The circadian input kinase gene (cikA) was first identified from a Tn5 mutant of Synechococcus elongatus PCC 7942. A cikA null strain shows a striking phenotype related to circadian gene regulation: all sampled loci show a shortened circadian period and reduced amplitude of oscillation and a failure to exhibit a wild-type resetting of the phase of the rhythm after an environmental signal. This global defect in response to the environment suggests a key role for CikA in the circadian input pathways. Bioinformatics results classify CikA as a divergent member of the bacteriophytochrome family, suggesting a role in light signal transduction. In vitro analysis previously showed that CikA is a bona fide histidine protein kinase (HPK), and its kinase activity is regulated by the presence of other domains. Its own pseudo-receiver (PsR) domain is not the cognate receiver domain of its kinase HPK domain, and its GAF domain does not likely bind a bilin chromophore as do photoreceptive phytochromes. Recent results suggested that CikA may function as a redox-sensor. In this study, we examined the function of each domain of CikA using different mutant cikA alleles, and determined their phenotypes with respect to complementation of a null mutant and overexpression in both wild type and cikA null strains. All domains except the featureless N-terminus were required for CikA function. Overexpression of all mutant alleles that encoded the PsR domain, whether or not the HPK was functional, caused a dominant arrhythmia phenotype. In the absence of PsR, overexpressed variants did not cause arrhythmia, but affected the amplitude and period of oscillation. The results suggest a model in which the PsR domain regulates kinase activity and mediates interaction with other input pathway components to allow CikA to reach the correct cellular position to fulfill its function. Cellular localization assays showed CikA can interact with a complex and showed a polar localization pattern, whereas its variant without PsR showed uniform distribution in the cell. In summary, CikA is an autoregulated kinase in which the PsR domain regulates activity of the HPK domain and also serves as an interaction module to lead the CikA to a specific cellular position.

Synechococcus elongatus PCC 7942 is a model organism used to study the circadian rhythm, a process that is driven by an endogenous biological clock that can be modulated by external cues such as light and temperature. Some proteins have been identified that are involved in circadian signal transduction in S. elongatus. Of them, KaiA, KaiB and KaiC comprise the central oscillator components, which are essential for internal timekeeping. SasA is an important protein in the output pathway, which passes the information from central oscillator to downstream components, and thus controls metabolic and behavioral processes. CikA is a major component in the input pathway, which maintains synchrony of the oscillator with the environment. CikA is an unusual phytochrome-like histidine protein kinase. It has a pseudo receiver domain which can not accept a phosphoryl group. CikA is thought to be located at the poles of the cell through interaction between PsR and some protein or protein complex that is also localized at the poles. One of the potential CikA-interacting proteins identified through a yeast two hybrid screen is called hypothetical protein 1. It specifically recognizes a PsR bait in a yeast two hybrid assay. A bioinformatics analysis showed that there are predicted signal peptide and transmembrane domains at the N-terminal and a cytochrome C homolog domain at the C-terminal of Hyp1. Elucidating the features and function of Hyp1 will provide us with useful information to understand the function and working mechanism of CikA, and therefore will help us to clarify the signal transduction in the clock. In this research, I used genetic, cell biological and biochemical approaches to study the features and function of this newly identified clock component Hyp1. To confirm the interaction between PsR and Hyp1 and complement the yeast two hybrid data, I truncated Hyp1 (Thyp1) and purified soluble Thyp1. At the same time, I obtained purified PsR. I tried to copurify the PsR and 6-histidine-tagged Hyp1 on a nickel affinity column. However, PsR non-specifically bound to the column, which eliminated the utility of this approach to study their interaction. In addition to using a biochemical approach to study Hyp1, I constructed three hyp1 overexpression alleles for genetic analysis and two hyp1-yfp overexpression fusion alleles for subcellular localization studies. All of them will help us to understand the features and function of Hyp1.