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

Study ID	ST001308
Study Title	1H NMR metabolomics corroborates serine hydroxymethyltransferase as the primary target of 2-aminoacrylate in a ridA mutant of Salmonella enterica
Study Type	NMR metabolomics on Salmonella enterica
Study Summary	The 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
Department	Microbiology, Biochemistry, Complex Carbohydrate Research Center
Laboratory	Edison Lab and Downs lab
Last Name	Gouveia
First Name	Goncalo
Address	315 riverbend road, Complex Carbohydrate Research Centre, ATHENS, GA, 30605, USA
Email	goncalog@uga.edu
Phone	7063087500
Submit Date	2020-01-22
Num Groups	4
Total Subjects	40
Raw Data Available	Yes
Raw Data File Type(s)	ft
Analysis Type Detail	NMR
Release Date	2020-03-03
Release Version	1

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Treatment:

Treatment ID:	TR001397
Treatment Summary:	Ten biologically independent wild-type and ridA mutant cultures were grown overnight in NB medium shaking at 37 °C and used to inoculate (1% inoculum) 250 mL non-baffled flasks holding 125 mL of medium. Each culture inoculated one each of the three media types (minimal medium, minimal medium with 1 mM L-isoleucine, and minimal medium with 1 mM glycine), for a total of 60 flasks. Flasks were randomly arranged in an Innova®44 incubator and cultures allowed to grow 16 h at 37 °C, shaking at 180 RPM. Cultures were chilled 5 min on ice and then harvested by centrifugation at 7,000 x G for 10 min at 4 °C. The supernatant was decanted, with 10 mL transferred to sterile 15 mL conical tubes and flash-frozen using liquid nitrogen for downstream analysis of external metabolites. Cell pellets were transferred to sterile 15 mL conical tubes after resuspension in 10 mL ddH2O, prior to a second pelleting at 7,000 x G for 10 min at 4 °C. The supernatant was decanted and pellets were flash-frozen using liquid nitrogen and stored at -80 °C.

Treatment ID:

TR001397

Treatment Summary:

Ten biologically independent wild-type and ridA mutant cultures were grown overnight in NB medium shaking at 37 °C and used to inoculate (1% inoculum) 250 mL non-baffled flasks holding 125 mL of medium. Each culture inoculated one each of the three media types (minimal medium, minimal medium with 1 mM L-isoleucine, and minimal medium with 1 mM glycine), for a total of 60 flasks. Flasks were randomly arranged in an Innova®44 incubator and cultures allowed to grow 16 h at 37 °C, shaking at 180 RPM. Cultures were chilled 5 min on ice and then harvested by centrifugation at 7,000 x G for 10 min at 4 °C. The supernatant was decanted, with 10 mL transferred to sterile 15 mL conical tubes and flash-frozen using liquid nitrogen for downstream analysis of external metabolites. Cell pellets were transferred to sterile 15 mL conical tubes after resuspension in 10 mL ddH2O, prior to a second pelleting at 7,000 x G for 10 min at 4 °C. The supernatant was decanted and pellets were flash-frozen using liquid nitrogen and stored at -80 °C.