Transcriptomic reprogramming of diatom Minutocellus polymorphus grown on urea

Minutocellus polymorphus MMDL5290, a minute diatom, can efficiently utilize organic nitrogen (N) urea as the sole N source and achieve equivalent growth rate and photosynthesis capacity as it does with nitrate. Interestingly, M. polymorphus MMDL5290 growing on urea-replete (400 µM) medium yields a similar growth rate to that on nitrate-replete (882 µM). So far, very few reports are available on the molecular regulation mechanisms of microalgae with similar growth potential under different N sources. To address this gap, our study aimed to characterize the differences in transcriptome-level responses of M. polymorphus MMDL5290 between nitrate-replete and urea-replete conditions. We identified 4075 differentially expressed genes between these two groups. Interestingly, gene expression in light-harvesting, electron transport chain, ATP synthesis, and chlorophyll and carotenoid synthesis was up-regulated under urea, while the expression of carbon fixation genes did not change significantly. Meanwhile, transcriptome profiling indicated that under the urea-replete condition, M. polymorphus MMDL5290 triggered massive gene expression reconfiguration, inducing cells to increase investment in protein synthesis and antioxidative stress. This may explain why higher photosynthetic capacity in urea-grown cells does not lead to higher growth. Furthermore, down-regulation of PT (signal peptide) genes was observed under the urea-replete condition, suggesting a repressed capacity of phosphate transport. In addition, we identified 139 stably and highly expressed genes, which have the potential to be used as candidate reference genes in future gene expression studies on M. polymorphus MMDL5290.