A Saccharomyces cerevisiae knockout screen for genes critical for growth under sulfur- and nitrogen-limited conditions reveals intracellular sorting via vesicular transport systems.

Abstract

It is understood that nutrient availability significantly impacts cellular growth and metabolism. The genetic basis for survival in nutrient-limited conditions, however, is not as thoroughly explored. The identification and description of the genes vital for growth in these conditions would therefore enhance the understanding of the signaling and biochemical pathways and processes crucial for cellular survival and growth under these constraints. A growth screen of a gene deletion library representing 4,934 genes of Saccharomyces cerevisiae was completed to discover genes required for normal growth under sulfur- and nitrogen-limited conditions. Genes were identified as required under these restrictive environments based on a comparison with their growth in a synthetic, defined control medium. After normalization and statistical analysis, 732 genes were noted as essential in sulfur-limited medium, and 761 genes were found for nitrogen-limited medium, with an overlap of 313 genes found to be needed in both, significantly more than expected by chance. Kyoto Encyclopedia of Genes and Genomes and Gene Ontologies were analyzed to investigate those processes involved. Proteins identified act in central metabolism and in metabolism of amino acids, glycerolipids, glycerophospholipids, and vitamins and in the pathways of mitogen-activated protein kinase and phosphatidylinositol signaling and the processes of vesicle trafficking, autophagy, mitophagy, and endocytosis. Of these, the metabolism and signaling of phosphatidylinositols are not frequently identified in screens examining nutrient starvation in yeast, nor are vesicular fusion, endocytosis, or trafficking to the early endosome, as we have discovered here. This study invites further exploration into the roles of these processes in adaptation to nutrient stress.