1. Computational and Systems Biology
  2. Microbiology and Infectious Disease
Download icon

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 0
  • Views 499
  • Annotations
Cite 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.

Article and author information

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 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 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, Reviewing Editor, 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)

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.

Metrics

  • 499
    Page views
  • 139
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Computational and Systems Biology
    2. Immunology and Inflammation
    Richard R Stein et al.
    Research Article
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics
    Wen Ma et al.
    Research Article