Precise circadian clocks in prokaryotic cyanobacteria

Current Issues in Molecular Biology

Volumn 6, Issue 2, 2004, Pages 103-110

  Johnson, Carl Hirschie ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; HELICASE; RECA PROTEIN; RIBOSOME RNA;

ACCURACY; ADAPTATION; BACTERIAL CHROMOSOME; BACTERIAL STRAIN; BIOLOGICAL RHYTHM; CELL CYCLE; CELL DIVISION; CIRCADIAN RHYTHM; CYANOBACTERIUM; EXPERIMENTATION; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE MUTATION; GENETIC SCREENING; MOLECULAR MODEL; NONHUMAN; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW; STRAIN DIFFERENCE;

BACTERIAL PROTEINS; CIRCADIAN RHYTHM; CYANOBACTERIA; LUMINESCENT MEASUREMENTS; TIME FACTORS;

CYANOBACTERIA; PROKARYOTA;

EID: 1942435934     PISSN: 14673037     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (58)

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, 527-542.
2. Aoki, S., Kondo, T., Wada, H., and Ishiura, M. (1997). Circadian rhythm of the cyanobacterium Synechocystis sp. PCC 6803 in the dark. J. Bacteriology 179, 5751-5755.
3. Chen, T.-H., Chen, T.-L., Huang, L.-M. and Huang, T.-C. (1991). Circadian rhythm in amino acid uptake by Synechococcus RF-1. Plant Physiol. 97, 55-59.
4. DasSarma, S., Kennedy, S.P., Berquist, B., Ng, W.V., Baliga, N.S., Spudich, J.L., Krebs, M.P., Eisen, J.A., Johnson, C.H., and Hood, L. (2001). Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynthesis Res. 70, 3-17.
5. Dvornyk, V., Vinogradova, O., and Nevo, E. (2002). Origin and evolution of circadian clock genes in prokaryotes. Proc Natl Acad Sci USA 100, 2495-2500.
6. Drilca K. (1992). Control of bacterial DNA supercoiling. Mol Microbiol 6, 425-433.
7. Gonze, D., Roussel, M.R., Goldbeter, A. (2002). A model for the enhancement of fitness in cyanobacteria based on resonance of a circadian oscillator with the external light-dark cycle. J. Theor. Biol. 214, 577-597.
8. 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, 173-177.
9. Hayashi, F., Suzuki, H., Iwase, R., Uzumaki, T., Miyake, A., Shen, J.-R., Imada, K., Furukawa, Y., Yonekura, K., Namba, K., and Ishiura, M. (2003). ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC. Genes to Cells 8, 287-296.
10. Hsieh, L.S., Rouviere-Yaniv, J., Drlica, K. (1991). Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock. J Bacteriol 173, 3914-3917.
11. Huang, T.-C., Chen, H.-M., Pen, S.-Y., and Chen, T.-H. (1994). Biological clock in the prokaryote Synechococcus RF-1. Planta 193, 131-136.
12. Ishiura, M., Kutsuna, S., Aoki, S., Iwasaki, H., Andersson, C.R., Tanabe, A., Golden, S.S., Johnson C.H., Kondo, T. (1998). Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281, 1519-1523.
13. Iwasaki, H., Taniguchi, Y., Kondo, T., Ishiura, M. (1999). Physical interactions among circadian clock proteins, KaiA, KaiB and KaiC, in Cyanobacteria. EMBO J. 18, 1137-45.
14. Iwasaki, H., Williams, S.B., Kitayama, Y., Ishiura, M., Golden, S.S. and Kondo, T. (2000). A KaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria. Cell 101, 223-233.
15. Iwasaki, H., Nishiwaki, T., Kitayama, Y., Nakajima, M., and Kondo, T. (2002). KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria. Proc. Natl. Acad. Sci. USA 99, 15788-15793.
16. Johnson, C.H., Golden, S.S., Ishiura, M., Kondo, T. (1996). Circadian clocks in prokaryotes. Mol. Microbiol. 21, 5-11.
17. Johnson, C.H. and Golden, S.S. (1999). Circadian programs in cyanobacteria: adaptiveness and mechanism. Annu. Rev. Microbiol. 53, 389-409.
18. Johnson, C.H. and Kondo, T. (2001). Circadian rhythms in unicellular organisms. In: Handbook of Behavioral Neurobiology, Chapter 3. Plenum Press, p. 61-77.
19. Kageyama, H., Kondo, T. and Iwasaki, H. (2003). Circadian formation of clock protein complexes by KaiA, KaiB, KaiC, and SasA in cyanobacteria. J. Biol. Chem. 278, 2388-2395.
20. 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, 3516-3524.
21. Katayama, M., Kondo, T., Xiong, J. and Golden, S.S. (2003). IdpA encodes an iron-sulfur protein involved in light-dependent modulation of the circadian period in the cyanobacterium Synechococcus elongatus PCC 7942. J. Bacteriol. 185, 1415-22.
22. Kippert, F. (1991). Essential clock proteins/circadian rhythms in prokaryotes - what is the evidence? Bot. Acta 104, 2-4.
23. Kitayama, Y., Iwasaki, H., Nishiwaki, T. and Kondo, T. (2003). KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system. EMBO J. 22, 1-8
24. 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. USA 90, 5672-5676.
25. Kondo, T. and Ishiura, M. (1994). Circadian rhythms of cyanobacteria: monitoring the biological clocks of individual colonies by bioluminescence. J. Bacteriol. 176, 1881-1885.
26. Kondo, T., Tsinoremas, N. F., Golden, S. S., Johnson, C. H., Kutsuna, S. and Ishiura, M. (1994a). Circadian clock mutants of cyanobacteria. Science 266, 1233-1236.
27. Kondo, T., Ishiura, M., Golden, S.S. and Johnson, C.H. (1994b). Circadian rhythms of cyanobacteria expressed from a luciferase reporter gene. In: Evolution of Circadian Clock. T. Hiroshige and K. Honma, eds. Hokkaido University Press, Sapporo. p. 59-73.
28. Kondo, T., Mori, T., Lebedeva, N.V., Aoki, S., Ishiura, M., Golden, S.S. (1997). Circadian rhythms in rapidly dividing cyanobacteria. Science 275, 224-227.
29. Leipe, D.D., Aravind, L., Grishin, N.V. and Koonin, E.V. (2000). The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res. 10, 5-16.
30. Lin, R.-F., Chou, H.-M., Huang, T.-C. (1999). Priority of light/dark entrainment over temperature in setting the circadian rhythms of the prokaryote Synechococcus RF-1. Planta 209, 202-206.
31. 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 and Dev. 9, 1469-1478.
32. 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. Mole. Microbiol. 20, 1071-1081.
33. 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, 129-133.
34. Menzel, R. and Gellert M. (1987). Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gurB promoters. Proc Natl Acad Sci USA 84, 4185-4189.
35. Min, H., Golden, S.S. (2000). A new circadian Class 2 gene, opcA, whose product is important for reductant production at night in Synechococcus elongatus PCC 7942. J Bacteriol 182, 6214-6221.
36. Mitsui, A., Kumazawa, S., Takahashi, A., Ikemoto, H., and Arai, T. (1986). Strategy by which nitrogen-fixing unicellular cyanobacteria grow photoautotrophically. Nature 323, 720-722.
37. Mori, T., Binder, B., 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 USA 93, 10183-10188.
38. Mori, T. and Johnson, C.H. (2000). Circadian control of cell division in unicellular organisms. In: Progress in Cell Cycle Research, Volume 4. L. Meijer, A. Jezequel, and B. Ducommun, eds. Kluwer Academic/Plenum Press, NY., p. 185-192.
39. Mori, T, and Johnson, C.H. (2001a). Independence of circadian timing from cell division in cyanobacteria. J. Bacteriol. 183, 2439-2444.
40. Mori, T. and Johnson, C.H. (2001b). Circadian programming in cyanobacteria. Sem. Cell Develop. Biol. 12, 271-278.
41. Mori, T., Saveliev, S.V., Xu, Y., Stafford, W.F., Cox, M.M., Inman, R.B., and Johnson, C.H. (2002). Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. Proc. Natl. Acad. Sci. USA 99, 17203-17208.
42. Mutsuda, M., Michel, K.P., Zhang, X., Montgomery, B.L. and Golden, S.S. (2003). Biochemical properties of CikA, an unusual phytochrome-like histidine protein kinase that resets the circadian clock in Synechococcus elongatus PCC 7942. J. Biol. Chem. 278, 19102-19110.
43. Nair, U., Ditty, J.L., Min, H., and Golden, S.S. (2002). Roles for sigma factors in global circadian regulation of the cyanobacterial genome. J. Bacteriol. 184, 3530-3538.
44. Nishimura, H., Nakahira, Y., Imai, K., Tsuruhara, A., Kondo, H., Hayashi, H., Hirai, M., Saito, H. and Kondo, T. (2002). Mutations in KaiA, a clock protein, extend the period of circadian rhythm in the cyanobacterium Synechococcus elongatus PCC 7942. Microbiol. 148, 2903-2909.
45. Nishiwaki, T., Iwasaki, H., Ishiura, M. and 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.
46. 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. USA 95, 8660-8664.
47. Pettijohn, D. (1976). Prokaryotic DNA in nucleiod structure. CRC Critical Rev. Biochem. 4, 175-202.
48. Pittendrigh, C.S. (1993). Temporal organization: reflections of a Darwinian clock-watcher. Annu. Rev. Physiol. 55, 17-54.
49. Pruss, G.J. and Drlica, K. (1989). DNA supercoiling and prokaryotic transcription. Cell 56, 521-523.
50. Salvador, M.L., Klein, U. and Bogorad, L. (1998). Endogenous fluctuations of DNA topology in the chloroplast of Chlamydomonas reinhardtii. Mole. Cell Biol. 18, 7235-7242.
51. Schmitz, O., Katayama, M., Williams, S.B., Kondo, T. and Golden, S.S. (2000). CikA, a bacteriophytochrome that resets the cyanobacterial circadian clock. Science 289, 765-768.
52. Taniguchi, Y., Yamaguchi, A., Hijikata, A, Iwasaki, H., Kamagata, K., Ishiura, M., Go, M. and Kondo, T. (2001). Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC. FEBS Letters 496, 86-90.
53. Trun, N.J. and Marko, J.F. (1998). Architecture of a bacterial chromosome. ASM News 64, 276-283.
54. Tsinoremas, N.F., Ishiura, M., Kondo, T., Andersson, C.R., Tanaka, K., Takahashi, H., Johnson, C.H. and Golden, S.S. (1996). A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria. EMBO Journal 15, 2488-2495.
55. Williams, S.B., Vakonakis, I., Golden, S.S., and LiWang, A.C. (2002). Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism. Proc. Natl. Acad. Sci. USA 99, 15357-15362.
56. Xu, Y., Piston, D. and C.H. Johnson. (1999). A bioluminescence resonance energy transfer (BRET) system: Application to interacting circadian clock proteins. Proc. Natl. Acad. Sci. USA 96, 151-156.
57. Xu, Y., Mori, T. and Johnson, C.H. (2000). Circadian clock-protein expression in cyanobacteria: rhythms and phase-setting. EMBO J. 19, 3349-57.
58. 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, 2117-2126.