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Barroso M, Puchwein-Schwepcke A, Buettner L, Goebel I, Küchler K, Muntau AC, Delgado A, Garcia-Collazo AM, Martinell M, Barril X, Cubero E, Gersting SW. Use of the Novel Site-Directed Enzyme Enhancement Therapy (SEE-Tx) Drug Discovery Platform to Identify Pharmacological Chaperones for Glutaric Acidemia Type 1. J Med Chem 2024. [PMID: 39312412 DOI: 10.1021/acs.jmedchem.4c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Allosteric regulators acting as pharmacological chaperones hold promise for innovative therapeutics since they target noncatalytic sites and stabilize the folded protein without competing with the natural substrate, resulting in a net gain of function. Exogenous allosteric regulators are typically more selective than active site inhibitors and can be more potent than competitive inhibitors when the natural substrate levels are high. To identify novel structure-targeted allosteric regulators (STARs) that bind to and stabilize the mitochondrial enzyme glutaryl-CoA dehydrogenase (GCDH), the computational site-directed enzyme enhancement therapy (SEE-Tx) technology was applied. SEE-Tx is an innovative drug discovery platform with the potential to identify drugs for treating protein misfolding disorders, such as glutaric acidemia type 1 (GA1) disease. Putative allosteric regulators were discovered using structure- and ligand-based virtual screening methods and validated using orthogonal biophysical and biochemical assays. The computational approach presented here could be used to discover allosteric regulators of other protein misfolding disorders.
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Affiliation(s)
- Madalena Barroso
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Alexandra Puchwein-Schwepcke
- Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich 80337, Germany
- Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital Basel, UKBB, Basel 4031, Switzerland
| | - Lars Buettner
- Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss 88397, Germany
| | - Ingrid Goebel
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Katrin Küchler
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
- German Center for Child and Adolescent Health (DZKJ), Partner Site Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Aida Delgado
- Gain Therapeutics Sucursal en España, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ana M Garcia-Collazo
- Gain Therapeutics Sucursal en España, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Marc Martinell
- Minoryx Therapeutics S.L., Tecno Campus Mataró-Maresme, Mataró, Barcelona 08302, Spain
| | - Xavier Barril
- Gain Therapeutics Sucursal en España, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Elena Cubero
- Gain Therapeutics Sucursal en España, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Søren W Gersting
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
- German Center for Child and Adolescent Health (DZKJ), Partner Site Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
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2
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Rashan EH, Bartlett AK, Khana DB, Zhang J, Jain R, Smith AJ, Baker ZN, Cook T, Caldwell A, Chevalier AR, Pfleger BF, Yuan P, Amador-Noguez D, Simcox JA, Pagliarini DJ. ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574893. [PMID: 38260250 PMCID: PMC10802472 DOI: 10.1101/2024.01.09.574893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Fatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)-fatty acids hydroxylated at the 4 (γ) position-which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs-conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
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Affiliation(s)
- Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Abigail K. Bartlett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daven B. Khana
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Raghav Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J. Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Zakery N. Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Taylor Cook
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Alana Caldwell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Autumn R. Chevalier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel Amador-Noguez
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith A. Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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3
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Tibelius A, Evers C, Oeser S, Rinke I, Jauch A, Hinderhofer K. Compilation of Genotype and Phenotype Data in GCDH-LOVD for Variant Classification and Further Application. Genes (Basel) 2023; 14:2218. [PMID: 38137040 PMCID: PMC10742628 DOI: 10.3390/genes14122218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Glutaric aciduria type 1 (GA-1) is a rare but treatable autosomal-recessive neurometabolic disorder of lysin metabolism caused by biallelic pathogenic variants in glutaryl-CoA dehydrogenase gene (GCDH) that lead to deficiency of GCDH protein. Without treatment, this enzyme defect causes a neurological phenotype characterized by movement disorder and cognitive impairment. Based on a comprehensive literature search, we established a large dataset of GCDH variants using the Leiden Open Variation Database (LOVD) to summarize the known genotypes and the clinical and biochemical phenotypes associated with GA-1. With these data, we developed a GCDH-specific variation classification framework based on American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. We used this framework to reclassify published variants and to describe their geographic distribution, both of which have practical implications for the molecular genetic diagnosis of GA-1. The freely available GCDH-specific LOVD dataset provides a basis for diagnostic laboratories and researchers to further optimize their knowledge and molecular diagnosis of this rare disease.
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Affiliation(s)
| | | | | | | | | | - Katrin Hinderhofer
- Institute of Human Genetics, Heidelberg University, 69120 Heidelberg, Germany
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4
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Barroso M, Gertzen M, Puchwein-Schwepcke AF, Preisler H, Sturm A, Reiss DD, Danecka MK, Muntau AC, Gersting SW. Glutaryl-CoA Dehydrogenase Misfolding in Glutaric Acidemia Type 1. Int J Mol Sci 2023; 24:13158. [PMID: 37685964 PMCID: PMC10487539 DOI: 10.3390/ijms241713158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/11/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Glutaric acidemia type 1 (GA1) is a neurotoxic metabolic disorder due to glutaryl-CoA dehydrogenase (GCDH) deficiency. The high number of missense variants associated with the disease and their impact on GCDH activity suggest that disturbed protein conformation can affect the biochemical phenotype. We aimed to elucidate the molecular basis of protein loss of function in GA1 by performing a parallel analysis in a large panel of GCDH missense variants using different biochemical and biophysical methodologies. Thirteen GCDH variants were investigated in regard to protein stability, hydrophobicity, oligomerization, aggregation, and activity. An altered oligomerization, loss of protein stability and solubility, as well as an augmented susceptibility to aggregation were observed. GA1 variants led to a loss of enzymatic activity, particularly when present at the N-terminal domain. The reduced cellular activity was associated with loss of tetramerization. Our results also suggest a correlation between variant sequence location and cellular protein stability (p < 0.05), with a more pronounced loss of protein observed with variant proximity to the N-terminus. The broad panel of variant-mediated conformational changes of the GCDH protein supports the classification of GA1 as a protein-misfolding disorder. This work supports research toward new therapeutic strategies that target this molecular disease phenotype.
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Affiliation(s)
- Madalena Barroso
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
| | - Marcus Gertzen
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
- Psychiatry and Psychotherapy, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Alexandra F. Puchwein-Schwepcke
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
- Department of Pediatric Neurology and Developmental Medicine, University of Basel Children’s Hospital, 4056 Basel, Switzerland
| | - Heike Preisler
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
| | - Andreas Sturm
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
| | - Dunja D. Reiss
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, 81377 Munich, Germany
| | - Marta K. Danecka
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
| | - Ania C. Muntau
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
- University Children’s Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Søren W. Gersting
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
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5
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Bian B, Liu Z, Feng D, Li W, Wang L, Li Y, Li D. Glutaric Aciduria Type 1: Comparison between Diffusional Kurtosis Imaging and Conventional MR Imaging. AJNR Am J Neuroradiol 2023; 44:967-973. [PMID: 37474264 PMCID: PMC10411849 DOI: 10.3174/ajnr.a7928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/07/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND AND PURPOSE Routine MR imaging has limited use in evaluating the severity of glutaric aciduria type 1. To better understand the mechanisms of brain injury in glutaric aciduria type 1, we explored the value of diffusional kurtosis imaging in detecting microstructural injury of the gray and white matter. MATERIALS AND METHODS This study included 17 patients with glutaric aciduria type 1 and 17 healthy controls who underwent conventional MR imaging and diffusional kurtosis imaging. The diffusional kurtosis imaging metrics of the gray and white matter were measured. Then, the MR imaging scores and diffusional kurtosis imaging metrics of all ROIs were further correlated with the morbidity scores and Barry-Albright dystonia scores. RESULTS The MR imaging scores showed no significant relation to the morbidity and Barry-Albright dystonia scores. Compared with healthy controls, patients with glutaric aciduria type 1 showed higher kurtosis values in the basal ganglia, corona radiata, centrum semiovale, and temporal lobe (P < .05). The DTI metrics of the basal ganglia were higher than those of healthy controls (P < .05). The fractional anisotropy value of the temporal lobe and the mean diffusivity values of basal ganglia in glutaric aciduria type 1 were lower than those in the control group (P < .05). The diffusional kurtosis imaging metrics of the temporal lobe and basal ganglia were significantly correlated with the Barry-Albright dystonia scores. The mean kurtosis values of the anterior and posterior putamen and Barry-Albright dystonia scores were most relevant (r = 0.721, 0.730, respectively). The mean kurtosis values of the basal ganglia had the best diagnostic efficiency with area under the curve values of 0.837 for the temporal lobe, and the mean diffusivity values of the basal ganglia in glutaric aciduria type 1 were lower than those in the control group (P < .05). The diffusional kurtosis imaging metrics of the temporal lobe and basal ganglia were significantly correlated with the Barry-Albright dystonia scores. The mean kurtosis values of the anterior and posterior putamen and Barry-Albright dystonia scores were most relevant (r = 0.721, 0.730, respectively). The mean kurtosis values of the basal ganglia had the best diagnostic efficiency with area under the curve values of 0.837. CONCLUSIONS Diffusional kurtosis imaging provides more comprehensive quantitative information regarding the gray and white matter micropathologic damage in glutaric aciduria type 1 than routine MR imaging scores.
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Affiliation(s)
- B Bian
- From the Departments of Radiology (B.B., Z.L., D.L.)
| | - Z Liu
- From the Departments of Radiology (B.B., Z.L., D.L.)
| | - D Feng
- Outpatient Pediatrics (D.F.)
| | - W Li
- State Key Laboratory of Stem Cell and Reproductive Biology (W.L., L.W.), Chinese Academy of Sciences and University, Beijing, China
| | - L Wang
- State Key Laboratory of Stem Cell and Reproductive Biology (W.L., L.W.), Chinese Academy of Sciences and University, Beijing, China
| | - Y Li
- Gene Therapy Laboratory (Y.L.), The First Hospital of Jilin University, Changchun, Jilin, China
| | - D Li
- From the Departments of Radiology (B.B., Z.L., D.L.)
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6
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Forny P, Hörster F, Baumgartner MR, Kölker S, Boy N. How guideline development has informed clinical research for organic acidurias (et vice versa). J Inherit Metab Dis 2023; 46:520-535. [PMID: 36591944 DOI: 10.1002/jimd.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
Organic acidurias, such as glutaric aciduria type 1 (GA1), methylmalonic (MMA), and propionic aciduria (PA) are a prominent group of inherited metabolic diseases involving accumulation of eponymous metabolites causing endogenous intoxication. For all three conditions, guidelines for diagnosis and management have been developed and revised over the last years, resulting in three revisions for GA1 and one revision for MMA/PA. The process of clinical guideline development in rare metabolic disorders is challenged by the scarcity and limited quality of evidence available. The body of literature is often fragmentary and where information is present, it is usually derived from small sample sizes. Therefore, the development of guidelines for GA1 and MMA/PA was initially confronted with a poor evidence foundation that hindered formulation of concrete recommendations in certain contexts, triggering specific research projects and initiation of longitudinal, prospective observational studies using patient registries. Reversely, these observational studies contributed to evaluate the value of newborn screening, phenotypic diversities, and treatment effects, thus significantly improving the quality of evidence and directly influencing formulation and evidence levels of guideline recommendations. Here, we present insights into interactions between guideline development and (pre)clinical research for GA1 and MMA/PA, and demonstrate how guidelines gradually improved from revision to revision. We describe how clinical studies help to unravel the relative impact of therapeutic interventions on outcome and conclude that despite new and better quality of research data over the last decades, significant shortcomings of evidence regarding prognosis and treatment remain. It appears that development of clinical guidelines can directly help to guide research, and vice versa.
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Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Friederike Hörster
- Division of Neuropaediatrics and Metabolic Medicine, Department of General Paediatrics, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Stefan Kölker
- Division of Neuropaediatrics and Metabolic Medicine, Department of General Paediatrics, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Nikolas Boy
- Division of Neuropaediatrics and Metabolic Medicine, Department of General Paediatrics, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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7
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Boy N, Mühlhausen C, Maier EM, Ballhausen D, Baumgartner MR, Beblo S, Burgard P, Chapman KA, Dobbelaere D, Heringer-Seifert J, Fleissner S, Grohmann-Held K, Hahn G, Harting I, Hoffmann GF, Jochum F, Karall D, Konstantopoulous V, Krawinkel MB, Lindner M, Märtner EMC, Nuoffer JM, Okun JG, Plecko B, Posset R, Sahm K, Scholl-Bürgi S, Thimm E, Walter M, Williams M, Vom Dahl S, Ziagaki A, Zschocke J, Kölker S. Recommendations for diagnosing and managing individuals with glutaric aciduria type 1: Third revision. J Inherit Metab Dis 2022; 46:482-519. [PMID: 36221165 DOI: 10.1002/jimd.12566] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 02/04/2023]
Abstract
Glutaric aciduria type 1 is a rare inherited neurometabolic disorder of lysine metabolism caused by pathogenic gene variations in GCDH (cytogenic location: 19p13.13), resulting in deficiency of mitochondrial glutaryl-CoA dehydrogenase (GCDH) and, consequently, accumulation of glutaric acid, 3-hydroxyglutaric acid, glutaconic acid and glutarylcarnitine detectable by gas chromatography/mass spectrometry (organic acids) and tandem mass spectrometry (acylcarnitines). Depending on residual GCDH activity, biochemical high and low excreting phenotypes have been defined. Most untreated individuals present with acute onset of striatal damage before age 3 (to 6) years, precipitated by infectious diseases, fever or surgery, resulting in irreversible, mostly dystonic movement disorder with limited life expectancy. In some patients, striatal damage develops insidiously. In recent years, the clinical phenotype has been extended by the finding of extrastriatal abnormalities and cognitive dysfunction, preferably in the high excreter group, as well as chronic kidney failure. Newborn screening is the prerequisite for pre-symptomatic start of metabolic treatment with low lysine diet, carnitine supplementation and intensified emergency treatment during catabolic episodes, which, in combination, have substantially improved neurologic outcome. In contrast, start of treatment after onset of symptoms cannot reverse existing motor dysfunction caused by striatal damage. Dietary treatment can be relaxed after the vulnerable period for striatal damage, that is, age 6 years. However, impact of dietary relaxation on long-term outcomes is still unclear. This third revision of evidence-based recommendations aims to re-evaluate previous recommendations (Boy et al., J Inherit Metab Dis, 2017;40(1):75-101; Kolker et al., J Inherit Metab Dis 2011;34(3):677-694; Kolker et al., J Inherit Metab Dis, 2007;30(1):5-22) and to implement new research findings on the evolving phenotypic diversity as well as the impact of non-interventional variables and treatment quality on clinical outcomes.
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Affiliation(s)
- Nikolas Boy
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Chris Mühlhausen
- Department of Paediatrics and Adolescent Medicine, University Medical Centre, Göttingen, Germany
| | - Esther M Maier
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, University of Munich Medical Centre, Munich, Germany
| | - Diana Ballhausen
- Paediatric Metabolic Unit, Paediatrics, Woman-Mother-Child Department, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Skadi Beblo
- Department of Women and Child Health, Hospital for Children and Adolescents, Centre for Paediatric Research Leipzig (CPL), University Hospitals, University of Leipzig, Leipzig, Germany
| | - Peter Burgard
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Kimberly A Chapman
- Rare Disease Institute, Children's National Health System, Washington, District of Columbia, USA
| | - Dries Dobbelaere
- Department of Paediatric Metabolism, Reference Centre of Inherited Metabolic Disorders, Jeanne de Flandre Hospital, Lille, France
| | - Jana Heringer-Seifert
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Fleissner
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, University of Munich Medical Centre, Munich, Germany
| | - Karina Grohmann-Held
- Centre for Child and Adolescent Medicine, University Hospital Greifswald, Greifswald, Germany
| | - Gabriele Hahn
- Department of Radiological Diagnostics, UMC, University of Dresden, Dresden, Germany
| | - Inga Harting
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Frank Jochum
- Evangelisches Waldkrankenhaus Spandau, Berlin, Germany
| | - Daniela Karall
- Clinic for Paediatrics I, Inherited Metabolic Disorders, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Michael B Krawinkel
- Institute of Nutritional Science, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Lindner
- Division of Metabolic Diseases, University Children's Hospital Frankfurt, Frankfurt, Germany
| | - E M Charlotte Märtner
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Jean-Marc Nuoffer
- University Institute of Clinical Chemistry, University of Bern, Bern, Switzerland
| | - Jürgen G Okun
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Barbara Plecko
- Department of Paediatrics and Adolescent Medicine, Division of General Paediatrics, University Children's Hospital Graz, Medical University Graz, Graz, Austria
| | - Roland Posset
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Katja Sahm
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Eva Thimm
- Division of Experimental Paediatrics and Metabolism, Department of General Paediatrics, Neonatology and Paediatric Cardiology, University Children's Hospital, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Magdalena Walter
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Monique Williams
- Department of Paediatrics, Centre for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Stephan Vom Dahl
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital, University of Düsseldorf, Düsseldorf, Germany
| | - Athanasia Ziagaki
- Centre of Excellence for Rare Metabolic Diseases, Interdisciplinary Centre of Metabolism: Endocrinology, Diabetes and Metabolism, University-Medicine Berlin, Berlin, Germany
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Stefan Kölker
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
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8
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Bhatt DP, Mills CA, Anderson KA, Henriques BJ, Lucas TG, Francisco S, Liu J, Ilkayeva OR, Adams AE, Kulkarni SR, Backos DS, Major MB, Grimsrud PA, Gomes CM, Hirschey MD. Deglutarylation of glutaryl-CoA dehydrogenase by deacylating enzyme SIRT5 promotes lysine oxidation in mice. J Biol Chem 2022; 298:101723. [PMID: 35157847 PMCID: PMC8969154 DOI: 10.1016/j.jbc.2022.101723] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
A wide range of protein acyl modifications has been identified on enzymes across various metabolic processes; however, the impact of these modifications remains poorly understood. Protein glutarylation is a recently identified modification that can be nonenzymatically driven by glutaryl-CoA. In mammalian systems, this unique metabolite is only produced in the lysine and tryptophan oxidative pathways. To better understand the biology of protein glutarylation, we studied the relationship between enzymes within the lysine/tryptophan catabolic pathways, protein glutarylation, and regulation by the deglutarylating enzyme sirtuin 5 (SIRT5). Here, we identify glutarylation on the lysine oxidation pathway enzyme glutaryl-CoA dehydrogenase (GCDH) and show increased GCDH glutarylation when glutaryl-CoA production is stimulated by lysine catabolism. Our data reveal that glutarylation of GCDH impacts its function, ultimately decreasing lysine oxidation. We also demonstrate the ability of SIRT5 to deglutarylate GCDH, restoring its enzymatic activity. Finally, metabolomic and bioinformatic analyses indicate an expanded role for SIRT5 in regulating amino acid metabolism. Together, these data support a feedback loop model within the lysine/tryptophan oxidation pathway in which glutaryl-CoA is produced, in turn inhibiting GCDH function via glutaryl modification of GCDH lysine residues and can be relieved by SIRT5 deacylation activity.
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9
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Tamhankar PM, Vasudevan L, Kondurkar P, Niazi S, Christopher R, Solanki D, Dholakia P, Muranjan M, Kamate M, Kalane U, Sheth J, Tamhankar V, Gulati R, Vasikarla M, Danda S, Naushad SM, Girisha KM, Patil S. Clinical Characteristics, Molecular Profile, and Outcomes in Indian Patients with Glutaric Aciduria Type 1. J Pediatr Genet 2021; 10:213-221. [PMID: 34504725 DOI: 10.1055/s-0040-1715528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
Abstract
Glutaric acidemia type 1 (GA-1, OMIM 231670) is an autosomal recessive inborn error of metabolism caused by the deficiency of glutaryl-coenzyme A (CoA) dehydrogenase with most children presenting in infancy with encephalopathy, dystonia, and macrocephaly. In this article, we presented the clinical characteristics, molecular profile, and outcomes in 29 unrelated families with affected children (30 cases total). The mean age at onset of illness was 10 months (±14.58), whereas the mean age at referral for molecular diagnosis was 29.44 months (±28.11). Patients were residents of nine different states of India. Clinical presentation varied from acute encephalitis followed by neuroregression and chronic/insidious developmental delay. Neurological sequelae varied from asymptomatic (no sequelae, 2 patients) to moderate (5 patients) and severe (23 patients) sequelae. All patients underwent blood tandem mass spectrometry (TMS on dried blood spots) and/or urine gas chromatography mass spectrometry (GCMS). Neuroimaging demonstrated batwing appearance in 95% cases. Sanger's sequencing of GCDH , covering all exons and exon-intron boundaries, was performed for all patients. Variants identified include 15 novel coding variants: p.Met100Thr, p.Gly107Ser, p.Leu179Val, p.Pro217Ser, p. Phe236Leufs*107, p.Ser255Pro, p.Met266Leufs*2, p.Gln330Ter, p.Thr344Ile, p.Leu345Pro, p.Lys377Arg, p.Leu424Pro, p.Asn373Lys, p.Lys377Arg, p.Asn392Metfs*9, and nine known genetic variants such as p.Arg128Gln, p.Leu179Arg, p.Trp225Ter, p.Met339Val, p.Gly354Ser, p.Arg402Gln, p.Arg402Trp, p.His403Tyr, and p.Ala433Val (Ensembl transcript ID: ENST00000222214). Using in silico analysis, genetic variants were shown to be affecting the residues responsible for homotetramer formation of the glutaryl-CoA dehydrogenase protein. Treatment included oral carnitine, riboflavin, protein-restricted diet, lysine-deficient special formulae, and management of acute crises with intravenous glucose and hydration. However, the mortality (9/30, 27.58%) and morbidity was high in our cohort with only two patients affording the diet. Our study is the largest multicentric, genetic variant-proven series of glutaric aciduria type 1 from India till date.
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Affiliation(s)
- Parag M Tamhankar
- Genetic Research Center, National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India.,Centre for Medical Genetics, Mumbai, Maharashtra, India.,Sandor Life Sciences Pvt. Ltd., Hyderabad, Andhra Pradesh, India
| | - Lakshmi Vasudevan
- Genetic Research Center, National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Pratima Kondurkar
- Genetic Research Center, National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Sarfaraj Niazi
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka, India
| | - Dhaval Solanki
- Mantra Child and Neurology and Epilepsy Clinic, Bhavnagar, Gujarat, India
| | | | - Mamta Muranjan
- Department of Pediatrics, Seth Gordhandas Sunderdas Medical College and King Edward Memorial hospital, Mumbai, Maharashtra, India
| | - Mahesh Kamate
- Department of Pediatric Neurology, Jawaharlal Nehru Medical College, Karnataka Lingayat Education University, Belgaum, Karnataka, India
| | - Umesh Kalane
- Pediatric Neurology Centre, Swargate, Pune, Maharashtra, India
| | - Jayesh Sheth
- Foundation for Research in Genetics and Endocrinology Institute of Human Genetics, Foundation for Research in Genetics and Endocrinology House, Satellite, Ahmedabad, Gujarat, India
| | | | - Reena Gulati
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Gorimedu, Puducherry, India
| | | | - Sumita Danda
- Department of Medical Genetics, Christian Medical College, Vellore, Tamil Nadu, India
| | - Shaik M Naushad
- Sandor Life Sciences Pvt. Ltd., Hyderabad, Andhra Pradesh, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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10
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Schühle K, Saft M, Vögeli B, Erb TJ, Heider J. Benzylmalonyl-CoA dehydrogenase, an enzyme involved in bacterial auxin degradation. Arch Microbiol 2021; 203:4149-4159. [PMID: 34059946 PMCID: PMC8360864 DOI: 10.1007/s00203-021-02406-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022]
Abstract
A novel acyl-CoA dehydrogenase involved in degradation of the auxin indoleacetate by Aromatoleum aromaticum was identified as a decarboxylating benzylmalonyl-CoA dehydrogenase (IaaF). It is encoded within the iaa operon coding for enzymes of indoleacetate catabolism. Using enzymatically produced benzylmalonyl-CoA, the reaction was characterized as simultaneous oxidation and decarboxylation of benzylmalonyl-CoA to cinnamoyl-CoA and CO2. Oxygen served as electron acceptor and was reduced to H2O2, whereas electron transfer flavoprotein or artificial dyes serving as electron acceptors for other acyl-CoA dehydrogenases were not used. The enzyme is homotetrameric, contains an FAD cofactor and is enantiospecific in benzylmalonyl-CoA turnover. It shows high catalytic efficiency and strong substrate inhibition with benzylmalonyl-CoA, but otherwise accepts only a few medium-chain alkylmalonyl-CoA compounds as alternative substrates with low activities. Its reactivity of oxidizing 2-carboxyacyl-CoA with simultaneous decarboxylation is unprecedented and indicates a modified reaction mechanism for acyl-CoA dehydrogenases, where elimination of the 2-carboxy group replaces proton abstraction from C2.
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Affiliation(s)
- Karola Schühle
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Martin Saft
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Marburg, Germany
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany. .,LOEWE-Center for Synthetic Microbiology, Marburg, Germany.
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11
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Cornelius LP, Raju V, Julin A. Pediatric Glutaric Aciduria Type 1: 14 Cases, Diagnosis and Management. Ann Indian Acad Neurol 2020; 24:22-26. [PMID: 33911375 PMCID: PMC8061498 DOI: 10.4103/aian.aian_42_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/05/2020] [Accepted: 04/17/2020] [Indexed: 11/04/2022] Open
Abstract
Introduction Glutaric aciduria type I is an autosomal recessive disorder of lysine metabolism due to the defect of the enzyme glutaryl-CoA dehydrogenase. The regression of milestones following an intercurrent infection with disabling dystonia is the common presentation. We report the clinical features, diagnosis, and management of 14 south Indian children with glutaric aciduria type I. Results Males predominated the study (57.1%). The mean age of onset of the symptoms was 8.57 ± 3.57 months. The mean age at the time of diagnosis was 35.21 ± 48.31 months. The history of consanguinity was noted in 57.1%. Development was normal prior to the onset of acute crises in nearly three fourths. Acute crises triggered by infection followed by the regression of milestones was the major presenting feature in 10 children (71.4%). Macrocephaly was another prominent feature in an equal number. Bat's wing appearance (fronto temporal atrophy) was present in all children. Nearly 80% had moderate to severe disability in the form of dystonic movement disorder and spastic quadriparesis. Conclusion Glutaric aciduria type Ihas to be identified and managed early to have a better outcome.
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Affiliation(s)
- Leema P Cornelius
- Department of Paediatric Neurology, Institute of Child Health and Hospital for Children, Madras Medical College, Chennai, Tamil Nadu, India
| | - Vivekasaravanan Raju
- Department of Paediatric Neurology, Institute of Child Health and Hospital for Children, Madras Medical College, Chennai, Tamil Nadu, India
| | - Asir Julin
- Department of Paediatric Neurology, Institute of Child Health and Hospital for Children, Madras Medical College, Chennai, Tamil Nadu, India
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12
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Chen YC, Huang CY, Lee YT, Wu CH, Chang SK, Cheng HL, Chang PH, Niu DM, Cheng YF. Audiological and otologic manifestations of glutaric aciduria type I. Orphanet J Rare Dis 2020; 15:337. [PMID: 33256818 PMCID: PMC7706203 DOI: 10.1186/s13023-020-01571-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/05/2020] [Indexed: 11/26/2022] Open
Abstract
Background Glutaric aciduria type 1 (GA-1) is a rare disease connected with speech delay and neurological deficits. However, the audiological and otologic profiles of GA-1 have not yet been fully characterized. To our knowledge, this is the largest study of comprehensive audiological and otologic evaluation in patients with GA-1 to date.
Methods Thirteen patients diagnosed with GA-1 between January 1994 and December 2019 with audiological, radiological and genetic manifestations were retrospectively analyzed. Hearing tests were performed in all patients. MRI was performed for radiological evaluation. Results Hearing loss was found in 76.9% (10/13) of GA-1 patients, including slight hearing loss in 46.1% (6/13) of patients, mild hearing loss in 15.4% (2/13) of patients, and moderate hearing loss in 7.7% (1/13) of patients. Normal hearing thresholds were seen in 23% (3/13) of patients. Patients with intensive care unit (ICU) admission history showed significantly worse hearing than those without (29.17 ± 12.47 vs 13.56 ± 3.93 dB HL, 95% CI 2.92–24.70, p = 0.0176). One patient had moderate sensorineural hearing loss and a past history of acute encephalopathic crisis. No usual causative gene mutations associated with hearing loss were found in these patients. MRI showed a normal vestibulocochlear apparatus and cochlear nerve. One patient with extensive injury of the basal ganglia on MRI after acute encephalopathic crisis was found to have moderate sensorineural hearing loss. Two patients with disability scores above 5 were found to have mild to moderate hearing impairment. No obvious correlation between macrocephaly and hearing loss was found. Conclusion A high prevalence of hearing impairment is found in GA-1 patients. Adequate audiological evaluation is essential for these patients, especially for those after encephalopathic crises or with ICU admission history.
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Affiliation(s)
- Yen-Chi Chen
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Kaoshiung Municipal Gangshan Hospital (Outsourceded by Show-Chwan Memorial Hospital), Kaoshiung, Taiwan
| | - Chii-Yuan Huang
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yen-Ting Lee
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Hung Wu
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Radiology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sheng-Kai Chang
- Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsiu-Lien Cheng
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Po-Hsiung Chang
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Dau-Ming Niu
- Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan. .,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Yen-Fu Cheng
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of Otolaryngology-Head and Neck Surgery, School of Medicine, National Yang-Ming University, Taipei, Taiwan. .,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan.
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13
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Leandro J, Houten SM. The lysine degradation pathway: Subcellular compartmentalization and enzyme deficiencies. Mol Genet Metab 2020; 131:14-22. [PMID: 32768327 DOI: 10.1016/j.ymgme.2020.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 02/07/2023]
Abstract
Lysine degradation via formation of saccharopine is a pathway confined to the mitochondria. The second pathway for lysine degradation, the pipecolic acid pathway, is not yet fully elucidated and known enzymes are localized in the mitochondria, cytosol and peroxisome. The tissue-specific roles of these two pathways are still under investigation. The lysine degradation pathway is clinically relevant due to the occurrence of two severe neurometabolic disorders, pyridoxine-dependent epilepsy (PDE) and glutaric aciduria type 1 (GA1). The existence of three other disorders affecting lysine degradation without apparent clinical consequences opens up the possibility to find alternative therapeutic strategies for PDE and GA1 through pathway modulation. A better understanding of the mechanisms, compartmentalization and interplay between the different enzymes and metabolites involved in lysine degradation is of utmost importance.
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Affiliation(s)
- João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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14
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Adult-onset glutaric aciduria type I: rare presentation of a treatable disorder. Neurogenetics 2020; 21:179-186. [PMID: 32306145 DOI: 10.1007/s10048-020-00610-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/26/2020] [Indexed: 02/07/2023]
Abstract
Glutaric aciduria type I (GA1; OMIM #231670) is an autosomal recessively inherited and treatable disorder characterized by the accumulation and irregular excretion of glutaric acid due to a defect in the glutaryl-CoA dehydrogenase enzyme involved in the catabolic pathways of L-lysine, L-hydroxylysine, and L-tryptophan. Glutaryl-CoA dehydrogenase is encoded by the GCDH gene (OMIM #608801), and several mutations in this gene are known to result in GA1. GA1 usually presents in the first 18-36 months of life with mild or severe acute encephalopathy, movement disorders, and striatal degeneration. Few cases of adult-onset GA1 have been described so far in the literature, often with non-specific and sometimes longstanding neurological symptoms. Since a preventive metabolic treatment is available, neurologists must be aware of this rare but likely underdiagnosed presentation, especially when typical neuroimaging features are identified. Here, we describe 35-year-old presenting with headache and subjective memory problems. There was no history of dystonic movement disorders. Neurological examination and neurocognitive tests were normal. Brain MRI scan revealed white matter abnormalities associated with subependymal nodules and mild frontotemporal hypoplasia suggestive of glutaric aciduria type 1 (GA1). Genetic testing confirmed the presence of homozygous c.1204C > T (p.R402W) variant in the GCDH gene, inherited from heterozygous parents.
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15
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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16
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Potential complementation effects of two disease-associated mutations in tetrameric glutaryl-CoA dehydrogenase is due to inter subunit stability-activity counterbalance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140269. [DOI: 10.1016/j.bbapap.2019.140269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/12/2019] [Accepted: 09/01/2019] [Indexed: 11/18/2022]
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17
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Jia Z, Zhao C, Wang M, Zhao X, Zhang W, Han T, Xia Q, Han Z, Lin R, Li X. Hepatotoxicity assessment of Rhizoma Paridis in adult zebrafish through proteomes and metabolome. Biomed Pharmacother 2020; 121:109558. [DOI: 10.1016/j.biopha.2019.109558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
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18
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Rani N, Hazra S, Singh A, Surolia A. Functional annotation of putative fadE9 of Mycobacterium tuberculosis as isobutyryl-CoA dehydrogenase involved in valine catabolism. Int J Biol Macromol 2019; 122:45-57. [DOI: 10.1016/j.ijbiomac.2018.10.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
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19
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Thapa HR, Robbins JM, Moore BS, Agarwal V. Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein. Biochemistry 2019; 58:918-929. [PMID: 30620182 DOI: 10.1021/acs.biochem.8b01177] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sequential enzymatic reactions on substrates tethered to carrier proteins (CPs) generate thiotemplated building blocks that are then delivered to nonribosomal peptide synthetases (NRPSs) to generate peptidic natural products. The underlying diversity of these thiotemplated building blocks is the principal driver of the chemical diversity of NRPS-derived natural products. Structural insights into recognition of CPs by tailoring enzymes that generate these building blocks are sparse. Here we present the crystal structure of a flavin-dependent prolyl oxidase that furnishes thiotemplated pyrrole as the product, in complex with its cognate CP in the holo and product-bound states. The thiotemplated pyrrole is an intermediate that is well-represented in natural product biosynthetic pathways. Our results delineate the interactions between the CP and the oxidase while also providing insights into the stereospecificity of the enzymatic oxidation of the prolyl heterocycle to the aromatic pyrrole. Biochemical validation of the interaction between the CP and the oxidase demonstrates that NRPSs recognize and bind to their CPs using interactions quite different from those of fatty acid and polyketide biosynthetic enzymes. Our results posit that structural diversity in natural product biosynthesis can be, and is, derived from subtle modifications of primary metabolic enzymes.
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Affiliation(s)
- Hem R Thapa
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Krone Engineered Biosystems Building , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Bradley S Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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20
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Banach M, Konieczny L, Roterman I. Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores. Methods Mol Biol 2019; 1958:347-378. [PMID: 30945229 DOI: 10.1007/978-1-4939-9161-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The traditional classification of protein structures (with regard to their supersecondary and tertiary conformation) is based on an assessment of conformational similarities between various polypeptide chains and particularly on the presence of specific secondary structural motifs. Mutual relations between secondary folds determine the overall shape of the protein and may be used to assign proteins to specific families (such as the immunoglobulin-like family). An alternative means of conducting structural assessment focuses on the structure of the protein's hydrophobic core. In this case, the protein is treated as a quasi-micelle, which exposes hydrophilic residues on its surface while internalizing hydrophobic residues. The accordance between the actual distribution of hydrophobicity in a protein and its corresponding theoretical ("idealized") distribution can be determined quantitatively, which, in turn, enables comparative analysis of structures regarded as geometrically similar (as well as geometrically divergent structures which are nevertheless regarded as similar in the sense of the fuzzy oil drop model). In this scope, the protein may be compared to an "intelligent micelle," where local disorder is often intentional and related to biological function-unlike traditional surfactant micelles which remain highly symmetrical throughout and do not carry any encoded information.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kraków, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University, Medical College, Kraków, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kraków, Poland.
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21
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Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat Commun 2018; 9:2114. [PMID: 29844506 PMCID: PMC5974017 DOI: 10.1038/s41467-018-04513-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/04/2018] [Indexed: 11/09/2022] Open
Abstract
Glutarate is a five carbon platform chemical produced during the catabolism of L-lysine. It is known that it can be catabolized through the glutaryl-CoA dehydrogenation pathway. Here, we discover that Pseudomonas putida KT2440 has an additional glutarate catabolic pathway involving L-2-hydroxyglutarate (L-2-HG), an abnormal metabolite produced from 2-ketoglutarate (2-KG). In this pathway, CsiD, a Fe2+/2-KG-dependent glutarate hydroxylase, is capable of converting glutarate into L-2-HG, and LhgO, an L-2-HG oxidase, can catalyze L-2-HG into 2-KG. We construct a recombinant strain that lacks both glutarate catabolic pathways. It can produce glutarate from L-lysine with a yield of 0.85 mol glutarate/mol L-lysine. Thus, L-2-HG anabolism and catabolism is a metabolic alternative to the glutaryl-CoA dehydrogenation pathway in P. putida KT2440; L-lysine can be both ketogenic and glucogenic.
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22
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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Schwander T, McLean R, Zarzycki J, Erb TJ. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. J Biol Chem 2017; 293:1702-1712. [PMID: 29275330 PMCID: PMC5798300 DOI: 10.1074/jbc.ra117.000764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to α,β-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 Å. The enzyme forms a homodimer of two 60-kDa subunits. Compared with other ACDs, MCD contains an ∼170-residue-long N-terminal extension that structurally mimics a dimer–dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an α-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homolog of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD toward succinyl-CoA through active-site mutagenesis.
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Affiliation(s)
- Thomas Schwander
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Richard McLean
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Jan Zarzycki
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Tobias J Erb
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and .,the LOEWE Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
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24
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Schmiesing J, Lohmöller B, Schweizer M, Tidow H, Gersting SW, Muntau AC, Braulke T, Mühlhausen C. Disease-causing mutations affecting surface residues of mitochondrial glutaryl-CoA dehydrogenase impair stability, heteromeric complex formation and mitochondria architecture. Hum Mol Genet 2017; 26:538-551. [PMID: 28062662 DOI: 10.1093/hmg/ddw411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/28/2016] [Indexed: 01/22/2023] Open
Abstract
The neurometabolic disorder glutaric aciduria type 1 (GA1) is caused by mutations in the GCDH gene encoding the mitochondrial matrix protein glutaryl-CoA dehydrogenase (GCDH), which forms homo- and heteromeric complexes. Twenty percent of all pathogenic mutations affect single amino acid residues on the surface of GCDH resulting in a severe clinical phenotype. We report here on heterologous expression studies of 18 missense mutations identified in GA1 patients affecting surface amino acids. Western blot and pulse chase experiments revealed that the stability of half of the GCDH mutants was significantly reduced. In silico analyses showed that none of the mutations impaired the 3D structure of GCDH. Immunofluorescence co-localisation studies in HeLa cells demonstrated that all GCDH mutants were correctly translocated into mitochondria. Surprisingly, the expression of p.Arg88Cys GCDH as well as further substitutions by alanine, lysine, or methionine but not histidine or leucine resulted in the disruption of mitochondrial architecture forming longitudinal structures composed of stacks of cristae and partial loss of the outer mitochondrial membrane. The expression of mitochondrial fusion or fission proteins was not affected in these cells. Bioluminescence resonance energy transfer analyses revealed that all GCDH mutants exhibit an increased binding affinity to electron transfer flavoprotein beta, whereas only p.Tyr155His GCDH showed a reduced interaction with dihydrolipoamide succinyl transferase. Our data underscore the impact of GCDH protein interactions mediated by amino acid residues on the surface of GCDH required for proper enzymatic activity.
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Affiliation(s)
- Jessica Schmiesing
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Lohmöller
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michaela Schweizer
- Center of Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging & Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Søren W Gersting
- Department of Molecular Pediatrics, Dr. von Hauner Childrens Hospital, Ludwig-Maximilians-University, Munich, Germany and
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Chris Mühlhausen
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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25
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Boy N, Mühlhausen C, Maier EM, Heringer J, Assmann B, Burgard P, Dixon M, Fleissner S, Greenberg CR, Harting I, Hoffmann GF, Karall D, Koeller DM, Krawinkel MB, Okun JG, Opladen T, Posset R, Sahm K, Zschocke J, Kölker S. Proposed recommendations for diagnosing and managing individuals with glutaric aciduria type I: second revision. J Inherit Metab Dis 2017; 40:75-101. [PMID: 27853989 DOI: 10.1007/s10545-016-9999-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
Glutaric aciduria type I (GA-I; synonym, glutaric acidemia type I) is a rare inherited metabolic disease caused by deficiency of glutaryl-CoA dehydrogenase located in the catabolic pathways of L-lysine, L-hydroxylysine, and L-tryptophan. The enzymatic defect results in elevated concentrations of glutaric acid, 3-hydroxyglutaric acid, glutaconic acid, and glutaryl carnitine in body tissues, which can be reliably detected by gas chromatography/mass spectrometry (organic acids) and tandem mass spectrometry (acylcarnitines). Most untreated individuals with GA-I experience acute encephalopathic crises during the first 6 years of life that are triggered by infectious diseases, febrile reaction to vaccinations, and surgery. These crises result in striatal injury and consequent dystonic movement disorder; thus, significant mortality and morbidity results. In some patients, neurologic disease may also develop without clinically apparent crises at any age. Neonatal screening for GA-I us being used in a growing number of countries worldwide and is cost effective. Metabolic treatment, consisting of low lysine diet, carnitine supplementation, and intensified emergency treatment during catabolism, is effective treatment and improves neurologic outcome in those individuals diagnosed early; treatment after symptom onset, however, is less effective. Dietary treatment is relaxed after age 6 years and should be supervised by specialized metabolic centers. The major aim of this second revision of proposed recommendations is to re-evaluate the previous recommendations (Kölker et al. J Inherit Metab Dis 30:5-22, 2007b; J Inherit Metab Dis 34:677-694, 2011) and add new research findings, relevant clinical aspects, and the perspective of affected individuals.
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Affiliation(s)
- Nikolas Boy
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany.
| | - Chris Mühlhausen
- University Children's Hospital, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, D-20246, Hamburg, Germany
| | - Esther M Maier
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, University of Munich Medical Centre, Munich, Germany
| | - Jana Heringer
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Birgit Assmann
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Peter Burgard
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Marjorie Dixon
- Dietetics, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Sandra Fleissner
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, University of Munich Medical Centre, Munich, Germany
| | - Cheryl R Greenberg
- Department of Pediatrics, Children's Hospital Health Sciences Centre and University of Manitoba, Winnipeg, MB, R3A 1R9, Canada
- Department of Biochemistry and Medical Genetics, Children's Hospital Health Sciences Centre and University of Manitoba, Winnipeg, MB, R3A 1R9, Canada
| | - Inga Harting
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Daniela Karall
- Clinic for Paediatrics I, Inherited Metabolic Disorders, Medical, University of Innsbruck, Innsbruck, Austria
| | - David M Koeller
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Michael B Krawinkel
- Justus Liebig University Giessen, Institute of Nutritional Science, Giessen, Germany
| | - Jürgen G Okun
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Thomas Opladen
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Roland Posset
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Katja Sahm
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Stefan Kölker
- Centre for Child and Adolescent Medicine, Department of General Paediatrics, Division of Neuropaediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, D-69120, Heidelberg, Germany
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26
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Radha Rama Devi A, Ramesh VA, Nagarajaram HA, Satish SPS, Jayanthi U, Lingappa L. Spectrum of mutations in Glutaryl-CoA dehydrogenase gene in glutaric aciduria type I--Study from South India. Brain Dev 2016; 38:54-60. [PMID: 26071121 DOI: 10.1016/j.braindev.2015.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Glutaric aciduria type I is an autosomal recessive organic acid disorder. The primary defect is the deficiency of Glutaryl-CoA dehydrogenase (EC number 1.3.99.7) enzyme that is involved in the catabolic pathways of the amino acids l-lysine, l-hydroxylysine, and l-tryptophan. It is a treatable neuro-metabolic disorder. Early diagnosis and treatment helps in preventing brain damage. METHODS The Glutaryl-CoA dehydrogenase gene (GCDH) gene was sequenced to identify disease causing mutations by direct sequencing of all the exons in twelve patients who were biochemically confirmed with GA I. RESULTS We identified eleven mutations of which nine are homozygous mutations, one heterozygous and two synonymous mutations. Among the eleven mutations, four mutations p.Q162R, p.P286S, p.W225X in two families and p.V410M are novel. A milder clinical presentation is observed in those families who are either heterozygous or with a benign synonymous SNP. Multiple sequence alignment (MSA) of GCDH with its homologues revealed that the observed novel mutations are not tolerated by protein structure and function. CONCLUSIONS The present study indicates genetic heterogeneity in GCDH gene mutations among South Indian population. Genetic analysis is useful in prenatal diagnosis and prevention. Mutation analysis is a useful tool in the absence of non-availability of enzyme assay in GA I.
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Affiliation(s)
- A Radha Rama Devi
- Genetic Metabolic Unit, Rainbow Children Hospital, India; Sandor Life Sciences, India.
| | - Vakkalagadda A Ramesh
- Laboratory of Computational Biology, CDFD, Gruhakalpa, Nampally, Hyderabad, India; Graduate Studies, Manipal University, India
| | - H A Nagarajaram
- Laboratory of Computational Biology, CDFD, Gruhakalpa, Nampally, Hyderabad, India
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27
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Zhang Y, Li H, Ma R, Mei L, Wei X, Liang D, Wu L. Clinical and molecular investigation in Chinese patients with glutaric aciduria type I. Clin Chim Acta 2015; 453:75-9. [PMID: 26656312 DOI: 10.1016/j.cca.2015.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/22/2015] [Accepted: 12/03/2015] [Indexed: 11/28/2022]
Abstract
Glutaric aciduria type I (GA-I) is a rare autosomal recessive metabolic disorder caused by deficiency of glutaryl-CoA dehydrogenase (GCDH), leading to an abnormal metabolism of lysine, hydroxylysine and tryptophan. It results in accumulations of glutaric acid, 3-hydroxyglutaric acid and glutaconic acid. Clinical features include the sudden onset of encephalopathy, hypotonia and macrocephaly usually before age 18months. Here we report five cases of GA-I confirmed with mutation analysis. GCDH gene mutations were identified in all five probands with GA-I. Three of them had compound heterozygous mutations and two had homozygous mutations. Mutations of two alleles (c.334G>T and IVS11-11A>G) were novel and both of them were confirmed to be splice site mutations by reverse transcription PCR.
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Affiliation(s)
- Yanghui Zhang
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Haoxian Li
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China; Hunan Jiahui Genetics Hospital, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Ruiyu Ma
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Libin Mei
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Xianda Wei
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Desheng Liang
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China; Hunan Jiahui Genetics Hospital, 110 Xiangya Road, Changsha, Hunan 410078, China.
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China; Hunan Jiahui Genetics Hospital, 110 Xiangya Road, Changsha, Hunan 410078, China.
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28
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Lund M, Olsen RKJ, Gregersen N. A short introduction to acyl-CoA dehydrogenases; deficiencies and novel treatment strategies. Expert Opin Orphan Drugs 2015. [DOI: 10.1517/21678707.2015.1092869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Abstract
Purpose Glutaric aciduria type 1 (GA1) is a rare metabolic disorder of glutaryl-CoA-dehydrogenase enzyme deficiency. Children with GA1 are reported to be predisposed to subdural hematoma (SDH) development due to stretching of cortical veins secondary to cerebral atrophy and expansion of CSF spaces. Therefore, GA1 testing is part of the routine work-up in abusive head trauma (AHT). This systematic review addresses the coexistence of GA1 and SDH and the validity of GA1 in the differential diagnosis of AHT. Methods A systematic literature review, with language restriction, of papers published before 1 Jan 2015, was performed using Pubmed, PsychINFO, and Embase. Inclusion criteria were reported SDHs, hygromas or effusions in GA1 patients up to 18 years of age. Of 1599 publications, 20 publications were included for analysis. Results In total 20 cases, 14 boys and 6 girls, were included. In eight cases (40 %) a child abuse work-up was performed, which was negative in all cases. Clinical history revealed the presence of trauma in eight cases (40 %). In only one case neuroradiology revealed no abnormalities related to GA1 according to the authors, although on evaluation we could not exclude AHT. Conclusion From this systematic review we conclude that SDHs in 19/20 children with GA1 are accompanied by other brain abnormalities specific for GA1. One case with doubtful circumstances was the exception to this rule.
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30
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Schürmann M, Meijers R, Schneider TR, Steinbüchel A, Cianci M. 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7(T): crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1360-72. [PMID: 26057676 PMCID: PMC4461206 DOI: 10.1107/s1399004715006616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/01/2015] [Indexed: 01/19/2023]
Abstract
3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase (AcdDPN7; EC 3.13.1.4) was identified during investigation of the 3,3'-dithiodipropionic acid (DTDP) catabolic pathway in the betaproteobacterium Advenella mimigardefordensis strain DPN7(T). DTDP is an organic disulfide and a precursor for the synthesis of polythioesters (PTEs) in bacteria, and is of interest for biotechnological PTE production. AcdDPN7 catalyzes sulfur abstraction from 3SP-CoA, a key step during the catabolism of DTDP. Here, the crystal structures of apo AcdDPN7 at 1.89 Å resolution and of its complex with the CoA moiety from the substrate analogue succinyl-CoA at 2.30 Å resolution are presented. The apo structure shows that AcdDPN7 belongs to the acyl-CoA dehydrogenase superfamily fold and that it is a tetramer, with each subunit containing one flavin adenine dinucleotide (FAD) molecule. The enzyme does not show any dehydrogenase activity. Dehydrogenase activity would require a catalytic base (Glu or Asp residue) at either position 246 or position 366, where a glutamine and a glycine are instead found, respectively, in this desulfinase. The positioning of CoA in the crystal complex enabled the modelling of a substrate complex containing 3SP-CoA. This indicates that Arg84 is a key residue in the desulfination reaction. An Arg84Lys mutant showed a complete loss of enzymatic activity, suggesting that the guanidinium group of the arginine is essential for desulfination. AcdDPN7 is the first desulfinase with an acyl-CoA dehydrogenase fold to be reported, which underlines the versatility of this enzyme scaffold.
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Affiliation(s)
- Marc Schürmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas R. Schneider
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Michele Cianci
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
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Gupta N, Singh PK, Kumar M, Shastri S, Gulati S, Kumar A, Agarwala A, Kapoor S, Nair M, Sapra S, Dubey S, Singh A, Kaur P, Kabra M. Glutaric Acidemia Type 1-Clinico-Molecular Profile and Novel Mutations in GCDH Gene in Indian Patients. JIMD Rep 2015; 21:45-55. [PMID: 25762492 PMCID: PMC4470956 DOI: 10.1007/8904_2014_377] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 02/05/2023] Open
Abstract
Glutaric acidemia I (GA I, #231670) is one of the treatable, autosomal recessively inherited metabolic disorders. Macrocephaly, acute encephalitis-like crises, dystonia and characteristic frontotemporal atrophy are the hallmarks of this disease. In this communication, we present the clinical, biochemical and molecular profile of seventeen GA I patients from 15 unrelated families from India and report seven novel mutations in GCDH gene (c.281G>A (p.Arg94Gln), c.401A>G (p.Asp134Gly), c.662T>C (p.Leu221Pro), c.881G>C (p.Arg294Pro), c.1173dupG (p.Asn392Glufs*5), c.1238A>G (p.Tyr413Cys) and c.1241A>C (p.Glu414Ala)). Out of these, c.662T>C (p.Leu221Pro) in exon 8 and c.281G>A (p.Arg94Gln) allele in exon 4 were low excretor alleles, whereas c.1241A>C (p.Glu414Ala), c.1173dupG and c.1207C>T (p.His403Tyr) in exon 11 were high excretor alleles. We conclude that c.1204C>T (p.Arg402Trp) is probably the most common mutant allele. Exons 11 and 8 are the hot spot regions of GCDH gene in Indian patients with GA I. An early diagnosis and timely intervention can improve the underlying prognosis. Molecular confirmation is helpful in providing genetic counselling and prenatal diagnosis in subsequent pregnancy.
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Affiliation(s)
- Neerja Gupta
- />Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Pawan Kumar Singh
- />Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Manoj Kumar
- />Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Shivaram Shastri
- />Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Sheffali Gulati
- />Division of Neurology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Atin Kumar
- />Department of Radiology, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Anuja Agarwala
- />Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Seema Kapoor
- />Maulana Azad Medical College, New Delhi, India
| | | | - Savita Sapra
- />Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Sudhisha Dubey
- />Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Ankur Singh
- />Maulana Azad Medical College, New Delhi, India
| | - Punit Kaur
- />Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Madhulika Kabra
- />Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029 India
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Sauer SW, Opp S, Komatsuzaki S, Blank AE, Mittelbronn M, Burgard P, Koeller DM, Okun JG, Kölker S. Multifactorial modulation of susceptibility to l-lysine in an animal model of glutaric aciduria type I. Biochim Biophys Acta Mol Basis Dis 2015; 1852:768-77. [PMID: 25558815 DOI: 10.1016/j.bbadis.2014.12.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/16/2014] [Accepted: 12/27/2014] [Indexed: 01/05/2023]
Abstract
Glutaric aciduria type I is an inherited defect in L-lysine, L-hydroxylysine and L-tryptophan degradation caused by deficiency of glutaryl-CoA dehydrogenase (GCDH). The majority of untreated patients presents with accumulation of neurotoxic metabolites - glutaric acid (GA) and 3-hydroxyglutaric acid (3-OHGA) - and striatal injury. Gcdh(-/-) mice display elevated levels of GA and 3-OH-GA but do not spontaneously develop striatal lesions. L-lysine-enriched diets (appr. 235 mg/d) were suggested to induce a neurological phenotype similar to affected patients. In our hands 93% of mice stressed according to the published protocol remained asymptomatic. To understand the underlying mechanism, we modified their genetic background (F1 C57BL6/Jx129/SvCrl) and increased the daily oral L-lysine supply (235-433 mg). We identified three modulating factors, (1) gender, (2) genetic background, and (3) amount of L-lysine. Male mice displayed higher vulnerability and inbreeding for more than two generations as well as elevating L-lysine supply increased the diet-induced mortality rate (up to 89%). Onset of first symptoms leads to strongly reduced intake of food and, thus, L-lysine suggesting a threshold for toxic metabolite production to induce neurological disease. GA and 3-OH-GA tissue concentrations did not correlate with dietary L-lysine supply but differed between symptomatic and asymptomatic mice. Cerebral activities of glyceraldehyde 3-phosphate dehydrogenase, 2-oxoglutarate dehydrogenase complex, and aconitase were decreased. Symptomatic mice did not develop striatal lesions or intracerebral hemorrhages. We found severe spongiosis in the hippocampus of Gcdh(-/-) mice which was independent of dietary L-lysine supply. In conclusion, the L-lysine-induced pathology in Gcdh(-/-) mice depends on genetic and dietary parameters.
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Affiliation(s)
- Sven W Sauer
- Department of General Pediatrics, Division of Inherited Metabolic Diseases, University Children's Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Silvana Opp
- Department of General Pediatrics, Division of Inherited Metabolic Diseases, University Children's Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Shoko Komatsuzaki
- Department of General Pediatrics, Division of Inherited Metabolic Diseases, University Children's Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Anna-Eva Blank
- Institute of Neurology (Edinger Institute), Goethe-University Frankfurt, D-60528 Frankfurt/Main, Germany
| | - Michel Mittelbronn
- Institute of Neurology (Edinger Institute), Goethe-University Frankfurt, D-60528 Frankfurt/Main, Germany
| | - Peter Burgard
- Department of General Pediatrics, Division of Inherited Metabolic Diseases, University Children's Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - D M Koeller
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Jürgen G Okun
- Department of General Pediatrics, Division of Inherited Metabolic Diseases, University Children's Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Stefan Kölker
- Department of General Pediatrics, Division of Inherited Metabolic Diseases, University Children's Hospital Heidelberg, D-69120 Heidelberg, Germany.
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Schmiesing J, Schlüter H, Ullrich K, Braulke T, Mühlhausen C. Interaction of glutaric aciduria type 1-related glutaryl-CoA dehydrogenase with mitochondrial matrix proteins. PLoS One 2014; 9:e87715. [PMID: 24498361 PMCID: PMC3912011 DOI: 10.1371/journal.pone.0087715] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/02/2014] [Indexed: 01/15/2023] Open
Abstract
Glutaric aciduria type 1 (GA1) is an inherited neurometabolic disorder caused by mutations in the GCDH gene encoding glutaryl-CoA dehydrogenase (GCDH), which forms homo- and heteromeric complexes in the mitochondrial matrix. GA1 patients are prone to the development of encephalopathic crises which lead to an irreversible disabling dystonic movement disorder. The clinical and biochemical manifestations of GA1 vary considerably and lack correlations to the genotype. Using an affinity chromatography approach we report here for the first time on the identification of mitochondrial proteins interacting directly with GCDH. Among others, dihydrolipoamide S-succinyltransferase (DLST) involved in the formation of glutaryl-CoA, and the β-subunit of the electron transfer flavoprotein (ETFB) serving as electron acceptor, were identified as GCDH binding partners. We have adapted the yellow fluorescent protein-based fragment complementation assay and visualized the oligomerization of GCDH as well as its direct interaction with DLST and ETFB in mitochondria of living cells. These data suggest that GCDH is a constituent of multimeric mitochondrial dehydrogenase complexes, and the characterization of their interrelated functions may provide new insights into the regulation of lysine oxidation and the pathophysiology of GA1.
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Affiliation(s)
- Jessica Schmiesing
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Department of Clinical Chemistry, Laboratory for Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kurt Ullrich
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (TB); (CM)
| | - Chris Mühlhausen
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (TB); (CM)
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Marlaire S, Van Schaftingen E, Veiga-da-Cunha M. C7orf10 encodes succinate-hydroxymethylglutarate CoA-transferase, the enzyme that converts glutarate to glutaryl-CoA. J Inherit Metab Dis 2014; 37:13-9. [PMID: 23893049 DOI: 10.1007/s10545-013-9632-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/14/2013] [Accepted: 06/21/2013] [Indexed: 10/26/2022]
Abstract
Glutarate, a side-product in the metabolism of tryptophan and lysine, is metabolized by conversion to glutaryl-CoA by a transferase using succinyl-CoA as a coenzyme donor. The enzyme catalyzing this conversion has not been formally identified. However, a benign form of glutaric aciduria (glutaric aciduria type III) is due to mutations in C7orf10, a putative member of the coenzyme A transferase class III family. In the present work, we show that recombinant human C7orf10 catalyzes the succinyl-CoA-dependent conversion of glutarate to glutaryl-CoA. C7orf10 could use many dicarboxylic acids as CoA acceptors, the best ones being glutarate, succinate, adipate, and 3-hydroxymethylglutarate. Confocal microscopy analysis of CHO cells transfected with a C7orf10-GFP fusion protein indicated that C7orf10 is a mitochondrial protein, in agreement with the presence of a predicted mitochondrial propeptide at its N-terminus. The effect of a missense mutation (p.Arg336Trp) found in the homozygous state in several patients with glutaric aciduria type III and present in the general population at a low frequency was also investigated. The p.Arg336Trp mutation led to the production of insoluble and inactive C7orf10 both in Escherichia coli and in HEK293T cells. These findings indicate that C7orf10 is implicated in the metabolism of glutarate, but possibly also of longer dicarboxylic acids. Homologues of this enzyme are found in numerous bacterial operons comprising also a putative glutaryl-CoA dehydrogenase, indicating that an enzyme with similar specificity exists in prokaryotes.
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Affiliation(s)
- Simon Marlaire
- de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium,
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Moncoq K, Regad L, Mann S, Méjean A, Ploux O. Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2340-52. [DOI: 10.1107/s0907444913021859] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/05/2013] [Indexed: 11/11/2022]
Abstract
Anatoxin-a and homoanatoxin-a are two potent cyanobacterial neurotoxins biosynthesized from L-proline by a short pathway involving polyketide synthases. Proline is first loaded onto AnaD, an acyl carrier protein, and prolyl-AnaD is then oxidized to 1-pyrroline-5-carboxyl-AnaD by a flavoprotein, AnaB. Three polyketide synthases then transform this imine into anatoxin-a or homoanatoxin-a. AnaB was crystallized in its holo form and its three-dimensional structure was determined by X-ray diffraction at 2.8 Å resolution. AnaB is a homotetramer and its fold is very similar to that of the acyl-CoA dehydrogenases (ACADs). The active-site base of AnaB, Glu244, superimposed very well with that of human isovaleryl-CoA dehydrogenase, confirming previous site-directed mutagenesis experiments and mechanistic proposals. The substrate-binding site of AnaB is small and is likely to be fitted for the pyrrolidine ring of proline. However, in contrast to ACADs, which use an electron-transport protein, AnaB uses molecular oxygen as the electron acceptor, as in acyl-CoA oxidases. Calculation of the solvent-accessible surface area around the FAD in AnaB and in several homologues showed that it is significantly larger in AnaB than in its homologues. A protonated histidine near the FAD in AnaB is likely to participate in oxygen activation. Furthermore, an array of water molecules detected in the AnaB structure suggests a possible path for molecular oxygen towards FAD. This is consistent with AnaB being an oxidase rather than a dehydrogenase. The structure of AnaB is the first to be described for a prolyl-ACP oxidase and it will contribute to defining the structural basis responsible for oxygen reactivity in flavoenzymes.
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36
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Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L. Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. Structure 2013; 21:1182-92. [PMID: 23791943 PMCID: PMC3701320 DOI: 10.1016/j.str.2013.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/17/2023]
Abstract
Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design. Structures of human and bacterial MCDs were determined at up to 2.3 Å resolution Distinct tetrameric and dimeric MCD oligomerizations were observed Unexpected homology to the GNAT superfamily gives insights into catalytic mechanism The structures provide the molecular basis for the disease-causing mutations in MCD
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Affiliation(s)
- D Sean Froese
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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Schürmann M, Deters A, Wübbeler JH, Steinbüchel A. A novel 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis strain DPN7T acting as a key enzyme during catabolism of 3,3'-dithiodipropionic acid is a member of the acyl-CoA dehydrogenase superfamily. J Bacteriol 2013; 195:1538-51. [PMID: 23354747 PMCID: PMC3624521 DOI: 10.1128/jb.02105-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/17/2013] [Indexed: 01/28/2023] Open
Abstract
3-Sulfinopropionyl coenzyme A (3SP-CoA) desulfinase (AcdDPN7) is a new desulfinase that catalyzes the sulfur abstraction from 3SP-CoA in the betaproteobacterium Advenella mimigardefordensis strain DPN7(T). During investigation of a Tn5::mob-induced mutant defective in growth on 3,3'-dithiodipropionate (DTDP) and also 3-sulfinopropionate (3SP), the transposon insertion was mapped to an open reading frame with the highest homology to an acyl-CoA dehydrogenase (Acd) from Burkholderia phenoliruptrix strain BR3459a (83% identical and 91% similar amino acids). An A. mimigardefordensis Δacd mutant was generated and verified the observed phenotype of the Tn5::mob-induced mutant. For enzymatic studies, AcdDPN7 was heterologously expressed in Escherichia coli BL21(DE3)/pLysS by using pET23a::acdDPN7. The purified protein is yellow and contains a noncovalently bound flavin adenine dinucleotide (FAD) cofactor, as verified by high-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS) analyses. Size-exclusion chromatography revealed a native molecular mass of about 173 kDa, indicating a homotetrameric structure (theoretically 179 kDa), which is in accordance with other members of the acyl-CoA dehydrogenase superfamily. In vitro assays unequivocally demonstrated that the purified enzyme converted 3SP-CoA into propionyl-CoA and sulfite (SO3(2-)). Kinetic studies of AcdDPN7 revealed a Vmax of 4.19 μmol min(-1) mg(-1), an apparent Km of 0.013 mM, and a kcat/Km of 240.8 s(-1) mM(-1) for 3SP-CoA. However, AcdDPN7 is unable to perform a dehydrogenation, which is the usual reaction catalyzed by members of the acyl-CoA dehydrogenase superfamily. Comparison to other known desulfinases showed a comparably high catalytic efficiency of AcdDPN7 and indicated a novel reaction mechanism. Hence, AcdDPN7 encodes a new desulfinase based on an acyl-CoA dehydrogenase (EC 1.3.8.x) scaffold. Concomitantly, we identified the gene product that is responsible for the final desulfination step during catabolism of 3,3'-dithiodipropionate (DTDP), a sulfur-containing precursor substrate for biosynthesis of polythioesters.
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Affiliation(s)
- Marc Schürmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Anika Deters
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Kormanik K, Kang H, Cuebas D, Vockley J, Mohsen AW. Evidence for involvement of medium chain acyl-CoA dehydrogenase in the metabolism of phenylbutyrate. Mol Genet Metab 2012; 107:684-9. [PMID: 23141465 PMCID: PMC3504130 DOI: 10.1016/j.ymgme.2012.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 10/12/2012] [Indexed: 11/28/2022]
Abstract
Sodium phenylbutyrate is used for treating urea cycle disorders, providing an alternative for ammonia excretion. Following conversion to its CoA ester, phenylbutyryl-CoA is postulated to undergo one round of β-oxidation to phenylacetyl-CoA, the active metabolite. Molecular modeling suggests that medium chain acyl-CoA dehydrogenase (MCAD; EC 1.3.99.3), a key enzyme in straight chain fatty acid β-oxidation, could utilize phenylbutyryl-CoA as substrate. Moreover, phenylpropionyl-CoA has been shown to be a substrate for MCAD and its intermediates accumulate in patients with MCAD deficiency. We have examined the involvement of MCAD and other acyl-CoA dehydrogenases (ACADs) in the metabolism of phenylbutyryl-CoA. Anaerobic titration of purified recombinant human MCAD with phenylbutyryl-CoA caused changes in the MCAD spectrum that are similar to those induced by octanoyl-CoA, its bona fide substrate, and unique to the development of the charge transfer ternary complex. The calculated apparent dissociation constant (K(D app)) for these substrates was 2.16 μM and 0.12 μM, respectively. The MCAD reductive and oxidative half reactions were monitored using the electron transfer flavoprotein (ETF) fluorescence reduction assay. The catalytic efficiency and the K(m) for phenylbutyryl-CoA were 0.2 mM 34(-1)·sec(-1) and 5.3 μM compared to 4.0 mM(-1)·sec(-1) and 2.8 μM for octanoyl-CoA. Extracts of wild type and MCAD-deficient lymphoblast cells were tested for the ability to reduce ETF using phenylbutyryl-CoA as substrate. While ETF reduction activity was detected in extracts of wild type cells, it was undetectable in extracts of cells deficient in MCAD. The results are consistent with MCAD playing a key role in phenylbutyrate metabolism.
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Affiliation(s)
- Kaitlyn Kormanik
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, 15224
- Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15213, United States
| | - Heejung Kang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, 15224
- Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15213, United States
| | - Dean Cuebas
- Department of Chemistry, Missouri State University, Springfield, MO 65897, United States
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, 15224
- Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15213, United States
| | - Al-Walid Mohsen
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, 15224
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Bross P, Frederiksen JB, Bie AS, Hansen J, Palmfeldt J, Nielsen MN, Duno M, Lund AM, Christensen E. Heterozygosity for an in-frame deletion causes glutaryl-CoA dehydrogenase deficiency in a patient detected by newborn screening: investigation of the effect of the mutant allele. J Inherit Metab Dis 2012; 35:787-96. [PMID: 22231382 DOI: 10.1007/s10545-011-9437-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/31/2011] [Accepted: 12/08/2011] [Indexed: 11/30/2022]
Abstract
A patient with suspected glutaric aciduria type 1 (GA-1) was detected by newborn screening. GA-1 is known as an autosomal recessively inherited disease due to defects in the gene coding for glutaryl-CoA dehydrogenase (GCDH), a mitochondrial enzyme involved in the catabolism of the amino acids hydroxylysine, lysine and tryptophan. DNA and cDNA sequencing revealed a 18 bp deletion (c.553_570del18) resulting in deletion of six amino acids (p.Gly185_Ser190del) in one allele and no sequence changes in the other allele. Confirmatory biochemical analysis of blood, urine and cultured fibroblasts from the proband were consistent with a mild biochemical GA-1 phenotype. Recombinant expression of the mutant variant in E. coli showed that the GCDH-(p.Gly185_Ser190del) protein displayed severely decreased assembly into tetramers and enzyme activity. To discover a potential dominant negative effect of the mutant protein, we engineered a prokaryotic expression system in which expression of a wild type and a mutant GCDH allele is controlled by separately inducible promoters. These cells displayed decreased levels of GCDH tetramer and enzyme activity when expressing both the wild type and the mutant GCDH variant protein compared to the situation when only the wild type allele was expressed. Further experiments suggest that the major impact of the GCDH-(p.Gly185_Ser190del) protein in heterozygous cells consists of hampering the assembly of wild type GCDH into tetramers. Our experimental data are consistent with the hypothesis that heterozygosity for this mutation confers a dominant negative effect resulting in a GCDH enzyme activity that is significantly lower than the expected 50%.
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Affiliation(s)
- Peter Bross
- Research Unit for Molecular Medicine, Aarhus University Hospital and Aarhus University, Institute of Clinical Medicine, Aarhus, Denmark.
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40
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Wu L, Qiao Y, Gao J, Deng G, Yu W, Chen G, Li D. Functional characterization of rat glutaryl-CoA dehydrogenase and its comparison with straight-chain acyl-CoA dehydrogenase. Bioorg Med Chem Lett 2011; 21:6667-73. [PMID: 21974953 DOI: 10.1016/j.bmcl.2011.09.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 09/16/2011] [Indexed: 11/17/2022]
Abstract
Glutaryl-CoA dehydrogenase catalyzes the oxidative decarboxylation of the γ-carboxylate of the substrate, glutaryl-CoA, to yield crotonyl-CoA and CO(2). The enzyme is a member of the acyl-CoA dehydrogenase (ACD) family of flavoproteins. In the present study, the catalytic properties of this enzyme, including its substrate specificity, isomerase activity, and interactions with inhibitors, were systematically studied. Our results indicated that the enzyme has its catalytic properties very similar to those of short-chain and medium-chain acyl-CoA dehydrogenase except its additional decarboxylation reaction. Therefore, the inhibitors of fatty acid oxidation targeting straight chain acyl-CoA dehydrogenase could also function as inhibitors for amino acid metabolism of lysine, hydroxylysine, and tryptophan.
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Affiliation(s)
- Long Wu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, PR China
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41
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Begley DW, Davies DR, Hartley RC, Hewitt SN, Rychel AL, Myler PJ, Van Voorhis WC, Staker BL, Stewart LJ. Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1060-9. [PMID: 21904051 PMCID: PMC3169403 DOI: 10.1107/s1744309111014436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/17/2011] [Indexed: 11/10/2022]
Abstract
Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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Kölker S, Christensen E, Leonard JV, Greenberg CR, Boneh A, Burlina AB, Burlina AP, Dixon M, Duran M, García Cazorla A, Goodman SI, Koeller DM, Kyllerman M, Mühlhausen C, Müller E, Okun JG, Wilcken B, Hoffmann GF, Burgard P. Diagnosis and management of glutaric aciduria type I--revised recommendations. J Inherit Metab Dis 2011; 34:677-94. [PMID: 21431622 PMCID: PMC3109243 DOI: 10.1007/s10545-011-9289-5] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/19/2011] [Accepted: 01/24/2011] [Indexed: 11/02/2022]
Abstract
Glutaric aciduria type I (synonym, glutaric acidemia type I) is a rare organic aciduria. Untreated patients characteristically develop dystonia during infancy resulting in a high morbidity and mortality. The neuropathological correlate is striatal injury which results from encephalopathic crises precipitated by infectious diseases, immunizations and surgery during a finite period of brain development, or develops insidiously without clinically apparent crises. Glutaric aciduria type I is caused by inherited deficiency of glutaryl-CoA dehydrogenase which is involved in the catabolic pathways of L-lysine, L-hydroxylysine and L-tryptophan. This defect gives rise to elevated glutaric acid, 3-hydroxyglutaric acid, glutaconic acid, and glutarylcarnitine which can be detected by gas chromatography/mass spectrometry (organic acids) or tandem mass spectrometry (acylcarnitines). Glutaric aciduria type I is included in the panel of diseases that are identified by expanded newborn screening in some countries. It has been shown that in the majority of neonatally diagnosed patients striatal injury can be prevented by combined metabolic treatment. Metabolic treatment that includes a low lysine diet, carnitine supplementation and intensified emergency treatment during acute episodes of intercurrent illness should be introduced and monitored by an experienced interdisciplinary team. However, initiation of treatment after the onset of symptoms is generally not effective in preventing permanent damage. Secondary dystonia is often difficult to treat, and the efficacy of available drugs cannot be predicted precisely in individual patients. The major aim of this revision is to re-evaluate the previous diagnostic and therapeutic recommendations for patients with this disease and incorporate new research findings into the guideline.
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Affiliation(s)
- Stefan Kölker
- Department of General Pediatrics, Division of Inborn Metabolic Diseases, University Children's Hospital, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.
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43
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Schaarschmidt J, Wischgoll S, Hofmann HJ, Boll M. Conversion of a decarboxylating to a non-decarboxylating glutaryl-coenzyme A dehydrogenase by site-directed mutagenesis. FEBS Lett 2011; 585:1317-21. [PMID: 21477586 DOI: 10.1016/j.febslet.2011.03.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 11/26/2022]
Abstract
Glutaryl-coenzyme A (CoA) dehydrogenases (GDHs) are acyl-CoA dehydrogenases, which usually dehydrogenate and decarboxylate the substrate to crotonyl-CoA. In some anaerobic bacteria, non-decarboxylating GDHs exist that release glutaconyl-CoA (2,3-dehydroglutaryl-CoA) without decarboxylation. The differing mechanisms of decarboxylating and non-decarboxylating GDHs were investigated by site-directed mutagenesis of the gene coding for the crotonyl-CoA-forming GDH from Geobacter metallireducens. Exchange of single amino acids involved in substrate carboxylate binding impaired the decarboxylation step, resulting in relative glutaconyl-CoA:crotonyl-CoA formation rates of 1:1 (S97A) or 13:1 (Y370A). The total amount of glutaconyl-CoA formed was maximal in the Y370V+S97A double mutant. The results obtained indicate that an invariant deprotonated Tyr plays a crucial role for optimizing the leaving group potential of CO(2) in decarboxylating GDHs.
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44
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Mushimoto Y, Fukuda S, Hasegawa Y, Kobayashi H, Purevsuren J, Li H, Taketani T, Yamaguchi S. Clinical and molecular investigation of 19 Japanese cases of glutaric acidemia type 1. Mol Genet Metab 2011; 102:343-8. [PMID: 21176883 DOI: 10.1016/j.ymgme.2010.11.159] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/12/2010] [Accepted: 11/14/2010] [Indexed: 10/18/2022]
Abstract
Glutaric acidemia type 1 (GA1) is a metabolic disease caused by a deficiency of glutaryl-CoA dehydrogenase (GCDH). Untreated patients mostly develop severe striatal degeneration. More than 200 mutations have been reported in the GCDH gene, and common R402W and IVS10-2A>C were found in Caucasian and Chinese/Taiwanese, respectively. However, in Japan, genetic mutations have only been reported in a few cases. Herein, we report the clinical and molecular basis of GA1 in 19 Japanese patients, including six previously reported patients. All cases showed high urinary glutaric acid excretion. Eleven patients were severely impaired (three patients died), three had mild impairment, and five showed normal development. Four of 5 patients that developed normally were detected in the presymptomatic stage by neonatal or sibling screening. Nineteen mutations in 26 alleles were identified, and eight of them (89 or 90delC, Y155C, IVS4+2T>C, G244S, Q352X, G354A, K361E, and 1144-1145delGC) were novel. S305L (12.1%, 4/34 alleles) was found in several cases, suggesting that this mutation is a common mutation. In contrast, R402W was not identified and IVS10-2A>C was only found in one allele, suggesting that Japanese patients with GA1 show allelic heterogeneity and have a different genetic background to patients from other countries. One of a pair of sisters with the same mutations (M339V/S305L) lacking residual activity was severely retarded, whereas the older girl remains asymptomatic at 22 years of age, indicating that genotype does not necessarily predict GA1 phenotype. We consistently found that there was no association between genotype and phenotype. However, children with mild impairment were diagnosed and treated earlier than severely impaired cases {4.7±2.5 months (range: 2-8 months) vs. 11.6±12.7 months (range: 4-51 months)}. Our results suggest that early detection and treatment but not genotype are associated with better patient outcome, reinforcing the importance of neonatal screening.
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Affiliation(s)
- Yuichi Mushimoto
- Department of Pediatrics, Shimane University Faculty of Medicine, Izumo, Shimane, Japan.
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Bhadauria V, Wang LX, Peng YL. Proteomic changes associated with deletion of the Magnaporthe oryzae conidial morphology-regulating gene COM1. Biol Direct 2010; 5:61. [PMID: 21040590 PMCID: PMC2989938 DOI: 10.1186/1745-6150-5-61] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 11/02/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Deletion of a conidial morphology regulating gene encoding putative transcriptional regulator COM1 in M. oryzae resulted in aberrant conidial shape, reduced conidiation and attenuated virulence. RESULTS In this study, a two-dimensional gel electrophoresis/matrix assisted laser desorption ionization- time of flight mass spectrometry (2-DE/MALDI-TOF MS) based proteomics approach was employed to identify the cellular and molecular components regulated by the COM1 protein (COM1p) that might contribute to the aberrant phenotypes in M. oryzae. By comparing the conidial proteomes of COM1 deletion mutant and its isogenic wild-type strain P131, we identified a potpourri of 31 proteins that exhibited statistically significant alterations in their abundance levels. Of these differentially regulated proteins, the abundance levels of nine proteins were elevated and twelve were reduced in the Δcom1 mutant. Three proteins were detected only in the Δcom1 conidial proteome, whereas seven proteins were apparently undetectable. The data obtained in the study suggest that the COM1p plays a key role in transcriptional reprogramming of genes implicated in melanin biosynthesis, carbon and energy metabolism, structural organization of cell, lipid metabolism, amino acid metabolism, etc. Semi-quantitative RT-PCR analysis revealed the down-regulation of genes encoding enzymes involved in melanin biosynthesis in the COM1 mutant. CONCLUSIONS Our results suggest that the COM1p may regulate the transcription of genes involved in various cellular processes indispensable for conidial development and appressorial penetration. These functions are likely to contribute to the effects of COM1p upon the aberrant phenotypes of M. oryzae.
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Affiliation(s)
- Vijai Bhadauria
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Molecular Plant Pathology, China Agricultural University, Beijing 100193, China
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Wischgoll S, Demmer U, Warkentin E, Günther R, Boll M, Ermler U. Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases. Biochemistry 2010; 49:5350-7. [PMID: 20486657 DOI: 10.1021/bi100317m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Glutaryl-coenzyme A dehydrogenases (GDHs) involved in amino acid degradation were thought to catalyze both the dehydrogenation and decarboxylation of glutaryl-coenzyme A to crotonyl-coenzyme A and CO(2). Recently, a structurally related but nondecarboxylating, glutaconyl-coenzyme A-forming GDH was characterized in the obligately anaerobic bacteria Desulfococcus multivorans (GDH(Des)) which conserves the free energy of decarboxylation by a Na(+)-pumping glutaconyl-coenzyme A decarboxylase. To understand the distinct catalytic behavior of the two GDH types on an atomic basis, we determined the crystal structure of GDH(Des) with and without glutaconyl-coenzyme A bound at 2.05 and 2.1 A resolution, respectively. The decarboxylating and nondecarboxylating capabilities are provided by complex structural changes around the glutaconyl carboxylate group, the key factor being a Tyr --> Val exchange strictly conserved between the two GDH types. As a result, the interaction between the glutaconyl carboxylate and the guanidinium group of a conserved arginine is stronger in GDH(Des) (short and planar bidentate hydrogen bond) than in the decarboxylating human GDH (longer and monodentate hydrogen bond), which is corroborated by molecular dynamics studies. The identified structural changes prevent decarboxylation (i) by strengthening the C4-C5 bond of glutaconyl-coenzyme A, (ii) by reducing the leaving group potential of CO(2), and (iii) by increasing the distance between the C4 atom (negatively charged in the dienolate transition state) and the adjacent glutamic acid.
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Affiliation(s)
- Simon Wischgoll
- Institute of Biochemistry, University of Leipzig, Leipzig, Germany
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Myler PJ, Stacy R, Stewart L, Staker BL, Van Voorhis WC, Varani G, Buchko GW. The Seattle Structural Genomics Center for Infectious Disease (SSGCID). Infect Disord Drug Targets 2010; 9:493-506. [PMID: 19594426 DOI: 10.2174/187152609789105687] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 03/17/2009] [Indexed: 11/22/2022]
Abstract
The NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium established to apply structural genomics approaches to potential drug targets from NIAID priority organisms for biodefense and emerging and re-emerging diseases. The mission of the SSGCID is to determine approximately 400 protein structures over the next five years. In order to maximize biomedical impact, ligand-based drug-lead discovery campaigns will be pursued for a small number of high-impact targets. Here we review the center's target selection processes, which include pro-active engagement of the infectious disease research and drug therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. This is followed by a brief overview of the SSGCID structure determination pipeline and ligand screening methodology. Finally, specifics of our resources available to the scientific community are presented. Physical materials and data produced by SSGCID will be made available to the scientific community, with the aim that they will provide essential groundwork benefiting future research and drug discovery.
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Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, 307 Westlake Ave N, Seattle, WA 98109-5219, USA.
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Li Z, Zhai Y, Fang J, Zhou Q, Geng Y, Sun F. Purification, crystallization and preliminary crystallographic analysis of very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:426-30. [PMID: 20383014 PMCID: PMC2852336 DOI: 10.1107/s1744309110005002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 02/08/2010] [Indexed: 11/10/2022]
Abstract
Acyl-CoA dehydrogenase [acyl-CoA:(acceptor) 2,3-oxidoreductase; EC 1.3.99.3] catalyzes the first reaction step in mitochondrial fatty-acid beta-oxidation. Here, the very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans (cVLCAD) has been cloned and overexpressed in Escherichia coli strain BL21 (DE3). Interestingly, unlike other very-long-chain acyl-CoA dehydrogenases, cVLCAD was found to form a tetramer by size-exclusion chromatography coupled with in-line static light-scattering, refractive-index and ultraviolet measurements. Purified cVLCAD (12 mg ml(-1)) was successfully crystallized by the hanging-drop vapour-diffusion method under conditions containing 100 mM Tris-HCl pH 8.0, 150 mM sodium chloride, 200 mM magnesium formate and 13% PEG 3350. The crystal has a tetragonal form and a complete diffraction data set was collected and processed to 1.8 A resolution. The crystal belonged to space group C2, with unit-cell parameters a = 138.6, b = 116.7, c = 115.3 A, alpha = gamma = 90.0, beta = 124.0 degrees . A self-rotation function indicated the existence of one noncrystallographic twofold axis. A preliminary molecular-replacement solution further confirmed the presence of two molecules in one asymmetric unit, which yields a Matthews coefficient V(M) of 2.76 A(3) Da(-1) and a solvent content of 55%.
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Affiliation(s)
- Zhijie Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education), College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Yujia Zhai
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Junnan Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Qiangjun Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yunqi Geng
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education), College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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Erb TJ, Fuchs G, Alber BE. (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Mol Microbiol 2009; 73:992-1008. [PMID: 19703103 DOI: 10.1111/j.1365-2958.2009.06837.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Many organic substrates are metabolized via acetyl-coenzyme A (CoA) and enter central carbon metabolism at the level of this compound. We recently described the outlines of the ethylmalonyl-CoA pathway, a new acetyl-CoA assimilation strategy that operates in a number of bacteria such as Rhodobacter sphaeroides, Methylobacterium extorquens and streptomycetes and replaces the glyoxylate cycle. This new pathway involves a unique central reaction sequence catalysed by characteristic enzymes. Here, we identified and characterized (2S)-methylsuccinyl-CoA dehydrogenase from R. sphaeroides, a flavin adenine dinucleotide-containing enzyme that catalyses the last unknown step in the central part of the ethylmalonyl-CoA pathway, the oxidation of (2S)-methylsuccinyl-CoA to mesaconyl-(C1)-CoA. This enzyme is highly specific for its substrate and forms a distinct subgroup within the superfamily of flavin-dependent acyl-CoA dehydrogenases. Homology modelling and comparative sequence analyses with well-studied members of this superfamily identified amino acids that may contribute to the narrow substrate specificity of (2S)-methylsuccinyl-CoA dehydrogenase. The central part of the ethylmalonyl-CoA pathway was reconstituted in vitro using four recombinant enzymes. By this work, the ethylmalonyl-CoA pathway and its stereochemical course have been completely solved. This allowed defining the minimum set of enzymes necessary for its operation and to screen for further organisms following this acetyl-CoA assimilation strategy.
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Affiliation(s)
- Tobias J Erb
- Mikrobiologie, Institut für Biologie II, Schänzlestr 1, Albert-Ludwigs-Universität Freiburg, Freiburg i Br, Germany
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Swigonová Z, Mohsen AW, Vockley J. Acyl-CoA dehydrogenases: Dynamic history of protein family evolution. J Mol Evol 2009; 69:176-93. [PMID: 19639238 DOI: 10.1007/s00239-009-9263-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 05/08/2009] [Accepted: 07/03/2009] [Indexed: 10/20/2022]
Abstract
The acyl-CoA dehydrogenases (ACADs) are enzymes that catalyze the alpha,beta-dehydrogenation of acyl-CoA esters in fatty acid and amino acid catabolism. Eleven ACADs are now recognized in the sequenced human genome, and several homologs have been reported from bacteria, fungi, plants, and nematodes. We performed a systematic comparative genomic study, integrating homology searches with methods of phylogenetic reconstruction, to investigate the evolutionary history of this family. Sequence analyses indicate origin of the family in the common ancestor of Archaea, Bacteria, and Eukaryota, illustrating its essential role in the metabolism of early life. At least three ACADs were already present at that time: ancestral glutaryl-CoA dehydrogenase (GCD), isovaleryl-CoA dehydrogenase (IVD), and ACAD10/11. Two gene duplications were unique to the eukaryotic domain: one resulted in the VLCAD and ACAD9 paralogs and another in the ACAD10 and ACAD11 paralogs. The overall patchy distribution of specific ACADs across the tree of life is the result of dynamic evolution that includes numerous rounds of gene duplication and secondary losses, interdomain lateral gene transfer events, alteration of cellular localization, and evolution of novel proteins by domain acquisition. Our finding that eukaryotic ACAD species are more closely related to bacterial ACADs is consistent with endosymbiotic origin of ACADs in eukaryotes and further supported by the localization of all nine previously studied ACADs in mitochondria.
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Affiliation(s)
- Zuzana Swigonová
- Department of Pediatrics, University of Pittsburgh, Children's Hospital of Pittsburgh, PA 15213, USA.
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