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 algaCyanidioschyzon 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 inC. 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 or retinoblastoma-related 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 deoxyribonucleotide triphosphate synthesis, were not affected in the transgenic lines, indicating that transcriptomic changes in most metabolic pathways are independent of the cell 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 algaChlamydomonas reinhardtii. The data set presented in this study will facilitate further studies on the cell cycle and its relationship with metabolism in eukaryotic algae. A data set of diel and cell-cycle-dependent transcriptomic changes in a eukaryotic alga with a minimal set of genes clarifies the relationship between metabolism and the cell cycle.