Circadian rhythms are a fundamental property of most organisms, from cyanobacteria to humans. In the unicellular obligately photoautotrophic cyanobacterium Synechococcus elongatus PCC 7942, essentially all promoter activities are controlled by the KaiABC-based clock under continuous light conditions. When Synechococcus cells are transferred from the light to continuous dark (DD) conditions, the expression of most genes, including the clock genes kaiA and kaiBC, is rapidly down-regulated, whereas the KaiC phosphorylation cycle persists. Therefore, we speculated that the posttranslational oscillator might not drive the transcriptional circadian output without de novo expression of the kai genes. Here we show that the cyanobacterial clock regulates the transcriptional output even in the dark. The expression of a subset of genes in the genomes of cells grown in the dark was dramatically affected by kaiABC nullification, and the magnitude of dark induction was dependent on the time at which the cells were transferred from the light to the dark. Moreover, under DD conditions, the expression of some dark-induced gene transcripts exhibited temperature-compensated damped oscillations, which were nullified in kaiABC-null strains and were affected by a kaiC period mutation. These results indicate that the Kai protein-based posttranslational oscillator can drive the circadian transcriptional output even without the de novo expression of the clock genes.M ost organisms exhibit circadian oscillations in their physiological activities, with a period of ≈24 h, as part of their adaptation to external environmental changes. The unicellular cyanobacterium Synechococcus elongatus PCC 7942 is an obligate photoautotroph and the simplest model organism in circadian biology. In S. elongatus, most genes display circadian expression rhythms that are regulated by three clock genes, kaiA, kaiB, and kaiC, under continuous light (LL) conditions (1, 2). When the cells are transferred to continuous dark (DD) conditions after 12 h in the light, expression of the kaiA and kaiBC genes is rapidly downregulated to zero, whereas the KaiC phosphorylation cycle persists in the dark, even in the presence of excess transcription/translation inhibitors (3). Therefore, the basic oscillation is generated via a posttranslational process and does not need a translation/transcription feedback loop in the kai genes. The reconstitution of the temperature-compensated KaiC phosphorylation rhythm in vitro when KaiC is incubated with KaiA, KaiB, and ATP (4) supports this conclusion. Kitayama et al. (5) demonstrated rhythmic kaiBC expression and KaiC accumulation with a lengthened period of ≈60 h, even after two phosphorylation sites in KaiC (Ser-431 and Thr-432) were replaced with Glu. However, the unstable rhythm observed in the mutant was not robust under different culture conditions and different ambient temperatures (6). In eukaryotic model organisms, the core process that generates and maintains self-sustaining circadian oscillations is reported to be driven ...