No promoter left behind: Global circadian gene expression in cyanobacteria

Journal of Biological Rhythms

Volumn 21, Issue 6, 2006, Pages 419-431

  Woelfle, Mark A ^a   Johnson, Carl Hirschie ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

Biological clock; Circadian; Global gene expression; Kai; Prokaryote; Supercoiling

Indexed keywords

CHROMOSOME; CIRCADIAN RHYTHM; CYANOBACTERIUM; EUKARYOTE; FEEDBACK SYSTEM; GENE CONTROL; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROMOTER REGION; REVIEW; RNA TRANSLATION; SYNECHOCOCCUS ELONGATUS; TRANSCRIPTION INITIATION;

BACTERIAL PROTEINS; BIOLOGICAL CLOCKS; CIRCADIAN RHYTHM; CYANOBACTERIA; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, BIOLOGICAL; PROMOTER REGIONS (GENETICS); SYNECHOCOCCUS; TRANSCRIPTION, GENETIC;

CYANOBACTERIA; EUKARYOTA; PROKARYOTA;

EID: 33750741439     PISSN: 07487304     EISSN: 15524531     Source Type: Journal    
DOI: 10.1177/0748730406294418     Document Type: Review

References (66)

1. Akhtar RA, Reddy AB, Maywood ES, Clayton JD, King VM, Smith AG, Gant TW, Hastings MH, and Kyriacou CP (2002) Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray is driven by the suprachiasmatic nucleus. Curr Biol 12:540-550.
2. Aoki S, Kondo T, and Ishiura M (1995) Circadian expression of the dnaK gene in the cyanobacterium Synechocystis sp. Strain PCC 6803. J Bacteriol 177:5606-5611.
3. Chen TH, Chen TL, Huang LM, and Huang TC (1991) Circadian rhythm in amino acid uptake by Synechococcus RF-1. Plant Physiol 97:55-59.
4. Chen YB, Dominic B, Zani S, Mellon MT, and Zehr JP (1999) Expression of photosynthesis genes in relation to nitrogen fixation in the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp. IMS 101. Plant Mol Biol 41:89-104.
5. Correa A, Lewis ZA, Greene AV, March IJ, Gomer RH, and Bell-Pedersen D (2003) Multiple oscillators regulate circadian gene expression in Neurospora. Proc Natl Acad Sci U S A 100:13597-13602.
6. Doi M, Hirayama J, and Sassone-Corsi P (2006) Circadian Regulator CLOCK is a histone acetyltransferase. Cell 125:497-508.
7. Dunlap JC, Loros JJ, and DeCoursey PJ (2004) Chronobiology: Biological Timekeeping. Sunderland (MA): Sinauer.
8. Etchegaray J-P, Lee C, Wade PA, and Reppert SM (2003) Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421:177-182.
9. Harmer SL, Hogenesch JB, Straume M, Chang H-S, Han B, Zhu T, Wang X, Kreps JA, and Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290:2110-2113.
10. Hastings JW and Johnson CH (2003) Bioluminescence and chemiluminescence. Methods Enzymol 360:75-104.
11. Huang TC, Lin RF, Chu MK, and Chen HM (1999) Organization and expression of nitrogen-fixation genes in the aerobic nitrogen-fixing unicellular cyanobacterium Synechococcus sp. Strain RF-1. Microbiology 145:743-753.
12. Imai K, Nishiwaki T, Kondo T, and Iwaski H (2004) Circadian rhythms in the synthesis and degradation of a master clock protein KaiC in cyanobacteria. J Biol Chem 279:36534-36539.
13. Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, and Kondo T (1998) Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281:1519-1523.
14. 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 U S A 99:15788-15793.
15. Iwasaki H, Taniguchi Y, Kondo T, and Ishiura M (1999) Physical interactions among circadian clock proteins, KaiA, KaiB and KaiC, in cyanobacteria. EMBO J 18:1137-1145.
16. Iwasaki H, Williams SB, Kitayama Y, Ishiura M, Golden SS, and Kondo T (2000) A KaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria. Cell 101:223-233.
17. Johnson CH (2004) Global orchestration of gene expression by the biological clock of cyanobacteria. Genome Biol 5:217.1-217.4.
18. 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.
19. Kao CC, Green S, Stein B, and Golden SS (2005) Diel infection of a cyanobacterium by a contractile bacteriophage. Appl Environ Microbiol 71:4276-4279.
20. Katayama M, Tsinoremas NF, Kondo T, and Golden SS (1999) cpmA, a gene involved in an output pathway of the cyanobacterial circadian system. J Bacteriol 181:3516-3524.
21. 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.
22. Kondo T, Mori T, Lebedeva NV, Aoki S, Ishiura M, and Golden SS (1997) Circadian rhythms in rapidly dividing cyanobacteria. Science 275:224-227.
23. Kondo T, Strayer CA, Kulkarni RD, Taylor W, Ishiura M, Golden SS, and Johnson CH (1993) Circadian rhythms in prokaryotes: Luciferase as a reporter of circadian gene expression in cyanobacteria. Proc Natl Acad Sci U S A 90:5672-5676.
24. Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, Kanehisa M, and Ishiura M (2005) Global analysis of circadian expression in the cyanobacterium Synechocystis sp. Strain PCC 6803. J Bacteriol 187:2190-2199.
25. Kucho K, Tauchiya Y, Okumoto Y, Harada M, Yamada M, and Ishiura M (2004) Construction of unmodified oligonucleotide-based microarrays in the thermophilic cyanobacterium Thermosynechococcus dongatus BP-1: Screening of the candidates for circadianly expressed genes. Genes Genet Syst 79:319-329.
26. Leipe DD, Aravind L, Grishin NV, and Koonin EV (2000) The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res 10:5-16.
27. Liu Y, Tsinoremas NF, Johnson CH, Lebedeva NV, Golden SS, Ishiura M, and Kondo T (1995) Circadian orchestration of gene expression in cyanobacteria. Genes Dev 9:1469-1478.
28. Lorne J, Scheffer J, Lee A, Painter M, and Miao VPW (2000) Genes controlling circadian rhythm are widely distributed in cyanobacteria. FEMS Microbiol Lett 189:129-133.
29. McDonald MJ and Rosbash M (2001) Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107:567-578.
30. Michael TP and McClung CR (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiol 132:629-639.
31. Min HY, Liu Y, Johnson CH, and Golden SS (2004) Phase determination of circadian gene expression in Synechococcus elongatus PCC 7942. J Biol Rhythms 19:103-112.
32. Mori T, Binder B, and Johnson CH (1996) Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours. Proc Natl Acad Sci U S A 93:10183-10188.
33. Mori T and Johnson CH (2001) Circadian programming in cyanobacteria. Semin Cell Dev Biol 12:271-278.
34. Mori T, Saveliev SV, Xu X Stafford WF, Cox MM, Inman RB, and Johnson CH (2002) Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. Proc Natl Acad Sci U S A 99:17203-17208.
35. Nair U, Ditty JL, Min H, and Golden SS (2002) Roles for sigma factors in global circadian regulation of the cyanobacterial genome. J Bacteriol 184:3530-3538.
36. 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 U S A 101:881-885.
37. 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 308:414-415.
38. 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 U S A 97:495-499.
39. Nowrousian M, Duffield GE, Loros JJ, and Dunlap JC (2003) The frequency gene is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa. Genetics 164:923-933.
40. Onai K, Morishita M, Itoh S, Okamoto K, and Ishiura M (2004) Circadian rhythms in the thermophilic cyanobacterium Thermosynechococcus elongatus: Compensation of period length over a wide temperature range. J Bacteriol 186:4972-4977.
41. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, and Hogenesch JB (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109:307-320.
42. Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, and Cozzarelli NR (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol 5:R87.
43. Pruss GJ and Drlica K (1989) DNA supercoiling and prokaryotic transcription. Cell 56:521-523.
44. Ripperger JA and Schibler U (2006) Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet 38:369-374.
45. Rossini C, Taylor W, Fagan T, and Hastings JW (2003) Lifetimes of mRNAs for clock-regulated proteins in a dinoflagellate. Chronobiol Int 20:963-976.
46. Salvador ML, Klein U, and Bogorad L (1998) Endogenous fluctuations of DNA topology in the chloroplast of Chlamydomonas reinhardtii. Mol Cell Biol 18:7235-7242.
47. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, and Wisman E (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13:113-123.
48. Schneegurt MA, Sherman DM, Nayar S, and Sherman LA (1994) Oscillating behavior of carbohydrate granule formation and dinitrogen fixation in the cyanobacterium Cyanothece sp. strain ATCC 51142. J Bacteriol 176:1586-1597.
49. Schneider R, Travers A, and Muskhelishvilli G (2000) The expression of the Escherichia coli fis gene is strongly dependent of the superhelical density of DNA. Mol Microbiol 38:167-175.
50. Smith RA and Williams SB (2006) Circadian rhythms of gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. Proc Natl Acad Sci U S A 103:8564-8569.
51. Stock AM, Robinson VL, and Goudreau PN (2000) Two-component signal transduction. Annu Rev Biochem 69:183-215.
52. Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, Wong WH, and Weitz CJ (2002) Extensive and divergent circadian gene expression in liver and heart. Nature 417:8-83.
53. Straney R, Krah R, and Menzel R (1994) Mutations in the -10 TATAAT sequence of the gyrA promoter affect both promoter strength and sensitivity to DNA supercoiling. J Bacteriol 176:5999-6006.
54. Takai N, Nakajima M, Oyama T, Kito R, Sugita C, Sugita M, Kondo T, and Iwasaki H (2006) A KaiC-associating SasA-RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria. Proc Natl Acad Sci U S A 103:12109-12114.
55. Tanaka K, Masuda S, and Takahasi H (1992) Multiple rpoD-related genes of cyanobacteria. Biosci Biotechnol Biochem 56:1113-1117.
56. 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 Lett 496:86-90.
57. Tomita J, Nakajima M, Kondo T, and Iwasaki H (2005) Circadian rhythm of KaiC phosphorylation without transcription-translation feedback. Science 307:251-254.
58. Trun NJ and Marko JF (1998) Architecture of a bacterial chromosome. ASM News 64:276-283.
59. Tsinoremas NF, Ishiura M, Kondo T, Andersson K, Tanaka K, Takahasi H, Johnson CH, and Golden SS (1996) A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria. EMBO J 19:2488-2495.
60. Ueda HR, Matsumoto A, Kawamura M, Iino M, Tanimura T, and Hashimoto S (2002) Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J Biol Chem 277:14048-14052.
61. Unniraman S and Nagaraja V (2001) Axial distortion as a sensor of supercoil changes: A molecular model for the homeostatic regulation of DNA gyrase. J Genet 80:119-124.
62. Williams SB, Vakonakis I, Golden SS, and LiWang AC (2002) Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: A potential clock input mechanism. Proc Natl Acad Sci U S A 99:15357-15362.
63. Xu Y, Mori T, and Johnson CH (2000) Circadian clock-protein expression in cyanobacteria: Rhythms and phase-setting. EMBO J 19:3349-3357.
64. Xu Y, Mori T, and Johnson CH (2003) Cyanobacterial circadian clockwork: Roles of KaiA, KaiB, and the kaiBC promoter in regulating KaiC. EMBO J 22:2117-2126.
65. Xu Y, Piston D, and Johnson CH (1999) A bioluminescence resonance energy transfer (BRET) system: Application to interacting circadian clock proteins. Proc Natl Acad Sci U S A 96:151-156.
66. Yen UC, Huang TC, and Yen TC (2004) Observation of the circadian photosynthetic rhythm in cyanobacteria with a dissolved-oxygen meter. Plant Sci 166:949-952.