Molecular Genetics and Genomics

, Volume 277, Issue 5, pp 589–600 | Cite as

Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants

Original Paper

Abstract

To examine the relationship between gene expression and DNA methylation, transcriptionally activated genes were screened in hypomethylated transgenic tobacco plants expressing an anti-DNA methyltransferase sequence. Among 16 genes initially identified, one clone was found to encode a glycerophosphodiesterase-like protein (NtGPDL), earlier reported to be responsive to aluminium stress. When detached leaves from wild type tobacco plants were treated with aluminium, NtGPDL transcripts were induced within 6 h, and corresponding genomic loci were demethylated at CCGG sites within 1 h. Direct bisulfite methylation mapping revealed that CG sites in coding regions were selectively demethylated, and that promoter regions were totally unmethylated regardless of the stress. Salt and low temperature treatments also induced similar demethylation patterns. Such effects could be attributable to oxidative stress, since reactive oxygen species generated by paraquat efficiently induced the same pattern of demethylation at coding regions. Pathogen infection induced neither transcripts nor genomic demethylation. These results suggested a close correlation between methylation and expression of NtGPDL upon abiotic stresses with a cause–effect relationship. Since DNA methylation is linked to histone modification, it is conceivable that demethylation at coding regions might induce alteration of chromatin structure, thereby enhancing transcription. We propose that environmental responses of plants are partly mediated through active alteration of the DNA methylation status.

Keywords

Aluminium 5-Methylcytosine DNA methylation Nicotiana tabacum Oxidative stress 

References

  1. Aguis F, Kapoor A, Zhu J-K (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103:11796–11801CrossRefGoogle Scholar
  2. Alina R, Sgorbati S, Santagostino A, Labra M, Ghiani A, Citterio S (2004) Specific hypomethylation of DNA is induced by heavy metals in white clover and industrial hemp. Physiol Plant 121:472–480CrossRefGoogle Scholar
  3. Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373–399PubMedCrossRefGoogle Scholar
  4. Bartee L, Malagnac F, Bender J (2001) Arabidopsis cmt3 chromomethylase mutations block non-CpG methylation and silencing of an endogenous gene. Genes Dev 15:1753–1758PubMedCrossRefGoogle Scholar
  5. Bender J (2004) DNA methylation and epigenetics. Ann Rev Plant Biol 55:41–68CrossRefGoogle Scholar
  6. Bird AP (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21PubMedCrossRefGoogle Scholar
  7. Borner GHH, Sherrier DJ, Stevens TJ, Arkin IT, Dupree P (2002) Prediction of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A genomic analysis. Plant Physiol 129:486–499PubMedCrossRefGoogle Scholar
  8. Borner GHH, Lilley KS, Stevens TJ, Dupree P (2003) Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol 132:568–577PubMedCrossRefGoogle Scholar
  9. Boscolo PRS, Menossi M, Jorge RA (2003) Aluminum-induced oxidative stress in maize. Phytochem 62:181–189CrossRefGoogle Scholar
  10. Bray EA, Bailey-Serres J, Wetertilnyk E (2000) Responses to abiotic stresses. In: Buchanan BB, Gruissem W, Jones RL (eds) Biochemistry and molecular biology of plants. American Society of Plant Physiologists, Rockville, pp 1158–1203Google Scholar
  11. Cerda S, Weitzman AS (1997) Influence of oxygen radical injury on DNA methylation. Mut Res 386:141–152Google Scholar
  12. Chan SW-L, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–60PubMedCrossRefGoogle Scholar
  13. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159PubMedCrossRefGoogle Scholar
  14. Ehrlich M (2000) DNA hypomethylation and cancer. In: Ehrlich M (ed) DNA alteration in cancer. Eaton Publishing, Natick, pp 273–291Google Scholar
  15. Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998) DNA methylation in plants. Ann Rev Plant Physiol Plant Mol Biol 49:223–247CrossRefGoogle Scholar
  16. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–201PubMedCrossRefGoogle Scholar
  17. Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns-from conservation to diversity. Trends Plant Sci 11:199–208PubMedCrossRefGoogle Scholar
  18. Galaud JP, Gaspar T, Boyer N (1993) Inhibition of internode growth due to mechanical stress in Bryonia dioica: relationship between changes in DNA methylation and ethylene metabolism. Physiol Plant 87:25–30CrossRefGoogle Scholar
  19. Gehring M, Huh JH, Hsieh T-F, Penterman J, Choi Y, Harada JJ, Goldberg R, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495–506PubMedCrossRefGoogle Scholar
  20. Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu J-K (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111:803–814PubMedCrossRefGoogle Scholar
  21. Gonzalez RG, Haxo RS. Schleich T (1980) Mechanism of action of polymer aurintricarboxylic acid, a potent inhibitor of protein-nucleic acid interaction. Biochem 19:4299–4303CrossRefGoogle Scholar
  22. Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 93:12406–12411PubMedCrossRefGoogle Scholar
  23. Ko YG, Nishino K, Hattori N, Arai Y, Tanaka S, Shiota K (2005) Stage-by-stage change in DNA methylation status of Dnmt1 locus during mouse early development. J Biol Chem 280:9627–9634PubMedCrossRefGoogle Scholar
  24. Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, Ruffini-Castiglione M, Bracale (2002) Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol 4:694–699CrossRefGoogle Scholar
  25. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080PubMedCrossRefGoogle Scholar
  26. Lizal P, Relichova J (2001) The effect of day length, vernalization and DNA demethylation on the flowering time in Arabidopsis thaliana. Physiol Plant 113:121–127CrossRefGoogle Scholar
  27. Martienssen R, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070–1074PubMedCrossRefGoogle Scholar
  28. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325PubMedCrossRefGoogle Scholar
  29. Nakano Y, Steward N, Koizumi N, Sano H (2000) A tobacco NtMET1 encoding a DNA methyltransferase: molecular characterization and abnormal phenotypes of antisence transgenic tobacco plants. Plant Cell Physiol 41:448–457PubMedCrossRefGoogle Scholar
  30. Papa CH, Springer NM, Muszynski MG, Meeley R, Kaeppler SM (2001) Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13:1919–1928PubMedCrossRefGoogle Scholar
  31. Paszkowski J, Whitham SA (2001) Gene silencing and DNA methylation processes. Curr Opin Plant Biol. 4:123–129PubMedCrossRefGoogle Scholar
  32. Peters AH, Schübeler D (2005) Methylation of histones: playing memory with DNA. Curr Opin Cell Biol. 17:230–238PubMedCrossRefGoogle Scholar
  33. Reik W, Dean W, Walter J (2001) Epigenetic reprogramming in mammalian development. Science 293:1089–1093PubMedCrossRefGoogle Scholar
  34. Shilatifard A (2006) Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem 75:243–269PubMedCrossRefGoogle Scholar
  35. Steward N, Kusano T, Sano H (2000) Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stresses quiescent cells. Nucleic Acids Res 28:3250–3259PubMedCrossRefGoogle Scholar
  36. Steward N, Ito M, Yamakuchi Y, Koizumi N, Sano H (2002) Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 277:37741–37746PubMedCrossRefGoogle Scholar
  37. Sugimoto M, Yamaguchi Y, Nakamura K, Tatsumi Y, Sano H (2004) A hypersensitive response-induced ATPase associated with various cellular activities (AAA) protein from tobacco plants. Plant Mol Biol 56:973–985PubMedCrossRefGoogle Scholar
  38. Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Plant Sci 6:244–251Google Scholar
  39. Wada Y, Ohya H, Yamaguchi Y, Koizumi N, Sano H (2003) Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants. J Biol Chem 278:42386–42393PubMedCrossRefGoogle Scholar
  40. Wada Y, Miyamoto K, Kusano H, Sano H (2004) Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in to tobacco plants. Mol Genet Genom 271:658–666Google Scholar
  41. Wada Y (2005) Physiological functions of plant DNA methyltransferases. Plant Biotechnol 22:71–80Google Scholar
  42. Xiao W, Gehring M, Chopi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL (2003) Imprinting of the MEA polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosilase. Dev Cell 5:891–901PubMedCrossRefGoogle Scholar
  43. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW-L, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1–13CrossRefGoogle Scholar
  44. Zilberman D, Henikoff S (2005) Epigenetic inheritance in Arabidopsis: selective silence. Curr Opin Genet Dev 15:557–562PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  1. 1.Research and Education Center for Genetic InformationNara Institute of Science and TechnologyNaraJapan

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