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Elife. 2018 Mar 9;7. pii: e32110. doi: 10.7554/eLife.32110.

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.

Author information

1
The Buck Institute for Research on Aging, Novato, United States.
2
Energy Biosciences Institute, Berkeley, United States.
3
United States Department of Energy Joint Genome Institute, Walnut Creek, United States.
4
Joint BioEnergy Institute, Emeryville, United States.
5
Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States.
6
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.
7
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
8
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
9
Department of Bioengineering, University of California, Berkeley, Berkeley, United States.
#
Contributed equally

Abstract

The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) 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 Agrobacterium tumefaciens 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.

KEYWORDS:

Rhodosporidium toruloides; TnSeq; computational biology; functional genomics; infectious disease; lipid droplet; lipid metabolism; microbiology; oleaginous yeast; systems biology

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