RpaB, Another Response Regulator Operating Circadian Clock-dependent Transcriptional Regulation in Synechococcus elongatus PCC 7942

Background: The circadian output pathway in cyanobacteria is mediated by a two-component system consisting of SasA/RpaA. Results: An additional response regulator, RpaB, directly binds to clock-regulated promoters during the night. Conclusion: RpaB is also a key regulator of the circadian output pathway; RpaA and RpaB function cooperatively. Significance: Clarification of output pathway details is crucial for understanding the circadian clock. The circadian clock of cyanobacteria is composed of KaiA, KaiB, and KaiC proteins, and the SasA-RpaA two-component system has been implicated in the regulation of one of the output pathways of the clock. In this study, we show that another response regulator that is essential for viability, the RpaA paralog, RpaB, plays a central role in the transcriptional oscillation of clock-regulated genes. In vivo and in vitro analyses revealed that RpaB and not RpaA could specifically bind to the kaiBC promoter, possibly repressing transcription during subjective night. This suggested that binding may be terminated by RpaA to activate gene transcription during subjective day. Moreover, we found that rpoD6 and sigF2, which encode group-2 and group-3 σ factors for RNA polymerase, respectively, were also targets of the RpaAB system, suggesting that a specific group of σ factors can propagate genome-wide transcriptional oscillation. Our findings thus reveal a novel mechanism for a circadian output pathway that is mediated by two paralogous response regulators.