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Pollegioni L, Campanini B, Good JM, Motta Z, Murtas G, Buoli Comani V, Pavlidou DC, Mercier N, Mittaz-Crettol L, Sacchi S, Marchesani F. L-serine deficiency: on the properties of the Asn133Ser variant of human phosphoserine phosphatase. Sci Rep 2024; 14:12463. [PMID: 38816452 PMCID: PMC11139964 DOI: 10.1038/s41598-024-63164-y] [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: 01/12/2024] [Accepted: 05/26/2024] [Indexed: 06/01/2024] Open
Abstract
The non-essential amino acid L-serine is involved in a number of metabolic pathways and in the brain its level is largely due to the biosynthesis from the glycolytic intermediate D-3-phosphoglycerate by the phosphorylated pathway (PP). This cytosolic pathway is made by three enzymes proposed to generate a reversible metabolon named the "serinosome". Phosphoserine phosphatase (PSP) catalyses the last and irreversible step, representing the driving force pushing L-serine synthesis. Genetic defects of the PP enzymes result in strong neurological phenotypes. Recently, we identified the homozygous missense variant [NM_004577.4: c.398A > G p.(Asn133Ser)] in the PSPH, the PSP encoding gene, in two siblings with a neurodevelopmental syndrome and a myelopathy. The recombinant Asn133Ser enzyme does not show significant alterations in protein conformation and dimeric oligomerization state, as well as in enzymatic activity and functionality of the reconstructed PP. However, the Asn133Ser variant is less stable than wild-type PSP, a feature also apparent at cellular level. Studies on patients' fibroblasts also highlight a strong decrease in the level of the enzymes of the PP, a partial nuclear and perinuclear localization of variant PSP and a stronger perinuclear aggregates formation. We propose that these alterations contribute to the formation of a dysfunctional serinosome and thus to the observed reduction of L-serine, glycine and D-serine levels (the latter playing a crucial role in modulating NMDA receptors). The characterization of patients harbouring the Asn133Ser PSP substitution allows to go deep into the molecular mechanisms related to L-serine deficit and to suggest treatments to cope with the observed amino acids alterations.
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Affiliation(s)
- Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy.
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | | | - Despina-Christina Pavlidou
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Noëlle Mercier
- Department of Epileptology, Institution of Lavigny, Lavigny, Switzerland
| | - Laureane Mittaz-Crettol
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy
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2
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Marchesani F, Comani VB, Bruno S, Mozzarelli A, Carcelli M, Pollegioni L, Caldinelli L, Peracchi A, Campanini B. Effect of l-serine and magnesium ions on the functional properties of human phosphoserine phosphatase and its pathogenetic variants. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167034. [PMID: 38278334 DOI: 10.1016/j.bbadis.2024.167034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
L-Ser supply in the central nervous system of mammals mostly relies on its endogenous biosynthesis by the phosphorylated pathway (PP). Defects in any of the three enzymes operating in the pathway result in a group of neurometabolic diseases collectively known as serine deficiency disorders (SDDs). Phosphoserine phosphatase (PSP) catalyzes the last, irreversible step of the PP. Here we investigated in detail the role of physiological modulators of human PSP activity and the properties of three natural PSP variants (A35T, D32N and M52T) associated with SDDs. Our results, partially contradicting previous reports, indicate that: i. PSP is almost fully saturated with Mg2+ under physiological conditions and fluctuations in Mg2+ and Ca2+ concentrations are unlikely to play a modulatory role on PSP activity; ii. Inhibition by L-Ser, albeit at play on the isolated PSP, does not exert any effect on the flux through the PP unless the enzyme activity is severely impaired by inactivating substitutions; iii. The so-far poorly investigated A35T substitution was the most detrimental, with a 50-fold reduction in catalytic efficiency, and a reduction in thermal stability (as well as an increase in the IC50 for L-Ser). The M52T substitution had similar, but milder effects, while the D32N variant behaved like the wild-type enzyme. iv. Predictions of the structural effects of the A35T and M52T substitutions with ColabFold suggest that they might affect the structure of the flexible helix-loop region.
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Affiliation(s)
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
| | | | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Loredano Pollegioni
- The Protein Factory 2.0, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Laura Caldinelli
- The Protein Factory 2.0, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; Biopharmanet-TEC, University of Parma, 43124 Parma, Italy.
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3
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Gomes Rodrigues F, Pipis M, Heeren TFC, Fruttiger M, Gantner M, Vermeirsch S, Okada M, Friedlander M, Reilly MM, Egan C. Description of a patient cohort with Hereditary Sensory Neuropathy Type 1 without retinal disease Macular Telangiectasia type 2 - implications for retinal screening in HSN1. J Peripher Nerv Syst 2022; 27:215-224. [PMID: 35837722 DOI: 10.1111/jns.12508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND AIMS Pathogenic variants in the genes encoding serine palmitoyl transferase (SPTLC1 or SPTLC2) are the most common causes of the rare peripheral nerve disorder Hereditary Sensory Neuropathy Type 1 (HSN1). Macular telangiectasia type 2 (MacTel), a retinal disorder associated with disordered serine-glycine metabolism and has been described in some patients with HSN1. This study aims to further investigate this association in a cohort of people with HSN1. METHODS Fourteen patients with a clinically and genetically confirmed diagnosis of HSN1 from the National Hospital for Neurology and Neurosurgery (NHNN, University College London Hospitals NHS Foundation Trust, London, United Kingdom) were recruited to the MacTel Registry, between July 2018 and April 2019. Two additional patients were identified from the dataset of the international clinical registry study (www.lmri.net). Ocular examination included fundus autofluorescence, blue light and infrared reflectance, macular pigment optical density mapping, and optical coherence tomography. RESULTS Twelve patients had a pathogenic variant in the SPTLC1 gene, with p.Cys133Trp in eleven cases (92%) and p.Cys133Tyr in one case (8%). Four patients had a variant in the SPTLC2 gene. None of the patients showed clinical evidence of MacTel. INTERPRETATION The link between HSN1 and MacTel seems more complex than can solely be explained by the genetic variants. An extension of the spectrum of SPTLC1/2-related disease with phenotypic pleiotropy is proposed. HSN1 patients should be screened for visual symptoms and referred for specialist retinal screening, but the association of the two diseases is likely to be variable and remains unexplained. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Filipa Gomes Rodrigues
- Medical Retina Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,University College London Institute of Ophthalmology, London, UK.,Ophthalmology Department, Hospital de Vila Franca de Xira, Vila Franca de Xira, Portugal
| | - Menelaos Pipis
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Tjebo F C Heeren
- Medical Retina Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,University College London Institute of Ophthalmology, London, UK
| | - Marcus Fruttiger
- University College London Institute of Ophthalmology, London, UK
| | | | - Sandra Vermeirsch
- Medical Retina Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,University College London Institute of Ophthalmology, London, UK.,Hôpital ophtalmique Jules-Gonin, Fondation asile des aveugles, Université de Lausanne, Switzerland
| | - Mali Okada
- Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | | | - Mary M Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Catherine Egan
- Medical Retina Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,University College London Institute of Ophthalmology, London, UK
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4
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Marchesani F, Zangelmi E, Bruno S, Bettati S, Peracchi A, Campanini B. A Novel Assay for Phosphoserine Phosphatase Exploiting Serine Acetyltransferase as the Coupling Enzyme. Life (Basel) 2021; 11:life11060485. [PMID: 34073563 PMCID: PMC8229081 DOI: 10.3390/life11060485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 01/01/2023] Open
Abstract
Phosphoserine phosphatase (PSP) catalyzes the final step of de novo L-serine biosynthesis—the hydrolysis of phosphoserine to serine and inorganic phosphate—in humans, bacteria, and plants. In published works, the reaction is typically monitored through the discontinuous malachite green phosphate assay or, more rarely, through a continuous assay that couples phosphate release to the phosphorolysis of a chromogenic nucleoside by the enzyme purine nucleoside phosphorylase (PNP). These assays suffer from numerous drawbacks, and both rely on the detection of phosphate. We describe a new continuous assay that monitors the release of serine by exploiting bacterial serine acetyltransferase (SAT) as a reporter enzyme. SAT acetylates serine, consuming acetyl-CoA and releasing CoA-SH. CoA-SH spontaneously reacts with Ellman’s reagent to produce a chromophore that absorbs light at 412 nm. The catalytic parameters estimated through the SAT-coupled assay are fully consistent with those obtained with the published methods, but the new assay exhibits several advantages. Particularly, it depletes L-serine, thus allowing more prolonged linearity in the kinetics. Moreover, as the SAT-coupled assay does not rely on phosphate detection, it can be used to investigate the inhibitory effect of phosphate on PSP.
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Affiliation(s)
- Francesco Marchesani
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (F.M.); (S.B.)
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (F.M.); (S.B.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy;
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
- Correspondence: (A.P.); (B.C.); Tel.: +39-0521-905137 (A.P.); +39-0521-906333 (B.C.)
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (F.M.); (S.B.)
- Correspondence: (A.P.); (B.C.); Tel.: +39-0521-905137 (A.P.); +39-0521-906333 (B.C.)
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5
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Murtas G, Marcone GL, Sacchi S, Pollegioni L. L-serine synthesis via the phosphorylated pathway in humans. Cell Mol Life Sci 2020; 77:5131-5148. [PMID: 32594192 PMCID: PMC11105101 DOI: 10.1007/s00018-020-03574-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
L-serine is a nonessential amino acid in eukaryotic cells, used for protein synthesis and in producing phosphoglycerides, glycerides, sphingolipids, phosphatidylserine, and methylenetetrahydrofolate. Moreover, L-serine is the precursor of two relevant coagonists of NMDA receptors: glycine (through the enzyme serine hydroxymethyltransferase), which preferentially acts on extrasynaptic receptors and D-serine (through the enzyme serine racemase), dominant at synaptic receptors. The cytosolic "phosphorylated pathway" regulates de novo biosynthesis of L-serine, employing 3-phosphoglycerate generated by glycolysis and the enzymes 3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase (the latter representing the irreversible step). In the human brain, L-serine is primarily found in glial cells and is supplied to neurons for D-serine synthesis. Serine-deficient patients show severe neurological symptoms, including congenital microcephaly, psychomotor retardation, and intractable seizures, thus highlighting the relevance of de novo production of this amino acid in brain development and morphogenesis. Indeed, the phosphorylated pathway is strictly linked to cancer. Moreover, L-serine has been suggested as a ready-to-use treatment, as also recently proposed for Alzheimer's disease. Here, we present our current state of knowledge concerning the three mammalian enzymes of the phosphorylated pathway and known mutations related to pathological conditions: although the structure of these enzymes has been solved, how enzyme activity is regulated remains largely unknown. We believe that an in-depth investigation of these enzymes is crucial to identify the molecular mechanisms involved in modulating concentrations of the serine enantiomers and for studying the interplay between glial and neuronal cells and also to determine the most suitable therapeutic approach for various diseases.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy.
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6
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Bonelli R, Woods SM, Ansell BRE, Heeren TFC, Egan CA, Khan KN, Guymer R, Trombley J, Friedlander M, Bahlo M, Fruttiger M. Systemic lipid dysregulation is a risk factor for macular neurodegenerative disease. Sci Rep 2020; 10:12165. [PMID: 32699277 PMCID: PMC7376024 DOI: 10.1038/s41598-020-69164-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/07/2020] [Indexed: 01/01/2023] Open
Abstract
Macular Telangiectasia type 2 (MacTel) is an uncommon bilateral retinal disease, in which glial cell and photoreceptor degeneration leads to central vision loss. The causative disease mechanism is largely unknown, and no treatment is currently available. A previous study found variants in genes associated with glycine-serine metabolism (PSPH, PHGDH and CPS1) to be associated with MacTel, and showed low levels of glycine and serine in the serum of MacTel patients. Recently, a causative role of deoxysphingolipids in MacTel disease has been established. However, little is known about possible other metabolic dysregulation. Here we used a global metabolomics platform in a case-control study to comprehensively profile serum from 60 MacTel patients and 58 controls. Analysis of the data, using innovative computational approaches, revealed a detailed, disease-associated metabolic profile with broad changes in multiple metabolic pathways. This included alterations in the levels of several metabolites that are directly or indirectly linked to glycine-serine metabolism, further validating our previous genetic findings. We also found changes unrelated to PSPH, PHGDH and CPS1 activity. Most pronounced, levels of several lipid groups were altered, with increased phosphatidylethanolamines being the most affected lipid group. Assessing correlations between different metabolites across our samples revealed putative functional connections. Correlations between phosphatidylethanolamines and sphingomyelin, and glycine-serine and sphingomyelin, observed in controls, were reduced in MacTel patients, suggesting metabolic re-wiring of sphingomyelin metabolism in MacTel patients. Our findings provide novel insights into metabolic changes associated with MacTel and implicate altered lipid metabolism as a contributor to this retinal neurodegenerative disease.
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Affiliation(s)
- Roberto Bonelli
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Sasha M Woods
- UCL Institute of Ophthalmology, University College London, 11-43 Bath St, London, EC1V 9EL, UK
| | - Brendan R E Ansell
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tjebo F C Heeren
- UCL Institute of Ophthalmology, University College London, 11-43 Bath St, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, EC1, UK
| | - Catherine A Egan
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, EC1, UK
| | - Kamron N Khan
- The Leeds Teaching Hospitals NHS Trust, St. James's Hospital, Leeds, LS9 7TF, UK
| | - Robyn Guymer
- Department of Surgery, Center for Eye Research Australia, Royal Victorian Eye and Ear Hospital, and Ophthalmology, 32 Gisborne St, East Melbourne, VIC, 3002, Australia
| | | | - Martin Friedlander
- Lowy Medical Research Institute, La Jolla, CA, USA
- The Scripps Research Institute, La Jolla, CA, USA
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Marcus Fruttiger
- UCL Institute of Ophthalmology, University College London, 11-43 Bath St, London, EC1V 9EL, UK.
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7
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Abdelfattah F, Kariminejad A, Kahlert AK, Morrison PJ, Gumus E, Mathews KD, Darbro BW, Amor DJ, Walsh M, Sznajer Y, Weiß L, Weidensee S, Chitayat D, Shannon P, Bermejo-Sánchez E, Riaño-Galán I, Hayes I, Poke G, Rooryck C, Pennamen P, Khung-Savatovsky S, Toutain A, Vuillaume ML, Ghaderi-Sohi S, Kariminejad MH, Weinert S, Sticht H, Zenker M, Schanze D. Expanding the genotypic and phenotypic spectrum of severe serine biosynthesis disorders. Hum Mutat 2020; 41:1615-1628. [PMID: 32579715 DOI: 10.1002/humu.24067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
Serine biosynthesis disorders comprise a spectrum of very rare autosomal recessive inborn errors of metabolism with wide phenotypic variability. Neu-Laxova syndrome represents the most severe expression and is characterized by multiple congenital anomalies and pre- or perinatal lethality. Here, we present the mutation spectrum and a detailed phenotypic analysis in 15 unrelated families with severe types of serine biosynthesis disorders. We identified likely disease-causing variants in the PHGDH and PSAT1 genes, several of which have not been reported previously. Phenotype analysis and a comprehensive review of the literature corroborates the evidence that serine biosynthesis disorders represent a continuum with varying degrees of phenotypic expression and suggest that even gradual differences at the severe end of the spectrum may be correlated with particular genotypes. We postulate that the individual residual enzyme activity of mutant proteins is the major determinant of the phenotypic variability, but further functional studies are needed to explore effects at the enzyme protein level.
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Affiliation(s)
- Fatima Abdelfattah
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | | | - Anne-Karin Kahlert
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Patrick J Morrison
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Evren Gumus
- Division of Medical Genetics, School of Medicine, Harran University, Sanliurfa, Turkey
| | | | | | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Maie Walsh
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Luisa Weiß
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - David Chitayat
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for SickKids, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Eva Bermejo-Sánchez
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies (UIAC), Institute of Rare Diseases Research (IIER), Institute of Health Carlos III, Ministry of Science and Innovation, Madrid, Spain
| | - Isolina Riaño-Galán
- AGC de Pediatría, Hospital Universitario Central de Asturias, Oviedo, Spain.,IUOPA-Departamento de Medicina-ISPA, Universidad de Oviedo, Oviedo, Spain.,CIBER de Epidemiologia y Salud Pública, Madrid, Spain
| | - Ian Hayes
- Genetic Health Service New Zealand, Auckland Hospital, Auckland, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington Regional Hospital, Wellington, New Zealand
| | - Caroline Rooryck
- MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, University of Bordeaux, Bordeaux, France
| | - Perrine Pennamen
- MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, University of Bordeaux, Bordeaux, France
| | | | - Annick Toutain
- Service de Génétique, CHU de Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Marie-Laure Vuillaume
- Service de Génétique, CHU de Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | | | | | - Sönke Weinert
- Department of Cardiology and Angiology, Internal Medicine, University Hospital Magdeburg, Magdeburg, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
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8
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Leherte L, Haufroid M, Mirgaux M, Wouters J. Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:3958-3974. [PMID: 32448044 DOI: 10.1080/07391102.2020.1772883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The human phosphoserine phosphatase (hPSP) catalyses the last step in the biosynthesis of L-serine. It involves conformational changes of the enzyme lid once the substrate, phosphoserine (PSer), is bound in the active site. Here, Elastic Network Model (ENM) is applied to the crystal structure of hPSP to probe the transition between open and closed conformations of hPSP. Molecular Dynamics (MD) simulations are carried out on several PSer-hPSP systems to characterise the intermolecular interactions and their effect on the dynamics of the enzyme lid. Systems involving either Ca++ or Mg++ are considered. The first ENM normal mode shows that an open-closed transition can be explained from a simple description of the enzyme in terms of harmonic potentials. Principal Component Analyses applied to the MD trajectories also highlight a trend for a closing/opening motion. Different PSer orientations inside the enzyme cavity are identified, i.e. either the carboxylate, the phosphate group of PSer, or both, are oriented towards the cation. The interaction patterns are analysed in terms of hydrogen bonds, electrostatics, and bond critical points of the electron density distributions. The latter approach yields a global description of the bonding intermolecular interactions. The PSer orientation determines the content of the cation coordination shell and the mobility of the substrate, while Lys158 and Thr182, involved in the reaction mechanism, are always in interaction with the substrate. Closed enzyme conformations involve Met52-Gln204, Arg49-Glu29, and Arg50-Glu29 interactions. Met52, as well as Arg49 and Arg50, also stabilize PSer inside the cavity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laurence Leherte
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Marie Haufroid
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Manon Mirgaux
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
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9
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Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, Keinan A, Schimenti JC, Clark AG, Yu H. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nat Commun 2019; 10:4141. [PMID: 31515488 PMCID: PMC6742646 DOI: 10.1038/s41467-019-11959-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022] Open
Abstract
Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at > 1% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual's genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.
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Affiliation(s)
- Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shayne D Wierbowski
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jin Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tina N Tran
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Juan F Beltran
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Christen A Rivera-Erick
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kaixiong Ye
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Li Yao
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Xiaomu Wei
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alon Keinan
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - John C Schimenti
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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10
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Scerri TS, Quaglieri A, Cai C, Zernant J, Matsunami N, Baird L, Scheppke L, Bonelli R, Yannuzzi LA, Friedlander M, Egan CA, Fruttiger M, Leppert M, Allikmets R, Bahlo M. Genome-wide analyses identify common variants associated with macular telangiectasia type 2. Nat Genet 2017; 49:559-567. [DOI: 10.1038/ng.3799] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/31/2017] [Indexed: 02/07/2023]
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11
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El-Hattab AW. Serine biosynthesis and transport defects. Mol Genet Metab 2016; 118:153-159. [PMID: 27161889 DOI: 10.1016/j.ymgme.2016.04.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/20/2016] [Accepted: 04/20/2016] [Indexed: 11/23/2022]
Abstract
l-serine is a non-essential amino acid that is biosynthesized via the enzymes phosphoglycerate dehydrogenase (PGDH), phosphoserine aminotransferase (PSAT), and phosphoserine phosphatase (PSP). Besides its role in protein synthesis, l-serine is a potent neurotrophic factor and a precursor of a number of essential compounds including phosphatidylserine, sphingomyelin, glycine, and d-serine. Serine biosynthesis defects result from impairments of PGDH, PSAT, or PSP leading to systemic serine deficiency. Serine biosynthesis defects present in a broad phenotypic spectrum that includes, at the severe end, Neu-Laxova syndrome, a lethal multiple congenital anomaly disease, intermediately, infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end, the childhood disease with intellectual disability. A serine transport defect resulting from deficiency of the ASCT1, the main transporter for serine in the central nervous system, has been recently described in children with neurological manifestations that overlap with those observed in serine biosynthesis defects. l-serine therapy may be beneficial in preventing or ameliorating symptoms in serine biosynthesis and transport defects, if started before neurological damage occurs. Herein, we review serine metabolism and transport, the clinical, biochemical, and molecular aspects of serine biosynthesis and transport defects, the mechanisms of these diseases, and the potential role of serine therapy.
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates.
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12
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El-Hattab AW, Shaheen R, Hertecant J, Galadari HI, Albaqawi BS, Nabil A, Alkuraya FS. On the phenotypic spectrum of serine biosynthesis defects. J Inherit Metab Dis 2016; 39:373-381. [PMID: 26960553 DOI: 10.1007/s10545-016-9921-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 12/11/2022]
Abstract
L-serine is a non-essential amino acid that is de novo synthesized via the enzymes phosphoglycerate dehydrogenase (PGDH), phosphoserine aminotransferase (PSAT), and phosphoserine phosphatase (PSP). Besides its role in protein synthesis, L-serine is a precursor of a number of important compounds. Serine biosynthesis defects result from deficiencies in PGDH, PSAT, or PSP and have a broad phenotypic spectrum ranging from Neu-Laxova syndrome, a lethal multiple congenital anomaly disease at the severe end to a childhood disease with intellectual disability at the mild end, with infantile growth deficiency, and severe neurological manifestations as an intermediate phenotype. In this report, we present three subjects with serine biosynthesis effects. The first was a stillbirth with Neu-Laxova syndrome and a homozygous mutation in PHGDH. The second was a neonate with growth deficiency, microcephaly, ichthyotic skin lesions, seizures, contractures, hypertonia, distinctive facial features, and a homozygous mutation in PSAT1. The third subject was an infant with growth deficiency, microcephaly, ichthyotic skin lesions, anemia, hypertonia, distinctive facial features, low serine and glycine in plasma and CSF, and a novel homozygous mutation in PHGDH gene. Herein, we also review previous reports of serine biosynthesis defects and mutations in the PHGDH, PSAT1, and PSPH genes, discuss the variability in the phenotypes associated with serine biosynthesis defects, and elaborate on the vital roles of serine and the potential consequences of its deficiency.
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jozef Hertecant
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Hassan I Galadari
- Department of Internal Medicine, College of Medicine and Health Sciences, UAE University, Al-Ain, United Arab Emirates
| | - Badi S Albaqawi
- Women Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Amira Nabil
- Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
- College of Medicine, King Saud University, Riyadh, Saudi Arabia.
- Developmental Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
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13
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Novel Report of Phosphoserine Phosphatase Deficiency in an Adult with Myeloneuropathy and Limb Contractures. JIMD Rep 2015; 30:103-108. [PMID: 26589312 DOI: 10.1007/8904_2015_510] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/24/2015] [Accepted: 10/01/2015] [Indexed: 12/05/2022] Open
Abstract
Serine is a nonessential amino acid that plays a vital role in proper development and functioning of the central nervous system (CNS). Serine deficiency leads to microcephaly, intellectual disability, seizures, and psychomotor retardation in children and severe axonal neuropathy in adults. Serine deficiency syndrome is due to a deficiency of one of three enzymes in the endogenous serine biosynthesis pathway: phosphoglycerate dehydrogenase, phosphoserine transaminase, or, most rarely, phosphoserine phosphatase. Of critical importance to clinical care, serine deficiency syndrome is treatable. Herein, we describe the novel presentation of phosphoserine phosphatase deficiency in an adult. The patient had intrauterine growth restriction, lifelong intellectual disability, childhood onset epilepsy, and borderline microcephaly. In adulthood, she developed progressively severe lower extremity hypertonia, axonal neuropathy, and hand contractures. Neuropathy was complicated by non-healing wounds. Fasting plasma amino acids showed low serine and glycine. Molecular analysis revealed compound heterozygous mutations in phosphoserine phosphatase (PSPH). Treatment with oral serine resulted in improvement of plasma serine levels, decreased neuropathic pain, and subjective improvement in energy level. Although the first case of phosphoserine phosphatase deficiency was described nearly 20 years ago, only eight cases have been reported, all in children. This is the first report of phosphoserine phosphatase deficiency in an adult.
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14
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Acuna-Hidalgo R, Schanze D, Kariminejad A, Nordgren A, Kariminejad M, Conner P, Grigelioniene G, Nilsson D, Nordenskjöld M, Wedell A, Freyer C, Wredenberg A, Wieczorek D, Gillessen-Kaesbach G, Kayserili H, Elcioglu N, Ghaderi-Sohi S, Goodarzi P, Setayesh H, van de Vorst M, Steehouwer M, Pfundt R, Krabichler B, Curry C, MacKenzie M, Boycott K, Gilissen C, Janecke A, Hoischen A, Zenker M. Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway. Am J Hum Genet 2014; 95:285-93. [PMID: 25152457 DOI: 10.1016/j.ajhg.2014.07.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 07/24/2014] [Indexed: 11/24/2022] Open
Abstract
Neu-Laxova syndrome (NLS) is a rare autosomal-recessive disorder characterized by a recognizable pattern of severe malformations leading to prenatal or early postnatal lethality. Homozygous mutations in PHGDH, a gene involved in the first and limiting step in L-serine biosynthesis, were recently identified as the cause of the disease in three families. By studying a cohort of 12 unrelated families affected by NLS, we provide evidence that NLS is genetically heterogeneous and can be caused by mutations in all three genes encoding enzymes of the L-serine biosynthesis pathway. Consistent with recently reported findings, we could identify PHGDH missense mutations in three unrelated families of our cohort. Furthermore, we mapped an overlapping homozygous chromosome 9 region containing PSAT1 in four consanguineous families. This gene encodes phosphoserine aminotransferase, the enzyme for the second step in L-serine biosynthesis. We identified six families with three different missense and frameshift PSAT1 mutations fully segregating with the disease. In another family, we discovered a homozygous frameshift mutation in PSPH, the gene encoding phosphoserine phosphatase, which catalyzes the last step of L-serine biosynthesis. Interestingly, all three identified genes have been previously implicated in serine-deficiency disorders, characterized by variable neurological manifestations. Our findings expand our understanding of NLS as a disorder of the L-serine biosynthesis pathway and suggest that NLS represents the severe end of serine-deficiency disorders, demonstrating that certain complex syndromes characterized by early lethality could indeed be the extreme end of the phenotypic spectrum of already known disorders.
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15
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Vincent J, Jamil T, Rafiq M, Anwar Z, Ayaz M, Hameed A, Nasr T, Naeem F, Khattak N, Carter M, Ahmed I, John P, Wiame E, Andrade D, Schaftingen E, Mir A, Ayub M. Phosphoserine phosphatase (PSPH) gene mutation in an intellectual disability family from Pakistan. Clin Genet 2014; 87:296-8. [DOI: 10.1111/cge.12445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 11/29/2022]
Affiliation(s)
- J.B. Vincent
- Molecular Neuropsychiatry and Development (MiND) Laboratory, The Campbell Family Brain Research Institute; The Centre for Addiction and Mental Health (CAMH); Toronto ON Canada
- Department of Psychiatry; University of Toronto; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
| | - T. Jamil
- Human Molecular Genetics Laboratory, Department of Bioinformatics and Biotechnology, FBAS; International Islamic University; Islamabad Pakistan
| | - M.A. Rafiq
- Molecular Neuropsychiatry and Development (MiND) Laboratory, The Campbell Family Brain Research Institute; The Centre for Addiction and Mental Health (CAMH); Toronto ON Canada
| | - Z. Anwar
- Human Molecular Genetics Laboratory, Department of Bioinformatics and Biotechnology, FBAS; International Islamic University; Islamabad Pakistan
| | - M. Ayaz
- Lahore Institute of Research and Development; Lahore Pakistan
| | - A. Hameed
- Institute of Biomedical and Genetic Engineering; Islamabad Pakistan
| | - T. Nasr
- Mayo Hospital, Lahore and Chaudry Hospital; Gujranwala Pakistan
| | - F. Naeem
- Lahore Institute of Research and Development; Lahore Pakistan
- Department of Psychiatry; Queen's University; Kingston ON Canada
| | - N.A. Khattak
- Department of Biochemistry; PMAS-Arid Agriculture University; Rawalpindi Pakistan
| | - M. Carter
- Department of Pediatrics, Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto ON Canada
| | - I. Ahmed
- Molecular Neuropsychiatry and Development (MiND) Laboratory, The Campbell Family Brain Research Institute; The Centre for Addiction and Mental Health (CAMH); Toronto ON Canada
- Atta-ur-Rehman School of Applied Biosciences (ASAB); National University of Sciences and Technology (NUST); Islamabad Pakistan
| | - P. John
- Krembil Neuroscience Centre; Toronto Western Research Institute; Toronto Canada
| | - E. Wiame
- Laboratory of Physiological Chemistry, de Duve Institute; Université Catholique de Louvain; B-1200 Brussels Belgium
| | - D.M. Andrade
- Krembil Neuroscience Centre; Toronto Western Research Institute; Toronto Canada
- Division of Neurology, Department of Medicine; University or Toronto; Toronto ON Canada
| | - E.V. Schaftingen
- Laboratory of Physiological Chemistry, de Duve Institute; Université Catholique de Louvain; B-1200 Brussels Belgium
| | - A. Mir
- Human Molecular Genetics Laboratory, Department of Bioinformatics and Biotechnology, FBAS; International Islamic University; Islamabad Pakistan
| | - M. Ayub
- Lahore Institute of Research and Development; Lahore Pakistan
- Department of Psychiatry; Queen's University; Kingston ON Canada
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16
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Varvagiannis K, Papoulidis I, Koromila T, Kefalas K, Ziegler M, Liehr T, Petersen MB, Gyftodimou Y, Manolakos E. De novo 393 kb microdeletion of 7p11.2 characterized by aCGH in a boy with psychomotor retardation and dysmorphic features. Meta Gene 2014; 2:274-82. [PMID: 25606410 PMCID: PMC4287824 DOI: 10.1016/j.mgene.2014.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/08/2014] [Accepted: 03/17/2014] [Indexed: 01/03/2023] Open
Abstract
We report on a 27 month old boy presenting with psychomotor delay and dysmorphic features, mainly mild facial asymmetry, prominent cup-shaped ears, long eyelashes, open mouth appearance and slight abnormalities of the hands and feet. Array comparative genomic hybridization revealed a 393 kb microdeletion in 7p11.2. We discuss the possible involvement of CHCHD2, GBAS, MRPS17, SEPT14 and PSPH on our patient's phenotype. Additionally, we studied the expression of two other genes deleted in the patient, CCT6A and SUMF2, for which there is scarce data in the literature. Based on current knowledge and the de novo occurrence of this finding in our proband we presume that the aberration is likely to be pathogenic in our case. However, a single gene disorder, elsewhere in the genome or in this very region cannot be ruled out. Further elucidation of the properties of this chromosomal region, as well as of the role of the genes involved will be needed in order to draw safe conclusions regarding the association of the chromosomal deletion with the patient's features. We report in detail the clinical and cytogenetic findings of a 27-month old male. We compare our findings with current literature and online databases. We discuss the possible involvement of certain genes in our patient’s phenotype.
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Affiliation(s)
| | | | - Theodora Koromila
- Laboratory of Human Genetics, Department of Biology, University of Athens, Athens, Greece
| | | | - Monika Ziegler
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | | | | | - Emmanouil Manolakos
- Eurogenetica S.A., Laboratory of Genetics, Athens-Thessaloniki, Greece ; Cattedra di Genetica Medica, Ospedale Binaghi, Cagliari, Italy
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17
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Williams SR, Yang Q, Chen F, Liu X, Keene KL, Jacques P, Chen WM, Weinstein G, Hsu FC, Beiser A, Wang L, Bookman E, Doheny KF, Wolf PA, Zilka M, Selhub J, Nelson S, Gogarten SM, Worrall BB, Seshadri S, Sale MM. Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke. PLoS Genet 2014; 10:e1004214. [PMID: 24651765 PMCID: PMC3961178 DOI: 10.1371/journal.pgen.1004214] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 01/14/2014] [Indexed: 12/31/2022] Open
Abstract
Circulating homocysteine levels (tHcy), a product of the folate one carbon metabolism pathway (FOCM) through the demethylation of methionine, are heritable and are associated with an increased risk of common diseases such as stroke, cardiovascular disease (CVD), cancer and dementia. The FOCM is the sole source of de novo methyl group synthesis, impacting many biological and epigenetic pathways. However, the genetic determinants of elevated tHcy (hyperhomocysteinemia), dysregulation of methionine metabolism and the underlying biological processes remain unclear. We conducted independent genome-wide association studies and a meta-analysis of methionine metabolism, characterized by post-methionine load test tHcy, in 2,710 participants from the Framingham Heart Study (FHS) and 2,100 participants from the Vitamin Intervention for Stroke Prevention (VISP) clinical trial, and then examined the association of the identified loci with incident stroke in FHS. Five genes in the FOCM pathway (GNMT [p = 1.60 × 10(-63)], CBS [p = 3.15 × 10(-26)], CPS1 [p = 9.10 × 10(-13)], ALDH1L1 [p = 7.3 × 10(-13)] and PSPH [p = 1.17 × 10(-16)]) were strongly associated with the difference between pre- and post-methionine load test tHcy levels (ΔPOST). Of these, one variant in the ALDH1L1 locus, rs2364368, was associated with incident ischemic stroke. Promoter analyses reveal genetic and epigenetic differences that may explain a direct effect on GNMT transcription and a downstream affect on methionine metabolism. Additionally, a genetic-score consisting of the five significant loci explains 13% of the variance of ΔPOST in FHS and 6% of the variance in VISP. Association between variants in FOCM genes with ΔPOST suggest novel mechanisms that lead to differences in methionine metabolism, and possibly the epigenome, impacting disease risk. These data emphasize the importance of a concerted effort to understand regulators of one carbon metabolism as potential therapeutic targets.
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Affiliation(s)
- Stephen R. Williams
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States of America
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Fang Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Xuan Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Keith L. Keene
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
- Center for Health Disparities Research, East Carolina University, Greenville, North Carolina, United States of America
| | - Paul Jacques
- Jean Mayer USDA Human Nutrition Research Center on Aging and Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, United States of America
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Galit Weinstein
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Fang-Chi Hsu
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Alexa Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Ebony Bookman
- National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Kimberly F. Doheny
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Philip A. Wolf
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Michelle Zilka
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jacob Selhub
- Jean Mayer USDA Human Nutrition Research Center on Aging and Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, United States of America
| | - Sarah Nelson
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Stephanie M. Gogarten
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Bradford B. Worrall
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Neurology University of Virginia, Charlottesville, Virginia, United States of America
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Michèle M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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18
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van der Crabben SN, Verhoeven-Duif NM, Brilstra EH, Van Maldergem L, Coskun T, Rubio-Gozalbo E, Berger R, de Koning TJ. An update on serine deficiency disorders. J Inherit Metab Dis 2013; 36:613-9. [PMID: 23463425 DOI: 10.1007/s10545-013-9592-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 01/17/2013] [Accepted: 01/21/2013] [Indexed: 11/28/2022]
Abstract
Serine deficiency disorders are caused by a defect in one of the three synthesising enzymes of the L-serine biosynthesis pathway. Serine deficiency disorders give rise to a neurological phenotype with psychomotor retardation, microcephaly and seizures in newborns and children or progressive polyneuropathy in adult patients. There are three defects that cause serine deficiency of which 3-phosphoglycerate dehydrogenase (3-PGDH) deficiency, the defect affecting the first step in the pathway, has been reported most frequently. The other two disorders in L-serine biosynthesis phosphoserine aminotransferase (PSAT) deficiency and phosphoserine phosphatase (PSP) deficiency have been reported only in a limited number of patients. The biochemical hallmarks of all three disorders are low concentrations of serine in cerebrospinal fluid and plasma. Prompt recognition of affected patients is important, since serine deficiency disorders are treatable causes of neurometabolic disorders. The use of age-related reference values for serine in CSF and plasma can be of great help in establishing a correct diagnosis of serine deficiency, in particular in newborns and young children.
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Affiliation(s)
- S N van der Crabben
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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19
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Su G, Zhang X, Raine JC, Xing L, Higley E, Hecker M, Giesy JP, Yu H. Mechanisms of toxicity of triphenyltin chloride (TPTC) determined by a live cell reporter array. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:803-811. [PMID: 23128992 DOI: 10.1007/s11356-012-1280-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 09/24/2012] [Indexed: 06/01/2023]
Abstract
Triphenyltin chloride (TPTC), which has been extensively used in industry and agriculture, can occur at concentrations in the environment sufficient to be toxic. Here, potency of TPTC to modulate genes in a library containing 1,820 modified green fluorescent protein (GFP)-expressing promoter reporter vectors constructed from Escherichia coli K12 strains was determined. Exposure to TPTC resulted in 22 (fold change > 2) or 71 (fold change > 1.5) differentially expressed genes. The no observed transcriptional effect (NOTEC) and median transcriptional effect concentrations (TEC50) were determined to be 0.036 and 0.45 mg/L in E. coli. These responses were 1,230 and 97 times more sensitive than the acute median effect concentration (EC50) required to inhibit growth of cells, which demonstrated that this live cell array represents a sensitive method to assess toxic potency of chemicals. The 71 differentially expressed genes could be classified into seven functional groups. Of all the altered genes, three groups which encoded for catalytic enzymes, regulatory proteins, and structural proteins accounted for 28 %, 18 %, and 14 % of all altered genes, respectively. The pattern of differential expression observed during this study was used to elucidate the mechanism of toxicity of TPTC. To determine potential relationships among genes that were changed greater than 2.0-fold by exposure to TPTC, a correlation network analysis was constructed, and four genes were related to aroH, which is the primary target for metabolic regulation of aromatic biosynthesis by feedback inhibition in bacteria. The genes rnC, cld, and glgS were selected as potential biomarkers for TPTC, since their expression was more than 2.0-fold greater after exposure to TPTC.
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Affiliation(s)
- Guanyong Su
- State Key Laboratory of Pollution Control and Resource Reuse & School of the Environment, Nanjing University, Nanjing, China
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20
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Abstract
Defects in the synthesis pathways of amino acids have only been discovered in recent years and are relatively unknown to most clinicians. In this chapter disorders neurological symptoms caused by genetic defects in the synthesis of the amino acids serine, glutamine and proline are discussed. Patients with serine deficiency invariably suffer from severe neurological symptoms such as microcephaly, psychomotor retardation and intractable seizures. The same is true for patients with a defect in the synthesis of glutamine who present with hypotonia and epileptic encephalopathy. Patients with a disorder in the synthesis proline have mental retardation in combination with symptoms of connective tissue disease. All amino acids synthesis disorders, except for one of the proline defects, can be diagnosed by routine amino acid analysis. Given the fact that the disorder discussed here lead to deficiencies of amino acids opens up possibilities to treat these patients with the amino acids that can't be synthesised. Prompt recognition and treatment of amino acid synthesis disorders are of outmost importance to obtain satisfactory treatment results.
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Affiliation(s)
- T J de Koning
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
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21
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Seifried A, Schultz J, Gohla A. Human HAD phosphatases: structure, mechanism, and roles in health and disease. FEBS J 2012; 280:549-71. [PMID: 22607316 DOI: 10.1111/j.1742-4658.2012.08633.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phosphatases of the haloacid dehalogenase (HAD) superfamily of hydrolases are an ancient and very large class of enzymes that have evolved to dephosphorylate a wide range of low- and high molecular weight substrates with often exquisite specificities. HAD phosphatases constitute approximately one-fifth of all human phosphatase catalytic subunits. While the overall sequence similarity between HAD phosphatases is generally very low, family members can be identified based on the presence of a characteristic Rossmann-like fold and the active site sequence DxDx(V/T). HAD phosphatases employ an aspartate residue as a nucleophile in a magnesium-dependent phosphoaspartyl transferase reaction. Although there is genetic evidence demonstrating a causal involvement of some HAD phosphatases in diseases such as cancer, cardiovascular, metabolic and neurological disorders, the physiological roles of many of these enzymes are still poorly understood. In this review, we discuss the structure and evolution of human HAD phosphatases, and summarize their known functions in health and disease.
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Affiliation(s)
- Annegrit Seifried
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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22
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Solomon BD, Hadley DW, Pineda-Alvarez DE, Kamat A, Teer JK, Cherukuri PF, Hansen NF, Cruz P, Young AC, Berkman BE, Chandrasekharappa SC, Mullikin JC, Mullikin JC. Incidental medical information in whole-exome sequencing. Pediatrics 2012; 129:e1605-11. [PMID: 22585771 PMCID: PMC3362899 DOI: 10.1542/peds.2011-0080] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genomic technologies, such as whole-exome sequencing, are a powerful tool in genetic research. Such testing yields a great deal of incidental medical information, or medical information not related to the primary research target. We describe the management of incidental medical information derived from whole-exome sequencing in the research context. We performed whole-exome sequencing on a monozygotic twin pair in which only 1 child was affected with congenital anomalies and applied an institutional review board-approved algorithm to determine what genetic information would be returned. Whole-exome sequencing identified 79525 genetic variants in the twins. Here, we focus on novel variants. After filtering artifacts and excluding known single nucleotide polymorphisms and variants not predicted to be pathogenic, the twins had 32 novel variants in 32 genes that were felt to be likely to be associated with human disease. Eighteen of these novel variants were associated with recessive disease and 18 were associated with dominantly manifesting conditions (variants in some genes were potentially associated with both recessive and dominant conditions), but only 1 variant ultimately met our institutional review board-approved criteria for return of information to the research participants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Benjamin E. Berkman
- Department of Bioethics, Clinical Center, and Office of the Clinical Director, and
| | - Settara C. Chandrasekharappa
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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23
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Keularts IMLW, Leroy PLJM, Rubio-Gozalbo EM, Spaapen LJM, Weber B, Dorland B, de Koning TJ, Verhoeven-Duif NM. Fatal cerebral edema associated with serine deficiency in CSF. J Inherit Metab Dis 2010; 33 Suppl 3:S181-5. [PMID: 20300853 PMCID: PMC3757259 DOI: 10.1007/s10545-010-9067-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 02/04/2010] [Accepted: 02/09/2010] [Indexed: 11/17/2022]
Abstract
Two young girls without a notable medical history except for asthma presented with an acute toxic encephalopathy with very low serine concentrations both in plasma and cerebrospinal fluid (CSF) comparable to patients with 3-phosphoglycerate dehydrogenase (3-PGDH) deficiency. Clinical symptoms and enzyme measurement (in one patient) excluded 3-PGDH deficiency. Deficiencies in other serine biosynthesis enzymes were highly unlikely on clinical grounds. On basis of the fasting state, ketone bodies and lactate in plasma, urine and CSF, we speculate that reduced serine levels were due to its use as gluconeogenic substrate, conversion to pyruvate by brain serine racemase or decreased L-serine production because of a lack of glucose. These are the first strikingly similar cases of patients with a clear secondary serine deficiency associated with a toxic encephalopathy.
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Affiliation(s)
- Irene M L W Keularts
- Laboratory for Biochemical Genetics, Dept Clinical Genetics, Maastricht University Medical Center, P Debyelaan 25, 6229 HX Maastricht, The Netherlands.
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24
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Ozeki Y, Pickard BS, Kano SI, Malloy MP, Zeledon M, Sun DQ, Fujii K, Wakui K, Shirayama Y, Fukushima Y, Kunugi H, Hashimoto K, Muir WJ, Blackwood DH, Sawa A. A novel balanced chromosomal translocation found in subjects with schizophrenia and schizotypal personality disorder: altered l-serine level associated with disruption of PSAT1 gene expression. Neurosci Res 2010; 69:154-60. [PMID: 20955740 DOI: 10.1016/j.neures.2010.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 10/04/2010] [Accepted: 10/10/2010] [Indexed: 12/19/2022]
Abstract
l-Serine is required for the synthesis of glycine and d-serine, both of which are NMDA receptor co-agonists. Although roles for d-serine and glycine have been suggested in schizophrenia, little is known about the role of the l-serine synthesizing cascade in schizophrenia or related psychiatric conditions. Here we report a patient with schizophrenia carrying a balanced chromosomal translocation with the breakpoints localized to 3q13.12 and 9q21.2. We examined this proband and her son with schizotypal personality disorder for chromosomal abnormalities, molecular expression profiles, and serum amino acids. Marked decrease of l-serine and glutamate was observed in the sera of the patient and her son, compared with those in normal controls. Interestingly, expression of PSAT1 gene, which is located next to the breakpoint and encodes one of the enzymes in the l-serine synthesizing cascade, was reduced in both patient and her son. Direct effect of impaired PSAT1 gene expression on decreased serum l-serine level was strongly implicated by rat astrocyte experiments. In summary, we propose an idea that PSAT1 may be implicated in altered serine metabolism and schizophrenia spectrum conditions.
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Affiliation(s)
- Yuji Ozeki
- Department of Psychiatry, Dokkyo Medical University, Japan
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25
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Tabatabaie L, Klomp LW, Berger R, de Koning TJ. L-serine synthesis in the central nervous system: a review on serine deficiency disorders. Mol Genet Metab 2010; 99:256-62. [PMID: 19963421 DOI: 10.1016/j.ymgme.2009.10.012] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/16/2009] [Accepted: 10/16/2009] [Indexed: 10/20/2022]
Abstract
The de novo synthesis of the amino acid L-serine plays an essential role in the development and functioning of the central nervous system (CNS). L-serine displays many metabolic functions during different developmental stages; among its functions providing precursors for amino acids, protein synthesis, nucleotide synthesis, neurotransmitter synthesis and L-serine derived lipids. Patients with congenital defects in the L-serine synthesizing enzymes present with severe neurological abnormalities and underscore the importance of this synthetic pathway. In this review, we will discuss the cellular functions of the L-serine pathway, structure and enzymatic properties of the enzymes involved and genetic defects associated with this pathway.
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Affiliation(s)
- L Tabatabaie
- Department of Metabolic and Endocrine Diseases, University Medical Center Utrecht and Netherlands Metabolomics Centre, The Netherlands.
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26
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Antflick JE, Baker GB, Hampson DR. The effects of a low protein diet on amino acids and enzymes in the serine synthesis pathway in mice. Amino Acids 2009; 39:145-53. [PMID: 19921396 DOI: 10.1007/s00726-009-0387-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 10/30/2009] [Indexed: 11/30/2022]
Abstract
L-serine is required for cellular and tissue growth and is particularly important in the immature brain where it acts as a crucial neurotrophic factor. In this study, the levels of amino acids and enzymes in the L-serine biosynthetic pathway were examined in the forebrain, cerebellum, liver, and kidney after the exposure of mice to protein-restricted diets. The levels of L-serine, D-serine, and L-serine-O-phosphate were quantified by HPLC and quantitative Western blotting was used to measure changes in protein levels of five enzymes in the pathway. The L-serine biosynthetic enzyme phosphoserine phosphatase was strongly upregulated, while the serine degradative enzymes serine racemase and serine dehydratase were downregulated in the livers and kidneys of mice fed low (6%) or very low (2%) protein diets for 2 weeks compared with mice fed a normal diet (18% protein). No changes in these enzymes were seen in the brain. The levels of L-serine increased in the livers of mice fed 2% protein; in contrast, D-serine levels were reduced below the limit of detection in the livers of mice given either the 6 or 2% diets. D-Serine is a co-agonist at the NMDA class of glutamate receptors; no alterations in NMDA-R1 subunit expression were observed in liver or brain after protein restriction. These findings demonstrate that the expression of L-serine synthetic and degradative enzymes display reciprocal changes in the liver and kidney to increase L-serine and decrease D-serine levels under conditions of protein restriction, and that the brain is insulated from such changes.
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Affiliation(s)
- Jordan E Antflick
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
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27
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Tabatabaie L, de Koning TJ, Geboers AJJM, van den Berg IET, Berger R, Klomp LWJ. Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. Hum Mutat 2009; 30:749-56. [PMID: 19235232 DOI: 10.1002/humu.20934] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Three-phosphoglycerate dehydrogenase (3-PGDH) deficiency is a rare recessive inborn error in the biosynthesis of the amino acid L-serine characterized clinically by congenital microcephaly, psychomotor retardation, and intractable seizures. The biochemical abnormalities associated with this disorder are low concentrations of L-serine, D-serine, and glycine in cerebrospinal fluid (CSF). Only two missense mutations (p.V425M and p.V490M) have been identified in PHGDH, the gene encoding 3-PGDH, but it is currently unclear how these mutations in the carboxy-terminal regulatory domain of the protein affect enzyme function. We now describe five novel mutations in five patients with 3-PGDH deficiency; one frameshift mutation (p.G238fsX), and four missense mutations (p.R135W, p.V261M, p.A373T, and p.G377S). The missense mutations were located in the nucleotide binding and regulatory domains of 3-PGDH and did not affect steady-state expression, protein stability, and protein degradation rates. Patients' fibroblasts displayed a significant, but incomplete, reduction in maximal enzyme activities associated with all missense mutations. In transient overexpression studies in HEK293T cells, the p.A373T, p.V425M, and p.V490M mutations resulted in almost undetectable enzyme activities. Molecular modeling of the p.R135W and p.V261M mutations onto the partial crystal structure of 3-PGDH predicted that these mutations affect substrate and cofactor binding. This prediction was confirmed by the results of kinetic measurements in fibroblasts and transiently transfected HEK293T cells, which revealed a markedly decreased V(max) and an increase in K(m) values, respectively. Taken together, these data suggest that missense mutations associated with 3-PGDH deficiency either primarily affect substrate binding or result in very low residual enzymatic activity.
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Affiliation(s)
- L Tabatabaie
- Department of Metabolic and Endocrine Diseases, UMC Utrecht, and Netherlands Metabolomics Centre, The Netherlands
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28
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Hart CE, Race V, Achouri Y, Wiame E, Sharrard M, Olpin SE, Watkinson J, Bonham JR, Jaeken J, Matthijs G, Van Schaftingen E. Phosphoserine aminotransferase deficiency: a novel disorder of the serine biosynthesis pathway. Am J Hum Genet 2007; 80:931-7. [PMID: 17436247 PMCID: PMC1852735 DOI: 10.1086/517888] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/01/2007] [Indexed: 11/03/2022] Open
Abstract
We present the first two identified cases of phosphoserine aminotransferase deficiency. This disorder of serine biosynthesis has been identified in two siblings who showed low concentrations of serine and glycine in plasma and cerebrospinal fluid. Clinically, the index patient presented with intractable seizures, acquired microcephaly, hypertonia, and psychomotor retardation and died at age 7 mo despite supplementation with serine (500 mg/kg/d) and glycine (200 mg/kg/d) from age 11 wk. The younger sibling received treatment from birth, which led to a normal outcome at age 3 years. Measurement of phosphoserine aminotransferase activity in cultured fibroblasts in the index patient was inconclusive, but mutational analysis revealed compound heterozygosity for two mutations in the PSAT1 gene--one frameshift mutation (c.delG107) and one missense mutation (c.299A-->C [p.Asp100Ala])--in both siblings. Expression studies of the p.Asp100Ala mutant protein revealed a V(max) of only 15% of that of the wild-type protein.
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Affiliation(s)
- Claire E Hart
- Departments of Clinical Chemistry, Sheffield Children's Hospital, Sheffield, UK
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29
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de Koning TJ. Treatment with amino acids in serine deficiency disorders. J Inherit Metab Dis 2006; 29:347-51. [PMID: 16763900 DOI: 10.1007/s10545-006-0269-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2005] [Accepted: 03/13/2006] [Indexed: 11/24/2022]
Abstract
Serine deficiency disorders are rare defects in the biosynthesis of the amino acid L-serine. At present two disorders have been reported: 3-phosphoglycerate dehydrogenase deficiency and 3-phosphoserine phosphatase deficiency. These enzyme defects lead to severe neurological symptoms such as congenital microcephaly and severe psychomotor retardation and in addition in patients with 3-phosphoglycerate dehydrogenase deficiency to intractable seizures. These symptoms respond to a variable degree to treatment with L-serine, sometimes combined with glycine. In this paper the current practice of amino acid treatment with L-serine and glycine in serine deficiency is reviewed.
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Affiliation(s)
- T J de Koning
- Department of Metabolic Diseases, University Medical Centre Utrecht, KC 03.063.0, PO Box 85090, 3508 AB, Utrecht, The Netherlands.
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