Characterization and RNA-seq transcriptomic analysis of a Scenedesmus obliqnus mutant with enhanced photosynthesis efficiency and lipid productivity

Abstract

Microalgae have received significant attention as potential next-generation microbiologic cell factories for biofuels. However, the production of microalgal biofuels is not yet sufficiently cost-effective for commercial applications. To screen higher lipid-producing strains, heavy carbon ion beams are applied to induce a genetic mutant. An RNA-seq technology is used to identify the pathways and genes of importance related to photosynthesis and biofuel production. The deep elucidation of photosynthesis and the fatty acid metabolism pathway involved in lipid yield is valuable information for further optimization studies. This study provided the photosynthetic efficiency and transcriptome profiling of a unicellular microalgae, Scenedesmus obliqnus mutant SO120G, with enhanced lipid production induced by heavy carbon ion beams. The lipid yield (52.5 mg L^-1) of SO120G mutant were enhanced 2.4 fold compared with that of the wild strain under the nitrogen deficient condition. In addition, the biomass and growth rate were 57% and 25% higher, respectively, in SO120G than in the wild type, likely owing to an improved maximum quantum efficiency (F_v/F_m) of photosynthesis. As for the major pigment compositions, the content of chlorophyll a and carotenoids was higher in SO120G than in the wild type. The transcriptome data confirmed that a total of 2077 genes with a change of at least twofold were recognized as differential expression genes (DEGs), of which 1060 genes were up-regulated and 1017 genes were down-regulated. Most of the DEGs involved in lipid biosynthesis were up-regulated with the mutant SO120G. The expression of the gene involved in the fatty acid biosynthesis and photosynthesis of SO120G was upregulated, while that related to starch metabolism decreased compared with that of the wild strain. This work demonstrated that heavy-ion irradiation is an promising strategy for quality improvement. In addition, the mutant SO120G was shown to be a potential algal strain for enhanced lipid production. Transcriptome sequencing and annotation of the mutant suggested the possible genes responsible for lipid biosynthesis and photosynthesis, and identified the putative target genes for future genetic manipulation and biotechnological applications.

Figure 1

Distribution histogram of the SO120G mutant phenotypes. (a) Distribution histogram of the photosynthesis efficiency mutants (PEMs); (b) distribution histogram of the lipid-over-production mutants (LOMs); and (c) the relationship between the lipid contents and F_v/F_m under stress conditions in the PEMs and LOMs of SO120G.

Figure 2

Biomass and total lipid contents of the WT and mutant SO120G under the N + and N- culture conditions. (a) Biomass of the WT and SO120G and (b) the TFA content of the WT and SO120G, *represents a significant effect (p < 0.05), and **represents a very significant effect (p < 0.01).

Figure 3

Chlorophyll fluorescence parameters of the WT and SO120G under the N+ and N− culture conditions. (a) The F_v/F_m values of the WT and SO120G; (b) the ΦPSII values of the WT and SO120G; (c) the NPQ values of the WT and SO120G; and (d) the rETR of the WT and SO120G.

Figure 4

(a) Correlation plot between the different samples. The control group (SOWT-1, SOWT-2, and SOWT-3), experimental group (SO120G-1, SO120G-2, and SO120G-3); (b) the MA plot of the differentially expressed genes (DE genes). Significantly up-regulated and down-regulated genes are shown as red and green dots, respectively. Genes with no significant changes are shown as black spots; (c) gene ontology (GO) classification analysis of all of the genes and DE genes. The X-axis shows the number of genes, the left Y-axis shows the GO function.

Figure 5

A mechanistic model for ¹²C⁶⁺ ion irradiation on S. obliqnus. FabG, 3-oxoacyl-[acyl-carrier protein] reductase; FAB2, SSI2, DESA1, acyl-[acyl-carrier-protein] desaturase; ACSL, long-chain acyl-CoA synthetase; FAD, fatty acid desaturase; Pet B, cytochrome b6; Pet J, cytochrome c6; UGDH, UDPglucose 6-dehydrogenase; GLGA, starch synthase; Lcy E, lycopene epsilon-cyclase. The boxes in red and blue indicate the up- and down-regulated pathways, respectively. Significantly up-regulated and down-regulated genes are shown as the red and blue rectangles.