芸薹属物种(B.napus,B.rapa,B.oleracea)防御素基因PDF1.1的生物信息学分析
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摘要
本研究利用生物信息学方法分析芸薹属物种PDF1.1家族的结构功能,探究芸薹属物种PDF1.1家族的分子进化,为芸薹属物种PDF1.1家族抗菌性提供理论基础。本研究以甘蓝型油菜,白菜,甘蓝为例,利用生物信息学方法,鉴定了这3个芸薹属物种共有8个PDF1.1,并分析其PDF1.1的基本特征、同源性及系统发生关系。结果显示,8个PDF1.1均有1个内含子和2个外显子;共有79～80个氨基酸残基;均具有Knot1结构域,具有多个磷酸化位点,其中丝氨酸磷酸化位点0～1个,苏氨酸磷酸化位点0～1个,酪氨酸磷酸化位点1个;它们的二级结构主要为随机卷曲;既是疏水性蛋白,也是稳定蛋白;在不同物种间芸薹属PDF1.1的同源性高于种内同源性。芸薹属的结构特点是防御素抗菌作用的重要条件之一;其三个物种的PDF1.1进化符合禹氏三角理论,且三个物种PDF1.1位点符合三倍化学说。本研究为芸薹属物种PDF1.1抗菌性提供了科学依据。
This research analyzed the struct ure and function of the PDF1.1 family of Brassica species by bioinformatics, and explored the molecular evolution of the PDF1.1 family of Brassica species, which provided a theoretical basis for the antibacterial properties of the PDF1.1 family of Brassica species. Taking Brassica napus,Brassica rapa and Brassica oleracea as examples, 8 PDF1.1, were identified by bioinformatics and their PDF1.1 characteristics, homology and phylogenetic relationship were analyzed. The results showed that all 8 PDF1.1 had one intron and two exons, and there were 79～80 amino acid residues. All of them have Knot1 domain, and have many phosphorylation sites, including one serine phosphorylation site, one threonine phosphorylation site and one tyrosine phosphorylation site, their secondary structures were mainly random crimp. The homology of PDF1.1 in different species is higher than that in species. The structural characteristics of Brassica are one of the important conditions for the antimicrobial action of defensing, an d the PDF1.1 evolution of three species conforms to the theory of Yu's triangle, and the PDF1.1 loci of three species conform to the triple chemical theory. This study provided a theoretical basis for the antibacterial properties of PDF1.1 family of Brassica species.
This research analyzed the struct ure and function of the PDF1.1 family of Brassica species by bioinformatics, and explored the molecular evolution of the PDF1.1 family of Brassica species, which provided a theoretical basis for the antibacterial properties of the PDF1.1 family of Brassica species. Taking Brassica napus,Brassica rapa and Brassica oleracea as examples, 8 PDF1.1, were identified by bioinformatics and their PDF1.1 characteristics, homology and phylogenetic relationship were analyzed. The results showed that all 8 PDF1.1 had one intron and two exons, and there were 79～80 amino acid residues. All of them have Knot1 domain, and have many phosphorylation sites, including one serine phosphorylation site, one threonine phosphorylation site and one tyrosine phosphorylation site, their secondary structures were mainly random crimp. The homology of PDF1.1 in different species is higher than that in species. The structural characteristics of Brassica are one of the important conditions for the antimicrobial action of defensing, an d the PDF1.1 evolution of three species conforms to the theory of Yu's triangle, and the PDF1.1 loci of three species conform to the triple chemical theory. This study provided a theoretical basis for the antibacterial properties of PDF1.1 family of Brassica species.
引文
Broekaert W.,1995,Plant defensins:novel antimicrobial peptides as components of the host defense system,Plant Physiol.,108(4):1353-1358
Brogden K.A.,2005,Antimicrobial peptides:pore formers or metabolic inhibitors in bacteria?Nat.Rev.Microbiol.,3(3):238-250
Cheng F.,Sun R.,and Hou X.,2016,Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea,Nat.Genet.,48(10):1218-1224
De Samblanx G.W.,Goderis I.J.,Thevissen K.,Raemaekers R.,Fant F.,Borremans F.,Acland D.P.,Osborn R.W.,Patel S.,and Broekaert W.F.,1997,Mutational analysis of a plant defensin from radish(Raphanus sativus L.)reveals two adjacent sites important for antifungal activity,J.Biol.Chem.,272(2):1171-1179
Francois I.E.J.A.,De Bolle M.F.C,Dwyer G.,Inge J.W.M.,Goderis I.J.W.M.,Woutors P.F.J.,Verhaert P.D.,Proost P.,Schaaper W.M.M.,Cammue B.P.A.,and Broekaert W.F.,2002,Transgenic expression in Arabidopsis of a polyprotein construct leading to production of two different antimicrobial proteins,Plant Physiol.,128(4):1346-1356
Gao A.G.,Hakimi S.M.,Mittanck C.A.,Wu Y.,Woerner B.M.,Stark D.M.,Shah D.M.,Liang J.,and Rommens C.M.,2000,Fungal pathogen protection in potato by expression of a plant defensing peptide,Nat.Biotechnol.,18(12):1307-1310
Harberd D.J.,2010,A contribution to the cyto-taxonomy of Brassica(Cruciferae)and its allies,Botanical Journal of the Linnean Society,65(1):1-23
Lu J.X.,Lu K.,Zhang K.,Cao T.,Li J.N.,and Liang Y.,2010,Cloning and analysis of SAMDC3genes and their promoters from Brassica napus,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),29(2):215-224(陆俊杏,卢坤,张凯,曹延,李加纳,梁颖,2010,甘蓝型油菜SAMDC3基因及其启动子的克隆与分析,基因组学与应用生物学,29(2):215-224)
Lu K.,Chai Y.R.,Zhang K.,Wang R.,Chen L.,Lei B.,Lu J.,Xu X.F.,and Li J.N.,2008,Cloning and characterization of phosphorus starvation inducible Brassica napus,purple acid phosphatase,12,gene family,and imprinting of a recently evolved MITE-minisatellite twin structure,Theor.Appl.Genet.,117(6):963-975
Mendez E.,Moreno A.,Colilla F.,Pelaez F.,Limas G.G.,Mendez R.,Soriano F.,Salinas M.,and De Haro C.,1990,Primary structure and inhibition of protein synthesis in eukaryotic cell-free system of a novel thionin,gamma-hordothionin,from barley endosper,Biochemistry,194(2):533-539
Nagaharu U.,1935,Genome analysis in Brassica with special reference to the experimental formation of B.napus and peculiar mode of fertilization,JPN.J.Bot.,7:389-452
Parashina E.V.,Serdobinskii L.A.,Kalle E.G.,and Lavrova N.V.,2000,Genetic engineering of oilseed rape and tomato plants expressing a radish defensin gene,Russian Journal of Plant Physiology,47(3):417-423
Penninckx I.A.,Eggermont K.,Terras F.R.,Thomma B.P.,De Samblanx G.W.,Buchala A.,Métraux J.P.,Manners J.M.,and Broekaert W.F.,1996,Pathogen-induced systemic activation of a plant defensin gene in Arabidopsis follows a salicylic acid-independent pathway,Plant Cell,8(12):2309-2323
Shi B.G.,Xie J.P.,Hu J.,Gao X.L.,Luo Y.Z.,Li S.B.,and Shi H.M.,2018,Sequence variation analysis of KAP6-1 and KAP6-4 genes in Yak,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(4):1383-1392(石斌刚,谢建鹏,胡江,高小莉,罗玉柱,李少斌,石红梅,2018,牦牛KAP6-1和KAP6-4基因序列变异分析,基因组学与应用生物学,37(4):1383-1392)
Terras F.R.,Schoofs H.M.,De Bolle M.F.,Van Leuven F.,Rees S.B.,Vanderleyden J.,Cammue B.P.,and Broekaert W.F.,1992,Analysis of two novel classes of plant antifungal proteins from radish(Raphanus sativus L.)seeds,Biol.Chem.,267(22):15301-15309
Terras F.R.G.,Eggermont K.,Kovaleva V.,Raikhel N.V.,Osborn R.W.,and Kester A.,1995,Small cysteine-rich antifungal proteins from radish:their role in host defense,Plant Cell,7(5):573-588
Wang J.L.,He Y.,Luan Y.F.,Dacizhuoga,and Zhang Y.Q.,2006,A Study on origin,evolution and spread of Brassica in China,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),22(8):489-494(王建林,何燕,栾运芳,大次卓嘎,张永青,2006,中国芸薹属植物的起源、演化与散布,中国农学通报,22(8):489-494)
Wang Y.,Nowak G.,Culley D.,Hadwiger L.A.,and Fristensky B.,1999,Constitutive expression of pea defense gene DRR-206 confers resistance to blackleg(Leptosphaeria maculans)disease in Transgenic canola(Brassica napus),Molecular Plant-Microbe Interactions,12(5):410-418
Xu J.,Zhu J.H.,Han Y.S.,Bai C.Y.,and Zhu H.L.,2018,Cloning and expression analysis of a new chalcone isomerase gene in Ipomoea batatas,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(2):845-849(徐靖,朱家红,韩义胜,白翠云,朱红林,2018,一个新的甘薯查尔酮异构酶基因的克隆和表达分析,基因组学与应用生物学,37(2):845-849)
Zhao G.H.,Zhang N.N.,Gao S.S.,Lu M.,Wang J.,Zhang T.Y.,and Li T.,2018,Cloning,expression characteristics and prokaryotic expression analysis of CYP83A1 gene from Isatis indigotica fort,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(1):302-312(赵桂红,张妮妮,高帅帅,陆苗,王晶,张天翼,李焘,2018,菘蓝CYP83A1基因的克隆、表达特性及原核表达分析,基因组学与应用生物学,37(1):302-312)
Zheng X.M.,Guo N.,Gan T.S.,Gong H.M.,and Zhang T.,2015,Cloning and expression analysis of defensin genes from Brassica napus,Zuowu Xuebao(Acta Agronomica Sinica),41(5):725-732(郑小敏,郭楠,高天姝,龚慧明,张涛,2015,甘蓝型油菜防御素基因的克隆与表达分析,作物学报,41(5):725-732)
Brogden K.A.,2005,Antimicrobial peptides:pore formers or metabolic inhibitors in bacteria?Nat.Rev.Microbiol.,3(3):238-250
Cheng F.,Sun R.,and Hou X.,2016,Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea,Nat.Genet.,48(10):1218-1224
De Samblanx G.W.,Goderis I.J.,Thevissen K.,Raemaekers R.,Fant F.,Borremans F.,Acland D.P.,Osborn R.W.,Patel S.,and Broekaert W.F.,1997,Mutational analysis of a plant defensin from radish(Raphanus sativus L.)reveals two adjacent sites important for antifungal activity,J.Biol.Chem.,272(2):1171-1179
Francois I.E.J.A.,De Bolle M.F.C,Dwyer G.,Inge J.W.M.,Goderis I.J.W.M.,Woutors P.F.J.,Verhaert P.D.,Proost P.,Schaaper W.M.M.,Cammue B.P.A.,and Broekaert W.F.,2002,Transgenic expression in Arabidopsis of a polyprotein construct leading to production of two different antimicrobial proteins,Plant Physiol.,128(4):1346-1356
Gao A.G.,Hakimi S.M.,Mittanck C.A.,Wu Y.,Woerner B.M.,Stark D.M.,Shah D.M.,Liang J.,and Rommens C.M.,2000,Fungal pathogen protection in potato by expression of a plant defensing peptide,Nat.Biotechnol.,18(12):1307-1310
Harberd D.J.,2010,A contribution to the cyto-taxonomy of Brassica(Cruciferae)and its allies,Botanical Journal of the Linnean Society,65(1):1-23
Lu J.X.,Lu K.,Zhang K.,Cao T.,Li J.N.,and Liang Y.,2010,Cloning and analysis of SAMDC3genes and their promoters from Brassica napus,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),29(2):215-224(陆俊杏,卢坤,张凯,曹延,李加纳,梁颖,2010,甘蓝型油菜SAMDC3基因及其启动子的克隆与分析,基因组学与应用生物学,29(2):215-224)
Lu K.,Chai Y.R.,Zhang K.,Wang R.,Chen L.,Lei B.,Lu J.,Xu X.F.,and Li J.N.,2008,Cloning and characterization of phosphorus starvation inducible Brassica napus,purple acid phosphatase,12,gene family,and imprinting of a recently evolved MITE-minisatellite twin structure,Theor.Appl.Genet.,117(6):963-975
Mendez E.,Moreno A.,Colilla F.,Pelaez F.,Limas G.G.,Mendez R.,Soriano F.,Salinas M.,and De Haro C.,1990,Primary structure and inhibition of protein synthesis in eukaryotic cell-free system of a novel thionin,gamma-hordothionin,from barley endosper,Biochemistry,194(2):533-539
Nagaharu U.,1935,Genome analysis in Brassica with special reference to the experimental formation of B.napus and peculiar mode of fertilization,JPN.J.Bot.,7:389-452
Parashina E.V.,Serdobinskii L.A.,Kalle E.G.,and Lavrova N.V.,2000,Genetic engineering of oilseed rape and tomato plants expressing a radish defensin gene,Russian Journal of Plant Physiology,47(3):417-423
Penninckx I.A.,Eggermont K.,Terras F.R.,Thomma B.P.,De Samblanx G.W.,Buchala A.,Métraux J.P.,Manners J.M.,and Broekaert W.F.,1996,Pathogen-induced systemic activation of a plant defensin gene in Arabidopsis follows a salicylic acid-independent pathway,Plant Cell,8(12):2309-2323
Shi B.G.,Xie J.P.,Hu J.,Gao X.L.,Luo Y.Z.,Li S.B.,and Shi H.M.,2018,Sequence variation analysis of KAP6-1 and KAP6-4 genes in Yak,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(4):1383-1392(石斌刚,谢建鹏,胡江,高小莉,罗玉柱,李少斌,石红梅,2018,牦牛KAP6-1和KAP6-4基因序列变异分析,基因组学与应用生物学,37(4):1383-1392)
Terras F.R.,Schoofs H.M.,De Bolle M.F.,Van Leuven F.,Rees S.B.,Vanderleyden J.,Cammue B.P.,and Broekaert W.F.,1992,Analysis of two novel classes of plant antifungal proteins from radish(Raphanus sativus L.)seeds,Biol.Chem.,267(22):15301-15309
Terras F.R.G.,Eggermont K.,Kovaleva V.,Raikhel N.V.,Osborn R.W.,and Kester A.,1995,Small cysteine-rich antifungal proteins from radish:their role in host defense,Plant Cell,7(5):573-588
Wang J.L.,He Y.,Luan Y.F.,Dacizhuoga,and Zhang Y.Q.,2006,A Study on origin,evolution and spread of Brassica in China,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),22(8):489-494(王建林,何燕,栾运芳,大次卓嘎,张永青,2006,中国芸薹属植物的起源、演化与散布,中国农学通报,22(8):489-494)
Wang Y.,Nowak G.,Culley D.,Hadwiger L.A.,and Fristensky B.,1999,Constitutive expression of pea defense gene DRR-206 confers resistance to blackleg(Leptosphaeria maculans)disease in Transgenic canola(Brassica napus),Molecular Plant-Microbe Interactions,12(5):410-418
Xu J.,Zhu J.H.,Han Y.S.,Bai C.Y.,and Zhu H.L.,2018,Cloning and expression analysis of a new chalcone isomerase gene in Ipomoea batatas,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(2):845-849(徐靖,朱家红,韩义胜,白翠云,朱红林,2018,一个新的甘薯查尔酮异构酶基因的克隆和表达分析,基因组学与应用生物学,37(2):845-849)
Zhao G.H.,Zhang N.N.,Gao S.S.,Lu M.,Wang J.,Zhang T.Y.,and Li T.,2018,Cloning,expression characteristics and prokaryotic expression analysis of CYP83A1 gene from Isatis indigotica fort,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(1):302-312(赵桂红,张妮妮,高帅帅,陆苗,王晶,张天翼,李焘,2018,菘蓝CYP83A1基因的克隆、表达特性及原核表达分析,基因组学与应用生物学,37(1):302-312)
Zheng X.M.,Guo N.,Gan T.S.,Gong H.M.,and Zhang T.,2015,Cloning and expression analysis of defensin genes from Brassica napus,Zuowu Xuebao(Acta Agronomica Sinica),41(5):725-732(郑小敏,郭楠,高天姝,龚慧明,张涛,2015,甘蓝型油菜防御素基因的克隆与表达分析,作物学报,41(5):725-732)