Identification, Expression and Interacting Protein Analysis of WOX Gene Family in Phalaenopsis equestris
ZHANG Ting, SHI Zi-Hao, ZHENG Tian-Tian, YU Xin, XU Yan, YI Qing-Ping, ZHU De-Yan*
College of Food and Biology/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen 448000, China
Abstract：WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor family with important regulatory roles in plant growth and stress adaptation. Phalaenopsis equestris is a widely cultivated flower and of great economic importance in orchids. The identification and analysis of WOX family members is helpful to speculate its function in P. equestris development. Ten members of PeWOX family were characterized by bioinformatics analysis in this study, which were low hydrophilic proteins and most were localized in the nucleus. Phylogenetic analysis showed that PeWOX13A and PeWOX13B belonged to ancient clade, PeWOX9, PeWOX11, and PeWOX12 belonged to intermediate clade, and others belonged to modern clade. Members of 3 clades showed obvious differences in protein structure. Expression profiling of PeWOX genes by qRT-PCR revealed their tissue-specific expression, suggesting that they might have functionally differentiation and were responsible for different organ development. Promoter analysis and the response of PeWOX genes to hormones and stresses by qRT-PCR suggested that PeWOX members were involved in the hormonal and stress response pathways. Interaction protein analysis revealed interaction relationships between PeWOX proteins and other transcription factors, epigenetic modifiers, and kinases, indicating that PeWOXs might have complex regulatory mechanisms. This study provides valuable information for further exploration of PeWOX function.
[1] Cai J, Liu X, Vanneste K, et al.2015. The genome sequence of the orchid Phalaenopsis equestris[J]. Nature Genetics, 47(1): 65-72. [2] Chen R, Xu N, Yu B, et al.2020. The WUSCHEL-related homeobox transcription factor OsWOX4 controls the primary root elongation by activating OsAUX1 in rice[J]. Plant Science, 298: 110575. [3] Cheng S, Tan F, Lu Y, et al.2018. WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice[J]. Nucleic Acids Research, 46(5): 2356-2369. [4] Cheng S, Zhou D X, Zhao Y.2016. WUSCHEL-related homeobox gene WOX11 increases rice drought resistance by controlling root hair formation and root system development[J]. Plant Signal & Behavior, 11(2): e1130198. [5] Gehring W J, Müller M, Affolter M, et al.1990. The structure of the homeodomain and its functional implications[J]. Trends in Genetics, 6(10): 323-329. [6] Geng L, Tan M, Deng Q, et al.2024. Transcription factors WOX11 and LBD16 function with histone demethylase JMJ706 to control crown root development in rice[J]. Plant Cell, 36(5): 1777-1790. [7] Gong X, Zhang T, Xing J, et al.2019. Positional effects on efficiency of CRISPR/Cas9-based transcriptional activation in rice plants[J]. aBIOTECH, 1(1): 1-5. [8] Guo L, Cao X, Liu Y, et al.2018. A chromatin loop represses WUSCHEL expression in Arabidopsis[J]. Plant Journal, 94(6): 1083-1097. [9] Honda E, Yew C L, Yoshikawa T, et al.2018. LEAF LATERAL SYMMETRY1, a member of the WUSCHEL-RELATED HOMEOBOX3 gene family, regulates lateral organ development differentially from other paralogs, NARROW LEAF2 and NARROW LEAF3 in rice[J]. Plant Cell Physiology, 59(2): 376-391. [10] Jiang G, Li Z, Ding X, et al.2024. WUSCHEL-related homeobox transcription factor SlWOX13 regulates tomato fruit ripening[J]. Plant Physiology, 194(4): 2322-2337. [11] Kawai T, Shibata K, Akahoshi R, et al.2022. WUSCHEL-related homeobox family genes in rice control lateral root primordium size[J]. Proceedings of the National Academy of Sciences of the USA, 119(1): e2101846119. [12] Laux T, Mayer K F, Berger J, et al.1996. The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis[J]. Development, 122(1): 87-96. [13] Li H, Li C, Wang Y, et al.2022. Genome-wide analysis of the WOX transcription factor genes in Dendrobium catenatum Lindl[J]. Genes (Basel), 13(8): 1481. [14] Liu M, Lei L, Miao F, et al.2018. The STENOFOLIA gene from Medicago alters leaf width, flowering time and chlorophyll content in transgenic wheat[J]. Plant Biotechnology, 16(1): 186-196. [15] Minh-Thu P T, Kim J S, Chae S, et al.2018. A WUSCHEL homeobox transcription factor, OsWOX13, enhances drought tolerance and triggers early flowering in rice[J]. Molecules and Cells, 41(8): 781-798. [16] Tsai W C, Lee P F, Chen H I, et al.2005. PeMADS6, a GLOBOSA/PISTILLATA-like gene in Phalaenopsis equestris involved in petaloid formation, and correlated with flower longevity and ovary development[J]. Plant & Cell Physiology, 46(7): 1125-1139. [17] Wang C, Zhao B, He L, et al.2021. The WOX family transcriptional regulator SlLAM1 controls compound leaf and floral organ development in Solanum lycopersicum[J]. Experimental Botany, 72(5): 1822-1835. [18] Wang Z, Cai Q, Xia H, et al.2022a. Genome-wide identification and comparative analysis of WOX genes in four euphorbiaceae species and their expression patterns in Jatropha curcas[J]. Frontiers in Genetics, 13: 878554. [19] Wang H, Li X, Wolabu T, et al.2022b. WOX family transcriptional regulators modulate cytokinin homeostasis during leaf blade development in Medicago truncatula and Nicotiana sylvestris[J]. Plant Cell, 34(10): 3737-3753. [20] Wu Y, Meng Y, Zhang L, et al.2024. PeFtsH5 negatively regulates the biological stress response in Phalaenopsis equestris mitochondria[J]. Plant Physiology, 292: 154159. [21] Xing L, Qi S, Zhou H, et al.2020. Epigenomic regulatory mechanism in vegetative phase transition of Malus hupehensis[J]. Agricultural and Food Chemistry, 68(17): 4812-4829. [22] Yang Y, Ren Z, Li L, et al.2024. WOX2 functions redundantly with WOX1 and WOX4 to positively regulate seed germination in Arabidopsis[J]. Planta, 259(4): 83. [23] Youngstrom C E, Withers K A, Irish E E, et al.2022. Vascular function of the T3/modern clade WUSCHEL-Related HOMEOBOX transcription factor genes predate apical meristem-maintenance function[J]. BMC Plant Biology, 22(1): 210. [24] Yuan H Y, Kagale S, Ferrie A M.2024. Multifaceted roles of transcription factors during plant embryogenesis[J]. Frontiers in Plant Science, 14: 1322728. [25] Zhang C, Wang J, Wang X, et al.2020. UF, a WOX gene, regulates a novel phenotype of un-fused flower in tomato[J]. Plant Science, 297: 110523. [26] Zhang D, Lan S, Yin W L, et al.2022. Genome-wide identification and expression pattern analysis of KNOX gene family in Orchidaceae[J]. Frontiers in Plant Science, 13: 901089. [27] Zhang F, Wang H, Kalve S, et al.2019. Control of leaf blade outgrowth and floral organ development by LEUNIG, ANGUSTIFOLIA3 and WOX transcriptional regulators[J]. New Phytologist, 223(4): 2024-2038. [28] Zhang F, Wang Y, Li G, et al.2014. STENOFOLIA recruits TOPLESS to repress ASYMMETRIC LEAVES2 at the leaf margin and promote leaf blade outgrowth in Medicago truncatula[J]. Plant Cell, 26(2): 650-664. [29] Zhang X, Zong J, Liu J, et al.2010. Genome-wide analysis of WOX gene family in rice, sorghum, maize, Arabidopsis and poplar[J]. Integrative Plant Biology, 52(11): 1016-1026. [30] Zhao Y, Hu Y, Dai M, et al.2009. The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice[J]. Plant Cell, 21(3): 736-748. [31] Zhou J, Qiao J, Wang J, et al.2022. OsQHB improves salt tolerance by scavenging reactive oxygen species in rice[J]. Frontier in Plant Science, 13: 848891. [32] Zhou S, Jiang W, Long F, et al.2017. Rice homeodomain protein WOX11 recruits a histone acetyltransferase complex to establish programs of cell proliferation of crown root meristem[J]. Plant Cell, 29(5): 1088-1104.
