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E-MTAB-10413

ABSTRACT: AmpliSeq Data of WT and SLC38A10 knockout primary cortex cells in amino acid starvation and refed conditions

PROVIDER: E-MTAB-10413 | ExpressionAtlas | 2025-07-07

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-10413-analysis-methods.tsv	Tabular
	E-MTAB-10413-analytics.tsv	Tabular
	E-MTAB-10413-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-10413-configuration.xml	Xml
	E-MTAB-10413-g2_g1-mvaPlot.png	Other

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AmpliSeq Data of WT and SLC38A10 knockout primary cortex cells in amino acid starvation and refed conditions

Project description:Samples-WT Basal condition primary cortex cells; WT B27 Starved-Primary cortex cells starved overnight without B27 supplement media. WT AA Starved-Primary cortex cell starved without amino acid for 2 hours. WT AA Refed-Primary cortex cell refed for 1 hour after amino acid starvation. KO Basal-SLC38 Knockout Primary cortex cells starved overnight without B27 supplement media. KO B27 Starved-SLC38 Knockout Primary cortex cell starved without amino acid for 2 hours. KO AA starved-SLC38 Knockout Primary cortex cell refed for 1 hour after amino acid starvation. KO AA Refed-SLC38 Knockout Primary cortex cell refed for 1 hour after amino acid starvation.

2021-06-03 | E-MTAB-10413 | biostudies-arrayexpress

AmpliSeq Data of WT and SLC38A10 knockout primary cortex cells in amino acid starvation and refed conditions

Project description:AmpliSeq Data of WT and SLC38A10 knockout primary cortex cells in amino acid starvation and refed conditions

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Project description:The stringent response is a conserved stress response employed by various bacteria to respond to and cope with conditions of amino acid starvation, carbon-source, fatty acid, oxygen/iron limitation, heat shock, antimicrobial challenge, and/or other environmental stressors. In S. aureus, the stringent response is mediated in part by enzyme RSH (relA spoT homologue) which synthesizes two nucleotide-based molecules, guanosine tetraphosphate (ppGpp) and pentaphosphate (pppGpp), collectively known as (p) ppGpp. This response is known to result in a number of diverse physiological and metabolic changes which we further characterized in the present study. Specifically, the global transcriptome of the RSH synthase mutant (rshsyn) was compared to the WT parent S. aureus strain (NCTC 8325) by RNA-Seq analysis under both normal and nutrient-limited media conditions. In order to mimic nutrient limitation, bacteria were treated with mupirocin, an antibiotic and isoleucine analogue known to lead to isoleucine starvation. In the WT strain, in response to mupirocin-induced isoleucine starvation, genes encoding protein synthesis machinery were suppressed while genes encoding amino acid biosynthetic machinery were upregulated. This response likely employed to compensate for amino acid deprivation, was not induced in the stringent response mutant. Furthermore, under starvation conditions, biofilm-related genes (i.e. icaA, icaC, fnbA, clfB, emp) were more upregulated in the WT than the stringent response mutant. Moreover, the effect of mupirocin caused a stronger upregulation of several proteases (i.e. sspA, sspP, sppB, aur), lipases (lip, geh) and phenol soluble modulin toxins in the WT as compared to the mutant. Overall, these results suggest that under starvation conditions, RSH plays an important role in helping the cell respond to nutritional stress as well as regulates the expression of numerous colonization and virulence factors.

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