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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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152
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Pai LM, Wang PY, Lin WC, Chakraborty A, Yeh CT, Lin YH. Ubiquitination and filamentous structure of cytidine triphosphate synthase. Fly (Austin) 2016; 10:108-14. [PMID: 27116391 PMCID: PMC4970526 DOI: 10.1080/19336934.2016.1182268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Living organisms respond to nutrient availability by regulating the activity of metabolic enzymes. Therefore, the reversible post-translational modification of an enzyme is a common regulatory mechanism for energy conservation. Recently, cytidine-5'-triphosphate (CTP) synthase was discovered to form a filamentous structure that is evolutionarily conserved from flies to humans. Interestingly, induction of the formation of CTP synthase filament is responsive to starvation or glutamine depletion. However, the biological roles of this structure remain elusive. We have recently shown that ubiquitination regulates CTP synthase activity by promoting filament formation in Drosophila ovaries during endocycles. Intriguingly, although the ubiquitination process was required for filament formation induced by glutamine depletion, CTP synthase ubiquitination was found to be inversely correlated with filament formation in Drosophila and human cell lines. In this article, we discuss the putative dual roles of ubiquitination, as well as its physiological implications, in the regulation of CTP synthase structure.
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Affiliation(s)
- Li-Mei Pai
- a Department of Biochemistry , Chang Gung University , Taoyuan City , Taiwan.,b Molecular Medicine Research Center, Chang Gung University , Taoyuan City , Taiwan.,c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan.,d Liver Research Center, Chang Gung Memorial Hospital , Taoyuan City , Taiwan
| | - Pei-Yu Wang
- a Department of Biochemistry , Chang Gung University , Taoyuan City , Taiwan.,b Molecular Medicine Research Center, Chang Gung University , Taoyuan City , Taiwan
| | - Wei-Cheng Lin
- b Molecular Medicine Research Center, Chang Gung University , Taoyuan City , Taiwan
| | - Archan Chakraborty
- c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan
| | - Chau-Ting Yeh
- c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan.,d Liver Research Center, Chang Gung Memorial Hospital , Taoyuan City , Taiwan
| | - Yu-Hung Lin
- c Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan City , Taiwan
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153
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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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154
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Shen QJ, Kassim H, Huang Y, Li H, Zhang J, Li G, Wang PY, Yan J, Ye F, Liu JL. Filamentation of Metabolic Enzymes in Saccharomyces cerevisiae. J Genet Genomics 2016; 43:393-404. [PMID: 27312010 PMCID: PMC4920916 DOI: 10.1016/j.jgg.2016.03.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/09/2016] [Accepted: 03/28/2016] [Indexed: 01/21/2023]
Abstract
Compartmentation via filamentation has recently emerged as a novel mechanism for metabolic regulation. In order to identify filament-forming metabolic enzymes systematically, we performed a genome-wide screening of all strains available from an open reading frame-GFP collection in Saccharomyces cerevisiae. We discovered nine novel filament-forming proteins and also confirmed those identified previously. From the 4159 strains, we found 23 proteins, mostly metabolic enzymes, which are capable of forming filaments in vivo. In silico protein-protein interaction analysis suggests that these filament-forming proteins can be clustered into several groups, including translational initiation machinery and glucose and nitrogen metabolic pathways. Using glutamine-utilising enzymes as examples, we found that the culture conditions affect the occurrence and length of the metabolic filaments. Furthermore, we found that two CTP synthases (Ura7p and Ura8p) and two asparagine synthetases (Asn1p and Asn2p) form filaments both in the cytoplasm and in the nucleus. Live imaging analyses suggest that metabolic filaments undergo sub-diffusion. Taken together, our genome-wide screening identifies additional filament-forming proteins in S. cerevisiae and suggests that filamentation of metabolic enzymes is more general than currently appreciated.
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Affiliation(s)
- Qing-Ji Shen
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Hakimi Kassim
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Yong Huang
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Hui Li
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jing Zhang
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Guang Li
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fangfu Ye
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK.
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155
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Protein aggregation as a mechanism of adaptive cellular responses. Curr Genet 2016; 62:711-724. [DOI: 10.1007/s00294-016-0596-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 11/26/2022]
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156
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Munder MC, Midtvedt D, Franzmann T, Nüske E, Otto O, Herbig M, Ulbricht E, Müller P, Taubenberger A, Maharana S, Malinovska L, Richter D, Guck J, Zaburdaev V, Alberti S. A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy. eLife 2016; 5. [PMID: 27003292 PMCID: PMC4850707 DOI: 10.7554/elife.09347] [Citation(s) in RCA: 282] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 02/13/2016] [Indexed: 01/19/2023] Open
Abstract
Cells can enter into a dormant state when faced with unfavorable conditions. However, how cells enter into and recover from this state is still poorly understood. Here, we study dormancy in different eukaryotic organisms and find it to be associated with a significant decrease in the mobility of organelles and foreign tracer particles. We show that this reduced mobility is caused by an influx of protons and a marked acidification of the cytoplasm, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability. We further demonstrate that this transition is required for cellular survival under conditions of starvation. Our findings have broad implications for understanding alternative physiological states, such as quiescence and dormancy, and create a new view of the cytoplasm as an adaptable fluid that can reversibly transition into a protective solid-like state.
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Affiliation(s)
| | - Daniel Midtvedt
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Titus Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oliver Otto
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Maik Herbig
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Elke Ulbricht
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Paul Müller
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anna Taubenberger
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jochen Guck
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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157
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Schuchmann K, Vonck J, Müller V. A bacterial hydrogen-dependent CO2 reductase forms filamentous structures. FEBS J 2016; 283:1311-22. [PMID: 26833643 DOI: 10.1111/febs.13670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 12/01/2022]
Abstract
Interconversion of CO2 and formic acid is an important reaction in bacteria. A novel enzyme complex that directly utilizes molecular hydrogen as electron donor for the reversible reduction of CO2 has recently been identified in the Wood-Ljungdahl pathway of an acetogenic bacterium. This pathway is utilized for carbon fixation as well as energy conservation. Here we describe the further characterization of the quaternary structure of this enzyme complex and the unexpected behavior of this enzyme in polymerizing into filamentous structures. Polymerization of metabolic enzymes into similar structures has been observed only in rare cases but the increasing number of examples point towards a more general characteristic of enzyme functioning. Polymerization of the purified enzyme into ordered filaments of more than 0.1 μm in length was only dependent on the presence of divalent cations. Polymerization was a reversible process and connected to the enzymatic activity of the oxygen-sensitive enzyme with the filamentous form being the most active state.
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Affiliation(s)
- Kai Schuchmann
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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158
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Aughey GN, Grice SJ, Liu JL. The Interplay between Myc and CTP Synthase in Drosophila. PLoS Genet 2016; 12:e1005867. [PMID: 26889675 PMCID: PMC4759343 DOI: 10.1371/journal.pgen.1005867] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/23/2016] [Indexed: 01/24/2023] Open
Abstract
CTP synthase (CTPsyn) is essential for the biosynthesis of pyrimidine nucleotides. It has been shown that CTPsyn is incorporated into a novel cytoplasmic structure which has been termed the cytoophidium. Here, we report that Myc regulates cytoophidium formation during Drosophila oogenesis. We have found that Myc protein levels correlate with cytoophidium abundance in follicle epithelia. Reducing Myc levels results in cytoophidium loss and small nuclear size in follicle cells, while overexpression of Myc increases the length of cytoophidia and the nuclear size of follicle cells. Ectopic expression of Myc induces cytoophidium formation in late stage follicle cells. Furthermore, knock-down of CTPsyn is sufficient to suppress the overgrowth phenotype induced by Myc overexpression, suggesting CTPsyn acts downstream of Myc and is required for Myc-mediated cell size control. Taken together, our data suggest a functional link between Myc, a renowned oncogene, and the essential nucleotide biosynthetic enzyme CTPsyn. The coordination of metabolism with cell growth is critical for regulation of organismal development. Therefore there is significant interplay between metabolic enzymes and key developmental regulators such as transcription factors. The enzyme CTP synthase (CTPsyn) is essential for metabolic homeostasis as well as growth and development, due to its role in synthesising precursors for many fundamental cellular macromolecules such as RNA and lipids. However, the mechanisms by which CTPsyn is regulated during development are little understood. Here we have shown that Myc, an oncogene and a key developmental regulator, is necessary and sufficient for the assembly of CTPsyn-containing macrostructures termed cytoophidia. We show that the presence of CTPsyn is required for Myc to mediate its effect on cell growth during Drosophila oogenesis. Roles for CTPsyn and Myc in tumourigenesis have been well established and both proteins have been considered promising therapeutic targets. By better understanding the relationship between these two proteins, we can gain important insights, not only into tumour pathology and aetiology, but also metazoan developmental processes.
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Affiliation(s)
- Gabriel N. Aughey
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Stuart J. Grice
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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159
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Vectors for Genetically-Encoded Tags for Electron Microscopy Contrast in Drosophila. Biol Proced Online 2016; 18:5. [PMID: 26839516 PMCID: PMC4736618 DOI: 10.1186/s12575-016-0034-1] [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] [Received: 07/07/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the most notable recent advances in electron microscopy (EM) was the development of genetically-encoded EM tags, including the fluorescent flavoprotein Mini-SOG (Mini-Singlet Oxygen Generator). Mini-SOG generates good EM contrast, thus providing a viable alternative to technically-demanding methods such as immuno-electron microcopy (immuno-EM). Based on the Mini-SOG technology, in this paper, we describe the construction, validation and optimization of a series of vectors which allow expression of Mini-SOG in the Drosophila melanogaster genetic model system. FINDINGS We constructed a Mini-SOG tag that has been codon-optimized for expression in Drosophila (DMS tag) using PCR-mediated gene assembly. The photo-oxidation reaction triggered by DMS was then tested using these vectors in Drosophila cell lines. DMS tag did not affect the subcellular localization of the proteins we tested. More importantly, we demonstrated the utility of the DMS tag for EM in Drosophila by showing that it can produce robust photo-oxidation reactions in the presence of blue light and the substrate DAB; the resultant electron micrographs contain electron-dense regions corresponding to the protein of interest. The vectors we generated allow protein tagging at both termini, for constitutive and inducible protein expression, as well as the generation of transgenic lines by P-element transformation. CONCLUSIONS We demonstrated the feasibility of Mini-SOG tagging in Drosophila. The constructed vectors will no doubt be a useful molecular tool for genetic tagging to facilitate high-resolution localization of proteins in Drosophila by electron microscopy.
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160
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Regulation of CTP Synthase Filament Formation During DNA Endoreplication in Drosophila. Genetics 2015; 201:1511-23. [PMID: 26482795 DOI: 10.1534/genetics.115.180737] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
CTP synthase (CTPsyn) plays an essential role in DNA, RNA, and lipid synthesis. Recent studies in bacteria, yeast, and Drosophila all reveal a polymeric CTPsyn structure, which dynamically regulates its enzymatic activity. However, the molecular mechanism underlying the formation of CTPsyn polymers is not completely understood. In this study, we found that reversible ubiquitination regulates the dynamic assembly of the filamentous structures of Drosophila CTPsyn. We further determined that the proto-oncogene Cbl, an E3 ubiquitin ligase, controls CTPsyn filament formation in endocycles. While the E3 ligase activity of Cbl is required for CTPsyn filament formation, Cbl does not affect the protein levels of CTPsyn. It remains unclear whether the regulation of CTPsyn filaments by Cbl is through direct ubiquitination of CTPsyn. In the absence of Cbl or with knockdown of CTPsyn, the progression of the endocycle-associated S phase was impaired. Furthermore, overexpression of wild-type, but not enzymatically inactive CTPsyn, rescued the endocycle defect in Cbl mutant cells. Together, these results suggest that Cbl influences the nucleotide pool balance and controls CTPsyn filament formation in endocycles. This study links Cbl-mediated ubiquitination to the polymerization of a metabolic enzyme and reveals a role for Cbl in endocycles during Drosophila development.
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161
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Chang CC, Lin WC, Pai LM, Lee HS, Wu SC, Ding ST, Liu JL, Sung LY. Cytoophidium assembly reflects upregulation of IMPDH activity. J Cell Sci 2015; 128:3550-5. [PMID: 26303200 PMCID: PMC4610212 DOI: 10.1242/jcs.175265] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/13/2015] [Indexed: 01/18/2023] Open
Abstract
Cytidine triphosphate synthase (CTPS) and inosine monophosphate dehydrogenase (IMPDH) (both of which have two isoforms) can form fiber-like subcellular structures termed 'cytoophidia' under certain circumstances in mammalian cells. Although it has been shown that filamentation of CTPS downregulates its activity by disturbing conformational changes, the activity of IMPDH within cytoophidia is still unclear. Most previous IMPDH cytoophidium studies were performed under conditions involving inhibitors that impair GTP synthesis. Here, we show that IMPDH forms cytoophidia without inhibition of GTP synthesis. First, we find that an elevated intracellular CTP concentration or treatment with 3'-deazauridine, a CTPS inhibitor, promotes IMPDH cytoophidium formation and increases the intracellular GTP pool size. Moreover, restriction of cell growth triggers the disassembly of IMPDH cytoophidia, implying that their presence is correlated with active cell metabolism. Finally, we show that the presence of IMPDH cytoophidia in mouse pancreatic islet cells might correlate with nutrient uptake in the animal. Collectively, our findings reveal that formation of IMPDH cytoophidia reflects upregulation of purine nucleotide synthesis, suggesting that the IMPDH cytoophidium plays a role distinct from that of the CTPS cytoophidium in controlling intracellular nucleotide homeostasis.
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Affiliation(s)
- Chia-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Wei-Cheng Lin
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China
| | - Li-Mei Pai
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China
| | - Hsuan-Shu Lee
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei 10051, Taiwan, Republic of China
| | - Shinn-Chih Wu
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Shih-Torng Ding
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, Republic of China
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162
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Kroschwald S, Maharana S, Mateju D, Malinovska L, Nüske E, Poser I, Richter D, Alberti S. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife 2015; 4:e06807. [PMID: 26238190 PMCID: PMC4522596 DOI: 10.7554/elife.06807] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/25/2015] [Indexed: 12/27/2022] Open
Abstract
RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine. DOI:http://dx.doi.org/10.7554/eLife.06807.001 Genes consist of long stretches of DNA that code for proteins. The DNA is first ‘transcribed’ to produce an RNA molecule, which is then translated into a protein. In most cells, RNA molecules are present within a structure called ribonucleoprotein (RNP for short) granules. These contain the protein machinery needed to transport, store, and break down RNAs. P bodies and stress granules are two types of RNP granules found in all cells, from yeast to human. P bodies are present at all times, whereas stress granules assemble when a cell experiences stressful conditions, such as a lack of nutrients or high temperatures. Once the stress has been overcome, the stress granules are disassembled. The precise details of how RNP granules assemble in cells remain poorly understood. One theory suggests that RNP granules form through a physical process called ‘phase separation’ in which RNA molecules and proteins above a certain critical concentration condense to form a liquid droplet. Other research has suggested that RNP granules arise when so-called prion-like proteins spontaneously clump together and start aggregating to form fibers. These granules would behave more like solids than liquids. Kroschwald et al. have now analyzed how P bodies and stress granules form in yeast and human cells using a chemical compound that can distinguish between liquid-like and solid-like structures. The results revealed that P bodies and stress granules behave very differently in yeast cells. While P bodies are indeed liquid droplets, stress granules are more solid in nature and act like protein aggregates. So why is there a difference between the two? It is known from previous work that when cells are stressed, many proteins misfold and start aggregating. Kroschwald et al. found that the formation of stress granules coincides with the formation of aggregates, suggesting that stress granules themselves are a type of aggregate. Furthermore, stress granule formation does not seem to involve prion-like fibers, but rather prion-like proteins can easily interact with other proteins in a promiscuous way, thus promoting the seeding of stress granules and their growth. Kroschwald et al. next studied human cells and observed that in these cells, both P bodies and stress granules were liquid droplets. These results together suggest that the physical properties and method of assembling P bodies and stress granules can vary from one organism to another. Future work will investigate whether the ability to form solid rather than liquid stress granules provides extra protection to yeast cells when they are stressed. It also remains to be tested whether and how stress granules convert into the pathological RNP aggregates that are often seen in neurodegenerative diseases. DOI:http://dx.doi.org/10.7554/eLife.06807.002
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Affiliation(s)
- Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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163
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Kroschwald S, Maharana S, Mateju D, Malinovska L, Nüske E, Poser I, Richter D, Alberti S. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife 2015; 4:e06807. [PMID: 26238190 DOI: 10.7554/elife.06807.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/25/2015] [Indexed: 05/23/2023] Open
Abstract
RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine.
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Affiliation(s)
- Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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164
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Laporte D, Courtout F, Pinson B, Dompierre J, Salin B, Brocard L, Sagot I. A stable microtubule array drives fission yeast polarity reestablishment upon quiescence exit. J Cell Biol 2015; 210:99-113. [PMID: 26124291 PMCID: PMC4494004 DOI: 10.1083/jcb.201502025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/01/2015] [Indexed: 11/22/2022] Open
Abstract
Cells perpetually face the decision to proliferate or to stay quiescent. Here we show that upon quiescence establishment, Schizosaccharomyces pombe cells drastically rearrange both their actin and microtubule (MT) cytoskeletons and lose their polarity. Indeed, while polarity markers are lost from cell extremities, actin patches and cables are reorganized into actin bodies, which are stable actin filament-containing structures. Astonishingly, MTs are also stabilized and rearranged into a novel antiparallel bundle associated with the spindle pole body, named Q-MT bundle. We have identified proteins involved in this process and propose a molecular model for Q-MT bundle formation. Finally and importantly, we reveal that Q-MT bundle elongation is involved in polarity reestablishment upon quiescence exit and thereby the efficient return to the proliferative state. Our work demonstrates that quiescent S. pombe cells assemble specific cytoskeleton structures that improve the swiftness of the transition back to proliferation.
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Affiliation(s)
- Damien Laporte
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France Centre National de la Recherche Scientifique, UMR5095 Bordeaux, 33077 Bordeaux, France
| | - Fabien Courtout
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France Centre National de la Recherche Scientifique, UMR5095 Bordeaux, 33077 Bordeaux, France
| | - Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France Centre National de la Recherche Scientifique, UMR5095 Bordeaux, 33077 Bordeaux, France
| | - Jim Dompierre
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France Centre National de la Recherche Scientifique, UMR5095 Bordeaux, 33077 Bordeaux, France
| | - Bénédicte Salin
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France Centre National de la Recherche Scientifique, UMR5095 Bordeaux, 33077 Bordeaux, France
| | - Lysiane Brocard
- Bordeaux Imaging Center, Pôle d'imagerie du végétal, Institut National de la Recherche Agronomique, 33140 Villenave d'Ornon, France
| | - Isabelle Sagot
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France Centre National de la Recherche Scientifique, UMR5095 Bordeaux, 33077 Bordeaux, France
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165
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Abstract
A yeast mother cell progressively ages with each cell division and yet produces daughter cells that are largely rejuvenated, suggesting that mothers accumulate aging factors. Two current studies address this issue by identifying mother-specific long-lived proteins and, in the case of Pma1, evidence that asymmetric distribution drives mother cell aging.
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Affiliation(s)
- Chuankai Zhou
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Rong Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
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166
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Tastan ÖY, Liu JL. CTP Synthase Is Required for Optic Lobe Homeostasis in Drosophila. J Genet Genomics 2015; 42:261-74. [PMID: 26059773 PMCID: PMC4458259 DOI: 10.1016/j.jgg.2015.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 10/31/2022]
Abstract
CTP synthase (CTPsyn) is a metabolic enzyme responsible for the de novo synthesis of the nucleotide CTP. Several recent studies have shown that CTPsyn forms filamentous subcellular structures known as cytoophidia in bacteria, yeast, fruit flies and humans. However, it remains elusive whether and how CTPsyn and cytoophidia play a role during development. Here, we show that cytoophidia are abundant in the neuroepithelial stem cells in Drosophila optic lobes. Optic lobes are underdeveloped in CTPsyn mutants as well as in CTPsyn RNAi. Moreover, overexpressing CTPsyn impairs the development of optic lobes, specifically by blocking the transition from neuroepithelium to neuroblast. Taken together, our results indicate that CTPsyn is critical for optic lobe homeostasis in Drosophila.
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Affiliation(s)
- Ömür Y Tastan
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom.
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167
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Keppeke GD, Calise SJ, Chan EKL, Andrade LEC. Assembly of IMPDH2-based, CTPS-based, and mixed rod/ring structures is dependent on cell type and conditions of induction. J Genet Genomics 2015; 42:287-99. [PMID: 26165495 DOI: 10.1016/j.jgg.2015.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 02/07/2023]
Abstract
Inhibition of guanosine triphosphate (GTP) and cytidine triphosphate (CTP) biosynthetic pathways induces cells to assemble rod/ring (RR) structures, also named cytoophidia, which consist of the enzymes cytidine triphosphate synthase (CTPS) and inosine-5'-monophosphate dehydrogenase 2 (IMPDH2). We aim to explore the interaction of CTPS and IMPDH2 in the generation of RR structures. HeLa and COS-7 cells were cultured in normal conditions or in the presence of 6-diazo-5-oxo-L-norleucine (DON), ribavirin, or mycophenolic acid (MPA). Over 90% of DON-treated cells presented RR structures. In HeLa cells, 35% of the RR structures were positive for IMPDH2 alone, 26% were CTPS alone, and 31% were IMPDH2/CTPS mixed, while in COS-7 cells, 42% of RR were IMPDH2 alone, 41% were CTPS alone, and 10% were IMPDH2/CTPS mixed. Ribavirin and MPA treatments induced only IMPDH2-based RR. Cells were also transfected with an N-terminal hemagglutinin (NHA)-tagged CTPS1 construct. Over 95% of NHA-CTPS1 transfected cells with DON treatment presented IMPDH2-based RR and almost 100% presented CTPS1-based RR; when treated with ribavirin, over 94% of transfected cells presented IMPDH2-based RR and 37% presented CTPS1-based RR, whereas 2% of untreated transfected cells presented IMPDH2-based RR and 28% presented CTPS1-based RR. These results may help in understanding the relationship between CTP and GTP biosynthetic pathways, especially concerning the formation of filamentous RR structures.
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Affiliation(s)
- Gerson Dierley Keppeke
- Rheumatology Division, Federal University of Sao Paulo, Sao Paulo SP 04023-062, Brazil; Department of Oral Biology, University of Florida, Gainesville FL 32610-0424, USA.
| | - S John Calise
- Department of Oral Biology, University of Florida, Gainesville FL 32610-0424, USA
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville FL 32610-0424, USA
| | - Luis Eduardo C Andrade
- Rheumatology Division, Federal University of Sao Paulo, Sao Paulo SP 04023-062, Brazil; Immunology Division, Fleury Medicine and Health Laboratories, Sao Paulo SP 04102-050, Brazil.
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168
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Shah S, Sanchez J, Stewart A, Piperakis MM, Cosstick R, Nichols C, Park CK, Ma X, Wysocki V, Bitinaite J, Horton NC. Probing the run-on oligomer of activated SgrAI bound to DNA. PLoS One 2015; 10:e0124783. [PMID: 25880668 PMCID: PMC4399878 DOI: 10.1371/journal.pone.0124783] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/05/2015] [Indexed: 02/04/2023] Open
Abstract
SgrAI is a type II restriction endonuclease with an unusual mechanism of activation involving run-on oligomerization. The run-on oligomer is formed from complexes of SgrAI bound to DNA containing its 8 bp primary recognition sequence (uncleaved or cleaved), and also binds (and thereby activates for DNA cleavage) complexes of SgrAI bound to secondary site DNA sequences which contain a single base substitution in either the 1st/8th or the 2nd/7th position of the primary recognition sequence. This modulation of enzyme activity via run-on oligomerization is a newly appreciated phenomenon that has been shown for a small but increasing number of enzymes. One outstanding question regarding the mechanistic model for SgrAI is whether or not the activating primary site DNA must be cleaved by SgrAI prior to inducing activation. Herein we show that an uncleavable primary site DNA containing a 3'-S-phosphorothiolate is in fact able to induce activation. In addition, we now show that cleavage of secondary site DNA can be activated to nearly the same degree as primary, provided a sufficient number of flanking base pairs are present. We also show differences in activation and cleavage of the two types of secondary site, and that effects of selected single site substitutions in SgrAI, as well as measured collisional cross-sections from previous work, are consistent with the cryo-electron microscopy model for the run-on activated oligomer of SgrAI bound to DNA.
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Affiliation(s)
- Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Jonathan Sanchez
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Genetics Graduate Program, University of Arizona, Tucson, AZ 85721, United States of America
| | - Michael M. Piperakis
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom, L69 7ZD, United States of America
| | - Richard Cosstick
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom, L69 7ZD, United States of America
| | - Claire Nichols
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Xin Ma
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, United States of America
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, United States of America
| | - Jurate Bitinaite
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, United States of America
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
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169
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Khachatoorian C, Ramirez RA, Hernandez F, Serna R, Kwok EY. Overexpressed Arabidopsis Annexin4 accumulates in inclusion body-like structures. Acta Histochem 2015; 117:279-87. [PMID: 25818562 PMCID: PMC4409563 DOI: 10.1016/j.acthis.2015.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 12/31/2022]
Abstract
Large protein complexes form in the cytosol of prokaryotes and eukaryotes as assemblies of functional enzymes or aggregates of misfolded proteins. Their roles in the cell range from critical components of metabolism to disease-causing agents. We have observed a novel structure in the cells of transgenic Arabidopsis thaliana that appears to be a form of inclusion body. These long, spindle-shaped structures form when Arabidopsis are transformed to express high levels of the protein Annexin4 fused to a fluorescent protein. These structures, previously named darts, are visible in all cells of the plant throughout development. Darts take on a variety of morphologies including rings and figure-eights. These structures are not associated with the endomembrane system and are not membrane bounded. Darts appear to be insoluble aggregates of protein analogous to bacterial inclusion bodies and eukaryotic aggresomes. Similar structures have not been observed in untransformed plants, suggesting darts are artifacts of transgenic overexpression.
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Affiliation(s)
- Careen Khachatoorian
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Rigoberto A Ramirez
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Fernando Hernandez
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Raphael Serna
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA
| | - Ernest Y Kwok
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA 91330-8303, USA.
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170
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Suresh HG, da Silveira Dos Santos AX, Kukulski W, Tyedmers J, Riezman H, Bukau B, Mogk A. Prolonged starvation drives reversible sequestration of lipid biosynthetic enzymes and organelle reorganization in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:1601-15. [PMID: 25761633 PMCID: PMC4436773 DOI: 10.1091/mbc.e14-11-1559] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/02/2015] [Indexed: 11/11/2022] Open
Abstract
Lipid homeostasis is modulated upon starvation at three different levels manifested in reversible 1) spatial confinement of lipid biosynthetic enzymes, 2) mitochondrial and endoplasmic reticular reorganization, and 3) loss of organelle contact sites, thus highlighting a novel mechanism regulating lipid biosynthesis by simply modulating flux through the pathway. Cells adapt to changing nutrient availability by modulating a variety of processes, including the spatial sequestration of enzymes, the physiological significance of which remains controversial. These enzyme deposits are claimed to represent aggregates of misfolded proteins, protein storage, or complexes with superior enzymatic activity. We monitored spatial distribution of lipid biosynthetic enzymes upon glucose depletion in Saccharomyces cerevisiae. Several different cytosolic-, endoplasmic reticulum–, and mitochondria-localized lipid biosynthetic enzymes sequester into distinct foci. Using the key enzyme fatty acid synthetase (FAS) as a model, we show that FAS foci represent active enzyme assemblies. Upon starvation, phospholipid synthesis remains active, although with some alterations, implying that other foci-forming lipid biosynthetic enzymes might retain activity as well. Thus sequestration may restrict enzymes' access to one another and their substrates, modulating metabolic flux. Enzyme sequestrations coincide with reversible drastic mitochondrial reorganization and concomitant loss of endoplasmic reticulum–mitochondria encounter structures and vacuole and mitochondria patch organelle contact sites that are reflected in qualitative and quantitative changes in phospholipid profiles. This highlights a novel mechanism that regulates lipid homeostasis without profoundly affecting the activity status of involved enzymes such that, upon entry into favorable growth conditions, cells can quickly alter lipid flux by relocalizing their enzymes.
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Affiliation(s)
- Harsha Garadi Suresh
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | | | - Wanda Kukulski
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Jens Tyedmers
- Department of Medicine I and Clinical Chemistry, University of Heidelberg, D-69120 Heidelberg, Germany
| | - Howard Riezman
- NCCR Chemical Biology, Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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171
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Tastan ÖY, Liu JL. Visualizing Cytoophidia Expression in Drosophila Follicle Cells via Immunohistochemistry. Methods Mol Biol 2015; 1328:179-189. [PMID: 26324438 DOI: 10.1007/978-1-4939-2851-4_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe a user-friendly immunohistochemical approach for the detection of protein localization in Drosophila ovaries, here focusing on CTP synthase. This approach mainly uses fluorescently labeled antibodies to detect single, double, or multiple antigens. We provide a step-by-step protocol with detailed notes and tips, a simplified method that can also be adapted to detect protein localization beyond Drosophila ovaries.
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Affiliation(s)
- Ömür Y Tastan
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
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172
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Lowe N, Rees JS, Roote J, Ryder E, Armean IM, Johnson G, Drummond E, Spriggs H, Drummond J, Magbanua JP, Naylor H, Sanson B, Bastock R, Huelsmann S, Trovisco V, Landgraf M, Knowles-Barley S, Armstrong JD, White-Cooper H, Hansen C, Phillips RG, Lilley KS, Russell S, St Johnston D. Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. Development 2014; 141:3994-4005. [PMID: 25294943 PMCID: PMC4197710 DOI: 10.1242/dev.111054] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although we now have a wealth of information on the transcription patterns of all the genes in the Drosophila genome, much less is known about the properties of the encoded proteins. To provide information on the expression patterns and subcellular localisations of many proteins in parallel, we have performed a large-scale protein trap screen using a hybrid piggyBac vector carrying an artificial exon encoding yellow fluorescent protein (YFP) and protein affinity tags. From screening 41 million embryos, we recovered 616 verified independent YFP-positive lines representing protein traps in 374 genes, two-thirds of which had not been tagged in previous P element protein trap screens. Over 20 different research groups then characterized the expression patterns of the tagged proteins in a variety of tissues and at several developmental stages. In parallel, we purified many of the tagged proteins from embryos using the affinity tags and identified co-purifying proteins by mass spectrometry. The fly stocks are publicly available through the Kyoto Drosophila Genetics Resource Center. All our data are available via an open access database (Flannotator), which provides comprehensive information on the expression patterns, subcellular localisations and in vivo interaction partners of the trapped proteins. Our resource substantially increases the number of available protein traps in Drosophila and identifies new markers for cellular organelles and structures.
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Affiliation(s)
- Nick Lowe
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Johanna S Rees
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK The Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - John Roote
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ed Ryder
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Irina M Armean
- The Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Glynnis Johnson
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Emma Drummond
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Helen Spriggs
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jenny Drummond
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jose P Magbanua
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Huw Naylor
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Bénédicte Sanson
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Rebecca Bastock
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sven Huelsmann
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Vitor Trovisco
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Matthias Landgraf
- The Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Seymour Knowles-Barley
- Institute for Adaptive and Neural Computation, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - J Douglas Armstrong
- Institute for Adaptive and Neural Computation, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - Helen White-Cooper
- Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Celia Hansen
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Roger G Phillips
- Centre for Advanced Microscopy, University of Sussex, School of Life Sciences, John Maynard Smith Building, Falmer, Brighton and Hove BN1 9QG, UK
| | | | - Kathryn S Lilley
- The Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Steven Russell
- The Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Daniel St Johnston
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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173
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Abstract
A general view is that Schizosaccharomyces pombe undergoes symmetric cell division with two daughter cells inheriting equal shares of the content from the mother cell. Here we show that CTP synthase, a metabolic enzyme responsible for the de novo synthesis of the nucleotide CTP, can form filamentous cytoophidia in the cytoplasm and nucleus of S. pombe cells. Surprisingly, we observe that both cytoplasmic and nuclear cytoophidia are asymmetrically inherited during cell division. Our time-lapse studies suggest that cytoophidia are dynamic. Once the mother cell divides, the cytoplasmic and nuclear cytoophidia independently partition into one of the two daughter cells. Although the two daughter cells differ from one another morphologically, they possess similar chances of inheriting the cytoplasmic cytoophidium from the mother cell, suggesting that the partition of cytoophidium is a stochastic process. Our findings on asymmetric inheritance of cytoophidia in S. pombe offer an exciting opportunity to study the inheritance of metabolic enzymes in a well-studied model system.
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Affiliation(s)
- Jing Zhang
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Lydia Hulme
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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174
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Protein kinases are associated with multiple, distinct cytoplasmic granules in quiescent yeast cells. Genetics 2014; 198:1495-512. [PMID: 25342717 DOI: 10.1534/genetics.114.172031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The cytoplasm of the eukaryotic cell is subdivided into distinct functional domains by the presence of a variety of membrane-bound organelles. The remaining aqueous space may be further partitioned by the regulated assembly of discrete ribonucleoprotein (RNP) complexes that contain particular proteins and messenger RNAs. These RNP granules are conserved structures whose importance is highlighted by studies linking them to human disorders like amyotrophic lateral sclerosis. However, relatively little is known about the diversity, composition, and physiological roles of these cytoplasmic structures. To begin to address these issues, we examined the cytoplasmic granules formed by a key set of signaling molecules, the protein kinases of the budding yeast Saccharomyces cerevisiae. Interestingly, a significant fraction of these proteins, almost 20%, was recruited to cytoplasmic foci specifically as cells entered into the G0-like quiescent state, stationary phase. Colocalization studies demonstrated that these foci corresponded to eight different granules, including four that had not been reported previously. All of these granules were found to rapidly disassemble upon the resumption of growth, and the presence of each was correlated with cell viability in the quiescent cultures. Finally, this work also identified new constituents of known RNP granules, including the well-characterized processing body and stress granule. The composition of these latter structures is therefore more varied than previously thought and could be an indicator of additional biological activities being associated with these complexes. Altogether, these observations indicate that quiescent yeast cells contain multiple distinct cytoplasmic granules that may make important contributions to their long-term survival.
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175
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Aughey GN, Grice SJ, Shen QJ, Xu Y, Chang CC, Azzam G, Wang PY, Freeman-Mills L, Pai LM, Sung LY, Yan J, Liu JL. Nucleotide synthesis is regulated by cytoophidium formation during neurodevelopment and adaptive metabolism. Biol Open 2014; 3:1045-56. [PMID: 25326513 PMCID: PMC4232762 DOI: 10.1242/bio.201410165] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The essential metabolic enzyme CTP synthase (CTPsyn) can be compartmentalised to form an evolutionarily-conserved intracellular structure termed the cytoophidium. Recently, it has been demonstrated that the enzymatic activity of CTPsyn is attenuated by incorporation into cytoophidia in bacteria and yeast cells. Here we demonstrate that CTPsyn is regulated in a similar manner in Drosophila tissues in vivo. We show that cytoophidium formation occurs during nutrient deprivation in cultured cells, as well as in quiescent and starved neuroblasts of the Drosophila larval central nervous system. We also show that cytoophidia formation is reversible during neurogenesis, indicating that filament formation regulates pyrimidine synthesis in a normal developmental context. Furthermore, our global metabolic profiling demonstrates that CTPsyn overexpression does not significantly alter CTPsyn-related enzymatic activity, suggesting that cytoophidium formation facilitates metabolic stabilisation. In addition, we show that overexpression of CTPsyn only results in moderate increase of CTP pool in human stable cell lines. Together, our study provides experimental evidence, and a mathematical model, for the hypothesis that inactive CTPsyn is incorporated into cytoophidia.
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Affiliation(s)
- Gabriel N Aughey
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stuart J Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Qing-Ji Shen
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Yichi Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chia-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China
| | - Ghows Azzam
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Pei-Yu Wang
- Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan, Republic of China Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China
| | - Luke Freeman-Mills
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Li-Mei Pai
- Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan, 333, Taiwan, Republic of China Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan, Republic of China
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan, Republic of China Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
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176
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Aughey GN, Tastan ÖY, Liu JL. Cellular serpents and dreaming spires: new frontiers in arginine and pyrimidine biology. J Genet Genomics 2014; 41:561-5. [PMID: 25438702 DOI: 10.1016/j.jgg.2014.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/30/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Gabriel N Aughey
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ömür Y Tastan
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom.
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177
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Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. Proc Natl Acad Sci U S A 2014; 111:14019-26. [PMID: 25228775 DOI: 10.1073/pnas.1416079111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long-lived proteins have been implicated in age-associated decline in metazoa, but they have only been identified in extracellular matrices or postmitotic cells. However, the aging process also occurs in dividing cells undergoing repeated asymmetric divisions. It was not clear whether long-lived proteins exist in asymmetrically dividing cells or whether they are involved in aging. Here we identify long-lived proteins in dividing cells during aging using the budding yeast, Saccharomyces cerevisiae. Yeast mother cells undergo a limited number of asymmetric divisions that define replicative lifespan. We used stable-isotope pulse-chase and total proteome mass-spectrometry to identify proteins that were both long-lived and retained in aging mother cells after ∼ 18 cells divisions. We identified ∼ 135 proteins that we designate as long-lived asymmetrically retained proteins (LARPS). Surprisingly, the majority of LARPs appeared to be stable fragments of their original full-length protein. However, 15% of LARPs were full-length proteins and we confirmed several candidates to be long-lived and retained in mother cells by time-lapse microscopy. Some LARPs localized to the plasma membrane and remained robustly in the mother cell upon cell division. Other full-length LARPs were assembled into large cytoplasmic structures that had a strong bias to remain in mother cells. We identified age-associated changes to LARPs that include an increase in their levels during aging because of their continued synthesis, which is not balanced by turnover. Additionally, several LARPs were posttranslationally modified during aging. We suggest that LARPs contribute to age-associated phenotypes and likely exist in other organisms.
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178
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Strochlic TI, Stavrides KP, Thomas SV, Nicolas E, O'Reilly AM, Peterson JR. Ack kinase regulates CTP synthase filaments during Drosophila oogenesis. EMBO Rep 2014; 15:1184-91. [PMID: 25223282 DOI: 10.15252/embr.201438688] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The enzyme CTP synthase (CTPS) dynamically assembles into macromolecular filaments in bacteria, yeast, Drosophila, and mammalian cells, but the role of this morphological reorganization in regulating CTPS activity is controversial. During Drosophila oogenesis, CTPS filaments are transiently apparent in ovarian germline cells during a period of intense genomic endoreplication and stockpiling of ribosomal RNA. Here, we demonstrate that CTPS filaments are catalytically active and that their assembly is regulated by the non-receptor tyrosine kinase DAck, the Drosophila homologue of mammalian Ack1 (activated cdc42-associated kinase 1), which we find also localizes to CTPS filaments. Egg chambers from flies deficient in DAck or lacking DAck catalytic activity exhibit disrupted CTPS filament architecture and morphological defects that correlate with reduced fertility. Furthermore, ovaries from these flies exhibit reduced levels of total RNA, suggesting that DAck may regulate CTP synthase activity. These findings highlight an unexpected function for DAck and provide insight into a novel pathway for the developmental control of an essential metabolic pathway governing nucleotide biosynthesis.
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Affiliation(s)
- Todd I Strochlic
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kevin P Stavrides
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sam V Thomas
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Alana M O'Reilly
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA, USA
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179
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Jékely G. Origin and evolution of the self-organizing cytoskeleton in the network of eukaryotic organelles. Cold Spring Harb Perspect Biol 2014; 6:a016030. [PMID: 25183829 DOI: 10.1101/cshperspect.a016030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing "active gel," the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming.
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Affiliation(s)
- Gáspár Jékely
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
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180
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Calise SJ, Carcamo WC, Krueger C, Yin JD, Purich DL, Chan EKL. Glutamine deprivation initiates reversible assembly of mammalian rods and rings. Cell Mol Life Sci 2014; 71:2963-73. [PMID: 24477477 PMCID: PMC11113311 DOI: 10.1007/s00018-014-1567-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 12/21/2013] [Accepted: 01/16/2014] [Indexed: 02/06/2023]
Abstract
Rods and rings (RR) are protein assemblies composed of cytidine triphosphate synthetase type 1 (CTPS1) and inosine monophosphate dehydrogenase type 2 (IMPDH2), key enzymes in CTP and GTP biosynthesis. Small-molecule inhibitors of CTPS1 or IMPDH2 induce RR assembly in various cancer cell lines within 15 min to hours. Since glutamine is an essential amide nitrogen donor in these nucleotide biosynthetic pathways, glutamine deprivation was examined to determine whether it leads to RR formation. HeLa cells cultured in normal conditions did not show RR, but after culturing in media lacking glutamine, short rods (<2 μm) assembled after 24 h, and longer rods (>5 μm) formed after 48 h. Upon supplementation with glutamine or guanosine, these RR underwent almost complete disassembly within 15 min. Inhibition of glutamine synthetase with methionine sulfoximine also increased RR assembly in cells deprived of glutamine. Taken together, our data support the hypothesis that CTP/GTP biosynthetic enzymes polymerize to form RR in response to a decreased intracellular level of glutamine. We speculate that rod and ring formation is an adaptive metabolic response linked to disruption of glutamine homeostasis.
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Affiliation(s)
- S. John Calise
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424 USA
| | - Wendy C. Carcamo
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424 USA
| | - Claire Krueger
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424 USA
| | - Joyce D. Yin
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424 USA
| | - Daniel L. Purich
- Department of Biochemistry and Molecular Biology, University of Florida, 1600 SW Archer Rd., Gainesville, FL 32610-0245 USA
| | - Edward K. L. Chan
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424 USA
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181
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Brown RWB, Collingridge PW, Gull K, Rigden DJ, Ginger ML. Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution. PLoS One 2014; 9:e103026. [PMID: 25050549 PMCID: PMC4106842 DOI: 10.1371/journal.pone.0103026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/27/2014] [Indexed: 11/18/2022] Open
Abstract
Classically viewed as a cytosolic pathway, glycolysis is increasingly recognized as a metabolic pathway exhibiting surprisingly wide-ranging variations in compartmentalization within eukaryotic cells. Trypanosomatid parasites provide an extreme view of glycolytic enzyme compartmentalization as several glycolytic enzymes are found exclusively in peroxisomes. Here, we characterize Trypanosoma brucei flagellar proteins resembling glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK): we show the latter associates with the axoneme and the former is a novel paraflagellar rod component. The paraflagellar rod is an essential extra-axonemal structure in trypanosomes and related protists, providing a platform into which metabolic activities can be built. Yet, bioinformatics interrogation and structural modelling indicate neither the trypanosome PGK-like nor the GAPDH-like protein is catalytically active. Orthologs are present in a free-living ancestor of the trypanosomatids, Bodo saltans: the PGK-like protein from B. saltans also lacks key catalytic residues, but its GAPDH-like protein is predicted to be catalytically competent. We discuss the likelihood that the trypanosome GAPDH-like and PGK-like proteins constitute molecular evidence for evolutionary loss of a flagellar glycolytic pathway, either as a consequence of niche adaptation or the re-localization of glycolytic enzymes to peroxisomes and the extensive changes to glycolytic flux regulation that accompanied this re-localization. Evidence indicating loss of localized ATP provision via glycolytic enzymes therefore provides a novel contribution to an emerging theme of hidden diversity with respect to compartmentalization of the ubiquitous glycolytic pathway in eukaryotes. A possibility that trypanosome GAPDH-like protein additionally represents a degenerate example of a moonlighting protein is also discussed.
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Affiliation(s)
- Robert W. B. Brown
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | | | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael L. Ginger
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- * E-mail:
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182
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Barry RM, Bitbol AF, Lorestani A, Charles EJ, Habrian CH, Hansen JM, Li HJ, Baldwin EP, Wingreen NS, Kollman JM, Gitai Z. Large-scale filament formation inhibits the activity of CTP synthetase. eLife 2014; 3:e03638. [PMID: 25030911 PMCID: PMC4126345 DOI: 10.7554/elife.03638] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
CTP Synthetase (CtpS) is a universally conserved and essential metabolic enzyme. While many enzymes form small oligomers, CtpS forms large-scale filamentous structures of unknown function in prokaryotes and eukaryotes. By simultaneously monitoring CtpS polymerization and enzymatic activity, we show that polymerization inhibits activity, and CtpS's product, CTP, induces assembly. To understand how assembly inhibits activity, we used electron microscopy to define the structure of CtpS polymers. This structure suggests that polymerization sterically hinders a conformational change necessary for CtpS activity. Structure-guided mutagenesis and mathematical modeling further indicate that coupling activity to polymerization promotes cooperative catalytic regulation. This previously uncharacterized regulatory mechanism is important for cellular function since a mutant that disrupts CtpS polymerization disrupts E. coli growth and metabolic regulation without reducing CTP levels. We propose that regulation by large-scale polymerization enables ultrasensitive control of enzymatic activity while storing an enzyme subpopulation in a conformationally restricted form that is readily activatable. DOI:http://dx.doi.org/10.7554/eLife.03638.001 Enzymes are proteins that perform reactions that can convert one or more chemicals (the substrates) into others (the products). The rate at which an enzyme produces its product is often carefully regulated. Some molecules slow or stop an enzyme by binding to and blocking the site where its substrates normally bind: its ‘active site’. Other molecules can also bind to sites other than the active site, which can cause the enzyme to become either more or less active. Almost all living things have an enzyme called CTP synthetase that makes one of the building blocks that is used to build DNA and a similar molecule called RNA. This enzyme converts a molecule called uridine triphosphate (or UTP) into another called cytidine triphosphate (CTP): a reaction that is powered by breaking down molecules of adenosine triphosphate (ATP). The amount of CTP synthetase made by a cell is carefully controlled. The enzyme's activity is also regulated by the levels of UTP and CTP, and by another molecule (called GTP) that binds to a site outside of its active site. Four copies of the CTP synthetase protein must work together before this enzyme can turn UTP into CTP. The enzyme also forms much larger aggregates, or polymers; however, it is not clear what causes these polymers to form, or what they do in a cell. Barry et al. have now discovered that CTP synthetase is almost completely inactivated when these polymers are formed. Furthermore, CTP encourages the polymers to form, whilst UTP and ATP cause them to disassemble. Therefore, this enzyme is least active when there is excess product in the cell, and most active when its substrates are plentiful. By determining the three-dimensional structure of a CTP synthetase polymer, Barry et al. reveal that although CTP is bound to the enzymes, their active sites are still freely accessible. However, the enzymes in the polymer appear to be locked into a shape that makes them unable to carry out their function. When Barry et al. then mutated the enzyme so that it was unable to form polymers it was also no longer inactivated in the same way by CTP. Bacterial cells with only these mutant versions of CTP synthetase are unable to properly control their levels of CTP. This suggests that polymer formation is important for regulating this enzyme in response to a build up of its product. Further work is needed to see whether the regulation of CTP synthetase activity by forming polymers is specific to this enzyme or a widespread mechanism that is used to control other enzymes too. DOI:http://dx.doi.org/10.7554/eLife.03638.002
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Affiliation(s)
- Rachael M Barry
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Anne-Florence Bitbol
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Alexander Lorestani
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Emeric J Charles
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Chris H Habrian
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Jesse M Hansen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Hsin-Jung Li
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Enoch P Baldwin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Justin M Kollman
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Canada
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, United States
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183
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Juda P, Smigová J, Kováčik L, Bártová E, Raška I. Ultrastructure of cytoplasmic and nuclear inosine-5'-monophosphate dehydrogenase 2 "rods and rings" inclusions. J Histochem Cytochem 2014; 62:739-50. [PMID: 24980853 DOI: 10.1369/0022155414543853] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Inosine-5'-monophosphate dehydrogenase catalyzes the critical step in the de novo synthesis of guanosine nucleotides: the oxidation of inosine monophosphate to xanthosine monophosphate. This reaction can be inhibited by specific inhibitors, such as ribavirin or mycophenolic acid, which are widely used in clinical treatment when required to inhibit the proliferation of viruses or cells. However, it was recently found that such an inhibition affects the cells, leading to a redistribution of IMPDH2 and the appearance of IMPDH2 inclusions in the cytoplasm. According to their shape, these inclusions have been termed "Rods and Rings" (R&R). In this work, we focused on the subcellular localization of IMPDH2 protein and the ultrastructure of R&R inclusions. Using microscopy and western blot analysis, we show the presence of nuclear IMPDH2 in human cells. We also show that the nuclear pool has an ability to form Rod structures after inhibition by ribavirin. Concerning the ultrastructure, we observed that R&R inclusions in cellulo correspond to the accumulation of fibrous material that is not surrounded by a biological membrane. The individual fibers are composed of regularly repeating subunits with a length of approximately 11 nm. Together, our findings describe the localization of IMPDH2 inside the nucleus of human cells as well as the ultrastructure of R&R inclusions.
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Affiliation(s)
- Pavel Juda
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Czech Republic (PJ, JS, LK, IR)Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic (EB)
| | - Jana Smigová
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Czech Republic (PJ, JS, LK, IR)Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic (EB)
| | - Lubomír Kováčik
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Czech Republic (PJ, JS, LK, IR)Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic (EB)
| | - Eva Bártová
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Czech Republic (PJ, JS, LK, IR)Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic (EB)
| | - Ivan Raška
- Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology, Czech Republic (PJ, JS, LK, IR)Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic (EB)
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184
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Coelho M, Lade SJ, Alberti S, Gross T, Tolić IM. Fusion of protein aggregates facilitates asymmetric damage segregation. PLoS Biol 2014; 12:e1001886. [PMID: 24936793 PMCID: PMC4061010 DOI: 10.1371/journal.pbio.1001886] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/09/2014] [Indexed: 02/02/2023] Open
Abstract
Fusion of harmful aggregated proteins into larger clumps increases the asymmetry of segregation of damage at cell division, favoring the production of rejuvenated cells. Asymmetric segregation of damaged proteins at cell division generates a cell that retains damage and a clean cell that supports population survival. In cells that divide asymmetrically, such as Saccharomyces cerevisiae, segregation of damaged proteins is achieved by retention and active transport. We have previously shown that in the symmetrically dividing Schizosaccharomyces pombe there is a transition between symmetric and asymmetric segregation of damaged proteins. Yet how this transition and generation of damage-free cells are achieved remained unknown. Here, by combining in vivo imaging of Hsp104-associated aggregates, a form of damage, with mathematical modeling, we find that fusion of protein aggregates facilitates asymmetric segregation. Our model predicts that, after stress, the increased number of aggregates fuse into a single large unit, which is inherited asymmetrically by one daughter cell, whereas the other one is born clean. We experimentally confirmed that fusion increases segregation asymmetry, for a range of stresses, and identified Hsp16 as a fusion factor. Our work shows that fusion of protein aggregates promotes the formation of damage-free cells. Fusion of cellular factors may represent a general mechanism for their asymmetric segregation at division. During their lifetime, cells accumulate damage that is inherited by the daughter cells when the mother cell divides. The amount of inherited damage determines how long the daughter cell will live and how fast it will age. We have discovered fusion of protein aggregates as a new strategy that cells use to apportion damage asymmetrically during division. By combining live-cell imaging with a mathematical model, we show that fission yeast cells divide the damage equally between the two daughter cells, but only as long as the amount of damage is low and harmless. However, when the cells are stressed and the damage accumulates to higher levels, the aggregated proteins fuse into a single clump, which is then inherited by one daughter cell, while the other cell is born clean. This form of damage control may be a universal survival strategy for a range of cell types, including stem cells, germ cells, and cancer cells.
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Affiliation(s)
- Miguel Coelho
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Steven J. Lade
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Thilo Gross
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Department of Engineering Mathematics, Merchant Venturers School of Engineering, University of Bristol, Bristol, United Kingdom
| | - Iva M. Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail: or
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185
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Noree C, Monfort E, Shiau AK, Wilhelm JE. Common regulatory control of CTP synthase enzyme activity and filament formation. Mol Biol Cell 2014; 25:2282-90. [PMID: 24920825 PMCID: PMC4116302 DOI: 10.1091/mbc.e14-04-0912] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTP synthase is one of many enzymes that form novel intracellular filaments/structures. A
structure–function approach is used to show that the same regulatory sites that control CTP
synthase enzyme activity also control filament formation. Close coupling of assembly to enzyme
regulation is proposed to be a general feature of these structures. The ability of enzymes to assemble into visible supramolecular complexes is a widespread
phenomenon. Such complexes have been hypothesized to play a number of roles; however, little is
known about how the regulation of enzyme activity is coupled to the assembly/disassembly of these
cellular structures. CTP synthase is an ideal model system for addressing this question because its
activity is regulated via multiple mechanisms and its filament-forming ability is evolutionarily
conserved. Our structure–function studies of CTP synthase in Saccharomyces
cerevisiae reveal that destabilization of the active tetrameric form of the enzyme
increases filament formation, suggesting that the filaments comprise inactive CTP synthase dimers.
Furthermore, the sites responsible for feedback inhibition and allosteric activation control
filament length, implying that multiple regions of the enzyme can influence filament structure. In
contrast, blocking catalysis without disrupting the regulatory sites of the enzyme does not affect
filament formation or length. Together our results argue that the regulatory sites that control CTP
synthase function, but not enzymatic activity per se, are critical for controlling filament
assembly. We predict that the ability of enzymes to form supramolecular structures in general is
closely coupled to the mechanisms that regulate their activity.
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Affiliation(s)
- Chalongrat Noree
- Section on Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Elena Monfort
- Section on Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Andrew K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093
| | - James E Wilhelm
- Section on Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
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186
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Fang Y, French J, Zhao H, Benkovic S. G-protein-coupled receptor regulation of de novo purine biosynthesis: a novel druggable mechanism. Biotechnol Genet Eng Rev 2014; 29:31-48. [PMID: 24568251 DOI: 10.1080/02648725.2013.801237] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Spatial organization of metabolic enzymes may represent a general cellular mechanism to regulate metabolic flux. One recent example of this type of cellular phenomenon is the purinosome, a newly discovered multi-enzyme metabolic assembly that includes all of the enzymes within the de novo purine biosynthetic pathway. Our understanding of the components and regulation of purinosomes has significantly grown in recent years. This paper reviews the purine de novo biosynthesis pathway and its regulation, and presents the evidence supporting the purinosome assembly and disassembly processes under the control of G-protein-coupled receptor (GPCR) signaling. This paper also discusses the implications of purinosome and GPCR regulation in drug discovery.
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Affiliation(s)
- Ye Fang
- a Biochemical Technologies, Science and Technology Division , Corning Incorporated , Corning , New York , USA
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187
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Petrovska I, Nüske E, Munder MC, Kulasegaran G, Malinovska L, Kroschwald S, Richter D, Fahmy K, Gibson K, Verbavatz JM, Alberti S. Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation. eLife 2014; 3:eLife.02409. [PMID: 24771766 PMCID: PMC4011332 DOI: 10.7554/elife.02409] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/10/2014] [Indexed: 01/20/2023] Open
Abstract
One of the key questions in biology is how the metabolism of a cell responds to changes in the environment. In budding yeast, starvation causes a drop in intracellular pH, but the functional role of this pH change is not well understood. Here, we show that the enzyme glutamine synthetase (Gln1) forms filaments at low pH and that filament formation leads to enzymatic inactivation. Filament formation by Gln1 is a highly cooperative process, strongly dependent on macromolecular crowding, and involves back-to-back stacking of cylindrical homo-decamers into filaments that associate laterally to form higher order fibrils. Other metabolic enzymes also assemble into filaments at low pH. Hence, we propose that filament formation is a general mechanism to inactivate and store key metabolic enzymes during a state of advanced cellular starvation. These findings have broad implications for understanding the interplay between nutritional stress, the metabolism and the physical organization of a cell.
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Affiliation(s)
- Ivana Petrovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Matthias C Munder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz Institute Dresden-Rossendorf, Dresden, Germany
| | - Kimberley Gibson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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188
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Abstract
The nucleus is a cellular compartment that hosts several macro-molecular machines displaying a highly complex spatial organization. This tight architectural orchestration determines not only DNA replication and repair but also regulates gene expression. In budding yeast microtubules play a key role in structuring the nucleus since they condition the Rabl arrangement in G1 and chromosome partitioning during mitosis through their attachment to centromeres via the kinetochore proteins. Recently, we have shown that upon quiescence entry, intranuclear microtubules emanating from the spindle pole body elongate to form a highly stable bundle that spans the entire nucleus. Here, we examine some molecular mechanisms that may underlie the formation of this structure. As the intranuclear microtubule bundle causes a profound re-organization of the yeast nucleus and is required for cell survival during quiescence, we discuss the possibility that the assembly of such a structure participates in quiescence establishment.
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Affiliation(s)
- Damien Laporte
- Université de Bordeaux; Institut de Biochimie et Génétique Cellulaires; Bordeaux, France; CNRS; UMR5095 Bordeaux France; Bordeaux, France
| | - Isabelle Sagot
- Université de Bordeaux; Institut de Biochimie et Génétique Cellulaires; Bordeaux, France; CNRS; UMR5095 Bordeaux France; Bordeaux, France
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189
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CTP synthase forms cytoophidia in the cytoplasm and nucleus. Exp Cell Res 2014; 323:242-253. [PMID: 24503052 DOI: 10.1016/j.yexcr.2014.01.029] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/24/2014] [Accepted: 01/26/2014] [Indexed: 02/07/2023]
Abstract
CTP synthase is an essential metabolic enzyme responsible for the de novo synthesis of CTP. Multiple studies have recently showed that CTP synthase protein molecules form filamentous structures termed cytoophidia or CTP synthase filaments in the cytoplasm of eukaryotic cells, as well as in bacteria. Here we report that CTP synthase can form cytoophidia not only in the cytoplasm, but also in the nucleus of eukaryotic cells. Both glutamine deprivation and glutamine analog treatment promote formation of cytoplasmic cytoophidia (C-cytoophidia) and nuclear cytoophidia (N-cytoophidia). N-cytoophidia are generally shorter and thinner than their cytoplasmic counterparts. In mammalian cells, both CTP synthase 1 and CTP synthase 2 can form cytoophidia. Using live imaging, we have observed that both C-cytoophidia and N-cytoophidia undergo multiple rounds of fusion upon glutamine analog treatment. Our study reveals the coexistence of cytoophidia in the cytoplasm and nucleus, therefore providing a good opportunity to investigate the intracellular compartmentation of CTP synthase.
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190
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O'Connell JD, Tsechansky M, Royal A, Boutz DR, Ellington AD, Marcotte EM. A proteomic survey of widespread protein aggregation in yeast. MOLECULAR BIOSYSTEMS 2014; 10:851-861. [PMID: 24488121 DOI: 10.1039/c3mb70508k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many normally cytosolic yeast proteins form insoluble intracellular bodies in response to nutrient depletion, suggesting the potential for widespread protein aggregation in stressed cells. Nearly 200 such bodies have been found in yeast by screening libraries of fluorescently tagged proteins. In order to more broadly characterize the formation of these bodies in response to stress, we employed a proteome-wide shotgun mass spectrometry assay in order to measure shifts in the intracellular solubilities of endogenous proteins following heat stress. As quantified by mass spectrometry, heat stress tended to shift the same proteins into insoluble form as did nutrient depletion; many of these proteins were also known to form foci in response to arsenic stress. Affinity purification of several foci-forming proteins showed enrichment for co-purifying chaperones, including Hsp90 chaperones. Tests of induction conditions and co-localization of metabolic enzymes participating in the same metabolic pathways suggested those foci did not correspond to multi-enzyme organizing centers. Thus, in yeast, the formation of stress bodies appears common across diverse, normally diffuse cytoplasmic proteins and is induced by multiple types of cell stress, including thermal, chemical, and nutrient stress.
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Affiliation(s)
- Jeremy D O'Connell
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Mark Tsechansky
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge, UK
| | - Ariel Royal
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel R Boutz
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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191
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Kinkhabwala A, Khmelinskii A, Knop M. Analytical model for macromolecular partitioning during yeast cell division. BMC BIOPHYSICS 2014; 7:10. [PMID: 25737777 PMCID: PMC4347614 DOI: 10.1186/s13628-014-0010-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell - which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles - can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. RESULTS Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. CONCLUSIONS In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning.
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Affiliation(s)
- Ali Kinkhabwala
- Abteilung Systemische Zellbiologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, Dortmund 44227, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
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192
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Carcamo WC, Calise SJ, von Mühlen CA, Satoh M, Chan EKL. Molecular cell biology and immunobiology of mammalian rod/ring structures. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:35-74. [PMID: 24411169 DOI: 10.1016/b978-0-12-800097-7.00002-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleotide biosynthesis is a highly regulated process necessary for cell growth and replication. Cytoplasmic structures in mammalian cells, provisionally described as rods and rings (RR), were identified by human autoantibodies and recently shown to include two key enzymes of the CTP/GTP biosynthetic pathways, cytidine triphosphate synthetase (CTPS) and inosine monophosphate dehydrogenase (IMPDH). Several studies have described CTPS filaments in mammalian cells, Drosophila, yeast, and bacteria. Other studies have identified IMPDH filaments in mammalian cells. Similarities among these studies point to a common evolutionarily conserved cytoplasmic structure composed of a subset of nucleotide biosynthetic enzymes. These structures appear to be a conserved metabolic response to decreased intracellular GTP and/or CTP pools. Antibodies to RR were found to develop in some hepatitis C patients treated with interferon-α and ribavirin. Additionally, the presence of anti-RR antibodies was correlated with poor treatment outcome.
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Affiliation(s)
- Wendy C Carcamo
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - S John Calise
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | | | - Minoru Satoh
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Florida, Gainesville, Florida, USA; Department of Clinical Nursing, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA.
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193
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Abstract
A rich and ongoing history of cell biology research has defined the major polymer systems of the eukaryotic cytoskeleton. Recent studies have identified additional proteins that form filamentous structures in cells and can self-assemble into linear polymers when purified. This suggests that the eukaryotic cytoskeleton is an even more complex system than previously considered. In this essay, I examine the case for an expanded definition of the eukaryotic cytoskeleton and present a series of challenges for future work in this area.
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Affiliation(s)
- James B Moseley
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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194
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Laporte D, Courtout F, Salin B, Ceschin J, Sagot I. An array of nuclear microtubules reorganizes the budding yeast nucleus during quiescence. ACTA ACUST UNITED AC 2013; 203:585-94. [PMID: 24247429 PMCID: PMC3840927 DOI: 10.1083/jcb.201306075] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The microtubule cytoskeleton is a highly dynamic network. In dividing cells, its complex architecture not only influences cell shape and movement but is also crucial for chromosome segregation. Curiously, nothing is known about the behavior of this cellular machinery in quiescent cells. Here we show that, upon quiescence entry, the Saccharomyces cerevisiae microtubule cytoskeleton is drastically remodeled. Indeed, while cytoplasmic microtubules vanish, the spindle pole body (SPB) assembles a long and stable monopolar array of nuclear microtubules that spans the entire nucleus. Consequently, the nucleolus is displaced. Kinetochores remain attached to microtubule tips but lose SPB clustering and distribute along the microtubule array, leading to a large reorganization of the nucleus. When cells exit quiescence, the nuclear microtubule array slowly depolymerizes and, by pulling attached centromeres back to the SPB, allows the recovery of a typical Rabl-like configuration. Finally, mutants that do not assemble a nuclear array of microtubules are impaired for both quiescence survival and exit.
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Affiliation(s)
- Damien Laporte
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, F-33077 Bordeaux Cedex, France
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195
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Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure 2013; 21:1848-58. [PMID: 24055317 PMCID: PMC3898938 DOI: 10.1016/j.str.2013.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
SgrAI is a sequence specific DNA endonuclease that functions through an unusual enzymatic mechanism that is allosterically activated 200- to 500-fold by effector DNA, with a concomitant expansion of its DNA sequence specificity. Using single-particle transmission electron microscopy to reconstruct distinct populations of SgrAI oligomers, we show that in the presence of allosteric, activating DNA, the enzyme forms regular, repeating helical structures characterized by the addition of DNA-binding dimeric SgrAI subunits in a run-on manner. We also present the structure of oligomeric SgrAI at 8.6 Å resolution, demonstrating the conformational state of SgrAI in its activated form. Activated and oligomeric SgrAI displays key protein-protein interactions near the helix axis between its N termini, as well as allosteric protein-DNA interactions that are required for enzymatic activation. The hybrid approach reveals an unusual mechanism of enzyme activation that explains SgrAI's oligomerization and allosteric behavior.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Heather Talley
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
- Genetics Interdisciplinary Graduate Program, University of Arizona, Tucson, AZ, 85721
| | - Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Florence Tama
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
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196
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SHAIKH Y, KRANTZ A, EL-FARRA Y. Anti-rods and rings autoantibodies can occur in the hepatitis c-naïve population. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2013; 54:175-80. [PMID: 24783898 PMCID: PMC4718377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
INTRODUCTION The anti-Rods and Rings autoantibody recently described in clinical populations is thought to occur in the setting of hepatitis C treatment, specifically in the context of cytidine triphosphate (CTP) and guanosine triphosphate (GTP) synthetic pathway inhibitors, and is important in its potential impact on response to therapy. This study asks the question: what is the epidemiology of anti-RR autoantibody in the general, non-clinical population? MATERIALS AND METHODS This is a cross-sectional study using the National Health and Nutrition Examination Survey (NHANES). Immunofluorescence assay for anti-Rods and Rings autoantibody were performed by NHANES labs and the results made publically available. Sample weights were used to calculate the prevalence and distribution of the autoantibody across demographics. A medication profile of the autoantibody positive population was also constructed RESULTS The study sample consisted of 4738 persons over the age of 12 years. Anti-Rods and Rings autoantibodies were found in 39 persons representing 1.3 million persons in the United States population. 38 of 39 persons with anti-Rods and Rings autoantibody had no prior history of hepatitis C virus infection. A majority of these persons were found to have poly-pharmacy. DISCUSSION This is the first study to show that anti-RR can occur in the general population without evidence of hepatits C virus infection, and that the majority of persons with anti-RR in the population have no evidence of prior hepatitis C infection. This indicates that there may be another undetermined etiology for anti-rods and rings autoantibodies besides the currently accepted exposure etiology of hepatitis C virus infection and treatment found in clinical studies.
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Affiliation(s)
- Y. SHAIKH
- Correspondence: Yahya Shaikh, UCLA David Geffen School of Medicine (310) 754-6367, 1735-213 Sawtelle blvd, Los Angeles, CA, 90025 - E-mail:
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197
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Kryndushkin D, Pripuzova N, Burnett BG, Shewmaker F. Non-targeted identification of prions and amyloid-forming proteins from yeast and mammalian cells. J Biol Chem 2013; 288:27100-27111. [PMID: 23926098 DOI: 10.1074/jbc.m113.485359] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The formation of amyloid aggregates is implicated both as a primary cause of cellular degeneration in multiple human diseases and as a functional mechanism for providing extraordinary strength to large protein assemblies. The recent identification and characterization of several amyloid proteins from diverse organisms argues that the amyloid phenomenon is widespread in nature. Yet identifying new amyloid-forming proteins usually requires a priori knowledge of specific candidates. Amyloid fibers can resist heat, pressure, proteolysis, and denaturation by reagents such as urea or sodium dodecyl sulfate. Here we show that these properties can be exploited to identify naturally occurring amyloid-forming proteins directly from cell lysates. This proteomic-based approach utilizes a novel purification of amyloid aggregates followed by identification by mass spectrometry without the requirement for special genetic tools. We have validated this technique by blind identification of three amyloid-based yeast prions from laboratory and wild strains and disease-related polyglutamine proteins expressed in both yeast and mammalian cells. Furthermore, we found that polyglutamine aggregates specifically recruit some stress granule components, revealing a possible mechanism of toxicity. Therefore, core amyloid-forming proteins as well as strongly associated proteins can be identified directly from cells of diverse origin.
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Affiliation(s)
| | - Natalia Pripuzova
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Barrington G Burnett
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
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198
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Spatial reorganization of Saccharomyces cerevisiae enolase to alter carbon metabolism under hypoxia. EUKARYOTIC CELL 2013; 12:1106-19. [PMID: 23748432 DOI: 10.1128/ec.00093-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hypoxia has critical effects on the physiology of organisms. In the yeast Saccharomyces cerevisiae, glycolytic enzymes, including enolase (Eno2p), formed cellular foci under hypoxia. Here, we investigated the regulation and biological functions of these foci. Focus formation by Eno2p was inhibited temperature independently by the addition of cycloheximide or rapamycin or by the single substitution of alanine for the Val22 residue. Using mitochondrial inhibitors and an antioxidant, mitochondrial reactive oxygen species (ROS) production was shown to participate in focus formation. Focus formation was also inhibited temperature dependently by an SNF1 knockout mutation. Interestingly, the foci were observed in the cell even after reoxygenation. The metabolic turnover analysis revealed that [U-(13)C]glucose conversion to pyruvate and oxaloacetate was accelerated in focus-forming cells. These results suggest that under hypoxia, S. cerevisiae cells sense mitochondrial ROS and, by the involvement of SNF1/AMPK, spatially reorganize metabolic enzymes in the cytosol via de novo protein synthesis, which subsequently increases carbon metabolism. The mechanism may be important for yeast cells under hypoxia, to quickly provide both energy and substrates for the biosynthesis of lipids and proteins independently of the tricarboxylic acid (TCA) cycle and also to fit changing environments.
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199
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Role of polyphosphate in thermophilic Synechococcus sp. from microbial mats. J Bacteriol 2013; 195:3309-19. [PMID: 23687278 DOI: 10.1128/jb.00207-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synechococcus OS-B', a thermophilic unicellular cyanobacterium, recently isolated from the microbial mats in Octopus Spring (Yellowstone National Park), induces a suite of genes, including phosphatases and transporters, in response to phosphorus (P) starvation. Here we describe two different approaches to examine the ability of Synechococcus OS-B' to synthesize and break down polyphosphate (poly P), a key storage compound in many prokaryotes. First, we developed a transformation protocol to create mutants in the polyphosphate kinase (ppk), the major enzyme responsible for the synthesis of poly P. The ppk mutant exhibited a pleiotropic phenotype with defects in poly P accumulation, aberrant levels of Pho regulon transcripts, growth defects, and changes in cell size and exopolysaccharide levels, among others. Second, we measured transcripts of ppk and ppx (encoding the polyphosphatase) directly from mat samples and found that the levels varied dramatically over a diel cycle. We also used Western blot analysis to quantify levels of PPK and PPX and found that these enzymes differentially accumulated during the diel cycle. Levels of polyphosphate kinase peaked at night, while polyphosphatase levels were highest during the early morning hours. We hypothesize that the opposing activities of these two enzymes allow cells to store and utilize poly P to optimize growth over a diel cycle.
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200
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MgATP regulates allostery and fiber formation in IMPDHs. Structure 2013; 21:975-85. [PMID: 23643948 DOI: 10.1016/j.str.2013.03.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 11/22/2022]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in nucleotide biosynthesis studied as an important therapeutic target and its complex functioning in vivo is still puzzling and debated. Here, we highlight the structural basis for the regulation of IMPDHs by MgATP. Our results demonstrate the essential role of the CBS tandem, conserved among almost all IMPDHs. We found that Pseudomonas aeruginosa IMPDH is an octameric enzyme allosterically regulated by MgATP and showed that this octameric organization is widely conserved in the crystal structures of other IMPDHs. We also demonstrated that human IMPDH1 adopts two types of complementary octamers that can pile up into isolated fibers in the presence of MgATP. The aggregation of such fibers in the autosomal dominant mutant, D226N, could explain the onset of the retinopathy adRP10. Thus, the regulatory CBS modules in IMPDHs are functional and they can either modulate catalysis or macromolecular assembly.
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