Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
- The Buck Institute for Research on Aging, United States
- University of California, Berkeley, United States
- United States Department of Energy Joint Genome Institute, United States
- Joint BioEnergy Institute, United States
- Cited 17
- Views 2,528
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Abstract
The basidiomycete yeast Rhodosporidium toruloides (a.k.a. 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 1337 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.
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Author details
Funding
Department of Energy, Office of Science, Office of Biological and Environmental Research (DE-SC-0012527)
- Samuel T Coradetti
- Dominic Pinel
- Gina Geiselman
- Masakazu Ito
- Ya-Fang Cheng
- Stefan Bauer
- Rachel Brem
- Adam P Arkin
- Jeffrey M Skerker
University of California Berkeley (OO1605)
- Dominic Pinel
- Adam P Arkin
- Jeffrey M Skerker
Department of Energy, Office of Science, Office of Biological and Environmental Research (DE-AC02-05CH11231)
- Stephen Mondo
- Igor Grigoriev
- John M Gladden
- Blake A Simmons
University of California Berkeley (OO6J01)
- Dominic Pinel
- Adam P Arkin
- Jeffrey M Skerker
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Joerg Bohlmann, University of British Columbia, Canada
Publication history
- Received: September 19, 2017
- Accepted: March 5, 2018
- Accepted Manuscript published: March 9, 2018 (version 1)
- Version of Record published: April 27, 2018 (version 2)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Further reading
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- Computational and Systems Biology
- Evolutionary Biology
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- Computational and Systems Biology
- Evolutionary Biology
