Cyanobacterial Circadian Rhythms
Scientific studies
1995 - present
Cyanobacteria are the simplest organisms known to exhibit circadian rhythms with a period of a day, which is comparable to our sleep/wake cycle. We have analysed molecular and physiological mechanism underlying genesis of the cellular rhythms. We have identified three genes, kaiABC, which are the core of cyanobacterial circadian rhythms (Ishiura et al. Science, 1998), and KaiC-associating two component regulatory factors, SasA and RpaA (Iwasaki et al. Cell, 2000; Takai et al. PNAS 2006). The SasA-RpaA constituents a major transcriptional output pathway to regulate genome-wide transcriptional control by the clock (Ito et al. PNAS 2009).
One of the most important contributions of our works was to falsify the TTFL (transcription-translation feedback loop) model. The TTFL model was theoretically predicted in 1965 by Goodwin, and experimentally supported to explain circadian cycling in Drosophila (fruit fly) in 1990. It has been widely supported in eukaryotic clock systems from fungi, plants, insects and higher animals in 1990s. The Novel prize for physiology and medicine in 2017 went to three U.S. biologists for pioneering establishment of the TTFL model. Nevertheless, in 2005 we reported that transcription and translation are not essential to sustain circadian oscillation in phosphorylation of the KaiC protein in cyanobacteria (Tomita et al. Science, 2005). Then, immediately we have demonstrated in vitro (in a test tube) that circadian enzymatic oscillation in KaiC phosphorylation is reconstituted by incubation of three Kai proteins (KaiA, KaiB and KaiC) in the presence of ATP (Nakajima et al. Science, 2005). This opened completely new phase in the history of chronobiology, and highly competitive research has been followed since then.
Our recent studies include demonstration of damped oscillation property described by Hopf bifurcation in low temperature (Murayama et al. PNAS, 2017), feed-forward system of transcriptional inhibition in the dark (Takano et al. BMC Biology, 2015), and circadian cycle in the dark without de novo kai gene expression (PNAS, 2013).
Now we are studying on physiological and molecular properties of the circadian system, such as
- Circadian control of metabolism and UV sensitivity in cyanobacteria.
- Damped oscillation which may be a prototype of sustained oscillation in cyanobacteria.
- Light-dependent modulation of transcriptional property in cyanobacteria.
- Transcriptional rhythms in the absence of KaiC phosphorylation cycle.
- Novel factors to link circadian cycle and cell division cycle.

Research articles (Representative)
Kon et al. (2021) "Na+/Ca2+ exchanger mediates cold Ca2+ signaling conserved for temperature-compensated circadian rhythms" Science Advances 7:18  doi:
Koji Kawasaki & Hideo Iwasaki (2020) "Involvement of glycogen metabolism in circadian control of UV resistance in cyanobacteria" PLOS Genetics 16:11 e1009230 doi:
Kawamoto N, Ito H, Tokuda IT, and Hideo Iwasaki (2020) "Damped circadian oscillation in the absence of KaiA in Synechococcus" Nature Communications, 11, 2242. doi: 10.1038/s41467-020-16087-x
Yoriko Murayama, Hiroshi Koric, Chiaki Oshima, Takao Kondo, Hideo Iwasaki, and Hiroshi Ito (2017) “Low temperature nullifies the circadian clock in cyanobacteria through Hopf bifurcation” Proc. Natl. Acad. Sci. USA, 2017 Apr 19. doi: 10.1073/pnas.1620378114
Takano S, Tomita J, Sonoike K, H. Iwasaki* (2015) "The initiation of nocturnal dormancy in Synechococcus as an active process." BMC Biol. 2015 Jun 10;13:36. doi: 10.1186/s12915-015-0144-2.
Umetani M, Hosokawa N, Kitayama Y, H. Iwasaki* (2014) "Hypersensitive photic responses and intact genome-wide transcriptional control without the KaiC phosphorylation cycle in the Synechococcus circadian system." J. Bacteriol.2014 Feb;196(3):548-55. doi: 10.1128/JB.00892-13. Epub 2013 Nov 15.
Xu Y, Weyman PD, Umetani M, Xiong J, Qin X, Xu Q, H. Iwasaki, Johnson CH. (2013) "Circadian yin-yang regulation and its manipulation to globally reprogram gene expression." Curr Biol..2013 Dec 2;23(23):2365-74. doi: 10.1016/j.cub.2013.10.011. Epub 2013 Nov 7.
N. Hosokawa, H. Kushige and H. Iwasaki* (2013) "Attenuation of the posttranslational oscillator via transcription?translation feedback enhances circadian-phase shifts in Synechococcus"  Proc. Natl. Acad. Sci. USA, Aug 27;110(35):14486-91. doi: 10.1073/pnas.1302243110. Epub 2013 Aug 12.
Kushige, H., Kugenuma, H., Matsuoka, M., Ehira, S., Ohmori, M., Iwasaki, H.* (2013) "Genome-wide and heterocyst-specific circadian gene expression in the filamentous cyanobacterium, Anabaena sp. PCC 7120". J. Bacteriol. 195: 1276-1284
M. Hanaoka*, N. Takai, N. Hosokawa, M. Fujiwara, Y. Akimoto, N. Kobori, H. Iwasaki, T. Kondo, K. Tanaka (2012) "RpaB, another response regulator operating circadian clock-dependent transcriptional regulation in Synechococcus elongatus PCC 7942" J. Biol. Chem., 287: 26321-26327
N. Hosokawa, T. Hatakeyama, T. Kojima, Y. Kikuchi, H. Ito and H. Iwasaki* (2011) "Circadian transcriptional regulation by the posttranslational oscillator without de novo clock gene expression in Synechococcus" Proc. Natl. Acad. Sci. USA, 108: 15396-15401.
H. Ito, M. Mutsuda, Y. Murayama, J. Tomita, N. Hosokawa, K. Terauchi, C. Sugita, M. Sugita, T. Kondo, H. Iwasaki* (2009) "Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus" Proc. Natl. Acad. Sci. USA, 106:14168-14173 (June 30, 2009)
H. Tozaki, T. Kobe, K. Aihara, H. Iwasaki* (2008) "An attempt to reveal a role of a transcription/translation feedback loop in the cyanobacterial KaiC protein-based circadian system by using a semi-synthetic method" Int. J. Bioinform. Res. Appl. , 4: 435-444
S.R. Mackey, JS. Cho, Y. Kitayama, H. Iwasaki, G. Dong, S.S. Golden (2008) "Proteins found in a CikA-interaction assay link the circadian clock, metabolism, and cell division in Synechococcus elongatus" J. Bacteriol., 190: 3738-3746
A. Seki, M. Hanaoka, Y. Akimoto, S. Masuda, H. Iwasaki, K. Tanaka (2007) "Induction of a group 2 sigma factor, RpoD3, by high light and the underlying mechanism in Synechococcus elongatus PCC 7942" J. Biol. Chem., 282: 36887-36894
F. Miyoshi, Y. Nakayama , K. Kaizu, H. Iwasaki, M. Tomita (2007) "A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria" J. Biol. Rhythms, 22: 69-80
N. Takai, M. Nakajima, T. Oyama, R. Kito, C. Sugita, M. Sugita, T. Kondo, H. Iwasaki* (2006) "A KaiC-associating SasA-RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria " Proc Natl Acad Sci USA, 103: 12109-12114
H. Kageyama, T. Nishiwaki, M. Nakajima, H. Iwasaki, T. Oyama, T. Kondo (2006) "Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro" Molecular Cell, 23: 161-171
M. Nakajima, K. Imai, H. Ito, T. Nishiwaki, Y. Murayama, H. Iwasaki, T. Oyama, T. Kondo (2005) "Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro" Science 308, 5720: 414-415
Tomita J, Nakajima M, Kondo T, Iwasaki H* (2005) "No transcription-translation feedback in circadian rhythm of KaiC phosphorylation." Science 307, 5707: 251-254
T. Nishiwaki, Satomi Y, Nakajima M, Lee C, Kiyohara R, Kageyama H, Kitayama Y, Temamoto M, Yamaguchi A, Hijikata A, Go M, Iwasaki H, Takao T, Kondo T. (2004) "Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942." Proc Natl Acad Sci USA 101:13927-32
Imai K, Nishiwaki T, Kondo T, Iwasaki H* (2004) "Circadian rhythms in the synthesis and degradation of a master clock protein KaiC in cyanobacteria."  J Biol Chem 279:36534-9
Nakahira Y, Katayama M, Miyashita H, Kutsuna S, Iwasaki H, Oyama T, Kondo T (2004) "Global gene repression by KaiC as a master process of prokaryotic circadian system." Proc Natl Acad Sci USA 101: 881-885
Kitayama Y, Iwasaki H, Nishiwaki T, Kondo T (2003) "KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system." EMBO J.22:2127-34
Kageyama H, Kondo T, Iwasaki H* (2003) "Circadian formation of clock protein complexes by KaiA, KaiB, KaiC, and SasA in cyanobacteria." J Biol Chem.278:2388-95
Iwasaki H*, Nishiwaki T, Kitayama Y, Nakajima M, Kondo T (2002) *corresponding author "KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria." Proc Natl Acad Sci USA 99:15788-93
Taniguchi Y, Yamaguchi A, Hijikata A, Iwasaki H, Kamagata K, Ishiura M, Go M, Kondo T (2001) "Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC." FEBS lett.496: 86-90
Iwasaki H, Williams SB, Kitayama Y, Ishiura M, Golden SS, Kondo T (2000) "A KaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria." Cell 101: 223-233
Nishiwaki T, Iwasaki H, Ishiura M, Kondo T (2000) "Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria." Proc Natl Acad Sci USA 97: 495-499
Iwasaki H, Taniguchi Y, Ishiura M, Kondo T (1999) "Physical interactions among circadian clock proteins, KaiA, KaiB and KaiC, in cyanobacteria." EMBO J 18: 1137-1145
NJ Cosper, C Stalhandske, H Iwasaki, T Oshima, R Scott, T Iwasaki (1999) "Structural conservation of the isolated zinc site in archaeal zinc-containing ferredoxins as revealed by X-ray absorption spectroscopic analysis and its evolutionary implications." J. Biol. Chem.274: 23160-23168
Ishiura, M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, Kondo T (1998) "Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria." Science 281: 1519-1523

Invited Review Articles & Chapters
Iwasaki H (2009) "A posttranslational chemical circadian oscillator in cyanobacteria" Systems Biology: The Challenge of Complexity (Eds. Nakanishi,S., Kageyama,R., Watanabe,D), Springer
Iwasaki H (2009) "Factors involved in transcriptional output from the Kai-protein-based circadian oscillator" Bacterial Circadian Programs (Eds. J. Ditty, S. Mackey, C.H. Johnson), Springer
Iwasaki H, Kondo T. (2004) "Circadian timing mechanism in the prokaryotic clock system of cyanobacteria." J. Biol. Rhythms 19: 436-444
Iwasaki H, Kondo T. (2002) "Histidine kinases in the cyanobacterial circadian system" Histidine Kinases (Eds. M. Inouye and R. Dutta), Academic Press
Iwasaki H, Kondo T (2000) "The current state and problems of circadian clock studies in cyanobacteria." Plant Cell Physiol 41: 1013-1020
Iwasaki H, Dunlap JC (2000) "Microbial circadian oscillatory systems in Neurospora and Synechococcus: models for cellular clocks." Curr. Opin. Microbiology 3: 189-19
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