Coordinated Transcriptional and miRNA Regulation of Phosphate Stress in Dinoflagellate

While gene regulation can occur at both transcriptional and epigenetic (microRNA) levels, combined transcriptomic and microRNAomic responses to environmental stress is unexplored for marine plankton. Here, we conducted transcriptome and microRNAome sequencing for the dinoflagellate Prorocentrum donghaiense understand molecular mechanisms by which this dinoflagellate copes with P-deficiency. Transcriptomic analysis revealed 1230 unigenes that were differentially expressed with ≥ 2-fold change. Genes related to DOP hydrolysis, cell cycle regulation, carbon fixation, nitrate assimilation, glycolysis and cellular motor were up-regulated under P-depleted condition. Both high- and low-affinity phosphate transporters as well as phosphatases such as 5′-Nucleotidase and alkaline phosphatase were actively expressed to facilitate tunable P uptake and scavenging. The up-regulated expression of ATP-generation and catabolism genes indicated accelerated ATP recycling under P-deficiency. Furthermore, miRNAome sequencing revealed 18 microRNAs, which presumably regulate 8228 protein-coding genes identified in our transcriptome. Among these microRNAs 4 were down- and 11 up-regulated under P-deficiency; functional enrichment analysis of their target genes predicted decreases in sulfolipid sulfatide catabolism under P-deficiency, which was corroborated by sulfolipid sulfatide increase detected by liquid chromatography-mass spectrometry (LC-MS) analysis. Proton-pump rhodopsin was predicted to be target of down-regulated microRNA, suggesting that this proton-pump were up-tuned to complement the transcriptional up-regulation of ATP synthesis and hence enhance cell survival under P-deficiency. Taken together, our data show that enhanced DOP utilization, accelerated recycle of ATP and repressed sulfolipids degradation through transcriptional and microRNA-mediated post-transcriptional regulations constitute a comprehensive strategy to cope with P deficiency in a dinoflagellate such as P. donghaiense.