Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

Abstract

The basidiomycete yeast Rhodosporidium toruloides (also known as 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 1,337 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.

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

“…It was interesting to note that the C/N ratio was dramatically higher during this time, which was mainly driven by a decrease in nitrogen level (Figure 4). Low levels of nitrogen are known to induce lipid accumulation in this and other organisms (Bellou, Triantaphyllidou, Mizerakis, & Aggelis, 2016; Coradetti et al, 2018). Thus, the higher FOH productivity during this period was likely caused by a higher flux towards the fatty acid pathway induced by elevated C/N ratios.…”

Genome‐scale model of Rhodotorula toruloides metabolism

“…The dotted line exemplifies perfect correlation. (c) Comparison of gene essentiality predictions from rhto‐GEM with gene essentiality inferred from a T‐DNA random insertion study (Coradetti et al, ). Shown are results from the 704 genes that are included in the model and that could be uniquely mapped to the T‐DNA study [Color figure can be viewed at http://wileyonlinelibrary.com]…”

“…While the exact culture conditions, media compositions, and R. toruloides strains used diverge between the literature‐derived growth rates, these variables do not relate to how well they correlate with model‐predicted growth rates. To evaluate the gene essentiality predictions, we used data from a recent study where a random mutant library was generated by T‐DNA insertion in over 6,000 genes (Coradetti et al, ). A total of 1,337 genes were identified as putative essential genes due to their recalcitrance to T‐DNA insertion, of which 207 genes are associated to reactions in rhto‐GEM .…”

Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery

“…Integration of large-scale data sets is crucial for a better understanding of the genomic organisation and metabolic pathways in living cells. Complete genome sequences are available for several R. toruloides strains (Kumar et al, 2012;Zhu et al, 2012;Morin et al, 2014;Hu and Ji, 2016;Sambles et al, 2017;Coradetti et al, 2018). The lipid formation process during different growth phases of cultivation on glucose has been investigated through proteomic analysis (Liu et al, 2009) and compared with cells grown on xylose (Tiukova et al, 2019b).…”