Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

a.
School of Life Sciences, Shanghai University, Shanghai 200444, China
b.
College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China

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Corresponding author: E-mail address: vvakevp@hotmail.com (Jian Wang)

摘要

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Abstract: The heat shock transcription factors (HSFs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (HSPs), which are critical in the protection against stress damage and many other important biological processes. Study of the HSF gene family is important for understanding the mechanism by which plants respond to stress. The completed genome sequences of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) constitute a valuable resource for comparative genomic analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. The identification of phylogenetic relationships among HSF proteins in these species is a fundamental step to unravel the functionality of new and yet uncharacterized genes belonging to this family. In this study, the full complement of HSF genes in rice and Arabidopsis has probably been identified through the genome-wide scan. Phylogenetic analyses resulted in the identification of three major clusters of orthologous genes that contain members belonging to both species, which must have been represented in their common ancestor before the taxonomic splitting of the angiosperms. Further analysis of the phylogenetic tree reveals a possible dicot specific gene group. We also identified nine pairs of paralogs, as evidence for studies on the evolution history of rice HSF family and rice genome evolution. Expression data analysis indicates that HSF proteins are widely expressed in plants. These results provide a solid base for future functional genomic studies of the HSF gene family in rice and Arabidopsis.
- heat stress transcription factor /
- Arabidopsis thaliana /
- phylogenetic analysis

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参考文献(61)

[1]	Amin, J., Ananthan, J., Voellmy, R. Key features of heat shock regulatory elements Mol. Cell Biol., 8 (1998),pp. 3761-3769
[2]	Bailey, T.L., Gribskov, M. Combining evidence using p-values: application to sequence homology searches Bioinformatics., 14 (1998),pp. 48-54
[3]	Bienz, M., Pelham, H.R. Mechanisms of heat-shock gene activation in higher eukaryotes Adv. Genet., 24 (1987),pp. 31-72
[4]	Cannon, S.B., Mitra, A., Baumgarten, A. et al. BMC Plant Biol., 4 (2004),p. 10
[5]	Chen, J.N., Zhang, X.T. New progress in research on functions of heat shock protein in human and plants Hereditas (Beijing), 19 (1997),pp. 45-48
[6]	Chen, X.J., Ye, C.J., Lu, H.Y. Acta Genet. Sin., 28 (2006),pp. 1411-1420
[7]	Chu, Y., Solski, P.A., Khosravi-Far, R. et al. J. Biol. Chem., 271 (1996),pp. 6497-6501
[8]	Cicero, M.P., Hubl, S.T., Harrison, C.J. et al. The wing in yeast heat shock transcription factor (HSF) DNA-binding domain is required for full activity Nucleic Acids Res., 29 (2001),pp. 1715-1723
[9]	Clos, J., Westwood, J.T., Becker, P.B. et al. Cell, 63 (1990),pp. 1085-1097
[10]	Cokol, M., Nair, R., Rost, B. Finding nuclear localization signals EMBO Rep., 1 (2000),pp. 411-415
[11]	Czarnecka-Verner, E., Yuan, C.X., Scharf, K.D. et al. Plants contain a novel multi-member class of heat shock factors without transcriptional activator potential Plant Mol. Biol., 43 (2000),pp. 459-471
[12]	Delorenzi, M., Speed, T. An HMM model for coiled-coil domains and a comparison with PSSM-based predictions Bioinformatics, 18 (2002),pp. 617-625
[13]	Doring, P., Treuter, E., Kistner, C. et al. Plant Cell, 12 (2000),pp. 265-278
[14]	Drees, B.L., Grotkopp, E.K., Nelson, H.C. J. Mol. Biol., 273 (1997),pp. 61-74
[15]	Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res., 32 (2004),pp. 1792-1797
[16]	Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2) Cladistics, 5 (1989),pp. 164-166
[17]	Feng, Y., Liu, Q.P., Xue, Q.Z. Acta Genet. Sin., 31 (2004),pp. 1284-1293
[18]	Gorlich, D., Kutay, U. Transport between the cell nucleus and the cytoplasm Annu. Rev. Cell Dev. Biol., 15 (1999),pp. 607-660
[19]	Guo, A., He, K., Liu, D. et al. Bioinformatics, 21 (2005),pp. 2568-2569
[20]	Harrison, C.J., Bohm, A.A., Nelson, H.C. Crystal structure of the DNA binding domain of the heat shock transcription factor Science, 263 (1994),pp. 224-227
[21]	Hartl, F.U., Hayer-Hartl, M. Molecular chaperones in the cytosol: from nascent chain to folded protein Science, 295 (2002),pp. 1852-1858
[22]	Heerklotz, D., Doring, P., Bonzelius, F. et al. Mol. Cell Biol., 21 (2001),pp. 1759-1768
[23]	Hubel, A., Schoffl, F. Plant Mol. Biol., 26 (1994),pp. 353-462
[24]	Kent, W.J., Baertsch, R., Hinrichs, A. et al. Evolution's cauldron: duplication. deletion. and rearrangement in the mouse and human genomes Proc. Natl. Acad. Sci. USA, 100 (2003),pp. 11484-11489
[25]	Kotak, S., Port, M., Ganguli, A. et al. Characterization of C-terminal domains of Arabidopsis heat stress transcription factors (Hsfs) and identification of a new signature combination of plant class A Hsfs with AHA and NES motifs essential for activator function and intracellular localization Plant J., 39 (2004),pp. 98-112
[26]	Kumar, S., Gadagkar, S.R. Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences Genetics, 158 (2001),pp. 1321-1327
[27]	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
[28]	Letunic, I., Copley, R.R., Schmidt, S. et al. SMART 4.0: towards genomic data integration Nucleic Acids Res., 32 (2004),pp. D142-D144
[29]	Li, C.X., Yang, Q. Acta Genet. Sin., 25 (2003),pp. 177-180
[30]	Li, X., Duan, X., Jiang, H. et al. Plant Physiol., 141 (2006),pp. 1167-1184
[31]	Link, V., Sinha, A.K., Vashista, P. et al. A heat-activated MAP kinase in tomato: a possible regulator of the heat stress response FEBS Lett., 531 (2002),pp. 179-183
[32]	Liu, J.G., Yao, Q.H., Zhang, Z. et al. Biochem Mol. Biol., 38 (2005),pp. 602-608
[33]	Lohmann, C., Eggers-Schumacher, G., Wunderlich, M. et al. Mol. Genet. Genomics., 271 (2004),pp. 11-21
[34]	Lyck, R., Harmening, U., Hohfeld, 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
[35]	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
[36]	Mehan, M.R., Freimer, N.B., Ophoff, R.A. A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture Hum Genomics, 1 (2004),pp. 335-344
[37]	Morimoto, R.I. Regulation of the heat shock transcriptional response: cross talk between a family of heat shock factors, molecular chaperones, and negative regulators Genes Dev., 12 (1998),pp. 3788-3796
[38]	Nover, L., Bharti, K., Doring, P. et al. Cell Stress Chaperones, 6 (2001),pp. 177-189
[39]	Nover, L., Scharf, K.D., Gagliardi, D. et al. Cell Stress Chaperones, 1 (1996),pp. 215-223
[40]	Ouyang, S., Zhu, W., Hamilton, J. et al. The TIGR rice genome annotation resource: improvements and new features Nucleic Acids Res., 35 (2007),pp. D846-D851
[41]	Page, R.D. TreeView: an application to display phylogenetic trees on personal computers Comput. Appl. Biosci., 12 (1996),pp. 357-358
[42]	Peteranderl, 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
[43]	Pruitt, K.D., Tatusova, T., Maglott, D.R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes. transcripts and proteins Nucleic Acids Res., 33 (2005),pp. D501-D504
[44]	Rabindran, S.K., Giorgi, G., Clos, J. et al. Proc. Natl. Acad. Sci. USA, 88 (1991),pp. 6906-6910
[45]	Richard Durbin, S.E., Anders, K., Graeme, M.
[46]	Sarge, K.D., Zimarino, V., Holm, K. et al. Cloning and characterization of two mouse heat shock factors with distinct inducible and constitutive DNA-binding ability Genes Dev., 5 (1991),pp. 1902-1911
[47]	Scharf, K.D., Heider, H., Hohfeld, I. et al. Mol. Cell Biol., 18 (1998),pp. 2240-2251
[48]	Scharf, K.D., Rose, S., Zott, W. et al. EMBO J., 9 (1990),pp. 4495-4501
[49]	Schuetz, T.J., Gallo, G.J., Sheldon, L. et al. Proc. Natl. Acad. Sci. USA, 88 (1991),pp. 6911-6915
[50]	Schultheiss, J., Kunert, O., Gase, U. et al. Eur. J. Biochem., 236 (1996),pp. 911-921
[51]	Sorger, P.K., Pelham, H.R. Yeast heat shock factor is an essential DNA-binding protein that exhibits temperature-dependent phosphorylation Cell, 54 (1988),pp. 855-864
[52]	Tatusov, R.L., Koonin, E.V., Lipman, D.J. A genomic perspective on protein families Science, 278 (1997),pp. 631-637
[53]	Thompson, J.D., Gibson, T.J., Plewniak, F. et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res., 25 (1997),pp. 4876-4882
[54]	Thornton, J.W., DeSalle, R. Gene family evolution and homology: genomics meets phylogenetics Annu. Rev. Genomics Hum. Genet., 1 (2000),pp. 41-73
[55]	Treuter, E., Nover, L., Ohme, K. et al. Promoter specificity and deletion analysis of three heat stress transcription factors of tomato Mol. Gen. Genet., 240 (1993),pp. 113-125
[56]	Wiederrecht, G., Seto, D., Parker, C.S. Cell, 54 (1988),pp. 841-853
[57]	Wu, C. Heat shock transcription factors: structure and regulation Annu Rev Cell Dev Biol., 11 (1995),pp. 441-469
[58]	Xiao, H., Lis, J.T. Germline transformation used to define key features of heat-shock response elements Science, 239 (1988),pp. 1139-1142
[59]	Young, J.C., Barral, J.M., Ulrich, H.F. More than folding: localized functions of cytosolic chaperones Trends Biochem Sci., 28 (2003),pp. 541-547
[60]	Yuan, Q., Ouyang, S., Liu, J. et al. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists Nucleic Acids Res, 31 (2003),pp. 229-233
[61]	Zhang, H.Y., Li, H.Y., Lin, J.T. Cloning and analysis of rat heat shock factor binding protein 1 Acat Geneti. Sin., 26 (2004),pp. 647-652