Transcriptomic study of zinc-deficient Saccharomyces cerevisiae wild-type, atg1?, and atg41? strains

Purpose: ATG41 is involved both in autophagy and zinc-deficient growth. The goal of this study is to compare transcriptomic profiles of wild-type and atg41? strains to discover autophagy-independent molecular phenotypes for the mutant. The atg1? mutant is a control for autophagy activity. Methods: Wild-type and mutant yeast were grown to mid-log phase in replete medium and shifted to zinc-deficient medium for 8 hours, after which, cells were harvested for RNA sequencing to detect differential gene expression. Results: Gene expression data for virtually every gene (~6,000) was obtained with ~12,000,000 reads per sample. Differential gene expression analysis showed that several hundred genes were differentially experessed in the atg41? mutant (greater than 2-fold) at an FDR of 0.5. Conclusions: Most strikingly, we found that the atg41? mutant transcriptome shows signs that sulfur metabolism is distrupted during zinc-deficinet growth. Expression of Met4 gene targets is increased. Overall design: mRNA from wild-type, atg1?, and atg41? yeast strains was prepared from zinc-deficient cultures in quadruplicate and sequenced. Single-end, 100bp sequencing was performed, using v4 SBS chemistry on an Illumina HiSeq2500 sequencer.

24

Bucci MD, Weisenhorn E, Haws S, Yao Z, Zimmerman G, Gannon M, Taggart J, Lee T, Klionsky DJ, Russell J, Coon J, Eide DJ