基于全基因组序列的核桃细菌性黑斑病菌分泌蛋白的预测及特征分析
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摘要
【目的】充分了解核桃黑斑病菌的侵染机制。【方法】以全基因组序列已经公布的7个核桃细菌性黑斑病菌菌株CFBP2528、CFBP7179、CFBP8253、DW3F3、J303、NCPPB1447、Xaj417等所具有的蛋白序列为预测数据,基于分泌蛋白所具有的主要特征,利用SignalP v4.1、ProtCompB v9.0、TMHMM v2.0、big-PI Fungal predictor、TargetP v1.1、LipoP v1.0等在线分析程序对分泌蛋白进行预测,同时分析其氨基酸组成及分布、信号肽长度、信号肽切割位点等特征。【结果】核桃细菌性黑斑病菌的分泌蛋白平均为74个,其氨基酸长度多集中于101～400氨基酸,所占比例为63.65%。信号肽氨基酸残基中以A最多,所占比例为22.04%;其次是L,所占比例为19.27%。信号肽长度以19～29个氨基酸的最多,所占比例为79.62%,信号肽切割位点属于A-X-A类型。【结论】核桃细菌性黑斑病菌中分泌蛋白的有效预测,可为深入解析核桃细菌性黑斑病菌中分泌蛋白在侵染过程中所发挥的功能提供理论依据。
【Objective】 Fully understand the infection mechanism of black spot pathogen of walnut. 【Method】 The genome sequence of seven bacterial pathogens causing black spot of walnut, CFBP2528, CFBP7179, CFBP8253, DW3 F3, J303, NCPPB1447 and Xaj417, whose complete genome sequence is known, were analyzed. Secretory proteins were predicted in the genome sequence based on the features of secretory protein using the online prediction programs such as SignalP v4.1, ProtCompB v9.0, TMHMM v2.0, big-PI Fungal predictor, TargetP v1.1, and LipoP v1.0. Additionally, the amino acid composition and distribution, signal peptide length, and signal peptide cleavage site of the secretory proteins were analyzed. 【Result】 The average number of secretory proteins predicted in the pathogens causing bacterial black spot of walnut was 74. The length of secretory proteins was mostly in the range of 101-400 amino acid residues, which accounted for about 63.65% of the total predicted secretory proteins. The abundant amino acid residue in the signal peptide was alanine, which accounted for 22.04%, followed by leucine, which accounted for 19.27% of the total amino acid residues. The length of signal peptide was mostly in the range of 19-29 amino acids residues, which accounted for 79.62% of the total predicted signal peptides. The signal peptide cleavage site belonged to the A-X-A type. 【Conclusion】The prediction of secreted proteins in the bacterial black spot pathogen of walnut is effe-ctively realized, which provides a theoretical foundation for further analysis of the secretory protein functions in the pathogens causing bacterial black spot of walnut during the process of infection.
【Objective】 Fully understand the infection mechanism of black spot pathogen of walnut. 【Method】 The genome sequence of seven bacterial pathogens causing black spot of walnut, CFBP2528, CFBP7179, CFBP8253, DW3 F3, J303, NCPPB1447 and Xaj417, whose complete genome sequence is known, were analyzed. Secretory proteins were predicted in the genome sequence based on the features of secretory protein using the online prediction programs such as SignalP v4.1, ProtCompB v9.0, TMHMM v2.0, big-PI Fungal predictor, TargetP v1.1, and LipoP v1.0. Additionally, the amino acid composition and distribution, signal peptide length, and signal peptide cleavage site of the secretory proteins were analyzed. 【Result】 The average number of secretory proteins predicted in the pathogens causing bacterial black spot of walnut was 74. The length of secretory proteins was mostly in the range of 101-400 amino acid residues, which accounted for about 63.65% of the total predicted secretory proteins. The abundant amino acid residue in the signal peptide was alanine, which accounted for 22.04%, followed by leucine, which accounted for 19.27% of the total amino acid residues. The length of signal peptide was mostly in the range of 19-29 amino acids residues, which accounted for 79.62% of the total predicted signal peptides. The signal peptide cleavage site belonged to the A-X-A type. 【Conclusion】The prediction of secreted proteins in the bacterial black spot pathogen of walnut is effe-ctively realized, which provides a theoretical foundation for further analysis of the secretory protein functions in the pathogens causing bacterial black spot of walnut during the process of infection.
引文
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[2] 韩长志,霍超.核桃炭疽病生物防治菌株YB-4-15的筛选和鉴定[J].经济林研究,2016,34(1):83-89.DOI:10.14067/j.cnki.1003-8981.2016.01.014.HAN C Z,HUO C.Isolation and identification of YB-4-15 strain against walnut anthracnose[J].Nonwood Forest Research,2016,34(1):83-89.
[3] 韩长志,霍超.核桃炭疽病生防菌yb33的鉴定及其次生代谢物特性分析[J].经济林研究,2015,33(3):63-67,74.DOI:10.14067/j.cnki.1003-8981.2015.03.011.HAN C Z,HUO C.Identiifcation of bio-control strain yb33 against walnut anthracnose and analysis of its secondary metabolite characteristics[J].Nonwood Forest Research,2015,33(3):63-67,74.
[4] 王琳莹.石棉县核桃黑斑病与炭疽病病原鉴定及其防治技术研究[D].雅安:四川农业大学,2015.WANG L Y.Identifieation and control of pathogens causing walnut anthracnoset and walnut blight in Shimian[D].Yaan:Sichuan Agricultural University,2015.
[5] 张永强,朱惠英,冯强,等.核桃黑斑病病原研究与防治试验初报[J].甘肃林业科技,2004,29(2):41-42.DOI:10.3969/j.issn.1006-0960.2004.02.013.ZHANG Y Q,ZHU H Y,FENG Q,et al.Preliminary report on pathogen studies of Xanthomonas campestris and its control trial[J].Journal of Gansu Forestry Science and Technology,2004,29(2):41-42.
[6] 曲文文,杨克强,刘会香,等.山东省核桃主要病害及其综合防治[J].植物保护,2011,37(2):136-140.DOI:10.3969/j.issn.0529-1542.2011.02.030.QU W W,YANG K Q,LIU H X,et al.Main diseases of walnut and integrated management in Shandong[J].Plant Protection,2011,37(2):136-140.
[7] SOLAR A,COLARI,et al.Seasonal variations of selected flavonoids,phenolic acids and quinones in annual shoots of common walnut (Juglans regia L.)[J].Plant Science,2006,170(3):453-461.DOI:10.1016/j.plantsci.2005.09.012.
[8] 张慧,乔旭,王云霞,等.陇南市核桃细菌性黑斑病的发生与防治[J].现代农业科技,2012(14):118-118.DOI:10.3969/j.issn.1007-5739.2012.14.082.ZHANG H,QIAO X,WANG Y X,et al.Occurrence and prevention of walnut bacterial black spot disease in Longnan City [J].Modern Agricultural Sciences and Technology,2012(14):118-118.
[9] 肖波,卢世栋,杨斌,等.云南核桃细菌性黑斑病病原菌的分离与鉴定[J].贵州农业科学,2017,45(12):55-58,63.XIAO B,LU S D,YANG B,et al.Isolation and identification of walnut bacterial black spot pathogen in Yunnan[J].Guizhou Agricultural Sciences,2017,45(12):55-58,63.
[10] 韩长志,许僖.植物病原丝状真菌分泌蛋白及CAZymes的研究进展[J].南京林业大学学报(自然科学版),2017,41(5):152-160.DOI:10.3969/j.issn.1000-2006.201607045.HAN C Z,XU X.Advance in functional research of secreted protein and CAZymes in plant pathogenic filamentous fungus[J].Journal of Nanjing Forestry University(Natural Sciences Edition),2017,41(5):152-160.
[11] 韩长志.全基因组预测禾谷炭疽菌的分泌蛋白[J].生物技术,2014,24(2):36-41.HAN C Z.Prediction for secreted proteins from Colletotrichum graminicola genome[J].Biotechnology,2014,24(2):36-41.
[12] 韩长志.全基因组预测希金斯炭疽菌的候选效应分子[J].生物技术,2015,25(6):546-551.HAN C Z.Prediction for candidate effectors from Colletotrichum higginsanum genome[J].Biotechnology,2015,25(6):546-551.
[13] 陈继圣,郑士琴,郑武,等.全基因组预测稻瘟菌的分泌蛋白[J].中国农业科学,2006,39(12):2474-2482.DOI:10.3321/j.issn:0578-1752.2006.12.011.CHEN J S,ZHENG S Q,ZHENG W,et al.Prediction for secreted proteins from Magnaporthe grisea genome[J].Scientia Agricultura Sinica,2006,39(12):2474-2482.
[14] 田李,陈捷胤,陈相永,等.大丽轮枝菌(Verticillium dahliae VdLs.17)分泌组预测及分析[J].中国农业科学,2011,44(15):3142-3153.TIAN L,CHEN J Y,CHEN X Y,et al.Prediction and analysis of Verticillium dahliae VdLs.17 secretome[J].Scientia Agricultura Sinica,2011,44(15):3142-3153.
[15] 韩长志.全基因组预测樟疫霉的候选效应分子[J].南京林业大学学报(自然科学版),2015,39(2):69-74.DOI:10.3969/j.issn.1000-2006.2015.02.012.HAN C Z.Prediction for candidate effector proteins from Phytophthora cinnamomi genome[J].Journal of Nanjing Forestry University (Natural Sciences Edition),2015,39(2):69-74.
[16] 周晓罡,侯思名,陈铎文,等.马铃薯晚疫病菌全基因组分泌蛋白的初步分析[J].遗传,2011,33(7):785-793.DOI:10.3724/SP.J.1005.2011.00785.ZHOU X G,HOU S M,CHEN D W,et al.Genome-wide analysis of the secreted proteins of phytophthora infestans[J].Hereditas,2011,33(7):785-793.
[17] 任文来,韩长志,刘通,等.全基因组预测枯草芽孢杆菌BEST195的分泌蛋白[J].西南林业大学学报,2016,36(6):106-111.DOI:10.11929/j.issn.2095-1914.2016.06.017.REN W L,HAN C Z,LIU T,et al.Prediction for secreted proteins from Bacillus subtilis subsp.natto BEST195 genome[J].Journal of Southwest Forestry University,2016,36(6):106-111.
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