Background: Nitrogen limitation can induce neutral lipid accumulation in microalgae, as well as inhibiting their growth. Therefore, to obtain cultures with both high biomass and high lipid contents, and explore the lipid accumulation mechanisms, we implemented nitrogen deprivation in a model diatom Phaeodactylum tricornutum at late exponential phase. Results: Neutral lipid contents per cell subsequently increased 2.4-fold, both the number and total volume of oil bodies increased markedly, and cell density rose slightly. Transcriptional profile analyzed by RNA-Seq showed that expression levels of 1213 genes (including key carbon fixation, TCA cycle, glycerolipid metabolism and nitrogen assimilation genes) increased, with a false discovery rate cut-off of 0.001, under N deprivation. However, most light harvesting complex genes were down-regulated, extensive degradation of chloroplast membranes was observed under an electron microscope, and photosynthetic efficiency declined. Further identification of lipid classes showed that levels of MGDG and DGDG, the main lipid components of chloroplast membranes, dramatically decreased and triacylglycerol (TAG) levels significantly rose, indicating that intracellular membrane remodeling substantially contributed to the neutral lipid accumulation. Conclusions: Our findings shed light on the molecular mechanisms of neutral lipid accumulation and the key genes involved in lipid metabolism in diatoms. They also provide indications of possible strategies for improving microalgal biodiesel production.

The fast growing photosynthetic microalgae have been widely used in aquaculture, food, health, and biofuels. Recent findings in the diatom has proposed a pivotal role of NADP-malic enzyme in generation of NADPH as an important supply of reducing power for fatty acid biosynthesis. To test the lipogenic malic enzyme for fatty acid synthesis in green algae, here the malic enzyme gene PtME from the oleaginous diatom Phaeodactylum tricornutum was expressed in a representative green microalga Chlorella pyrenoidosa. The engineered C. pyrenoidosa strain showed higher enzymatic activity of malic enzyme which subsequently promoted fatty acid synthesis. The neutral lipid content was significantly increased by up to 3.2-fold than wild type determined by Nile red staining, and total lipid content reached 40.9 % (dry cell weight). The engineered strain exhibited further lipid accumulation subjected to nitrogen deprivation condition. Upon nitrogen deprivation, engineered microalgae accumulated total lipid up to 58.7 % (dry cell weight), a 4.6-fold increase over the wild type cells under normal culture condition. At cellular level, increased volume and number of oil bodies were observed in the engineered microalgal cells. These findings suggested that malic enzyme is a pivotal regulator in lipid accumulation in green microalga C. pyrenoidosa, and presenting a breakthrough of generating ideal algal strains for algal nutrition and biofuels.