Identification and Expression Analysis of PP2C Gene Family in Phyllostachys edulis
HU Qiu-Tao1, HOU Dan1, ZHAO Zhong-Yu1, WEI Han-Tian1, LIN Xin-Chun1,2,*
1 State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an 311300, China; 2 Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an 311300, China
Abstract：2C type protein phosphatases (PP2C) widely exist in organisms and play important regulatory roles. Many studies have indicated that PP2C play important roles in plant stress resistance and response to hormone regulation. However, the PP2C in moso bamboo (Phyllostachys edulis) have not been investigated. In this study, moso bamboo was used as experimental material and bioinformatics method was used to identify 125 genes with complete PP2C conserved domain from the whole genome of moso bamboo. The length of the proteins encoded by PP2C ranged from 110 to 1 086 aa with molecular weights from 12.07 to 121.02 kD. According to phylogenetic analysis result, 125 PP2Cs were clustered into 9 subgroups, and 4 genes (PH02Gene36278.t1, PH02Gene48541.t1, PH02Gene37946.t1, PH02Gene29918.t1) were not divided into any subgroups and formed a branch independently; According to expression profile analysis of transcriptome, 121 PP2Cs exhibited different levels in different tissues and growth stages. Most PP2Cs were highly expressed in different stages of bamboo shoot development and some PP2Cs had high expression in roots and leaves; qRT-PCR results showed that 9 PP2Cs were up-regulated and 1 PP2C was down-regulated after abscisic acid treatment; whereas 6 PP2Cs were up-regulated and 5 PP2Cs were down-regulated after salt stress and methyl jasmonate treatment, which indicated that PP2Cs might play different roles in the regulation of stress and hormone responses. The present study could provide some reference for further functional study of PP2C gene family in Phyllostachys edulis.
胡秋涛, 侯丹, 赵钟毓, 魏涵天, 林新春. 毛竹PP2C基因家族鉴定与表达分析[J]. 农业生物技术学报, 2020, 28(10): 1776-1787.
HU Qiu-Tao, HOU Dan, ZHAO Zhong-Yu, WEI Han-Tian, LIN Xin-Chun. Identification and Expression Analysis of PP2C Gene Family in Phyllostachys edulis. 农业生物技术学报, 2020, 28(10): 1776-1787.
[1] 白羽聪, 李翔宇, 程占超, 等. 2019. 毛竹PIN基因家族的鉴定与生物信息学分析[J]. 分子植物育种, 17(16): 5238-5247. (Bai Y C, Li X Y, Cheng Z C, et al.2019. Identification and bioinformatics analysis of PIN gene family in moso bamboo (Phyllostachys edulis)[J]. Molecular Plant Breeding, 17(16): 5238-5247.) [2] 程梅. 2014. 玉米脱落酸受体(PYL3)与2C型丝氨/苏氨酸蛋白磷酸酶(PP2C)的互作分析[D].硕士学位论文, 四川农业大学, 导师: 付凤玲, pp. 20-22. (Cheng M.2014. Interaction between abscisic acid receptor (PYL3) and Serine/Threonine protein phosphatase type 2C in maize[D]. Thesis for M.S., Sichuan Agricultural University, Supervisor: Fu F L, pp. 20-22.) [3] 程占超, 侯丹, 马艳军, 等. 2017. 毛竹生长素反应因子基因的生物信息学分析及差异表达[J]. 浙江农林大学学报, 34(4): 574-580. (Cheng Z C, Hou D, Ma Y J, et al.2017. Bioinformatic analysis and differential expression of auxin response factor (ARF) gene in Phyllostachys edulis[J]. Journal of Zhejiang A & F University, 34(4): 574-580.) [4] 郭安源, 朱其慧, 陈新, 等. 2007. GSDS: 基因结构显示系统[J]. 遗传, 29(8): 1023-1026. (Guo A Y, Zhu Q H, Chen X, et al.2007. GSDS: A gene structure display server[J]. Hereditas (Beijing), 29(8): 1023-1026.) [5] 何红红, 路志浩, 马宗桓, 等. 2018. 葡萄PP2C家族基因的鉴定与表达分析[J]. 园艺学报, 45(7): 1237-1250. (He H H, Lu Z H, Ma Z H, et al.2018. Genome-wide identification and expression analysis of the PP2C gene family in Vitis vinifera[J]. Acta Horticulturae Sinica, 45(7): 1237-1250.) [6] 黎帮勇, 胡尚连, 曹颖, 等. 2015. 毛竹NAC转录因子家族生物信息学分析[J]. 基因组学与应用生物学, 34(8): 1769-1777. (Li B Y, Hu S L, Cao Y, et al.2015. Bioinformatics analysis of NAC gene family in moso bamboo[J]. Genomics and Applied Biology, 34(8): 1769-1777.) [7] 柳丽娜, 董敦义, 李云, 等. 2014. 浙江安吉县毛竹林高温干旱灾害调研报告[J]. 世界竹藤通讯, 12(1): 24-28. (Liu L N, Dong D Y, Li Y, et al.2014. Investigation of moso bamboo forest under high temperature and drought disaster[J]. World Bamboo and Rattan, 12(1): 24-28.) [8] 闵东红, 薛飞洋, 马亚男, 等. 2013. 谷子PP2C基因家族的特性[J]. 作物学报, 39(12): 2135-2144. (Min D H, Xue F Y, Ma Y N, et al.2013. Characteristics of PP2C gene family in foxtail millet (Setaria italica)[J]. Acta Agronomica Sinica, 39(12): 2135-2144.) [9] 阮海华, 徐郎莱. 2007. 2C类蛋白磷酸酶的结构与功能研究进展[J]. 南京农业大学学报, 30(1): 136-141. (Ruan H H, Xu L L.2007. Progress in the structure and function of PP2C-type protein in phosphatases[J]. Journal of Nanjing Agricultural University, 30(1): 136-141.) [10] 陶贵耘, 傅鹰, 周明兵. 2018. 竹类植物快速生长的机理研究进展[J]. 农业生物技术学报, 26(5): 871-887. (Tao G Y, Fu Y, Zhou M B.2018. Advances in studies on molecular mechanisms of rapid growth of bamboo species[J]. Journal of Agricultural Biotechnology, 26(5): 871-887.) [11] 吴佳军, 俞率成, 刘志刚, 等. 2019. 毛竹B3家族全基因组鉴定及表达模式分析[J]. 农业生物技术学报, 27(1): 43-54. (Wu J J, Yu S C, Liu Z G, et al.2019. Genome identification and expression pattern analysis of Phyllostachys edulis B3 family[J]. Journal of Agricultural Biotechnology, 27(1): 43-54.) [12] 徐秀荣, 杨克彬, 王思宁, 等. 2019. 毛竹bHLH转录因子的鉴定及其在干旱和盐胁迫条件下的表达分析[J]. 植物科学学报, 37(5): 610-620. (Xu X R, Yang K B, Wang S N, et al.2019. Identification of bHLH transcription factors in moso bamboo (Phyllostachys edulis) and their expression analysis under drought and salt stress[J]. Plant Science Journal, 37(5): 610-620.) [13] 张弛, 蔚静玲, 储谟立, 等. 2018. 拟南芥蛋白磷酸酶PP2C31的盐胁迫响应功能研究[J]. 中国科技论文, 13(18): 19-24. (Zhang C, Yu J L, Chu M L, et al.2018 Functional analysis of protein phosphatase PP2C31 in salt response in Arabidopsis thaliana[J]. China Sciencepaper, 13(18): 19-24.) [14] 赵钟毓, 侯丹, 胡秋涛, 等. 2020. 毛竹PeNAC047基因的克隆与表达分析[J]. 农业生物技术学报, 28(1): 58-71. (Zhao Z Y, Hou D, Hu Q T, et al.2020. Cloning and expression analysis of PeNAC047 gene from Phyllostachys edulis[J]. Journal of Agricultural Biotechnology, 28(1): 58-71) [15] Anna S, Agata D G, Iwona S.2016. The role and regulation of ABI5 (ABA-Insensitive 5) in plant development, abiotic stress responses and phytohormone crosstalk[J]. Frontiers in Plant Science, 7: 1884. [16] Bailey T L, Boden M, Buske F A, et al.2009. MEME suite: Tools for motif discovery and searching[J]. Nucleic Acids Research, 37(1): 202-208. [17] Cao J, Jiang M, Li P, et al.2016. Genome-wide identification and evolutionary analyses of the PP2C gene family with their expression profiling in response to multiple stresses in Brachypodium distachyon[J]. BMC Genomics, 17(1): 175. [18] Fan C, Ma J, Guo Q, et al.2013. Selection of reference genes for quantitative real-time PCR in bamboo (Phyllostachys edulis)[J]. PLOS ONE, 8(2): e56573. [19] Fuchs S, Grill E, Meskiene I,et al.2013. Type 2C protein phosphatases in plants[J]. The FEBS Journal, 280(2): 681-693. [20] Gagne J M, Clark S E.2010. The Arabidopsis stem cell factor POLTERGEIST is membrane localized and phospholipid stimulated[J]. Plant Cell, 22(3): 729-743. [21] Gfeller A, Dubugnon L, Liechti R, et al.2010. Jasmonate biochemical pathway[J]. Science Signaling, 3(109): 1-6. [22] Haider M S, Khan N, Pervaiz T, et al.2019. Genome-wide identification, evolution, and molecular characterization of the PP2C gene family in woodland strawberry[J]. Gene, 702(1): 27-35. [23] Haur W J, K S A, Yeon P M, et al.2019. Mutation of a conserved motif of PP2C.D phosphatases confers SAUR immunity and constitutive activity[J]. Plant Physiology, 181(1): 353-366. [24] Kerk D, Bulgrien J, Smith D W, et al.2002. The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis[J]. Plant Physiology, 129(2): 908-925. [25] Khan N, Ke H, Hu C M, et al.2019. Genome-wide identification, evolution, and transcriptional profiling of PP2C gene family in Brassica rapa[J]. BioMed Research International, 2019: 2965035. [26] Kumar Sudhir, Stecher Glen, Tamura Koichiro.2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 33(7): 1870-1874. [27] Lescot M, Dehais P, Thijs G, et al.2002. PlantCARE, database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J]. Nucleic Acids Research, 30(1): 325-327. [28] Luan S.2003. Protein phosphatases in plants[J]. Annual Review of Plant Biology, 54: 63-92. [29] Ma Y, Szostkiewicz I, Korte A, et al.2019. Regulators of PP2C phosphatase activity function as abscisic acid sensors[J]. Science, 324(5930): 1064-1068. [30] Marchler B A, Lu S N, Anderson J B, et al.2011. CDD: A conserved domain database for the functional annotation of proteins[J]. Nucleic Acids Research, 39(1): 225-229. [31] Nishimura N, Yoshida T, Kitahata N, et al.2007. ABA-hypersensitive germination1 encodes a protein phosphatase 2C, an essential component of abscisic acid signaling in Arabidopsis seed[J]. Plant Journal, 50(6): 935-949. [32] Peng Z, Lu Y, Li L, et al.2013. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)[J]. Nature Genetics, 45(4): 456-461. [33] Qi Y, Kun L, Xiaocui N, et al.2018. Genome-wide identification of PP2C genes and their expression profiling in response to drought and cold stresses in Medicago truncatula[J]. Scientific Reports, 8(1): 12841. [34] Raghavendra A S, Gonugunta V K, Christmann A, et al.2010. ABA perception and signaling[J]. Trends in Plant Science, 15(7): 395-401. [35] Schweighofer A, Hirt H, Meskiene I.2004. Plant PP2C phosphatases: Emerging functions in stress signaling[J]. Trends in Plant Science, 9(5): 236-243. [36] Schweighofer A, Kazanaviciute V, Scheikl E, et al.2007. PP2C-Type phosphatase AP2C1, which negatively regulates MPK4 and MPK6, modulates innate immunity, jasmonic acid, and ethylene levels in Arabidopsis[J]. Plant Cell, 19(7): 2213-2224. [37] Shazadee H, Khan N, Wang J, et al.2019. Identification and expression profiling of protein phosphatases (PP2C) gene family in Gossypium hirsutum L.[J]. International Journal of Molecular Sciences, 20(6): 1395. [38] Singh A, Giri J, Kapoor S, et al.2010. Protein phosphatase complement in rice: Genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development[J]. BMC Genomics, 11(1): 435. [39] Singh A, Jha S K, Bagri J, et al.2015. ABA inducible rice protein phosphatase 2C confers ABA insensitivity and abiotic stress tolerance in Arabidopsis[J]. PLOS ONE, 10(4): e0125168. [40] Wilkins M R, Gasteiger E, Bairoch A, et al.1999. Protein identification and analysis tools in the ExPASy server[J]. Methods in Molecular Biology, 112(1): 531-532. [41] Xue T, Wang D, Zhang S, et al.2008. Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis[J]. BMC Genomics, 9(1): 550. [42] Yamaguchi-Shinozaki K, Shinozaki K.2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses[J]. Annual Review of Plant Biology, 57(1): 781-803. [43] Yang K, Li Y, Wang S, et al.2019. Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)[J]. PeerJ, 6(1): e6242. [44] Yu X, Han J, Wang E, et al.2019. Genome-wide identification and homoeologous expression analysis of PP2C genes in wheat (Triticum aestivum L.)[J]. Frontiers in Genetics, 10: 561. [45] Zhao H, Gao Z, Wang L, et al.2018. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)[J]. GigaScience, 7(10): 1-12.
