Analysis of the residue variation of the circadian clock protein KaiA

Regulation of daily physiological functions with approximate a 24-hour periodicity, or circadian rhythms, is a characteristic of eukaryotes. So far, cyanobacteria are only known prokaryotes reported to possess circadian rhythmicity. The circadian system in cyanobacteria comprises both a post-translational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) with the existence of ATP. Phase of the nanoclockwork has been associated with the phosphorylation states of KaiC, with KaiA promoting the phosphorylation of KaiC, and KaiB dephosphorylating KaiC. Here we studied the sequence variation of 65 KaiA proteins in evolution, and determined some key residues in KaiA by analyzing the site variation rates of the protein sequences. These key residues could be used to study the key interactions of KaiA with KaiB and KaiC.