RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism - Supplementary Data
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RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism. David K.Y. Lim, Holger Schuhmann, Skye R. Thomas-Hall, Kenneth C.K. Chan, Taylor J. Wass, Felipe Aguilera, T. Catalina Adarme-Vega, Cristiana G.O. Dal'Molin, Glen J. Thorpe, Jacqueline Batley, David Edwards, Peer M. Schenk. Bioresource Technology 244:1281-1293 (2017). https://doi.org/10.1016/j.biortech.2017.06.003
Abstract
To map out key lipid-related pathways that lead to rapid triacylglyceride accumulation in oleaginous microalgae, RNA-Seq was performed with Tetraselmis sp. M8 at 24 h after exhaustion of exogenous nitrogen to reveal molecular changes during early stationary phase. Further gene expression profiling by quantitative real-time PCR at 16–72 h revealed a distinct shift in expression of the fatty acid/triacylglyceride biosynthesis and β-oxidation pathways, when cells transitioned from log-phase into early-stationary and stationary phase. Metabolic reconstruction modeling combined with real-time PCR and RNA-Seq gene expression data indicates that the increased lipid accumulation is a result of a decrease in lipid catabolism during the early-stationary phase combined with increased metabolic fluxes in lipid biosynthesis during the stationary phase. During these two stages, Tetraselmis shifts from reduced lipid consumption to active lipid production. This process appears to be independent from DGAT expression, a key gene for lipid accumulation in microalgae.
- David K.Y. Lim (first author - PhD student)
- Felipe Aguilera (PhD student)
- Peer M. Schenk (corresponding author)
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01-Supplementary-Figures.pdf contains supplementary figures used in this study.
- Supplementary Figure 1. Nitrogen and phosphate contents of growth medium during Tetraselmis sp. M8 cultivation and harvesting for RNA-Seq and qRT-PCR experiments.
- Supplementary Figure 2. DiffKAP dataflow diagram.
- Supplementary Figure 3. Flux map of the central carbon metabolism for Tetraselmis sp. M8 under nitrogen limiting conditions at 72 h.
- Supplementary Figure 4. Distribution of Gene ontology (GO) terms assigned to annotated differentially expressed reads (DERs) in Control and Nitrogen-starved treatments.
- Supplementary Figure 5. Growth and lipid accumulation of Tetraselmis sp. M8 in a time-course experiment using control and nitrogen-starved cultures.
- Supplementary Figure 6. Flux map of the central carbon metabolism under the lipid accumulation for Tetraselmis sp. M8 under nitrogen limiting conditions at 24 h.
- Supplementary Figure 7. qRT-PCR data of fatty acid pathway genes.
- Supplementary Figure 8. qRT-PCR data of TAG pathway genes.
- Supplementary Figure 9. qRT-PCR data of lipid catabolism pathway genes.
02-List-primers-qPCR.xlsx contains the list of primers used for qRT-PCR.
03-DiffKAP-and-DERs.xlsx contains the Differential Kmer Analysis Pipeline (DiffKAP) with Differentially Expressed Reads (DERs).
04-Distribution-DERs-and-GO-terms.xlsx contains the distribution of annotated Differentially Expressed Reads (DERs) assigned with Gene Ontology (GO) terms, presented as a percentage of the total annotated DERs for each treatment.