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Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress

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Abstract

Wild soybean (Glycine soja L. G07256) exhibits a greater adaptability to soil bicarbonate stress than cultivated soybean, and recent discoveries show that TIFY family genes are involved in the response to several abiotic stresses. A genomic and transcriptomic analysis of all TIFY genes in G. soja, compared with G. max, will provide insight into the function of this gene family in plant bicarbonate stress response. This article identified and characterized 34 TIFY genes in G. soja. Sequence analyses indicated that most GsTIFY proteins had two conserved domains: TIFY and Jas. Phylogenetic analyses suggested that these GsTIFY genes could be classified into two groups. A clustering analysis of all GsTIFY transcript expression profiles from bicarbonate stress treated G. soja showed that there were five different transcript patterns in leaves and six different transcript patterns in roots when the GsTIFY family responds to bicarbonate stress. Moreover, the expression level changes of all TIFY genes in cultivated soybean, treated with bicarbonate stress, were also verified. The expression comparison analysis of TIFYs between wild and cultivated soybeans confirmed that, different from the cultivated soybean, GsTIFY (10a, 10b, 10c, 10d, 10e, 10f, 11a, and 11b) were dramatically up-regulated at the early stage of stress, while GsTIFY 1c and 2b were significantly up-regulated at the later period of stress. The frequently stress responsive and diverse expression profiles of the GsTIFY gene family suggests that this family may play important roles in plant environmental stress responses and adaptation.

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References

  • Alhendawi RA, Römheld V, Kirkby EA, Marschner H (1997) Influence of increasing bicarbonate concentration on plant growth, organic acid accumulation in roots and iron uptake by barley, sorghum and maize. J Plant Nutr 20:1731–1753

    Article  CAS  Google Scholar 

  • Anas SSM, Vivekanandan M (2000) Influence of NaCI salinity on the behavior of hydrolases and phosphatases in mulberry genotype: relationship to salt tolerance. J Plant Biol 43:217–225

    Article  CAS  Google Scholar 

  • Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME Suite: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208

    Article  PubMed  CAS  Google Scholar 

  • Busch H, Camacho-Trullio D, Rogon Z, Breuhahn K, Angel P, Eils R, Szabowski A (2008) Gene network dynamics controlling keratinocyte migration. Mol Syst Biol 4:199

    Article  PubMed  Google Scholar 

  • Cheong MS, Yun DJ (2007) Salt-Stress Signaling. J. Plant Biol 50:148–155

    Article  CAS  Google Scholar 

  • 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 signaling. Nature 448:666–671

    Article  PubMed  CAS  Google Scholar 

  • 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 21:131–145

    Article  PubMed  CAS  Google Scholar 

  • Creelman RA, Mullet JE (1995) Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress. Proc Natl Acad Sci USA 92:4114–4119

    Article  PubMed  CAS  Google Scholar 

  • Davies DD (1986) The fine control of cytosolic pH. Physiol Plant 67:702–706

    Article  CAS  Google Scholar 

  • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763

    Article  PubMed  CAS  Google Scholar 

  • Ge Y, Zhu YM, Lv DK, Dong TT, Wang WS, Tan SJ, Liu CH, Zou P (2009) Research on responses of wild soybean to alkaline stress. Pratacultural Science 26:47–52

    CAS  Google Scholar 

  • Ge Y, Li Y, Zhu YM, Bai X, Lv DK, Guo DJ, Ji W, Cai H (2010) Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC Plant Biol 10:153

    Article  PubMed  Google Scholar 

  • Ge Y, Li Y, Lv DK, Bai X, Ji W, Hua C, Wang AX, Zhu YM (2011) Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. Funct Integr Genomics 11:369–379

    Article  PubMed  CAS  Google Scholar 

  • Gout E, Bligny R, Douce R (1992) Regulation of in tracellular pH values in higher plant cells: carbon-13 and phosphorus-31 nuclear magnetic resonance studies. J Biol Chem 267:13903–13909

    PubMed  CAS  Google Scholar 

  • Janes K, Gaudet S, Albeck J, Nielsen U, Lauffenburger D, Sorger P (2006) The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 124(6):1225–1239

    Article  PubMed  CAS  Google Scholar 

  • Jiang Y, Deyholos MK (2006) Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes, BMC. Plant Biol 12:6–25

    Google Scholar 

  • Kang HG, Kim J, Kim B, Jeong H, Choi SH, Kim EK, Lee HY, Lim PO (2011) Overexpression of FTL1/DDF1, an AP2 transcription factor, enhances tolerance to cold, drought, and heat stresses in Arabidopsis thaliana. Plant Sci 180:634–641

    Article  PubMed  CAS  Google Scholar 

  • Kim MY, Lee S, Van K, Kim TH, Jeong SC (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107:22032–22037

    Article  PubMed  CAS  Google Scholar 

  • Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306

    Article  PubMed  CAS  Google Scholar 

  • Li XY, Dhaubhadel S (2011) Soybean 14-3-3 gene family: identification and molecular characterization. Planta 233:569–582

    Article  PubMed  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−△△CT method. Methods 25:402–408

    Article  PubMed  CAS  Google Scholar 

  • Major IT, Constabel CP (2006) Molecular analysis of poplar defense against herbivory: comparison of wound-and insect elicitor induced gene expression. New Phytol 172:617–635

    Article  PubMed  CAS  Google Scholar 

  • Mazzucotellia E, Mastrangeloa AM, Crosattib C, Guerrab D, Stancab AM, Cattivelli L (2008) Abiotic stress response in plants: when post-transcriptional and post-translational regulations control transcription. Plant Sci 174:420–431

    Article  Google Scholar 

  • Mulder NJ, Apweiler R (2008) The InterPro database and tools for protein domain analysis. Wiley, London

    Google Scholar 

  • Nishii A, Takemura M, Fujita H, Shikata M, Yokota A, Kohchi T (2000) Characterization of a novel gene encoding a putative single zincfinger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. Biosci Biotechnol Biochem 64:1402–1409

    Article  PubMed  CAS  Google Scholar 

  • Rao MV, Lee H, Creelman RA, Mullet JE, Davis KR (2000) Jasmonic acid signaling modulates ozone induced hypersensitive cell death. Plant Cell 12:1633–1646

    PubMed  CAS  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    PubMed  CAS  Google Scholar 

  • Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34:374–378

    PubMed  CAS  Google Scholar 

  • Sakano K (1998) Revision of biochemical pH-stat: involvement of alternative pathway metabolisms. Plant Cell Physiol 39(5):467–473

    Article  CAS  Google Scholar 

  • 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 55:631–639

    Article  PubMed  CAS  Google Scholar 

  • Staswick PE (2008) JAZing up jasmonate signaling. Trends Plant Sci 13:66–71

    Article  PubMed  CAS  Google Scholar 

  • Tang CX, Robson AD (1993) pH above 6.0 reduces nodulation in Lupinus species. Plant Soil 152:269–276

    Article  Google Scholar 

  • 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 signaling. Nature 448:661–665

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  • Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G (2007) The TIFY family previously known as ZIM. Trends Plant Sci 12:239–244

    Article  PubMed  CAS  Google Scholar 

  • White DW (2006) PEAPOD regulates lamina size and curvature in Arabidopsis. Proc Natl Acad Sci USA 103:13238–13243

    Article  PubMed  CAS  Google Scholar 

  • Willems E, Leyns L, Vandesompele J (2008) Standardization of real-time PCR gene expression data from independent biological replicates. Anal Biochem 379:127–129

    Article  PubMed  CAS  Google Scholar 

  • Xiong L, Schumaker K, Zhu J (2002) Cell signaling during cold, drought, and salt stress. Plant Cell Online 14:165–183

    Article  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803

    Article  PubMed  CAS  Google Scholar 

  • 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 19:2470–2483

    Article  PubMed  CAS  Google Scholar 

  • Yang CW, Shi DC, Wang DL (2008) Comparative effects of salt stress and alkali stress on growth, osmotic adjustment and ionic balance of an alkali resistant halophyteSuaeda glauca(Bge.). Plant Growth Regul 56:179–190

    Article  CAS  Google Scholar 

  • Ye HY, Du H, Tang N, Li XH, Xiong LZ (2009) Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol 71:291–305

    Article  PubMed  CAS  Google Scholar 

  • Zhu D, Bai X, Chen C, Chen Q, Cai H, Li Y, Ji W, Zhai H, Lv DK, Luo X, Zhu YM (2011) GsTIFY10, a novel positive regulator of plant tolerance to bicarbonate stress and a repressor of jasmonate signaling. Plant Mol Biol 77:285–297

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Suk-Ha Lee (Seoul National University) for providing G. soja genome sequences. The authors thank Neil. Hobson (University of Alberta) for edit and suggestions to the manuscript. This study was supported by the National Natural Science Foundation of China (30570990, 30471059), the “863” project (2008AA10Z153), the National Major Project for Cultivation of Transgenic Crops (2008ZX08004), the Key Research Plan of Heilongjiang Province (GA06B103-3), the Innovation Research Group of NEAU (CXT004), and the Basic Research Preliminary Study Foundation of the Ministry of Science and Technology of the PRC (2003CCA03500).

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Authors and Affiliations

  1. Plant Bioengineering Laboratory, The College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China

    Dan Zhu, Xi Bai, Xiao Luo, Hua Cai, Wei Ji & Yanming Zhu

  2. Lethbridge Research Centre Agriculture and Agri-Food Canada, 5403-1 Ave, South P.O. Box 3000, Lethbridge, AB, T1J 4B1, Canada

    Qin Chen

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  1. Dan Zhu
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  2. Xi Bai
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  3. Xiao Luo
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  4. Qin Chen
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  5. Hua Cai
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  6. Wei Ji
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  7. Yanming Zhu
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Correspondence to Yanming Zhu.

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Communicated by H. Judelson.

Dan Zhu and Xi Bai contributed equally to this study.

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Zhu, D., Bai, X., Luo, X. et al. Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress. Plant Cell Rep 32, 263–272 (2013). https://doi.org/10.1007/s00299-012-1360-7

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  • DOI: https://doi.org/10.1007/s00299-012-1360-7

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