Genome-Wide Analysis and Molecular Characterization of Heat Shock Transcription Factor Family in Glycine max

Eunsook Chung; Kyoung-Mi Kim; Jai-Heon Lee

doi:10.1016/j.jgg.2012.12.002

Volume 40 Issue 3

Mar. 2013

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2013 > 40(3): 127-135

PDF( 985 KB)

Genome-Wide Analysis and Molecular Characterization of Heat Shock Transcription Factor Family in Glycine max

doi: 10.1016/j.jgg.2012.12.002

BK21 Center for Silver-Bio Industrialization, College of Natural Resources and Life Science, Dong-A University, Hadan 2 dong, Sahagu, Busan 604-714, Republic of Korea

More Information

Corresponding author: E-mail address: jhnlee@dau.ac.kr (Jai-Heon Lee)
Received Date: 2012-07-25
Accepted Date: 2012-12-07
Rev Recd Date: 2012-12-04

Available Online: 2012-12-28

Publish Date: 2013-03-20

Abstract

Abstract

Heat shock transcription factors (Hsfs) play an essential role on the increased tolerance against heat stress by regulating the expression of heat-responsive genes. In this study, a genome-wide analysis was performed to identify all of the soybean (Glycine max) GmHsf genes based on the latest soybean genome sequence. Chromosomal location, protein domain, motif organization, and phylogenetic relationships of 26 non-redundant GmHsf genes were analyzed compared with AtHsfs (Arabidopsis thaliana Hsfs). According to their structural features, the predicted members were divided into the previously defined classes A–C, as described for AtHsfs. Transcript levels and subcellular localization of five GmHsfs responsive to abiotic stresses were analyzed by real-time RT-PCR. These results provide a fundamental clue for understanding the complexity of the soybean GmHsf gene family and cloning the functional genes in future studies.
- Abiotic stress,
- Expression patterns,
- Heat shock transcription factor,
- Phylogenetic analysis

FullText(HTML)

References(56)

References

[1]	Abel, S., Theologis, A. Plant J., 5 (1994),pp. 421-427
[2]	Almoguera, C., Rojas, A., Diaz-Martin, J. et al. Seed-specific heat-shock transcription factor involved in developmental regulation during embryogenesis in sunflower J. Biol. Chem., 277 (2002),pp. 43866-43872
[3]	Bailey, T.L., Gribskov, M. Bioinformatics, 14 (1998),pp. 48-54
[4]	Bharti, K., Schmidt, E., Lyck, R. et al. Plant J., 22 (2000),pp. 355-365
[5]	Bienz, M., Pelham, H.R.B. Mechanisms of heat-shock gene activation in higher eukaryotes Adv. Genet., 24 (1987),pp. 31-72
[6]	Charng, Y.Y., Liu, H.C., Liu, N.Y. et al. Plant Physiol., 143 (2007),pp. 251-262
[7]	Chung, E., Seong, E., Kim, Y.-C. et al. Mol. Cells, 17 (2004),pp. 377-380
[8]	Chung, E., Cho, C.W., Yun, B.H. et al. Molecular cloning and characterization of the soybean DEAD-box RNA helicase gene induced by low temperature stress Gene, 443 (2009),pp. 91-99
[9]	Czarnecka-Verner, E., Yuan, C.-X., Fox, P.C. et al. Isolation and characterization of six heat shock transcription factor cDNA clones from soybean Plant Mol. Biol., 29 (1995),pp. 37-51
[10]	Davletova, S., Rizhsky, L., Liang, H. et al. Plant Cell, 17 (2005),pp. 268-281
[11]	Delorenzi, M., Speed, T. An HMM model for coiled-coil domains and a comparison with PSSM-based predictions Bioinformatics, 18 (2002),pp. 617-625
[12]	Díaz-Martín, J., Almoguera, C., Prieto-Dapena, P. et al. Functional interaction between two transcription factors involved in the developmental regulation of a small heat stress protein gene promoter Plant Physiol., 139 (2005),pp. 1483-1494
[13]	Doring, P., Treuter, E., Kistner, C. et al. The role of AHA motifs in the activator function of tomato heat stress transcription factors HsfA1 and HsfA2 Plant Cell, 12 (2000),pp. 265-278
[14]	Fields, K.A., Fischer, E., Haakstadt, T. Infect. Immun., 70 (2002),pp. 3816-3823
[15]	Gorlich, D., Kutay, U. Transport between the cell nucleus and the cytoplasm Annu. Rev. Cell. Dev. Biol., 15 (1999),pp. 607-660
[16]	Guo, J., Wu, J., Qian, J. et al. J. Genet. Genomics, 35 (2008),pp. 105-118
[17]	Heerklotz, D., Doring, P., Bonzelius, F. et al. The balance of nuclear import and export determines the intracellular distribution and function of tomato heat stress transcription factor HsfA2 Mol. Cell. Biol., 21 (2001),pp. 1759-1768
[18]	Higgins, D.G., Thompson, J.D., Gibson, T.J. Using CLUSTAL for multiple sequence alignments Methods Enzymol., 266 (1996),pp. 383-402
[19]	Kotak, S., Port, M., Ganguli, A. et al. Plant J., 39 (2004),pp. 98-112
[20]	Kotak, S., Larkindale, J., Lee, U. et al. Complexity of the heat stress response in plants Curr. Opin. Plant Biol., 10 (2007),pp. 310-316
[21]	Kotak, S., Vierling, E., Bäumlein, H. et al. Plant Cell, 19 (2007),pp. 182-195
[22]	la Cour, T., Kiemer, L., Molgaard, A. et al. Analysis and prediction of leucine-rich nuclear export signals Protein Eng. Des. Sel., 17 (2004),pp. 527-536
[23]	Larkindale, J., Knight, M.R. Plant Physiol., 128 (2002),pp. 682-695
[24]	Larkindale, J., Hall, J.D., Knight, M.R. et al. Plant Physiol., 138 (2005),pp. 882-897
[25]	Letunic, I., Copley, R.R., Schmidt, S. et al. SMART 4.0: towards genomic data integration Nucleic Acids Res., 32 (2004),pp. D142-D144
[26]	Lyck, R., Harmening, U., Höhfeld, I. et al. Intracellular distribution and identification of the nuclear localization signals of two plant heat-stress transcription factors Planta, 202 (1997),pp. 117-125
[27]	Lin, Y.-X., Jiang, H.-Y., Chu, Z.-X. et al. Genome-wide identification, classification and analysis of heat shock transcription factor family in maize BMC Genomics, 12 (2011),p. 76
[28]	McGinnis, S., Madden, T.L. BLAST: at the core of a powerful and diverse set of sequence analysis tools Nucleic Acids Res., 32 (2004),pp. W20-W25
[29]	Miller, G., Mittler, R. Could heat shock transcription factors function as hydrogen peroxide sensors in plants? Ann. Bot., 98 (2006),pp. 279-288
[30]	Mishra, S.K., Tripp, J., Winkelhaus, S. et al. In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermotolerance in tomato Genes Dev., 16 (2002),pp. 1555-1567
[31]	Mochida, K., Yoshida, T., Sakurai, T. et al. DNA Res., 16 (2009),pp. 353-369
[32]	Nishizawa, A., Ybuta, Y., Yoshida, E. et al. Plant J., 48 (2006),pp. 535-547
[33]	Nover, L. Expression of heat stress genes I homologous and heterologous systems Enzyme Microb. Technol., 9 (1987),pp. 130-144
[34]	Nover, L., Bharti, K., Döring, P. et al. Cell Stress Chaperon, 6 (2001),pp. 177-189
[35]	Panchuk, I.I., Volkov, R.A., Schöffl, F. Plant Physiol., 129 (2002),pp. 838-853
[36]	Panikulangara, T.J., Eggers-Schumacher, G., Wunderlich, M. et al. Plant Physiol., 136 (2004),pp. 3148-3158
[37]	Peteranderi, R., Rabenstein, M., Shin, Y.K. et al. Biochemical and biophysical characterization of the trimerization domain from the heat shock transcription factor Biochemistry, 38 (1999),pp. 3559-3569
[38]	Port, M., Tripp, J., Zielinski, D. et al. Role of Hsp17.4-CII as coregulator and cytoplasmic retention factor of tomato heat stress transcription factor HsfA2 Plant Physiol., 135 (2004),pp. 1457-1470
[39]	Qin, F., Kakimoto, M., Sakuma, Y. et al. Plant J., 50 (2007),pp. 54-59
[40]	Rizhsky, L., Liang, H., Shuman, J. et al. Plant Physiol., 134 (2004),pp. 1683-1696
[41]	Sakuma, Y., Maruyama, K., Qin, F. et al. Proc. Natl. Acad. Sci. USA, 103 (2006),pp. 18822-18827
[42]	Scharf, K.D., Rose, S., Zott, W. et al. EMBO J., 9 (1990),pp. 4495-4501
[43]	Scharf, K.D., Heider, H., Hohfeld, I. et al. The tomato Hsf system: HsfA2 needs interaction with HsfA1 for efficient nuclear import and may be localized in cytoplasmic heat shock granules Mol. Cell. Biol., 18 (1998),pp. 2240-2251
[44]	Schmutz, J., Cannon, S.B., Schlueter, J. et al. Genome sequence of the palaeopolyploid soybean Nature, 463 (2010),pp. 178-183
[45]	Schramm, F., Larkindale, J., Kiehlmann, E. et al. Plant J., 53 (2008),pp. 264-274
[46]	Schultheiss, J., Kunert, O., Gase, U. et al. Solution structure of the DNA-binding domain of the tomato heat-stress transcription factor Hsf24 Eur. J. Biochem., 236 (1996),pp. 911-921
[47]	Shim, D., Hwang, J.-U., Lee, J. et al. Orthologs of class A4 heat shock transcription factor HsfA4a confer cadmium tolerance in wheat and rice Plant J., 21 (2009),pp. 4031-4034
[48]	Shultz, J.L., Kurunam, D., Shopinski, K. et al. The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max Nucleic Acids Res., 34 (2006),pp. D758-D765
[49]	Swindell, W.R., Huebner, M., Weber, A.P. BMC Genomics, 8 (2007),p. 25
[50]	Volkov, R.A., Panchuk, I.I., Mullineaux, P.M. et al. Plant Mol. Biol., 61 (2006),pp. 733-746
[51]	von Koskull-Döring, P., Scharf, K.-D., Nover, L. The diversity of plant heat stress transcription factors Trends Plant Sci., 12 (2007),pp. 452-457
[52]	Wang, Z., Libault, M., Joshi, T. et al. Soy DB: a knowledge database of soybean transcription factors BMC Plant Biol., 10 (2010),p. 14
[53]	Yamanouchi, U., Yano, M., Lin, H. et al. Proc. Natl. Acad. Sci. USA, 99 (2002),pp. 7530-7535
[54]	Yokotani, N., Ichikawa, T., Kondou, Y. et al. Planta, 227 (2008),pp. 957-967
[55]	Yoshida, T., Sakuma, Y., Todaka, D. et al. Biochem. Biophys. Res. Commun., 368 (2008),pp. 515-521
[56]	Zhu, B., Ye, C., Lü, H. et al. J. Plant Res., 119 (2006),pp. 247-256