Bacterial circadian programs

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 72, Issue , 2007, Pages 395-404

  Johnson, C H ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR CLOCK; BACTERIAL PROTEIN; KAIA PROTEIN, CYANOBACTERIA; KAIB PROTEIN, CYANBACTERIA; KAIC PROTEIN, CYANOBACTERIA;

CELL DIVISION; CIRCADIAN RHYTHM; CYANOBACTERIUM; FEEDBACK SYSTEM; GENE EXPRESSION; IN VITRO STUDY; NONHUMAN; OSCILLATOR; ADAPTATION; BACTERIAL GENE; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CYTOLOGY; GENETICS; MULTIGENE FAMILY; PHYSIOLOGY; REVIEW;

ADAPTATION, PHYSIOLOGICAL; BACTERIA; BACTERIAL PHYSIOLOGY; BACTERIAL PROTEINS; CELL DIVISION; CIRCADIAN RHYTHM; CYANOBACTERIA; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION; GENES, BACTERIAL; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MULTIGENE FAMILY;

EID: 48249120313     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2007.72.027     Document Type: Conference Paper

References (74)

1. Andersson C.A., Tsinoremas N.F., Shelton J., Lebedeva N.V., Yarrow J., Min H., and Golden, S.S. 2000. Application of bioluminescence to the study of circadian rhythms in cyanobacteria. Methods Enzymol. 305: 527.
2. Aoki S., Kondo T., Wada H., and Ishiura M. 1997. Circadian rhythm of the cyanobacterium Synechocystis sp. PCC 6803 in the dark. J. Bacteriol. 179: 5751.
3. Bruce V.G. 1961. Environmental entrainment of circadian rhythms. Cold Spring Harbor Symp. Quant. Biol. 25: 29.
4. -. 1970. The biological clock in Chlamydomonas reinhardtii. J. Protozool. 17: 328.
5. Chen T.-H., Chen T.-L., Hung L.-M., and Huang T.-C. 1991. Circadian rhythm in amino acid uptake by Synechococcus RF-1. Plant Physiol. 97: 55.
6. Clodong S., Duhring U., Kronk L., Wilde A., Axmann I., Herzel H., and Kollmann M. 2007. Functioning and robustness of a bacterial circadian clock. Mol. Syst. Biol. 3: 90.
7. Dodd A.N., Salathia N., Hall A., Kevei E., Toth R., Nagy F., Hibberd J.M., Millar A.J., and Webb A.A. 2005. Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630.
8. Doi M., Hirayama J., and Sassone-Corsi P. 2006. Circadian regulator CLOCK is a histone acetyltransferase. Cell 125: 497.
9. Dunlap J.C. 1999. Molecular bases for circadian clocks. Cell 96: 271.
10. Dvornyk V. and Knudsen B. 2005. Functional divergence of the circadian clock proteins in prokaryotes. Genetica 124: 247.
11. Edmunds L.N. 1988. Cellular and molecular bases of biological clocks. Springer-Verlag, New York.
12. Ehret C.F. 1961. Action spectra and nucleic acid metabolism in circadian rhythms at the cellular level. Cold Spring Harbor Symp. Quant. Biol. 25: 149.
13. Ehret C.F. and Trucco E. 1967. Molecular models for the circadian clock. I. The chronon concept. J. Theor. Biol. 15: 240.
14. Etchegaray J.P., Lee C., Wade P.A., and Reppert S.M. 2003. Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421: 177.
15. Garces R.G., Wu N., Gillon W., and Pai E.F. 2004. Anabaena circadian clock proteins KaiA and KaiB reveal potential common binding site to their partner KaiC. EMBO J. 23: 1688.
16. Grobbelaar N., Huang T.-C., Lin H.Y., and Chow T.J. 1986. Dinitrogen-fixing endogenous rhythm in Synechococcus RF-1. FEMS Microbiol. Lett. 37: 173.
17. Halberg F. and Conner R.L. 1961. Circadian organization and microbiology: Variance spectra and a periodogram on behavior of Escherichia coli growing in fluid culture. Proc. Minn. Acad. Sci. 29: 227.
18. Hastings J.W. 1961. Biochemical aspects of rhythms: Phase shifting by chemicals. Cold Spring Harbor Symp. Quant. Biol. 25: 131.
19. Hitomi K., Oyama T., Han S., Arvai A.S., and Getzoff E.D. 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.
20. Huang T.-C. and Grobbelaar N. 1995. The circadian clock in the prokaryote Synechococcus RF-1. Microbiology 141: 535.
21. Hunt T. and Sassone-Corsi P. 2007. Riding tandem: Circadian clocks and the cell cycle. Cell 129: 461.
22. Ishiura M., Kutsuna S., Aoki S., Iwasaki H., Andersson C.R., Tanabe A., Golden S.S., Johnson C.H., and Kondo T. 1998. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281: 1519.
23. Ivleva N.B., Gao T., LiWang A.C., and Golden S.S. 2006. Quinone sensing by the circadian input kinase of the cyanobacterial circadian clock. Proc. Natl. Acad. Sci. 103: 17468.
24. Johnson C.H. 1994. Illuminating the clock: Circadian photobiology. Semin. Cell Biol. 5: 355.
25. -. 2004. Global orchestration of gene expression by the biological clock of cyanobacteria. Genome Biol. 5: 217.
26. -. 2005. Testing the adaptive value of circadian systems. Methods Enzymol. 393: 818.
27. Johnson C.H. and Kondo T. 2001. Circadian rhythms in unicellular organisms. In Handbook of behavioral neurobiology, vol. 13: Developmental psychobiology (ed. J.S. Takahashi et al.), Chap. 3, p. 61. Plenum Press, New York.
28. Johnson C.H. and Kyriacou C.P. 2005. Clock evolution and adaptation: Whence and whither? In Endogenous plant rhythms (ed. A.J.W. Hall and H. McWatters), chap. 10, p. 237. Blackwell Publishing, Oxford, United Kingdom.
29. Johnson C.H., Elliott J.A., and Foster R.G. 2003. Entrainment of circadian programs. Chronobiol. Int. 20: 741.
30. Johnson C.H., Golden S.S., Ishiura M., and Kondo T. 1996. Circadian clocks in prokaryotes. Mol. Microbiol. 21: 5.
31. Kageyama H., Nishiwaki T., Nakajima M., Iwasaki H., Oyama T., and Kondo T. 2006. Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro. Mol. Cell 23: 161.
32. Katayama M., Tsinoremas N.F., Kondo T., and Golden S.S. 1999. cpmA, a gene involved in an output pathway of the cyanobacterial circadian system. J. Bacteriol. 181: 3516.
33. Kippert F. 1986. Endocytobiotic coordination, intracellular calcium signalling, and the origin of endogenous rhythms. Ann. N.Y. Acad. Sci. 503: 476.
34. Kondo T. and Ishiura M. 1994. Circadian rhythms of cyanobacteria: Monitoring the biological clocks of individual colonies by bioluminescence. J. Bacteriol. 176: 1881-1885.
35. Kondo T., Mori T., Lebedeva N.V., Aoki S., Ishiura M., and Golden S.S. 1997. Circadian rhythms in rapidly dividing cyanobacteria. Science 275: 224.
36. Kondo T., Tsinoremas N.F., Golden S.S., Johnson C.H., Kutsuna S., and Ishiura M. 1994. Circadian clock mutants of cyanobacteria. Science 266: 1233.
37. Kondo T., Strayer C.A., Kulkarni R.D., Taylor W., Ishiura M., Golden S.S., and Johnson C.H. 1993. Circadian rhythms in prokaryotes: Luciferase as a reporter of circadian gene expression in cyanobacteria. Proc. Natl. Acad. Sci. 90: 5672.
38. Liu Y., Tsinoremas N.F., Golden S.S., Kondo T., and Johnson C.H. 1996. Circadian expression of genes involved in the purine biosynthetic pathway of the cyanobacterium Synechococcus sp. strain PCC 7942. Mol. Microbiol. 20: 1071.
39. Liu Y., Tsinoremas N.F., Johnson C.H., Lebedeva N.V., Golden S.S., Ishiura M., and Kondo T. 1995. Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 9: 1469.
40. Lorne J., Scheffer J., Lee A., Painter M., and Miao V.P. 2000. Genes controlling circadian rhythm are widely distributed in cyanobacteria. FEMS Microbiol. Lett. 189: 129.
41. Min H., Guo H., and Xiong J. 2005. Rhythmic gene expression in a purple photosynthetic bacterium, Rhodobacter sphaeroides. FEBS Lett. 579: 808.
42. Mitsui A., Kumazawa S., Takahashi A., Ikemoto H., and Arai T. 1986. Strategy by which nitrogen-fixing unicellular cyanobacteria grow photoautotrophically. Nature 323: 720.
43. Mittag M., Kiaulehn S., and Johnson C.H. 2005. The circadian clock in Chlamydomonas reinhardtii: What is it for? What is it similar to? Plant Physiol. 137: 399.
44. Mori T. and Johnson C.H. 2000. Circadian control of cell division in unicellular organisms. Prog. Cell Cycle Res. 4: 185.
45. -. 2001a. Circadian programming in cyanobacteria. Semin. Cell Dev. Biol. 12: 271.
46. -. 2001b. Independence of circadian timing from cell division in cyanobacteria. J. Bacteriol. 183: 2439.
47. Mori T., Binder B., and Johnson C.H. 1996. Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours. Proc. Natl. Acad. Sci. 93: 10183.
48. Mori T., Williams D.R., Byrne M.O., Qin X., Mchaourab H.S., Egli M., Stewart P.L., and Johnson C.H. 2007. Elucidating the ticking of an in vitro circadian clockwork. PLoS Biol. 5: e93.
49. Nakahira Y., Katayama M., Miyashita H, Kutsuna S., Iwasaki H., Oyama T., and Kondo T. 2004. Global gene repression by KaiC as a master process of prokaryotic circadian system. Proc. Natl. Acad. Sci. 101: 881.
50. Nakajima M., Imai K., Ito H., Nishiwaki T., Murayama Y., Iwasaki H., Oyama T., and Kondo T. 2005. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308: 414.
51. Nishiwaki T., Satomi Y., Nakajima M., Lee C., Kiyohara R., Kageyama H., Kitayama Y., Temamoto M., Yamaguchi A., Hijikata A., Go M., Iwasaki H., Takao T., and Kondo T. 2004. Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942. Proc. Natl. Acad. Sci. 101: 13927.
52. Ouyang Y., Andersson C.R., Kondo T., Golden S.S., and Johnson C.H. 1998. Resonating circadian clocks enhance fitness in cyanobacteria. Proc. Natl. Acad. Sci. 95: 8660.
53. Pattanayek R., Wang J., Mori T., Xu Y., Johnson C.H., and Egli M. 2004. Visualizing a circadian clock protein: Crystal structure of KaiC and functional insights. Mol. Cell 15: 375.
54. Pattanayek R., Williams D.R., Pattanayek S., Xu Y., Mori T., Johnson C.H., Stewart P.L., and Egli M. 2006. Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J. 25: 2017.
55. Pittendrigh C.S., Bruce V.G., Rosensweig N.S., and Rubin M.L. 1959. Growth patterns in Neurospora: A biological clock in Neurospora. Nature 184: 169.
56. Schweiger H.-G. and Schweiger M. 1977. Circadian rhythms in unicellular organisms: An endeavor to explain the molecular mechanism. Int. Rev. Cytol. 51: 315.
57. Smith R.M. and Williams S.B. 2006. Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. Proc. Natl. Acad. Sci. 103: 8564.
58. Stal L.J. and Krumbein W.E. 1985. Nitrogenase activity in the non-heterocystous cyanobacterium Oscillatoria sp. grown under alternating light-dark cycles. Arch. Microbiol. 143: 67.
59. Sturtevant R.P. 1973. Circadian variability in Klebsiella demonstrated by cosinor analysis. Int. J. Chronobiol. 1: 141.
60. Sweeney B.M. 1961. The photosynthetic rhythm in single cells of Gonyaulax polyedra. Cold Spring Harbor Symp. Quant. Biol. 25: 145.
61. Sweeney B.M. and Borgese M.B. 1989. A circadian rhythm in cell division in a prokaryote, the cyanobacterium Synechococcus WH7803. J. Phycol. 25: 183.
62. Sweeney B.M. and Hastings J.W. 1961. Effects of temperature upon diurnal rhythms. Cold Spring Harbor Symp. Quant. Biol. 25: 87.
63. Taylor W.R. 1979. "Studies on the bioluminescent glow rhythm of Gonyaulax polyedra." Ph.D. thesis, University of Michigan, Ann Arbor.
64. Tomita J., Nakajima M., Kondo T., and Iwasaki H. 2005. Circadian rhythm of KaiC phosphorylation without transcription-translation feedback. Science 307: 251.
65. Vakonakis I. and LiWang A.C. 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. 101: 10925.
66. Vakonakis I., Sun J., Wu T., Holzenburg A., Golden S.S., and LiWang A.C. 2004. NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: Implications for the KaiA-KaiC Interaction. Proc. Natl. Acad. Sci. 101: 1479.
67. van Zon J.S., Lubensky D.K., Altena P.R., and ten Wolde P.R. 2007. An allosteric model of circadian KaiC phosphorylation. Proc. Natl. Acad. Sci. 104: 7420.
68. Woelfle M.A. and Johnson C.H. 2006. No promoter left behind: Global orchestration of circadian gene expression in cyanobacteria. J. Biol. Rhythms 21: 419.
69. Woelfle M.A., Ouyang Y., Phanvijhitsiri K., and Johnson C.H. 2004. The adaptive value of circadian clocks: An experimental assessment in cyanobacteria. Curr. Biol. 14: 1481.
70. Woelfle M.A., Xu Y., Qin X., and Johnson C.H. 2007. Circadian rhythms of superhelical status of DNA in cyanobacteria. Proc. Natl. Acad. Sci. (in press).
71. Xu Y., Mori T., and Johnson C.H. 2003. Cyanobacterial circadian clockwork: Roles of KaiA, KaiB, and the kaiBC promoter in regulating KaiC. EMBO J. 22: 2117.
72. Xu Y., Mori T., Pattanayek R., Pattanayek S., Egli M., and Johnson C.H. 2004. Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses. Proc. Natl. Acad. Sci. 101: 13933.
73. Ye S., Vakonakis I., Ioerger T.R., LiWang A.C., and Sacchettini J.C. 2004. Crystal structure of circadian clock protein KaiA from Synechococcus elongatus. J. Biol. Chem. 279: 20511.
74. Yoda M., Eguchi K., Terada T.P., and Sasai M. 2007. Monomer-shuffling and allosteric transition in KaiC circadian oscillation. PLoS ONE 2: e408.