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Title: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

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. Lastly, 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.
Authors:
ORCiD logo [1] ;  [2] ;  [2] ;  [2] ; ORCiD logo [3] ;  [4] ;  [2] ;  [2] ;  [5] ; ORCiD logo [6] ;  [7] ;  [8] ; ORCiD logo [9] ; ORCiD logo [9]
  1. The Buck Institute for Research on Aging, Novato, CA (United States)
  2. Univ. of California, Berkeley, CA (United States)
  3. United States Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
  4. Joint BioEnergy Institute, Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  5. United States Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Joint BioEnergy Institute, Emeryville, CA (United States)
  7. Joint BioEnergy Institute, Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  8. The Buck Institute for Research on Aging, Novato, CA (United States); Univ. of California, Berkeley, CA (United States)
  9. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Grant/Contract Number:
AC05-76RL01830; AC02-05CH11231; Office of Biological and Environmental Research, DE-SC-0012527; Office of Biological and Environmental Research, DE-AC02-05CH11231
Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1466439
Alternate Identifier(s):
OSTI ID: 1437152; OSTI ID: 1459403; OSTI ID: 1466441

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., and Skerker, Jeffrey M.. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. United States: N. p., Web. doi:10.7554/eLife.32110.
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.. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. United States. doi:10.7554/eLife.32110.
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., and Skerker, Jeffrey M.. 2018. "Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides". United States. doi:10.7554/eLife.32110.
@article{osti_1466439,
title = {Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides},
author = {Coradetti, Samuel T. and Pinel, Dominic and Geiselman, Gina M. and Ito, Masakazu and Mondo, Stephen J. and Reilly, Morgann C. and Cheng, Ya -Fang and Bauer, Stefan and Grigoriev, Igor V. and Gladden, John M. and Simmons, Blake A. and Brem, Rachel B. and Arkin, Adam P. and Skerker, Jeffrey M.},
abstractNote = {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. Lastly, 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.},
doi = {10.7554/eLife.32110},
journal = {eLife},
number = ,
volume = 7,
place = {United States},
year = {2018},
month = {3}
}

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