Sorgum [Sorghum bicolor (L.) Moench] Genomunda BES1 Transkripsiyon Faktör Ailesinin Genom Çaplı Analizi

Year 2020, Volume: 7 Issue: 1, 85 - 95, 29.02.2020

Ayşe Gül Kasapoğlu , Emre İlhan , Damla Kızılkaya , Arash Hossein Pour , Kamil Haliloğlu

https://doi.org/10.19159/tutad.671605

Cited By: 9

Abstract

BES1 transkripsiyon faktörü ailesi brassinosteroidlerin biyosentezinde önemli bir role sahiptir. Bitki büyüme ve gelişme

süreçlerini ve çevresel streslere yanıt mekanizmasını etkileyen bir steroid hormonudur. Bu çalışmanın amacı sorgum

[Sorghum bicolor (L.) Moench] bitkisinin farklı dokularında farklı azot kaynakları (kontrol gübresi, amonyak, nitrat, üre)

uygulanarak bu dokulardaki BES1 transkripsiyon faktörünün ifade profillerini belirlemek ve in siliko olarak BES1 gen

ailesinin üyelerini genom çapında tespit ederek karakterize etmektir. Sorgum genomunda amino asit sayıları 190 ile 716,

moleküler ağırlıkları 35.27 ile 80.54 kDa ve izoelektrik noktaları 5.0 ile 10.07 arasında değişen 9 Sobic-BES1 proteini

belirlenmiştir. Gen yapısı analizlerinde tahmini ekzonların sayısı 2 ile 10 arasında değişmiştir. S. bicolor, Arabidopsis

thaliana ve Oryza sativa türlerinin BES1 proteinleri kullanılarak filogenetik ilişki tespit edilmiştir. Evrimsel süreçte Sobic-

BES1-4 ve Sobic-BES1-9 genlerinin segmental duplike olduğu belirlenmiştir. İn siliko gen ifade analizlerine göre farklı azot

kaynaklarının ve su kontrolünün uygulandığı kök ve sürgün dokularında Sobic-BES1-4 ve -9 genlerinin ifade seviyelerinin

en yüksek olduğu, diğer taraftan kullanılan azot kaynağına ve dokuya göre Sobic-BES1-1, Sobic-BES1-2 ve Sobic-BES1-8

genlerinin ifade seviyelerinin farklılık gösterdiği belirlenmiştir. Bu çalışmanın sonuçları fonksiyonel gen araştırmaları için

bir temel sağlayacak olup, sorgum bitkisinde BES1 gen ailesinin anlaşılmasına katkı sunacaktır.

Keywords

Biyoinformatik analizler, fitohormon, brassinosteroid, gen ailesi, gen ifadesi

Genome-Wide Analysis of BES1 Transcription Factor Family in Sorghum [Sorghum bicolor (L.) Moench] Genome

Abstract

The BES1 transcription factor family has an important role in the biosynthesis of brassinosteroids. It is a steroid

hormone that affects plant growth and development processes and the mechanism of response to environmental stresses. The

aim of this study was to determine the expression profiles of BES1 transcription factor in different tissues of sorghum

[Sorghum bicolor (L.) Moench] by applying different nitrogen sources (controlled fertilized, ammonia, nitrate and urea) and

to characterize BES1 gene family members through in silico methods. In sorghum genome, 9 Sobic-BES1 proteins with

amino acid numbers ranged from 190 and 716, molecular weights between 35.27 and 80.54 kDa and isoelectric points

between 5.0 and 10.07 were determined. In gene structure analysis, the number of estimated exons ranged from 2 to 10.

Phylogenetic relationship was determined using BES1 proteins of S. bicolor, Arabidopsis thaliana and Oryza sativa species.

Sobic-BES1-4 and Sobic-BES1-9 genes were found to be segmental duplicated in the evolutionary process. According to the

silico gene expression analysis, the expression levels of Sobic-BES1-4 and -9 genes were the highest in the root and shoot

tissues where different nitrogen sources and irrigation control were applied. On the other hand, the expression levels of

Sobic-BES1-1, Sobic-BES1-2 and Sobic-BES1-8 genes were differed according to the nitrogen source and tissue used. The

results of this study will provide a basis for functional gene research and contribute to the understanding of the BES1 gene

family in Sorghum bicolor.

Keywords

Bioinformatic analysis, phytohormone, brassinosteroids, gene family, gene expression

References

• Anabousi, O.A.N., Hattar, B.J., Suwwan, M.A., 1997. Effect of rate and source of nitrogen on growth, yield and quality of potato (Solanum tuberosum) under jordon valley conditions. Agricultural Sciences, 24(2): 242-259.
• Anonymous, 2019a. Phytozome Database. (https:// phytozome.jgi.doe.gov/pz/portal.html), (Erişim tarihi: 18.09.2019).
• Anonymous, 2019b. Hidden Markov Model (HMM). (http://www.ebi.ac.uk), (Erişim tarihi: 18.09.2019).
• Anonymous, 2019c. Decrease Redundancy Tool. (http:// web.expasy.org/decrease_redundancy/), (Erişim tarihi: 18.09.2019).
• Anonymous, 2019d. HMMER. (http://www.ebi.ac.uk), (Erişim tarihi: 18.09.2019).
• Anonymous, 2019e. ProtParam. (http://web. expasy.org/protparam), (Erişim tarihi: 18.09.2019).
• Anonymous, 2019f. Plant Genome Duplication Database. (http://chibba.agtec.uga.edu/duplication/ index/locus), (Erişim Tarihi: 25.09.2019).
• Anonymous, 2019g. CIMMiner. (https://discover. nci.nih.gov/cimminer/), (Erişim tarihi: 02.10.2019).
• Bailey, T.L., Williams, N., Misleh, C., Li, W.W., 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34: W369-W373.
• Bajguz A., Hayat S., 2009. Effects of brassinosteroids on the plant responses to environmental stresses. Plant Physiol Biochem, 47(1): 1-8.
• Bhol, B.B., Rao G., Lenka, D.D., 1989. Relative efficiency of sources of nitrogen on the yield of potato. Indian Journal of Agronomy, 34(1): 132-133.
• Blanc, G., Wolfe, K.H., 2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. The Plant Cell, 16(7): 1679-1691.
• Campos, M.L., De Almeida, M., Rossi, M.L., Martinelli, A.P., Litholdo Junior, C.G., Figueira, A., Pereira, Peres, L.E., 2009. Brassinosteroids interact negatively with jasmonates in the formation of anti-herbivory traits in tomato. Journal of Experimental Botany, 60(15): 4347-4361.
• Clouse, S.D., 1996. Molecular genetic studies confirm the role of brassinosteroids in plant growth and development. Plant Journal, 10(1): 1-8.
• Crooks, G.E., Hon, G., Chandonia, J.M., Brenner, S.E., 2004. WebLogo: A sequence logo generator. Genome Research, 14(6): 1188-1190.
• Cusack, B.P., Wolfe, K.H., 2007. When gene marriages don’t work out: divorce by subfunctionalization. Trends in Genetics, 23(6): 270-272.
• Flagel, L.E., Wendel, J.F., 2009. Gene duplication and evolutionary novelty in plants. New Phytologist, 183(3): 557-564.
• Fujioka, S., Yokota, T., 2003. Biosynthesis and metabolism of brassinosteroids. Annual Review of Plant Biology, 54(1): 137-164.
• Glazebrook, J., 2001. Genes controlling expression of defense responses in Arabidopsis-2001 status. Current Opinion Plant Biology, 4(4): 301-308.
• Grenier, C., Bramel-Cox, P.J., Hamon, P., 2001. Core collection of sorghum: I. Stratification based on eco-geographical data. Crop Science, 41(1): 234-240.
• Guo, A., Zhu, Q., Chen, X., Luo, J., 2007. GSDS: a gene structure display server. Yi Chuan= Hereditas, 29(8): 1023-1026.
• Guo, R., Qian, H., Shen, W., Liu, L., Zhang, M., Cai, C., Zhao, Y., Qiao, J., Wang, Q., 2013. BZR1 and BES1 participate in regulation of glucosinolate biosynthesis by brassinosteroids in Arabidopsis. Journal of Experimental Botany, 64(8): 2401-2412.
• He, J.X., Gendron, J.M., Sun, Y., Gampala, S.S., Gendron, N., Sun, C.Q., Wang, Z.Y., 2005. BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses. Science, 307(5715): 1634-1638.
• Juretic, N., Hoen, D.R., Huynh, M.L., Harrison, P.M., Bureau, T.E., 2005. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Research, 15(9): 1292-1297.
• Kara, B., 2006. Çukurova koşullarında değişik bitki sıklıkları ve farklı azot dozlarında değişik bitki sıklıkları ve farklı azot dozlarında mısırın verim ve verim özellikleri ile azot alım ve kullanım etkinliğinin belirlenmesi. Doktora tezi, Çukurova Üniversitesi Fen Bilimleri Enstitüsü, Adana.
• Khripach, V., Zhabinskii, V., de Groot, A., 2000. Twenty years of brassinosteroids: steroidal plant hormones warrant better crops for the XXI century. Annals Botany, 86(3): 441-447.
• Kondrashov, F.A., Rogozin, I.B., Wolf, Y.I., Koonin, E.V., 2002. Selection in the evolution of gene duplications. Genome biology, 3(2002): research0008-1.
• Lee, T.H., Tang, H.B., Wang, X.Y., Paterson, A.H., 2013. PGDD: A database of gene and genome duplication in plants. Nucleic Acids Research, 41(D1): D1152-D1158.
• Li, B., Hu, Q., Xu, R., Ren, H., Fei, E., Chen, D., Wang, G., 2012. Hax-1 is rapidly degraded by the proteasome dependent on its PEST sequence. BMC Cell Biology, 13(1): 1-10.
• Li, J., Chory, J., 1999. Brassinosteroid actions in plants. Journal of Experimental Botany, 50(332): 275-282.
• Li, L., 2010. The mechanism and network of BES1 mediated transcriptional regulation in Brassinosteroids (BR) pathway in Arabidopsis. Graduate Theses and Dissertations, pp. 11326.
• Li, Q., Guo, L., Wang, H., Zhang, Y., Fan, C., Shen, Y., 2019. In silico genome-wide identification and comprehensive characterization of the BES1 gene family in soybean. Heliyon, 5(6): e01868.
• Lorenz, O.A., Weir, B.L., Bishop, J.C., 1974. Effect of sources of nitrogen on yield and nitrogen absorption of potatoes. American Potato Journal, 51(2): 56-65.
• Menz, M.A., Klein, R.R., Mullet, J.E., Obert, J.A., Unruh, N.C., Klein, P.E., 2002. A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers. Plant molecular biology, 48(5-6): 483-499.
• Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229): 551-556.
• Öztürk, E., Kara, K., Polat, T., 2007. Azotlu gübre formları ve uygulama zamanlarının patatesin verimi ile yumru büyüklüğü üzerine etkisi. Tekirdağ Ziraat Fakültesi Dergisi, 4(2): 127-135.
• Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., Lopez, R., 2005. InterProScan: Protein domains identifier. Nucleic Acids Research, 33(Suppl_2): W116-W120.
• Sharma, U.C., 1990. Effect of sources and methods of nitrogen application on yield and nitrogen uptake of potato (Solanum tuberosum) in Meghalaya. Indian Journal of Agricultural Sciences, 60(2): 119-122.
• Singh, D., Singh, M., Sandhu, H.S., 1979. Effects of different nitrogen sources and of biuret in urea on the growth and yield of potato and ıts nutrient uptake. Indian Journal of Agricultural Sciences, 49: 641-648.
• Smith, R.H., Bhaskaran, S., 1986. Sorghum [Sorghum bicolor (L.) Moench]. Crops I, pp: 220-233.
• Suyama, M., Torrents, D., Bork, P., 2006. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 34: W609-W612.
• Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731-2739.
• Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25(24): 4876-4882.
• Timm, H., Riekels, J.W., 1964. Growth, yield, and composition of onion, barley, and potato plants as affected by phosphorus and ammoniacal nitrogen fertilization. Agronomy Journal, 56(3): 335-340.
• Toledo-Ortiz, G., Huq, E., Quail, P.H., 2003. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 15(8): 1749-1770.
• Trapnell, C., Roberts, A., Goffl, O., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., Pachter, L., 2013. Differential gene and transcript expression analysis of RNAseq experiments with TopHat and Cufflinks. Nature Protocols, 7(3): 562-578.
• Voorrips, R.E., 2002. MapChart: Software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93(1): 77-78.
• Wang, Z.Y., Nakano, T., Gendron, J., He, J., Chen, M., Vafeados, D., Chory, J., 2002. Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Developmental Cell, 2(4): 505-513.
• Wendel, J.F., 2000. Genome evolution in polyploids. In Plant Molecular Evolution, 42: 225-249.
• Wu, P., Song, X., Wang, Z., Duan, W., Hu, R., Wang, W., Hou, X., 2016. Genome-wide analysis of the BES1 transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis). Plant Growth Regulation, 80(3): 291-301.
• Xu, G., Guo, C., Shan, H., Kong, H., 2012. Divergence of duplicate genes in exon–intron structure. Proceedings of the National Academy of Sciences, 109(4): 1187-1192.
• Xu, H., Ding, A., Chen, S., Marowa, P., Wang, D., Chen, M., Zhou, G., 2018. Genome-wide analysis of sorghum GT47 family reveals functional divergences of MUR3-like genes. Frontiers in Plant Science, 9: 1773.
• Yang, D.H., Hettenhausen, C., Baldwin, I.T., Wu, J., 2011. BAK1 regulates the accumulation of jasmonic acid and the levels of trypsin proteinase inhibitors in Nicotiana attenuata's responses to herbivory. Journal of Experimental Botany, 62(2): 641-652.
• Yang, Z.H., 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8): 1586-1591.
• Yin, Y., Vafeados, D., Tao, Y., Yoshida, S., Asami, T., Chory, J., 2005. A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell, 120(2): 249-259.
• Yin, Y., Wang, Z.Y., Mora-Garcia, S., Li, J., Yoshida, S., Asami, T., Chory, J., 2002. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell, 109(2): 181-191.
• Yu, X., Li, L., Li, L., Guo, M., Chory, J., Yin, Y., 2008. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proceedings of the National Academy of Sciences, 105(21): 7618-7623.
• Zhao, J., Peng, P., Schmitz, R.J., Decker, A.D., Tax, F.E., Li, J., 2002. Two putative BIN2 substrates are nuclear components of brassinosteroid signaling. Plant Physiology, 130(3): 1221-1229.
• Zheng, Y., Jiao, C., Sun, H., Rosli, H. G., Pombo, M. A., Zhang, P., Zhao, P.X., 2016. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant, 9(12): 1667-1670.