Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Characterization of the connection between protein synthesis and amino acid biosynthesis gene expression to growth rate in budding yeast

ABSTRACT: In unicellular organisms, growth rate is the major phenotype that is being selected through evolution. In order to grow efficiently, living cells should synchronize the quantity of their ribosome and RNA polymerase levels according to the respective rates by which amino acids and nucleotides pool are replenished. Gene expression patterns and their relationship with growth rate have been widely investigated in various conditions, and a large set of transcripts which included genes associated with ribosome biogenesis (Ribi) and with the stress response, was shown to be expressed in coordination with cell growth rate. Interestingly, decoupling of this correlation was found for certain mutants and conditions, including in my lab when mutant growth rate was examined and when yeast were grown on xylulose, a carbon source not available in the wild. Under those conditions, amino-acid biosynthesis genes regulated by the GCN4 transcription factor were found to have a strong inverse correlation with growth rate, while Ribi and stress genes showed no such correlation. I hypothesized that this decoupling of the general coupling between growth rate and gene expression is a result of a lack of evolutionary optimization to this carbon source or to genetic mutations. The goal of my study was to examine this hypothesis at a greater depth. To this end, I defined the growth rate and genome-wide expression profile of 328 strains deleted of individual genes that show different levels of growth defect. As predicted, growth rate of those strains was correlated with the expression level of GCN4-dependent genes, but not with the Ribi or stress genes, similar to the correlation observed in our xylulose experiment. 328 S. Cerevisiae deletion strains relatively to the wild type strain

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Noam Ohana

PROVIDER: E-GEOD-54748 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Limited systems-level understanding of oil synthesis in wild oleaginous algae has hindered the development of microalgal feedstock. Nannochloropsis is a small unicellular microalgae widely distributed in oceans and fresh water. In many large-scale and pilot-scale outdoor cultivation facilities, Nannochloropsis strains have been found to be capable of robust growth when supplied with flue gases, naturally accumulating large quantities of oils in a stationary phase, and exhibiting resistance to environmental contaminants. The rich genomic resources, compact genomes, resistance to foreign DNA invasion, wide ecological adaptation, large collections of natural strains and the demonstrated ability to grow on a large scale suggested Nannochloropsis can serve as research models and platform strains for economical and scalable photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying the robust biomass accumulation and oil production in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal triacylglycerol (TAG) production in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolutiontranscript change for the complete time-courses of nitrogen-depletion-induced TAG synthesis. Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 50 M-BM-5mol photons m-2 s-1) at 25M-bM-^DM-^C and aerated by bubbling with a mixture of 1.5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in nitrogen replete medium (Control condition or C, i.e. N+) and nitrogen deprived medium (N deficiency or N, i.e. N-) with 50M-BM-5mol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 4h, 6h, 12h, 24h and 48h. Three biological replicates of algal cultures were established under each of the above M-bM-^@M-^\CM-bM-^@M-^] (i.e. N+) and M-bM-^@M-^\NM-bM-^@M-^] (i.e. N-) conditions, respectively. In total, 36 samples collected at six time points (3h,4h,6h,12h,24h and 48h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.

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Characterization of the connection between protein synthesis and amino acid biosynthesis gene expression to growth rate in budding yeast

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