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Lipidomic characterization of Jurkat-derived T cell line in which the chaperonin complex CCT has been partially silenced

ABSTRACT: When the chaperonin complex CCT is partially silenced in Jurkat-derived T cell line J77 E61, we observe changes in the production of exosomes and in their composition. Thus, to explore the bases of these alterations and find possible new mechanisms of exosome biosynthesis regulation we characterized the lipidome content in cells where the chaperonin complex CCT was partially silent (CCT) and controls (CTRL). We analyzed 5 biological replicates containing 3 × 106 cells using LC-MS in positive and negative polarity mode. For quality control, 5 QCs samples and 4 blanks were also included in the analysis (total 19 samples and 2 groups).

ORGANISM(S): Human Homo Sapiens

TISSUE(S): T-cells

SUBMITTER: Alessia Ferrarini

PROVIDER: ST002185 | MetabolomicsWorkbench | Fri Jun 03 00:00:00 BST 2022

REPOSITORIES: MetabolomicsWorkbench

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Project description:BACKGROUND:Isobutanol is a promising next generation biofuel with demonstrated high yield microbial production, but the toxicity of this molecule reduces fermentation volumetric productivity and final titers. Organic solvent tolerance is a complex, multigenic phenotype that has been recalcitrant to rational engineering approaches. We apply experimental evolution followed by genome resequencing and a gene expression study to elucidate genetic bases on adaptation to exogenous isobutanol stress. RESULTS:The adaptations acquired in our evolved lineages exhibit antagonistic pleiotropy between minimal and rich medium, and appear to be specific to the effects of longer chain alcohols. By examining genotypic adaptation in multiple independent lineages, we find evidence of parallel evolution in hfq, mdh, acrAB, gatYZABCD, and rph genes. Many isobutanol tolerant lineages show reduced rpoS activity, perhaps related to mutations in hfq or acrAB. Consistent with the complex, multigenic nature of solvent tolerance, we observe adaptations in a diversity of cellular processes. Many adaptations appear to involve epistasis between different mutations, implying a rugged fitness landscape for isobutanol tolerance. We observe a trend of evolution targeting post-transcriptional regulation and high centrality nodes of biochemical networks. Collectively, the genotypic adaptations we observe suggest mechanisms of adaptation to isobutanol stress based on remodelling the cell envelope and surprisingly, stress response attenuation. CONCLUSIONS:We have discovered a set of genotypic adaptations that confer increased tolerance to exogenous isobutanol stress. Our results are immediately useful to efforts to engineer more isobutanol tolerant host strains of E. coli for isobutanol production. We suggest that rpoS and post-transcriptional regulators, such as hfq, RNA helicases, and sRNAs may be interesting mutagenesis targets for futurue global phenotype engineering. Two strains (WT strain and G3.2 mutant strain), each with two culture conditions (with and without isobutanol in medium). Three biological replicates for each strain/culture condition. Twelve samples in total.

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Lipidomic characterization of Jurkat-derived T cell line in which the chaperonin complex CCT has been partially silenced

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