Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>

ABSTRACT The reactive intermediate deaminase RidA (EC 3.5.99.10) is conserved across all domains of life and deaminates reactive enamine species. When Salmonella enterica ridA mutants are grown in minimal medium, 2-aminoacrylate (2AA) accumulates, damages several pyridoxal 5′-phosphate (PLP)-depende...

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Autores principales:	Andrew J. Borchert, Goncalo J. Gouveia, Arthur S. Edison, Diana M. Downs
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	1H NMR 2-aminoacrylate stress RidA metabolomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/40280bad67c446c1aa128e306c7065e7
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spelling	oai:doaj.org-article:40280bad67c446c1aa128e306c7065e72021-12-02T19:46:19ZProton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>10.1128/mSystems.00843-192379-5077https://doaj.org/article/40280bad67c446c1aa128e306c7065e72020-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00843-19https://doaj.org/toc/2379-5077ABSTRACT The reactive intermediate deaminase RidA (EC 3.5.99.10) is conserved across all domains of life and deaminates reactive enamine species. When Salmonella enterica ridA mutants are grown in minimal medium, 2-aminoacrylate (2AA) accumulates, damages several pyridoxal 5′-phosphate (PLP)-dependent enzymes, and elicits an observable growth defect. Genetic studies suggested that damage to serine hydroxymethyltransferase (GlyA), and the resultant depletion of 5,10-methelenetetrahydrofolate (5,10-mTHF), was responsible for the observed growth defect. However, the downstream metabolic consequence from GlyA damage by 2AA remains relatively unexplored. This study sought to use untargeted proton nuclear magnetic resonance (1H NMR) metabolomics to determine whether the metabolic state of an S. enterica ridA mutant was accurately reflected by characterizing growth phenotypes. The data supported the conclusion that metabolic changes in a ridA mutant were due to the IlvA-dependent generation of 2AA, and that the majority of these changes were a consequence of damage to GlyA. While many of the metabolic differences for a ridA mutant could be explained, changes in some metabolites were not easily modeled, suggesting that additional levels of metabolic complexity remain to be unraveled. IMPORTANCE The accumulation of the reactive enamine intermediate 2-aminoacrylate (2AA) elicits global metabolic stress in many prokaryotes and eukaryotes by simultaneously damaging multiple pyridoxal 5′-phosphate (PLP)-dependent enzymes. This work employed 1H NMR to expand our understanding of the consequence(s) of 2AA stress on metabolite pools and effectively identify the metabolic changes stemming from one damaged target: GlyA. This study shows that nutrient supplementation during 1H NMR metabolomics experiments can disentangle complex metabolic outcomes stemming from a general metabolic stress. Metabolomics shows great potential to complement classical reductionist approaches to cost-effectively accelerate the rate of progress in expanding our global understanding of metabolic network structure and physiology. To that end, this work demonstrates the utility in implementing nutrient supplementation and genetic perturbation into metabolomics workflows as a means to connect metabolic outputs to physiological phenomena and establish causal relationships.Andrew J. BorchertGoncalo J. GouveiaArthur S. EdisonDiana M. DownsAmerican Society for Microbiologyarticle1H NMR2-aminoacrylate stressRidAmetabolomicsMicrobiologyQR1-502ENmSystems, Vol 5, Iss 2 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	1H NMR 2-aminoacrylate stress RidA metabolomics Microbiology QR1-502
spellingShingle	1H NMR 2-aminoacrylate stress RidA metabolomics Microbiology QR1-502 Andrew J. Borchert Goncalo J. Gouveia Arthur S. Edison Diana M. Downs Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>
description	ABSTRACT The reactive intermediate deaminase RidA (EC 3.5.99.10) is conserved across all domains of life and deaminates reactive enamine species. When Salmonella enterica ridA mutants are grown in minimal medium, 2-aminoacrylate (2AA) accumulates, damages several pyridoxal 5′-phosphate (PLP)-dependent enzymes, and elicits an observable growth defect. Genetic studies suggested that damage to serine hydroxymethyltransferase (GlyA), and the resultant depletion of 5,10-methelenetetrahydrofolate (5,10-mTHF), was responsible for the observed growth defect. However, the downstream metabolic consequence from GlyA damage by 2AA remains relatively unexplored. This study sought to use untargeted proton nuclear magnetic resonance (1H NMR) metabolomics to determine whether the metabolic state of an S. enterica ridA mutant was accurately reflected by characterizing growth phenotypes. The data supported the conclusion that metabolic changes in a ridA mutant were due to the IlvA-dependent generation of 2AA, and that the majority of these changes were a consequence of damage to GlyA. While many of the metabolic differences for a ridA mutant could be explained, changes in some metabolites were not easily modeled, suggesting that additional levels of metabolic complexity remain to be unraveled. IMPORTANCE The accumulation of the reactive enamine intermediate 2-aminoacrylate (2AA) elicits global metabolic stress in many prokaryotes and eukaryotes by simultaneously damaging multiple pyridoxal 5′-phosphate (PLP)-dependent enzymes. This work employed 1H NMR to expand our understanding of the consequence(s) of 2AA stress on metabolite pools and effectively identify the metabolic changes stemming from one damaged target: GlyA. This study shows that nutrient supplementation during 1H NMR metabolomics experiments can disentangle complex metabolic outcomes stemming from a general metabolic stress. Metabolomics shows great potential to complement classical reductionist approaches to cost-effectively accelerate the rate of progress in expanding our global understanding of metabolic network structure and physiology. To that end, this work demonstrates the utility in implementing nutrient supplementation and genetic perturbation into metabolomics workflows as a means to connect metabolic outputs to physiological phenomena and establish causal relationships.
format	article
author	Andrew J. Borchert Goncalo J. Gouveia Arthur S. Edison Diana M. Downs
author_facet	Andrew J. Borchert Goncalo J. Gouveia Arthur S. Edison Diana M. Downs
author_sort	Andrew J. Borchert
title	Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>
title_short	Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>
title_full	Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>
title_fullStr	Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>
title_full_unstemmed	Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>
title_sort	proton nuclear magnetic resonance metabolomics corroborates serine hydroxymethyltransferase as the primary target of 2-aminoacrylate in a <italic toggle="yes">rida</italic> mutant of <named-content content-type="genus-species">salmonella enterica</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/40280bad67c446c1aa128e306c7065e7
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Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a <italic toggle="yes">ridA</italic> Mutant of <named-content content-type="genus-species">Salmonella enterica</named-content>

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