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Title: Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis

Abstract

Yarrowia lipolytica is an oleaginous ascomycete yeast that accumulates large amounts of lipids and has potential as a biofuel producing organism. Despite a growing scientific literature focused on lipid production by Y. lipolytica, there remain significant knowledge gaps regarding the key biological processes involved. We applied a combination of metabolomic and lipidomic profiling approaches as well as microscopic techniques to identify and characterize the key pathways involved in de novo lipid accumulation from glucose in batch cultured, wild-type Y. lipolytica. We found that lipids accumulated rapidly and peaked at 48 hours during the five day experiment, concurrent with a shift in amino acid metabolism. We also report that Y. lipolytica secretes disaccharides early in batch culture and reabsorbs them when extracellular glucose is depleted. Exhaustion of extracellular sugars coincided with thickening of the cell wall, suggesting that genes involved in cell wall biogenesis may be a useful target for improving the efficiency of lipid producing yeast strains.

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1179505
Report Number(s):
PNNL-SA-105704
48167; 47736; KP1601010
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
PLoS One, 10(4):e0123188
Additional Journal Information:
Journal Name: PLoS One, 10(4):e0123188; Journal Volume: 10; Journal Issue: 4
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; yarrowia plos paper; Environmental Molecular Sciences Laboratory

Citation Formats

Pomraning, Kyle R., Wei, Siwei, Karagiosis, Sue A., Kim, Young-Mo, Dohnalkova, Alice, Arey, Bruce W., Bredeweg, Erin L., Orr, Galya, Metz, Thomas O., and Baker, Scott E. Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0123188.
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Pomraning, Kyle R., Wei, Siwei, Karagiosis, Sue A., Kim, Young-Mo, Dohnalkova, Alice, Arey, Bruce W., Bredeweg, Erin L., Orr, Galya, Metz, Thomas O., & Baker, Scott E. Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis. United States. https://doi.org/10.1371/journal.pone.0123188
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Pomraning, Kyle R., Wei, Siwei, Karagiosis, Sue A., Kim, Young-Mo, Dohnalkova, Alice, Arey, Bruce W., Bredeweg, Erin L., Orr, Galya, Metz, Thomas O., and Baker, Scott E. Thu . "Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis". United States. https://doi.org/10.1371/journal.pone.0123188. https://www.osti.gov/servlets/purl/1179505.
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@article{osti_1179505,
title = {Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis},
author = {Pomraning, Kyle R. and Wei, Siwei and Karagiosis, Sue A. and Kim, Young-Mo and Dohnalkova, Alice and Arey, Bruce W. and Bredeweg, Erin L. and Orr, Galya and Metz, Thomas O. and Baker, Scott E.},
abstractNote = {Yarrowia lipolytica is an oleaginous ascomycete yeast that accumulates large amounts of lipids and has potential as a biofuel producing organism. Despite a growing scientific literature focused on lipid production by Y. lipolytica, there remain significant knowledge gaps regarding the key biological processes involved. We applied a combination of metabolomic and lipidomic profiling approaches as well as microscopic techniques to identify and characterize the key pathways involved in de novo lipid accumulation from glucose in batch cultured, wild-type Y. lipolytica. We found that lipids accumulated rapidly and peaked at 48 hours during the five day experiment, concurrent with a shift in amino acid metabolism. We also report that Y. lipolytica secretes disaccharides early in batch culture and reabsorbs them when extracellular glucose is depleted. Exhaustion of extracellular sugars coincided with thickening of the cell wall, suggesting that genes involved in cell wall biogenesis may be a useful target for improving the efficiency of lipid producing yeast strains.},
doi = {10.1371/journal.pone.0123188},
journal = {PLoS One, 10(4):e0123188},
number = 4,
volume = 10,
place = {United States},
year = {Thu Apr 23 00:00:00 EDT 2015},
month = {Thu Apr 23 00:00:00 EDT 2015}
}
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https://doi.org/10.1371/journal.pone.0123188
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Accumulation of a Cocoa-Butter-Like Lipid by Yarrowia lipolytica Cultivated on Agro-Industrial Residues
journal, February 2003

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  • DOI: 10.1007/s00284-002-3833-3

Production of erythritol and mannitol by Yarrowia lipolytica yeast in media containing glycerol
journal, May 2012

  • Tomaszewska, Ludwika; Rywińska, Anita; Gładkowski, Witold
  • Journal of Industrial Microbiology & Biotechnology, Vol. 39, Issue 9
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Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeast species
journal, September 2013

Yarrowia lipolytica as a model for bio-oil production
journal, November 2009

  • Beopoulos, Athanasios; Cescut, Julien; Haddouche, Ramdane
  • Progress in Lipid Research, Vol. 48, Issue 6, p. 375-387
  • DOI: 10.1016/j.plipres.2009.08.005

Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production
journal, January 2013

MetaboliteDetector: Comprehensive Analysis Tool for Targeted and Nontargeted GC/MS Based Metabolome Analysis
journal, May 2009

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Accumulation of High-Value Lipids in Single-Cell Microorganisms: A Mechanistic Approach and Future Perspectives
journal, March 2014

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Production of Alkaline Extracellular Protease by Yarrowia Lipolytica
journal, January 1988

Comparative Lipidomic Profiling of S. cerevisiae and Four Other Hemiascomycetous Yeasts
journal, March 2012

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    journal, November 2017

    MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses
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    • Bobbie-Jo, Webb-Robertson,; D., Smith, Richard; S., Nakayasu, Ernesto
    • The University of North Carolina at Chapel Hill University Libraries
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    Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids
    journal, January 2016

    Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica
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    Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica
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    Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica
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    Engineering Yarrowia lipolytica to produce biodiesel from raw starch
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    • Biotechnology for Biofuels, Vol. 8, Issue 1
    • DOI: 10.1186/s13068-015-0335-7

    A molecular genetic toolbox for Yarrowia lipolytica
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    • Biotechnology for Biofuels, Vol. 10, Issue 1
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    Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity
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