Two circadian oscillators in one cyanobacterium

Abstract

The rotation of the Earth results in predictable environmental changes that pose challenges for organisms and force them to adapt. To address this daily rhythm, organisms from all kingdoms of life have evolved diverse timing mechanisms. In the cyanobacterium Synechococcus elongatus PCC 7942, the three proteins KaiA, KaiB, and KaiC constitute the central timing mechanism that drives circadian oscillations. In addition to the standard oscillator, named KaiAB1C1, Synechocystis sp. PCC 6803 harbors several, diverged clock homologs. The nonstandard KaiB3-KaiC3 system was suggested to impact the metabolic switch in response to darkness. Here, we demonstrate the direct interaction of KaiC3 with Sll0485, which is a potential new chimeric KaiA homolog that we named KaiA3. The existence of a functional link between these proteins is further supported by the co occurrence of genes encoding KaiA3 with the KaiB3-KaiC3-like gene products in 10 cyanobacterial and five other bacterial species. KaiA3 is annotated as a NarL-type response regulator due to its similarity to the response regulator receiver domains. However, its similarity to canonical NarL drastically decreases in the C-terminal domain, which resembles the circadian clock protein KaiA. In line with this, we detected the stimulation of KaiC3 phosphorylation by KaiA3 in vitro. Furthermore, we showed that deletion of the kaiA3 gene led to growth defects during mixotrophic growth conditions and, like a kaiC3-deficient mutant, viability was impaired during chemoheterotrophic growth in complete darkness. In summary, we suggest KaiA3 as a novel, nonstandard KaiA homolog within the cyanobacterial phylum, extending the KaiB3-KaiC3 system in Cyanobacteria and other prokaryotes.

Diel Cycle Proteomics: Illuminating Molecular Dynamics in Purple Bacteria for Optimized Biotechnological Applications

“…The role of Kai proteins in R. rubrum is still unknown and their function might be related to a timing system that has yet to be identified. Upon closer examination of the position of kai genes in the genome of R. rubrum, we observe that kaiB2 and kaiC2 are preceded by the gene Rru_A3293, recently identified as an ortholog of the kaiA3 gene in Synechocystis by Köbler and colleagues [14]. Further investigations into the transcriptional and translational expression of kai gene homologs should incorporate Rru_A3293 to provide a more comprehensive understanding of clock component regulation.…”

“…In contrast, Synechocystis sp. PCC 6803 encodes multiple Kai proteins, suggested to play a role in fine-tuning the core oscillator [11][12][13][14]. Importantly, the presence of Kai proteins is not exclusive to Cyanobacteria.…”

“…R. rubrum possesses two homologs of the circadian clock kaiB and kaiC genes and one potential homolog of one of the gene kaiA of Synechocystis sp. PCC 6803 [14]. Interestingly, rhythmic activity of the uptake hydrogenase (Hup), an enzyme involved in the consumption of H2, was reported using an enzyme assay [23].…”