Prediction of secretory protein in walnut bacterial black spot pathogen

ZHU Youpeng, LIU Hongli, HAN Changzhi

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2019, Vol. 43 ›› Issue (03) : 17-22.

PDF(1698981 KB)
南京林业大学学报（自然科学版）
PDF(1698981 KB)
Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2019, Vol. 43 ›› Issue (03) : 17-22. DOI: 10.3969/j.issn.1000-2006.201807003

Prediction of secretory protein in walnut bacterial black spot pathogen

  • ZHU Youpeng1, LIU Hongli1, HAN Changzhi1,2*
Author information +
History +

Abstract

【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, DW3F3, 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.

Cite this article

EndNote

Ris (Procite)

Bibtex

Download Citations
ZHU Youpeng, LIU Hongli, HAN Changzhi. Prediction of secretory protein in walnut bacterial black spot pathogen[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 2019, 43(03): 17-22 https://doi.org/10.3969/j.issn.1000-2006.201807003

References

[1] 李娅, 余红红. 基于全产业链视角的云南省核桃产业国内竞争力分析[J]. 林业经济问题, 2018, 38(5): 38-43,104. DOI:10.16832/j.cnki.1005-9709.2018.05.006.
LI Y, YU H H.Analysis on the domestic competitiveness of walnut industry in Yunnan Province from the perspective of whole industry chain[J]. Issues of Forestry Economics, 2018, 38(5): 38-43,104.
[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, COLARIC^ M, USENIK V, 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.
[18] GOMEZ M, JOHNSON S, GENNARO M L. Identification of secreted proteins of Mycobacterium tuberculosis by a bioinformatic approach[J]. Infection and Immunity, 2000, 68(4): 2323-2327.
[19] 肖文超, 范会云, 白亭亭, 等. 香蕉细菌性软腐病菌XJ8-3-3基因组中ORFs的信号肽及分泌蛋白功能预测分析[J]. 果树学报,2014, 31(6): 1057-1064.
XIAO W C, FAN H Y, BAI T T, et al. Prediction and analysis of the signal peptide and secreted proteins in softrot bacteria XJ8-3-3 genome ORFs of banana [J]. Journal of Fruit Science, 2014, 31(6): 1057-1064.
[20] 黄俊丽, 吴金钟, 肖崇刚, 等. 植物病原细菌Ralstonia solanacearum GMI1000中分泌蛋白信号肽分析[J]. 遗传, 2007, 29(11): 1409-1416. DOI:10.16288/j.yczz.2007.11.022.
HUANG J L, WU J Z, XIAO C G, et al. Analysis of signal peptides of the secreted proteins in Ralstonia solanacearum GMI1000[J]. Hereditas, 2007, 29(11): 1409-1416.
[21] 刘雅婷, 李正跃, 朱有勇, 等. 植物病原细菌Pseudomonas syringae pv.tomato基因组中的信号肽分析[J]. 遗传, 2005, 27(6): 959-964. DOI:10.3321/j.issn:0253-9772.2005.06.019.
LIU Y T, LI Z Y, ZHU Y Y, et al. Analysis of the coding region for signal peptide-containing proteins in Pseudomonas syringae pv. tomato genome[J]. Hereditas, 2005, 27(6): 959-964.
[22] 吕伟强, 刘聪, 黄丽丽, 等. 内生菌KM-1-2全基因组ORFs信号肽和分泌蛋白预测及功能分析[J]. 微生物学报, 2017, 57(3): 411-421. DOI:10.13343/j.cnki.wsxb.20160281.
LÜ W Q, LIU C, HUANG L L, et al. Genome-wide prediction and analysis of the secretory proteins and ORFs signal peptide of ginkgo endophyte KM-1-2[J]. Acta Microbiologica Sinica, 2017, 57(3): 411-421.
[23] 韩长志, 祝友朋, 许僖. 枯草芽孢杆菌XF-1的碳水化合物活性酶类(CAZymes)蛋白预测与遗传关系分析[J]. 河南师范大学学报(自然科学版), 2018, 46(3): 95-100.
HAN C Z, ZHU Y P, XU X. Prediction for CAZymes proteins from Bacillus subtilis XF-1 genome[J]. Journal of Henan Normal University(Natural Science), 2018, 46(3): 95-100.
[24] 韩长志. 全基因组预测枯草芽孢杆菌 XF-1的分泌蛋白[J]. 福建农业学报, 2016, 31(4): 384-388. DOI:10.19303/j.issn.1008-0384.2016.04.010.
HAN C Z. Prediction algorithm on secretory proteins of Bacillus subtilis XF-1[J]. Fujian Journal of Agricultural Sciences, 2016, 31(4): 384-388.
[25] 韩长志, 王娟. 基于全基因组序列预测里氏木霉QM6a的分泌蛋白[J]. 华中农业大学学报, 2017, 36(2): 28-32. DOI:10.13300/j.cnki.hnlkxb.20170213.017.
HAN C Z, WANG J. Predicting forsecreted proteins from Trichoderma reesei QM6a genome[J]. Journal of Huazhong Agricultural University, 2017, 36(2): 28-32.
[26] 陈琦光, 王陈骄子, 杨媚, 等. 希金斯刺盘孢全基因组候选效应分子的预测[J]. 热带作物学报, 2015, 36(6): 1105-1111.
CHEN Q G, WANG C J Z, YANG M, et al. Prediction of candidate effectors from the genome of Colletotrichum higginsianum [J]. Chinese Journal of Tropical Crops, 2015, 36(6): 1105-1111.
[27] 陈相永, 陈捷胤, 肖红利, 等. 植物病原真菌寄生性与分泌蛋白组CAZymes的比较分析[J]. 植物病理学报, 2014, 44(2): 163-172.
CHEN X Y, CHEN J Y, XIAO H L, et al. The comparative analysis of secreted CAZymes in phytopathogenic fungi with different lifestyle[J]. Acta Phytopathologica Sinica, 2014, 44(2): 163-172.
[28] 陈建森, 佘菲菲. 全基因组预测幽门螺杆菌的分泌蛋白[J]. 中国人兽共患病学报, 2008, 24(7): 607-611. DOI:10.3969/j.issn.1002-2694.2008.07.004.
CHEN J S, SHE F F. Whole genome prediction for secreted proteins from Helicobacter pylori[J]. Chinese Journal of Zoonoses, 2008, 24(7): 607-611.
[29] 孙阳. 不同药剂防治核桃细菌性黑斑病田间药效试验[J]. 山东农业科学, 2012, 44(1): 93-94. DOI:10.3969/j.issn.1001-4942.2012.01.027.
SUN Y. Field efficacy test of different pesticides against walnut bacterial black spot disease[J]. Shandong Agricultural Sciences, 2012, 44(1): 93-94.
[30] 宫永红. 核桃细菌性黑斑病研究进展[J]. 北方果树, 2012(6): 1-4. DOI:10.3969/j.issn.1001-5698.2012.06.001.
GONG Y H. Advance in research on walnut blight[J]. Northern Fruits, 2012(6): 1-4.
PDF(1698981 KB)

Accesses

Citation

Detail
Sections
Recommended
The full text is translated into English by AI, aiming to facilitate reading and comprehension. The core content is subject to the explanation in Chinese.

Author

Reader

Reviewer

www.nldxb.njfu.edu.cn

Edited ＆ Published by Editorial Department of Nanjing Forestry University(Natural Sciences Edition)
Address： No.159 Longpan Road,Nanjing 210037 Jiangsu,P.R.China
E-mail ：xuebao@njfu.edu.cn , xuebao@njfu.com.cn
Telephone +86-25-85428247,85427076
Distributed by China International Book Trading Corporation P.O. Box 399, Beijing ,P.R. China

/

〈 〉