Minimal tool set for a prokaryotic circadian clock

Abstract

BackgroundCircadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.ResultsUsing a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.ConclusionOur analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0999-7) contains supplementary material, which is available to authorized users.

Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea

“…This nonredundant set was used to build a dendrogram by using a combination of the FastTree method and the unweighted pair group method using average linkages (UPGMA) (Text S1; see Materials and Methods for details). The resulting tree topology was largely consistent with results of previous phylogenetic analyses (34,39).…”

“…Several halobacterial KaiC-like proteins have been studied with respect to their potential involvement in light-dependent gene expression (38). Very recently, KaiC proteins from the hyperthermophiles Thermococcus litoralis and Pyrococcus horikoshii were shown to be capable of KaiA-independent autophosphorylation at both 30°C and 75°C (34,39). Finally, structural analysis of a distinct family of archaea-specific uncharacterized proteins (DUF835, PF05763 in the Pfam database [40]) has shown that these proteins are inactivated ATPases that are most closely related to KaiC (41).…”

Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights

“…Evolutionarily, W331 and W462 are highly conserved among KaiC proteins found in KaiABC clusters in the cyanobacterial phylum, a clade known as KaiC1 (SI Appendix, Table S2) (60). W331 is also conserved among the KaiC3 clade, proteins which have not been functionally characterized (61).…”

Identification of circadian rhythms inNannochloropsisspecies using bioluminescence reporter lines

“…Under constant light conditions no oscillations of gene expression and chlorophyll fluorescence have been detected in the gymnosperm Norway Spruce ( Picea abies ) in spite of containing the canonical plant clock genes (Gyllenstrand et al , 2014). In contrast to the widely studied Synechococcus elongatus , other cyanobacteria such as the abundant Prochlorococcus genus lack a functional kaiA gene and no rhythms have been detected under constant light conditions (Holtzendorff et al , 2008, Schmelling et al , 2017). It has been hypothesized that an hour-glass oscillator that is reset every day is sufficient for these Prochlorococcus species because they originate from southern latitudes where they do not experience large changes in daylength, and their marine environment is more stable than fresh water habitats (Mullineaux and Stanewsky 2009).…”