Mathematical modeling of the in vitro cyanobacterial circadian oscillator

Bacterial Circadian Programs

Volumn , Issue , 2009, Pages 283-300

  Byrne, Mark ^a  

^a SPRING HILL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79955791406     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-540-88431-6_16     Document Type: Chapter

References (27)

1. Clodong S, Düring U, Kronk L, Axmann I, Wilde A, Herzel H, Kollmann M (2007) Functioning and robustness of a bacterial circadian clock. Mol Sys Bio 3:90
2. Emberly E, Wingreen NS (2006) Hourglass model for a protein-based circadian oscillator. Phys Rev Lett 96:038303
3. Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22:403-444
4. Hitomi K, Oyama T, Han S, Arvai AS, Getzoff ED (2005) Tetrameric architecture of the circadian clock protein KaiB: a novel interface for intermolecular interactions and its impact on the circadian rhythm. J Biol Chem 280:19127-19135
5. Ito H, Kageyama H, Mutsuda M, Nakajima M, Oyama T, Kondo T (2007) Autonomous synchronization of the circadian KaiC phosphorylation rhythm. Nat Stat Mol Biol 14:11
6. 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
7. Kageyama H, Nishiwaki T, Nakajima M, Iwasaki H, Oyama T, Kondo T (2006) Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro. Mol Cell 23:161-171
8. 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 22:2127-2134
9. Kurosawa G, Aihara K, Iwasa Y (2006) A model for the circadian rhythm of cyanobacteria that maintains oscillation without gene expression. Biophys J 91(6):2015-2023
10. Li S, Fang YH (2007) Modelling circadian rhythms of protein KaiA, KaiB and KaiC interactions in cyanobacteria. Biol Rhythm Res 38:43-53
11. Mehra A, Hong C, Shi M, Loros J, Dunlap J, Ruoff P (2006) Circadian rhythmicity by autocatalysis. PLoS Comput Biol 2:e96
12. Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. J Biol Rhythms 22:69-80
13. Mori T, Saveliev SV, Xu Y, Stafford WF, Cox MM, Inman RB, Johnson CH (2002) Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. Proc Natl Acad Sci USA 99:17203-17208
14. Mori T, Williams DR, Byrne MO, Qin X, Egli M, Mchaourab HS, Stewart PL, Johnson CH (2007) Elucidating the ticking of an in vitro circadian clockwork. PLoS Biol 4:e93
15. Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T (2005) Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308:414-415
16. Nishiwaki T, Satomi Y, Kitayama Y, Terauchi K, Kiyohara R, Takao T, Kondo T (2007) A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria. EMBO J 26:4029-4037
17. Pattanayek, R, Wang J, Mori T, Xu Y, Johnson CH, Egli M (2004) Visualizing a circadian clock protein: crystal structure of KaiC and functional insights. Mol Cell 15:375-388
18. Pattanayek R, Williams DR, Pattanayek S, Xu Y, Mori T, Johnson CH, Stewart PL, Egli M (2006) Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J 25:2017-2028
19. Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK (2007) Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science 318:809-812
20. Takigawa-Imamura H, Mochizuki A (2006) Predicting regulation of the phosphorylation cycle of KaiC clock protein using mathematical analysis. J Biol Rhythms 21(5):405-416
21. Terauchi K, Kitayama Y, Nishiwaki T, Miwa K, Murayama Y, Oyama T, Kondo T (2007) ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria. Proc Natl Acad Sci USA 104:16377-16381
22. Tomita J, Nakajima M, Kondo T, Iwasaki H (2005) No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 307:251-254
23. Vakonakis I, LiWang AC (2004) Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation. Proc Natl Acad Sci USA 101:10925-10930
24. Van Zon JS, Lubensky DK, Altena PR, ten Wolde PR (2007) An allosteric model of circadian KaiC phosphorylation. Proc Natl Acad Sci USA 104:7420
25. Xu Y, Mori T, Pattanayek R, Pattanayek S, Egli M, Johnson CH (2004) Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses. Proc Natl Acad Sci USA 101:13933-13938
26. Ye S, Vakonakis I, Ioerger TR, LiWang AC, Sacchettini JC (2004) Crystal structure of circadian clock protein KaiA from Synechococcus elongatus. J Biol Chem 279:20511-20518
27. Yoda M, Eguchi K, Terada TP, Sasai M (2007) Monomer-shuffling and allosteric transition in KaiC circadian oscillation. PLoS ONE 2:e408