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UTR Analysis of bZIP Transcription Factor Family in Barley | ||
| دوفصلنامه فن آوری زیستی در کشاورزی | ||
| Article 5, Volume 7, Issue 2, March 2017, Pages 45-52 PDF (583.43 K) | ||
| Document Type: research | ||
| DOI: 10.22084/ab.2016.2062 | ||
| Authors | ||
| Farzan Ghanegolmohamadi1; Zahra Sadat Shobbar* 2; Ehsan Pourabed1; Farrokh Ghanatir3 | ||
| 1M.Sc. Graduated, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj | ||
| 2Assistant Professor, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj | ||
| 3M.Sc. Graduated, Department of Computer Engineering, Islamic Azad University, Behbahan Branch, Behbahan | ||
| Abstract | ||
| bZIP family is one of the most diverse transcription factors in plants playing critical roles in response to biotic and abiotic stresses. Regulation of gene expression at translation level is determined based on the mRNA features which untranslated regions (UTRs) are among the most important ones. In the present study, we attempted to survey the features of UTRs and their probable effect on transcription and translation of bZIP family in barley (78 members) through in silico approaches. Based on the results, mean length of 5´-UTRs were more than 3´-UTR but 5´-UTRs had more GC content. Context of initial codons had 49.23% guanine at +4 and 56.70% purine at -3 positions. Totally, 18 abiotic stress responsive Cis-acting elements were found which GA-regulated myb element was prevalent. Ribosome should consume more than 50 Kcal/mol energy to reach the start codon of 50 members. However, 23 members had Internal Ribosome Entry Site (IRES). sRNA targets were only detected in 5´-UTR (HvbZIP4) and in 3´-UTR(HvbZIP44). 225 Upstream Open Reading Frame (uORFs) were extracted where the minimum length was 12 nt. uORF of HvbZIP24 (at frame +3) was similar to an upstream protein of Theobroma cacao (XM_007017561.1). In general, mRNAs of the bZIP family in barley had different regulatory structures, which might be a natural solution for accurate regulation of these regulatory proteins. | ||
| Keywords | ||
| Transcription factor; bZIP family; Untranslated region; Barley | ||
| References | ||
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Alves, M. S., Dadalto, S. P., Gonçalves, A. B., De Souza, G. B., Barros, V. A. and Fietto, L. G. 2013. Plant bZIP transcription factors responsive to pathogens: a review. International Journal of Molecular Sciences, 14(4): 7815-7828. Araujo, P. R., Yoon, K., Ko, D., Smith, A. D., Qiao, M., Suresh, U., Burns, S. C. and Penalva, L. O. F. 2012. Before It Gets Started: Regulating Translation at the 5′ UTR. Comparative and Functional Genomics. Calvo, S. E., Pagliarini, D. J. and Mootha, V. K. 2009. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proceedings of the National Academy of Sciences of the United State, 106(18): 7507-7512. Chappell, S. A., Edelman, G. M. and Mauro, V. P. 2000. A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity. Proceedings of the National Academy of Sciences of the United States, 97(4): 1536-1541. Chatterjee, S. and Pal, J. K. 2009. Role of 5′‐and 3′‐untranslated regions of mRNAs in human diseases. Biology of the Cell, 101(5): 251-262. Chia-Pei, C., Shun-Jia, C., Chen-Huan, L., Tzu-Ling, W. and Chien-Chia, W. 2010. A single sequence context cannot satisfy all non-AUG initiator codons in yeast. BMC Microbiology, 10: 188. Churbanov, A., Rogozin, I. B., Babenko, V. N., Ali, H. and Koonin, E. V. 2005. Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes. Nucleic Acids Research, 33(17): 5512-5520. Crowe, M., Wang, X. Q. and Rothnagel, J. 2006. Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides. BMC Genomics, 7(1): 16. Gubler, F., Raventos, D., Keys, M., Watts, R., Mundy, J. and Jacobsen, J. V. 1999. Target genes and regulatory domains of the GAMYB transcriptional activator in cereal aleurone. The Plant Journal, 17(1): 1-9. Dai, X. and Zhao, P. X. 2011. psRNATarget: A plant small RNA target analysis server. Nucleic Acids Research, 39(suppl 2): W155-W159. Davuluri, R. V., Suzuki, Y., Sugano, S. and Zhang, M. Q. 2000. CART classification of human 5′ UTR sequences. Genome Research, 10(11): 1807-1816. Dever, T. E. 2002. Gene-specific regulation by general translation factors. Cell, 108(4): 545-556. Dunn, M. A., White, A. J., Vural, S. and Hughes, M. A. 1998. Identification of promoter elements in a low-temperature-responsive gene (blt4. 9) from barley (Hordeum vulgare L.). Plant Molecular Biology, 38(4): 551-564. Esposito, D., Hicks, A. J. and Stern, D. B. 2001. A role for initiation codon context in chloroplast translation. The Plant Cell Online, 13(10): 2373-2384. Gray, N. K. and Wickens, M. 1998. Control of translation initiation in animals. Annual Review of Cell and Developmental Biology, 14(1): 399-458. Grillo, G., Turi, A., Licciulli, F., Mignone, F., Liuni, S., Banfi, S., Gennarino, V. A., Horner, D. S., Pavesi, G. and Picardi, E. 2010. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Research, 38(suppl 1): D75-D80. Jakoby, M., Weisshaar, B., Dröge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T. and Parcy, F. 2002. bZIP transcription factors in Arabidopsis. Trends in Plant Science, 7(3): 106-111. Jones-Rhoades, M. W., Bartel, D. P. and Bartel, B. 2006. MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology, 57: 19-53. Jordan, I. K., Rogozin, I. B., Glazko, G. V. and Koonin, E. V. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends in Genetics, 19(2): 68-72. Kochetov, A., Syrnik, O., Rogozin, I., Glazko, G., Komarova, M. and Shumnyĭ, V. 2002. Context organization of mRNA 5'-untranslated regions of higher plants. Molekuliarnaia Biologiia, 36(4): 649-656. Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P. and Rombauts, S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30(1): 325-327. Littlefield, O. and Nelson, H. C. 1999. A new use for the'wing' of the 'winged' helix-turn-helix motif in the HSF-DNA cocrystal. Nature Structural and Molecular Biology, 6(5): 464-470. Liu, C., Wu, Y. and Wang, X. 2012. bZIP transcription factor OsbZIP52/RISBZ5: a potential negative regulator of cold and drought stress response in rice. Planta, 235(6): 1157-1169. Liu, J., Chen, N., Chen, F., Cai, B., Dal Santo, S., Tornielli, G. B., Pezzotti, M. and Cheng, Z. M. M. 2014. Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera). BMC Genomics, 15(1): 281. Medenbach, J., Seiler, M. and Hentze, M. W. 2011. Translational control via protein-regulated upstream open reading frames. Cell, 145(6): 902-913. Mignone, F., Gissi, C., Liuni, S. and Pesole, G. 2002. Untranslated regions of mRNAs. Genome Biology, 3(3): 0004.0001-0004.0010. Mihailovich, M., Thermann, R., Grohovaz, F., Hentze, M. W. and Zacchetti, D. 2007. Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5′ untranslated region. Nucleic Acids Research, 35(9): 2975-2985. Mohanty, B., Krishnan, S., Swarup, S. and Bajic, V. B. 2005. Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species. Annals of Botany, 96(4): 669-681. Motamayor, J. C., Mockaitis, K., Schmutz, J., Haiminen, N., Donald III, L., Cornejo, O., Findley, S. D., Zheng, P., Utro, F. and Royaert, S. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology, 14(6): r53. Morita, A., Umemura, T. A., Kuroyanagi, M., Futsuhara, Y., Perata, P. and Yamaguchi, J. 1998. Functional dissection of a sugar-repressed α-amylase gene (RAmy1A) promoter in rice embryos. FEBS letters, 423(1): 81-85. Morris, D. R. and Geballe, A. P. 2000. Upstream open reading frames as regulators of mRNA translation. Molecular and Cellular Biology, 20(23): 8635-8642. Neafsey, D. E. and Galagan, J. E. 2007. Dual modes of natural selection on upstream open reading frames. Molecular Biology and Evolution, 24(8): 1744-1751. Nijhawan, A., Jain, M., Tyagi, A. K. and Khurana, J. P. 2008. Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiology, 146(2): 333-350. Pandey, B., Sharma, P., Pandey, D., Varshney, J., Sheoran, S., Singh, M., Singh, R., Sharma, I. and Chatrath, R. 2012. Comprehensive computational analysis of different classes of Glutathione S-transferases in Triticum aestivum L., Plant Omics, 5(6): 518. Park, E. H., Lee, J. M. and Pelletier, J. 2006. The Tie2 5′untranslated region is inhibitory to 5′ end-mediated translation initiation. FEBS letters, 580(5): 1309-1319. Pourabed, E., Golmohamadi, F. G., Monfared, P. S., Razavi, S. M. and Shobbar, Z. S. 2015. Basic leucine zipper family in barley: Genome-wide characterization of members and expression analysis. Molecular Biotechnology, 57(1): 12-26. Rahmani, F., Hummel, M., Schuurmans, J., Wiese-Klinkenberg, A., Smeekens, S. and Hanson, J. 2009. Sucrose control of translation mediated by an upstream open reading frame-encoded peptide. Plant Physiology, 150(3): 1356-1367. Rangan, L., Vogel, C. and Srivastava, A. 2008. Analysis of context sequence surrounding translation initiation site from complete genome of model plants. Molecular Biotechnology, 39(3): 207-213. Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B. and Bartel, D. P. 2002. MicroRNAs in plants. Genes and Development, 16(13): 1616-1626. Ringner, M. and Krogh, M. 2005. Folding free energies of 5′-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLOS Computational Biology, 1(7): e72. Rogozin, I. B., Kochetov, A. V., Kondrashov, F. A., Koonin, E. V. and Milanesi, L. 2001. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a weak context of the start codon. Bioinformatics, 17(10): 890-900. Siberil, Y., Doireau, P. and Gantet, P. 2001. Plant bZIP G‐box binding factors. European Journal of Biochemistry, 268(22): 5655-5666. Singh, K. B., Foley, R. C. and Oñate-Sánchez, L. 2002. Transcription factors in plant defense and stress responses. Current Opinion in Plant Biology, 5(5): 430-436. Touriol, C., Bornes, S., Bonnal, S., Audigier, S., Prats, H., Prats, A. C. and Vagner, S. 2003. Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons. Biology of the Cell, 95(3): 169-178. Wegrzyn, J., Drudge, T., Valafar, F. and Hook, V. 2008. Bioinformatics analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites. BMC Bioinformatics, 9(1): 232. Wei, K., Chen, J., Wang, Y., Chen, Y., Chen, S., Lin, Y., Pan, S., Zhong, X. and Xie, D. 2012. Genome-wide analysis of bZIP-encoding genes in maize. DNA Research, 19(6): 463-476. Xiong, J. 2006. Essential bioinformatics, Cambridge University Press, pp. 231-240. Xue, G.P. 2002. An AP2 domain transcription factor HvCBF1 activates expression of cold-responsive genes in barley through interaction with a (G/a) (C/t) CGAC motif. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression, 1577(1): 63-72. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Proceedings of the National Academy of Sciences of the United States, 31(13): 3406-3415. | ||
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