Transcriptome analysis reveals global regulation in response to CO(2) supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169

BACKGROUND: Microalgae are emerging as suitable feedstock for renewable biofuel production and providing a promising way to alleviate green house gas CO(2). Characterizing the metabolic pathways involved in the biosynthesis of energy-rich compounds and their global regulation upon elevated CO(2) is necessary to explore the mechanism underlying rapid growth and lipid accumulation, so as to realize the full potential of these organisms as energy resources. RESULTS: In the present study, 2 and 5 % CO(2) increased growth rate and lipid accumulation in autotrophically cultured green alga Coccomyxa subellipsoidea C-169. Overall biomass productivity as 222 mg L(−1) day(−1) and fatty acid content as 48.5 % dry cell weight were attained in 2 % CO(2), suggesting C-169 as a great candidate for lipid production via CO(2) supplementation. Transcriptomic analysis of 2 % against 0.04 % CO(2)-cultured C-169 unveiled the global regulation of important metabolic processes. Other than enhancing gene expression in the Calvin cycle, C-169 upregulated the expression of phosphoenolpyruvate carboxylase, pyruvate carboxylase and carbamoyl-phosphate synthetase II to enhance the anaplerotic carbon assimilation reactions upon elevated CO(2). Upregulation of ferredoxin and ferredoxin–NADP(+) reductase implied that plentiful energy captured through photosynthesis was transferred through ferredoxin to sustain rapid growth and lipid accumulation. Genes involved in the glycolysis, TCA cycle and oxidative phosphorylation were predominantly upregulated presumably to provide abundant intermediates and metabolic energy for anabolism. Coordinated upregulation of nitrogen acquisition and assimilation genes, together with activation of specific carbamoyl-phosphate synthetase and ornithine pathway genes, might help C-169 to maintain carbon/nitrogen balance upon elevated CO(2). Significant downregulation of fatty acid degradation genes, as well as the upregulation of fatty acid synthesis genes at the later stage might contribute to the tremendous lipid accumulation. CONCLUSION: Global and collaborative regulation was employed by C-169 to assimilate more carbon and maintain carbon/nitrogen balance upon elevated CO(2), which provide abundant carbon skeleton and affluent metabolic energy to sustain rapid growth and lipid accumulation. Data here for the first time bring significant insights into the regulatory profile of metabolism and acclimation to elevated CO(2) in C-169, which provide important information for future metabolic engineering in the development of sustainable microalgae-based biofuels. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13068-016-0571-5) contains supplementary material, which is available to authorized users.