Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

• Published in: eLife 2018-03, Vol.7
• Main Authors: Coradetti, Samuel T, Pinel, Dominic, Geiselman, Gina M, Ito, Masakazu, Mondo, Stephen J, Reilly, Morgann C, Cheng, Ya-Fang, Bauer, Stefan, Grigoriev, Igor V, Gladden, John M, Simmons, Blake A, Brem, Rachel B, Arkin, Adam P, Skerker, Jeffrey M
• Format: Article
• Language: English
• Subjects: Agrobacterium tumefaciens; Amino acids; Autophagy; BASIC BIOLOGICAL SCIENCES; Bioengineering; Biomass; Carbon sources; Carotenoids; Carotenoids - biosynthesis; Carotenoids - genetics; Cellular biology; Clonal deletion; Computational and Systems Biology; Deoxyribonucleic acid; DNA; Experiments; Fatty acids; functional genomics; Fungi; Gene deletion; Gene expression; Gene Expression Regulation, Fungal - genetics; Genes; Genomics; Insertion; Laboratories; lipid droplet; Lipid metabolism; Lipid Metabolism - genetics; Lipids; Lipids - biosynthesis; Metabolic Engineering; Metabolism; Microbiology and Infectious Disease; Microscopy; Mutagenesis; Mutagenesis, Insertional; Nitrogen; Nucleotide sequence; oleaginous yeast; Phagocytosis; Phenotype; Protein transport; Proteins; Rhodosporidium toruloides; Rhodotorula - genetics; Rhodotorula - metabolism; Rhodotorula toruloides; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; T-DNA; TnSeq; Transformation, Genetic; tRNA; tRNA Ala
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.32110

The basidiomycete yeast (also known as ) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.