An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins

Abstract

The biological clock of cyanobacteria is composed of three proteins, KaiA, KaiB, and KaiC. The KaiB-KaiC binding brings the slowness into the system, which is essential for the long period of the circadian rhythm. However, there is no consensus as to the origin of the slowness due to the pre-binding conformational transition of either KaiB or KaiC. In this study, we propose a simple KaiB-KaiC binding scheme in a hexameric form with an attractive interaction between adjacent bound KaiB monomers, which is independent of KaiB’s conformational change. We then show that the present scheme can explain several important experimental results on the binding, including that used as evidence for the slow conformational transition of KaiB. The present result thus indicates that the slowness arises from KaiC rather than KaiB.

Ring-shaped multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by the ADP/ATP exchange inhibition

“…The comparison between the hexameric and monomeric models shows that the simultaneous promotion and acceleration of the complex formation arises from the cooperative binding of six KaiB to C1. Our previous study has shown that this cooperative binding originates from the attractive adjacent KaiB-KaiB interaction in the KaiB-KaiC complex [20]. In particular, this KaiB-KaiB interaction much more largely stabilizes the KaiB 6 KaiC 6 complex than the other smaller complexes KaiB n KaiC 6…”

“…Remarkably, in light of the kinetic theory [19], the result indicates that the pre-binding conformational transition of KaiC is the rate limiting process. Moreover, we have theoretically shown that the slow KaiB-KaiC binding of the former experiment can be explained by the attractive KaiB-KaiB interaction in the ring-shaped KaiB-KaiC complex [15], without assuming the slow conformational transition of KaiB [20]. Thus, it is now conceivable that the slowness of the binding arises from KaiC rather than KaiB.…”

“…Lastly, Assumption (v) is consistent with the experimental result that the ATPase activity of C1 affects the period [22,24], which implies that the other processes involved in the KaiB-KaiC binding are fast. Moreover, the conformational transition of KaiB is theoretically shown to be not necessary slow [20].…”

“…The present model explicitly considers the hexameric form of KaiC and imposes several restrictive conditions for the binding. Specifically, reflecting that KaiB 6 KaiC 6 complex is much more stable than KaiB n KaiC 6 (n < 6) due to the strong attractive adjacent KaiB-KaiB interaction [15,20,25,26], the present model assumes that six KaiB monomers immediately bind to C1 only when C1 binds six ADP. Moreover, the ADP/ATP exchange rate of the binding-competent C1 is assumed to be smaller than that of the binding-incompetent C1.…”

Functional and Regulatory Roles of Fold-Switching Proteins

“…Since only KaiB fs is active (Tseng et al, 2017), this phenotypic readout suggests that the low abundance of KaiB fs probably plays an important role in maintaining the cyanobacterial circadian clock. The mechanistic details of this role are still up for debate, however (Chang et al, 2015;Koda and Saito, 2020).…”