Studies of the Molecular Machinery of Biological Clocks

Organisms that live under 24-hour day-night cycles have evolved circadian clocks so that they are able to adapt to these cyclic conditions. Circadian clocks control physiological activities, such as wake-sleep activity and endocrine activity; therefore, they show circadian rhythms with a period of about 24 hours. 

Circadian clock genes have been cloned from cyanobacteria (even bacteria have circadian clocks), Neurospora, Drosophila, and mammals including mouse and human. These clocks have been analyzed in detail. However, central questions remain to be answered: How does the clock generates circadian oscillation? How is the period of the circadian oscillation is precisely regulated to 24 hours (the circadian clock of cyanobacteria is very precise, with a variance of less than 5 minutes per day)? Finally, how is the period precisely temperature-compensated?
Recognizing the circadian clock as molecular machinery (a complex or complexes of clock proteins), we seek to elucidate its atomic structure and to understand the operation of the machinery at the atomic level. Because thermotolerant proteins derived from thermophilic organisms are most suitable for protein research, we are using the thermophilic cyanobacterium Thermosynechococcus elongatus BP1. We cloned the kaiA, kaiB, and kaiC genes from T. elongatus, expressed them in Esherichia coli, purified them, and characterized them in detail biochemically and biophysically (see Fig. 1; KaiA acts as an accelerator, KaiC as a brake, and the function of KaiB is not known).  We analyzed the structures of the Kai proteins by electron microscopy, X-ray crystallography, and NMR analysis; we solved the 3-D structure of KaiC and the atomic structures of KaiA and KaiB; and we clarified the relationships between the structure and clock function of the Kai proteins at the atomic level.
In order to clarify the operation of the circadian clock molecular machinery, we are trying to solve the structures in various states and to reconstitute the machinery in vitro.  In addition, by isolating rhythm mutants and cloning clock genes, we are investigating clock molecular mechanisms in higher plants and algae.

Genomics of Mitochondria

Virtually all aerobic eukaryotic cells contain mitochondria, which play an important role as the site of aerobic respiration and ATP generation. We have analyzed the structure and replication of mitochondrial DNA, as well as the transcription and translation of mitochondrial genes in higher plants. We hope to understand the evolution of mitochondria in plant cells.

Genomics of Archaea

Plants and other organisms are able to capture and transform light energy from the sun into chemical energy, such as ATP. We aim to dissect the molecular machinery that performs this type of energy conversion in Archaea.