参薯BBR-BPC基因家族的挖掘和特征分析

Identification and characteristic analysis of BBR-BPC gene family in greater yam (Dioscorea alata L.)

摘要

为了解参薯(Dioscorea alata)中BBR-BPC基因家族对其生长发育的调控作用，对参薯BBR-BPC基因家族的基因结构、系统进化、保守基序和编码蛋白理化性质进行分析，同时对BBR-BPC蛋白二级、三级结构进行预测，并验证了BBR-BPC基因与DELLA基因之间的互作关系。通过HMMsearch和BLAST分析，共在参薯基因组鉴定了6个BBR-BPC家族成员。这些基因蛋白特性存在差别明显，且存在可变剪切，共检测到10个剪接本。亚细胞定位分析发现，参薯BBR-BPC家族在细胞核内均有定位。Da4BBR-BPC2与参薯DaDELLA2的酵母双杂互作结果表明，Da4BBR-BPC2与DaDELLA2存在互作关系，且发生在DaDELLA2基因的N端。

Abstract

In order to understand the regulatory role of the BBR-BPC gene family in the growth and development of Dioscorea alata (greater yam), we analyzed the gene structure, phylogenetic evolution, conserved motifs, and physicochemical properties of the BBR-BPC gene family in greater yam. We also predicted the secondary and tertiary structures of BBR-BPC proteins and verified the interaction between the BBR-BPC gene and the DELLA gene. Through HMMsearch and BLAST analyses, we identified six members of the BBR-BPC family in the greater yam genome. These gene proteins exhibited significant differences and alternative splicing events, with a total of 10 splice variants detected. Subcellular localization analysis revealed that all members of the BBR-BPC family in greater yam are located in the nucleus. The yeast two-hybrid interaction results between Da4BBR-BPC2 and DaDELLA2 indicate that there is an interaction between Da4BBR-BPC2 and DaDELLA2, occurring at the N-terminus of the DaDELLA2 gene.

关键词

DaBBR-BPC基因 / DaDELLA2 / 赤霉素 / 酵母双杂 / 生物信息分析

Key words

DaBBR-BPC gene / DaDELLA2 / Gibberellin / Yeast two-hybrid / Bioinformatics analysis

参考文献

[1] 索宁宁, 张艳芳, 高圆丽, 等. 山药块茎膨大期淀粉积累及淀粉合成相关基因表达分析[J]. 中国瓜菜, 2023, 36(3): 69-76. https://doi.org/10.3969/j.issn.1673-2871.2023.03.012

[2] 夏薇, 吴文嫱, 许云, 等. 大薯种质资源多样性研究进展[J]. 植物生理学报, 2017, 53(5): 781-784.

[3] 张青, 赵景梅, 黄东益, 等. 大薯病程相关蛋白1(PR1)基因及其启动子序列的克隆与分析[J]. 分子植物育种, 2018, 16(7): 2078-2084.

[4] 刘林娅, 黄亚成, 黄小龙, 等. 薯蓣植物块茎特异蛋白Dioscorin的研究进展[J]. 植物学报, 2016, 51(2): 274-280. https://doi.org/10.11983/CBB15072

[5] Zhu J K. Abiotic stress signaling and responses in plants[J]. Cell, 2016, 167(2): 313-324. https://doi.org/10.1016/j.cell.2016.08.029

[6] 龚蓉. 水稻OsGBP转录因子家族基因的功能研究及雌雄配子不育基因MFS的定位与功能分析[D]. 武汉: 华中农业大学, 2018.

[7] 赵东波, 管培燕, 郭智慧, 等. 玉米BBR-BPC基因家族全基因组鉴定及表达分析[J]. 玉米科学, 2023, 31(3): 58-66.

[8] Lee Y C, Tsai P T, Huang X X, et al. Family members additively repress the ectopic expression of BASIC PENTACYSTEINE3 to prevent disorders in Arabidopsis circadian vegetative development[J]. Frontiers in Plant Science, 2022, 13: 919946. https://doi.org/10.3389/fpls.2022.919946

[9] Theune M L, Bloss U, Brand L H, et al. Phylogenetic analyses and GAGA-motif binding studies of BBR/BPC proteins lend to clues in GAGA-motif recognition and a regulatory role in brassinosteroid signaling[J]. Frontiers in Plant Science, 2019, 10: 466. https://doi.org/10.3389/fpls.2019.00466

[10] Mishra K, Chopra V S, Srinivasan A, et al. Trl-GAGA directly interacts with Lola like and both are part of the repressive complex of Polycomb group of genes[J]. Mechanisms of Development, 2003, 120(6): 681-689. https://doi.org/10.1016/S0925-4773(03)00046-7

[11] Ogiyama Y, Schuettengruber B, Papadopoulos G L, et al. Polycomb-dependent chromatin looping contributes to gene silencing during Drosophila development[J]. Molecular Cell, 2018, 71(1): 73-88. https://doi.org/10.1016/j.molcel.2018.05.032

[12] Lang D, Weiche B, Timmerhaus G, et al. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity[J]. Genome Biology and Evolution, 2010, 2: 488-503. https://doi.org/10.1093/gbe/evq032

[13] Wanke D, Hohensxtatt M L, Dynowski M, et al. Alanine zipper-like coiled-coil domains are necessary for homotypic dimerization of plant GAGA-factors in the nucleus and nucleolus[J]. PLoS One, 2011, 6(2): e16070. https://doi.org/10.1371/journal.pone.0016070

[14] Santi L, Wang Y, Stile M R, et al. The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3[J]. Plant Journal, 2010, 34(6): 813-826.

[15] Monfared M M, Simon M K, Meister R J, et al. Overlapping and antagonistic activities of BASIC PENTACYSTEINE genes affect a range of developmental processes in Arabidopsis[J]. The Plant Journal, 2011, 66(6): 1020-1031. https://doi.org/10.1111/j.1365-313X.2011.04562.x

[16] Hecker A, Brand L H, Peter S, et al. The Arabidopsis gaga-Binding factor basic pentacysteine6 recruits the polycomb-repressive complex1 component like heterochromatin protein1 toGaga DNA motifs[J]. Plant Physiology, 2015, 168(3): 1013-1024. https://doi.org/10.1104/pp.15.00409

[17] Simonini S , Kater M M. Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance[J]. Journal of Experimental Botany, 2014, 65(6): 1455-1465. https://doi.org/10.1093/jxb/eru003

[18] Mu Y, Zou M, Sun X, et al. BASIC PENTACYSTEINE proteins repress ABSCISIC ACID INSENSITIVE4 expression via direct recruitment of the polycomb-repressive complex 2 in Arabidopsis root development[J]. Plant & Cell Physiology, 2017, 58(3): 607-621.

[19] Meister R J, Williams L A, Monfared M M, et al. Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter[J]. Plant Journal, 2004, 37(3): 426-438. https://doi.org/10.1046/j.1365-313X.2003.01971.x

[20] Kooiker M, Airoldi C A, Losa A, et al. BASIC PENTACYSTEINE1 a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK[J]. The Plant Cell, 2005, 17(3): 722-729. https://doi.org/10.1105/tpc.104.030130

[21] Simonini S , Roig-villanova I , GREGIS V , et al. Basic pentacysteine proteins mediate MADS domain complex binding to the DNA for tissue-specific expression of target genes in Arabidopsis[J]. Plant Cell, 2012, 24(10): 4163-4172. https://doi.org/10.1105/tpc.112.103952

[22] Wu J, Mohamed D, Dowhanik S, et al. Spatiotemporal restriction of FUSCA3 expression by class I BPCs promotes ovule development and coordinates embryo and endosperm growth[J]. The Plant Cell, 2020, 32(6): 1886-1904. https://doi.org/10.1105/tpc.19.00764

[23] Lao Z, Mao J, Chen R, et al. Genome-wide identification and characterization of BASIC PENTACYSTEINE transcription factors and their binding motifs in coconut palm[J]. Frontiers in Plant Science, 2024, 15: 1491139. https://doi.org/10.3389/fpls.2024.1491139

[24] Wai A H, Divya D, Park J I, et al. Genome wide identification of BBP/BPC transcription factor in tomato and its expression profiling in response to abiotic stress[J]. Plant Biotechnology Reports, 2024, 18(6): 759-776. https://doi.org/10.1007/s11816-024-00927-z

[25] Berger N, Dubreucq B. Evolution goes GAGA: GAGA binding proteins across Kingdoms[J]. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2012, 1819(8): 863-868. https://doi.org/10.1016/j.bbagrm.2012.02.022

[26] Sun H, Pang B, Yan J, et al. Comprehensive analysis of cucumber gibberellin oxidase family genes and functional characterization of CsGA20ox1 in root development in Arabidopsis[J]. International Journal of Molecular Sciences, 2018, 19(10): 3135. https://doi.org/10.3390/ijms19103135

[27] Sahu A, Singh R, Verma P K. Plant BBR/BPC transcription factors: unlocking multilayered regulation in development, stress and immunity[J]. Planta, 2023, 258(2): 31. https://doi.org/10.1007/s00425-023-04188-y

[28] Yang Q, Li B, Rizwan H M, et al. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis[J]. Frontiers in Plant Science, 2022, 13: 972734. https://doi.org/10.3389/fpls.2022.972734

[29] Akond Z, Rahman H, Ahsan M A, et al. Comprehensive In silico analysis of RNA silencing-related genes and their regulatory elements in wheat (Triticum aestivum L.)[J]. BioMed Research International, 2022, 2022: 4955209. https://doi.org/10.1155/2022/4955209

[30] 程文杰. 大薯种质资源遗传多样性分析[D]. 海口: 海南大学, 2010.

[31] Kumar D, Wareing P F. Factors controlling stolon development in the potato plant[J]. New Phytologist, 1972, 71(4): 639-648. https://doi.org/10.1111/j.1469-8137.1972.tb01274.x

[32] Li W, Zhang J, Sun H, et al. FveRGA1, encoding a DELLA protein, negatively regulates runner production inFragaria vesca[J]. Planta, 2018, 247(4): 941-951. https://doi.org/10.1007/s00425-017-2839-9

[33] Zentella R, Zhang Z L, Park M, et al. Global analysis of della direct targets in early gibberellin signaling in Arabidopsis[J]. The Plant Cell, 2007, 19(10): 3037-3057. https://doi.org/10.1105/tpc.107.054999

[34] Li S, Sun M, Miao L, et al. Multifaceted regulatory functions of CsBPC2 in cucumber under salt stress conditions[J]. Horticulture Research, 2023, 10(5): 142-154.

[35] Zhao H, Wan S, Huang Y, et al. The transcription factor MdBPC2 alters apple growth and promotes dwarfing by regulating auxin biosynthesis[J]. The Plant Cell, 2024, 36(3): 585-604. https://doi.org/10.1093/plcell/koad297

基金资助

国家自然科学基金项目(32160470)

国家自然科学基金项目(32160472)

海南省海南大学2023年研究生创研课题(Qhys2023-266)