Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The genomic basis of lipid accumulation in Mucor circinelloides VI 04473

ABSTRACT: The filamentous fungus Mucor circinelloides VI 04473 (indicated by MC1 in these data) was exposed to treatments known to trigger the accumulation of lipids in fungal cells, in order to investigate the genomic basis of this trait. Treatments consisted of different levels of calcium and inorganic phosphorus substrate in the growth media used for cultivation: For calcium, the two levels were calcium present in a concentration of 0.1 g/L (Ca1), and absence of calcium (Ca0). For phosphorus, there were three different levels: The reference concentration P1 (phosphate salts in a concentration of 7 g/L KH2PO4 and 2 g/L Na2HPO4), four times the reference concentration (P4), and half the reference concentration (P0.5). The combination of the different levels of calcium and phosphorus resulted in six different growth media, indicated in these data by numbers _1 - _6: 1 = Ca1P1, 2 = Ca1P4, 3 = Ca1P0.5, 4 = Ca0P1, 5 = Ca0P4, 6 = Ca0P0.5. There were 3-4 replicates per unique growth media, indicated by R1-R4 . The biomass was washed and harvested after 5 days of cultivation. RNA was extracted from the biomass and sequenced, followed by analysis of the transcriptome (genes differentially expressed between treatments).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mucor circinelloides

SUBMITTER: Veronica Aarvik Bøe

PROVIDER: E-MTAB-13309 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Renewable biodiesel produced by microalgae has great potential as a portable source of high-density energy that can replace certain traditional hydrocarbon sources. One limitation of scaling up algal cultivation to industrial levels is the availability of key macronutrients, particularly inorganic phosphorus (Pi), which is a finite and dwindling resource. Here, Auxenochlorella protothecoides was adapted to low Pi conditions through continuous cultivation in 100 times less Pi media for 285 days, or ~41 generations. The adapted populations demonstrated significantly higher growth rates than wild type (WT) cells in low Pi, with average maximum growth rates of 0.72 d-1 and 0.54 d-1, respectively in batch-culture experiments. Based on UPLC/MS analyses, the total lipid content of the adapting A. protothecoides populations showed a shift from their typical profile in nutrient replete media to the accumulation of non-phosphorus glycerolipids, with 306% MGDG and 189% SQDG, relative to WT at initial exposure, followed by a decline, and a steady increase until the final time point was reached. Transcriptome profiling by Illumina RNA-seq collected at 5 time points throughout the experiment, and results of the lipid analyses revealed a trend of increased transcript levels during the first ~11 generations of adaptation, followed by an overall decrease in gene expression after ~34 generations. The short-term changes in gene expression were associated with shifts in major metabolic pathways including carbon metabolism, oxidative phosphorylation, glycolysis, and gluconeogenesis. By comparison, certain transcripts showing decreased expression, reflected increased fatty acid turnover, and a stable decrease in photosynthesis-related gene expression. These results illustrate the utility of laboratory-directed evolution for the selection of microalgae populations with altered cultivation traits, revealing distinct phases of adaptation, based on expression profiles. The results further demonstrate the use of metabolic engineering to select a microalga variant after only ~40 generations of growth in low-phosphate conditions that utilizes Pi more efficiently for growth than its wild type parent population and produces 1.22 times more biomass in batch growth experiments.

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The genomic basis of lipid accumulation in Mucor circinelloides VI 04473

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