Genome wide bioinformatics analysis BES1 gene family in Vitis vinifera L.

Ladan Moghdam, Alireza

doi:10.30473/cb.2020.54046.1813

Genome wide bioinformatics analysis BES1 gene family in Vitis vinifera L.

Document Type : Research Paper

Author

Alireza Ladan Moghdam

Department of Horticulture, Garmsar Branch, Islamic Azad University, Garmsar, Iran

10.30473/cb.2020.54046.1813

Abstract

Brassinosteroids (BRs) are the plant-specific steroidal hormones that regulate a broad spectrum of plant growth and developmental processes under normal conditions and various biotic, and abiotic stresses. BES1 transcription factors regulate the expression of brassinosteroid-responsive genes. Completion of the grape genome sequencing enabled us to undertake a genome-wide identification of the gene families in this plant. Therefore, we performed a genome-wide investigation of BES genes in grape. The physicochemical properties, phylogeny tree, gene structure, conserved motifs, cis-acting elements, miRNA, and gene chip expression of the grape BES1 transcription factors were analyzed using the bioinformatics tools. The results showed that the grape BES1 transcription factors had seven members, which clustered into three subgroups according to the phylogenetic analysis. Each subgroup was well defined by the conserved motifs, implying that close genetic relationships could be identified among the members of each subgroup. According to the chromosomal locations, 1, 1, 2, 1, 1, and 1 genes were located on chromosomes 2, 4, 10, 15, 18, and 19, respectively. The analysis of cis-acting elements indicated that BES1 genes contained response elements of hormones and abiotic stresses, as well as organ-specific elements. The miRNA target analysis indicated that VvBES1-1, VvBES1-3, and VvBES1-5 contained miRNA target position in grape. Gene chip expression profile analysis revealed that the expression patterns of the grape BES1 genes were different in different organs and developmental stages. The analysis of this gene family would provide some theoretical basis for understanding the evolution and function of the BES1 genes in the grape.

Keywords

20.1001.1.22520783.1399.10.30.6.0

Main Subjects

Bioinformatics

References

Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, De Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E (2012) ExPASy: SIB bioinformatics resource portal. Nucleic acids research. 40 (W1): W597-W603.

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 research. 37 (suppl_2): W202-W208.

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M (2012) NCBI GEO: archive for functional genomics data sets-update. Nucleic acids research. 41 (D1): D991-D995.

Cao X, Khaliq A, Lu S, Xie M, Ma Z, Mao J, Chen B (2020) Genome‐wide identification and characterization of the BES1 gene family in apple (Malus domestica). Plant Biology.

Century K, Reuber TL, Ratcliffe O (2008) Regulating the regulators: the future prospects for transcription-factor-based agricultural biotechnology products. Plant physiology. 147 (1): 20-29.

Clouse SD (2011) Brassinosteroid signal transduction: from receptor kinase activation to transcriptional networks regulating plant development. The Plant Cell. 23 (4): 1219-1230.

Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic acids research. 46 (W1): W49-W54.

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A (2019) The Pfam protein families database in 2019. Nucleic acids research. 47 (D1): D427-D432.

Feng Y, Yin Y, Fei S (2015) Down-regulation of BdBRI1, a putative brassinosteroid receptor gene produces a dwarf phenotype with enhanced drought tolerance in Brachypodium distachyon. Plant Science .234: 163-173.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2012) Phytozome: a comparative platform for green plant genomics. Nucleic acids research. 40 (D1): D1178-D1186.

Haider MS, Jogaiah S, Pervaiz T, Yanxue Z, Khan N, Fang J (2019) Physiological and transcriptional variations inducing complex adaptive mechanisms in grapevine by salt stress. Environmental Experimental Botany. 162: 455-467.

Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G (2015) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 31 (8): 1296-1297.

Jiang J, Zhang C, Wang X (2015) A recently evolved isoform of the transcription factor BES1 promotes brassinosteroid signaling and development in Arabidopsis thaliana. The Plant Cell. 27 (2): 361-374.

Jiang K, Asami T (2018) Chemical regulators of plant hormones and their applications in basic research and agriculture. Bioscience, biotechnology, biochemistry. 82 (8): 1265-1300.

Jiu S, Xu Y, Wang J, Wang L, Wang S, Ma C, Guan L, Abdullah M, Zhao M, Xu W (2019) Genome-wide Identification, Characterization and Transcript Analysis of the TCP Transcription Factors in Vitis vinifera. Frontiers in genetics. 10: 1276.

Koul A, Sharma D, Kaul S, Dhar MK (2019) Identification and in silico characterization of cis-acting elements of genes involved in carotenoid biosynthesis in tomato. 3 Biotech. 9 (7): 287.

Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology evolution. 33 (7): 1870-1874.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics. 23 (21): 2947-2948.

Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, 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.

Li J, Nagpal P, Vitart V, McMorris TC, Chory J (1996) A role for brassinosteroids in light-dependent development of Arabidopsis. Science 272 (5260):398-401

Li J, Nam KH, Vafeados D, Chory J (2001) BIN2, a new brassinosteroid-insensitive locus in Arabidopsis. Plant physiology. 127 (1): 14-22.

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.

Li Y, He L, Li J, Chen J, Liu C (2018) Genome-wide identification, characterization, and expression profiling of the legume BZR transcription factor gene family. Frontiers in plant science. 9: 1332.

Liang T, Mei S, Shi C, Yang Y, Peng Y, Ma L, Wang F, Li X, Huang X, Yin Y (2018) UVR8 interacts with BES1 and BIM1 to regulate transcription and photomorphogenesis in Arabidopsis. Developmental cell. 44 (4): 512-523.

Liu B, Ouyang Z, Zhang Y, Li X, Hong Y, Huang L, Liu S, Zhang H, Li D, Song F (2014) Tomato NAC transcription factor SlSRN1 positively regulates defense response against biotic stress but negatively regulates abiotic stress response. PLoS One. 9 (7): e102067.

Liu Z, Qanmber G, Lu L, Qin W, Liu J, Li J, Ma S, Yang Z, Yang Z (2018) Genome-wide analysis of BES1 genes in Gossypium revealed their evolutionary conserved roles in brassinosteroid signaling. Science China Life Sciences. 61 (12): 1566-1582.

Long M, Deutsch M (1999) Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Molecular biology evolution. 16 (11): 1528-1534.

Lopez‐Molina L, Mongrand S, McLachlin DT, Chait BT, Chua NH (2002) ABI5 acts downstream of ABI3 to execute an ABA‐dependent growth arrest during germination. The Plant Journal. 32 (3): 317-328.

Luo X-M, Lin W-H, Zhu S, Zhu J-Y, Sun Y, Fan X-Y, Cheng M, Hao Y, Oh E, Tian M (2010) Integration of light-and brassinosteroid-signaling pathways by a GATA transcription factor in Arabidopsis. Developmental cell. 19 (6): 872-883.

Lv J, Li Y, Liu Z, Li X, Lei X, Gao C (2020) Response of BpBZR genes to abiotic stress and hormone treatment in Betula platyphylla. Plant Physiology Biochemistry. 151: 157-165.

Manoli A, Trevisan S, Quaggiotti S, Varotto S (2018) Identification and characterization of the BZR transcription factor family and its expression in response to abiotic stresses in Zea mays L. Plant growth regulation. 84 (3): 423-436.

Metsalu T, Vilo J (2015) ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic acids research. 43 (W1): W566-W570.

Nolan T, Chen J, Yin Y (2017) Cross-talk of Brassinosteroid signaling in controlling growth and stress responses. Biochemical Journal. 474 (16): 2641-2661.

Peres ALG, Soares JS, Tavares RG, Righetto G, Zullo MA, Mandava NB, Menossi M (2019) Brassinosteroids, the sixth class of phytohormones: a molecular view from the discovery to hormonal interactions in plant development and stress adaptation. International Journal of Molecular Sciences. 20 (2): 331.

Roy SW, Penny D (2007) A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Molecular biology evolution. 24 (7): 1447-1457.

Ruvinsky A, Eskesen S, Eskesen F, Hurst L (2005) Can codon usage bias explain intron phase distributions and exon symmetry? Journal of molecular evolution. 60 (1): 99-104.

Saha G, Park JI, Jung HJ, Ahmed NU, Kayum MA, Kang JG, Nou (2015) Molecular characterization of BZR transcription factor family and abiotic stress induced expression profiling in Brassica rapa. Plant Physiology Biochemistry. 92: 92-104.

Sami Z, Alemzadeh A (2016) Isolation and molecular characterization of a novel Na+/H+ antiporter gene, AlNHX2, from'Aeluropus littoralis' and comparison of AlNHX1 and AlNHX2. Plant Omics. 9 (3): 205.

Sharma R, De Vleesschauwer D, Sharma MK, Ronald PC (2013) Recent advances in dissecting stress-regulatory crosstalk in rice. Molecular Plant. 6 (2): 250-260.

Song X, Ma X, Li C, Hu J, Yang Q, Wang T, Wang L, Wang J, Guo D, Ge W (2018) Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. BMC genomics. 19 (1): 346.

Sun Y, Fan X-Y, Cao D-M, Tang W, He K, Zhu J-Y, He J-X, Bai M-Y, Zhu S, Oh E (2010) Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Developmental cell. 19 (5): 765-777.

Sunkar R, Jagadeeswaran G (2008) In silicoidentification of conserved microRNAs in large number of diverse plant species. BMC plant biology. 37 (1): 8.

Tang W, Yuan M, Wang R, Yang Y, Wang C, Oses-Prieto JA, Kim T-W, Zhou H-W, Deng Z, Gampala SS (2011) PP2A activates brassinosteroid-responsive gene expression and plant growth by dephosphorylating BZR1. Nature cell biology. 13 (2): 124-131.

Waese J, Provart NJ (2016) The Bio-Analytic Resource: Data visualization and analytic tools for multiple levels of plant biology. Current Plant Biology. 7: 2-5.

Wang W, Sun Y-Q, Li G-L, Zhang S-Y (2019) Genome-wide identification, characterization, and expression patterns of the BZR transcription factor family in sugar beet (Beta vulgaris L.). BMC plant biology. 19 (1): 191.

Wang Z-Y, Nakano T, Gendron J, He J, Chen M, Vafeados D, Yang Y, Fujioka S, Yoshida S, Asami T (2002) Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Developmental cell. 2 (4): 505-513.

Wani SH, Kumar V, Khare T, Tripathi P, Shah T, Ramakrishna C, Aglawe S, Mangrauthia SK (2020) miRNA applications for engineering abiotic stress tolerance in plants. Biologia. 1-19.

Wu P, Song X, Wang Z, Duan W, Hu R, Wang W, Li Y, 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.

Yang C-J, Zhang C, Lu Y-N, Jin J-Q, Wang X-L (2011) The mechanisms of brassinosteroids' action: from signal transduction to plant development. Molecular plant. 4 (4): 588-600.

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.

Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins: Structure, Function, Bioinformatic. 64 (3): 643-651.

Yu H, Feng W, Sun F, Zhang Y, Qu J, Liu B, Lu F, Yang L, Fu F, Li W (2018) Cloning and characterization of BES1/BZR1 transcription factor genes in maize. Plant growth regulation. 86 (2): 235-249.

Yu H, Sun F, Feng W, Lu F, Li W, Fu FYc (2019) The BES1/BZR1 transcription factors regulate growth, development and stress resistance in plants. Hereditas. 41 (3): 206-214.

Zhang C, Xian Z, Huang W, Li Z (2015) Evidence for the biological function of miR403 in tomato development. Scientia Horticulturae. 197: 619-626.

Zhang X, Guo W, Du D, Pu L, Zhang C (2020) Overexpression of a maize BR transcription factor ZmBZR1 in Arabidopsis enlarges organ and seed size of the transgenic plants. Plant Science. 292: 110378.

Zhao J, Zhai Z, Li Y, Geng S, Song G, Guan J, Jia M, Wang F, Sun G, Feng N (2018) Genome-wide identification and expression profiling of the TCP family genes in spike and grain development of wheat (Triticum aestivum L.). Frontiers in Plant Science. 9: 1282.

Zhao Y, Wen H, Teotia S, Du Y, Zhang J, Li J, Sun H, Tang G, Peng T, Zhao Q (2017) Suppression of microRNA159 impacts multiple agronomic traits in rice (Oryza sativa L.). BMC plant biology. 17 (1): 215.

Zhou Y, Yuan C, Ruan S, Zhang Z, Meng J, Xi Z (2018) Exogenous 24-epibrassinolide interacts with light to regulate anthocyanin and proanthocyanidin biosynthesis in cabernet sauvignon (Vitis vinifera L.). Molecules. 23 (1): 93.