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Pomraning KR, Wei S, Karagiosis SA, Kim YM, Dohnalkova AC, Arey BW, Bredeweg EL, Orr G, Metz TO, Baker SE. Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis. PLoS One 2015; 10:e0123188. [PMID: 25905710 PMCID: PMC4408067 DOI: 10.1371/journal.pone.0123188] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/17/2015] [Indexed: 11/24/2022] Open
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 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.
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Affiliation(s)
- Kyle R. Pomraning
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Siwei Wei
- Fundamental and Computer Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Sue A. Karagiosis
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Young-Mo Kim
- Fundamental and Computer Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Bruce W. Arey
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Erin L. Bredeweg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Thomas O. Metz
- Fundamental and Computer Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Scott E. Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
- * E-mail:
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Knutsen AK, Robert V, Poot GA, Epping W, Figge M, Holst-Jensen A, Skaar I, Smith MT. Polyphasic re-examination of Yarrowia lipolytica strains and the description of three novel Candida species: Candida oslonensis sp. nov., Candida alimentaria sp. nov. and Candida hollandica sp. nov. Int J Syst Evol Microbiol 2007; 57:2426-2435. [PMID: 17911320 DOI: 10.1099/ijs.0.65200-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The type strain of Yarrowia lipolytica and 38 strains identified as Yarrowia lipolytica, four strains of Candida deformans, including the type and two subcultures of the type, two strains of Candida galli and six unidentified strains that resembled Y. lipolytica were examined by PCR fingerprints using primers M13 and (GAC)5. The same strains, together with four strains of the recently introduced Candida yakushimensis nom. inval., were sequenced for the D1/D2 domain of the 26S rRNA gene and parts of the ITS domain and also studied for their physiological properties. Of the strains identified previously as Y. lipolytica, CBS 2076 had the same fingerprint as the type of C. deformans and strain CBS 4855 was distinct from all other strains. The six strains that resembled Y. lipolytica were separated into two groups distinct from any of the other clades. A total of six groups obtained by fingerprint and sequence data were evaluated by performing DNA reassociation reactions. Mating experiments among the 35 strains of Y. lipolytica
sensu stricto showed that 15 strains represented one mating type and 16 strains represented the opposite mating type, while four strains were self-sporulating. Teleomorph states were not produced by C. deformans, C. galli or any of the unidentified isolates. However, positive mating reactions were rarely observed in crosses among C. galli and some strains of Y. lipolytica and C. deformans. Consequently, sharing the same mating type system, C. deformans and C. galli could be considered anamorphs of unnamed Yarrowia species. Results from PCR fingerprints, sequencing and mating studies support the grouping of the studied strains into Y. lipolytica, C. galli, C. deformans, C. yakushimensis nom. inval. and three novel species in the Yarrowia clade: Candida oslonensis sp. nov. (type strain CBS 10146T =NRRL Y-48252T; Mycobank number MB 510769), Candida alimentaria sp. nov. (type strain CBS 10151T =NRRL Y-48253T; Mycobank number MB 510770) and Candida hollandica sp. nov. (type strain CBS 4855T =NRRL Y-48254T; Mycobank number MB 510771).
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MESH Headings
- Candida/classification
- Candida/genetics
- DNA Fingerprinting
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Genes, Mating Type, Fungal
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Polymerase Chain Reaction
- RNA, Ribosomal/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Yarrowia/classification
- Yarrowia/genetics
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Affiliation(s)
- Ann Kristin Knutsen
- National Veterinary Institute, Ullevålsveien 68, PO Box 8156 Dep., 0033 Oslo, Norway
| | - V Robert
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G A Poot
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Wendy Epping
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marian Figge
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - A Holst-Jensen
- National Veterinary Institute, Ullevålsveien 68, PO Box 8156 Dep., 0033 Oslo, Norway
| | - Ida Skaar
- National Veterinary Institute, Ullevålsveien 68, PO Box 8156 Dep., 0033 Oslo, Norway
| | - Maudy Th Smith
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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