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Timm S, Klaas N, Niemann J, Jahnke K, Alseekh S, Zhang Y, Souza PVL, Hou LY, Cosse M, Selinski J, Geigenberger P, Daloso DM, Fernie AR, Hagemann M. Thioredoxins o1 and h2 jointly adjust mitochondrial dihydrolipoamide dehydrogenase-dependent pathways towards changing environments. PLANT, CELL & ENVIRONMENT 2024; 47:2542-2560. [PMID: 38518065 DOI: 10.1111/pce.14899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/24/2024]
Abstract
Thioredoxins (TRXs) are central to redox regulation, modulating enzyme activities to adapt metabolism to environmental changes. Previous research emphasized mitochondrial and microsomal TRX o1 and h2 influence on mitochondrial metabolism, including photorespiration and the tricarboxylic acid (TCA) cycle. Our study aimed to compare TRX-based regulation circuits towards environmental cues mainly affecting photorespiration. Metabolite snapshots, phenotypes and CO2 assimilation were compared among single and multiple TRX mutants in the wild-type and the glycine decarboxylase T-protein knockdown (gldt1) background. Our analyses provided evidence for additive negative effects of combined TRX o1 and h2 deficiency on growth and photosynthesis. Especially metabolite accumulation patterns suggest a shared regulation mechanism mainly on mitochondrial dihydrolipoamide dehydrogenase (mtLPD1)-dependent pathways. Quantification of pyridine nucleotides, in conjunction with 13C-labelling approaches, and biochemical analysis of recombinant mtLPD1 supported this. It also revealed mtLPD1 inhibition by NADH, pointing at an additional measure to fine-tune it's activity. Collectively, we propose that lack of TRX o1 and h2 perturbs the mitochondrial redox state, which impacts on other pathways through shifts in the NADH/NAD+ ratio via mtLPD1. This regulation module might represent a node for simultaneous adjustments of photorespiration, the TCA cycle and branched chain amino acid degradation under fluctuating environmental conditions.
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Affiliation(s)
- Stefan Timm
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Nicole Klaas
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Janice Niemann
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Kathrin Jahnke
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Youjun Zhang
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Paulo V L Souza
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Liang-Yu Hou
- Department Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Maike Cosse
- Department of Plant Cell Biology, Botanical Institute, Christian-Albrechts University Kiel, Kiel, Germany
| | - Jennifer Selinski
- Department of Plant Cell Biology, Botanical Institute, Christian-Albrechts University Kiel, Kiel, Germany
| | - Peter Geigenberger
- Department Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Danilo M Daloso
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Martin Hagemann
- Plant Physiology Department, University of Rostock, Rostock, Germany
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Moore KH, Boitet LM, Chandrashekar DS, Traylor AM, Esman SK, Erman EN, Srivastava RK, Khan J, Athar M, Agarwal A, George JF. Cutaneous Arsenical Exposure Induces Distinct Metabolic Transcriptional Alterations of Kidney Cells. J Pharmacol Exp Ther 2024; 388:605-612. [PMID: 37699712 PMCID: PMC10801764 DOI: 10.1124/jpet.123.001742] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Arsenicals are deadly chemical warfare agents that primarily cause death through systemic capillary fluid leakage and hypovolemic shock. Arsenical exposure is also known to cause acute kidney injury, a condition that contributes to arsenical-associated death due to the necessity of the kidney in maintaining whole-body fluid homeostasis. Because of the global health risk that arsenicals pose, a nuanced understanding of how arsenical exposure can lead to kidney injury is needed. We used a nontargeted transcriptional approach to evaluate the effects of cutaneous exposure to phenylarsine oxide, a common arsenical, in a murine model. Here we identified an upregulation of metabolic pathways such as fatty acid oxidation, fatty acid biosynthesis, and peroxisome proliferator-activated receptor (PPAR)-α signaling in proximal tubule epithelial cell and endothelial cell clusters. We also revealed highly upregulated genes such as Zbtb16, Cyp4a14, and Pdk4, which are involved in metabolism and metabolic switching and may serve as future therapeutic targets. The ability of arsenicals to inhibit enzymes such as pyruvate dehydrogenase has been previously described in vitro. This, along with our own data, led us to conclude that arsenical-induced acute kidney injury may be due to a metabolic impairment in proximal tubule and endothelial cells and that ameliorating these metabolic effects may lead to the development of life-saving therapies. SIGNIFICANCE STATEMENT: In this study, we demonstrate that cutaneous arsenical exposure leads to a transcriptional shift enhancing fatty acid metabolism in kidney cells, indicating that metabolic alterations might mechanistically link topical arsenical exposure to acute kidney injury. Targeting metabolic pathways may generate promising novel therapeutic approaches in combating arsenical-induced acute kidney injury.
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Affiliation(s)
- Kyle H Moore
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Laurence M Boitet
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Darshan S Chandrashekar
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Amie M Traylor
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Stephanie K Esman
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Elise N Erman
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Ritesh K Srivastava
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Jasim Khan
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Mohammad Athar
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - Anupam Agarwal
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
| | - James F George
- Division of Nephrology, Department of Medicine (K.H.M., A.M.T., S.K.E., E.N.E., A.A.), Nephrology Research and Training Center (K.H.M., L.M.B., A.A., J.F.G.), Division of Cardiothoracic Surgery, Department of Surgery (K.H.M., E.N.E., J.F.G.), Molecular and Cellular Pathology, Department of Pathology (D.S.C.), Genomic Diagnostics and Bioinformatics, Department of Pathology (D.S.C.), and Research Center of Excellence in Arsenicals, Department of Dermatology, School of Medicine (R.K.S., J.K., M.A.), University of Alabama at Birmingham, Birmingham, Alabama
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3
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Liu J, Zhang H, Xu Y, Meng H, Zeng AP. Turn air-captured CO 2 with methanol into amino acid and pyruvate in an ATP/NAD(P)H-free chemoenzymatic system. Nat Commun 2023; 14:2772. [PMID: 37188719 DOI: 10.1038/s41467-023-38490-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
The use of gaseous and air-captured CO2 for technical biosynthesis is highly desired, but elusive so far due to several obstacles including high energy (ATP, NADPH) demand, low thermodynamic driving force and limited biosynthesis rate. Here, we present an ATP and NAD(P)H-free chemoenzymatic system for amino acid and pyruvate biosynthesis by coupling methanol with CO2. It relies on a re-engineered glycine cleavage system with the NAD(P)H-dependent L protein replaced by biocompatible chemical reduction of protein H with dithiothreitol. The latter provides a higher thermodynamic driving force, determines the reaction direction, and avoids protein polymerization of the rate-limiting enzyme carboxylase. Engineering of H protein to effectively release the lipoamide arm from a protected state further enhanced the system performance, achieving the synthesis of glycine, serine and pyruvate at g/L level from methanol and air-captured CO2. This work opens up the door for biosynthesis of amino acids and derived products from air.
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Affiliation(s)
- Jianming Liu
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China
| | - Han Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China
| | - Yingying Xu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Hao Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - An-Ping Zeng
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China.
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4
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Arribas-Carreira L, Dallabona C, Swanson MA, Farris J, Østergaard E, Tsiakas K, Hempel M, Aquaviva-Bourdain C, Koutsoukos S, Stence NV, Magistrati M, Spector EB, Kronquist K, Christensen M, Karstensen HG, Feichtinger RG, Achleitner MT, Lawrence Merritt II J, Pérez B, Ugarte M, Grünewald S, Riela AR, Julve N, Arnoux JB, Haldar K, Donnini C, Santer R, Lund AM, Mayr JA, Rodriguez-Pombo P, Van Hove JLK. Pathogenic variants in GCSH encoding the moonlighting H-protein cause combined nonketotic hyperglycinemia and lipoate deficiency. Hum Mol Genet 2023; 32:917-933. [PMID: 36190515 PMCID: PMC9990993 DOI: 10.1093/hmg/ddac246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/09/2022] [Accepted: 09/26/2022] [Indexed: 11/14/2022] Open
Abstract
Maintaining protein lipoylation is vital for cell metabolism. The H-protein encoded by GCSH has a dual role in protein lipoylation required for bioenergetic enzymes including pyruvate dehydrogenase and 2-ketoglutarate dehydrogenase, and in the one-carbon metabolism through its involvement in glycine cleavage enzyme system, intersecting two vital roles for cell survival. Here, we report six patients with biallelic pathogenic variants in GCSH and a broad clinical spectrum ranging from neonatal fatal glycine encephalopathy to an attenuated phenotype of developmental delay, behavioral problems, limited epilepsy and variable movement problems. The mutational spectrum includes one insertion c.293-2_293-1insT, one deletion c.122_(228 + 1_229-1) del, one duplication of exons 4 and 5, one nonsense variant p.Gln76*and four missense p.His57Arg, p.Pro115Leu and p.Thr148Pro and the previously described p.Met1?. Via functional studies in patient's fibroblasts, molecular modeling, expression analysis in GCSH knockdown COS7 cells and yeast, and in vitro protein studies, we demonstrate for the first time that most variants identified in our cohort produced a hypomorphic effect on both mitochondrial activities, protein lipoylation and glycine metabolism, causing combined deficiency, whereas some missense variants affect primarily one function only. The clinical features of the patients reflect the impact of the GCSH changes on any of the two functions analyzed. Our analysis illustrates the complex interplay of functional and clinical impact when pathogenic variants affect a multifunctional protein involved in two metabolic pathways and emphasizes the value of the functional assays to select the treatment and investigate new personalized options.
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Affiliation(s)
- Laura Arribas-Carreira
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Institute for Molecular Biology-IUBM, Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Michael A Swanson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Joseph Farris
- Boler-Parseghian Center for Rare and Neglected Disease, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- Department of Biology, Saginaw Valley State University, University Center, MI, USA
| | - Elsebet Østergaard
- Centre for Inherited Metabolic Diseases, Departments of Clinical Genetics and Pediatrics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Cecile Aquaviva-Bourdain
- Service Biochimie et Biologie Moléculaire, UM Pathologies Héréditaires du Métabolisme et du Globule Rouge, Centre de Biologie Est, CHU de Lyon, Lyon, France
| | - Stefanos Koutsoukos
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | | | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Elaine B Spector
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
- Molecular Genetics Lab, Precision DX, Children's Hospital Colorado, Aurora, CO, USA
| | - Kathryn Kronquist
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
- Molecular Genetics Lab, Precision DX, Children's Hospital Colorado, Aurora, CO, USA
| | - Mette Christensen
- Centre for Inherited Metabolic Diseases, Departments of Clinical Genetics and Pediatrics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Helena G Karstensen
- Centre for Inherited Metabolic Diseases, Departments of Clinical Genetics and Pediatrics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - René G Feichtinger
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Melanie T Achleitner
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | | | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Institute for Molecular Biology-IUBM, Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Institute for Molecular Biology-IUBM, Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain
| | | | | | - Natalia Julve
- Department of Pediatrics, IMED Valencia Hospital, Valencia, Spain
| | - Jean-Baptiste Arnoux
- Centre de Reference des Maladies Hereditaires, Necker Enfants Malades, Paris, France
| | - Kasturi Haldar
- Boler-Parseghian Center for Rare and Neglected Disease, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Allan M Lund
- Centre for Inherited Metabolic Diseases, Departments of Clinical Genetics and Pediatrics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Johannes A Mayr
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Pilar Rodriguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Institute for Molecular Biology-IUBM, Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
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5
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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6
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Xu Y, Ren J, Wang W, Zeng A. Improvement of glycine biosynthesis from one-carbon compounds and ammonia catalyzed by the glycine cleavage system in vitro. Eng Life Sci 2022; 22:40-53. [PMID: 35024026 PMCID: PMC8727733 DOI: 10.1002/elsc.202100047] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/26/2022] Open
Abstract
Glycine cleavage system (GCS) plays a central role in one-carbon (C1) metabolism and receives increasing interest as a core part of the recently proposed reductive glycine pathway (rGlyP) for assimilation of CO2 and formate. Despite decades of research, GCS has not yet been well understood and kinetic data are barely available. This is to a large degree because of the complexity of GCS, which is composed of four proteins (H, T, P, and L) and catalyzes reactions involving different substrates and cofactors. In vitro kinetics of reconstructed microbial multi-enzyme glycine cleavage/synthase system is desired to better implement rGlyP in microorganisms like Escherichia coli for the use of C1 resources. Here, we examined in vitro several factors that may affect the rate of glycine synthesis via the reverse GCS reaction. We found that the ratio of GCS component proteins has a direct influence on the rate of glycine synthesis, namely higher ratios of P protein and especially H protein to T and L proteins are favorable, and the carboxylation reaction catalyzed by P protein is a key step determining the glycine synthesis rate, whereas increasing the ratio of L protein to other GCS proteins does not have significant effect and the ratio of T protein to other GCS proteins should be kept low. The effect of substrate concentrations on glycine synthesis is quite complex, showing interdependence with the ratios of GCS component proteins. Furthermore, adding the reducing agent dithiothreitol to the reaction mixture not only results in great tolerance to high concentration of formaldehyde, but also increases the rate of glycine synthesis, probably due to its functions in activating P protein and taking up the role of L protein in the non-enzymatic reduction of Hox to Hred. Moreover, the presence of some monovalent and divalent metal ions can have either positive or negative effect on the rate of glycine synthesis, depending on their type and their concentration.
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Affiliation(s)
- Yingying Xu
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijingP. R. China
| | - Jie Ren
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijingP. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri‐product Quality and SafetyMinistry of AgricultureInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingP. R. China
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyHamburgGermany
| | - An‐Ping Zeng
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijingP. R. China
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyHamburgGermany
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7
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Understanding and Engineering Glycine Cleavage System and Related Metabolic Pathways for C1-Based Biosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:273-298. [DOI: 10.1007/10_2021_186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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da Fonseca-Pereira P, Souza PVL, Fernie AR, Timm S, Daloso DM, Araújo WL. Thioredoxin-mediated regulation of (photo)respiration and central metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5987-6002. [PMID: 33649770 DOI: 10.1093/jxb/erab098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Thioredoxins (TRXs) are ubiquitous proteins engaged in the redox regulation of plant metabolism. Whilst the light-dependent TRX-mediated activation of Calvin-Benson cycle enzymes is well documented, the role of extraplastidial TRXs in the control of the mitochondrial (photo)respiratory metabolism has been revealed relatively recently. Mitochondrially located TRX o1 has been identified as a regulator of alternative oxidase, enzymes of, or associated with, the tricarboxylic acid (TCA) cycle, and the mitochondrial dihydrolipoamide dehydrogenase (mtLPD) involved in photorespiration, the TCA cycle, and the degradation of branched chain amino acids. TRXs are seemingly a major point of metabolic regulation responsible for activating photosynthesis and adjusting mitochondrial photorespiratory metabolism according to the prevailing cellular redox status. Furthermore, TRX-mediated (de)activation of TCA cycle enzymes contributes to explain the non-cyclic flux mode of operation of this cycle in illuminated leaves. Here we provide an overview on the decisive role of TRXs in the coordination of mitochondrial metabolism in the light and provide in silico evidence for other redox-regulated photorespiratory enzymes. We further discuss the consequences of mtLPD regulation beyond photorespiration and provide outstanding questions that should be addressed in future studies to improve our understanding of the role of TRXs in the regulation of central metabolism.
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Affiliation(s)
| | - Paulo V L Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stefan Timm
- University of Rostock, Plant Physiology Department, Albert- Einstein-Str. 3, Rostock, Germany
| | - Danilo M Daloso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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9
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mTORC1 activity regulates post-translational modifications of glycine decarboxylase to modulate glycine metabolism and tumorigenesis. Nat Commun 2021; 12:4227. [PMID: 34244482 PMCID: PMC8270999 DOI: 10.1038/s41467-021-24321-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/09/2021] [Indexed: 11/08/2022] Open
Abstract
Glycine decarboxylase (GLDC) is a key enzyme of glycine cleavage system that converts glycine into one-carbon units. GLDC is commonly up-regulated and plays important roles in many human cancers. Whether and how GLDC is regulated by post-translational modifications is unknown. Here we report that mechanistic target of rapamycin complex 1 (mTORC1) signal inhibits GLDC acetylation at lysine (K) 514 by inducing transcription of the deacetylase sirtuin 3 (SIRT3). Upon inhibition of mTORC1, the acetyltransferase acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes GLDC K514 acetylation. This acetylation of GLDC impairs its enzymatic activity. In addition, this acetylation of GLDC primes for its K33-linked polyubiquitination at K544 by the ubiquitin ligase NF-X1, leading to its degradation by the proteasomal pathway. Finally, we find that GLDC K514 acetylation inhibits glycine catabolism, pyrimidines synthesis and glioma tumorigenesis. Our finding reveals critical roles of post-translational modifications of GLDC in regulation of its enzymatic activity, glycine metabolism and tumorigenesis, and provides potential targets for therapeutics of cancers such as glioma.
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10
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Guo J, Gong BQ, Li JF. Arabidopsis lysin motif/F-box-containing protein InLYP1 fine-tunes glycine metabolism by degrading glycine decarboxylase GLDP2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:394-408. [PMID: 33506579 DOI: 10.1111/tpj.15171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Lysin motif (LysM) is a carbohydrate-binding module often found in secreted or transmembrane proteins in living organisms from prokaryotes to eukaryotes. Thus far, all characterized LysM-containing proteins in plants are plasma membrane-resident receptors or co-receptors playing roles in plant-microbe interactions. Here, we interrogate the Arabidopsis LysM/F-box-containing protein InLYP1 and reveal its function in glycine metabolism. InLYP1 was mainly expressed by vigorously growing tissues, encoding a nuclear-cytoplasmic protein. We validated InLYP1 as part of the SKP1-CULLIN1-F-box E3 complex for mediating protein degradation. The glycine decarboxylase P-protein 1 (GLDP1) was identified as an InLYP1-interacting protein by both immunoprecipitation/mass spectrometry and yeast two-hybrid library screening. InLYP1 could also interact with GLDP2, a paralog of GLDP1 with weaker catalytic activity, and could mediate the degradation of GLDP2 but not GLDP1. Interestingly, both GLDPs could be O-glycosylated and form homodimers or heterodimers. Overexpression of InLYP1L9A encoding a dominant-negative variant could cause seedling germination retardation on the medium containing glycine. Collectively, these results shed light on the function of plant intracellular LysM-containing proteins, and suggest that InLYP1 may deplete GLDP2 to facilitate glycine decarboxylation in Arabidopsis.
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Affiliation(s)
- Jianhang Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ben-Qiang Gong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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11
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Farris J, Alam MS, Rajashekara AM, Haldar K. Genomic analyses of glycine decarboxylase neurogenic mutations yield a large-scale prediction model for prenatal disease. PLoS Genet 2021; 17:e1009307. [PMID: 33524012 PMCID: PMC7850488 DOI: 10.1371/journal.pgen.1009307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 11/18/2022] Open
Abstract
Hundreds of mutations in a single gene result in rare diseases, but why mutations induce severe or attenuated states remains poorly understood. Defect in glycine decarboxylase (GLDC) causes Non-ketotic Hyperglycinemia (NKH), a neurological disease associated with elevation of plasma glycine. We unified a human multiparametric NKH mutation scale that separates severe from attenuated neurological disease with new in silico tools for murine and human genome level-analyses, gathered in vivo evidence from mice engineered with top-ranking attenuated and a highly pathogenic mutation, and integrated the data in a model of pre- and post-natal disease outcomes, relevant for over a hundred major and minor neurogenic mutations. Our findings suggest that highly severe neurogenic mutations predict fatal, prenatal disease that can be remedied by metabolic supplementation of dams, without amelioration of persistent plasma glycine. The work also provides a systems approach to identify functional consequences of mutations across hundreds of genetic diseases. Our studies provide a new framework for a large scale understanding of mutation functions and the prediction that severity of a neurogenic mutation is a direct measure of pre-natal disease in neurometabolic NKH mouse models. This framework can be extended to analyses of hundreds of monogenetic rare disorders where the underlying genes are known but understanding of the vast majority of mutations and why and how they cause disease, has yet to be realized. Building models of human genetic disease, both computational and animal, is an essential part of understanding the disease, designing treatments, and testing therapies. Here, we have developed new in silico tools to build models for the rare neurological disorder non-ketotic hyperglycinemia (NKH), which is caused by mutations in glycine decarboxylase (GLDC), a protein that degrades glycine. We first applied a mutation scoring tool to GLDC in both the human and mouse genomes, and then used this data to develop a computational model for predicting which mutations would be well-modeled in mice, and how severe their disease would be. We then validated this computational model by genetically-engineering a mutation predicted to cause mild disease and another predicted to cause severe disease. Our predictions were correct and we used them to develop a model relevant for over a hundred major and minor neurogenic mutations that suggests that the more severe the mutation, the greater chance it will cause disease that starts before birth and is likely to be fatal unless rescued by modifying diet. This study also demonstrates the power of in silico analyses for guiding the development of genetic disease models and incorporating them into scalable models that can be applied to understand hundreds of mutations that cause disease.
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Affiliation(s)
- Joseph Farris
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
| | - Md Suhail Alam
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
| | - Arpitha Mysore Rajashekara
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
| | - Kasturi Haldar
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
- * E-mail:
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12
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Wittmiß M, Mikkat S, Hagemann M, Bauwe H. Stoichiometry of two plant glycine decarboxylase complexes and comparison with a cyanobacterial glycine cleavage system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:801-813. [PMID: 32311173 DOI: 10.1111/tpj.14773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
The multienzyme glycine cleavage system (GCS) converts glycine and tetrahydrofolate to the one-carbon compound 5,10-methylenetetrahydrofolate, which is of vital importance for most if not all organisms. Photorespiring plant mitochondria contain very high levels of GCS proteins organised as a fragile glycine decarboxylase complex (GDC). The aim of this study is to provide mass spectrometry-based stoichiometric data for the plant leaf GDC and examine whether complex formation could be a general property of the GCS in photosynthesizing organisms. The molar ratios of the leaf GDC component proteins are 1L2 -4P2 -8T-26H and 1L2 -4P2 -8T-20H for pea and Arabidopsis, respectively, as determined by mass spectrometry. The minimum mass of the plant leaf GDC ranges from 1550 to 1650 kDa, which is larger than previously assumed. The Arabidopsis GDC contains four times more of the isoforms GCS-P1 and GCS-L1 in comparison with GCS-P2 and GCS-L2, respectively, whereas the H-isoproteins GCS-H1 and GCS-H3 are fully redundant as indicated by their about equal amounts. Isoform GCS-H2 is not present in leaf mitochondria. In the cyanobacterium Synechocystis sp. PCC 6803, GCS proteins concentrations are low but above the complex formation threshold reported for pea leaf GDC. Indeed, formation of a cyanobacterial GDC from the individual recombinant GCS proteins in vitro could be demonstrated. Presence and metabolic significance of a Synechocystis GDC in vivo remain to be examined but could involve multimers of the GCS H-protein that dynamically crosslink the three GCS enzyme proteins, facilitating glycine metabolism by the formation of multienzyme metabolic complexes. Data are available via ProteomeXchange with identifier PXD018211.
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Affiliation(s)
- Maria Wittmiß
- Department of Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical Center, Schilling-Allee 69, D-18057, Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Hermann Bauwe
- Department of Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
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13
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Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity. PLoS Comput Biol 2020; 16:e1007871. [PMID: 32421718 PMCID: PMC7259800 DOI: 10.1371/journal.pcbi.1007871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 04/13/2020] [Indexed: 12/14/2022] Open
Abstract
Monogenetic diseases provide unique opportunity for studying complex, clinical states that underlie neurological severity. Loss of glycine decarboxylase (GLDC) can severely impact neurological development as seen in non-ketotic hyperglycinemia (NKH). NKH is a neuro-metabolic disorder lacking quantitative predictors of disease states. It is characterized by elevation of glycine, seizures and failure to thrive, but glycine reduction often fails to confer neurological benefit, suggesting need for alternate tools to distinguish severe from attenuated disease. A major challenge has been that there are 255 unique disease-causing missense mutations in GLDC, of which 206 remain entirely uncharacterized. Here we report a Multiparametric Mutation Score (MMS) developed by combining in silico predictions of stability, evolutionary conservation and protein interaction models and suitable to assess 251 of 255 mutations. In addition, we created a quantitative scale of clinical disease severity comprising of four major disease domains (seizure, cognitive failure, muscular and motor control and brain-malformation) to comprehensively score patient symptoms identified in 131 clinical reports published over the last 15 years. The resulting patient Clinical Outcomes Scores (COS) were used to optimize the MMS for biological and clinical relevance and yield a patient Weighted Multiparametric Mutation Score (WMMS) that separates severe from attenuated neurological disease (p = 1.2 e-5). Our study provides understanding for developing quantitative tools to predict clinical severity of neurological disease and a clinical scale that advances monitoring disease progression needed to evaluate new treatments for NKH. Neurodegenerative disorders frequently have diverse, severe symptoms and health outcomes that can be difficult to predict. The rare disease non-ketotic hyperglycinemia (NKH) additionally has a wide range of disease-causing mutations in glycine decarboxylase (GLDC), a protein that breaks down glycine. But measuring glycine is not sufficient to foretell disease outcome. A method to predict whether a mutation will cause severe or more mild forms of NKH would be very helpful to both understanding the disease as well as developing treatments for it. We used computation-based approaches to develop a mutation score that comprehensively predicts how mutations decrease GLDC function. After training against clinical data, the score was able to predict whether a mutation will cause severe or attenuated disease. This study utilizes the power of computational and multidisciplinary analyses to advance understanding and treatment of genetically caused neurodegenerative diseases.
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14
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Frukh A, Siddiqi TO, Khan MIR, Ahmad A. Modulation in growth, biochemical attributes and proteome profile of rice cultivars under salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:55-70. [PMID: 31733605 DOI: 10.1016/j.plaphy.2019.11.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/06/2019] [Accepted: 11/06/2019] [Indexed: 05/06/2023]
Abstract
One of the major abiotic stresses that affect productivity of rice is salinity. Rice cultivars showed significant genetic variation in response to salt stress. In the present investigation, differential growth pattern and physio-chemical traits-based screening of high yielding rice cultivars of various salt affected areas of India was carried out, and salt-sensitive and salt-tolerant cultivars were identified. Differential responses of antioxidant enzyme activity and tolerance index at maximum level of salt treatment depicted that Jhelum and Vytilla-4 cultivars of rice were sensitive and tolerant to salt stress, respectively. Analysis of growth, morpho-physiological, and biochemical parameters also confirmed the salt-tolerant and salt-sensitive characters of cv. Vytilla-4 and cv. Jhelum, respectively. Nano-LCMS/MS-based proteome profile of these two cultivars was carried out to find out the mechanism lying behind the salt tolerance. A total number of 514 and 770 protein spots were reported in the most salt-tolerant (cv. Vytilla-4) and salt-sensitive (cv. Jhelum) cultivars, respectively. The differentially expressed proteins (DEPs) were found associated with major metabolic pathways including photosynthesis, energy metabolism, amino acid metabolism, nitrogen assimilation and stress and signalling pathways. The changes in the major proteins like Ribulose bisphosphate carboxylase small chain, chlorophyll a-b binding protein, phosphoglycerate kinase, cytochrome c oxidase subunit 5C, glutamine synthetase, glutathione S-transferase, peroxidase, and thioredoxin elucidated the mechanism activated by salt-tolerant cv. Vytilla-4. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the proteomic results. Outcomes of this work could help in finding out the potential cross-links of different pathways involved in salt-tolerance mechanisms operating in the studied here rice cultivars under salt stress.
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Affiliation(s)
- Arajmand Frukh
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Tariq Omar Siddiqi
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - M Iqbal R Khan
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
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15
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Florez-Sarasa I, Obata T, Del-Saz NSFN, Reichheld JP, Meyer EH, Rodriguez-Concepcion M, Ribas-Carbo M, Fernie AR. The Lack of Mitochondrial Thioredoxin TRXo1 Affects In Vivo Alternative Oxidase Activity and Carbon Metabolism under Different Light Conditions. PLANT & CELL PHYSIOLOGY 2019; 60:2369-2381. [PMID: 31318380 DOI: 10.1093/pcp/pcz123] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/17/2019] [Indexed: 05/04/2023]
Abstract
The alternative oxidase (AOX) constitutes a nonphosphorylating pathway of electron transport in the mitochondrial respiratory chain that provides flexibility to energy and carbon primary metabolism. Its activity is regulated in vitro by the mitochondrial thioredoxin (TRX) system which reduces conserved cysteines residues of AOX. However, in vivo evidence for redox regulation of the AOX activity is still scarce. In the present study, the redox state, protein levels and in vivo activity of the AOX in parallel to photosynthetic parameters were determined in Arabidopsis knockout mutants lacking mitochondrial trxo1 under moderate (ML) and high light (HL) conditions, known to induce in vivo AOX activity. In addition, 13C- and 14C-labeling experiments together with metabolite profiling were performed to better understand the metabolic coordination between energy and carbon metabolism in the trxo1 mutants. Our results show that the in vivo AOX activity is higher in the trxo1 mutants at ML while the AOX redox state is apparently unaltered. These results suggest that mitochondrial thiol redox systems are responsible for maintaining AOX in its reduced form rather than regulating its activity in vivo. Moreover, the negative regulation of the tricarboxylic acid cycle by the TRX system is coordinated with the increased input of electrons into the AOX pathway. Under HL conditions, while AOX and photosynthesis displayed similar patterns in the mutants, photorespiration is restricted at the level of glycine decarboxylation most likely as a consequence of redox imbalance.
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Affiliation(s)
- Igor Florez-Sarasa
- Max-Planck-Institut f�r Molekulare Pflanzenphysiologie, Am M�hlenberg 1, Potsdam-Golm, Germany
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Toshihiro Obata
- Max-Planck-Institut f�r Molekulare Pflanzenphysiologie, Am M�hlenberg 1, Potsdam-Golm, Germany
- University of Nebraska Lincoln, 1901 Vine Street, Lincoln, NE, USA
| | - Nï Stor Fernï Ndez Del-Saz
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterranies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, Palma de Mallorca, Spain
- Departamento de Bot�nica, Facultad de Ciencias Naturales y Oceanogr�ficas, Universidad de Concepci�n, Concepci�n, Chile
| | | | - Etienne H Meyer
- Max-Planck-Institut f�r Molekulare Pflanzenphysiologie, Am M�hlenberg 1, Potsdam-Golm, Germany
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Miquel Ribas-Carbo
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterranies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, Palma de Mallorca, Spain
| | - Alisdair R Fernie
- Max-Planck-Institut f�r Molekulare Pflanzenphysiologie, Am M�hlenberg 1, Potsdam-Golm, Germany
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16
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Reinholdt O, Schwab S, Zhang Y, Reichheld JP, Fernie AR, Hagemann M, Timm S. Redox-Regulation of Photorespiration through Mitochondrial Thioredoxin o1. PLANT PHYSIOLOGY 2019; 181:442-457. [PMID: 31413204 PMCID: PMC6776843 DOI: 10.1104/pp.19.00559] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/30/2019] [Indexed: 05/02/2023]
Abstract
Photorespiration sustains photosynthesis in the presence of oxygen due to rapid metabolization of 2-phosphoglycolate, the major side-product of the oxygenase activity of Rubisco that also directly impedes carbon assimilation and allocation. Despite the fact that both the biochemical reactions and the underlying genetics are well characterized, information concerning the regulatory mechanisms that adjust photorespiratory flux is rare. Here, we studied the impact of mitochondrial-localized thioredoxin o1 (TRXo1) on photorespiratory metabolism. The characterization of an Arabidopsis (Arabidopsis thaliana) transfer DNA insertional line (trxo1-1) revealed an increase in the stoichiometry of photorespiratory CO2 release and impaired Gly-to-Ser turnover after a shift from high-to-low CO2 without changes in Gly decarboxylase (GDC) gene or protein expression. These effects were distinctly pronounced in a double mutant, where the TRXo1 mutation was combined with strongly reduced GDC T-protein expression. The double mutant (TxGT) showed reduced growth in air but not in high CO2, decreased photosynthesis, and up to 54-fold more Gly alongside several redox-stress-related metabolites. Given that GDC proteins are potential targets for redox-regulation, we also examined the in vitro properties of recombinant GDC l-proteins (lipoamide dehydrogenase) from plants and the cyanobacterium Synechocystis species strain PCC6803 and observed a redox-dependent inhibition by either artificial reducing agents or TRXo1 itself. Collectively, our results demonstrate that TRXo1 potentially adjusts photorespiration via redox-regulation of GDC in response to environmental changes.
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Affiliation(s)
- Ole Reinholdt
- University of Rostock, Plant Physiology Department, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
| | - Saskia Schwab
- University of Rostock, Plant Physiology Department, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
| | - Youjun Zhang
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Martin Hagemann
- University of Rostock, Plant Physiology Department, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
| | - Stefan Timm
- University of Rostock, Plant Physiology Department, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
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17
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Riediger M, Kadowaki T, Nagayama R, Georg J, Hihara Y, Hess WR. Biocomputational Analyses and Experimental Validation Identify the Regulon Controlled by the Redox-Responsive Transcription Factor RpaB. iScience 2019; 15:316-331. [PMID: 31103851 PMCID: PMC6525291 DOI: 10.1016/j.isci.2019.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 11/24/2022] Open
Abstract
Oxygenic photosynthesis requires the coordination of environmental stimuli with the regulation of transcription. The transcription factor RpaB is conserved from the simplest unicellular cyanobacteria to complex eukaryotic algae, representing more than 1 billion years of evolution. To predict the RpaB-controlled regulon in the cyanobacterium Synechocystis, we analyzed the positional distribution of binding sites together with high-resolution mapping data of transcriptional start sites (TSSs). We describe more than 150 target promoters whose activity responds to fluctuating light conditions. Binding sites close to the TSS mediate repression, whereas sites centered ∼50 nt upstream mediate activation. Using complementary experimental approaches, we found that RpaB controls genes involved in photoprotection, cyclic electron flow and state transitions, photorespiration, and nirA and isiA for which we suggest cross-regulation with the transcription factors NtcA or FurA. The deep integration of RpaB with diverse photosynthetic gene functions makes it one of the most important and versatile transcriptional regulators. RpaB controls a complex regulon, widely beyond the photosynthetic machinery The expression of the RNA regulators IsrR, PsrR1, and others depends on RpaB RpaB exhibits cross-regulations with other transcription factors, NtcA and Fur RpaB is a crucial transcriptional regulator in a photosynthetic microorganism
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Affiliation(s)
- Matthias Riediger
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Ryuta Nagayama
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Jens Georg
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany.
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18
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Rossignoli G, Grottesi A, Bisello G, Montioli R, Borri Voltattorni C, Paiardini A, Bertoldi M. Cysteine 180 Is a Redox Sensor Modulating the Activity of Human Pyridoxal 5'-Phosphate Histidine Decarboxylase. Biochemistry 2018; 57:6336-6348. [PMID: 30346159 DOI: 10.1021/acs.biochem.8b00625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histidine decarboxylase is a pyridoxal 5'-phosphate enzyme catalyzing the conversion of histidine to histamine, a bioactive molecule exerting its role in many modulatory processes. The human enzyme is involved in many physiological functions, such as neurotransmission, gastrointestinal track function, cell growth, and differentiation. Here, we studied the functional properties of the human enzyme and, in particular, the effects exerted at the protein level by two cysteine residues: Cys-180 and Cys-418. Surprisingly, the enzyme exists in an equilibrium between a reduced and an oxidized form whose extent depends on the redox state of Cys-180. Moreover, we determined that (i) the two enzymatic redox species exhibit modest structural changes in the coenzyme microenvironment and (ii) the oxidized form is slightly more active and stable than the reduced one. These data are consistent with the model proposed by bioinformatics analyses and molecular dynamics simulations in which the Cys-180 redox state could be responsible for a structural transition affecting the C-terminal domain reorientation leading to active site alterations. Furthermore, the biochemical properties of the purified C180S and C418S variants reveal that C180S behaves like the reduced form of the wild-type enzyme, while C418S is sensitive to reductants like the wild-type enzyme, thus allowing the identification of Cys-180 as the redox sensitive switch. On the other hand, Cys-418 appears to be a residue involved in aggregation propensity. A possible role for Cys-180 as a regulatory switch in response to different cellular redox conditions could be suggested.
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Affiliation(s)
- Giada Rossignoli
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | | | - Giovanni Bisello
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | - Carla Borri Voltattorni
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli" , University "La Sapienza", Rome , P.zale A. Moro 5 , 00185 Roma , Italy
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
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Keech O, Gardeström P, Kleczkowski LA, Rouhier N. The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations. PLANT, CELL & ENVIRONMENT 2017; 40:553-569. [PMID: 26791824 DOI: 10.1111/pce.12713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/28/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
Photorespiration is a complex and tightly regulated process occurring in photosynthetic organisms. This process can alter the cellular redox balance, notably via the production and consumption of both reducing and oxidizing equivalents. Under certain circumstances, these equivalents, as well as reactive oxygen or nitrogen species, can become prominent in subcellular compartments involved in the photorespiratory process, eventually promoting oxidative post-translational modifications of proteins. Keeping these changes under tight control should therefore be of primary importance. In order to review the current state of knowledge about the redox control of photorespiration, we primarily performed a careful description of the known and potential redox-regulated or oxidation sensitive photorespiratory proteins, and examined in more details two interesting cases: the glycerate kinase and the glycine cleavage system. When possible, the potential impact and subsequent physiological regulations associated with these changes have been discussed. In the second part, we reviewed the extent to which photorespiration contributes to cellular redox homeostasis considering, in particular, the set of peripheral enzymes associated with the canonical photorespiratory pathway. Finally, some recent biotechnological strategies to circumvent photorespiration for future growth improvements are discussed in the light of these redox regulations.
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Affiliation(s)
- Olivier Keech
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | - Per Gardeström
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | | | - Nicolas Rouhier
- INRA, UMR 1136 Interactions Arbres/Microorganismes, Centre INRA Nancy Lorraine, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, 54506, Vandoeuvre-lès-Nancy, France
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20
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Bravo-Alonso I, Navarrete R, Arribas-Carreira L, Perona A, Abia D, Couce ML, García-Cazorla A, Morais A, Domingo R, Ramos MA, Swanson MA, Van Hove JLK, Ugarte M, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P. Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease. Hum Mutat 2017; 38:678-691. [PMID: 28244183 DOI: 10.1002/humu.23208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 11/08/2022]
Abstract
The rapid analysis of genomic data is providing effective mutational confirmation in patients with clinical and biochemical hallmarks of a specific disease. This is the case for nonketotic hyperglycinemia (NKH), a Mendelian disorder causing seizures in neonates and early-infants, primarily due to mutations in the GLDC gene. However, understanding the impact of missense variants identified in this gene is a major challenge for the application of genomics into clinical practice. Herein, a comprehensive functional and structural analysis of 19 GLDC missense variants identified in a cohort of 26 NKH patients was performed. Mutant cDNA constructs were expressed in COS7 cells followed by enzymatic assays and Western blot analysis of the GCS P-protein to assess the residual activity and mutant protein stability. Structural analysis, based on molecular modeling of the 3D structure of GCS P-protein, was also performed. We identify hypomorphic variants that produce attenuated phenotypes with improved prognosis of the disease. Structural analysis allows us to interpret the effects of mutations on protein stability and catalytic activity, providing molecular evidence for clinical outcome and disease severity. Moreover, we identify an important number of mutants whose loss-of-functionality is associated with instability and, thus, are potential targets for rescue using folding therapeutic approaches.
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Affiliation(s)
- Irene Bravo-Alonso
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
| | - Laura Arribas-Carreira
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
| | | | - David Abia
- Servicio de Bioinformática, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - María Luz Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Service of Neonatology, Department of Pediatrics, Hospital Clínico Universitario de Santiago, CIBERER, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Angels García-Cazorla
- Institut de Recerca Pediàtrica-Hospital Sant Joan de Déu (IRP-HSJD), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Ana Morais
- Unidad de Nutrición Infantil y Enfermedades Metabólicas, Hospital Universitario Infantil La Paz, Madrid, Spain
| | - Rosario Domingo
- Servicio de Pediatría, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - María Antonia Ramos
- Servicio de Genética, Hospital B del Complejo Hospitalario de Navarra, Pamplona, Navarra, Spain
| | - Michael A Swanson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, Colorado
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, Colorado
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
| | - Celia Pérez-Cerdá
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, CBM-CSIC, Departamento de Biología Molecular, Universidad Autónoma Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIPAZ, Madrid, Spain
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21
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Smolko A, Šupljika F, Martinčić J, Jajčanin-Jozić N, Grabar-Branilović M, Tomić S, Ludwig-Müller J, Piantanida I, Salopek-Sondi B. The role of conserved Cys residues in Brassica rapa auxin amidohydrolase: Cys139 is crucial for the enzyme activity and Cys320 regulates enzyme stability. Phys Chem Chem Phys 2017; 18:8890-900. [PMID: 26959939 DOI: 10.1039/c5cp06301a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Brassica rapa auxin amidohydrolase (BrILL2) participates in the homeostasis of the plant hormones auxins by hydrolyzing the amino acid conjugates of auxins, thereby releasing the free active form of hormones. Herein, the potential role of the two conserved Cys residues of BrILL2 (at sequence positions 139 and 320) has been investigated by using interdisciplinary approaches and methods of molecular biology, biochemistry, biophysics and molecular modelling. The obtained results show that both Cys residues participate in the regulation of enzyme activity. Cys320 located in the satellite domain of the enzyme is mainly responsible for protein stability and regulation of enzyme activity through polymer formation, as has been revealed by enzyme kinetics and differential scanning calorimetry analysis of the BrILL2 wild type and mutants C320S and C139S. Cys139 positioned in the active site of the catalytic domain is involved in the coordination of one Mn(2+) ion of the bimetal center and is crucial for the enzymatic activity. Although the point mutation Cys139 to Ser causes the loss of enzyme activity, it does not affect the metal binding to the BrILL2 enzyme, as has been shown by isothermal titration calorimetry, circular dichroism spectropolarimetry and differential scanning calorimetry data. MD simulations (200 ns) revealed a different active site architecture of the BrILL2C139S mutant in comparison to the wild type enzyme. Additional possible reasons for the inactivity of the BrILL2C139S mutant have been discussed based on MD simulations and MM-PBSA free energy calculations of BrILL2 enzyme complexes (wt and C139S mutant) with IPA-Ala as a substrate.
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Affiliation(s)
- Ana Smolko
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Filip Šupljika
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Jelena Martinčić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Nina Jajčanin-Jozić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | | | - Sanja Tomić
- Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | | | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
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22
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Loviglio MN, Beck CR, White JJ, Leleu M, Harel T, Guex N, Niknejad A, Bi W, Chen ES, Crespo I, Yan J, Charng WL, Gu S, Fang P, Coban-Akdemir Z, Shaw CA, Jhangiani SN, Muzny DM, Gibbs RA, Rougemont J, Xenarios I, Lupski JR, Reymond A. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Med 2016; 8:105. [PMID: 27799067 PMCID: PMC5088687 DOI: 10.1186/s13073-016-0359-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/16/2016] [Indexed: 02/13/2023] Open
Abstract
Background Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. Methods We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes. Results Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1–/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1–/– mouse model. Conclusions These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Nicla Loviglio
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marion Leleu
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicolas Guex
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Anne Niknejad
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Crespo
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Jiong Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Laboratory Medicine Program, UHN, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 2C4, Canada
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Fang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: WuXiNextCODE, 101Main Street, Cambridge, MA, 02142, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacques Rougemont
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
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23
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Abstract
Sesamin is one of the major lignans found in sesame oil. Although some microbial metabolites of sesamin have been identified, sesamin-metabolic pathways remain uncharacterized at both the enzyme and gene levels. Here, we isolated microorganisms growing on sesamin as a sole-carbon source. One microorganism showing significant sesamin-degrading activity was identified as Sinomonas sp. no. 22. A sesamin-metabolizing enzyme named SesA was purified from this strain and characterized. SesA catalyzed methylene group transfer from sesamin or sesamin monocatechol to tetrahydrofolate (THF) with ring cleavage, yielding sesamin mono- or di-catechol and 5,10-methylenetetrahydrofolate. The kinetic parameters of SesA were determined to be as follows: Km for sesamin = 0.032 ± 0.005 mM, Vmax = 9.3 ± 0.4 (μmol⋅min(-1)⋅mg(-1)), and kcat = 7.9 ± 0.3 s(-1) Next, we investigated the substrate specificity. SesA also showed enzymatic activity toward (+)-episesamin, (-)-asarinin, sesaminol, (+)-sesamolin, and piperine. Growth studies with strain no. 22, and Western blot analysis revealed that SesA formation is inducible by sesamin. The deduced amino acid sequence of sesA exhibited weak overall sequence similarity to that of the protein family of glycine cleavage T-proteins (GcvTs), which catalyze glycine degradation in most bacteria, archaea, and all eukaryotes. Only SesA catalyzes C1 transfer to THF with ring cleavage reaction among GcvT family proteins. Moreover, SesA homolog genes are found in both Gram-positive and Gram-negative bacteria. Our findings provide new insights into microbial sesamin metabolism and the function of GcvT family proteins.
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24
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Zhu L, Zhang YH, Su F, Chen L, Huang T, Cai YD. A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana. PLoS One 2016; 11:e0159519. [PMID: 27434024 PMCID: PMC4951011 DOI: 10.1371/journal.pone.0159519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.
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Affiliation(s)
- Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Fangchu Su
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
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25
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The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT. Genet Med 2016; 19:104-111. [PMID: 27362913 DOI: 10.1038/gim.2016.74] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/25/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The study's purpose was to delineate the genetic mutations that cause classic nonketotic hyperglycinemia (NKH). METHODS Genetic results, parental phase, ethnic origin, and gender data were collected from subjects suspected to have classic NKH. Mutations were compared with those in the existing literature and to the population frequency from the Exome Aggregation Consortium (ExAC) database. RESULTS In 578 families, genetic analyses identified 410 unique mutations, including 246 novel mutations. 80% of subjects had mutations in GLDC. Missense mutations were noted in 52% of all GLDC alleles, most private. Missense mutations were 1.5 times as likely to be pathogenic in the carboxy terminal of GLDC than in the amino-terminal part. Intragenic copy-number variations (CNVs) in GLDC were noted in 140 subjects, with biallelic CNVs present in 39 subjects. The position and frequency of the breakpoint for CNVs correlated with intron size and presence of Alu elements. Missense mutations, most often recurring, were the most common type of disease-causing mutation in AMT. Sequencing and CNV analysis identified biallelic pathogenic mutations in 98% of subjects. Based on genotype, 15% of subjects had an attenuated phenotype. The frequency of NKH is estimated at 1:76,000. CONCLUSION The 484 unique mutations now known in classic NKH provide a valuable overview for the development of genotype-based therapies.Genet Med 19 1, 104-111.
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Structure of the PLP-Form of the Human Kynurenine Aminotransferase II in a Novel Spacegroup at 1.83 Å Resolution. Int J Mol Sci 2016; 17:446. [PMID: 27023527 PMCID: PMC4848902 DOI: 10.3390/ijms17040446] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/10/2016] [Accepted: 03/22/2016] [Indexed: 11/16/2022] Open
Abstract
Kynurenine aminotransferase II (KAT-II) is a 47 kDa pyridoxal phosphate (PLP)-dependent enzyme, active as a homodimer, which catalyses the transamination of the amino acids kynurenine (KYN) and 3-hydroxykynurenine (3-HK) in the tryptophan pathway, and is responsible for producing metabolites that lead to kynurenic acid (KYNA), which is implicated in several neurological diseases such as schizophrenia. In order to fully describe the role of KAT-II in the pathobiology of schizophrenia and other brain disorders, the crystal structure of full-length PLP-form hKAT-II was determined at 1.83 Å resolution, the highest available. The electron density of the active site reveals an aldimine linkage between PLP and Lys263, as well as the active site residues, which characterize the fold-type I PLP-dependent enzymes.
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27
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Swanson MA, Coughlin CR, Scharer GH, Szerlong HJ, Bjoraker KJ, Spector EB, Creadon-Swindell G, Mahieu V, Matthijs G, Hennermann JB, Applegarth DA, Toone JR, Tong S, Williams K, Van Hove JLK. Biochemical and molecular predictors for prognosis in nonketotic hyperglycinemia. Ann Neurol 2015; 78:606-18. [PMID: 26179960 PMCID: PMC4767401 DOI: 10.1002/ana.24485] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 12/22/2022]
Abstract
Objective Nonketotic hyperglycinemia is a neurometabolic disorder characterized by intellectual disability, seizures, and spasticity. Patients with attenuated nonketotic hyperglycinemia make variable developmental progress. Predictive factors have not been systematically assessed. Methods We reviewed 124 patients stratified by developmental outcome for biochemical and molecular predictive factors. Missense mutations were expressed to quantify residual activity using a new assay. Results Patients with severe nonketotic hyperglycinemia required multiple anticonvulsants, whereas patients with developmental quotient (DQ) > 30 did not require anticonvulsants. Brain malformations occurred mainly in patients with severe nonketotic hyperglycinemia (71%) but rarely in patients with attenuated nonketotic hyperglycinemia (7.5%). Neonatal presentation did not correlate with outcome, but age at onset ≥ 4 months was associated with attenuated nonketotic hyperglycinemia. Cerebrospinal fluid (CSF) glycine levels and CSF:plasma glycine ratio correlated inversely with DQ; CSF glycine > 230 μM indicated severe outcome and CSF:plasma glycine ratio ≤ 0.08 predicted attenuated outcome. The glycine index correlated strongly with outcome. Molecular analysis identified 99% of mutant alleles, including 96 novel mutations. Mutations near the active cleft of the P‐protein maintained stable protein levels. Presence of 1 mutation with residual activity was necessary but not sufficient for attenuated outcome; 2 such mutations conferred best outcome. Divergent outcomes for the same genotype indicate a contribution of other genetic or nongenetic factors. Interpretation Accurate prediction of outcome is possible in most patients. A combination of 4 factors available neonatally predicted 78% of severe and 49% of attenuated patients, and a score based on mutation severity predicted outcome with 70% sensitivity and 97% specificity. Ann Neurol 2015;78:606–618
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Affiliation(s)
| | | | | | | | | | | | | | - Vincent Mahieu
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Julia B Hennermann
- Department of Pediatric and Adolescent Medicine, University Medical Center Mainz, Mainz, Germany
| | - Derek A Applegarth
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer R Toone
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suhong Tong
- Department of Pediatrics, University of Colorado, Aurora, CO
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Go MK, Zhang WC, Lim B, Yew WS. Glycine Decarboxylase Is an Unusual Amino Acid Decarboxylase Involved in Tumorigenesis. Biochemistry 2014; 53:947-56. [DOI: 10.1021/bi4014227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Maybelle Kho Go
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Wen Cai Zhang
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Bing Lim
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Wen Shan Yew
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
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