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Vähätupa M, Nättinen J, Aapola U, Uusitalo-Järvinen H, Uusitalo H, Järvinen TAH. Proteomics Analysis of R-Ras Deficiency in Oxygen Induced Retinopathy. Int J Mol Sci 2023; 24:ijms24097914. [PMID: 37175621 PMCID: PMC10178533 DOI: 10.3390/ijms24097914] [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: 03/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Small GTPase R-Ras regulates vascular permeability in angiogenesis. In the eye, abnormal angiogenesis and hyperpermeability are the leading causes of vision loss in several ischemic retinal diseases such as proliferative diabetic retinopathy (PDR), retinal vein occlusion (RVO), and retinopathy of prematurity (ROP). Oxygen-induced retinopathy (OIR) is the most widely used experimental model for these ischemic retinopathies. To shed more light on how the R-Ras regulates vascular permeability in pathological angiogenesis, we performed a comprehensive (>2900 proteins) characterization of OIR in R-Ras knockout (KO) and wild-type (WT) mice by sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics. OIR and age-matched normoxic control retinas were collected at P13, P17, and P42 from R-Ras KO and WT mice and were subjected to SWATH-MS and data analysis. The most significant difference between the R-Ras KO and WT retinas was an accumulation of plasma proteins. The pathological vascular hyperpermeability during OIR in the R-Ras KO retina took place very early, P13. This led to simultaneous hypoxic cell injury/death (ferroptosis), glycolytic metabolism as well compensatory mechanisms to counter the pathological leakage from angiogenic blood vessels in the OIR retina of R-Ras deficient mice.
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Affiliation(s)
- Maria Vähätupa
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
| | - Janika Nättinen
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Ulla Aapola
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Hannele Uusitalo-Järvinen
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Hannu Uusitalo
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Tero A H Järvinen
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
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Briso-Montiano A, Del Caño-Ochoa F, Vilas A, Velázquez-Campoy A, Rubio V, Pérez B, Ramón-Maiques S. Insight on molecular pathogenesis and pharmacochaperoning potential in phosphomannomutase 2 deficiency, provided by novel human phosphomannomutase 2 structures. J Inherit Metab Dis 2022; 45:318-333. [PMID: 34859900 DOI: 10.1002/jimd.12461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/12/2021] [Accepted: 12/01/2021] [Indexed: 12/22/2022]
Abstract
Phosphomannomutase 2 (PMM2) deficiency, the most frequent congenital disorder of glycosylation (PMM2-CDG), is a severe condition, which has no cure. Due to the identification of destabilizing mutations, our group aims at increasing residual activity in PMM2-CDG patients, searching for pharmacochaperones. Detailed structural knowledge of hPMM2 might help identify variants amenable to pharmacochaperoning. hPMM2 structural information is limited to one incomplete structure deposited in the Protein Databank without associated publication, which lacked ligands and residues from a crucial loop. Here we report five complete crystal structures of hPMM2, three for wild-type and two for the p.Thr237Met variant frequently found among Spanish PMM2-CDG patients, free and bound to the essential activator glucose-1,6-bisphosphate (Glc-1,6-P2 ). In the hPMM2 homodimer, each subunit has a different conformation, reflecting movement of the distal core domain relative to the dimerization cap domain, supporting an opening/closing process during catalysis. Two Mg2+ ions bind to the core domain, one catalytic and one structural. In the cap domain, the site for Glc-1,6-P2 is well delineated, while a Cl- ion binding at the intersubunit interface is predicted to strengthen dimerization. Patient-found amino acid substitutions are nonhomogeneously distributed throughout hPMM2, reflecting differential functional or structural importance for various parts of the protein. We classify 93 of 101 patient-reported single amino acid variants according to five potential pathogenetic mechanism affecting folding of the core and cap domains, linker 2 flexibility, dimerization, activator binding, and catalysis. We propose that ~80% and ~50% of the respective core and cap domains substitutions are potential candidates for pharmacochaperoning treatment.
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Affiliation(s)
- Alvaro Briso-Montiano
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Group CB06/07/0004 in the Universidad Autónoma de Madrid of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Investigación La Paz, IdiPAZ, Madrid, Spain
| | - Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Alicia Vilas
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Group CB06/07/0004 in the Universidad Autónoma de Madrid of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Investigación La Paz, IdiPAZ, Madrid, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Departament of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
- Protein Targets Group, Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain
- Group CB06/04/0066, Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), Madrid, Spain
- Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
- Group CB06/07/0077 at the Instituto de Biomedicina de Valencia (IBV-CSIC) of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Group CB06/07/0004 in the Universidad Autónoma de Madrid of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Investigación La Paz, IdiPAZ, Madrid, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
- Group CB06/07/0077 at the Instituto de Biomedicina de Valencia (IBV-CSIC) of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
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Frasse PM, Miller JJ, Polino AJ, Soleimani E, Zhu JS, Jakeman DL, Jez JM, Goldberg DE, Odom John AR. Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria-causing parasites. J Biol Chem 2022; 298:101550. [PMID: 34973333 PMCID: PMC8808168 DOI: 10.1016/j.jbc.2021.101550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/05/2022] Open
Abstract
The malaria-causing parasite Plasmodium falciparum is responsible for over 200 million infections and 400,000 deaths per year. At multiple stages during its complex life cycle, P. falciparum expresses several essential proteins tethered to its surface by glycosylphosphatidylinositol (GPI) anchors, which are critical for biological processes such as parasite egress and reinvasion of host red blood cells. Targeting this pathway therapeutically has the potential to broadly impact parasite development across several life stages. Here, we characterize an upstream component of parasite GPI anchor biosynthesis, the putative phosphomannomutase (PMM) (EC 5.4.2.8), HAD5 (PF3D7_1017400). We confirmed the PMM and phosphoglucomutase activities of purified recombinant HAD5 by developing novel linked enzyme biochemical assays. By regulating the expression of HAD5 in transgenic parasites with a TetR-DOZI-inducible knockdown system, we demonstrated that HAD5 is required for malaria parasite egress and erythrocyte reinvasion, and we assessed the role of HAD5 in GPI anchor synthesis by autoradiography of radiolabeled glucosamine and thin layer chromatography. Finally, we determined the three-dimensional X-ray crystal structure of HAD5 and identified a substrate analog that specifically inhibits HAD5 compared to orthologous human PMMs in a time-dependent manner. These findings demonstrate that the GPI anchor biosynthesis pathway is exceptionally sensitive to inhibition in parasites and that HAD5 has potential as a specific, multistage antimalarial target.
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Affiliation(s)
- Philip M Frasse
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Justin J Miller
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alexander J Polino
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ebrahim Soleimani
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Chemistry, Razi University, Kermanshah, Iran
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Daniel E Goldberg
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Morava E, Schatz UA, Torring PM, Abbott MA, Baumann M, Brasch-Andersen C, Chevalier N, Dunkhase-Heinl U, Fleger M, Haack TB, Nelson S, Potelle S, Radenkovic S, Bommer GT, Van Schaftingen E, Veiga-da-Cunha M. Impaired glucose-1,6-biphosphate production due to bi-allelic PGM2L1 mutations is associated with a neurodevelopmental disorder. Am J Hum Genet 2021; 108:1151-1160. [PMID: 33979636 PMCID: PMC8206387 DOI: 10.1016/j.ajhg.2021.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/22/2021] [Indexed: 11/25/2022] Open
Abstract
We describe a genetic syndrome due to PGM2L1 deficiency. PGM2 and PGM2L1 make hexose-bisphosphates, like glucose-1,6-bisphosphate, which are indispensable cofactors for sugar phosphomutases. These enzymes form the hexose-1-phosphates crucial for NDP-sugars synthesis and ensuing glycosylation reactions. While PGM2 has a wide tissue distribution, PGM2L1 is highly expressed in the brain, accounting for the elevated concentrations of glucose-1,6-bisphosphate found there. Four individuals (three females and one male aged between 2 and 7.5 years) with bi-allelic inactivating mutations of PGM2L1 were identified by exome sequencing. All four had severe developmental and speech delay, dysmorphic facial features, ear anomalies, high arched palate, strabismus, hypotonia, and keratosis pilaris. Early obesity and seizures were present in three individuals. Analysis of the children's fibroblasts showed that glucose-1,6-bisphosphate and other sugar bisphosphates were markedly reduced but still present at concentrations able to stimulate phosphomutases maximally. Hence, the concentrations of NDP-sugars and glycosylation of the heavily glycosylated protein LAMP2 were normal. Consistent with this, serum transferrin was normally glycosylated in affected individuals. PGM2L1 deficiency does not appear to be a glycosylation defect, but the clinical features observed in this neurodevelopmental disorder point toward an important but still unknown role of glucose-1,6-bisphosphate or other sugar bisphosphates in brain metabolism.
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Affiliation(s)
- Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ulrich A Schatz
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Pernille M Torring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, MA 01199, USA
| | - Matthias Baumann
- Department of Pediatrics I, Division of Pediatric Neurology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark; Human Genetics, Faculty of Health, University of Southern Denmark, 5000 Odense, Denmark
| | | | | | - Martin Fleger
- Department of Pediatrics, Landeskrankenhaus Bregenz, 6900 Bregenz, Austria
| | - Tobias B Haack
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; Centre for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Stephen Nelson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Sven Potelle
- de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Silvia Radenkovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Metabolomics Expertise Center, VIB-KU Leuven, 3000 Leuven, Belgium
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Zhang Y, Fang W, Raimi OG, Lockhart DEA, Ferenbach AT, Lu L, van Aalten DMF. Genetic and structural validation of phosphomannomutase as a cell wall target in Aspergillus fumigatus. Mol Microbiol 2021; 116:245-259. [PMID: 33629421 DOI: 10.1111/mmi.14706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 11/29/2022]
Abstract
Aspergillus fumigatus is an opportunistic mold responsible for severe life-threatening fungal infections in immunocompromised patients. The cell wall, an essential structure composed of glucan, chitin, and galactomannan, is considered to be a target for the development of antifungal drugs. The nucleotide sugar donor GDP-mannose (GDP-Man) is required for the biosynthesis of galactomannan, glycosylphosphatidylinositol (GPI) anchors, glycolipid, and protein glycosylation. Starting from fructose-6-phosphate, GDP-Man is produced by the sequential action of the enzymes phosphomannose isomerase, phosphomannomutase (Pmm), and GDP-mannose pyrophosphorylase. Here, using heterokaryon rescue and gene knockdown approaches we demonstrate that the phosphomannomutase encoding gene in A. fumigatus (pmmA) is essential for survival. Reduced expression of pmmA is associated with significant morphological defects including retarded germination, growth, reduced conidiation, and abnormal polarity. Moreover, the knockdown strain exhibited an altered cell wall organization and sensitivity toward cell wall perturbing agents. By solving the first crystal structure of A. fumigatus phosphomannomutase (AfPmmA) we identified non-conservative substitutions near the active site when compared to the human orthologues. Taken together, this work provides a genetic and structural foundation for the exploitation of AfPmmA as a potential antifungal target.
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Affiliation(s)
- Yuanwei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Wenxia Fang
- School of Life Sciences, University of Dundee, Dundee, UK.,National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | | | | | | | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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