Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway

Plant Physiology

Volumn 138, Issue 4, 2005, Pages 2374-2385

  Lidder, Preetmoninder ^a,c,e   Gutiérrez, Rodrigo A ^b,e   Salomé, Patrice A ^d   McClung, C Robertson ^d   Green, Pamela J ^c  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b Michigan State University   (United States)

^c UNIVERSITY OF DELAWARE   (United States)

^d Lamont Doherty Earth Observatory   (United States)

^e NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEGRADATION; GENES;

CIRCADIAN REGULATION; FREE-RUNNING CONDITIONS; MUTANTS;

RNA;

DEGRADATION; GENES; NUCLEIC ACIDS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; MESSENGER RNA; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; BIOSYNTHESIS; CHEMISTRY; CIRCADIAN RHYTHM; LIGHT; METABOLISM;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CIRCADIAN RHYTHM; LIGHT; PLANT PROTEINS; RNA, MESSENGER;

EID: 33644669368     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.105.060368     Document Type: Article

References (59)

1. Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Más P, Kay SA (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293: 880-883
2. Baggs JE, Green CB (2003) Nocturnin, a deadenylase in Xenopus laevis retina: a mechanism for posttranscriptional control of circadian-related mRNA. Curr Biol 13: 189-198
3. Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99: 9697-9702
4. Bognar LK, Hall A, Adam E, Thain SC, Nagy F, Millar AJ (1999) The circadian clock controls the expression pattern of the circadian input photoreceptor, phytochrome B. Proc Natl Acad Sci USA 96: 14652-14657
5. Chen CY, Shyu AB (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem Sci 20: 465-470
6. Chen Y, Hunter-Ensor M, Schotland P, Sehgal A (1998) Alterations of per RNA in noncoding regions affect periodicity of circadian behavioral rhythms. J Biol Rhythms 13: 364-379
7. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743
8. 2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding. BMC Genomics 2: 9
9. Edery I (1999) Role of posttranscriptional regulation in circadian clocks: lessons from Drosophila. Chronobiol Int 16: 377-414
10. Feinberg AP, Vogelstein B (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6-13
11. Feldbrugge M, Arizti P, Sullivan ML, Zamore PD, Belasco JG, Green PJ (2002) Comparative analysis of the plant mRNA-destabilizing element, DST, in mammalian and tobacco cells. Plant Mol Biol 49: 215-223
12. Frisch B, Hardin PE, Hamblen-Coyle MJ, Rosbash M, Hall JC (1994) A promoterless period gene mediates behavioral rhythmicity and cyclical per expression in a restricted subset of the Drosophila nervous system. Neuron 12: 555-570
13. Glossop NR, Lyons LC, Hardin PE (1999) Interlocked feedback loops within the Drosophila circadian oscillator. Science 286: 766-768
14. Green RM, Tingay S, Wang ZY, Tobin EM (2002) Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol 129: 576-584
15. Gutierrez RA, Ewing RM, Cherry JM, Green PJ (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci USA 99: 11513-11518
16. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock Science 290: 2110-2113
17. Harmer SL, Panda S, Kay SA (2001) Molecular bases of circadian rhythms. Annu Rev Cell Dev Biol 17: 215-253
18. Heintzen C, Nater M, Apel K, Staiger D (1997) AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc Natl Acad Sci USA 94: 8515-8520
19. Iwamoto M, Higo H, Higo K (2000) Differential diurnal expression of rice catalase genes: the 5′-flanking region of CatA is not sufficient for circadian control. Plant Sci 151: 39-46
20. Johnson MA, Pérez-Amador MA, Lidder P, Green PJ (2000) Mutants of Arabidopsis defective in a sequence-specific mRNA degradation pathway. Proc Natl Acad Sci USA 97: 13991-13996
21. Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK (2003) Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421: 948-952
22. Majercak J, Sidote D, Hardin PE, Edery I (1999) How a circadian clock adapts to seasonal decreases in temperature and day length. Neuron 24: 219-230
23. McClung CR (2001) Circadian rhythms in plants. Annu Rev Plant Physiol Plant Mol Biol 52: 139-162
24. McNeil GP, Zhang X, Genova G, Jackson FR (1998) A molecular rhythm mediating circadian clock output in Drosophila. Neuron 20: 297-303
25. Michael TP, McClung CR. (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiol 132: 629-639
26. Millar AJ, Carré IA, Strayer CA, Chua NH, Kay SA (1995) Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267: 1161-1163
27. Millar AJ, Kay SA (1991) Circadian control of cab gene transcription and mRNA accumulation in Arabidopsis. Plant Cell 3: 541-550
28. Mittag M (2003) The function of circadian RNA-binding proteins and their cis-acting elements in microalgae. Chronobiol Int 20: 529-541
29. Mittag M, Lee DH, Hastings JW (1994) Circadian expression of the luciferin-binding protein correlates with the binding of a protein to the 3′ untranslated region of its mRNA. Proc Natl Acad Sci USA 91: 5257-5261
30. Morse D, Pappenheimer AM Jr, Hastings JW (1989) Role of a luciferin-binding protein in the circadian bioluminescent reaction of Gonyaulax polyedra. J Biol Chem 264: 11822-11826
31. Newman TC, Ohme-Takagi M, Taylor CB, Green PJ (1993) DST sequences, highly conserved among plant SAUR genes, target reporter transcripts for rapid decay in tobacco. Plant Cell 5: 701-714
32. Oh SA, Lee SY, Chung IK, Lee CH, Nam HG (1996) A senescence-associated gene of Arabidopsis thaliana is distinctively regulated during natural and artificially induced leaf senescence. Plant Mol Biol 30: 739-754
33. Ohme-Takagi M, Taylor CB, Newman TC, Green PJ (1993) The effect of sequences with high AU content on mRNA stability in tobacco. Proc Natl Acad Sci USA 90: 11811-11815
34. Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH (1998) Resonating circadian clocks enhance fitness in cyanobacteria. Proc Natl Acad Sci USA 95: 8660-8664
35. Panda S, Hogenesch JB, Kay SA (2002) Circadian rhythms from flies to human. Nature 417: 329-335
36. Perez-Amador MA, Lidder P, Johnson MA, Landgraf J, Wisman E, Green PJ (2001) New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis. Plant Cell 13: 2703-2717
37. Pilgrim ML, Caspar T, Quail PH, McClung CR (1993) Circadian and light-regulated expression of nitrate reductase in Arabidopsis. Plant Mol Biol 23: 349-364
38. Plautz JD, Straume M, Stanewsky R, Jamison CF, Brandes C, Dowse HB, Hall JC, Kay SA (1997) Quantitative analysis of Drosophila period gene transcription in living animals. J Biol Rhythms 12: 204-217
39. Robinson BG, Frim DM, Schwartz WJ, Majzoub JA (1988) Vasopressin mRNA in the suprachiasmatic nuclei: daily regulation of polyadenylate tail length. Science 241: 342-344
40. Sahai H, Ageel MI (2000) The Analysis of Variance: Fixed, Random and Mixed Models. Birkhauser, Boston
41. Salomé PA, Michael TP, Kearns EV, Fett-Neto AG, Sharrock RA, McClung CR (2002) The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis. Plant Physiol 129: 1674-1685
42. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13: 113-123
43. Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, Carre IA, Coupland G (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93: 1219-1229
44. Seeley KA, Byrne DH, Colbert JT (1992) Red light-independent instability of oat phytochrome mRNA in vivo. Plant Cell 4: 29-38
45. So WV, Rosbash M (1997) Post-transcriptional regulation contributes to Drosophila clock gene mRNA cycling. EMBO J 16: 7146-7155
46. Staiger D (2001) RNA-binding proteins and circadian rhythms in Arabidopsis thaliana. Philos Trans R Soc Lond B Biol Sci 356: 1755-1759
47. Staiger D, Zecca L, Wieczorek Kirk DA, Apel K, Eckstein L (2003) The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant J 33: 361-371
48. Stanewsky R (2002) Clock mechanisms in Drosophila. Cell Tissue Res 309: 11-26
49. Stanewsky R, Jamison CF, Plaute JD, Kay SA, Hall JC (1997) Multiple circadian-regulated elements contribute to cycling period gene expression in Drosophila. EMBO J 16: 5006-5018
50. Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Más P, Panda S, Kreps JA, Kay SA (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289: 768-771
51. Sullivan ML, Green PJ (1996) Mutational analysis of the DST element in tobacco cells and transgenic plants: identification of residues critical for mRNA instability. RNA 2: 308-315
52. Taylor CB, Bariola PA, delCardayre SB, Raines RT, Green PJ (1993) RNS2: a senescence-associated RNase of Arabidopsis that diverged from the S-RNases before speciation. Proc Natl Acad Sci USA 90: 5118-5122
53. Taylor CB, Green PJ (1991) Genes with homology to fungal and S-gene RNases are expressed in Arabidopsis thaliana. Plant Physiol 96: 980-984
54. Tijsterman M, Ketting RF, Plasterk RH (2002) The genetics of RNA silencing. Annu Rev Genet 36: 489-519
55. Waltenberger H, Schneid C, Grosch JO, Bareiss A, Mittag M (2001) Identification of target mRNAs for the clock-controlled RNA-binding protein Chlamy 1 from Chlamydomonas reinhardtii. Mol Genet Genomics 265: 180-188
56. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 99: 5860-5865
57. Wang ZV, Tobin EM (1998) Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93: 1207-1217
58. Wuarin J, Falvey E, Lavery D, Talbot D, Schmidt E, Ossipow V, Fonjallaz P, Schibler U (1992) The role of the transcriptional activator protein DBP in circadian liver gene expression. J Cell Sci Suppl 16: 123-127
59. Zhong HH, Resnick AS, Straume M, McClung CR (1997) Effects of synergistic signaling by phytochrome A and cryptochromel on circadian clock-regulated catalase expression. Plant Cell 9: 947-955