The ins and outs of circadian regulated gene expression

Current Opinion in Plant Biology

Volumn 2, Issue 2, 1999, Pages 114-120

  Strayer, Carl A ^a,b   Kay, Steve A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA;

EID: 0033119880     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(99)80023-5     Document Type: Article

References (72)

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4. 4. Somers DE, Devlin PF, Kay SA: Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 1998, 282:1488-1490. These authors measured circadian period length over a range of light intensities to determine fluence response curves (FRC) - a thorough assay that revealed subtle effects of changes in single photorecepters in a complex system. A model for further dissection of circadian light input pathways in plants as well as animals.
5. 5. Liu Y, Merrow M, Loros JJ, Dunlap JC: How temperature changes reset a circadian oscillator. Science 1998, 281:825-829. A thorough characterization of temperature effects on the products of the frq clock gene locus in Neurospora. The bottom line is that FRQ protein cycles over different ranges at different temperatures. The answer referred to in the title is, therefore, that the same level of FRQ denotes different clock times at different temperatures.
6. 6. Luo CH, Loros JJ, Dunlap JC: Nuclear localization is required for function of the essential clock protein FRQ. EMBO J 1998, 17:1228-1235. Although FRQ is known to negatively regulate its own transcription, the mechanism of this is still not known, but is suspected to lie close to the gene. Like its fly counterpart PER, it has been suspected to be, or at least interact with, a transcription factor. The conclusion of the title supports this hypothesis.
7. 7. Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, Kondo T: Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 1998, 281:1519-1523. In this classic paper, the first components of a prokaryotic clock are defined. From a single locus, both negative (KaiC) and positive (KaiA) elements of a transcriptional feedback loop are identified, showing that the oscillator is functionally conserved in all organisms in which it has been identified.
8. 8. Shinohara ML, Loros JJ, Dunlap JC: Glyceraldehyde-3-phosphate dehydrogenase is regulated on a daily basis by the circadian clock. J Biol Chem 1998, 273:446-452. The gene encoding GAPDH, ccg-7, was identified in a differential screen for cycling mRNAs, as the name implies. The identity of the gene product was confirmed by enzyme activity assays, which also showed that the circadian regulation extended to the level of function.
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10. 10. Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, Carré IA, Coupland G: The late-elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 1998, 93:1219-1229. This report describes the cloning of the gene and its similar expression profiles and similar circadian phenotypes of overexpression as compared to CCA1. lhy was identified as a transposon (tn)-tagged mutant (the tn was found to cause overexpression of the LHY locus) which was day-neutral in its flowering response - another phenotype consistent with loss of clock function. Taken together, all these phenotypes suggest the clock is not functioning in lhy plants. As with CCA1, feedback regulation of the endogenous locus in the transgenic LHY-overexpressor is intriguing.
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32. 32. Nakahira Y, Baba K, Yoneda A, Shiina T, Toyoshima Y: Circadian-regulated transcription of the psbD light-responsive promoter in wheat chloroplasts. Plant Physiol 1998, 118:1079-1088. Nuclease protection assays uncovered a robust circadian rhythm of psbD mRNA levels. An in vitro assay, in which chloroplast extracts from plants were assayed for their ability to promote transcription of plasmid-borne promoter targets, was used to dissect cis elements mediating transcriptional regulation. Interesting implications for circadian studies, as well as genome coupling in general, were gained from this work.
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38. 38. Halaban R: Effect of light quality on the circadian rhythm of leaf movement of a short-day plant. Plant Physiol 1969, 44:973-977.
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40. 40. Cashmore AR: The cryptochrome family of photoreceptors. Plant Cell Environ 1997, 20:764-767.
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43. 43. Somers DE, Webb AAR, Pearson M, Kay S: The short-period mutant, toc1-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana. Development 1998, 125:485-494. The affects of toc1 on clock function in multiple tissue types at different developmental stages suggest there is a common circadian oscillator underlying all these rhythms. These results and the toc1 fluence response curve results also support the idea that TOC1 lies in, or very near, this oscillator. Also, the quantitative flowering-time defect reported in a mutant with a quantitative period phenotype provides strong genetic proof that daylength measurement by the clock underlies photoperiodic induction of flowering.
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48. 48. Thresher RJ, Vitaterna MH, Miyamoto Y, Kazantsev A, Hsu DS, Petit C, Selby CP, Dawut L, Smithies O, Takahashi JS, Sancar A: Role of mouse cryptochrome blue-light photoreceptor in circadian photoresponses. Science 1998, 282:1490-1494. These papers [44-47,48•] describe the identification and initial characterization of animal cryptochromes. Taken together, they predict a story so far similar to that in plants - CRY is a circadian photoreceptor, but not the only one. The identification of all photoreceptors, and how their signal transduction pathways interact with the clock awaits elucidation in all models.
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51. 51. Sun ZS, Albrecht U, Zhuchenko O, Bailey J, Eichele G, Lee CC: RIGUI, a putative mammalian ortholog of the Drosophila period gene. Cell 1997, 90:1003-1011. See [61•] for annotation.
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55. 55. Allada R, White NE, So WV, Hall JC, Rosbash M: A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell 1998, 93:791-804. See [61•] for annotation.
56. 56. Darlington TK, Wager-Smith K, Ceriani MF, Staknis D, Genkakis N, Steeves TDL, Weitz CJ, Tahakashi JS: Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science 1998, 280:1599-1603. See [61•] for annotation.
57. 57. Rutila JE, Suri V, Le M, So WV, Rosbash M, Hall JC: CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless. Cell 1998, 93:805-814. See [61•] for annotation.
58. 58. Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, Takahashi JS, Weitz CJ : Role of the CLOCK protein in the mammalian circadian mechanism. Science 1998, 280:1564-1569. See [61•] for annotation.
59. 59. Hogenesch JB, Gu Y-Z, Jain S, Bradfield CA: The basic helix-loop helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci USA 1998, 95:5474-5479. See [61•] for annotation.
60. 60. Sangoram AM, Saez L, Antoch MP, Gekakis N, Staknis D, Whiteley A, Fruechte EM, Vitaterna MH, Shimomura K, King KP et al.: Mammalian circadian autoregulatory loop: a timeless ortholog and mPer1 interact and negatively regulate CLOCK-BMAL1-induced transcription. Neuron 1998, 21:1101-1113. See [61•] for annotation.
61. 61. Zylka MJ, Shearman LP, Levine JD, Jin X, Weaver DR, Reppert SM: Molecular analysis of mammalian timeless. Neuron 1998, 21:1115-1122. This is the golden age of circadian biology, as these papers collectively illustrate [50•-61•]. The conservation of oscillator mechanisms among evolutionarily diverse organisms (Synechococcus, Neurospora, Drosophila, mouse and humans), and the conservation of components among animals, are the take-home messages. For reviews that give a more detailed treatment of the progress in animals models, see [61•,62].
62. 62. Dunlap JC: Common threads in eukaryotic circadian systems. Curr Opin Genet Dev 1998, 8:400-406.
63. 63. Wilsbacher LD, Takahashi JS: Circadian rhythms: molecular basis of the clock. Curr Opin Genet Dev 1998, 8:595-602.
64. 64. Crosthwaite SK, Dunlap JC, Loros JJ: Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity. Science 1997, 276:763-769. Both genes were identified by mutation as essential for all light responses in Neurospora. Both are involved in light entrainment of the clock, and both act as positive regulators of frq expression. Differences are that only WC-2 is absolutely required for rhythmic frq expression, and only WC-1 is absolutely required for acute light induction of frq.
65. 65. Kolar C, Fejes E, Adám E, Schäfer E, Kay S, Nagy F: Transcription of Arabidopsis and wheat Cab genes in single tobacco transgenic seedlings exhibits independent rhythms in a developmentally regulated fashion. Plant J 1998, 13:563-569. [43••] and [63] show that the clock runs in Arabidopsis throughout development, from seedling to floral phase. In this paper, we see that circadian inputs, outputs, and/or oscillators are connecting/disconnecting to the same CAB gene early in development. The one thing that seems certain is that the circadian system does itself develop in tobacco.
66. 66. Zhong HH, Painter JE, Salome PA, Straume M, McClung CR: Imbibition, but not release from stratification, sets the circadian clock in Arabidopsis seedlings. Plant Cell 1998, 10:2005-2018. Nice demonstration of a novel zeitgeber, or entraining signal, of plant clocks - imbibition. Now the question is - does this signal initiate rhythms of a dormant clock or synchronize extant rhythms in these embryos?
67. 67. Ni M, Tepperman J, Quail P: PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 1998, 95:657-667. Another well executed yeast two-hybrid screen turns up PIF3. One interesting property of the protein not listed in the title is that it also contains a PAS domain - it is the first plant gene with both this motif and an identifiable motif suggesting a role in transcriptional regulation, features of several known clock genes. That it interacts with photoreceptors now known to mediate circadian entrainment (see [4••]) raises interesting possibilities.
68. 68. Heintzen C, Nater M, Apel K, Staiger D: AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc Natl Acad Sci USA 1997, 94:8515-8520.
69. 69. Plautz JD, Kaneko M, Hall JC, Kay SA: Independent photoreceptive clocks throughout Drosophila. Science 1997, 278:1632-1635.
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72. 72. Mittag M, Li L, Hastings JW: The mRNA level of the circadian regulated Gonyaulax luciferase remains constant over the cycle. Chronobiology International 1998, 15:93-98. The luciferase protein is known to cycle - that the message does not suggests translational regulation by the clock, as is known to occur for expression of luciferase binding protein. Use of this control point by the clock is becoming something of a hallmark for this species.