Entrainment mechanism of the cyanobacterial circadian clock induced by oxidized quinone

doi:10.1088/1674-1056/aba615

Abstract The circadian clock is a self-sustained biological oscillator which can be entrained by environmental signals. The cyanobacteria circadian clock is the simplest one, which is composed of the proteins KaiA, KaiB and KaiC. The phosphorylation/dephosphorylation state of KaiC exhibits a circadian oscillator. KaiA and KaiB activate KaiC phosphorylation and dephosphorylation respectively. CikA competing with KaiA for the same binding site on KaiB affects the phosphorylation state of KaiC. Quinone is a signaling molecule for entraining the cyanobacterial circadian clock which is oxidized at the onset of darkness and reduced at the onset of light, reflecting the environmental light-dark cycle. KaiA and CikA can sense external signals by detecting the oxidation state of quinone. However, the entrainment mechanism is far from clear. We develop an enhanced mathematical model including oxidized quinone sensed by KaiA and CikA, with which we present a detailed study on the entrainment of the cyanobacteria circadian clock induced by quinone signals. We find that KaiA and CikA sensing oxidized quinone pulse are related to phase advance and delay, respectively. The time of oxidized quinone pulse addition plays a key role in the phase shifts. The combination of KaiA and CikA is beneficial to the generation of entrainment, and the increase of signal intensity reduces the entrainment phase. This study provides a theoretical reference for biological research and helps us understand the dynamical mechanisms of cyanobacteria circadian clock.

Keywords: mathematical model entrainment cyanobacterial circadian clock phase response curve

Received: 04 June 2020
Revised: 02 July 2020
Accepted manuscript online: 15 July 2020

PACS:	87.18.Yt	(Circadian rhythms)
	87.85.Tu	(Modeling biomedical systems)
	87.18.Vf	(Systems biology)

Fund: Project supported by the National Natural Science Foundation of China (Grant No. 11672177).

Corresponding Authors: Ying Li
E-mail: leeliying@163.com

Cite this article:

Ying Li(李莹), Guang-Kun Zhang(张广鹍), Zi-Gen Song(宋自根) Entrainment mechanism of the cyanobacterial circadian clock induced by oxidized quinone 2020 Chin. Phys. B 29 098703

[1]	Takahashi J S 2004 J. Biol. Rhythms 19 339
[2]	Bell-Pedersen D, Cassone V M, Earnest D J, Golden S S, Hardin P E, Thomas T L and Zoran M J 2005 Nat. Rev. Genet. 6 544
[3]	Iwasaki H and Kondo T 2004 J. Biol. Rhythms 19 436
[4]	Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T and Kondo T 2005 Science 308 414
[5]	Tseng R, Chang Y, Bravo I, Latham R, Chaudhary A R, Kuo N and Liwang A 2014 J. Mol. Biol. 426 389
[6]	Tseng R, Goularte N F, Chavan A et al. 2017 Science 355 1174
[7]	Nishiwaki T, Iwasaki H, Ishiura M and Kondo T 2000 Proc. Natl. Acad. Sci. USA 97 495
[8]	Xu Y, Mori T and Johnson C H 2003 EMBO J. 22 2117
[9]	Nishiwaki T, Satomi Y, Nakajima M et al. 2004 Proc. Natl. Acad. Sci. USA 101 13927
[10]	Xu Y, Mori T, Pattanayek R, Pattanayek S, Egli M and Johnson C H 2004 Proc. Natl. Acad. Sci. USA 101 13933
[11]	Iwasaki H, Nishiwaki T, Kitayama Y, Nakajima M and Kondo T 2002 Proc. Natl. Acad. Sci. USA 99 15788
[12]	Akiyama S, Nohara A, Ito K and Maeda Y 2008 Mol. Cell 29 703
[13]	Schmitz O, Katayama M, Williams S B, Kondo T and Golden S S 2000 Science 289 765
[14]	Kaur M, Ng A, Kim P, Diekman C O and Kim Y 2019 J. Biol. Rhythms 34 218
[15]	Rust M J, Golden S S and Oshea E K 2011 Science 331 220
[16]	Kim Y, Vinyard D J, Ananyev G, Dismukes G C and Golden S S 2012 Proc. Natl Acad. Sci. USA 109 17765
[17]	Ivleva N B, Gao T, Liwang A and Golden S S 2006 Proc. Natl. Acad. Sci. USA 103 17468
[18]	Kim P, Porr B, Mori T, Kim Y, Johnson C H, Diekman C O and Kim Y 2020 J. Biol. Rhythms 35 227
[19]	Li Y and Liu Z 2014 Int. J. Bifurcat. Chaos 24 1450161
[20]	Li Y and Liu Z 2016 Physica A 457 62
[21]	Gu C, Wang P and Yang H 2019 Chin. Phys. B 28 018701
[22]	Zhu B, Zhou J, Jia M, Yang H and Gu C 2020 Chin. Phys. B 29 068702
[23]	Takigawaimamura H and Mochizuki A 2006 J. Theor. Biol. 241 178
[24]	Rust M J, Markson J S, Lane W S, Fisher D S and Oshea E K 2007 Science 318 809
[25]	Jeong Y M, Dias C L, Diekman C O, Brochon H, Kim P, Kaur M and Kim Y 2019 J. Biol. Rhythms 34 380
[26]	Shalitkaneh A, Kumimoto R W, Filkov V and Harmer S L 2018 Proc. Natl. Acad. Sci. USA 115 7147
[27]	Roenneberg T, Daan S and Merrow M 2003 J. Biol. Rhythms 18 183
[28]	Mihalcescu I, Hsing W and Leibler S 2004 Nature 430 81
[29]	Mihalcescu I 2009 Stability and Noise in the Cyanobacterial Circadian Clock in Bacterial Circadian Programs ed Ditty J L, Mackey S R and Johnson C H (Berlin: Springer) pp. 223-239
[30]	Amdaoud M, Vallade M, Weiss-Schaber C and Mihalcescu I 2007 Proc. Natl. Acad. Sci. USA 104 7051

[1]	Dynamic behavior of the cyanobacterial circadian clock with regulation of CikA Ying Li(李莹), Guang-Kun Zhang(张广鹍), and Yan-Ming Ge (葛焰明). Chin. Phys. B, 2021, 30(10): 108702.
[2]	Entrainment range affected by the difference in sensitivity to light-information between two groups of SCN neurons Bao Zhu(朱宝), Jian Zhou(周建), Mengting Jia(贾梦婷), Huijie Yang(杨会杰), Changgui Gu(顾长贵). Chin. Phys. B, 2020, 29(6): 068702.
[3]	Quantitative modeling of bacterial quorum sensing dynamics in time and space Xiang Li(李翔), Hong Qi(祁宏), Xiao-Cui Zhang(张晓翠), Fei Xu(徐飞), Zhi-Yong Yin(尹智勇), Shi-Yang Huang(黄世阳), Zhao-Shou Wang(王兆守)†, and Jian-Wei Shuai(帅建伟)‡. Chin. Phys. B, 2020, 29(10): 108702.
[4]	Entrainment range affected by the heterogeneity in the amplitude relaxation rate of suprachiasmatic nucleus neurons Chang-Gui Gu(顾长贵), Ping Wang(王萍), Hui-Jie Yang(杨会杰). Chin. Phys. B, 2019, 28(1): 018701.
[5]	Dynamically tunable terahertz passband filter based on metamaterials integrated with a graphene middle layer MaoSheng Yang(杨茂生), LanJu Liang(梁兰菊), DeQuan Wei(韦德泉), Zhang Zhang(张璋), Xin Yan(闫昕), Meng Wang(王猛), JianQuan Yao(姚建铨). Chin. Phys. B, 2018, 27(9): 098101.
[6]	Numerical investigation of the interaction of the turbulent dual-jet and acoustic propagation Yi-Ming Li(李一明), Bao-Kuan Li(李宝宽), Feng-Sheng Qi(齐凤升), Xi-Chun Wang(王喜春). Chin. Phys. B, 2017, 26(2): 024701.
[7]	Interaction function of coupled bursting neurons Xia Shi(石霞), Jiadong Zhang(张佳栋). Chin. Phys. B, 2016, 25(6): 060502.
[8]	Structure-dependent behaviors of diode-triggered silicon controlled rectifier under electrostatic discharge stress Li-Zhong Zhang(张立忠), Yuan Wang(王源), Yan-Dong He(何燕冬). Chin. Phys. B, 2016, 25(12): 128501.
[9]	Collective behaviors of suprachiasm nucleus neurons under different light-dark cycles Gu Chang-Gui (顾长贵), Zhang Xin-Hua (张新华), Liu Zong-Hua (刘宗华). Chin. Phys. B, 2014, 23(7): 078702.
[10]	Large eddy simulations of a circular orifice jet with and without a cross-sectional exit plate Zhang Jian-Peng (张健鹏), Xu Min-Yi (徐敏义), Mi Jian-Chun (米建春). Chin. Phys. B, 2014, 23(4): 044704.
[11]	Mean and fluctuating velocity fields of a diamond turbulent jet Xu Min-Yi (徐敏义), Zhang Jian-Peng (张健鹏), Mi Jian-Chun (米建春), Nathan G. J., Kalt P. A. M.. Chin. Phys. B, 2013, 22(3): 034701.
[12]	Mathematical modelling of gain-switched RF-excited CO₂ waveguide laser Hussain Badran (巴德), Tian Zhao-Shuo (田兆硕), Wang Qi (王骐). Chin. Phys. B, 2004, 13(4): 501-504.
[13]	An open plus nonlinear closed loop control of chaotic oscillators Chen Li-Qun (陈立群). Chin. Phys. B, 2002, 11(9): 900-904.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Metrics
Related Articles

Entrainment mechanism of the cyanobacterial circadian clock induced by oxidized quinone

Cite this article:

Online attention