Summary of study ST001308

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000889. The data can be accessed directly via it's Project DOI: 10.21228/M8S39G This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST001308
Study Title1H NMR metabolomics corroborates serine hydroxymethyltransferase as the primary target of 2-aminoacrylate in a ridA mutant of Salmonella enterica
Study TypeNMR metabolomics on Salmonella enterica
Study SummaryThe reactive intermediate deaminase RidA (EC: 3.5.99.10) is conserved across all domains of life and deaminates reactive enamine species. When S. 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 1H NMR metabolomics to determine whether the metabolic state of a 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 shifts in the metabolome of 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.
Institute
University of Georgia
DepartmentMicrobiology, Biochemistry, Complex Carbohydrate Research Center
LaboratoryEdison Lab and Downs lab
Last NameGouveia
First NameGoncalo
Address315 riverbend road, Complex Carbohydrate Research Centre, ATHENS, GA, 30605, USA
Emailgoncalog@uga.edu
Phone7063087500
Submit Date2020-01-22
Num Groups4
Total Subjects40
Raw Data AvailableYes
Raw Data File Type(s).par, pdata, info, .xml
Analysis Type DetailNMR
Release Date2020-03-03
Release Version1
Goncalo Gouveia Goncalo Gouveia
https://dx.doi.org/10.21228/M8S39G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Factors:

Subject type: Bacteria; Subject species: Salmonella enterica serovar Typhimurium (Factor headings shown in green)

mb_sample_id local_sample_id Sample_group Genotype Suplement
SA094489media_3480 +Gly 6mut_gly rid1-knockout glycine
SA094490media_3480 +Gly 10mut_gly rid1-knockout glycine
SA094491media_3480 +Gly 8mut_gly rid1-knockout glycine
SA0944923480 +Gly 1mut_gly rid1-knockout glycine
SA0944933480 +Gly 8mut_gly rid1-knockout glycine
SA094494media_3480 +Gly 3mut_gly rid1-knockout glycine
SA0944953480 +Gly 7mut_gly rid1-knockout glycine
SA0944963480 +Gly 9mut_gly rid1-knockout glycine
SA0944973480 +Gly 2mut_gly rid1-knockout glycine
SA0944983480 +Gly 5mut_gly rid1-knockout glycine
SA0944993480 +Gly 4mut_gly rid1-knockout glycine
SA094500media_3480 +Gly 5mut_gly rid1-knockout glycine
SA094501media_3480 +Gly 7mut_gly rid1-knockout glycine
SA094502media_3480 +Gly 2mut_gly rid1-knockout glycine
SA094503media_3480 +Gly 1mut_gly rid1-knockout glycine
SA0945043480 +Gly 3mut_gly rid1-knockout glycine
SA094505media_3480 +Gly 4mut_gly rid1-knockout glycine
SA094506media_3480 +Gly 9mut_gly rid1-knockout glycine
SA0945073480 +Gly 10mut_gly rid1-knockout glycine
SA0945083480 +Gly 6mut_gly rid1-knockout glycine
SA094509media_3480 +Ile 10mut_ile rid1-knockout isoleucine
SA094510media_3480 +Ile 6mut_ile rid1-knockout isoleucine
SA0945113480 +Ile 7mut_ile rid1-knockout isoleucine
SA094512media_3480 +Ile 5mut_ile rid1-knockout isoleucine
SA0945133480 +Ile 1mut_ile rid1-knockout isoleucine
SA0945143480 +Ile 4mut_ile rid1-knockout isoleucine
SA0945153480 +Ile 6mut_ile rid1-knockout isoleucine
SA0945163480 +Ile 5mut_ile rid1-knockout isoleucine
SA094517media_3480 +Ile 3mut_ile rid1-knockout isoleucine
SA094518media_3480 +Ile 9mut_ile rid1-knockout isoleucine
SA094519media_3480 +Ile 2mut_ile rid1-knockout isoleucine
SA094520media_3480 +Ile 1mut_ile rid1-knockout isoleucine
SA094521media_3480 +Ile 4mut_ile rid1-knockout isoleucine
SA0945223480 +Ile 8mut_ile rid1-knockout isoleucine
SA094523media_3480 +Ile 7mut_ile rid1-knockout isoleucine
SA094524media_3480 +Ile 8mut_ile rid1-knockout isoleucine
SA0945253480 +Ile 9mut_ile rid1-knockout isoleucine
SA0945263480 +Ile 2mut_ile rid1-knockout isoleucine
SA0945273480 +Ile 3mut_ile rid1-knockout isoleucine
SA0945283480 +Ile 10mut_ile rid1-knockout isoleucine
SA094529media_3480 Min 8mut_min rid1-knockout minimal
SA0945303480 Min 5mut_min rid1-knockout minimal
SA094531media_3480 Min 4mut_min rid1-knockout minimal
SA0945323480 Min 1mut_min rid1-knockout minimal
SA094533media_3480 Min 3mut_min rid1-knockout minimal
SA094534media_3480 Min 1mut_min rid1-knockout minimal
SA094535media_3480 Min 9mut_min rid1-knockout minimal
SA094536media_3480 Min 6mut_min rid1-knockout minimal
SA0945373480 Min 3mut_min rid1-knockout minimal
SA094538media_3480 Min 10mut_min rid1-knockout minimal
SA094539media_3480 Min 7mut_min rid1-knockout minimal
SA094540media_3480 Min 2mut_min rid1-knockout minimal
SA094541media_3480 Min 5mut_min rid1-knockout minimal
SA0945423480 Min 4mut_min rid1-knockout minimal
SA0945433480 Min 10mut_min rid1-knockout minimal
SA0945443480 Min 8mut_min rid1-knockout minimal
SA0945453480 Min 6mut_min rid1-knockout minimal
SA0945463480 Min 2mut_min rid1-knockout minimal
SA0945473480 Min 9mut_min rid1-knockout minimal
SA0945483480 Min 7mut_min rid1-knockout minimal
SA0945499404 +Gly 9wt_gly wild-type glycine
SA0945509404 +Gly 1wt_gly wild-type glycine
SA094551media_9404 +Gly 4wt_gly wild-type glycine
SA094552media_9404 +Gly 3wt_gly wild-type glycine
SA094553media_9404 +Gly 1wt_gly wild-type glycine
SA0945549404 +Gly 7wt_gly wild-type glycine
SA094555media_9404 +Gly 9wt_gly wild-type glycine
SA094556media_9404 +Gly 10wt_gly wild-type glycine
SA094557media_9404 +Gly 5wt_gly wild-type glycine
SA0945589404 +Gly 3wt_gly wild-type glycine
SA0945599404 +Gly 5wt_gly wild-type glycine
SA0945609404 +Gly 2wt_gly wild-type glycine
SA094561media_9404 +Gly 7wt_gly wild-type glycine
SA094562media_9404 +Gly 2wt_gly wild-type glycine
SA0945639404 +Gly 8wt_gly wild-type glycine
SA094564media_9404 +Gly 8wt_gly wild-type glycine
SA094565media_9404 +Gly 6wt_gly wild-type glycine
SA0945669404 +Gly 6wt_gly wild-type glycine
SA0945679404 +Gly 4wt_gly wild-type glycine
SA0945689404 +Gly 10wt_gly wild-type glycine
SA094569media_9404 +Ile 6wt_ile wild-type isoleucine
SA0945709404 +Ile 10wt_ile wild-type isoleucine
SA0945719404 +Ile 5wt_ile wild-type isoleucine
SA094572media_9404 +Ile 1wt_ile wild-type isoleucine
SA094573media_9404 +Ile 5wt_ile wild-type isoleucine
SA0945749404 +Ile 7wt_ile wild-type isoleucine
SA094575media_9404 +Ile 2wt_ile wild-type isoleucine
SA094576media_9404 +Ile 3wt_ile wild-type isoleucine
SA0945779404 +Ile 3wt_ile wild-type isoleucine
SA094578media_9404 +Ile 9wt_ile wild-type isoleucine
SA0945799404 +Ile 4wt_ile wild-type isoleucine
SA094580media_9404 +Ile 4wt_ile wild-type isoleucine
SA0945819404 +Ile 6wt_ile wild-type isoleucine
SA094582media_9404 +Ile 7wt_ile wild-type isoleucine
SA0945839404 +Ile 9wt_ile wild-type isoleucine
SA0945849404 +Ile 2wt_ile wild-type isoleucine
SA094585media_9404 +Ile 10wt_ile wild-type isoleucine
SA0945869404 +Ile 1wt_ile wild-type isoleucine
SA094587media_9404 +Ile 8wt_ile wild-type isoleucine
SA0945889404 +Ile 8wt_ile wild-type isoleucine
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