactions with metabolites themselves or via post-translational modifications triggered by intracellular signal transduction pathways. More recently, enzyme regulation has attracted the attention of cell biologists who noticed that change in growth conditions often triggers the condensation of diffusely localized enzymes into one or more discrete foci, easily visible by light microscopy. This reorganization from a soluble to a condensed state is best described as a phase separation. As summarized in this review, stimulus-induced phase separation has now been observed for dozens of enzymes suggesting that this could represent a widespread mode of activity regulation, rather than, or in addition to, a storage form of temporarily superfluous enzymes. Building on our recent structure determination of TOROIDs (TORc1 Organized in Inhibited Domain), the condensate formed by the protein kinase Target Of Rapamycin Complex 1 (TORC1), we will highlight that the molecular organization of enzyme condensates can vary dramatically and that future work aimed at the structural characterization of enzyme condensates will be critical to understand how phase separation regulates enzyme activity and consequently metabolic homeostasis. This information may ultimately facilitate the design of strategies to target the assembly or disassembly of specific enzymes condensates as a therapeutic approach to restore metabolic homeostasis in certain diseases.
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Affiliation(s)
- Manoël Prouteau
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Sciences II, Room 3-308, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
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63
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Calise SJ, Abboud G, Kasahara H, Morel L, Chan EKL. Immune Response-Dependent Assembly of IMP Dehydrogenase Filaments. Front Immunol 2018; 9:2789. [PMID: 30555474 PMCID: PMC6283036 DOI: 10.3389/fimmu.2018.02789] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to xanthosine monophosphate, the rate-limiting step in de novo guanosine monophosphate (GMP) synthesis. In cultured cells, IMPDH polymerizes into micron-scale filamentous structures when GMP synthesis is inhibited by depletion of purine precursors or by various drugs, including mycophenolic acid, ribavirin, and methotrexate. IMPDH filaments also spontaneously form in undifferentiated mouse embryonic stem cells and induced pluripotent stem cells, hinting they might function in various highly proliferative cell types. Therefore, we investigated IMPDH filament formation in human and murine T cells, which rely heavily on de novo guanine nucleotide synthesis to rapidly proliferate in response to antigenic challenge. We discovered extensive in vivo IMPDH filament formation in mature T cells, B cells, and other proliferating splenocytes of normal, adult B6 mice. Both cortical and medullary thymocytes in young and old mice also showed considerable assembly of IMPDH filaments. We then stimulated primary human peripheral blood mononuclear cells ex vivo with T cell mitogens phytohemagglutinin (PHA), concanavalin A (ConA), or antibodies to CD3 and CD28 for 72 h. We detected IMPDH filaments in 40–60% of T cells after activation compared to 0–10% of unstimulated T cells. Staining of activated T cells for the proliferation marker Ki-67 also showed an association between IMPDH filament formation and proliferation. Additionally, we transferred ovalbumin-specific CD4+ T cells from B6.OT-II mice into B6.Ly5a recipient mice, challenged these mice with ovalbumin, and harvested spleens 6 days later. In these spleens, we identified abundant IMPDH filaments in transferred T cells by immunofluorescence, indicating that IMPDH also polymerizes during in vivo antigen-specific T cell activation. Overall, our data indicate that IMPDH filament formation is a novel aspect of T cell activation and proliferation, and that filaments might be useful morphological markers for T cell activation. The data also suggest that in vivo IMPDH filament formation could be occurring in a variety of proliferating cell types throughout the body. We propose that T cell activation will be a valuable model for future experiments probing the molecular mechanisms that drive IMPDH polymerization, as well as how IMPDH filament formation affects cell function.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Georges Abboud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
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64
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Zhang S, Ding K, Shen QJ, Zhao S, Liu JL. Filamentation of asparagine synthetase in Saccharomyces cerevisiae. PLoS Genet 2018; 14:e1007737. [PMID: 30365499 PMCID: PMC6221361 DOI: 10.1371/journal.pgen.1007737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 11/07/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022] Open
Abstract
Asparagine synthetase (ASNS) and CTP synthase (CTPS) are two metabolic enzymes crucial for glutamine homeostasis. A genome-wide screening in Saccharomyces cerevisiae reveal that both ASNS and CTPS form filamentous structures termed cytoophidia. Although CTPS cytoophidia were well documented in recent years, the filamentation of ASNS is less studied. Using the budding yeast as a model system, here we confirm that two ASNS proteins, Asn1 and Asn2, are capable of forming cytoophidia in diauxic and stationary phases. We find that glucose deprivation induces ASNS filament formation. Although ASNS and CTPS form distinct cytoophidia with different lengths, both structures locate adjacently to each other in most cells. Moreover, we demonstrate that the Asn1 cytoophidia colocalize with the Asn2 cytoophidia, while Asn2 filament assembly is largely dependent on Asn1. In addition, we are able to alter Asn1 filamentation by mutagenizing key sites on the dimer interface. Finally, we show that ASN1D330V promotes filamentation. The ASN1D330V mutation impedes cell growth in an ASN2 knockout background, while growing normally in an ASN2 wild-type background. Together, this study reveals a connection between ASNS and CTPS cytoophidia and the differential filament-forming capability between two ASNS paralogs. Asparagine synthetase (ASNS) is an essential enzyme for biosynthesis of asparagine. We have recently shown that ASNS, similar to CTP synthase (CTPS), can assemble into snake-shaped structures termed cytoophidia. In this study, we reveal that the ASNS cytoophidium stays close with the CTPS cytoophidium in most cells. Two ASNS proteins, Asn1 and Asn2, localize in the same structure. The Asn1 protein is important for the formation of the Asn2 filaments. Mutant cells with branching Asn1 cytoophidia grow slower than wild-type cells. Our findings provide a better understanding of the ASNS cytoophidium as well as its relationship with the CTPS cytoophidium.
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Affiliation(s)
- Shanshan Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Shanghai Institute of Biochemistry and Cell biology, Chinese Academy of Sciences, Shanghai, China
| | - Kang Ding
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Qing-Ji Shen
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: ,
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65
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Chang CC, Keppeke GD, Sung LY, Liu JL. Interfilament interaction between IMPDH and CTPS cytoophidia. FEBS J 2018; 285:3753-3768. [PMID: 30085408 PMCID: PMC6220823 DOI: 10.1111/febs.14624] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 07/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) and cytidine triphosphate synthase (CTPS) are two metabolic enzymes that perform rate‐limiting steps in the de novo synthesis of purine and pyrimidine nucleotides, respectively. It has been shown that IMPDH and CTPS can comprise a filamentous macrostructure termed the cytoophidium, which may play a role in regulation of their catalytic activity. Although these two proteins may colocalise in the same cytoophidium, how they associate with one another is still elusive. As reported herein, we established a model HeLa cell line coexpressing OFP‐tagged IMPDH2 and GFP‐tagged CTPS1 and recorded the assembly, disassembly and movement of the cytoophidium in live cells. Moreover, by using super‐resolution confocal imaging, we demonstrate how IMPDH‐ and CTPS‐based filaments are aligned or intertwined in the mixed cytoophidium. Collectively, our findings provide a panorama of cytoophidium dynamics and suggest that IMPDH and CTPS cytoophidia may coordinate by interfilament interaction.
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Affiliation(s)
- Chia-Chun Chang
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Gerson D Keppeke
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK.,School of Life Science and Technology, ShanghaiTech University, China
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66
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Atomic insights into the genesis of cellular filaments by globular proteins. Nat Struct Mol Biol 2018; 25:705-714. [PMID: 30076408 PMCID: PMC6185745 DOI: 10.1038/s41594-018-0096-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/21/2018] [Indexed: 02/04/2023]
Abstract
Self-assembly of proteins into filaments, such as actin and tubulin filaments, underlies essential cellular processes in all three domains of life. The early emergence of filaments in evolutionary history suggests that filament genesis might be a robust process. Here we describe the fortuitous construction of GFP fusion proteins that self-assemble as fluorescent polar filaments in Escherichia coli. Filament formation is achieved by appending as few as 12 residues. Crystal structures reveal that the protomers each donate an appendage to fill a groove between two following protomers along the filament. This exchange of appendages resembles runaway domain swapping but is distinguished by higher efficiency because monomers cannot competitively bind their own appendages. Ample evidence of this “runaway domain coupling” mechanism in nature suggests it could facilitate the evolutionary pathway from globular protein to polar filament, requiring a minimal extension of protein sequence and no significant refolding.
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67
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Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. The run-on oligomer filament enzyme mechanism of SgrAI: Part 1. Assembly kinetics of the run-on oligomer filament. J Biol Chem 2018; 293:14585-14598. [PMID: 30068553 DOI: 10.1074/jbc.ra118.003680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/30/2018] [Indexed: 01/06/2023] Open
Abstract
Filament or run-on oligomer formation by metabolic enzymes is now recognized as a widespread phenomenon having potentially unique enzyme regulatory properties and biological roles, and its dysfunction is implicated in human diseases such as cancer, diabetes, and developmental disorders. SgrAI is a bacterial allosteric type II restriction endonuclease that binds to invading phage DNA, may protect the host DNA from off-target cleavage activity, and forms run-on oligomeric filaments with enhanced DNA-cleavage activity and altered DNA sequence specificity. However, the mechanisms of SgrAI filament growth, cooperativity in filament formation, sequestration of enzyme activity, and advantages over other filament mechanisms remain unknown. In this first of a two-part series, we developed methods and models to derive association and dissociation rate constants of DNA-bound SgrAI in run-on oligomers and addressed the specific questions of cooperativity and filament growth mechanisms. We show that the derived rate constants are consistent with the run-on oligomer sizes determined by EM analysis and are most consistent with a noncooperative growth mode of the run-on oligomer. These models and methods are extended in the accompanying article to include the full DNA-cleavage pathway and address specific questions related to the run-on oligomer mechanism including the sequestration of DNA-cleavage activity and trapping of products.
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Affiliation(s)
- Chad K Park
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jonathan L Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Claudia Barahona
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - L Emilia Basantes
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Juan Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Christian Hernandez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - N C Horton
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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68
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Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. The run-on oligomer filament enzyme mechanism of SgrAI: Part 2. Kinetic modeling of the full DNA cleavage pathway. J Biol Chem 2018; 293:14599-14615. [PMID: 30054273 DOI: 10.1074/jbc.ra118.003682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/17/2018] [Indexed: 11/06/2022] Open
Abstract
Filament or run-on oligomer formation by enzymes is now recognized as a widespread phenomenon with potentially unique enzyme regulatory properties and biological roles. SgrAI is an allosteric type II restriction endonuclease that forms run-on oligomeric filaments with activated DNA cleavage activity and altered DNA sequence specificity. In this two-part work, we measure individual steps in the run-on oligomer filament mechanism to address specific questions of cooperativity, trapping, filament growth mechanisms, and sequestration of activity using fluorophore-labeled DNA, kinetic FRET measurements, and reaction modeling with global data fitting. The final models and rate constants show that the assembly step involving association of SgrAI-DNA complexes into the run-on oligomer filament is relatively slow (3-4 orders of magnitude slower than diffusion limited) and rate-limiting at low to moderate concentrations of SgrAI-DNA. The disassembly step involving dissociation of complexes of SgrAI-DNA from each other in the run-on oligomer filament is the next slowest step but is fast enough to limit the residence time of any one copy of SgrAI or DNA within the dynamic filament. Further, the rate constant for DNA cleavage is found to be 4 orders of magnitude faster in the run-on oligomer filament than in isolated SgrAI-DNA complexes and faster than dissociation of SgrAI-DNA complexes from the run-on oligomer filament, making the reaction efficient in that each association into the filament likely leads to DNA cleavage before filament dissociation.
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Affiliation(s)
- Chad K Park
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jonathan L Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Claudia Barahona
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - L Emilia Basantes
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Juan Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Christian Hernandez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - N C Horton
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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69
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Structural basis for regulation of human acetyl-CoA carboxylase. Nature 2018; 558:470-474. [DOI: 10.1038/s41586-018-0201-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 04/24/2018] [Indexed: 11/08/2022]
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70
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Li H, Ye F, Ren JY, Wang PY, Du LL, Liu JL. Active transport of cytoophidia in Schizosaccharomyces pombe. FASEB J 2018; 32:5891-5898. [PMID: 29782206 PMCID: PMC6292696 DOI: 10.1096/fj.201800045rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The metabolic enzyme cytidine triphosphate synthase has recently been found to form micrometer-sized filamentous structures termed cytoophidia, which are evolutionarily conserved across prokaryotes and eukaryotes. The cytoophidium represents a novel type of membraneless organelle and behaves dynamically inside the cell. The question of how cytoophidia transport is mediated, however, remains unanswered. For the first time, we detected in this study the active transport of cytoophidia, taking advantage of the fission yeast Schizosaccharomyces pombe as an excellent model for studying membraneless organelles. We demonstrated that actin filaments, not microtubules, are responsible for this transport. Furthermore, we determined that Myo52, a type of myosin V, is required for the active transport of cytoophidia. These results reveal the major players critical to the dynamics of cytoophidia and extend our understanding of intracellular transport of membraneless organelles.—Li, H., Ye, F., Ren, J.-Y., Wang, P.-Y., Du, L.-L., Liu, J.-L. Active transport of cytoophidia in Schizosaccharomyces pombe.
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Affiliation(s)
- Hui Li
- Department of Physiology, Anatomy, and Genetics, Medical Research Council Functional Genomics Unit, University of Oxford, Oxford, United Kingdom.,Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Fangfu Ye
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Yi Ren
- National Institute of Biological Sciences, Beijing, China; and
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China; and
| | - Ji-Long Liu
- Department of Physiology, Anatomy, and Genetics, Medical Research Council Functional Genomics Unit, University of Oxford, Oxford, United Kingdom.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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71
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Extramitochondrial Assembly of Mitochondrial Targeting Signal Disrupted Mitochondrial Enzyme Aldehyde Dehydrogenase. Sci Rep 2018; 8:6186. [PMID: 29670139 PMCID: PMC5906672 DOI: 10.1038/s41598-018-24586-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/06/2018] [Indexed: 11/17/2022] Open
Abstract
Supramolecular assembly of metabolic enzymes has been studied both in vivo and in vitro for nearly a decade. Experimental evidence has suggested a close relationship between enzymatic activity and enzyme assembly/disassembly. However, most cases were studied with the cytosolic enzymes. Here, I report the evidence for a mitochondrial enzyme with its ability in forming visible intracellular structures. By removing the mitochondrial targeting sequence, yeast mitochondrial enzyme aldehyde dehydrogenase (Ald4p) exhibits reversible supramolecular assembly in the cytoplasm, thus creating a useful system for further characterization of the regulatory factors that modulate the assembly/disassembly of this mitochondrial enzyme.
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72
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Biophysical Analysis of Bacterial CTP Synthase Filaments Formed in the Presence of the Chemotherapeutic Metabolite Gemcitabine-5'-triphosphate. J Mol Biol 2018; 430:1201-1217. [PMID: 29501573 DOI: 10.1016/j.jmb.2018.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 11/21/2022]
Abstract
While enzyme activity is often regulated by a combination of substrate/effector availability and quaternary structure, many cytosolic enzymes may be further regulated through oligomerization into filaments. Cytidine-5'-triphosphate (CTP) synthase (CTPS) forms such filaments-a process that is promoted by the product CTP. The CTP analog and active chemotherapeutic metabolite gemcitabine-5'-triphosphate (dF-dCTP) is a potent inhibitor of CTPS; however, its effect on the enzyme's ability to form filaments is unknown. Alongside electron microscopy studies, dynamic light scattering showed that dF-dCTP induces Escherichia coli CTPS (EcCTPS) to form filaments in solution with lengths ≥30 nm in the presence of CTP or dF-dCTP. The substrate UTP blocks formation of filaments and effects their disassembly. EcCTPS variants were constructed to investigate the role of CTP-binding determinants in CTP- and dF-dCTP-dependent filament formation. Substitution of Glu 149 (i.e., E149D), which interacts with the ribose of CTP, caused reduced affinity for both CTP and dF-dCTP, and obviated filament formation. Phe 227 appears to interact with CTP through an edge-on interaction with the cytosine ring, yet the F227A and F227L variants bound CTP and dF-dCTP. F227A EcCTPS did not form filaments, while F227L EcCTPS formed shorter filaments in the presence of CTP or dF-dCTP. Hence, Phe 227 plays a role in filament formation, although replacement by a bulky hydrophobic amino acid is sufficient for limited filament formation. That dF-dCTP can induce filament formation highlights the fact that nucleotide analogs employed as chemotherapeutic agents may affect the filamentous states of enzymes and potentially alter their regulation in vivo.
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73
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Stoddard PR, Williams TA, Garner E, Baum B. Evolution of polymer formation within the actin superfamily. Mol Biol Cell 2017; 28:2461-2469. [PMID: 28904122 PMCID: PMC5597319 DOI: 10.1091/mbc.e15-11-0778] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/13/2017] [Accepted: 07/18/2017] [Indexed: 01/02/2023] Open
Abstract
While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes. It is not known whether these polymers descended from a single ancestral polymer or arose multiple times by convergent evolution from monomeric actin-like proteins. In this work, we provide an overview of the structures, dynamics, and functions of this diverse set. Then, using a phylogenetic analysis to examine actin evolution, we show that the actin-related protein families that form polymers are more closely related to one another than they are to other nonpolymerizing members of the actin superfamily. Thus all the known actin-like polymers are likely to be the descendants of a single, ancestral, polymer-forming actin-like protein.
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Affiliation(s)
- Patrick R Stoddard
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Ethan Garner
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Institute of Physics of Living Systems, University College London, London WC1E 6BT, UK
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74
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Anthony SA, Burrell AL, Johnson MC, Duong-Ly KC, Kuo YM, Simonet JC, Michener P, Andrews A, Kollman JM, Peterson JR. Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations. Mol Biol Cell 2017; 28:mbc.E17-04-0263. [PMID: 28794265 PMCID: PMC5620369 DOI: 10.1091/mbc.e17-04-0263] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/02/2017] [Accepted: 08/04/2017] [Indexed: 01/01/2023] Open
Abstract
Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and metabolic homeostasis. The guanine nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) forms octamers that polymerize into helical chains. In mammalian cells, IMPDH filaments can associate into micron-length assemblies. Polymerization and enzyme activity are regulated in part by binding of purine nucleotides to an allosteric regulatory domain. ATP promotes octamer polymerization, whereas GTP promotes a compact, inactive conformation whose ability to polymerize is unknown. Also unclear is whether polymerization directly alters IMPDH catalytic activity. To address this, we identified point mutants of human IMPDH2 that either prevent or promote polymerization. Unexpectedly, we found that polymerized and non-assembled forms of recombinant IMPDH have comparable catalytic activity, substrate affinity, and GTP sensitivity and validated this finding in cells. Electron microscopy revealed that substrates and allosteric nucleotides shift the equilibrium between active and inactive conformations in both the octamer and the filament. Unlike other metabolic filaments, which selectively stabilize active or inactive conformations, recombinant IMPDH filaments accommodate multiple states. These conformational states are finely tuned by substrate availability and purine balance, while polymerization may allow cooperative transitions between states.
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Affiliation(s)
- Sajitha A Anthony
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Krisna C Duong-Ly
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Yin-Ming Kuo
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Jacqueline C Simonet
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Peter Michener
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102
| | - Andrew Andrews
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Jeffrey R Peterson
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
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75
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Zaganjor E, Spinelli JB, Haigis MC. Strength in numbers: Phosphofructokinase polymerization prevails in the liver. J Cell Biol 2017; 216:2239-2241. [PMID: 28716843 PMCID: PMC5551721 DOI: 10.1083/jcb.201706005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Zaganjor et al. preview work from Webb et al. that shows that the liver-specific isoform of the glycolysis enzyme PFK1 can assemble into filaments and localize to distinct puncta near the plasma membrane. Numerous metabolic enzymes assemble into filamentous structures, which are thought to serve additional regulatory functions. In this issue, Webb et al. (2017. J. Cell Biol.https://doi.org/10.1083/jcb.201701084) show that the liver-specific isoform of phosphofructokinase-1 forms filaments in vitro and localizes as puncta in cells along the plasma membrane. This suggests spatial organization of glycolysis in higher organisms.
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Affiliation(s)
- Elma Zaganjor
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | | | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA
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76
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Webb BA, Dosey AM, Wittmann T, Kollman JM, Barber DL. The glycolytic enzyme phosphofructokinase-1 assembles into filaments. J Cell Biol 2017. [PMID: 28646105 PMCID: PMC5551713 DOI: 10.1083/jcb.201701084] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Despite abundant knowledge of the regulation and biochemistry of glycolytic enzymes, we have limited understanding on how they are spatially organized in the cell. Emerging evidence indicates that nonglycolytic metabolic enzymes regulating diverse pathways can assemble into polymers. We now show tetramer- and substrate-dependent filament assembly by phosphofructokinase-1 (PFK1), which is considered the "gatekeeper" of glycolysis because it catalyzes the step committing glucose to breakdown. Recombinant liver PFK1 (PFKL) isoform, but not platelet PFK1 (PFKP) or muscle PFK1 (PFKM) isoforms, assembles into filaments. Negative-stain electron micrographs reveal that filaments are apolar and made of stacked tetramers oriented with exposed catalytic sites positioned along the edge of the polymer. Electron micrographs and biochemical data with a PFKL/PFKP chimera indicate that the PFKL regulatory domain mediates filament assembly. Quantified live-cell imaging shows dynamic properties of localized PFKL puncta that are enriched at the plasma membrane. These findings reveal a new behavior of a key glycolytic enzyme with insights on spatial organization and isoform-specific glucose metabolism in cells.
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Affiliation(s)
- Bradley A Webb
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Anne M Dosey
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
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Abstract
The organization of metabolic multienzyme complexes has been hypothesized to benefit metabolic processes and provide a coordinated way for the cell to regulate metabolism. Historically, their existence has been supported by various in vitro techniques. However, it is only recently that the existence of metabolic complexes inside living cells has come to light to corroborate this long-standing hypothesis. Indeed, subcellular compartmentalization of metabolic enzymes appears to be widespread and highly regulated. On the other hand, it is still challenging to demonstrate the functional significance of these enzyme complexes in the context of the cellular milieu. In this review, we discuss the current understanding of metabolic enzyme complexes by primarily focusing on central carbon metabolism and closely associated metabolic pathways in a variety of organisms, as well as their regulation and functional contributions to cells.
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Affiliation(s)
- Danielle L Schmitt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC) , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Songon An
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC) , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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78
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Lynch EM, Hicks DR, Shepherd M, Endrizzi JA, Maker A, Hansen JM, Barry RM, Gitai Z, Baldwin EP, Kollman JM. Human CTP synthase filament structure reveals the active enzyme conformation. Nat Struct Mol Biol 2017; 24:507-514. [PMID: 28459447 PMCID: PMC5472220 DOI: 10.1038/nsmb.3407] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/06/2017] [Indexed: 12/11/2022]
Abstract
The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we show that for human CTPS, polymerization increases catalytic activity. The cryo-EM structures of bacterial and human CTPS filaments differ considerably in overall architecture and in the conformation of the CTPS protomer, explaining the divergent consequences of polymerization on activity. The structure of human CTPS filament, the first structure of the full-length human enzyme, reveals a novel active conformation. The filament structures elucidate allosteric mechanisms of assembly and regulation that rely on a conserved conformational equilibrium. The findings may provide a mechanism for increasing human CTPS activity in response to metabolic state and challenge the assumption that metabolic filaments are generally storage forms of inactive enzymes. Allosteric regulation of CTPS polymerization by ligands likely represents a fundamental mechanism underlying assembly of other metabolic filaments.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
| | - Matthew Shepherd
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - James A Endrizzi
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
| | - Allison Maker
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, Washington, USA
| | - Rachael M Barry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Enoch P Baldwin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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79
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Huang Y, Wang JJ, Ghosh S, Liu JL. Critical roles of CTP synthase N-terminal in cytoophidium assembly. Exp Cell Res 2017; 354:122-133. [PMID: 28342900 PMCID: PMC5405848 DOI: 10.1016/j.yexcr.2017.03.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/18/2017] [Accepted: 03/20/2017] [Indexed: 01/27/2023]
Abstract
Several metabolic enzymes assemble into distinct intracellular structures in prokaryotes and eukaryotes suggesting an important functional role in cell physiology. The CTP-generating enzyme CTP synthase forms long filamentous structures termed cytoophidia in bacteria, yeast, fruit flies and human cells independent of its catalytic activity. However, the amino acid determinants for protein-protein interaction necessary for polymerisation remained unknown. In this study, we systematically analysed the role of the conserved N-terminal of Drosophila CTP synthase in cytoophidium assembly. Our mutational analyses identified three key amino acid residues within this region that play an instructive role in organisation of CTP synthase into a filamentous structure. Co-transfection assays demonstrated formation of heteromeric CTP synthase filaments which is disrupted by protein carrying a mutated N-terminal alanine residue thus revealing a dominant-negative activity. Interestingly, the dominant-negative activity is supressed by the CTP synthase inhibitor DON. Furthermore, we found that the amino acids at the corresponding position in the human protein exhibit similar properties suggesting conservation of their function through evolution. Our data suggest that cytoophidium assembly is a multi-step process involving N-terminal-dependent sequential interactions between correctly folded structural units and provide insights into the assembly of these enigmatic structures. CTP synthase mutational analyses reveal N-terminal amino acids that regulate filament self-assembly. Amino acid 20 of CTP synthase plays key role in protein interactions necessary for polymerisation. The dominant-negative activity is supressed by CTP synthase inhibitor DON. The functional properties of the amino acids are conserved in Drosophila and human CTP synthases.
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Affiliation(s)
- Yong Huang
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom; Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Sanjay Ghosh
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom.
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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80
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Liu JL. The Cytoophidium and Its Kind: Filamentation and Compartmentation of Metabolic Enzymes. Annu Rev Cell Dev Biol 2016; 32:349-372. [DOI: 10.1146/annurev-cellbio-111315-124907] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China;
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81
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Data on dynamic study of cytoophidia in Saccharomyces cerevisiae. Data Brief 2016; 8:40-4. [PMID: 27274529 PMCID: PMC4885114 DOI: 10.1016/j.dib.2016.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 04/18/2016] [Accepted: 05/09/2016] [Indexed: 11/30/2022] Open
Abstract
The data in this paper are related to the research article entitled “Filamentation of metabolic enzymes in Saccharomyces cerevisiae” Q.J. Shen et al. (2016) [1]. Cytoophidia are filamentous structures discovered in fruit flies (doi:10.1016/S1673-8527(09)60046-1) J.L. Liu (2010) [2], bacteria (doi:10.1038/ncb2087) M. Ingerson-Mahar et al. (2010) [3], yeast (doi:10.1083/jcb.201003001; doi:10.1242/bio.20149613) C. Noree et al. (2010) and J. Zhang, L. Hulme, J.L. Liu (2014) [4], [5] and human cells (doi:10.1371/journal.pone.0029690; doi:10.1016/j.jgg.2011.08.004) K. Chen et al. (2011) and W.C. Carcamo et al. (2011) ( [6], [7]. However, there is little research on the motility of the cytoophidia. Here we selected cytoophidia formed by 6 filament-forming proteins in the budding yeast S. cerevisiae, and performed living-cell imaging of cells expressing the proteins fused with GFP. The dynamic features of the six types of cytoophidia were analyzed. In the data, both raw movies and analysed results of the dynamics of cytoophidia are presented.
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82
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Abstract
Determining the mechanisms of enzymatic regulation is central to the study of cellular metabolism. Regulation of enzyme activity via polymerization-mediated strategies has been shown to be widespread, and plays a vital role in mediating cellular homeostasis. In this review, we begin with an overview of the filamentation of CTP synthase, which forms filamentous structures termed cytoophidia. We then highlight other important examples of the phenomenon. Moreover, we discuss recent data relating to the regulation of enzyme activity by compartmentalization into cytoophidia. Finally, we hypothesize potential roles for enzyme filament formation in the regulation of metabolism, development and disease.
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Affiliation(s)
- Gabriel N Aughey
- a MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK
| | - Ji-Long Liu
- a MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics , University of Oxford , Oxford , UK
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