title: Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169.
abstract: BACKGROUND
  Microalgae are emerging as suitable feedstock for renewable biofuel production and providing a promising way to alleviate green house gas CO2. Characterizing the metabolic pathways involved in the biosynthesis of energy-rich compounds and their global regulation upon elevated CO2 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 % CO2 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 % CO2, suggesting C-169 as a great candidate for lipid production via CO2 supplementation. Transcriptomic analysis of 2 % against 0.04 % CO2-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 CO2. 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 CO2. 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.
  
  
  CONCLUSIONS
  Global and collaborative regulation was employed by C-169 to assimilate more carbon and maintain carbon/nitrogen balance upon elevated CO2, 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 CO2 in C-169, which provide important information for future metabolic engineering in the development of sustainable microalgae-based biofuels.
authors.affiliation: School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People's Republic of China.
authors.forename: Huifeng
authors.initials: H
authors.lastname: Peng
authors.affiliation: School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People's Republic of China.
authors.forename: Dong
authors.initials: D
authors.lastname: Wei
authors.affiliation: School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People's Republic of China.
authors.forename: Gu
authors.initials: G
authors.lastname: Chen
authors.affiliation: School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People's Republic of China ; Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 People's Republic of China.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
keywords: Carbamoyl-phosphate synthetase II; Clavaminate synthase; Coccomyxa subellipsoidea C-169; Elevated CO2; Ferredoxin; Lipid accumulation; Phosphoenolpyruvate carboxylase; Pyruvate carboxylase; Transcriptomic analysis; Vacuolar H+-ATPase