Genome-wide identification and expression analysis of wheat NPR1 gene family
-
摘要: 【目的】对小麦NPR1基因家族成员进行鉴定及表达分析，为探究该家族基因的作用机制及小麦遗传改良提供理论参考。【方法】以拟南芥NPR1家族蛋白序列为参考序列，从小麦基因组中鉴定出小麦NPR1基因家族成员，利用生物信息学软件对其序列特征进行分析，并分别利用RNA-Seq原始数据和实时荧光定量PCR（qRT-PCR）分析小麦NPR1家族基因在不同组织及不同胁迫下的表达水平。通过STRING在线网站构建TaNPR1s蛋白的互作网络。【结果】共鉴定获得20个小麦NPR1基因家族成员，其编码蛋白的不稳定指数均大于40，为不稳定蛋白；平均总亲水性值（GRAVY）均为负值（除TaNPR5-D为正值外），为亲水蛋白；主要分布于细胞核内，在叶绿体、线粒体、内质网和细胞质等部位也有分布；二级结构均由α-螺旋、延伸链、β-转角和无规卷曲组成，以α-螺旋和无规则卷曲为主；对应的三级结构模型有10种。20个TaNPR1s蛋白均可与转录因子HBP-1b及未知蛋白A、B、C、D发生相互作用，这5种蛋白均含有bZIP结构域（含TGACG基序）和种子休眠特异基因结构域（DOG1）。TaNPR1s基因在不同组织中的表达模式不同，可分为在多个组织中表达、在特定的组织或发育阶段表达和在不同组织发育阶段均低表达或不表达，共三大类。随机挑选的8个TaNPR1s基因中，有3个基因在禾谷镰刀菌胁迫下表达量降低，但在白粉病菌胁迫下表达量升高；有2个基因在这两种菌胁迫下表达量均升高，有2个基因在两种菌胁迫下表达量均下降。TaNPR1s基因对6种非生物胁迫处理均有响应，但表达模式存在差异。【结论】小麦NPR1基因家族成员在不同组织生长发育过程和生物和非生物胁迫响应中发挥重要调控作用，且基因的可变剪接体也表现出不同组织表达特性，丰富了NPR1s蛋白功能。TaNPR1s蛋白可能通过与bZIP和DOG1结构域结合发挥其生物学功能。Abstract: 【Objective】 The identification and expression analysis of NPR1 gene family members in wheat provided theoretical reference for exploring the mechanism of this family gene and wheat genetic improvement.【Method】 Wheat NPR1 gene family members from wheat genome were identified based on NPR1 family protein sequence from arabidopsis. The sequence characteristics were analyzed by bioinformatics software, and the expression levels of wheat NPR1 family genes under different tissues and different stresses were analyzed by RNA-Seq data and real-time fluorescence quantitative PCR(qRT-PCR). The online website STRING was used to predict and analyze the interaction relationship between related proteins of TaNPR1 family members.【Result】 A total of 20 members of wheat NPR1 gene family were identified,and the TaNPR1s encoded by them were unstable proteins with instability index greater than 40. The average total hydrophilic value(GRAVY)was negative(except TaNPR5-D was positive),which was hydrophilic protein. It was mainly distributed in the nucleus,chloroplast,mitochondria,endoplasmic reticulum and cytoplasm. The secondary structure was composed of α-helix,extended strand,β-turn and random coil,and α-helix and random coil were the main components. There were 10 kinds of tertiary structure models. All 20 TaNPR1s proteins could interact with the transcription factor HBP-1b and unknown proteins A,B,C and D,the five proteins all contained bZIP domain (containing TGACG motif)and seed dormancy specific gene domain(DOG1). The expression pattern of TaNPR1s gene in different tissues was different,which could be divided into three categories:expressed in multiple tissues,expressed in specific tissues or developmental stages,and all low expression or no expression in different tissue development stages. Among the 8 randomly selected TaNPR1s genes,the expression levels of 3 genes decreased under Fusarium graminearum stress,but increased under powdery mildew stress. The expression levels of two genes increased under both strains,and the expression levels of two genes decreased under both strains. TaNPR1s gene responded to all six abiotic stress treatments,but their expression patterns were different.【Conclusion】 Members of wheat NPR1 gene family play an important role in regulating the growth and development of different tissues and the response to biological and abiotic stresses,and the variable spliceosomes of genes also show different tissue expression characteristics,enriching the function of NPR1s protein. TaNPR1s protein may play its biological function by binding to bZIP and DOG1 domains.
-
Keywords:
- wheat /
- NPR1 gene family /
- identification /
- bioinformatics analysis /
- expression analysis
-
-
蔡韡韡,曾志芳,魏春,杨华丽,佘文琴,陈桂信.2019.㮏NPR1同源基因全长cDNA的分离与表达分析[J].园艺学报,46(3):567-576.[Cai W W,Zeng Z F,Wei C,Yang H L,She W Q,Chen G X.2019.Isolation and expression analysis of full-length cDNA of NPR1 homologous genes in Nai(Prunus salicina var.cordata)[J].Acta Horticulturae Sinica,46(3):567-576.]doi: 10.16420/j.issn.0513-353x.2019-0030. 陈文烨,杨帆,刘永伟,董福双,赵和,柴建芳,吕孟雨,周硕.2020.小麦Ta NAC-B072基因的克隆和表达分析[J].江西农业学报,32(8):1-7.[Chen W Y,Yang F,Liu Y W,Dong F S,Zhao H,Chai J F,Lü M Y,Zhou S.2020Cloning and expression analysis of TaNAC-B072 in wheat[J].Acta Agriculturae Jiangxi,32(8):1-7.]doi: 10.19386/j.cnki.jxnyxb.2020.08.01. 韩永光,马利刚,赵乐,冯卫生,郑晓珂.2018.植物抗性基因NPR1研究进展[J].安徽农业科学,46(26):18-20.[Han Y G,Ma L G,Zhao L,Feng W S,Zheng X K.2018.Research progress on resistance gene NPR1 in plants[J].Journal of Anhui Agricultural Sciences,46(26):18-20.]doi: 10.13989/j.cnki.0517-6611.2018.26.006. 焦鹏.2016.苹果NPR1基因家族的全基因组鉴定与表达分析[D].杨凌:西北农林科技大学.[Jiao P.2016.Genomewide identification and expression analysis of NPR1 gene family in apple[D].Yangling:Northwest A & F University.] 李微巍.2014.杨树NPR-like基因家族抗病相关基因的鉴定及功能研究[D].合肥:安徽农业大学.[Li W W.2014.Identification of disease-resistance cancer-critical genes and functional research of NPR-Like family in poplar[D].Hefei:Anhui Agricultural University.] 任陪娣,谢碧玉,陈翠,贾彩红,王静毅,张建斌.2019.香蕉NPR1基因家族的鉴定及在枯萎病菌胁迫下表达分析[J].植物遗传资源学报,20(6):1621-1629.[Ren P D,Xie B Y,Chen C,Jia C H,Wang J Y,Zhang J B.2019.Genome-wide survey of the NPR1 gene family in banana(Musa spp.)and expression pattern analysis upon infection with Foc TR4[J].Journal of Plant Genetic Resources,20(6):1621-1629.]doi: 10.13430/j.cnki.jpgr.20190416002. 宋松泉,刘军,徐恒恒,刘旭,黄荟.2020.脱落酸代谢与信号传递及其调控种子休眠与萌发的分子机制[J].中国农业科学,53(5):857-873.[Song S Q,Liu J,Xu H H,Liu X,Huang H.2020.ABA metabolism and signaling and their molecular mechanism regulating seed dormancy and germination[J].Scientia Agricultura Sinica,53(5):857-873.]doi: 10.3864/j.issn.0578-1752.2020.05.001. 郑世仲,王培育,张春柳,江胜滔,江金兰,颜沛沛,叶炜,赖钟雄.2020.文心兰NPR1基因的克隆与诱导抗性过程中的表达分析[J].福建农业学报,35(2):140-149.[Zheng SZ,Wang P Y,Zhang C L,Jiang S T,Jiang J L,Yan P P,Ye W,Lai Z X.2020.NPR1 Cloning and expression during development of induced systemic resistance in Oncidium hybridum[J].Fujian Journal of Agricultural Sciences,35(2):140-149.]doi: 10.19303/j.issn.1008-0384.2020.02.004. Altschul S F,Madden T L,Schäffer A A,Zhang J,Zhang Z,Miller W,Lipman D J.1997.Gapped BLAST and PSI-BLAST:A new generation of protein database search programs[J].Nucleic Acids Research,25(17):3389-3402.doi: 10.1093/nar/25.17.3389.
Aravind L,Koonin E V.1999.Fold prediction and evolutionary analysis of the POZ domain:Structural and evolutionary relationship with the potassium channel tetramerization domain[J].Journal of Molecular Biology,285(4):1353-1361.doi: 10.1006/jmbi.1998.2394.
Backer R,Naidoo S,Berg N.2019.The NONEXPRESSOROF PATHOGENESIS-RELATED GENES 1(NPR1) and related family:mechanistic insights in plant disease resistance[J].Frontiers in Plant Science,10:102.doi: 10.3389/fpls.2019.00102.
Boyle P,Su E L,Rochon A,Shearer H L,Murmu J,Chu J Y,Fobert P R,Després C.2009.The BTB/POZ domain of the Arabidopsis disease resistance protein NPR1 interacts with the repression domain of TGA2 to negate its function[J].The Plant Cell,21(11):3700-3713.doi: 10.1105/tpc.109.069971.
Cao H,Bowling S A,Gordon A S,Dong X.1994.Characterization of an Arabidopsis mutant that is nonresponsive to inducers of systemic acquired resistance[J].The Plant Cell,6(11):1583.doi: 10.1105/tpc.6.11.1583.
Cao H,Glazebrook J,Clarke J D,Volko S,Dong X.1997.The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats[J].The Cell,88(1):57-63.doi: 10.1016/S0092-8674(00)81858-9.
Castelló M J,Medina-puche L,Lamilla J,Tornero P.2018.NPR1 paralogs of Arabidopsis and their role in salicylic acid perception[J].PLoS One,13(12):e0209835.doi: 10.1371/journal.pone.0209835.
Fan W H,Dong X N.2002.In vivo interaction between NPR1 and transcription factor TGA2 leads to salicylic acidmediated gene activation in Arabidopsis[J].The Plant Cell,14(6):1377-1389.doi: 10.1105/tpc.001628.
Finn R D,Mistry J,Schuster-böckler B,Griffiths-jones S,Hollich V,Lassmann T,Moxon S,Marshall M,Khanna A,Durbin R,Eddy S R,Sonnhammer E L L,Bateman A.2006.Pfam:Clans,web tools and services[J].Nucleic Acids Research,34(S1):247-251.doi: 10.1093/nar/gkj149.
Hepworth S R,Zhang Y,Mckim S,Li X,Haughn G W.2005.BLADE-ON-PETIOLE-dependent signaling controls leaf and floral patterning in Arabidopsis[J].The Plant Cell,17(5):1434-1448.doi: 10.1105/tpc.104.030536.
Horton P,Park K J,Obayashi T,Fujita N,Harada H,Adamscollier C J,Nakai K.2007.WoLF PSORT:Protein localization predictor[J].Nucleic Acids Research,35(S2):585-587.doi: 10.1093/nar/gkm259.
Initiative T A G.2000.Analysis of the genome sequence of the fowering plant Arabidopsis thaliana[J].Nature,408(6814):796-815.doi: 10.1038/35048692.
Jiang W Q,Yang L,He Y Q,Zhang H T,Li W,Chen H G,Ma D F,Yin J L.2019.Genome-wide identification and transcriptional expression analysis of superoxide dismutase(SOD) family in wheat[J].PeerJ,7(2):e8062.doi: 10.7287/peerj.preprints.27402.
Jones J D G,Dangl J L.2006.The plant immune system[J].Nature,444(7117):323-329.doi: 10.1038/nature05286.
Kinkema M,Fan W,Dong X.2000.Nuclear localization of NPR1 is required for activation of PR gene expression[J].The Plant Cell,12(12):2339-2350.doi: 10.1105/tpc.12.12.2339.
Kogel K,Langen G.2005.Induced disease resistance and gene expression in cereals[J].Cellular Microbiology,7(11):1555-1564.doi: 10.1111/j.1462-5822.2005.00592.x.
Liu X,Liu Z G,Niu X H,Xu Q,Yang L.2019.Genomewide identification and analysis of the NPR1-Like gene family in bread wheat and its relatives[J].International Journal of Molecular Sciences,20(23):5974.doi: 10.3390/ijms20235974.
Liu Y,Schiff M,Marathe R,Dinesh-kumar S P.2002.Tobacco Rar1,EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus[J].The Plant Journal,30(4):415-429.doi: 10.1046/j.1365-313x.2002.01297.x.
Ma S,Bohnert H J.2007.Integration of Arabidopsis thaliana stress-related transcript profiles,promoter structures,and cell-specific expression[J].Genome Biology,8(4):R49.doi: 10.1186/gb-2007-8-4-r49.
Malnoy M,Jin Q,Borejsza-wysocka E E,He S Y,Aldwinckle H S.2007.Overexpression of the apple MpNPR1 gene confers increased disease resistance in Malus x domestica[J].Molecular Plant-Microbe Interactions,20(12):1568-1580.doi: 10.1094/MPMI-20-12-1568.
Mhamdi A.2019.NPR1 has everything under control[J].Plant Physiology,181(1):6-7.doi: 10.1104/pp.19.00890.
Mikael N,Mattias H,Ove N.2005.The BLADE ON PETI-OLE genes act redundantly to control the growth and development of lateral organs[J].Development,132(9):2203-2213.doi: 10.1242/dev.01815.
Mulder N,Apweiler R.2007.InterPro and InterProScan:Tools for protein sequence classification and comparison[J].Methods in Molecular Biology,396:59-70.doi: 10.1007/978-1-59745-515-2_5.
Olate E,Jiménez-gómez J M,Holuigue L,Salinas J.2018.NPR1 mediates a novel regulatory pathway in cold acclimation by interacting with HSFA1 factors[J].Nature Plants,4(10):811-23.doi: 10.1038/s41477-018-0254-2.
Peraza-echeverria S,Santamaría J M,Fuentes G,Menéndezcerón M,Vallejo-reyna M,Herrera-valencia V A.2012.The NPR1 family of transcription cofactors in papaya:Insights into its structure,phylogeny and expression[J].Genes & Genomics,34(4):379-390.doi: 10.1007/s13258-011-0218-7.
Pieterse C M J,Van Wees S C M,Van Pelt J A,Knoester M,Laan R,Gerrits H,Weisbeek P J,Van Loon L C.1998.Anovel signaling pathway controlling induced systemic resistance in Arabidopsis[J].The Plant Cell,10(9):1571-1580.doi: 10.1105/tpc.10.9.1571.
Rochon A,Boyle P,Wignes T,Fobert P R,Despres C.2006.The coactivator function of Arabidopsis NPR1 requires the core of its BTB/POZ domain and the oxidation of C-terminal cysteines[J].The Plant Cell,18(12):3670-3685.doi: 10.1105/tpc.106.046953.
Schwede T,Kopp J,Guex N,Peitsch M C.2003.SWISS-MODEL:An automated protein homology-modeling server[J].Nucleic Acids Research,31(13):3381-3385.doi: 10.1093/nar/gkg520.
Silva K J P,Brunings A,Peres N A,Mou Z,Folta K M.2015.The Arabidopsis NPR1 gene confers broad-spectrum disease resistance in strawberry[J].Transgenic Research,24(4):693-704.doi: 10.1007/s11248-015-9869-5.
Spoel S H,Koornneef A,Claessens S M C,Korzelius J P,Van Pelt J A,Mueller M J,Buchala A J,Métraux J,Brown R,Kazan K,Van Loon L C,Dong X,Pieterse C.2003.NPR1 modulates cross-talk between salicylate-and jasmonate-dependent defense pathways through a novel function in the cytosol[J].The Plant Cell,15(3):760-770.doi: 10.1105/tpc.009159.
Szklarczyk D,Gable A L,Lyon D,Junge A,Wyder S,Huertacepas J,Simonovic M,Doncheva N T,Morris J H,Bork P,Jensen L J,Mering C.2018.STRING v11:Protein-protein association networks with increased coverage,supporting functional discovery in genome-wide experimental datasets[J].Nucleic Acids Research,47(D1):D607-D613.doi: 10.1093/nar/gky1131.
Tripathi D,Raikhy G,Kumar D.2019.Chemical elicitors of systemic acquired resistance-Salicylic acid and its functional analogs[J].Current Plant Biology,17:48-59.doi: 10.1016/j.cpb.2019.03.002.
Wang X D,Bi W S,Gao J,Yu X M,Wang H Y,Liu D Q.2018.Systemic acquired resistance,NPR1,and pathogenesis-related genes in wheat and barley[J].Journal of Integrative Agriculture,17(11):60345-60347.doi: 10.1016/S2095-3119(17)61852-5.
Wang X D,Yang B J,Li K,Kang Z S,Cantu D,Dubcovsky J.2016.A conserved Puccinia striiformis protein interacts with wheat NPR1 and reduces induction of pathogenesis-related genes in response to pathogens[J].Molecular Plant-Microbe Interactions,29(12):977-989.doi: 10.1094/MPMI-10-16-0207-R.
Wang Y,Liu J,Huang B O,Xu Y M,Li J,Huang L F,Lin J,Zhang J,Min Q H,Yang W M,Wang X Z.2015.Mechanism of alternative splicing and its regulation[J].Biomedical Reports,3(2):152-158.doi: 10.3892/br.2014.407.
Wang Z,Ma L Y,Li X,Zhao F Y,Sarwar R,Cao J,Li Y L,Ding L N,Zhu K M,Yang Y H,Tan X L.2020.Genome-wide identification of the NPR1 like gene family in Brassica napus and functional characterization of BnaNPR1 in resistance to Sclerotinia sclerotiorum[J].Plant Cell Reports,39:709-722.doi: 10.1007/s00299-020-02525-z.
Wilkins M R,Gasteiger E,Bairoch A,Sanchez J C,Williams K L,Appel R D.1999.Protein identification and analysis tools in the ExPASy Server[J].Methods in Molecular Biology,112(112):531-552.doi: 10.1385/1-59259-584-7:531.
Yuan Y X,Zhong S H,Li Q,Zhu Z R,Lou Y G,Wang L Y,Wang J J,Wang M Y,Li Q L,Yang D L,He Z H.2007.Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility[J].Plant Biotechnology Journal,5(2):313-324.doi: 10.1111/j.1467-7652.2007.00243.x.
Zhang Y L,Cheng Y T,Qu N,Zhao Q G,Bi D L,Li X.2006.Negative regulation of defense responses in Arabidopsis by two NPR1 paralogs[J].The Plant Journal,48(5):647-656.doi: 10.1111/j.1365-313X.2006.02903.x.
Zhang Y L,Fan W H,Kinkema M,Li X,Dong X N.1999.Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene[J].Proceedings of the National Academy of Sciences,96(11):6523-6528.doi: 10.1073/pnas.96.11.6523.
Zhou J,Trifa Y,Silva H,Pontier D,Lam E,Jyoti S,Klessig DF,Zhou J M,Shah J.2000.NPR1 differentially interacts with members of the TGA/OBF family of transcription factors that bind an element of the PR-1 gene required for induction by salicylic acid[J].Molecular Plant-Microbe Interactions,13(2):191-202.doi: 10.1016/S1369-5266(00)80027-8.
-
期刊类型引用(3)
1. 葛仕杰，刘怡德，张华东，宁强，朱展望，王书平，刘易科. 小麦蛋白质二硫键异构酶基因家族的鉴定与表达. 生物技术通报. 2025(02): 85-96 . 
百度学术
2. 刘冰琪，颜沛沛，王培育，李尊文，吴铭俊，李汉生，林敏水，江金兰，叶炜. 金线兰NPR1基因克隆及其抗性响应表达分析. 东南园艺. 2024(05): 403-410 . 百度学术
3. 李登高，林睿，穆青慧，周娜，张焱如，白薇. 马铃薯StNPR4基因的克隆与功能分析. 植物研究. 2022(05): 821-829 . 百度学术
其他类型引用(5)
计量
- 文章访问数: 73
- HTML全文浏览量: 4
- PDF下载量: 9
- 被引次数: 8
下载: