Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator

PLoS ONE

Volumn 5, Issue 9, 2010, Pages 1-14

  Hayes, Kevin R ^a   Beatty, Mary ^a   Meng, Xin ^a   Simmons, Carl R ^a   Habben, Jeffrey E ^a   Danilevskaya, Olga N ^a  

^a PIONEER HI BRED INTERNATIONAL INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CIRCADIAN RHYTHM; DNA FLANKING REGION; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; LEAF DEVELOPMENT; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOSYNTHESIS; PLANT DEVELOPMENT; PLANT EAR; PLANT GENE; PLANT GENOME; PLANT LEAF; TRANSCRIPTOMICS; BIOLOGICAL RHYTHM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYSIOLOGY;

ARABIDOPSIS; ZEA MAYS;

VEGETABLE PROTEIN;

BIOLOGICAL CLOCKS; CIRCADIAN RHYTHM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; PLANT LEAVES; PLANT PROTEINS; ZEA MAYS;

EID: 77958612183     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012887     Document Type: Article

References (58)

1. Barak S, Tobin EM, Andronis C, Sugano S, Green RM (2000) All in good time: the Arabidopsis circadian clock. Trends Plant Sci 5: 517-522.
2. Harmer SL (2009) The circadian system in higher plants. Annu Rev Plant Biol 60: 357-377.
3. Dodd AN, Salathia N, Hall A, Kevei E, Toth R, et al. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633.
4. Ni Z, Kim ED, Ha M, Lackey E, Liu J, et al. (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327-331.
5. Mas P (2008) Circadian clock function in Arabidopsis thaliana: time beyond transcription. Trends Cell Biol 18: 273-281.
6. de Montaigu A, Toth R, Coupland G (2010) Plant development goes like clockwork. Trends Genet 26: 296-306.
7. Nemhauser JL (2008) Dawning of a new era: photomorphogenesis as an integrated molecular network. Curr Opin Plant Biol 11: 4-8.
8. Pruneda-Paz JL, Breton G, Para A, Kay SA (2009) A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323: 1481-1485.
9. Nakamichi N, Kiba T, Henriques R, Mizuno T, Chua NH, et al. (2010) PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell 22: 594-605.
10. Mas P, Kim WY, Somers DE, Kay SA (2003) Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426: 567-570.
11. Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, et al. (2007) Rhythmic growth explained by coincidence between internal and external cues. Nature 448: 358-361.
12. Nozue K, Maloof JN (2006) Diurnal regulation of plant growth. Plant Cell Environ 29: 396-408.
13. Lagercrantz U (2009) At the end of the day: a common molecular mechanism for photoperiod responses in plants? J Exp Bot 60: 2501-2515.
14. Sun N, Ma L, Pan D, Zhao H, Deng XW (2003) Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Mol Biol 53: 467-478.
15. Gutierrez RA, Stokes TL, Thum K, Xu X, Obertello M, et al. (2008) Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A 105: 4939-4944.
16. Covington MF, Harmer SL (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5: e222.
17. Michaels SD (2009) Flowering time regulation produces much fruit. Curr Opin Plant Biol 12: 75-80.
18. Tsuji H, Tamaki S, Komiya R KS (2008) Florigen and photoperiodic control of flowering in rice. Rice 1: 25-35.
19. Rawat R, Schwartz J, Jones MA, Sairanen I, Cheng Y, et al. (2009) REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. Proc Natl Acad Sci U S A 106: 16883-16888.
20. Fukushima A, Kusano M, Nakamichi N, Kobayashi M, Hayashi N, et al. (2009) Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proc Natl Acad Sci U S A 106: 7251-7256.
21. Legnaioli T, Cuevas J, Mas P (2009) TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought. EMBO J 28: 3745-3757.
22. Blasing OE, Gibon Y, Gunther M, Hohne M, Morcuende R, et al. (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17: 3257-3281.
23. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, et al. (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14.
24. Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL (2008) Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9: R130.
25. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, et al. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13: 113-123.
26. Facella P, Lopez L, Carbone F, Galbraith DW, Giuliano G, et al. (2008) Diurnal and circadian rhythms in the tomato transcriptome and their modulation by cryptochrome photoreceptors. PLoS One 3: e2798.
27. Hudson K (2010) The Circadian Clock-controlled Transcriptome of Developing Soybean Seeds. The Plant Genome 3: 3-13.
28. Ptitsyn A (2008) Comprehensive analysis of circadian periodic pattern in plant transcriptome. BMC Bioinformatics 9 Suppl 9: S18.
29. Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, et al. (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10: R17.
30. Graf A, Schlereth A, Stitt M, Smith AM (2010) Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proc Natl Acad Sci U S A 107: 9458-9463.
31. Kalt-Torres W, Huber SC (1987) Diurnal Changes in Maize Leaf Photosyn-thesis: III. Leaf Elongation Rate in Relation to Carbohydrates and Activities of Sucrose Metabolizing Enzymes in Elongating Leaf Tissue. Plant Physiol 83: 294-298.
32. Kalt-Torres W, Kerr PS, Usuda H, Huber SC (1987) Diurnal Changes in Maize Leaf Photosynthesis: I. Carbon Exchange Rate, Assimilate Export Rate, and Enzyme Activities. Plant Physiol 83: 283-288.
33. Ciceri P, Locatelli F, Genga A, Viotti A, Schmidt RJ (1999) The activity of the maize Opaque2 transcriptional activator is regulated diurnally. Plant Physiol 121: 1321-1328.
34. Redinbaugh MG, Sabre M, Scandalios JG (1990) Expression of the maize Cat3 catalase gene is under the influence of a circadian rhythm. Proc Natl Acad Sci U S A 87: 6853-6857.
35. Miller TA, Muslin EH, Dorweiler JE (2008) A maize CONSTANS-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods. Planta 227: 1377-1388.
36. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, et al. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110-2113.
37. Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, et al. (2007) The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol 72: 353-363.
38. Wichert S, Fokianos K, Strimmer K (2004) Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 20: 5-20.
39. Hughes M, Deharo L, Pulivarthy SR, Gu J, Hayes K, et al. (2007) High-resolution time course analysis of gene expression from pituitary. Cold Spring Harb Symp Quant Biol 72: 381-386.
40. Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, et al. (2009) Harmonics of circadian gene transcription in mammals. PLoS Genet 5: e1000442.
41. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
42. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, et al. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res 16: 1241-1251.
43. Murakami M, Ashikari M, Miura K, Yamashino T, Mizuno T (2003) The evolutionarily conserved OsPRR quintet: rice pseudo-response regulators implicated in circadian rhythm. Plant Cell Physiol 44: 1229-1236.
44. Murakami M, Tago Y, Yamashino T, Mizuno T (2007) Characterization of the rice circadian clock-associated pseudo-response regulators in Arabidopsis thaliana. Biosci Biotechnol Biochem 71: 1107-1110.
45. Somers DE, Schultz TF, Milnamow M, Kay SA (2000) ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis. Cell 101: 319-329.
46. Nelson DC, Lasswell J, Rogg LE, Cohen MA, Bartel B (2000) FKF1, a clock-controlled gene that regulates the transition to flowering in Arabidopsis. Cell 101: 331-340.
47. Schultz TF, Kiyosue T, Yanovsky M, Wada M, Kay SA (2001) A role for LKP2 in the circadian clock of Arabidopsis. Plant Cell 13: 2659-2670.
48. Murakami M, Tago Y, Yamashino T, Mizuno T (2007) Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Plant Cell Physiol 48: 110-121.
49. Bieniawska Z, Espinoza C, Schlereth A, Sulpice R, Hincha DK, et al. (2008) Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol 147: 263-279.
50. Michael TP, Breton G, Hazen SP, Priest H, Mockler TC, et al. (2008) A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol 6: e225.
51. Jahn D, Verkamp E, Soll D (1992) Glutamyl-transfer RNA: a precursor of heme and chlorophyll biosynthesis. Trends Biochem Sci 17: 215-218.
52. James AB, Monreal JA, Nimmo GA, Kelly CL, Herzyk P, et al. (2008) The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots. Science 322: 1832-1835.
53. Ueda HR (2006) Systems biology flowering in the plant clock field. Mol Syst Biol 2: 60.
54. Ritchie SW HJ, Benson GO (1997) How a corn plant develops. Special report Ames, Iowa 48.
55. te Velde AA, de Kort F, Sterrenburg E, Pronk I, ten Kate FJ, et al. (2007) Comparative analysis of colonic gene expression of three experimental colitis models mimicking inflammatory bowel disease. Inflamm Bowel Dis 13: 325-330.
56. Kaufmann K, Wellmer F, Muino JM, Ferrier T, Wuest SE, et al. (2010) Orchestration of floral initiation by APETALA1. Science 328: 85-89.
57. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
58. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.