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Gene expression analysis of yeast lacking Set4 under normal and stress conditions

ABSTRACT: Genome-wide gene expression data were generated for wildtype and set4 mutant yeast under aerobic and hypoxic conditions to determine the contribution of Set4 to gene expression. Illumina-based sequencing was performed on strand-specific libraries prepared from mRNA purified from yeast grown in rich medium aerobically or under hypoxia. Reads were processed for qualiy control, mapped to the genome, and differential gene expression was determined based on log fold-change differences between set4 mutants and wildtype.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE173901 | GEO | 2021/10/05

REPOSITORIES: GEO

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Project description:Pseudomonas aeruginosa is a Gram-negative, opportunistic bacterium and a major etiological agent in monogenic disease cystic fibrosis (CF). High density colonies of P. aeruginosa are often isolated from hypoxic mucus plugs in respiratory tract of CF patients, indicating high adaptive capacities of the bacterium. Despite the high prevalence and related patient mortality, the protein machinery enabling the bacterium to adapt to this hypoxic environment remains to be fully elucidated. We investigated this by performing both SWATH mass spectrometry and data-dependent SPS-MS3 of TMT labelled peptides to profile the proteomes of two P. aeruginosa CF isolates, PASS2 and PASS3, and a laboratory reference strain, PAO1, grown under hypoxic stress (O2<1%) and aerobic conditions in media that mimics the nutrient components of the CF lung. 3,967 P. aeruginosa proteins were quantitated (FDR <1%) across all three strains, reflecting approximately 71% of predicted ORFs in PAO1 and representing the most comprehensive proteome of clinically relevant P. aeruginosa to date. Comparative analysis revealed 735, 640 and 364 proteins were altered by two-fold or more when comparing low oxygen to aerobic growth in PAO1, PASS2 and PASS3 respectively. Strikingly, under hypoxic stress, all strains showed concurrent increased abundance of proteins required for both aerobic (cbb3-1 and cbb3-2 terminal oxidases) and anaerobic denitrification and arginine fermentation, with the two clinical isolates showing higher relative expression of proteins in these pathways. Additionally, functional annotation revealed that clinical strains portray a unique expression profile of replication, membrane biogenesis and virulence proteins during hypoxia which may endow these bacteria with a survival advantage. These protein profiles illuminate the diversity of P. aeruginosa mechanisms to adapt to low oxygen and shows that CF isolates initiate a robust molecular response to persist under these conditions.

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Gene expression analysis of yeast lacking Set4 under normal and stress conditions

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