Aoki Lab

Life-Informatics Unit, Department of Complex System Sciences

Graduate School of Informatics, Nagoya University

Research themes:

The aim of our lab is to understand the genetic and molecular mechanisms underlying various types of adaptation processes mainly in photosynthetic organisms and microorganisms, especially from the viewpoints of evolution and diversity. One example of the research themes we are focusing on is the mechanisms of the circadian clocks (=biological clocks) in photosynthetic organisms and their evolution. Circadian clocks, the endogenous timekeeping systems that tick with a period of ~24 h, enable various biological processes to occur in appropriate times of day, thereby making organisms better adapt to environmental changes of day-night cycles, which is ultimately attributed to the rotation of the Earth. The circadian clocks in photosynthetic organisms, such as plants, algae and cyanobacteria, regulate a variety of activities ranging from gene expression and photosynthesis to leaf and flower movements.


We are using the moss Physcomitrella patens for experiments, because P. patens is a highly established model plant and various techniques and tools for studying gene function can be effectively applied to this species. Importantly, the genome of P. patens was completely sequenced (Rensing et al. (2008) Science 319(5859): 64-69), enhancing the potential of P. patens as a model organism in this genomic/post-genomic era. The other reason we use P. patens is that moss plants are known to have diverged from the lineages leading to extant "higher plants" at least 450 million years ago, which makes mosses attractive from the viewpoint of evolution and diversity of plants. We expect that important insights will be obtained about the evolution and origin of the plant circadian clocks by using P. patens. We are also using Chlamydomonas reinhardtii (green alga), Arabidopsis thaliana (angiosperm) and cyanobacteria (bacteria), largely in collaboration with other labs, to get insights by comparisons between the mechanisms of these phylogenetically distant species.


We also study under other related research themes, e.g., evolution of two-component systems in green (photosynthetic) organisms and the bioluminescence burst in Escherichia coli. For details, take a look at the list of recent publications shown below.

To foreign students:

Aoki lab always welcomes eager students from foreign countries. Please take a look at a web page provided by our faculty. If you have any question, do not hesitate to contact us:


Tel&fax, +81-52-789-5376


Circadian clock, Circadian rhythm, Biological clock, Moss, Physcomitrella patens, Bryophyte, Two-component system, Signal transduction, Regulation of gene expression, Environmental adaptation, Photosynthetic organisms, Evolution, Reporter gene techniques.

Recent publications:

"PAS-histidine kinases PHK1 and PHK2 exert oxygen-dependent dual and opposite effects on gametophore formation in the moss Physcomitrella patens" Masashi Ryo, Takafumi Yamashino, Hisanori Yamakawa, Yuichi Fujita and Setsuyuki Aoki. Biochemical and Biophysical Research Communications. (2018) 503(4):2861-2865.


"Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens" Masashi Ryo, Takafumi Yamashino, Yuji Nomoto, Yuki Goto, Mizuho Ichinose, Kensuke Sato, Mamoru Sugita and Setsuyuki Aoki. Journal of Experimental Botany. (2018) 69(20):4839-4851.


"Diversity of plant circadian clocks: insights from studies of Chlamydomonas reinhardtii and Physcomitrella patens" Masashi Ryo, Takuya Matsuo, Takafumi Yamashino*, Mizuho Ichinose, Mamoru Sugita and Setsuyuki Aoki. Plant Signaling & Behavior. (2016) 11(1):E1116661.


"Posttranslationally caused bioluminescence burst of the Escherichia coli luciferase reporter strain" Yamato ideguchi, Yuta Oshikoshi, Masashi Ryo, Shogo Motoki, Takashi Kuwano, Takafumi Tezuka and Setsuyuki Aoki. Archives of Microbiology. (2016) 198(1):35-41.


"Transformation and measurement of bioluminescence rhythms in the moss Physcomitrella patens" Setsuyuki Aoki, Ryo Okada and Santosh B. Satbhai. In Plant Circadian Networks (Methods in Molecular Biology, Vol. 1158), pp. 325-336, Edited by Dorothee Staiger. (2014) Humana Press, New York.


"Firefly luciferase as the reporter for transcriptional response to the environment in Escherichia coli" Masashi Ryo, Yuta Oshikoshi, Shosei Doi, Shogo Motoki, Atsuko Niimi and Setsuyuki Aoki. Analytical Biochemistry (2013) 443(2):211-213.