Genome-wide in silico identification, characterization and transcriptional analysis of the family of growth-regulating factors in common bean (Phaseolus vulgaris l.) subjected to polyethylene glycol-induced drought stress
Keywords:growth regulating factor, PhvGRF, drought stress, genome-wide in silico identification, common bean
According to most recent findings, growth regulating factors (GRFs) are plant-specific transcription factors (TFs) that play important roles in many processes, including abiotic and biotic stress response mechanisms. Completion of the common bean (Phaseolus vulgaris) genome project has provided researchers with the opportunity to identify all GRF genes in this species. With this aim, a genome-wide in silico study was performed and 10 GRF proteins (called PhvGRFs) were identified in the common bean genome. Conserved and mandatory motifs (QLQ and WRC) were confirmed in all identified PhvGRFs and two segmental duplication events were determined. Most of the PhvGRFs were found to be more similar to Arabidopsis thaliana GRFs than to Zea mays GRFs in a phylogenetic tree. According to the expression analysis of 10 PhvGRFs, inversely related expression patterns were observed in the roots of Yakutiye and Zulbiye cultivars based on their capacity to adopt to drought stress. After drought treatment of the Zulbiye cultivar, a drought-sensitive common bean cultivar, PhvGRF1, PhvGRF2, PhvGRF3, PhvGRF5, PhvGRF6, PhvGRF9 and PhvGRF10 genes were upregulated 2- to 4-fold in root tissues, as compared to the untreated control. The trend of PhvGRF1, PhvGRF2, PhvGRF3, PhvGRF5, PhvGRF6, PhvGRF7, PhvGRF9 and PhvGRF10 genes showed a consistent decline of 2- to 6-fold in root tissues of the drought-tolerant Yakutiye cultivar subjected to 24 h of drought stress. We demonstrated that the expression patterns of the identified PhvGRFs correlated with the drought-stress response in a cultivar-specific manner in the common bean. We suggest that members of the GRF family can also be used for genetic engineering applications in the common bean.
Received: February 4, 2016; Revised: March 21, 2016; Accepted: March 25, 2016; Published online: April 4, 2016
How to cite this article: Büyük İ, Aras S. Genome-wide in silico identification, characterization and transcriptional analysis of the family of growth-regulating factors in common bean (Phaseolus vulgaris l.) subjected to polyethylene glycolinduced drought stress. Arch Biol Sci. 2017;69(1):5-14.
Van der Knaap E, Kim JH, Kende H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant Physiol. 2000;122(3):695-704.
Liu H, Guo S, Xu Y, Li C, Zhang Z, Zhang D, Xu S, Zhang C, Chong K. OsmiR396d-regulated OsGRFs function in floral organogenesis in rice through binding to their targets OsJMJ706 and OsCR4. Plant Physiol. 2014;165(1):160-74.
Pajoro A, Madrigal P, Muino JM, Matus JT, Jin J, Mecchia MA, Debernardi JM, Palatnik JF, Balazadeh S, Arif M, Ó’Maoiléidigh DS, Wellmer F, Krajewski P, Riechmann JL, Angenent GC, Kaufmann K. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol. 2014;15(3):R41.
Omidbakhshfard MA, Proost S, Fujikura U, Mueller-Roeber B. Growth-Regulating Factors (GRFs): A small transcription factor family with important functions in plant biology. Mol Plant. 2015;8(7):998-1010.
Kim JS, Mizoi J, Kidokoro S, Maruyama K, Nakajima J, Nakashima K, Mitsuda N, Takiguchi Y, Ohme-Takagi M, Kondou Y, Yoshizumi T, Matsui M, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis growth-regulating factor7 functions as a transcriptional repressor of abscisic acid- and osmotic stress-responsive genes, including DREB2A. Plant Cell. 2012;24(8):3393-405.
Hewezi T, Maier TR, Nettleton D, Baum TJ. The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant Physiol. 2012;159(1):321-35.
Zhang DF, Li B, Jia GQ, Zhang TF, Dai JR, Li JS, Wang SC. Isolation and characterization of genes encoding GRF transcription factors and GIF transcriptional coactivators in maize (Zea mays L.). Plant Sci. 2008;175(6):809-17.
Yang FX, Liang G, Liu DM, Yu DQ. Arabidopsis MiR396 Mediates the development of leaves and flowers in transgenic tobacco. J Plant Biol. 2009;52(5):475-81.
Osnato M, Stile MR, Wang Y, Meynard D, Curiale S, Guiderdoni E, Liu Y, Horner DS, Ouwerkerk PB, Pozzi C, Müller KJ, Salamini F, Rossini L. Cross talk between the KNOX and ethylene pathways is mediated by intron-binding transcription factors in barley. Plant Physiol. 2010;154(4):1616-32.
Baloglu MC, Eldem V, Hajyzadeh M, Unver T. Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS One. 2014;9(4):e96014.
Filiz E, Koc I, Ozyigit, II. Comparative analysis and modeling of superoxide dismutases (SODs) in Brachypodium distachyon L. Appl Biochem Biotechnol. 2014;173(5):1183-96.
Kuijt SJ, Greco R, Agalou A, Shao J, t Hoen CC, Overnas E, Osnato M, Curiale S, Meynard D, van Gulik R, de Faria Maraschin S, Atallah M, de Kam RJ, Lamers GE, Guiderdoni E, Rossini L, Meijer AH, Ouwerkerk PB. Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors. Plant Physiol. 2014;164(4):1952-66.
Wang F, Qiu N, Ding Q, Li J, Zhang Y, Li H, Gao J. Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics. 2014;15:807.
Choi D, Kim JH, Kende H. Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice (Oryza sativa L.). Plant Cell Physiol. 2004;45(7):897-904.
Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J. PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res. 2011;39:D1114-D1117.
Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2012;40:D302-D305.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290-D301.
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;3:W202-W208.
Thompson JD, Higgins DG, Gibson TJ. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673-80.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731-9.
Yang S, Zhang X, Yue JX, Tian D, Chen JQ. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics. 2008;280(3):187-98.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674-6.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25(4):402-8.
Zhang JZ. Evolution by gene duplication: an update. Trends in Ecology & Evolution. 2003;18(6):292-8.
Casati P. Analysis of UV-B regulated miRNAs and their targets in maize leaves. Plant Signal Behav. 2013;8(10):e26758.
Pucholt P, Sjodin P, Weih M, Ronnberg-Wastljung AC, Berlin S. Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes. BMC Plant Biol. 2015;15:244.
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