Identification of novel clock-controlled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii

Circadian rhythms are self-sustaining oscillations whose period length under constant conditions is about 24 h. Circadian rhythms are widespread and involve functions as diverse as human sleep-wake cycles and cyanobacterial nitrogen fixation. In spite of a long research history, knowledge about clock-controlled genes is limited in Chlamydomonas reinhardtii. Using a cDNA macroarray containing 10 368 nuclear-encoded genes, we examined global circadian regulation of transcription in Chlamydomonas. We identified 269 candidates for circadianly expressed gene. Northern blot analysis confirmed reproducible and sustainable rhythmicity for 12 genes. Most genes exhibited peak expression at the transition point between day and night. One hundred and eighteen genes were assigned predicted annotations. The functions of the cycling genes were diverse and included photosynthesis, respiration, cellular structure, and various metabolic pathways. Surprisingly, 18 genes encoding chloroplast ribosomal proteins showed a coordinated circadian pattern of expression and peaked just at the beginning of subjective day. The co-regulation of genes bearing a similar function was also observed in genes involved in cellular structure. They peaked at the end of the subjective night, which is when the regeneration of cell walls and flagella in daughter cells occurs. Expression of the chlamyopsin gene, which encodes an opsin-type photoreceptor, also exhibited circadian rhythm.