Minimal tool set for a prokaryotic circadian clock

Jul 23, 2017BMC evolutionary biology

Basic components needed for a daily biological clock in simple bacteria

AI simplified

Circadian Biology on OpenScience ↗PubMed ↗DOI ↗

Abstract

Analysis of 11,264 genomes shows that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea.

Putative KaiC-based timing systems were identified in organisms outside of Cyanobacteria, along with variations within cyanobacterial strains.
Differences in circadian gene expression among cyanobacterial strains may correlate with the diversity of clock components encoded in their genomes.
Statistical analyses suggest networks of either reduced or fully functional clock systems based on the co-occurrence of clock component homologs.
Biochemical studies show that kinase activity is consistently present in cyanobacterial KaiC proteins and homologs from two thermophilic Archaea.
Phosphorylation by KaiA is only detectable in KaiC1 orthologs, indicating variability in functional mechanisms among different KaiC proteins.

AI simplified

BACKGROUND: Circadian 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.

RESULTS: Using 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.

CONCLUSION: Our 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.

Full Text

We can’t show the full text here under this license. Use the link below to read it at the source.

View full text (PDF) ↗

Minimal tool set for a prokaryotic circadian clock

Abstract

Full Text

You found one interesting study. We’ll send the next 7.

what lands in your inbox each week:

Recent issues from the circadian biology brief

Abstract

Full Text

Related papers

You found one interesting study. We’ll send the next 7.

what lands in your inbox each week:

Recent issues from the circadian biology brief