Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2-4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response.

Automated summary

It is essential to investigate the molecular mechanism of salt stress response in green algae to understand the evolutionary cues of abiotic stress response in plants. In this study, we conducted a comprehensive temporal investigation of transcriptomes in Chlamydomonas reinhardtii GY-D55 cells at different time points. The results revealed a set of common upregulated/downregulated genes and candidate regulatory mechanisms for salt stress responses. Short-term salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis, while the cells employed transcriptional regulation, protein folding, and osmotic stress coping mechanisms. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. Additionally, we identified several transcription factors (TFs) with potential roles in algal salt stress response, including Alfin, C2C2, and the MYB family TFs.