Identification of ABF/AREB Gene Family and Their Expression Analysis in Jujube Fruit

doi:10.13560/j.cnki.biotech.bull.1985.2024-0328

Abstract

Abstract:

【Objective】 ABFs（ABRE binding factors）/AREB（ABA responsive element binding）transcription factors, which not only participate in the plant stress response, but also affect the development of plants and fruits. Understanding its role in jujube fruit development provides a basis for further study of jujube ABF gene function. 【Method】 We conducted genome-wide identification of jujube ABF gene and analyzed the physicochemical analysis, subcellular localization, gene structure, motifs, phylogenetic relationships, promoter cis-acting elements and expression patterns. 【Result】 Five ABF genes were found in the jujube genome and located on five different pseudochromosomes. The length of the coding amino acid sequence of ZjABF was 321 to 474 aa, the isoelectric point was 7.75 to 9.85, the hydrophilic coefficient was between -0.807 and -0.592, and all five members were hydrophilic proteins. The instability coefficient ranged from 35.62 to 61.51. Gene structure and motif analysis showed that all ABF family members had UTR, containing 3 to 5 exons and 6 to 7 motifs. Phylogenetic trees grouped the ABF family into three large classes. Promoter cis-acting element analysis showed that jujube ABF gene family promoters had multiple cis-acting elements related to response hormones and abiotic stress. By analyzing the transcriptome data at different stages of fruit development, all ZjABFs except ZjABF4 were differently expressed, indicating that the ABF family played a regulatory role in fruit development. Interacting proteins of ZjABF3, ZjABF4, and ZjABF5 were predicted using homologous proteins. 【Conclusion】 The structure of ABF family in jujube is conserved, and there are multiple cis-acting elements in the promoter region that respond to hormones and abiotic stress, with different expression patterns during different stages of fruit development.

Key words: Ziziphus jujuba Mill., ABF/AREB gene family, bioinformatics analysis, fruit development

YANG Chong, CHENG Sha-sha, AI Chang-feng, ZHAO Xuan, LIU Meng-jun. Identification of ABF/AREB Gene Family and Their Expression Analysis in Jujube Fruit[J]. Biotechnology Bulletin, 2024, 40(11): 184-191.

Figures/Tables 7

Table 1 Physicochemical properties of jujube ABF

基因名称Gene name	基因编号 Gene ID	编码氨基酸长度 Length of encoded amino acids/aa	蛋白质分子量 Molecular weight of protein/kD	等电点 pI	染色体定位 Chromosome location	亲水性GRAVY	不稳定系数 Instability index	脂肪族氨基酸指数 Aliphatic index	亚细胞定位 Subcellular localization
ZjABF1	XP_048337122.1	436	46.24	9.85	Chr.9	-0.614	52.33	66.93	nucl: 14
ZjABF2	XP_060673229.1	470	50.76	7..75	Chr.5	-0.592	35.62	68.09	nucl: 14
ZjABF3	XP_015898748.2	438	48.07	8.47	Chr.11	-0.787	61.51	63.88	nucl: 14
ZjABF4	XP_015872556.3	474	52.64	8.82	Chr.10	-0.798	55.84	64.58	chlo: 6, pero: 5, nucl: 2.5, cyto_nucl: 2
ZjABF5	XP_048326228.1	321	35.58	8.5	Chr.8	-0.807	59.61	66.88	nucl: 14

Fig. 1 Analysis of gene structure of ABF gene family in jujube

Fig. 2 Analysis of conserved motif of ABF family protein in jujube

Fig. 3 Phylogenetic tree analysis of ABF families from jujube, Arabidopsis and peach（Prunus persica）

Fig. 4 Prediction of cis-acting elements of ABF genes in jujube

Fig. 5 Expression analysis of ABFs at different fruit development stages S1: Early stage of young fruit. S2: Middle stage of young fruit. S3: Pre hard core stage. S4: Hard core stage. S5: White ripening stage. S6: Late stage of white ripening. S7: Quarter coloring stage. S8: Half-red stage. S9: Full-red stage

Fig. 6 Interacting protein prediction of ABF in jujube A: The interacting protein prediction of ZjABF3. B: The interacting protein prediction of ZjABF4. C: The interacting protein prediction of ZjABF5

References 35

[1]	Liu MJ, Wang JR, Wang LL, et al. The historical and current research progress on jujube-a superfruit for the future[J]. Hortic Res, 2020, 7: 119.
[2]	Romera-Branchat M, Severing E, Pocard C, et al. Functional divergence of the Arabidopsis florigen-interacting bZIP transcription factors FD and FDP[J]. Cell Rep, 2020, 31(9): 107717.
[3]	Zou MJ, Guan YC, Ren HB, et al. A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance[J]. Plant Mol Biol, 2008, 66(6): 675-683.
[4]	Collin A, Daszkowska-Golec A, Szarejko I. Updates on the role of abscisic acid insensitive 5(ABI5)and abscisic acid-responsive element binding factors(ABFs)in ABA signaling in different developmental stages in plants[J]. Cells, 2021, 10(8): 1996.
[5]	Brocard IM, Lynch TJ, Finkelstein RR. Regulation and role of the Arabidopsis abscisic acid-insensitive 5 gene in abscisic acid, sugar, and stress response[J]. Plant Physiol, 2002, 129(4): 1533-1543.
[6]	Xiang Y, Tang N, Du H, et al. Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice[J]. Plant Physiol, 2008, 148(4): 1938-1952.
[7]	洪方蕾, 陆瑶, 俞世姣, 等. 桂花OfABFs基因克隆和表达分析[J]. 浙江农林大学学报, 2023, 40(3): 481-491.
	Hong FL, Lu Y, Yu SJ, et al. Cloning and expression analysis of OfABFs gene in Osmanthus fragrans[J]. J Zhejiang A F Univ, 2023, 40(3): 481-491.
[8]	Li FF, Mei FM, Zhang YF, et al. Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis[J]. BMC Plant Biol, 2020, 20(1): 558.
[9]	Liu TF, Zhou TT, Lian MT, et al. Genome-wide identification and characterization of the AREB/ABF/ABI5 subfamily members from Solanum tuberosum[J]. Int J Mol Sci, 2019, 20(2): 311.
[10]	Yong X, Zheng TC, Zhuo XK, et al. Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei(Prunus mume)[J]. PeerJ, 2021, 9: e10785.
[11]	庞少萍, 董翠翠, 马岩岩, 等. CsAREB转录因子在柑橘果实发育中的作用[J]. 园艺学报, 2017, 44(3): 441-451.
	Pang SP, Dong CC, Ma YY, et al. The roles of two CsAREB transcription factors in the development of citrus fruit[J]. Acta Hortic Sin, 2017, 44(3): 441-451.
[12]	杨玲. 烟草ABF转录因子基因的克隆及功能分析[D]. 重庆: 重庆大学, 2014.
	Yang L. Cloning and functional analysis of ABF transcription factor gene in Nicotiana tabacum[D]. Chongqing: Chongqing University, 2014.
[13]	涂明星. 葡萄转录因子VlbZIP30抗旱功能及其调控机理研究[D]. 杨凌: 西北农林科技大学, 2021
	Tu MX. Drought resistance function and regulation mechanism analysis of grapevine transcription factor VlbZIP30 gene[D]. Yangling: Northwest A&F University, 2021.
[14]	Yang XL, Yue YZ, Li HY, et al. The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans[J]. Hortic Res, 2018, 5: 72.
[15]	郭树娟, 孙月, 郑昊元, 等. 小麦ABF/AREB/ABI5基因家族全基因组鉴定与表达分析[J]. 农业生物技术学报, 2023, 31(4): 667-681.
	Guo SJ, Sun Y, Zheng HY, et al. Genome-wide identification and expression analysis of ABF/AREB/ABI5 gene family in Wheat(Triticum aestivum)[J]. J Agric Biotechnol, 2023, 31(4): 667-681.
[16]	Mou WS, Li DD, Bu JW, et al. Comprehensive analysis of ABA effects on ethylene biosynthesis and signaling during tomato fruit ripening[J]. PLoS One, 2016, 11(4): e0154072.
[17]	牟望舒. 脱落酸及脱落酸-乙烯互作调控番茄果实成熟的效应与机理[D]. 杭州: 浙江大学, 2019.
	Mou WS. The roles and mechanism of abscisic acid and abscisic acid-ethylene crosstalk in the regulation of tomato fruit ripening[D]. Hangzhou: Zhejiang University, 2019.
[18]	方燕. AREB/ABF/ABI5 基因家族调控草莓果实成熟机理解析[D]. 合肥: 安徽农业大学, 2020.
	Fang Y. Analysis of mechanism of strawberry fruit ripening regulated by AREB/ABF/ABI5 gene family[D]. Hefei: Anhui Agricultural University, 2020.
[19]	苟琦敏, 王新文, 马建忠. 拟南芥ABI5亚家族转录因子-回顾与展望[J]. 植物生理学报, 2022, 58(6): 1068-1076.
	Gou QM, Wang XW, Ma JZ. The ABI5 subfamily transcription factors in Arabidopsis thaliana: retrospect and prospect[J]. Plant Physiol J, 2022, 58(6): 1068-1076.
[20]	Zhang Y, Gao WL, Li HT, et al. Genome-wide analysis of the bZIP gene family in Chinese jujube(Ziziphus jujuba Mill.)[J]. BMC Genomics, 2020, 21(1): 483.
[21]	李天杰, 吴颖, 高龙飞, 等. 蓝莓ABF转录因子VcABF2基因的克隆与表达分析[J]. 分子遗传育种, 2021: 1-14.
	Li TJ, Wu Y, Gao LF, et al. Cloning and expression analysis of ABF transcription factor gene VcABF2 in Blueberry[J]. Mol Plant Breed, 2021: 1-14.
[22]	靳蜜静. 脱落酸处理对猕猴桃果实抗冷性的影响及转录因子Achn ABF1的功能研究[D]. 杨凌: 西北农林科技大学, 2021.
	Jin MJ. Effects of abscisic acid treatment on cold resistance of Kiwifruit and functional identification of transcription factor Achn ABF1[D]. Yangling: Northwest A&F University, 2021.
[23]	徐子健. 脱落酸及转录因子SlAREB1调控番茄盐碱和低温抗性的机制研究[D]. 杨凌: 西北农林科技大学, 2022.
	Xu ZJ. The mechanism of abscisic acid and transcription factor SlAREB1 in regulating saline-alkaline and low-temperature tolerance in tomato[D]. Yangling: Northwest A&F University, 2022.
[24]	王双成. 苹果属垂丝海棠MhABF和MhPYL基因的克隆及耐盐碱性功能鉴定[D]. 兰州: 甘肃农业大学, 2022.
	Wang SC. Cloning of MhABF and MhPYL genes and identification of their saline-alkali tolerance function in Malus halliana[D]. Lanzhou: Gansu Agricultural University, 2022.
[25]	陈乃钰, 张国香, 张力爽, 等. ABF转录因子在植物响应非生物胁迫中的作用[J]. 植物遗传资源学报, 2021, 22(4): 930-938.
	Chen NY, Zhang GX, Zhang LS, et al. Chang-hong, The role of ABF transcription factors in response to abiotic stress in plant[J]. J Plant Genet Resour, 2021, 22(4): 930-938.
[26]	Contreras-López O, Vidal EA, Riveras E, et al. Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate[J]. Proc Natl Acad Sci USA, 2022, 119(4): e2107879119.
[27]	Yang YL, Li HG, Wang J, et al. ABF3 enhances drought tolerance via promoting ABA-induced stomatal closure by directly regulating ADF5 in Populus euphratica[J]. J Exp Bot, 2020, 71(22): 7270-7285.
[28]	Li XY, Liu X, Yao Y, et al. Overexpression of Arachis hypogaea AREB1 gene enhances drought tolerance by modulating ROS scavenging and maintaining endogenous ABA content[J]. Int J Mol Sci, 2013, 14(6): 12827-12842.
[29]	Nitsch L, Kohlen W, Oplaat C, et al. ABA-deficiency results in reduced plant and fruit size in tomato[J]. J Plant Physiol, 2012, 169(9): 878-883.
[30]	Sun L, Sun YF, Zhang M, et al. Suppression of 9-cis-epoxycarotenoid dioxygenase, which encodes a key enzyme in abscisic acid biosynthesis, alters fruit texture in transgenic tomato[J]. Plant Physiol, 2012, 158(1): 283-298.
[31]	Wang SS, Saito T, Ohkawa K, et al. Abscisic acid is involved in aromatic ester biosynthesis related with ethylene in green apples[J]. J Plant Physiol, 2018, 221: 85-93.
[32]	崔春晓. 番茄成熟过程中ABA相关转录因子调控乙烯合成的研究[D]. 郑州: 河南工业大学, 2023.
	Cui CX. Regulations of ethylene synthesisby ABA-regulated transcription factors during tomato fruit ripening[D]. Zhenzhou: Henan University of Technology, 2023.
[33]	Wu Q, Tao XY, Ai XZ, et al. Contribution of abscisic acid to aromatic volatiles in cherry tomato(Solanum lycopersicum L.) fruit during postharvest ripening[J]. Plant Physiol Biochem, 2018, 130: 205-214.
[34]	邓璇. 转录因子MaJOINTLESS及上游调控因MaABI5、MaABF1在桑葚落果中的功能研究[D]. 重庆: 西南大学, 2023.
	Deng X. Study on the Function of transcription factor MaJOINTLESS and upstream regulatory factors MaABI5 and MaABF1 during fruit abscission in mulberry(Morus alba L.)[D]. Chongqing: Southwest University, 2023
[35]	Feng G, Wu J, Xu Y, et al. High-spatiotemporal-resolution transcriptomes provide insights into fruit development and ripening in Citrus sinensis[J]. Plant Biotechnol J, 2021, 19: 1337-1353.