1. Computational and Systems Biology
  2. Microbiology and Infectious Disease
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Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

  1. Samuel T Coradetti
  2. Dominic Pinel
  3. Gina Geiselman
  4. Masakazu Ito
  5. Stephen Mondo
  6. Morgann C Reilly
  7. Ya-Fang Cheng
  8. Stefan Bauer
  9. Igor Grigoriev
  10. John M Gladden
  11. Blake A Simmons
  12. Rachel Brem
  13. Adam P Arkin  Is a corresponding author
  14. Jeffrey M Skerker  Is a corresponding author
  1. The Buck Institute for Research on Aging, United States
  2. University of California, Berkeley, United States
  3. United States Department of Energy Joint Genome Institute, United States
  4. Joint BioEnergy Institute, United States
Research Article
  • Cited 40
  • Views 4,441
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Cite this article as: eLife 2018;7:e32110 doi: 10.7554/eLife.32110

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

  1. Samuel T Coradetti

    The Buck Institute for Research on Aging, Novato, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Dominic Pinel

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Gina Geiselman

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Masakazu Ito

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Stephen Mondo

    United States Department of Energy Joint Genome Institute, Walnut Creek, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Morgann C Reilly

    Joint BioEnergy Institute, Emeryville, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Ya-Fang Cheng

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Stefan Bauer

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Igor Grigoriev

    United States Department of Energy Joint Genome Institute, Walnut Creek, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. John M Gladden

    Joint BioEnergy Institute, Emeryville, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6985-2485

  11. Blake A Simmons

    Joint BioEnergy Institute, Emeryville, United States
    Competing interests
    The authors declare that no competing interests exist.

  12. Rachel Brem

    The Buck Institute for Research on Aging, Novato, United States
    Competing interests
    The authors declare that no competing interests exist.

  13. Adam P Arkin

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    For correspondence
    aparkin@lbl.gov
    Competing interests
    The authors declare that no competing interests exist.

  14. Jeffrey M Skerker

    Energy Biosciences Institute, University of California, Berkeley, Berkeley, United States
    For correspondence
    SKERKER@BERKELEY.EDU
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2653-1566

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

  1. Joerg Bohlmann, University of British Columbia, Canada

Publication history

  1. Received: September 19, 2017
  2. Accepted: March 5, 2018
  3. Accepted Manuscript published: March 9, 2018 (version 1)
  4. 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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    Funding: GJW and MJD accepted funding from BioNexus KC for funding on this project, but BioNexus KC had no direct role in this article.

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