基于生物信息学的胶孢炭疽菌效应分子的筛选
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摘要
隶属炭疽菌属的胶孢炭疽菌(C. gloeosporioides)是农业和林业生产上重要的病原真菌,可以引起两百多种植物产生病害,对农林业造成严重的经济损失。效应蛋白在胶孢炭疽菌侵染寄主植物的过程发挥了关键作用。为了能筛选出胶孢炭疽菌(Colletotrichum gloeosporioides)的效应蛋白,以便开展对该菌与寄主的互作研究。本研究利用已经发表的胶孢炭疽菌的基因组序列,根据效应蛋白的主要特征,利用一系列生物信息分析服务器(SignalP, TMHMM, Protcomp, big-PI Predictor, TargetP和Blast),对该菌的效应蛋白进行预测和分析。我们共分析了胶孢炭疽菌的15 381个蛋白质序列,最后获得了443个符合效应蛋白特征的候选效应子,其中有86个具有预测功能。本研究为阐明炭疽病与植物寄主之间的相互作用提供理论依据。
C. gloeosporioides, belonging to the genus Colletotrichum, is an important phytopathogenic fungi in agricultural and forestry production. C. gloeosporioides can infect more than 200 varieties host plants and causes serious economic losses to agriculture and forestry. Effectors of C. gloeosporioides play a key role during the infection process of fungal pathogens on their host plants.The purpose of this study is to screen out effector proteins in Colletotrichum gloeosporioides for carrying out the plant-pathogen interaction researches between the bacteria and the host. Here, effector proteins from C. gloeosporioides, which genome sequence has been published,were predicted and analyzed with a series of bioinformatics analysis servers(SignalP, TMHMM, Protcomp, big-PI Predictor, TargetP and Blast). 15 381 protein sequences of C. gloeosporioides were analyzed, and 443 candidate effectors that match the profile of effector proteins were obtained. Among them, we have known 86 effector proteins with known function. This study might provide a theoretical basis for elucidating the interaction between C. gloeosporioides and plant hosts.
C. gloeosporioides, belonging to the genus Colletotrichum, is an important phytopathogenic fungi in agricultural and forestry production. C. gloeosporioides can infect more than 200 varieties host plants and causes serious economic losses to agriculture and forestry. Effectors of C. gloeosporioides play a key role during the infection process of fungal pathogens on their host plants.The purpose of this study is to screen out effector proteins in Colletotrichum gloeosporioides for carrying out the plant-pathogen interaction researches between the bacteria and the host. Here, effector proteins from C. gloeosporioides, which genome sequence has been published,were predicted and analyzed with a series of bioinformatics analysis servers(SignalP, TMHMM, Protcomp, big-PI Predictor, TargetP and Blast). 15 381 protein sequences of C. gloeosporioides were analyzed, and 443 candidate effectors that match the profile of effector proteins were obtained. Among them, we have known 86 effector proteins with known function. This study might provide a theoretical basis for elucidating the interaction between C. gloeosporioides and plant hosts.
引文
Cesari S.,Thilliez G.,Ribot C.,Chalvon V.,Michel C.,Jauneau A.,Rivas S.,Alaux L.,Kanzaki H.,and Okuyama Y.,2013,The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39by direct binding,Plant Cell,25(4):1463-1481
Chen J.S.,Zheng S.Q.,Zheng W.,Zhou J.,Lu G.D.,and Wang Z.H.,2006,Prediction for secreted proteins from Magnaporthe grisea genome,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),39(12):2474-2482(陈继圣,郑士琴,郑武,周洁,鲁国东,王宗华,2006,全基因组预测稻瘟菌的分泌蛋白,中国农业科学,39(12):2474-2482)
Chen Q.G.,Wang C.J.Z.,Yang M.,and Zhou E.X.,2015,Prediction of candidate effectors from the genome of Colletotrichum higginsianum,Redai Zuowu Xuebao(Chinese Journal of Tropical Crops),36(6):1105-1111(陈琦光,王陈骄子,杨媚,周而勋,2015,希金斯刺盘孢全基因组候选效应分子的预测,热带作物学报,36(6):1105-1111)
Gan P.,Ikeda K.,Irieda H.,Narusaka M.,O'Connell R.J.,Narusaka Y.,Takano Y.,Kubo Y.,and Shirasu K.,2013,Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi,New Phytol.,197(4):1236-1249
Han C.Z.,2014a,Research advances on genes in infection process of Colletotrichum gloeosporioides,Guangdong Nongye Kexue(Guangdong Agricultural Sciences),41(9):165-169(韩长志,2014a,胶孢炭疽菌侵染过程相关基因研究进展,广东农业科学,41(9):165-169)
Han C.Z.,2014b,Prediction for secreted proteins from Colletotrichum graminicola genome,Shengwu Jishu(Biotechnology),24(2):36-41(韩长志,2014b,全基因组预测禾谷炭疽菌的分泌蛋白,生物技术,24(2):36-41)
Han M.,Wang X.W.,Zhu X.Q.,and Guo L.Y.,2016,Distribution of RXLR effectors Avr3a,Avr4 and IPI-O in Phytophthora infestans isolates in China,Zhiwu Bingli Xuebao(Acta Phytopathologica Sinica),46(3):347-356(韩淼,汪晓雯,朱小琼,国立耘,2016,RxLR效应因子Avr3a,Avr4和IP-I-O在中国致病疫霉菌株中的组成,植物病理学报,46(3):347-356)
Huang J.F.,Chen B.Y.,Li J.F.,Gao Z.H.,Mi L.,Zhang Z.,Li G.P.,and Qiao Y.S.,2012,Isolation and identification ofpathogenic fungus Colletotrichum gloeosporioides(Penz.)Sacc.causing strawberry anthracnose,Xinan Nongye Xuebao(Southwest China Journal of Agricultural Sciences),25(5):1714-1719(黄金凤,陈丙义,李金凤,高志红,糜林,章镇,李国平,乔玉山,2012,草莓上胶孢炭疽菌的分离与鉴定,西南农业学报,25(5):1714-1719)
Jones J.D.,and Dangl J.L.,2006,The plant immune system,Nature,444(7117):323-329
Kong X.J.,Shi J.,Kong F.F.,Wang Z.Y.,and Zhang H.,2016,I-dentification of the signal peptide of candidate effector protein RXLR5 from Plasmopara viticola,Zhiwu Baohu(Plant Protection),42(1):40-44(孔祥久,石洁,孔繁芳,王忠跃,张昊,2016,葡萄霜霉菌候选效应子RXLR5信号肽的鉴定,植物保护,42(1):40-44)
Kumar G.V.,Pandey A.,Kumar P.,Pandey B.K.,Gaur R.K.,Bajpai V.,Sharma N.,and Sharma S.,2012,Genetic characterization of mango anthracnose pathogen Colletotrichum gloeosporioides Penz.by random amplified polymorphic DNAanalysis,African J.Biotechnology,9(26):4009-4013
Li H.,Zhu D.X.,Xu J.P.,Zhou G.Y.,Hu M.,and Tian F.,2014,Population genetic structure of Colletotrichum gloeosporioides causing anthracnose of Camellia oleifera in China,Zhi wu Bingli Xuebao(Acta Phytopathologica Sinica),44(6):620-628(李河,朱丹雪,徐建平,周国英,胡茉,田丰,2014,引起油茶炭疽病胶孢炭疽菌种群遗传结构研究,植物病理学报,44(6):620-628)
Liu Y.N.,Pu J.J.,Zhang H.,Zhou F.X.,Yang Y.L.,Zhang K.L.,and Liu X.M.,2017,Cloning and construction of knock out vector of scytalone dehydratase gene SCD1 from mango an thracnose(Colletotrichum gloeosporioides),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(3):894-899(刘娅楠,蒲金基,张贺,周芳雪,杨永利,张恺莉,刘晓妹,2017,芒果炭疽病菌小柱孢酮脱水酶基因SCD1的克隆与敲除载体构建,基因组学与应用生物学,36(3):894-899)
Stergiopoulos I.,and De Wit P.J.G.M.,2009,Fungal effector proteins,Annu.Rev.Phytopathol.,47(1):233-263
Valent B.,and Khang C.H.,2010,Recent advances in rice blast effector research,Curr.Opin.Plant Biol.,13(4):434-441
Wang Z.,Yang M.,Yang Y.Q.,Peng Z.K.,and Zhou E.X.,2010,Morphological and molecular identification of citrus anthracnose pathogen from Guangdong province,Junwu Xuebao(Mycosystema),29(4):488-493(王震,杨媚,杨迎青,彭正凯,周而勋,2010,广东省柑橘炭疽病病原菌的形态与分子鉴定,菌物学报,29(4):488-493)
Weir B.S.,Johnston P.R.,and Damm U.,2012,The Colletotrichum gloeosporioides species complex,Stud.Mycol.,73(1):115-180
Wu M.L.,Li X.Y.,Zhang N.,Xu S.,and Liu Z.Q.,2017,Gene cloning and biological function of CgRGS2 in Colletotrichum gloeosporioides,Weishengwu Xuebao(Acta Microbiologica Sinica),57(1):66-76(吴曼莉,李晓宇,张楠,徐爽,柳志强2017,胶孢炭疽菌CgRGS2基因的克隆及生物学功能,微生物学报,57(1):66-76)
Xu S.,Wu M.L.,Ke Z.J.,Liu Z.Q.,and Li X.Y.,2017,CgR GS4regulates vegetative growth,osmotic pressure response,oxidative stress response and pathogenicity in Colletotrichum gloeosporioides,Zhejiang Nongye Xuebao(Acta Agriculturae Zhejiangensis),29(2):277-285(徐爽,吴曼莉,柯智健,柳志强,李晓宇,2017,胶孢炭疽菌CgR GS4调控营养生长、渗透压响应、氧化应激反应和致病性,浙江农业学报,29(2):277-285)
Zhang N.,Liu Z.Q.,Wu M.L.,and Li X.Y.,2017,Gene cloning and functional analysis of CgSho1 in Colletotrichum gloeosporioides,Zhiwu Bingli Xuebao(Acta Phytopathologica Sinica),47(1):40-49(张楠,柳志强,吴曼莉,李晓宇,2017,胶孢炭疽菌CgSho1基因的克隆与功能分析,植物病理学报,47(1):40-49)
Zhou X.G.,Li C.Y.,Zhao Z.W.,Su Y.,Zhang S.S.,Li J.B.,Yang J.,Liu L.,and Ye Y.F.,2006,Analysis of the secreted proteins encoded by genes in genome of filamental fungus(Neurospora crassa),Yichuan(Hereditas),28(2):200-207(周晓罡,李成云,赵之伟,苏源,张绍松,李进斌,杨静,刘林,业艳芬,2006,粗糙脉孢菌基因组分泌蛋白的初步分析,遗传,28(2):200-207)
Chen J.S.,Zheng S.Q.,Zheng W.,Zhou J.,Lu G.D.,and Wang Z.H.,2006,Prediction for secreted proteins from Magnaporthe grisea genome,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),39(12):2474-2482(陈继圣,郑士琴,郑武,周洁,鲁国东,王宗华,2006,全基因组预测稻瘟菌的分泌蛋白,中国农业科学,39(12):2474-2482)
Chen Q.G.,Wang C.J.Z.,Yang M.,and Zhou E.X.,2015,Prediction of candidate effectors from the genome of Colletotrichum higginsianum,Redai Zuowu Xuebao(Chinese Journal of Tropical Crops),36(6):1105-1111(陈琦光,王陈骄子,杨媚,周而勋,2015,希金斯刺盘孢全基因组候选效应分子的预测,热带作物学报,36(6):1105-1111)
Gan P.,Ikeda K.,Irieda H.,Narusaka M.,O'Connell R.J.,Narusaka Y.,Takano Y.,Kubo Y.,and Shirasu K.,2013,Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi,New Phytol.,197(4):1236-1249
Han C.Z.,2014a,Research advances on genes in infection process of Colletotrichum gloeosporioides,Guangdong Nongye Kexue(Guangdong Agricultural Sciences),41(9):165-169(韩长志,2014a,胶孢炭疽菌侵染过程相关基因研究进展,广东农业科学,41(9):165-169)
Han C.Z.,2014b,Prediction for secreted proteins from Colletotrichum graminicola genome,Shengwu Jishu(Biotechnology),24(2):36-41(韩长志,2014b,全基因组预测禾谷炭疽菌的分泌蛋白,生物技术,24(2):36-41)
Han M.,Wang X.W.,Zhu X.Q.,and Guo L.Y.,2016,Distribution of RXLR effectors Avr3a,Avr4 and IPI-O in Phytophthora infestans isolates in China,Zhiwu Bingli Xuebao(Acta Phytopathologica Sinica),46(3):347-356(韩淼,汪晓雯,朱小琼,国立耘,2016,RxLR效应因子Avr3a,Avr4和IP-I-O在中国致病疫霉菌株中的组成,植物病理学报,46(3):347-356)
Huang J.F.,Chen B.Y.,Li J.F.,Gao Z.H.,Mi L.,Zhang Z.,Li G.P.,and Qiao Y.S.,2012,Isolation and identification ofpathogenic fungus Colletotrichum gloeosporioides(Penz.)Sacc.causing strawberry anthracnose,Xinan Nongye Xuebao(Southwest China Journal of Agricultural Sciences),25(5):1714-1719(黄金凤,陈丙义,李金凤,高志红,糜林,章镇,李国平,乔玉山,2012,草莓上胶孢炭疽菌的分离与鉴定,西南农业学报,25(5):1714-1719)
Jones J.D.,and Dangl J.L.,2006,The plant immune system,Nature,444(7117):323-329
Kong X.J.,Shi J.,Kong F.F.,Wang Z.Y.,and Zhang H.,2016,I-dentification of the signal peptide of candidate effector protein RXLR5 from Plasmopara viticola,Zhiwu Baohu(Plant Protection),42(1):40-44(孔祥久,石洁,孔繁芳,王忠跃,张昊,2016,葡萄霜霉菌候选效应子RXLR5信号肽的鉴定,植物保护,42(1):40-44)
Kumar G.V.,Pandey A.,Kumar P.,Pandey B.K.,Gaur R.K.,Bajpai V.,Sharma N.,and Sharma S.,2012,Genetic characterization of mango anthracnose pathogen Colletotrichum gloeosporioides Penz.by random amplified polymorphic DNAanalysis,African J.Biotechnology,9(26):4009-4013
Li H.,Zhu D.X.,Xu J.P.,Zhou G.Y.,Hu M.,and Tian F.,2014,Population genetic structure of Colletotrichum gloeosporioides causing anthracnose of Camellia oleifera in China,Zhi wu Bingli Xuebao(Acta Phytopathologica Sinica),44(6):620-628(李河,朱丹雪,徐建平,周国英,胡茉,田丰,2014,引起油茶炭疽病胶孢炭疽菌种群遗传结构研究,植物病理学报,44(6):620-628)
Liu Y.N.,Pu J.J.,Zhang H.,Zhou F.X.,Yang Y.L.,Zhang K.L.,and Liu X.M.,2017,Cloning and construction of knock out vector of scytalone dehydratase gene SCD1 from mango an thracnose(Colletotrichum gloeosporioides),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(3):894-899(刘娅楠,蒲金基,张贺,周芳雪,杨永利,张恺莉,刘晓妹,2017,芒果炭疽病菌小柱孢酮脱水酶基因SCD1的克隆与敲除载体构建,基因组学与应用生物学,36(3):894-899)
Stergiopoulos I.,and De Wit P.J.G.M.,2009,Fungal effector proteins,Annu.Rev.Phytopathol.,47(1):233-263
Valent B.,and Khang C.H.,2010,Recent advances in rice blast effector research,Curr.Opin.Plant Biol.,13(4):434-441
Wang Z.,Yang M.,Yang Y.Q.,Peng Z.K.,and Zhou E.X.,2010,Morphological and molecular identification of citrus anthracnose pathogen from Guangdong province,Junwu Xuebao(Mycosystema),29(4):488-493(王震,杨媚,杨迎青,彭正凯,周而勋,2010,广东省柑橘炭疽病病原菌的形态与分子鉴定,菌物学报,29(4):488-493)
Weir B.S.,Johnston P.R.,and Damm U.,2012,The Colletotrichum gloeosporioides species complex,Stud.Mycol.,73(1):115-180
Wu M.L.,Li X.Y.,Zhang N.,Xu S.,and Liu Z.Q.,2017,Gene cloning and biological function of CgRGS2 in Colletotrichum gloeosporioides,Weishengwu Xuebao(Acta Microbiologica Sinica),57(1):66-76(吴曼莉,李晓宇,张楠,徐爽,柳志强2017,胶孢炭疽菌CgRGS2基因的克隆及生物学功能,微生物学报,57(1):66-76)
Xu S.,Wu M.L.,Ke Z.J.,Liu Z.Q.,and Li X.Y.,2017,CgR GS4regulates vegetative growth,osmotic pressure response,oxidative stress response and pathogenicity in Colletotrichum gloeosporioides,Zhejiang Nongye Xuebao(Acta Agriculturae Zhejiangensis),29(2):277-285(徐爽,吴曼莉,柯智健,柳志强,李晓宇,2017,胶孢炭疽菌CgR GS4调控营养生长、渗透压响应、氧化应激反应和致病性,浙江农业学报,29(2):277-285)
Zhang N.,Liu Z.Q.,Wu M.L.,and Li X.Y.,2017,Gene cloning and functional analysis of CgSho1 in Colletotrichum gloeosporioides,Zhiwu Bingli Xuebao(Acta Phytopathologica Sinica),47(1):40-49(张楠,柳志强,吴曼莉,李晓宇,2017,胶孢炭疽菌CgSho1基因的克隆与功能分析,植物病理学报,47(1):40-49)
Zhou X.G.,Li C.Y.,Zhao Z.W.,Su Y.,Zhang S.S.,Li J.B.,Yang J.,Liu L.,and Ye Y.F.,2006,Analysis of the secreted proteins encoded by genes in genome of filamental fungus(Neurospora crassa),Yichuan(Hereditas),28(2):200-207(周晓罡,李成云,赵之伟,苏源,张绍松,李进斌,杨静,刘林,业艳芬,2006,粗糙脉孢菌基因组分泌蛋白的初步分析,遗传,28(2):200-207)