## 2 Entrainment through the Input Pathway
Truly, the ability to become entrained with variation in ATP/ADP concentration is a remarkable discovery, but there must be some other mechanism that ensures cyanobacteria's more acute response to a dark pulse since a dark-induced drop in the ATP/ADP ratio only becomes apparent after at least 2 h [33]. This is because, if the onset of darkness is directly related to survival, cyanobacteria must have a way to send this vital information about imminent darkness to the circadian clock at a faster rate. In addition, a recent study reported that cyanobacteria subjected to darkness experience only a slight reduction in energy charge [2], and cyanobacteria's resilience can be attributed to its ability to maintain a steady-state level of reduced power. Therefore, some other pathway is needed to explain cyanobacteria's rather quick response to the sudden absence of light. As previously mentioned, both photosynthetic and respiratory electrons eventually flow through the PQ pool (Figure 1) and measuring the redox state of the PQ pool has shown a profile that is in agreement with this notion [34]. Cyanobacteria try to maintain a steady-state level of the redox state, but darkness quickly oxidizes its quinone pool. Applying oxidized quinone to cyanobacteria makes KaiA become inactivated in vivo [35; 36; 37; 38]. To test this effect in a more isolated and detailed manner by mimicking it in vitro, oxidized quinone's effect was tested in a standard oscillator mixture KaiABC [34]. In this study, KaiA became inactivated by oxidized quinone in vitro, and more surprising was KaiA's time dependency regarding this response. This is because inactivated KaiA can no longer induce KaiC phosphorylation and it depends on the time point of quinone application. KaiA inactivation with oxidized quinone shifted the phase of the oscillation, causing premature dephosphorylation of KaiC and forcing the rhythm to oscillate early; thus, a phase advance occurs. However, an expected phase delay was not produced; therefore, an in vitro approach using oxidized quinone to mimic the in vivo dark pulse entrainment process remained somewhat incomplete at this point. Commonly, a photosynthetic organism detects the environmental day/night transition through the use of photoreceptors, such as a phytochrome [39; 40]. Furthermore, the initial discovery of a phytochrome-like protein in cyanobacteria suggested a possibility that this might be one of the input components that convey the vital information about light or darkness to the circadian oscillator [37]. This protein was named \"circadian input kinase A\" (CikA); however, while phytochromes normally bind a chromophore called bilin in other light-harvesting organisms, CikA seemed unresponsive to bilin [35]. A crystal structure of CikA bound to the KaiB-KaiC complex confirmed its common binding spot on KaiB [41]. Later, it turned out that CikA competes with KaiA for the same binding site on KaiB during the time when KaiC-KaiB complexation takes place [42]. Again, KaiB's role as an oscillator component is to sequester KaiA away from the A-loop in such a way that the isolated KaiA cannot lock it in its exposed conformation, leading to KaiC dephosphorylation. Adding CikA in the in vitro mixture shortened the oscillatory KaiC phosphorylation [43], which is an effect that is like adding more KaiA [43]. In agreement with this finding, an ectopic expression of CikA in vivo showed period shortening [44]. The displaced KaiA can bind to the A-loop to activate the kinase activity of KaiC. This may be because KaiB cannot sequester KaiA when CikA is occupying the same spot, leading to premature KaiC phosphorylation. KaiA is composed of a KaiC-interacting C-terminal domain, a linker, and a pseudoreceiver (PsR) domain, and it is this PsR domain where oxidized quinone binds and inactivates KaiA. CikA also has a PsR domain, which resembles that of KaiA [45], and oxidized quinone inactivates CikA in a similar manner.