Analysis of autotrophic, mixotrophic and heterotrophic phenotypes in the microalgae Chlorella vulgaris using time-resolved proteomics and transcriptomics approaches

Some microalgae species including Chlorella vulgaris can, under light exposure, concurrently metabolize organic and inorganic carbon sources in a metabolic mode known as mixotrophy. In many cases the cells can generate high biomass yield under mixotrophy, which is highly desirable for future massive applications of microalgae biomass as industrial feedstock. However, there is no complete understanding of the molecular physiology of microalgae in mixotrophy. Therefore, we performed a time-series analysis of the proteome and transcriptome of Chlorella vulgaris during the transition from autotrophy to mixotrophy under continuous light, and then to heterotrophy in darkness in controlled bioreactor conditions. The results from biomass and cell growth characterization demonstrated that under mixotrophic growth the cells have enhanced growth rate, and transcriptomics data showed overexpressed genes related to chromosome organization, DNA-repair, and DNA replication. Moreover, our proteomics data revealed differentially expressed proteins and overrepresentation of proteins related to translation mechanism. The transcriptomics and proteomics analysis also indicated that the expression of genes of the glyoxylate cycle, oxylipin metabolism, myoinositol synthesis pathway and a subset of thioredoxins were also modulated. Moreover, we performed the annotation of transcription factor and transcriptional regulator genes and the results revealed novel candidate regulator genes that were exclusively expressed during mixotrophic growth phase including members of MYB (V-myb avian myeloblastosis viral oncogene homolog) and bZIP (Basic Leucine Zipper) protein families. Thus, our findings indicated that the high specific growth rate observed in cells under mixotrophy is likely supported by the induction of abiotic stress tolerance mechanisms via inositol and its derivatives and increased resistance to oxidative stress through the modulation of the expression of thioredoxins. Therefore, the identification of novel candidate genes in mixotrophy may contribute to the development of microalgae strains with higher growth capacity and better performance for biomass production.