1
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Flores-Mendez M, Ohl L, Roule T, Zhou Y, Tintos-Hernández JA, Walsh K, Ortiz-González XR, Akizu N. IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency. EMBO Rep 2024:10.1038/s44319-024-00218-2. [PMID: 39075237 DOI: 10.1038/s44319-024-00218-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use mouse models of a childhood neurodegenerative disorder caused by AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that mouse models of AMPD2 deficiency exhibit predominant degeneration of the hippocampal dentate gyrus, despite a general reduction of brain GTP levels. Neurodegeneration-resistant regions accumulate micron-sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis, while these filaments are barely detectable in the hippocampal dentate gyrus. Furthermore, we show that IMPDH2 filament disassembly reduces GTP levels and impairs growth of neural progenitor cells derived from individuals with human AMPD2 deficiency. Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation, opening the possibility of exploring the induction of IMPDH2 assembly as a therapy for neurodegeneration.
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Affiliation(s)
- Marco Flores-Mendez
- Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Ohl
- Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Roule
- Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yijing Zhou
- Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesus A Tintos-Hernández
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelsey Walsh
- Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xilma R Ortiz-González
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Naiara Akizu
- Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. J Cell Biol 2024; 223:e202310139. [PMID: 38323936 PMCID: PMC10849882 DOI: 10.1083/jcb.202310139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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3
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Toyoda S, Handa T, Yong H, Takahashi H, Shiwaku H. IMPDH2 forms spots at branching sites and distal ends of astrocyte stem processes. Genes Cells 2024; 29:150-158. [PMID: 38009721 DOI: 10.1111/gtc.13088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in the de novo GTP biosynthesis pathway. Recent studies suggest that IMPDH2, an isoform of IMPDH, can localize to specific subcellular compartments under certain conditions and regulate site-specific GTP availability and small GTPase activity in invasive cancer cells. However, it is unclear whether IMPDH2 plays a site-specific regulatory role in subcellular functions in healthy cells. In this study, we focused on brain cells and examined the localization pattern of IMPDH2. We discovered that IMPDH2 forms localized spots in the astrocytes of the adult mouse hippocampus. Further analysis of spot distribution in primary astrocyte cultures revealed that IMPDH2 spots are predominantly localized on branching sites and distal ends of astrocyte stem processes. Our findings suggest a potential unidentified role for IMPDH2 and GTP synthesis specifically at specialized nodes of astrocyte branches.
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Affiliation(s)
- Saori Toyoda
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Takehisa Handa
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Huang Yong
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Hiroki Shiwaku
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
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4
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Flores-Mendez M, Ohl L, Roule T, Zhou Y, Tintos-Hernández JA, Walsh K, Ortiz-González XR, Akizu N. IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576443. [PMID: 38328116 PMCID: PMC10849482 DOI: 10.1101/2024.01.20.576443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use mouse models of AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that AMPD deficiency in mice primarily leads to hippocampal dentate gyrus degeneration despite causing a generalized reduction of brain GTP levels. Remarkably, we found that neurodegeneration resistant regions accumulate micron sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis. In contrast, IMPDH2 filaments are barely detectable in the hippocampal dentate gyrus, which shows a progressive neuroinflammation and neurodegeneration. Furthermore, using a human AMPD2 deficient neural cell culture model, we show that blocking IMPDH2 polymerization with a dominant negative IMPDH2 variant, impairs AMPD2 deficient neural progenitor growth. Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation in neurons with available GTP precursor molecules, providing resistance to neurodegeneration. Our findings open the possibility of exploring the involvement of IMPDH2 assembly as a therapeutic intervention for neurodegeneration.
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Affiliation(s)
- Marco Flores-Mendez
- Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Ohl
- Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Roule
- Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yijing Zhou
- Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesus A Tintos-Hernández
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Kelsey Walsh
- Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xilma R Ortiz-González
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Naiara Akizu
- Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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5
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558867. [PMID: 37790411 PMCID: PMC10542554 DOI: 10.1101/2023.09.21.558867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanosine triphosphate (GTP) synthesis and is controlled by feedback inhibition and allosteric regulation. IMPDH assembles into micron-scale filaments in cells, which desensitizes the enzyme to feedback inhibition by GTP and boosts nucleotide production. The vertebrate retina expresses two tissue-specific splice variants IMPDH1(546) and IMPDH1(595). IMPDH1(546) filaments adopt high and low activity conformations, while IMPDH1(595) filaments maintain high activity. In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of phosphorylation in IMPDH1 variants. The S477D mutation re-sensitized both variants to GTP inhibition, but only blocked assembly of IMPDH1(595) filaments and not IMPDH1(546) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of the high activity assembly interface, still allowing assembly of low activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, phosphorylation at S477 acts as a mechanism for downregulating retinal GTP synthesis in the dark, when nucleotide turnover is decreased. Like IMPDH1, many other metabolic enzymes dynamically assemble filamentous polymers that allosterically regulate activity. Our work suggests that posttranslational modifications may be yet another layer of regulatory control to finely tune activity by modulating filament assembly in response to changing metabolic demands.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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6
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O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM. Neurodevelopmental disorder mutations in the purine biosynthetic enzyme IMPDH2 disrupt its allosteric regulation. J Biol Chem 2023; 299:105012. [PMID: 37414152 PMCID: PMC10407431 DOI: 10.1016/j.jbc.2023.105012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023] Open
Abstract
Inosine 5' monophosphate dehydrogenase (IMPDH) is a critical regulatory enzyme in purine nucleotide biosynthesis that is inhibited by the downstream product GTP. Multiple point mutations in the human isoform IMPDH2 have recently been associated with dystonia and other neurodevelopmental disorders, but the effect of the mutations on enzyme function has not been described. Here, we report the identification of two additional missense variants in IMPDH2 from affected individuals and show that all of the disease-associated mutations disrupt GTP regulation. Cryo-EM structures of one IMPDH2 mutant suggest this regulatory defect arises from a shift in the conformational equilibrium toward a more active state. This structural and functional analysis provides insight into IMPDH2-associated disease mechanisms that point to potential therapeutic approaches and raises new questions about fundamental aspects of IMPDH regulation.
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Affiliation(s)
- Audrey G O'Neill
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Simon Edvardson
- Alyn Hospital, Hebrew University School of Medicine, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alyssa L Rippert
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tomoki Nomakuchi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kosuke Izumi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.
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7
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O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Shaked HM, Rippert AL, Nomakuchi T, Izumi K, Kollman JM. Point mutations in IMPDH2 which cause early-onset neurodevelopmental disorders disrupt enzyme regulation and filament structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532669. [PMID: 36993700 PMCID: PMC10055058 DOI: 10.1101/2023.03.15.532669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Inosine 5' monophosphate dehydrogenase (IMPDH) is a critical regulatory enzyme in purine nucleotide biosynthesis that is inhibited by the downstream product GTP. Multiple point mutations in the human isoform IMPDH2 have recently been associated with dystonia and other neurodevelopmental disorders, but the effect of the mutations on enzyme function has not been described. Here, we report identification of two additional affected individuals with missense variants in IMPDH2 and show that all of the disease-associated mutations disrupt GTP regulation. Cryo-EM structures of one IMPDH2 mutant suggest this regulatory defect arises from a shift in the conformational equilibrium toward a more active state. This structural and functional analysis provides insight into IMPDH2-associated disease mechanisms that point to potential therapeutic approaches and raises new questions about fundamental aspects of IMPDH regulation.
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Affiliation(s)
- Audrey G O'Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Simon Edvardson
- Alyn Hospital, Hebrew University School of Medicine, Jerusalem, Israel
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alyssa L Rippert
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tomoki Nomakuchi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kosuke Izumi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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8
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Meng J, Yang G, Li S, Luo Y, Bai Y, Deng C, Song N, Li M, Zeng X, Hu C. The clinical value of indirect immunofluorescence for screening anti-rods and rings antibodies: A retrospective study of two centers in China. Front Immunol 2022; 13:1007257. [PMID: 36238277 PMCID: PMC9552219 DOI: 10.3389/fimmu.2022.1007257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Objective To investigate the distribution and clinical significance of the rods and rings (RR) pattern in various diseases. Methods A total of 169,891 patients in Peking Union Medical College Hospital (PUMCH) and 29,458 patients in Inner Mongolia People’s Hospital (IMPH) from January 2018 to December 2020 were included, and the results of ANA (antinuclear antibodies) and special antibodies were analyzed retrospectively. Results The positive rates of ANA and RR patterns were 34.84%, 0.16% in PUMCH, and 44.73%, 0.23% in IMPH. Anti-RR antibodies mainly appear in adults (≥ 41 years), mostly of low or medium fluorescence titers. Isolated RR patterns were mostly presented (60.30% and 69.12%, respectively), and the RR pattern mixed with the speckled pattern was most commonly observed among patients having two or more patterns. The RR pattern existed in a variety of diseases including hepatitis C, AIDs, pulmonary diseases, nephropathy diseases, and even healthy people. The highest prevalence of the RR pattern was observed in hepatic diseases, such as hepatic dysfunction (0.79%), hepatic cirrhosis (1.05%), PBC (0.85%), and AIH (0.65%), etc. The positive rate of specific antibodies in RR pattern cases was 31.25%, and anti-Ro52 (27, 20.61%) was the most common target antibody. Conclusion The RR pattern had a low prevalence in ANAs test samples and varied in different nationalities and regions. Except for hepatitis C, it could be observed in AIDs, pulmonary diseases, nephropathy, other hepatic diseases, and even healthy people, but the positive rate was slightly higher in hepatic diseases. Its mechanism of action and clinical relevance still need clarification.
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Affiliation(s)
- Jingjing Meng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
- Department of Clinical Laboratory, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guoxiang Yang
- Department of Clinical Laboratory, Inner Mongolia People’s Hospital, Hohhot, China
| | - Siting Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Yueming Luo
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine (TCM) (Affiliated Jiangmen TCM Hospital of Ji’nan University), Jiangmen, China
| | - Yina Bai
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Chuiwen Deng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Ning Song
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
- *Correspondence: Chaojun Hu, ; Xiaofeng Zeng,
| | - Chaojun Hu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
- *Correspondence: Chaojun Hu, ; Xiaofeng Zeng,
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9
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Buey RM, Fernández‐Justel D, Jiménez A, Revuelta JL. The gateway to guanine nucleotides: Allosteric regulation of IMP dehydrogenases. Protein Sci 2022; 31:e4399. [PMID: 36040265 PMCID: PMC9375230 DOI: 10.1002/pro.4399] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022]
Abstract
Inosine 5′‐monophosphate dehydrogenase (IMPDH) is an evolutionarily conserved enzyme that mediates the first committed step in de novo guanine nucleotide biosynthetic pathway. It is an essential enzyme in purine nucleotide biosynthesis that modulates the metabolic flux at the branch point between adenine and guanine nucleotides. IMPDH plays key roles in cell homeostasis, proliferation, and the immune response, and is the cellular target of several drugs that are widely used for antiviral and immunosuppressive chemotherapy. IMPDH enzyme is tightly regulated at multiple levels, from transcriptional control to allosteric modulation, enzyme filamentation, and posttranslational modifications. Herein, we review recent developments in our understanding of the mechanisms of IMPDH regulation, including all layers of allosteric control that fine‐tune the enzyme activity.
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Affiliation(s)
- Rubén M. Buey
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
| | - David Fernández‐Justel
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
| | - José L. Revuelta
- Metabolic Engineering Group, Department of Microbiology and Genetics Universidad de Salamanca Salamanca Spain
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10
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Chang CC, Peng M, Zhong J, Zhang Z, Keppeke GD, Sung LY, Liu JL. Molecular crowding facilitates bundling of IMPDH polymers and cytoophidium formation. Cell Mol Life Sci 2022; 79:420. [PMID: 35833994 PMCID: PMC11072341 DOI: 10.1007/s00018-022-04448-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
The cytoophidium is a unique type of membraneless compartment comprising of filamentous protein polymers. Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step of de novo GTP biosynthesis and plays critical roles in active cell metabolism. However, the molecular regulation of cytoophidium formation is poorly understood. Here we show that human IMPDH2 polymers bundle up to form cytoophidium-like aggregates in vitro when macromolecular crowders are present. The self-association of IMPDH polymers is suggested to rely on electrostatic interactions. In cells, the increase of molecular crowding with hyperosmotic medium induces cytoophidia, while the decrease of that by the inhibition of RNA synthesis perturbs cytoophidium assembly. In addition to IMPDH, CTPS and PRPS cytoophidium could be also induced by hyperosmolality, suggesting a universal phenomenon of cytoophidium-forming proteins. Finally, our results indicate that the cytoophidium can prolong the half-life of IMPDH, which is proposed to be one of conserved functions of this subcellular compartment.
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Affiliation(s)
- Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Gerson Dierley Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, 04023-062, Brazil
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.
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11
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IMPDH dysregulation in disease: a mini review. Biochem Soc Trans 2022; 50:71-82. [PMID: 35191957 PMCID: PMC9022972 DOI: 10.1042/bst20210446] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
Abstract
Inosine-5′-monophosphate dehydrogenase (IMPDH) is a highly conserved enzyme in purine metabolism that is tightly regulated on multiple levels. IMPDH has a critical role in purine biosynthesis, where it regulates flux at the branch point between adenine and guanine nucleotide synthesis, but it also has a role in transcription regulation and other moonlighting functions have been described. Vertebrates have two isoforms, IMPDH1 and IMPDH2, and point mutations in each are linked to human disease. Mutations in IMPDH2 in humans are associated with neurodevelopmental disease, but the effects of mutations at the enzyme level have not yet been characterized. Mutations in IMPDH1 lead to retinal degeneration in humans, and recent studies have characterized how they cause functional defects in regulation. IMPDH1 is expressed as two unique splice variants in the retina, a tissue with very high and specific demands for purine nucleotides. Recent studies have revealed functional differences among splice variants, demonstrating that retinal variants up-regulate guanine nucleotide synthesis by reducing sensitivity to feedback inhibition by downstream products. A better understanding of the role of IMPDH1 in the retina and the characterization of an animal disease model will be critical for determining the molecular mechanism of IMPDH1-associated blindness.
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12
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Burrell AL, Nie C, Said M, Simonet JC, Fernández-Justel D, Johnson MC, Quispe J, Buey RM, Peterson JR, Kollman JM. IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat Struct Mol Biol 2022; 29:47-58. [PMID: 35013599 PMCID: PMC9044917 DOI: 10.1038/s41594-021-00706-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/23/2021] [Indexed: 01/06/2023]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized. IMPDH1 plays a unique role in retinal metabolism, and point mutants cause blindness. Here, in a series of cryogenic-electron microscopy structures we show that human IMPDH1 assembles polymorphic filaments with different assembly interfaces in extended and compressed states. Retina-specific splice variants introduce structural elements that reduce sensitivity to GTP inhibition, including stabilization of the extended filament form. Finally, we show that IMPDH1 disease mutations fall into two classes: one disrupts GTP regulation and the other has no effect on GTP regulation or filament assembly. These findings provide a foundation for understanding the role of IMPDH1 in retinal function and disease and demonstrate the diverse mechanisms by which metabolic enzyme filaments are allosterically regulated.
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Affiliation(s)
- Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Chuankai Nie
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Meerit Said
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jacqueline C Simonet
- Cancer Epigenetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Biology, Arcadia University, Glenside, PA, USA
| | - David Fernández-Justel
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Jeffrey R Peterson
- Cancer Epigenetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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13
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Dobrut A, Brzychczy-Włoch M. Immunogenic Proteins of Group B Streptococcus-Potential Antigens in Immunodiagnostic Assay for GBS Detection. Pathogens 2021; 11:43. [PMID: 35055991 PMCID: PMC8778278 DOI: 10.3390/pathogens11010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen, which asymptomatically colonizes the gastrointestinal and genitourinary tract of up to one third of healthy adults. Nevertheless, GBS carriage in pregnant women may lead to several health issues in newborns causing life threatening infection, such as sepsis, pneumonia or meningitis. Recommended GBS screening in pregnant women significantly reduced morbidity and mortality in infants. Nevertheless, intrapartum antibiotic prophylaxis, recommended following the detection of carriage or in case of lack of a carriage test result for pregnant women who demonstrate certain risk factors, led to the expansion of the adverse phenomenon of bacterial resistance to antibiotics. In our paper, we reviewed some immunogenic GBS proteins, i.e., Alp family proteins, β protein, Lmb, Sip, BibA, FsbA, ScpB, enolase, elongation factor Tu, IMPDH, and GroEL, which possess features characteristic of good candidates for immunodiagnostic assays for GBS carriage detection, such as immunoreactivity and specificity. We assume that they can be used as an alternative diagnostic method to the presently recommended bacteriological cultivation and MALDI.
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Affiliation(s)
| | - Monika Brzychczy-Włoch
- Department of Molecular Medical Microbiology, Faculty of Medicine, Medical College, Jagiellonian University, 31-121 Krakow, Poland;
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14
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Simonet JC, Burrell AL, Kollman JM, Peterson JR. Freedom of assembly: metabolic enzymes come together. Mol Biol Cell 2021; 31:1201-1205. [PMID: 32463766 PMCID: PMC7353150 DOI: 10.1091/mbc.e18-10-0675] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many different enzymes in intermediate metabolism dynamically assemble filamentous polymers in cells, often in response to changes in physiological conditions. Most of the enzyme filaments known to date have only been observed in cells, but in a handful of cases structural and biochemical studies have revealed the mechanisms and consequences of assembly. In general, enzyme polymerization functions as a mechanism to allosterically tune enzyme kinetics, and it may play a physiological role in integrating metabolic signaling. Here, we highlight some principles of metabolic filaments by focusing on two well-studied examples in nucleotide biosynthesis pathways—inosine-5’-monophosphate (IMP) dehydrogenase and cytosine triphosphate (CTP) synthase.
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Affiliation(s)
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
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15
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Keppeke GD, Chang CC, Antos CL, Peng M, Sung LY, Andrade LEC, Liu JL. IMPDH forms the cytoophidium in zebrafish. Dev Biol 2021; 478:89-101. [PMID: 34048735 DOI: 10.1016/j.ydbio.2021.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in de novo guanine nucleotide biosynthesis. Its activity is negatively regulated by the binding of GTP. IMPDH can form a membraneless subcellular structure termed the cytoophidium in response to certain changes in the metabolic status of the cell. The polymeric form of IMPDH, which is the subunit of the cytoophidium, has been shown to be more resistant to the inhibition by GTP at physiological concentrations, implying a functional correlation between cytoophidium formation and the upregulation of GTP biosynthesis. Herein we demonstrate that zebrafish IMPDH1b and IMPDH2 isoforms can assemble abundant cytoophidium in most of cultured cells under stimuli, while zebrafish IMPDH1a shows distinctive properties of forming the cytoophidium in different cell types. Point mutations that disrupt cytoophidium structure in mammalian models also prevent the aggregation of zebrafish IMPDHs. In addition, we discover the presence of the IMPDH cytoophidium in various tissues of larval and adult fish under normal growth conditions. Our results reveal that polymerization and cytoophidium assembly of IMPDH can be a regulatory machinery conserved among vertebrates, and with specific physiological purposes.
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Affiliation(s)
- Gerson Dierley Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, 04023-062, Brazil
| | - Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Christopher L Antos
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Luis Eduardo Coelho Andrade
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, 04023-062, Brazil
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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16
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Calise SJ, Chan EKL. Anti-rods/rings autoantibody and IMPDH filaments: an update after fifteen years of discovery. Autoimmun Rev 2020; 19:102643. [PMID: 32805424 DOI: 10.1016/j.autrev.2020.102643] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
Autoantibodies to unknown subcellular rod and ring-shaped structures were first discovered in sera from hepatitis C patients in 2005. Early studies showed a strong association between these anti-rods/rings antibodies (anti-RR) and the standard of care interferon-α plus ribavirin combination therapy (IFN/RBV), suggesting that anti-RR are drug-induced autoantibodies. In the context of hepatitis C, anti-RR have been linked with relapse from or lack of response to IFN/RBV in some patient cohorts. However, examples of anti-RR in other diseases and healthy individuals have also been reported over the years, although anti-RR remains a rare autoantibody response in general. The advent of new direct-acting antiviral drugs for chronic hepatitis C and studies of anti-RR from different parts of the world are also beginning to change the perception of anti-RR. The nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) has been identified as the major autoantigen recognized by anti-RR. Coincidentally, the assembly of IMPDH into micron-scale rod and ring-shaped structures was discovered around the same time as anti-RR. Knowledge of the fundamental biological properties and cellular functions of these structures, referred to as "IMPDH filaments" by cell biologists, has advanced in parallel to anti-RR antibodies. Recent studies have revealed that IMPDH filament assembly is a mechanism to prevent feedback inhibition of IMPDH and is therefore important for the increased nucleotide production required in hyperproliferating cells, like activated T cells. Fifteen years later, we review the history and current knowledge in both the anti-RR autoantibody and IMPDH filament fields. TAKE-HOME MESSAGE: Anti-rods/rings are recognized as an example of a drug-induced autoantibody in hepatitis C patients treated with interferon and ribavirin, although new studies suggest anti-rods/rings may be detected in other contexts and may depend on unknown environmental or genetic factors in different populations. Recent data suggest that the assembly of IMPDH into rod and ring structures, the targets of anti-rods/rings autoantibody, is a mechanism for hyperproliferating cells, like activated T cells, to maintain increased guanine nucleotide levels to support rapid cell division.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA.
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA.
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17
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Johnson MC, Kollman JM. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. eLife 2020; 9:e53243. [PMID: 31999252 PMCID: PMC7018514 DOI: 10.7554/elife.53243] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
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Affiliation(s)
- Matthew C Johnson
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Justin M Kollman
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
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18
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Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story. Cancers (Basel) 2019; 11:cancers11091346. [PMID: 31514446 PMCID: PMC6770829 DOI: 10.3390/cancers11091346] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 01/15/2023] Open
Abstract
The purine nucleotides ATP and GTP are essential precursors to DNA and RNA synthesis and fundamental for energy metabolism. Although de novo purine nucleotide biosynthesis is increased in highly proliferating cells, such as malignant tumors, it is not clear if this is merely a secondary manifestation of increased cell proliferation. Suggestive of a direct causative effect includes evidence that, in some cancer types, the rate-limiting enzyme in de novo GTP biosynthesis, inosine monophosphate dehydrogenase (IMPDH), is upregulated and that the IMPDH inhibitor, mycophenolic acid (MPA), possesses anti-tumor activity. However, historically, enthusiasm for employing IMPDH inhibitors in cancer treatment has been mitigated by their adverse effects at high treatment doses and variable response. Recent advances in our understanding of the mechanistic role of IMPDH in tumorigenesis and cancer progression, as well as the development of IMPDH inhibitors with selective actions on GTP synthesis, have prompted a reappraisal of targeting this enzyme for anti-cancer treatment. In this review, we summarize the history of IMPDH inhibitors, the development of new inhibitors as anti-cancer drugs, and future directions and strategies to overcome existing challenges.
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19
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Fernández-Justel D, Núñez R, Martín-Benito J, Jimeno D, González-López A, Soriano EM, Revuelta JL, Buey RM. A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity. J Mol Biol 2019; 431:956-969. [PMID: 30664871 DOI: 10.1016/j.jmb.2019.01.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/29/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo GTP biosynthetic pathway and plays essential roles in cell proliferation. As a clinical target, IMPDH has been studied for decades, but it has only been within the last years that we are starting to understand the complexity of the mechanisms of its physiological regulation. Here, we report structural and functional insights into how adenine and guanine nucleotides control a conformational switch that modulates the assembly of the two human IMPDH enzymes into cytoophidia and allosterically regulates their catalytic activity. In vitro reconstituted micron-length cytoophidia-like structures show catalytic activity comparable to unassembled IMPDH but, in turn, are more resistant to GTP/GDP allosteric inhibition. Therefore, IMPDH cytoophidia formation facilitates the accumulation of high levels of guanine nucleotides when the cell requires it. Finally, we demonstrate that most of the IMPDH retinopathy-associated mutations abrogate GTP/GDP-induced allosteric inhibition and alter cytoophidia dynamics.
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Affiliation(s)
- David Fernández-Justel
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Rafael Núñez
- Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jaime Martín-Benito
- Centro Nacional de Biotecnología (CNB), Spanish National Research Council (CSIC), Darwin 3, 28039 Madrid, Spain
| | - David Jimeno
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Adrián González-López
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Eva María Soriano
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Rubén M Buey
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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20
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Calise SJ, Abboud G, Kasahara H, Morel L, Chan EKL. Immune Response-Dependent Assembly of IMP Dehydrogenase Filaments. Front Immunol 2018; 9:2789. [PMID: 30555474 PMCID: PMC6283036 DOI: 10.3389/fimmu.2018.02789] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to xanthosine monophosphate, the rate-limiting step in de novo guanosine monophosphate (GMP) synthesis. In cultured cells, IMPDH polymerizes into micron-scale filamentous structures when GMP synthesis is inhibited by depletion of purine precursors or by various drugs, including mycophenolic acid, ribavirin, and methotrexate. IMPDH filaments also spontaneously form in undifferentiated mouse embryonic stem cells and induced pluripotent stem cells, hinting they might function in various highly proliferative cell types. Therefore, we investigated IMPDH filament formation in human and murine T cells, which rely heavily on de novo guanine nucleotide synthesis to rapidly proliferate in response to antigenic challenge. We discovered extensive in vivo IMPDH filament formation in mature T cells, B cells, and other proliferating splenocytes of normal, adult B6 mice. Both cortical and medullary thymocytes in young and old mice also showed considerable assembly of IMPDH filaments. We then stimulated primary human peripheral blood mononuclear cells ex vivo with T cell mitogens phytohemagglutinin (PHA), concanavalin A (ConA), or antibodies to CD3 and CD28 for 72 h. We detected IMPDH filaments in 40–60% of T cells after activation compared to 0–10% of unstimulated T cells. Staining of activated T cells for the proliferation marker Ki-67 also showed an association between IMPDH filament formation and proliferation. Additionally, we transferred ovalbumin-specific CD4+ T cells from B6.OT-II mice into B6.Ly5a recipient mice, challenged these mice with ovalbumin, and harvested spleens 6 days later. In these spleens, we identified abundant IMPDH filaments in transferred T cells by immunofluorescence, indicating that IMPDH also polymerizes during in vivo antigen-specific T cell activation. Overall, our data indicate that IMPDH filament formation is a novel aspect of T cell activation and proliferation, and that filaments might be useful morphological markers for T cell activation. The data also suggest that in vivo IMPDH filament formation could be occurring in a variety of proliferating cell types throughout the body. We propose that T cell activation will be a valuable model for future experiments probing the molecular mechanisms that drive IMPDH polymerization, as well as how IMPDH filament formation affects cell function.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Georges Abboud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
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21
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Autoantibodies to cytoplasmic rods and rings in patients with hepatitis C virus infection treated with direct-acting antivirals: The role of prior treatment with interferon plus ribavirin. GASTROENTEROLOGIA Y HEPATOLOGIA 2018; 42:82-89. [PMID: 30446175 DOI: 10.1016/j.gastrohep.2018.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/27/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The cytoplasmic rods-rings (RR) pattern is found in hepatitis C (HCV) patients treated with interferon-ribavirin when studied with ANA-IIF. Ribavirin aggregates/induces antigenic changes in IMPDH-2, an enzyme necessary for ribavirin action. PATIENTS AND METHOD Prospective search for anti-RR autoantibodies (HEp-2, INOVA) in patients treated with direct-acting antivirals (DAAs) from October 2015 to June 2017. HCV-negative patients from up to June 2016 acted as controls. Anti-RR was analyzed at baseline and, mainly, during treatment and follow-up. The Chi-square test, Student's t-test and a logistic regression analysis were performed. RESULTS Between October 2015 and June 2016, 1258 men and 2389 women who were HCV-negative and 137 men and 112 women who were HCV-positive patients were studied. Approximately 22.9% of HCV-negative and 13.2% of HCV-positive were ANA-IIF-positive (p<0.05). Three HCV-negative (0.08%) and 23 (9.2%) HCV-positive patients had anti-RR (p<0.001). A total of 122 patients received DAAs; 30 received DAA+RBV; 46 pre-treated with IFN-RBV received DAA; 31 pre-treated with IFN-RBV received DAA+RBV; 16 received IFNpeg-RBV; and 24 received IFN-RBV-DAA. None of the 122 DAA-treated patients showed anti-RR; anti-RR were identified in 14.8% of those treated with DAA-RBV; in 25.9% of those pre-treated with IFN-RBV receiving DAA; in 22.2% of IFN-RBV-pre-treated patients who received DAA+RBV; in 7.4% of those treated with IFNpeg-RBV and in 29.6% of those treated with IFNpeg-RBV-DAA. The multivariate analysis showed significant associations between anti-RR and "Exposure to IFN" and "Time of exposure to RBV". CONCLUSIONS Anti-RR autoantibodies were detected only in patients with current or past treatments with RBV, even in cases in which only DAAs were later administered.
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22
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Dobrut A, Brzozowska E, Górska S, Pyclik M, Gamian A, Bulanda M, Majewska E, Brzychczy-Włoch M. Epitopes of Immunoreactive Proteins of Streptococcus Agalactiae: Enolase, Inosine 5'-Monophosphate Dehydrogenase and Molecular Chaperone GroEL. Front Cell Infect Microbiol 2018; 8:349. [PMID: 30333963 PMCID: PMC6176014 DOI: 10.3389/fcimb.2018.00349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/11/2018] [Indexed: 11/13/2022] Open
Abstract
Three Streptococcus agalactiae (group B streptococci, GBS) immunoreactive proteins: enolase (47.4 kDa), inosine 5'-monophosphate dehydrogenase (IMPDH) (53 kDa) and molecular chaperone GroEL (57 kDa) were subjected to investigation. Enolase protein was described in our previous paper, whereas IMPDH and GroEL were presented for the first time. The aim of our paper was to provide mapping of specific epitopes, highly reactive with umbilical cord blood serum. Bioinformatic analyses allowed to select 32 most likely epitopes for enolase, 36 peptides for IMPDH and 41 immunoreactive peptides for molecular chaperone GroEL, which were synthesized by PEPSCAN. Ten peptides: two in enolase, one in IMPDH and seven in molecular chaperone GroEL have been identified as potentially highly selective epitopes that can be used as markers in rapid immunological diagnostic tests or constitute a component of an innovative vaccine against GBS infections.
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Affiliation(s)
- Anna Dobrut
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Ewa Brzozowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Sabina Górska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Marcelina Pyclik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Andrzej Gamian
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Małgorzata Bulanda
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Elzbieta Majewska
- Department of Clinical Obstetrics and Perinatology, University Hospital, Krakow, Poland
| | - Monika Brzychczy-Włoch
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
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23
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Chang CC, Keppeke GD, Sung LY, Liu JL. Interfilament interaction between IMPDH and CTPS cytoophidia. FEBS J 2018; 285:3753-3768. [PMID: 30085408 PMCID: PMC6220823 DOI: 10.1111/febs.14624] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 07/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) and cytidine triphosphate synthase (CTPS) are two metabolic enzymes that perform rate‐limiting steps in the de novo synthesis of purine and pyrimidine nucleotides, respectively. It has been shown that IMPDH and CTPS can comprise a filamentous macrostructure termed the cytoophidium, which may play a role in regulation of their catalytic activity. Although these two proteins may colocalise in the same cytoophidium, how they associate with one another is still elusive. As reported herein, we established a model HeLa cell line coexpressing OFP‐tagged IMPDH2 and GFP‐tagged CTPS1 and recorded the assembly, disassembly and movement of the cytoophidium in live cells. Moreover, by using super‐resolution confocal imaging, we demonstrate how IMPDH‐ and CTPS‐based filaments are aligned or intertwined in the mixed cytoophidium. Collectively, our findings provide a panorama of cytoophidium dynamics and suggest that IMPDH and CTPS cytoophidia may coordinate by interfilament interaction.
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Affiliation(s)
- Chia-Chun Chang
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Gerson D Keppeke
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK.,School of Life Science and Technology, ShanghaiTech University, China
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24
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Schiavon CR, Griffin ME, Pirozzi M, Parashuraman R, Zhou W, Jinnah HA, Reines D, Kahn RA. Compositional complexity of rods and rings. Mol Biol Cell 2018; 29:2303-2316. [PMID: 30024290 PMCID: PMC6249804 DOI: 10.1091/mbc.e18-05-0274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Maxwell E Griffin
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Marinella Pirozzi
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Raman Parashuraman
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - H A Jinnah
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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25
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Keppeke GD, Chang CC, Peng M, Chen LY, Lin WC, Pai LM, Andrade LEC, Sung LY, Liu JL. IMP/GTP balance modulates cytoophidium assembly and IMPDH activity. Cell Div 2018; 13:5. [PMID: 29946345 PMCID: PMC6004095 DOI: 10.1186/s13008-018-0038-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/06/2018] [Indexed: 02/07/2023] Open
Abstract
Background Inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme in de novo GTP biosynthesis, plays an important role in cell metabolism and proliferation. It has been demonstrated that IMPDH can aggregate into a macrostructure, termed the cytoophidium, in mammalian cells under a variety of conditions. However, the regulation and function of the cytoophidium are still elusive. Results In this study, we report that spontaneous filamentation of IMPDH is correlated with rapid cell proliferation. Intracellular IMP accumulation promoted cytoophidium assembly, whereas elevated GTP level triggered disassociation of aggregates. By using IMPDH2 CBS domain mutant cell models, which are unable to form the cytoophidium, we have determined that the cytoophidium is of the utmost importance for maintaining the GTP pool and normal cell proliferation in the condition that higher IMPDH activity is required. Conclusions Together, our results suggest a novel mechanism whereby cytoophidium assembly upregulates IMPDH activity and mediates guanine nucleotide homeostasis. Electronic supplementary material The online version of this article (10.1186/s13008-018-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerson Dierley Keppeke
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK
| | - Chia Chun Chang
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK.,2Institute of Biotechnology, National Taiwan University, Taipei, 106 Taiwan, ROC
| | - Min Peng
- 2Institute of Biotechnology, National Taiwan University, Taipei, 106 Taiwan, ROC
| | - Li-Yu Chen
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK
| | - Wei-Cheng Lin
- 3Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC
| | - Li-Mei Pai
- 3Molecular Medicine Research Center, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC.,4Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC.,5Department of Biochemistry, College of Medicine, Chang Gung University, Tao-Yuan, 333 Taiwan, ROC
| | - Luis Eduardo Coelho Andrade
- 6Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP 04023-062 Brazil
| | - Li-Ying Sung
- 2Institute of Biotechnology, National Taiwan University, Taipei, 106 Taiwan, ROC.,7Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan, ROC
| | - Ji-Long Liu
- 1Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT UK.,8School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China
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26
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Anthony SA, Burrell AL, Johnson MC, Duong-Ly KC, Kuo YM, Simonet JC, Michener P, Andrews A, Kollman JM, Peterson JR. Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations. Mol Biol Cell 2017; 28:mbc.E17-04-0263. [PMID: 28794265 PMCID: PMC5620369 DOI: 10.1091/mbc.e17-04-0263] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/02/2017] [Accepted: 08/04/2017] [Indexed: 01/01/2023] Open
Abstract
Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and metabolic homeostasis. The guanine nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) forms octamers that polymerize into helical chains. In mammalian cells, IMPDH filaments can associate into micron-length assemblies. Polymerization and enzyme activity are regulated in part by binding of purine nucleotides to an allosteric regulatory domain. ATP promotes octamer polymerization, whereas GTP promotes a compact, inactive conformation whose ability to polymerize is unknown. Also unclear is whether polymerization directly alters IMPDH catalytic activity. To address this, we identified point mutants of human IMPDH2 that either prevent or promote polymerization. Unexpectedly, we found that polymerized and non-assembled forms of recombinant IMPDH have comparable catalytic activity, substrate affinity, and GTP sensitivity and validated this finding in cells. Electron microscopy revealed that substrates and allosteric nucleotides shift the equilibrium between active and inactive conformations in both the octamer and the filament. Unlike other metabolic filaments, which selectively stabilize active or inactive conformations, recombinant IMPDH filaments accommodate multiple states. These conformational states are finely tuned by substrate availability and purine balance, while polymerization may allow cooperative transitions between states.
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Affiliation(s)
- Sajitha A Anthony
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Krisna C Duong-Ly
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Yin-Ming Kuo
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Jacqueline C Simonet
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Peter Michener
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102
| | - Andrew Andrews
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Box 357350, Seattle, WA 98195
| | - Jeffrey R Peterson
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
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27
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Chitrakar I, Kim-Holzapfel DM, Zhou W, French JB. Higher order structures in purine and pyrimidine metabolism. J Struct Biol 2017; 197:354-364. [PMID: 28115257 DOI: 10.1016/j.jsb.2017.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
The recent discovery of several forms of higher order protein structures in cells has shifted the paradigm of how we think about protein organization and metabolic regulation. These dynamic and controllable protein assemblies, which are composed of dozens or hundreds of copies of an enzyme or related enzymes, have emerged as important players in myriad cellular processes. We are only beginning to appreciate the breadth of function of these types of macromolecular assemblies. These higher order structures, which can be assembled in response to varied cellular stimuli including changing metabolite concentrations or signaling cascades, give the cell the capacity to modulate levels of biomolecules both temporally and spatially. This provides an added level of control with distinct kinetics and unique features that can be harnessed as a subtle, yet powerful regulatory mechanism. Due, in large part, to advances in structural methods, such as crystallography and cryo-electron microscopy, and the advent of super-resolution microscopy techniques, a rapidly increasing number of these higher order structures are being identified and characterized. In this review, we detail what is known about the structure, function and control mechanisms of these mesoscale protein assemblies, with a particular focus on those involved in purine and pyrimidine metabolism. These structures have important implications both for our understanding of fundamental cellular processes and as fertile ground for new targets for drug discovery and development.
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Affiliation(s)
- Iva Chitrakar
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Deborah M Kim-Holzapfel
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Weijie Zhou
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States
| | - Jarrod B French
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States.
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28
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Noble JW, Hunter DV, Roskelley CD, Chan EKL, Mills J. Loukoumasomes Are Distinct Subcellular Structures from Rods and Rings and Are Structurally Associated with MAP2 and the Nuclear Envelope in Retinal Cells. PLoS One 2016; 11:e0165162. [PMID: 27798680 PMCID: PMC5087950 DOI: 10.1371/journal.pone.0165162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 10/07/2016] [Indexed: 12/19/2022] Open
Abstract
“Rods and rings” (RR) and loukoumasomes are similarly shaped, subcellular macromolecular structures with as yet unknown function. RR, so named because of their shape, are formed in response to inhibition in the GTP or CTP synthetic pathways and are highly enriched in the two key enzymes of the nucleotide synthetic pathway. Loukoumasomes also occur as linear and toroidal bodies and were initially inferred to be the same as RR, largely due to their shared shape and size and the fact that it was unclear if they shared the same subcomponents. In human retinoblastoma tissue and cells we have observed toroidal, perinuclear, macromolecular structures of similar size and antigenicity to those previously reported in neurons (neuronal-loukoumasomes). To further characterize the subcomponents of the retinal-loukoumasomes, confocal analysis following immunocytochemical staining for alpha-tubulin, beta-III tubulin and detyrosinated tubulin was performed. These studies indicate that retinal-loukoumasomes are enriched for beta-III tubulin and other tubulins associated with microtubules. Immunofluorescence together with the in situ proximity ligation assay (PLA), confirmed that beta-III tubulin colocalized with detyrosinated tubulin within loukoumasomes. Our results indicate that these tissues contain only loukoumasomes because these macromolecular structures are immunoreactive with an anti-tubulin antibody but are not recognized by the prototype anti-RR/inosine monophosphate dehydrogenase (IMPDH) antibody (It2006). To further compare the RR and retinal-loukoumasomes, retinoblastoma cells were exposed to the IMPDH-inhibitor ribavirin, a drug known to induce the formation of RR. In contrast to RR, the production of retinal-loukoumasomes was unaffected. Coimmunostaining of Y79 cells for beta-III tubulin and IMPDH indicate that these cells, when treated with ribavirin, can contain both retinal-loukoumasomes and RR and that these structures are antigenically distinct. Subcellular fractionation studies indicate that ribavirin increased the RR subcomponent, IMPDH, in the nuclear fraction of Y79 cells from 21.3 ± 5.8% (0 mM ribavirin) to 122.8 ± 7.9% (1 mM ribavirin) while the subcellular localization of the retinal-loukoumasome subcomponent tubulin went unaltered. Further characterization of retinal-loukoumasomes in retinoblastoma cells reveals that they are intimately associated with lamin folds within the nuclear envelope. Using immunofluorescence and the in situ PLA in this cell type, we have observed colocalization of beta-III tubulin with MAP2. As MAP2 is a microtubule-associated protein implicated in microtubule crosslinking, this supports a role for microtubule crosslinkers in the formation of retinal-loukoumasomes. Together, these results suggest that loukoumasomes and RR are distinct subcellular macromolecular structures, formed by different cellular processes and that there are other loukoumasome-like structures within retinal tissues and cells.
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Affiliation(s)
- Jake W. Noble
- Department of Biology, Trinity Western University, Langley, British Columbia, Canada
| | - Diana V. Hunter
- International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin D. Roskelley
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Edward K. L. Chan
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - Julia Mills
- Department of Biology, Trinity Western University, Langley, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
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29
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Keppeke GD, Prado MS, Nunes E, Perazzio SF, Rodrigues SH, Ferraz MLG, Chan EKL, Andrade LEC. Differential capacity of therapeutic drugs to induce Rods/Rings structures in vitro and in vivo and generation of anti-Rods/Rings autoantibodies. Clin Immunol 2016; 173:149-156. [PMID: 27746381 DOI: 10.1016/j.clim.2016.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/26/2016] [Accepted: 10/09/2016] [Indexed: 12/27/2022]
Abstract
Some HCV patients using ribavirin and interferon alpha (IFN-α) develop anti-rods and rings (RR) autoantibodies, the main target of which is inosine monophosphate dehydrogenase (IMPDH), the rate-determining enzyme in de novo GTP biosynthesis. In vitro inhibition of IMPDH by ribavirin induces RR formation. Here we investigate whether other commonly used drugs that interfere with GTP biosynthesis can induce RR structures in vitro and vivo and elicit generation of autoantibodies. HEp-2 cells treated for 24h with ribavirin, mycophenolic acid (MPA), azathioprine, methotrexate or acyclovir were positive for RR structures. However, adefovir, entecavir, tenofovir and lamivudine did not induce RR structures in these cells. Structures induced by ribavirin in HEp-2 cells are stable after 24h drug-washout, while structures induced by other drugs are relatively labile, disappearing within 2h. Looking at patients treated with these drugs, HCV patients treated with ribavirin (n=17) showed higher average percentage of RR-positive peripheral mononuclear cells than autoimmune patients treated with RR-inducing immunosuppressant drugs (n=21). Serum from 173 autoimmune patients who had been treated with MPA, azathioprine or methotrexate was tested for presence of anti-RR autoantibodies, and only one sample was found to be positive. Conversely, of 48 anti-RR autoantibody positive samples identified at Fleury Laboratories over 30months, 94% were from HCV patients treated with ribavirin plus IFN-α. These data indicate that RR structures can be induced by a variety of drugs in vitro and in vivo, but anti-RR autoantibody production is mostly restricted to HCV patients under ribavirin+IFN-α treatment.
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Affiliation(s)
- Gerson Dierley Keppeke
- Rheumatology Division, Federal University of Sao Paulo, Sao Paulo, SP 04023-062, Brazil.
| | - Monica Simon Prado
- Rheumatology Division, Federal University of Sao Paulo, Sao Paulo, SP 04023-062, Brazil
| | - Eunice Nunes
- Gastroenterology Division, Federal University of Sao Paulo, Sao Paulo, SP 04023-062, Brazil
| | - Sandro Felix Perazzio
- 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
| | | | | | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610-0424, USA
| | - Luis Eduardo Coelho 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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30
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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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31
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Climent J, Morandeira F, Castellote J, Xiol J, Niubó J, Calatayud L, Mestre M, Bas J. Clinical correlates of the "rods and rings" antinuclear antibody pattern. Autoimmunity 2015; 49:102-8. [PMID: 26699543 DOI: 10.3109/08916934.2015.1118762] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The "rods and rings" (RR) antinuclear antibody (ANA) pattern is believed to be restricted to hepatitis C virus (HCV) infection and related to the treatment. This is a 4-year retrospective study of all patients with RR pattern from the 20,000 serum samples received at the Hospital Universitari de Bellvitge for ANA testing. Two control groups with HCV patients without RR pattern: ANA-positive (n = 74) and ANA negative (n = 75) were included. Eighty-seven patients had samples with the RR pattern. Seventy-three were infected with HCV (prevalence of 15% in the HCV population). The RR pattern could not be related to ribavirin treatment, clinical status, biochemistry data, hepatic fibrosis, IL28B genotype, HCV genotype or the presence of autoantibodies related with autoimmune hepatitis. As 14 cases presented other diseases, mainly of autoimmune origin, the presence of RR antibodies may also be explained by alterations in immune regulation caused by autoimmunity or HCV in a particular genetic background.
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Affiliation(s)
| | | | | | | | - Jordi Niubó
- c Department of Microbiology , Hospital Universitari de Bellvitge , Catalonia , Spain
| | - Laura Calatayud
- c Department of Microbiology , Hospital Universitari de Bellvitge , Catalonia , Spain
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32
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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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