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Minimal tool set for a prokaryotic circadian clock.

Nicolas M Schmelling1, Robert Lehmann2, Paushali Chaudhury3

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BMC Evolutionary Biology
|July 23, 2017
PubMed
Summary

Circadian clocks, driven by KaiABC proteins in cyanobacteria, have homologs in Bacteria and Archaea. These organisms may possess simpler KaiC-based timing systems, suggesting widespread, albeit reduced, circadian functions across domains.

Keywords:
ArchaeaBLASTCircadian clockCo-occurrenceCyanobacteriaInput factorsKinase activityLength distributionOutput factors

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Area of Science:

  • Microbiology
  • Biochemistry
  • Genomics

Background:

  • Circadian clocks are widespread, with cyanobacteria utilizing a unique KaiABC protein system.
  • Homologs of KaiABC proteins exist in Bacteria and Archaea, but their function remains unclear.
  • Understanding these homologs is crucial for deciphering the evolution and diversity of circadian rhythms.

Purpose of the Study:

  • To investigate the presence and diversity of KaiC-based circadian systems in Bacteria and Archaea.
  • To analyze the conservation and functional regions of KaiC homologs.
  • To propose potential network structures of circadian clock systems outside of cyanobacteria.

Main Methods:

  • Universal BLAST analysis for identifying KaiC homologs.
  • Systematic analysis of public microarray data for gene expression variations.
  • Statistical analysis of co-occurrences for network inference.
  • Sequence conservation analysis and biochemical characterization of KaiC proteins.

Main Results:

  • Putative KaiC-based timing systems identified in organisms beyond Cyanobacteria.
  • Variations in circadian gene expression observed across different cyanobacterial strains.
  • KaiC homologs from Archaea exhibit kinase activity, but KaiA-mediated phosphorylation is limited to KaiC1 orthologs.
  • Proposed models for reduced and fully functional circadian clock networks.

Conclusions:

  • Circadian clock components homologous to Synechococcus elongatus PCC 7942 are present in Bacteria and Archaea.
  • These components are less abundant outside of cyanobacteria, suggesting simpler or reduced timing systems.
  • The findings indicate the potential for diurnal oscillations driven by KaiC-based systems in diverse prokaryotes.