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A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle

Journal Article · · Nature Communications

Abstract

A prevalent side-reaction of succinate dehydrogenase oxidizes malate to enol-oxaloacetate (OAA), a metabolically inactive form of OAA that is a strong inhibitor of succinate dehydrogenase. We purified from cow heart mitochondria an enzyme (OAT1) with OAA tautomerase (OAT) activity that converts enol-OAA to the physiological keto-OAA form, and determined that it belongs to the highly conserved and previously uncharacterized Fumarylacetoacetate_hydrolase_domain-containing protein family. From all three domains of life, heterologously expressed proteins were shown to have strong OAT activity, and ablating the OAT1 homolog caused significant growth defects. In Escherichia coli , expression of succinate dehydrogenase was necessary for OAT1-associated growth defects to occur, and ablating OAT1 caused a significant increase in acetate and other metabolites associated with anaerobic respiration. OAT1 increased the succinate dehydrogenase reaction rate by 35% in in vitro assays with physiological concentrations of both succinate and malate. Our results suggest that OAT1 is a universal metabolite repair enzyme that is required to maximize aerobic respiration efficiency by preventing succinate dehydrogenase inhibition.

Sponsoring Organization:
USDOE
Grant/Contract Number:
SC0019148
OSTI ID:
2283115
Alternate ID(s):
OSTI ID: 2472080
Journal Information:
Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 15; ISSN 2041-1723
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (64)

The mitochondrial enzyme FAHD1 regulates complex II activity in breast cancer cells and is indispensable for basal BT‐20 cells in vitro journal August 2022
l‐2‐Hydroxyglutaric aciduria: Neuropathological correlations and first report of severe neurodegenerative disease and neonatal death journal March 1995
D‐2‐hydroxyglutaric aciduria: Case report and biochemical studies journal January 1980
l‐2‐Hydroxyglutaric aciduria, a defect of metabolite repair journal June 2007
l‐2‐Hydroxyglutaric aciduria, a disorder of metabolite repair journal November 2008
Oxidation of malate by the mitochondrial succinate-ubiquinone reductase journal October 1988
Isolation and properties of oxaloacetate keto-enol-tautomerases from bovine heart mitochondria journal October 1988
Tightly bound oxalacetate and the activation of succinate dehydrogenase journal November 1972
Identification of the high‐molecular‐mass mitochondrial oxaloacetate keto‐enol tautomerase as inactive aconitase journal March 1989
Direct demonstration of enol -oxaloacetate as an immediate product of malate oxidation by the mammalian succinate dehydrogenase journal July 1991
Regulation of succinate dehydrogenase and tautomerization of oxaloacetate journal January 1989
Oxalacetate Keto-Enol Tautomerase journal April 1969
Studies on succinate dehydrogenase. II. On the nature of the reaction of competitive inhibitors and substrates with succinate dehydrogenase journal January 1965
Crystal structure and mechanism of a carbon–carbon bond hydrolase journal September 1999
A spectrophotometric coupled enzyme assay to measure the activity of succinate dehydrogenase journal November 2013
The gene mutated in l-2-hydroxyglutaric aciduria encodes l-2-hydroxyglutarate dehydrogenase journal January 2006
Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency? journal August 2014
Approaches for completing metabolic networks through metabolite damage and repair discovery journal December 2021
Recent advances in stable isotope-enabled mass spectrometry-based plant metabolomics journal February 2017
Depletion of oxaloacetate decarboxylase FAHD1 inhibits mitochondrial electron transport and induces cellular senescence in human endothelial cells journal June 2017
Identification of a S-(2-succino)cysteine breakdown pathway that uses a novel S-(2-succino) lyase journal December 2022
Structural Insight into Substrate Binding and Catalysis of a Novel 2-Keto-3-deoxy-d-arabinonate Dehydratase Illustrates Common Mechanistic Features of the FAH Superfamily journal May 2008
Stable Isotope Assisted Assignment of Elemental Compositions for Metabolomics journal September 2007
Escherichia coli fumarase A catalyzes the isomerization of enol and keto oxalacetic acid journal January 1993
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters journal May 2011
Catalysis of keto-enol tautomerism of oxaloacetic acid and its ions studied by proton nuclear magnetic resonance journal December 1977
D‐2‐Hydroxyglutaric aciduria: Further clinical delineation journal June 1999
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate journal November 2009
Overflow metabolism in Escherichia coli results from efficient proteome allocation journal December 2015
A cross-platform toolkit for mass spectrometry and proteomics journal October 2012
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking journal August 2016
Metabolite damage and its repair or pre-emption journal January 2013
A non-canonical tricarboxylic acid cycle underlies cellular identity journal March 2022
Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1 journal November 2018
Identification of a dehydrogenase acting on D-2-hydroxyglutarate journal June 2004
‘Nothing of chemistry disappears in biology’: the Top 30 damage-prone endogenous metabolites journal June 2016
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS: Metabolic flux profiling in E.���coli journal March 2003
Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli journal January 1998
A gene encoding a putative FAD-dependent l -2-hydroxyglutarate dehydrogenase is mutated in l -2-hydroxyglutaric aciduria journal November 2004
Design and analysis of synthetic carbon fixation pathways journal April 2010
Glycolytic strategy as a tradeoff between energy yield and protein cost journal April 2013
Alteration of the Specificity of Malate Dehydrogenase by Chemical Modulation of an Active Site Arginine journal August 2001
Superoxide Is Produced by the Reduced Flavin in Mitochondrial Complex I journal May 2011
Identification of Human Fumarylacetoacetate Hydrolase Domain-containing Protein 1 (FAHD1) as a Novel Mitochondrial Acylpyruvase journal October 2011
Identification of FAH Domain-containing Protein 1 (FAHD1) as Oxaloacetate Decarboxylase journal March 2015
Identification of a metabolic disposal route for the oncometabolite S-(2-succino)cysteine in Bacillus subtilis journal May 2018
The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism journal December 2020
Characterization of the human fumarylacetoacetate hydrolase gene and identification of a missense mutation abolishing enzymatic activity journal January 1993
ECMDB: The E. coli Metabolome Database journal October 2012
The Phylogenetic Extent of Metabolic Enzymes and Pathways journal March 2003
Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle journal March 2020
Tissue-based map of the human proteome journal January 2015
YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl journal August 2016
Identification of Escherichia coli YgaF as an l -2-Hydroxyglutarate Oxidase journal June 2008
Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization journal January 2024
Pathway of acetate assimilation in autotrophic and heterotrophic methanococci. journal November 1987
Isotope rate Effects in the Enolization of Oxalacetic acid journal July 1962
Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective journal June 2010
Tricarboxylic acid cycle intermediates in human muscle at rest and during prolonged cycling journal February 1997
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data journal July 2010
Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family journal May 2015
Protein kinase A controls yeast growth in visible light journal November 2020
FAH Domain Containing Protein 1 (FAHD-1) Is Required for Mitochondrial Function and Locomotion Activity in C. elegans journal August 2015
X-ray structure of fumarylacetoacetate hydrolase family member Homo sapiens FLJ36880 journal October 2004

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