Relationship between cell cycle and diel transcriptomic changes in metabolism in a unicellular red alga

Metabolism, cell cycle stages, and related transcriptomes in eukaryotic algae change with the diel cycle of light availability. In the unicellular red alga Cyanidioschyzon merolae, the S and M phases occur at night. To examine how diel transcriptomic changes in metabolic pathways are related to the cell cycle and to identify all genes, for which mRNA levels change depending on the cell cycle, we examined diel transcriptomic changes in C. merolae. In addition, we compared transcriptomic changes between the wild type and transgenic lines, in which the cell cycle was uncoupled from the diel cycle by the depletion of either cyclin-dependent kinase A (CDKA) or retinoblastoma-related (RBR) protein. Of 4,775 nucleus-encoded genes, the mRNA levels of 1,979 genes exhibited diel transcriptomic changes in the wild type. Of these, the periodic expression patterns of 454 genes were abolished in the transgenic lines, suggesting that the expression of these genes is dependent on cell cycle progression. The periodic expression patterns of most metabolic genes, except those involved in starch degradation and de novo dNTP synthesis, were not affected in the transgenic lines, indicating that the cell cycle and transcriptomic changes in most metabolic pathways are independent of the diel cycle. Approximately 40% of the cell–cycle–dependent genes were of unknown function, and approximately 19% of these genes of unknown function are shared with the green alga Chlamydomonas reinhardtii. The dataset presented in this study will facilitate further studies on the cell cycle and its relationship with metabolism in eukaryotic algae. The C. merolae wild type, G1-arrested HA-CDKA-conditional knockdown (cKD) and RBR-KO cells cultured in the 12-h light and dark cycle at 42°C. The algal cells were collected every four hours (8 samples through the diurnal LD cycle). To obtain two replicates of the data sets, pairs of LD cultures of the wild type and HA-CDKA-cKD were performed twice 1 month apart as biological replicates [WT1 vs. HA-CDKA-cKD1 (rep. 1) and WT2 vs. HA-CDKA-cKD2 (rep.2)] and pairs of LD cultures of the wild type and RBR-KO were performed twice 1 month apart as biological replicates [WT3 vs. RBR-KO1 (rep.1) and WT4 vs. RBR-KO2 (rep.2)].