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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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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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3
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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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4
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Darekar S, Laín S. Asymmetric inheritance of cytoophidia could contribute to determine cell fate and plasticity: The onset of alternative differentiation patterns in daughter cells may rely on the acquisition of either CTPS or IMPDH cytoophidia: The onset of alternative differentiation patterns in daughter cells may rely on the acquisition of either CTPS or IMPDH cytoophidia. Bioessays 2022; 44:e2200128. [PMID: 36209393 DOI: 10.1002/bies.202200128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 12/20/2022]
Abstract
Two enzymes involved in the synthesis of pyrimidine and purine nucleotides, CTP synthase (CTPS) and IMP dehydrogenase (IMPDH), can assemble into a single or very few large filaments called rods and rings (RR) or cytoophidia. Most recently, asymmetric cytoplasmic distribution of organelles during cell division has been described as a decisive event in hematopoietic stem cell fate. We propose that cytoophidia, which could be considered as membrane-less organelles, may also be distributed asymmetrically during mammalian cell division as previously described for Schizosaccharomyces pombe. Furthermore, because each type of nucleotide intervenes in distinct processes (e.g., membrane synthesis, glycosylation, and G protein-signaling), alterations in the rate of synthesis of specific nucleotide types could influence cell differentiation in multiple ways. Therefore, we hypothesize that whether a daughter cell inherits or not CTPS or IMPDH filaments determines its fate and that this asymmetric inheritance, together with the dynamic nature of these structures enables plasticity in a cell population.
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Affiliation(s)
- Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
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Zaffagni M, Harris JM, Patop IL, Pamudurti NR, Nguyen S, Kadener S. SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome. eLife 2022; 11:71945. [PMID: 35293857 PMCID: PMC9054133 DOI: 10.7554/elife.71945] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/10/2022] [Indexed: 11/15/2022] Open
Abstract
Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in the presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy. Viruses are parasites, relying on the cells they infect to make more of themselves. In doing so they change how an infected cell turns its genes on and off, forcing it to build new virus particles and turning off the immune surveillance that would allow the body to intervene. This is how SARS-CoV-2, the virus that causes COVID, survives with a genome that carries instructions to make just 29 proteins. One of these proteins, known as Nsp14, is involved in both virus reproduction and immune escape. Previous work has shown that it interacts with IMPDH2, the cellular enzyme that controls the production of the building blocks of the genetic code. The impact of this interaction is not clear. To find out more, Zaffagni et al. introduced 26 of the SARS-CoV-2 proteins into human cells one at a time. Nsp14 had the most dramatic effect, dialing around 4,000 genes up or down and changing how the cell interprets over 1,000 genes. Despite being just one protein, it mimicked the genetic changes seen during real SARS-CoV-2 infection. Blocking IMPDH2 partially reversed the effects, which suggests that the interaction of Nsp14 with the enzyme might be responsible for the effects of SARS-CoV-2 on the genes of the cell. Understanding how viral proteins affect cells can explain what happens during infection. This could lead to the discovery of new treatments designed to counteract the effects of the virus. Further work could investigate whether interfering with Nsp14 helps cells to overcome infection.
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Affiliation(s)
- Michela Zaffagni
- Department of Biology, Brandeis University, Waltham, United States
| | - Jenna M Harris
- Department of Biology, Brandeis University, Waltham, United States
| | - Ines L Patop
- Department of Biology, Brandeis University, Waltham, United States
| | | | - Sinead Nguyen
- Department of Biology, Brandeis University, Waltham, United States
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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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Zaffagni M, Harris JM, Patop IL, Pamudurti NR, Nguyen S, Kadener S. SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.07.02.450964. [PMID: 35194610 PMCID: PMC8863146 DOI: 10.1101/2021.07.02.450964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1,000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.
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