Transcriptome analysis of germinating maize kernels exposed to smoke-water and the active compound KAR1

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Soós, Vilmos ^a   Sebestyén, Endre ^a   Juhász, Angéla ^a   Light, Marnie E ^b   Kohout, Ladislav ^c   Szalai, Gabriella ^a   Tandori, Júlia ^a   Van Staden, Johannes ^b   Balázs, Ervin ^a  

^a AGRICULTURAL INSTITUTE   (Hungary)

^b UNIVERSITY OF KWAZULU NATAL   (South Africa)

^c INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ZEA MAYS;

3 METHYL 2H FURO(2,3 C)PYRAN 2 ONE; 3-METHYL-2H-FURO(2,3-C)PYRAN-2-ONE; FURAN DERIVATIVE; PYRAN DERIVATIVE; VEGETABLE PROTEIN; WATER;

ARTICLE; CLUSTER ANALYSIS; DNA MICROARRAY; DRUG EFFECT; FIRE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GERMINATION; GROWTH, DEVELOPMENT AND AGING; IMMUNOBLOTTING; MAIZE; MASS FRAGMENTOGRAPHY; METABOLISM; PLANT SEED; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SMOKE;

CLUSTER ANALYSIS; FIRES; FURANS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GERMINATION; IMMUNOBLOTTING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT PROTEINS; PYRANS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEEDS; SMOKE; WATER; ZEA MAYS;

EID: 77958545976     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-236     Document Type: Article

References (46)

1. Soós V, Sebestyén E, Juhász A, Pintér J, Light ME, Van Staden J, Balázs E. Stress-related genes define essential steps in the response of maize seedlings to smoke-water. Funct Integr Genomics 2009, 9:231-42. 10.1007/s10142-008-0105-8, 19139936.
2. Van Staden J, Jäger AK, Light ME, Burger BV. Isolation of the major germination cue from plant-derived smoke. S Afr J Bot 2004, 70:654-659.
3. Flematti GR, Ghisalberti EL, Dixon KW, Trengove RD. A compound from smoke that promotes seed germination. Science 2004, 305:977. 10.1126/science.1099944, 15247439.
4. Light ME, Daws MI, Van Staden J. Smoke-derived butenolide: towards understanding its biological effects. S Afr J Bot 2009, 75:1-7.
5. Flematti GR, Ghisalberti EL, Dixon KW, Trengove RD. Identification of alkyl substituted 2H-Furo[2,3-c]pyran-2-ones as germination stimulants present in smoke. J Agric Food Chem 2009, 57:9475-9480. 10.1021/jf9028128, 19785418.
6. Drewes FE, Smith MT, Van Staden J. The effect of plant-derived smoke extract on the germination of light-sensitive lettuce seed. Plant Growth Regul 1995, 16:205-209.
7. Light ME, Gardner MJ, Jäger AK, Van Staden J. Dual regulation of seed germination by smoke solutions. Plant Growth Regul 2002, 37:135-141.
8. Light ME, Burger BV, Staerk D, Kohout L, Van Staden J. Butenolides from plant-derived smoke: natural plant-growth regulators with antagonistic actions on seed germination. J Nat Prod 2010, 73:267-269. 10.1021/np900630w, 20078110.
9. Soós V, Juhász A, Light ME, Van Staden J, Balázs E. Smoke-water-induced changes of expression pattern in Grand Rapids lettuce achenes. Seed Sci Res 2009, 19:37-49.
10. Nelson DC, Riseborough JA, Flematti GR, Stevens J, Ghisalberti EL, Dixon KW, Smith SM. Karrikins discovered in smoke trigger Arabidopsis seed germination by a mechanism requiring gibberellic acid synthesis and light. Plant Physiol 2009, 149:863-873. 10.1104/pp.108.131516, 2633839, 19074625.
11. Van Staden J, Sparg SG, Kulkarni MG, Light ME. Post-germination effects of the smoke-derived compound 3-methyl-2H-furo[2,3-c]pyran-2-one, and its potential as a preconditioning agent. Field Crops Research 2006, 98:98-105.
12. Jain N, Ascough GD, Van Staden J. A smoke-derived butenolide alleviates HgCl2 and ZnCl2 inhibition of water uptake during germination and subsequent growth of tomato - Possible involvement of aquaporins. J Plant Physiol 2009, 165:1422-1427.
13. Ghebrehiwot HM, Kulkarni MG, Kirkman KP, Van Staden J. Smoke-water and a smoke-isolated butenolide improve germination and seedling vigour of Eragrostis tef (Zucc) Trotter under high temperature and low osmotic potential. J Agric Crop Sci 2008, 194:270-277.
14. Nettleton D. A discussion of statistical methods for design and analysis of microarray experiments for plant scientists. Plant Cell 2006, 18:2112-2121. 10.1105/tpc.106.041616, 1560901, 16968907.
15. Niemietz CM, Tyerman SD. New potent inhibitors of aquaporins: silver and gold compounds inhibit aquaporins of plant and human origin. FEBS Letters 2002, 531:443-447. 10.1016/S0014-5793(02)03581-0, 12435590.
16. Zhong GV, Burns JK. Profiling ethylene-regulated gene expression in Arabidopsis thaliana by microarray analysis. Plant Mol Biol 2003, 53:117-131. 10.1023/B:PLAN.0000009270.81977.ef, 14756311.
17. Cho YH, Yoo SD. Emerging Complexity of Ethylene Signal Transduction. J Plant Biol 2009, 52:283-288.
18. Conaway RC, Brower CS, Conaway JW. Emerging roles of ubiquitin in transcription regulation. Science 2002, 296:1254-1258. 10.1126/science.1067466, 12016299.
19. Ferreira RMB, Rodrigues-Ramos PC, Franco E, Ricardo CPP, Teixeira ARN. Changes in ubiquitin and ubiquitin-protein conjugates during seed formation and germination. J Exp B 1995, 46:211-219.
20. Takizawa M, Goto A, Watanabe Y. The tobacco ubiquitin-activating enzymes NtE1A and NtE1B are induced by tobacco mosaic virus, wounding and stress hormones. Mol Cells 2009, 19:228-231.
21. Rey P, Becuwe N, Barrault MB, Rumeau D, Havaux M, Biteau B, Toledano MB. The Arabidopsis thaliana sulfiredoxin is a plastidic cysteine-sulfinic acid reductase involved in the photooxidative stress response. Plant J 2007, 49:505-514. 10.1111/j.1365-313X.2006.02969.x, 17217469.
22. Pandey GK, Cheong YH, Kim KN, Grant JJ, Li L, Hung W, D'Angelo C, Weinl S, Kudla J, Luan S. The calcium sensor calcineurin B-like 9 modulates abscisic acid sensitivity and biosynthesis in Arabidopsis. Plant Cell 2004, 16:1912-1924. 10.1105/tpc.021311, 514170, 15208400.
23. Liu Q, Umeda M, Uchimiya H. Isolation and expression analysis of two rice genes encoding the major intrinsic protein. Plant Mol Biol 1994, 26:2003-2007. 10.1007/BF00019511, 7858235.
24. Li DD, Tai FJ, Zhang ZT, Li Y, Zheng Y, Wu YF, Li XB. A cotton gene encodes a tonoplast aquaporin that is involved in cell tolerance to cold stress. Gene 2009, 438:26-32. 10.1016/j.gene.2009.02.023, 19303046.
25. Maggio A, De Pascale S. Hydraulic conductivity of cut flower stems and aquaporins function. Acta Hort 2007, 755:225-230.
26. Maggio A, Joly RJ. Effects of mercuric chloride on the hydraulic conductivity of tomato root systems (Evidence for a channel-mediated water pathway). Plant Physiol 1995, 109:331-335. 157593, 12228599.
27. Zhao XC, Qu X, Mathews DE, Schaller GE. Effect of ethylene pathway mutations upon expression of the ethylene receptor ETR1 from Arabidopsis. Plant Physiol 2002, 130:1983-1991. 10.1104/pp.011635, 166709, 12481081.
28. Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucl Acids Res 2009, 37:11-13.
29. Somers DE, Fujiwara S. Thinking outside the F-box: novel ligands for novel receptors. Trends Plant Sci 2009, 14:206-13. 10.1016/j.tplants.2009.01.003, 19285909.
30. D'Auria JC, Gershenzon J. The secondary metabolism of Arabidopsis thaliana: growing like a weed. Curr Opin Plant Biol 2005, 8:308-316. 10.1016/j.pbi.2005.03.012, 15860428.
31. Taylor LP, Grotewold E. Flavonoids as developmental regulators. Curr Opin Plant Biol 2005, 8:317-323. 10.1016/j.pbi.2005.03.005, 15860429.
32. Baxter BJM, Van Staden J, Granger JE, Brown NAC. Plant-derived smoke and smoke extracts stimulate seed germination of the fire-climax grass Themeda triandra Forssk. Env Exp Bot 1994, 34:217-223.
33. Flematti GR, Ghisalberti EL, Dixon KW, Trengove RD. Synthesis of the seed germination stimulant 3-methyl-2H-furo[2,3-c]pyran-2-one. Tetrahedron Lett 2005, 46:5719-5721.
34. R Development Core Team R A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. 2008, Vienna, Austria, ISBN 3-900051-07-0, R Development Core Team R., http://www.R-project.org
35. Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN. On the utility of pooling biological samples in microarray experiments. PNAS 2005, 102:4252-4257. 10.1073/pnas.0500607102, 552978, 15755808.
36. Dobbin KK, Shih JH, Simon RM. Comment on 'Evaluation of the gene-specific dye bias in cDNA microarray experiments'. Bioinformatics 2005, 21:2803-2804. 10.1093/bioinformatics/bti428, 15817695.
37. 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 VJ, Huber W, Irizarry RA, Dudoit S.
38. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit D, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
39. Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007, 23:2700-2707. 10.1093/bioinformatics/btm412, 17720982.
40. Yang YH, Dudoits S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucl Acids Res 2002, 30:e15. 10.1093/nar/30.4.e15, 100354, 11842121.
41. Smyth GK, Speed TP. Normalization of cDNA microarray data. Methods 2003, 31:265-273. 10.1016/S1046-2023(03)00155-5, 14597310.
42. Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 31:1-25.
43. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc 1995, 57:289-300.
44. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Gen 2000, 25:25-29.
45. Castillo-Davis CI, Hartl DL. GeneMerge: Post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 2003, 19:891-892. 10.1093/bioinformatics/btg114, 12724301.
46. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 2005, 139:5-17. 10.1104/pp.105.063743, 1203353, 16166256.