Advertisement

Plant Molecular Biology

, Volume 71, Issue 3, pp 291–305 | Cite as

Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice

  • Haiyan Ye
  • Hao Du
  • Ning Tang
  • Xianghua Li
  • Lizhong Xiong
Article

Abstract

The TIFY family is a novel plant-specific gene family involved in the regulation of diverse plant-specific biologic processes, such as development and responses to phytohormones, in Arabidopsis. However, there is limited information about this family in monocot species. This report identifies 20 TIFY genes in rice, the model monocot species. Sequence analysis indicated that rice TIFY proteins have conserved motifs beyond the TIFY domain as was previously shown in Arabidopsis. On the basis of their protein structures, members of the TIFY family can be divided into two groups. Transcript level analysis of OsTIFY genes in tissues and organs revealed different tempo-spatial expression patterns, suggesting that expression and function vary by stage of plant growth and development. Most of the OsTIFY genes were predominantly expressed in leaf. Nine OsTIFY genes were responsive to jasmonic acid and wounding treatments. Interestingly, almost all the OsTIFY genes were responsive to one or more abiotic stresses including drought, salinity, and low temperature. Over-expression of OsTIFY11a, one of the stress-inducible genes, resulted in significantly increased tolerance to salt and dehydration stresses. These results suggest that the OsTIFY family may have important roles in response to abiotic stresses. The data presented in this report provide important clues for further elucidating the functions of the genes in the OsTIFY family.

Keywords

Oryza ZIM Abiotic stress Expression profile JAZ 

Abbreviations

ABA

Abscisic acid

GA

Gibberellic acid

JA

Jasmonic acid

Jas

JASMONATE-ASSOCIATED

JAZ

JASMONATE ZIM-DOMAIN

SA

Salicylic acid

ZIM

Zinc-finger protein expressed in inflorescence meristem

Notes

Acknowledgments

We thank our colleagues Lei Wang for providing Ghd7-CFP construct, and Jian Xu for providing the pM999 vector, and Yubing He for assistance in proline content measurement. This work was supported by grants from the National Special Key Project of China on Functional Genomics of Major Plants and Animals, the National Program on the Development of Basic Research, the National Natural Science Foundation of China, the Ministry of Education of China (NO 707045), and the EU FP6 INCO-MPC2 project CEDROME (INCOCT-2005-015468).

Supplementary material

11103_2009_9524_MOESM1_ESM.doc (835 kb)
(DOC 835 kb)

References

  1. Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15:63–78PubMedCrossRefGoogle Scholar
  2. Baker SS, Wilhelm KS, Thomashow MF (1994) The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol 24:701–713PubMedCrossRefGoogle Scholar
  3. Boudsocq M, Lauriere C (2005) Osmotic signaling in plants: multiple pathways mediated by emerging kinase families. Plant Physiol 138:1185–1194PubMedCrossRefGoogle Scholar
  4. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10PubMedCrossRefGoogle Scholar
  5. Chini A, Fonseca S, Fernandez G, Adie B, Chico JM, Lorenzo O, Garcia-Casado G, Lopez-Vidriero I, Lozano FM, Ponce MR, Micol JL, Solano R (2007) The JAZ family of repressors is the missing link in jasmonate signalling. Nature 448:666–671PubMedCrossRefGoogle Scholar
  6. Chung HS, Howe GA (2009) A critical role for the TIFY motif in repression of jasmonate signaling by a stabilized splice variant of the JASMONATE ZIM-domain protein JAZ10 in Arabidopsis. Plant Cell 21:131–145PubMedCrossRefGoogle Scholar
  7. Chung HS, Koo AJ, Gao X, Jayanty S, Thines B, Jones AD, Howe GA (2008) Regulation and function of Arabidopsis JASMONATE ZIM-domain genes in response to wounding and herbivory. Plant Physiol 146:952–964PubMedCrossRefGoogle Scholar
  8. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763PubMedCrossRefGoogle Scholar
  9. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251PubMedCrossRefGoogle Scholar
  10. Garg AK, Kim JK, Owens TG, Ranwala AP, Choi YD, Kochian LV, Wu RJ (2002) Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proc Natl Acad Sci USA 99:15898–15903PubMedCrossRefGoogle Scholar
  11. Gilmour SJ, Thomashow MF (1991) Cold acclimation and cold-regulated gene expression in ABA mutants of Arabidopsis thaliana. Plant Mol Biol 17:1233–1240PubMedCrossRefGoogle Scholar
  12. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29(8):1023–1026PubMedGoogle Scholar
  13. Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271–282PubMedCrossRefGoogle Scholar
  14. Katsir L, Schilmiller AL, Staswick PE, He SY, Howe GA (2008) COI1 is a critical component of a receptor for jasmonate and the bacterial virulence factor coronatine. Proc Natl Acad Sci USA 105:7100–7105PubMedCrossRefGoogle Scholar
  15. Liu J, Zhu JK (1997) Proline accumulation and salt-stress-induced gene expression in a salt-hypersensitive mutant of Arabidopsis. Plant Physiol 114:591–596PubMedCrossRefGoogle Scholar
  16. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408PubMedCrossRefGoogle Scholar
  17. Lorenzo O, Chico JM, Sanchez-Serrano JJ, Solano R (2004) JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell 16:1938–1950PubMedCrossRefGoogle Scholar
  18. Melotto M, Mecey C, Niu Y, Chung HS, Katsir L, Yao J, Zeng W, Thines B, Staswick P, Browse J, Howe G, He SY (2008) A critical role of two positively charged amino acids in the Jas motif of Arabidopsis JAZ proteins in mediating coronatine- and jasmonoyl isoleucine-dependent interaction with the COI1 F-box protein. Plant J 55:979–988PubMedCrossRefGoogle Scholar
  19. Mulder NJ, Apweiler R (2008) The InterPro database and tools for protein domain analysis. Current protocols in bioinformatics chapter 2: unit 2.7. Wiley, LondonGoogle Scholar
  20. Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34:D731–D735PubMedCrossRefGoogle Scholar
  21. Nishii A, Takemura M, Fujita H, Shikata M, Yokota A, Kohchi T (2000) Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. Biosci Biotechnol Biochem 64:1402–1409PubMedCrossRefGoogle Scholar
  22. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:D883–D887PubMedCrossRefGoogle Scholar
  23. Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339:62–66PubMedCrossRefGoogle Scholar
  24. Retief JD (2000) Phylogenetic analysis using PHYLIP. Methods Mol Biol 132:243–258PubMedGoogle Scholar
  25. Reyes JC, Muro-Pastor MI, Florencio FJ (2004) The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol 134:1718–1732PubMedCrossRefGoogle Scholar
  26. Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 23:319–327PubMedCrossRefGoogle Scholar
  27. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, New YorkGoogle Scholar
  28. Shikata M, Matsuda Y, Ando K, Nishii A, Takemura M, Yokota A, Kohchi T (2004) Characterization of Arabidopsis ZIM, a member of a novel plant-specific GATA factor gene family. J Exp Bot 55:631–639PubMedCrossRefGoogle Scholar
  29. Staswick PE (2008) JAZing up jasmonate signaling. Trends Plant Sci 13:66–71PubMedCrossRefGoogle Scholar
  30. Su J, Shen Q, David Ho TH, Wu R (1998) Dehydration-stress-regulated transgene expression in stably transformed rice plants. Plant Physiol 117:913–922PubMedCrossRefGoogle Scholar
  31. Thines B, Katsir L, Melotto M, Niu Y, Mandaokar A, Liu G, Nomura K, He SY, Howe GA, Browse J (2007) JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling. Nature 448:661–665PubMedCrossRefGoogle Scholar
  32. Thompson JD, Gibson TJ et al (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882CrossRefGoogle Scholar
  33. Troll W, Lindsley J (1955) A photometric method for the determination of proline. J Biol Chem 215:655–660PubMedGoogle Scholar
  34. Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G (2007) The TIFY family previously known as ZIM. Trends Plant Sci 12:239–244PubMedCrossRefGoogle Scholar
  35. Verslues PE, Agarwal M, Katiyar-Agarwal S, Zhu J, Zhu JK (2006) Methods and concepts in quantifying resistance to drought, salt and freezing, abiotic stresses that affect plant water status. Plant J 45:523–539PubMedCrossRefGoogle Scholar
  36. Wang H, Cutler AJ (1995) Promoters from kin1 and cor6.6, two Arabidopsis thaliana low-temperature- and ABA-inducible genes, direct strong β-glucuronidase expression in guard cells, pollen and young developing seeds. Plant Mol Biol 28:619–634PubMedCrossRefGoogle Scholar
  37. White DW (2006) PEAPOD regulates lamina size and curvature in Arabidopsis. Proc Natl Acad Sci USA 103:13238–13243PubMedCrossRefGoogle Scholar
  38. Xiao B, Huang Y, Tang N, Xiong L (2007) Over-expression of a LEA gene in rice improves drought resistance under the field conditions. Theor Appl Genet 115:35–46PubMedCrossRefGoogle Scholar
  39. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767PubMedCrossRefGoogle Scholar
  40. Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6:251–264PubMedCrossRefGoogle Scholar
  41. Yan Y, Stolz S, Chetelat A, Reymond P, Pagni M, Dubugnon L, Farmer EE (2007) A downstream mediator in the growth repression limb of the jasmonate pathway. Plant Cell 19:2470–2483PubMedCrossRefGoogle Scholar
  42. Yoo SD, Cho YH, Sheen J (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2:1565–1572PubMedCrossRefGoogle Scholar
  43. Yu J, Hu S, Wang GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92PubMedCrossRefGoogle Scholar
  44. Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Haiyan Ye
    • 1
  • Hao Du
    • 1
  • Ning Tang
    • 1
  • Xianghua Li
    • 1
  • Lizhong Xiong
    • 1
  1. 1.National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina

Personalised recommendations