Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Casati, Paula ^a   Campi, Mabel ^a   Morrow, Darren J ^b   Fernandes, John F ^b   Walbot, Virginia ^b  

^a UNIVERSIDAD NACIONAL DE ROSARIO   (Argentina)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOACCUMULATION; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; GENE EXPRESSION; MAIZE; METABOLOMICS; NONHUMAN; PLANT EAR; PLANT GENE; PLANT LEAF; RADIATION EXPOSURE; RADIATION RESPONSE; RADIATION SHIELD; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; ULTRAVIOLET B RADIATION; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METABOLOME; TIME; ULTRAVIOLET RADIATION;

ZEA MAYS;

PROTEOME;

GENE EXPRESSION PROFILING; METABOLOME; PLANT LEAVES; PROTEOME; SIGNAL TRANSDUCTION; TIME FACTORS; ULTRAVIOLET RAYS; ZEA MAYS;

EID: 79959207993     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-321     Document Type: Article

References (37)

1. Kerr RA, McElroy CT. Evidence of large upward trends of ultraviolet-B radiation linked to ozone depletion. Science 1993, 262:1032-1034. 10.1126/science.262.5136.1032, 17782050.
2. Rowland FS. Stratospheric ozone depletion. Philos Trans R Soc London B 2006, 361:769-790.
3. Casati P, Walbot V. Gene expression profiling in response to ultraviolet radiation in Zea mays genotypes with varying flavonoid content. Plant Physiol 2003, 132:1739-1754. 10.1104/pp.103.022871, 181262, 12913132.
4. Casati P, Walbot V. Differential accumulation of maysin and rhamnosylisorientin in leaves of high altitude landraces of maize after UV-B exposure. Plant Cell Environ 2005, 28:788-799.
5. Casati P, Campi M, Chu F, Suzuki N, Maltby D, Guan S, Burlingame AL, Walbot V. Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize. Plant Cell 2008, 20:827-842. 10.1105/tpc.107.056457, 2390752, 18398050.
6. Casati P, Stapleton AE, Blum JE, Walbot V. Genome wide analysis of high altitude maize and gene knockdown stocks implicates chromatin remodeling proteins in responses to UV-B. Plant J 2006, 46:613-627. 10.1111/j.1365-313X.2006.02721.x, 16640598.
7. Izaguirre MM, Scopel AL, Baldwin IT, Ballaré CL. Convergent responses to stress. Solar ultraviolet-B radiation and Manduca sexta herbivory elicit overlapping transcriptional responses in field-grown plants of Nicotiana longiflora. Plant Physiol 2003, 132:1755-1767. 10.1104/pp.103.024323, 181263, 12913133.
8. Ulm R, Baumann A, Oravecz A, Maté Z, Adam E, Oakeley EJ, Schafer E, Nagy F. Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis. Proc Natl Acad Sci USA 2004, 101:1397-1402. 10.1073/pnas.0308044100, 337064, 14739338.
9. Brown BA, Cloix C, Jiang GH, Kaiserli E, Herzyk P, Kliebenstein DJ, Jenkins GI. A UV-B-specific signaling component orchestrates plant UV protection. Proc Natl Acad Sci USA 2005, 102:18225-18230. 10.1073/pnas.0507187102, 1312397, 16330762.
10. Casati P, Walbot V. Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues. Genome Biol 2004, 5:R16. 10.1186/gb-2004-5-3-r16, 395766, 15003119.
11. Kerr KM, Churchill GA. Statistical design and the analysis of gene expression microarray data. Genet Res 2001, 77:123-128.
12. Blum JE, Casati P, Walbot V, Stapleton AE. Split-plot microarray design allows sensitive detection of expression differences after ultraviolet radiation in the inbred parental lines of a key maize mapping population. Plant Cell Environ 2004, 27:1374-1386.
13. Meng PH, Raynaud C, Tcherkez G, Blanchet S, Massoud K, Domenichini S, Henry Y, Soubigou-Taconnat L, Lelarge-Trouverie C, Saindrenan P, Renou JP, Bergounioux C. Crosstalks between myo-Inositol metabolism, programmed cell death and basal immunity in Arabidopsis. PLoS ONE 2009, 4:e7364. 10.1371/journal.pone.0007364, 2754662, 19812700.
14. Favory JJ, Stec A, Gruber H, Rizzini L, Oravecz A, Funk M, Albert A, Cloix C, Jenkins GI, Oakeley EJ, Seidlitz HK, Nagy F, Ulm R. Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J 2009, 28:591-601. 10.1038/emboj.2009.4, 2657586, 19165148.
15. Gadjev I, Stone JM, Gechev TS. Chapter 3: Programmed cell death in plants. New insights into redox regulation and the role of hydrogen peroxide. Int Rev Cell Mol Biol 2008, 270:87-144.
16. Simoes I, Faro C. Structure and function of plant aspartic proteinases. Eur J Biochem 2004, 271:2067-2075. 10.1111/j.1432-1033.2004.04136.x, 15153096.
17. Chen XY, Kim JY. Callose synthesis in higher plants. Plant Signal Behav 2009, 4:489-492. 10.4161/psb.4.6.8359, 2688293, 19816126.
18. Matos AR, Pham-Thi AT. Lipid deacylating enzymes in plants: Old activities, new genes. Plant Physiol Biochem 2009, 47:491-503. 10.1016/j.plaphy.2009.02.011, 19324564.
19. Malik S, Roeder RG. Epigenetics? Mediator does that too!. Mol Cell 2008, 31:305-306. 10.1016/j.molcel.2008.07.011, 18691961.
20. Casati P, Zhang X, Burlingame AL, Walbot V. Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity. Mol Cel Proteomics 2005, 4:1673-1685.
21. Mackerness SAH, Thomas B, Jordan BR. The effect of supplementary ultraviolet-B radiation on transcripts, translation and stability of chloroplast proteins and pigment formation in Pisum sativum L. J Exp Bot 1997, 48:729-738.
22. Jansen MAK, Le Martret B, Koornneef M. Variations in constitutive and inducible UV-B tolerance; dissecting photosystem II protection in Arabidopsis thaliana accessions. Physiol Plant 2010, 138:22-34. 10.1111/j.1399-3054.2009.01293.x, 19843242.
23. Smart CC, Flores S. Overexpression of D-myo-inositol-3-phosphate synthase leads to elevated levels of inositol in Arabidopsis. Plant Mol Biol 1997, 33:811-820. 10.1023/A:1005754425440, 9106505.
24. Loewus FA, Murthy PP. Myo-Inositol metabolism in plants. Plant Sci 2000, 150:1-19.
25. Bohnert HJ, Nelson DE, Jensen RG. Adaptations to environmental stresses. Plant Cell 1995, 7:1099-1111. 160917, 12242400.
26. Oravecz A, Baumann A, Maté Z, Brzezinska A, Molinier J, Oakeley EJ, Adam E, Schafer E, Nagy F, Ulm R. CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis. Plant Cell 2006, 18:1975-1990. 10.1105/tpc.105.040097, 1533968, 16829591.
27. Brown BA, Headland LR, Jenkins GI. UV-B action spectrum for UVR8-mediated HY5 transcript accumulation in Arabidopsis. Photochem Photobiol 2009, 85:1147-1155. 10.1111/j.1751-1097.2009.00579.x, 19558421.
28. Cerdán PD, Chory J. Regulation of flowering time by light quality. Nature 2003, 423:881-885. 10.1038/nature01636, 12815435.
29. Wollenberg AC, Strasser B, Cerdán PD, Amasino RM. Acceleration of flowering during shade-avoidance in Arabidopsis thaliana alters the balance between FLOWERING LOCUS C-mediated repression and photoperiodic induction of flowering. Plant Physiol 2008, 148:1681-1694. 10.1104/pp.108.125468, 2577263, 18790998.
30. Kidd BN, Edgar CI, Kumar KK, Aitken EA, Schenk PM, Manners JM, Kazan K. The mediator complex subunit PFT1 is a key regulator of jasmonate-dependent defense in Arabidopsis. Plant Cell 2009, 8:2237-2252.
31. Casati P, Walbot V. Maize lines expressing RNAi to chromatin remodeling factors are similarly hypersensitive to UV-B radiation but exhibit distinct transcriptome responses. Epigenetics 2008, 3:216-229. 10.4161/epi.3.4.6631, 2551322, 18719398.
32. Skibbe DS, Fernandes JF, Medzihradszky KF, Burlingame AL, Walbot V. Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers. Plant J 2009, 59:622-633. 10.1111/j.1365-313X.2009.03901.x, 19453454.
33. Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. New York: Springer, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W.
34. Falcone Ferreyra ML, Pezza A, Biarc J, Burlingame AL, Casati P. Plant L10 ribosomal proteins have different roles during development and translation under UV-B stress. Plant Physiol 2010, 153:1878-1894. 10.1104/pp.110.157057, 2923885, 20516338.
35. Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie A. Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat Protoc 2006, 1:387-396. 10.1038/nprot.2006.59, 17406261.
36. Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D. GMD@CSB. DB: the golm metabolome database. Bioinformatics 2005, 21:1635-1638. 10.1093/bioinformatics/bti236, 15613389.
37. Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, Lundgren K, Roessner-Tunali U, Forbes MG, Willmitzer L, Fernie AR, Kopka J. GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett 2005, 579:1332-1337. 10.1016/j.febslet.2005.01.029, 15733837.