Tracing ancient cyanobacteria reveals early origins of circadian clocks

Tracing ancient cyanobacteria reveals early origins of circadian clocks
by Riko Seibo
Tokyo, Japan (SPX) May 21, 2025

To shed light on the evolutionary roots of the cyanobacterial circadian clock, a Japanese research team has traced the development of timekeeping proteins from ancient bacterial ancestors. Their study focused on the oscillatory behavior of KaiA, KaiB, and KaiC proteins, comparing the mechanisms in modern cyanobacteria to those of ancestral versions.

"Extant cyanobacteria utilize a circadian clock to predict the light-dark environmental cycle by Earth's rotation in order to achieve efficient photosynthetic reactions. We wanted to know the evolutionary history of when ancient bacteria acquired the circadian clock and how this property was inherited by the present cyanobacteria," explained Associate Professor Atsushi Mukaiyama of Fukui Prefectural University.

Cyanobacteria, known for their role in shaping the planet's oceans and atmosphere, emerged around 3 billion years ago. These bacteria survived critical planetary shifts, including the Great Oxidation event about 2.3 billion years ago, and two global glaciation periods known as Snowball Earth events, before undergoing further evolutionary transformation during the Neoproterozoic Oxygenation event.

Using fossil evidence and molecular models, researchers believe early cyanobacteria already had basic oxygenic photosynthesis systems. Given the importance of light-dark cycles for photosynthetic efficiency, the team investigated whether a circadian clock existed during these ancient eras.

The researchers utilized the cyanobacteria strain Synechococcus elongatus to study circadian rhythms. By reconstituting the KaiC protein oscillator in vitro, they analyzed how the structure and function of these proteins evolved. Their findings show that early clock proteins displayed rhythmic cycles of 18 to 20 hours, suggesting Earth's faster rotation during that era. "The ancient cyanobacterial clock was synchronized to the cycle of 18 to 20 hours. This means that the history of the Earth's rotation period has been restored by tracing the evolution of clock protein molecules," said Assistant Professor Yoshihiko Furuike from the Institute for Molecular Science.

Originally, the oldest KaiC proteins lacked the features necessary for rhythmic oscillation. However, during pivotal evolutionary periods such as the Great Oxidation and Snowball Earth events, these proteins gained the molecular structure needed to support self-sustained circadian function. This adaptation was later inherited by modern photosynthetic cyanobacteria.

The study not only enhances understanding of how biological clocks evolved but also has implications for synthetic biology. "Our ultimate goal is to design modified cyanobacteria that can adapt to the rotation period of planets and satellites other than Earth by shortening or lengthening the period of the Kai-protein oscillator. Cyanobacteria have taken a long time to tune their clock to 24 hours, but we may be able to achieve even faster evolution using modern knowledge and technology," said Professor Shuji Akiyama of the Institute for Molecular Science.

Research Report:Evolutionary Origins of Self-Sustained Kai protein Circadian Oscillators in Cyanobacteria