From primordial clocks to circadian oscillators

Nature. 2023 Apr;616(7955):183-189. doi: 10.1038/s41586-023-05836-9. Epub 2023 Mar 22.


Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock2. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood3-6, but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism7-9. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.

MeSH terms

  • Adenosine Diphosphate / metabolism
  • Adenosine Triphosphate / metabolism
  • Allosteric Regulation
  • Bacterial Proteins* / chemistry
  • Bacterial Proteins* / metabolism
  • Bacterial Proteins* / ultrastructure
  • Circadian Clocks*
  • Circadian Rhythm*
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Kinetics
  • Phosphorylation
  • Protein Conformation
  • Protein Folding
  • Rhodobacter sphaeroides* / chemistry
  • Rhodobacter sphaeroides* / metabolism


  • Bacterial Proteins
  • Adenosine Triphosphate
  • Adenosine Diphosphate