Secreted Protein and Peptaibols Synthetase of Trichoerma harzianum Tr1: Bioinformatics Analysis

doi:10.11924/j.issn.1000-6850.casb18040012

Abstract

Abstract: The paper aims to analyze the secreted proteins and Peptaibols synthetase of Trichoerma harzianum by bioinformatics methods. Using the 11264 hypothetical proteins of Trichoerma harzianum Tr1 as the objects of this study, we applied the bioinformatics methods such as SignalP, Protparam and Swissmodel to predict the secreted proteins, and analyzed their signal peptides, in order to select the secreted proteins and Peptaibols synthetase associating with the biocontrol mechanism, and analyzed the properties, structures and functions of these proteins. The results showed that: a total of 403 secreted proteins were found in Trichoerma harzianumTr1, thereinto PNP53160 and PNP56908 might act as cellulase and chitinase respectively; the intermediate region of signal peptide was rich in leucine and alanine, while the C terminals of signal peptides belonged to A-X-A type; the 16862-20750 aa of PNP58822 which contained 5 kinds of functional regions including acetyl coenzyme A synthetase Ⅰ, CT domain of TaqA, and surfactin synthetase subunit Ⅲ and so on, probably acted as Peptaibols synthetase. In this study, 403 secreted proteins and their signal peptides are analyzed by bioinformatics methods, and the characteristics, structures and functions of the proteins which are probably associated with the biocontrol mechanism of Trichoerma harzianum are predicted, so as to provide a fundamental basis for further study on its biocontrol mechanism.

戴陈伟,李静,蔡标,张爽,童琳 and 叶红. Secreted Protein and Peptaibols Synthetase of Trichoerma harzianum Tr1: Bioinformatics Analysis[J]. Chinese Agricultural Science Bulletin, 2018, 34(23): 46-52.

References

[1]吕黎, 许丽媛, 罗志威,等. 哈茨木霉生物防治研究进展[J]. 湖南农业科学, 2013(17):92-95.
[2]管怀骥, 陈莉. 哈茨木霉TH-1菌株对小麦纹枯病的控制效果研究[J]. 安徽农业科学, 2011, 39(16):9664-9665.
[3]刘爱荣, 陈双臣, 陈凯,等. 哈茨木霉对黄瓜尖孢镰刀菌的抑制作用和抗性相关基因表达[J]. 植物保护学报, 2010, 37(3):249-254.
[4]Zimand G, Elad Y, Chet I. Effect of Trichoderma harzianum on Botrytis cinerea pathogenicity.[J]. Phytopathology, 1996, 86(11):1255-1260.
[5]陈方新, 齐永霞, 戴庆怀,等. 哈茨木霉对几种植物病原真菌的拮抗作用及其抗药性测定[J]. 中国农学通报, 2005, 21(11):314-317.
[6]李琼芳, 曾华兰, 叶鹏盛,等. 哈茨木霉(Trichoerma harzianum)T23生防菌筛选及防治中药材根腐病的研究[J]. 西南大学学报(自然科学版), 2007, 29(11):119-122.
[7]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.
[8]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.
[9]Martinez D. The Phanerochaete chrysosporium secretome: database predictions and initial mass spectrometry peptide identifications in cellulose-grown medium.[J]. Journal of Biotechnology, 2005, 118(1):17-34.
[10]韩长志, 刘艳, 任雪敏. 全基因组预测褐环乳牛肝菌的分泌蛋白[J]. 江苏农业科学, 2017, 45(23):45-48.
[11]杨静, 李成云, 王云月,等. 酿酒酵母分泌蛋白组的计算机分析[J]. 中国农业科学, 2005, 38(3):516-522.
[12]潘顺. 哈茨木霉菌发酵液中Peptaibols类抗菌肽的分离纯化、鉴定及活性研究[D]. 中国计量学院, 2013.
[13]宋晓妍, 张玉忠, 王元秀. 木霉peptaibols抗菌肽的研究进展[J]. 微生物学报, 2011, 51(4):438-444.
[14]Aric W, Darlene G, Xu B W, et al. Identification of peptaibols from Trichoderma virens and cloning of a peptaibol synthetase[J]. Journal of Biological Chemistry, 2002, 277(23):20862.
[15]Vizcaíno J A, Cardoza R E, Dubost L, et al. Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene from T. harzianum CECT 2413[J]. Folia Microbiologica, 2006, 51(2):114-20.
[16]宋伟, 李鼎立, 王然,等. 蔷薇科植物DELLA蛋白的生物信息学分析[J]. 中国农学通报, 2013, 29(19):142-148.
[17]田新生, 吴培星. 四种真菌基因组编码的细胞壁降解酶生物信息学分析[J]. 中国农学通报, 2009, 25(19):26-31.
[18]张亮, 张智俊, 李疆,等. 扁桃CBF1基因的克隆与生物信息学分析[J]. 中国农学通报, 2014, 30(34):16-23.
[19]陈建荣, 郭清泉, 张学文,等. 苎麻咖啡酰辅酶A甲基转移酶基因原核表达及其结构分析[J]. 中国农学通报, 2008, 24(12):50-53.
[20]邢家强, 刘晓凡, 窦强,等. 风疹病毒E1蛋白与受体结合特定结合域的预测[J]. 中国生物制品学杂志, 2014, 27(6):756-760.
[21]Petersen T N, Brunak S, Von H G, et al. SignalP 4.0: discriminating signal peptides from transmembrane regions.[J]. Nature Methods, 2011, 8(10):785-6.
[22]Blum T, Briesemeister S, Kohlbacher O. MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction.[J]. Bmc Bioinformatics, 2009, 10(1):274.
[23]Krogh A, Larsson B, Heijne G V, et al. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes 1[J]. Journal of Molecular Biology, 2001, 305(3):567-580.
[24]Lukas K, Anders K, Sonnhammer E L L. Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server[J]. Nucleic Acids Research, 2007, 35(Web Server issue):429-32.
[25]Eisenhaber B, Schneider G, Wildpaner M, et al. A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe.[J]. Journal of Molecular Biology, 2004, 337(2):243-253.
[26]Emanuelsson O, Nielsen H, Brunak S, et al. Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence[J]. Journal of Molecular Biology, 2000, 300(4):1005-1016.
[27]Biasini M, Bienert S, Waterhouse A, et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information[J]. Nucleic Acids Research, 2014, 42(Web Server issue):W252.
[28]Kopp J, Schwede T. The SWISS-MODEL Repository: new features and functionalities[J]. Nucleic Acids Research, 2006, 34(Database issue):D315.
[29]Guex N, Peitsch M C, Schwede T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.[J]. Electrophoresis, 2009, 30(S1):S162–S173.
[30]Benkert P, Biasini M, Schwede T. Toward the estimation of the absolute quality of individual protein structure models[J]. Bioinformatics, 2011, 27(3):343-350.
[31]Bertoni M, Kiefer F, Biasini M, et al. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology[J]. Sci Rep, 2017, 7(1).
[32]Dundas J, Ouyang Z, Tseng J, et al. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues.[J]. Nucleic Acids Research, 2006, 34(Web Server issue):116-8.
[33]Waterhouse A M, Procter J B, Martin D M, et al. Jalview Version 2--a multiple sequence alignment editor and analysis workbench[J]. Bioinformatics, 2009, 25(9):1189.
[34]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(6):546-551.
[35]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.
[36]郑斌, 詹希美. 信号肽序列及其在蛋白质表达中的应用[J]. 生物技术通讯, 2005, 16(3):296-298.
[37]李红玲. 非核糖体肽合成酶结构研究进展[J]. 临床合理用药杂志, 2013, 6(28):180-181.
[38]Zhang J, Liu N, Cacho R A, et al. Structural basis of nonribosomal peptide macrocyclization in fungi[J]. Nature Chemical Biology, 2016, 12(12):1001.
[39]And G J, Tong L. Crystal Structure of Yeast Acetyl-Coenzyme A Synthetase in Complex with AMP?[J]. Biochemistry, 2004, 43(6):1425-1431.
[40]Tanovic A, Samel S A, Essen L O, et al. Crystal structure of the termination module of a nonribosomal peptide synthetase.[J]. Science, 2008, 321(5889):659.
[41]Barajas, Jesus , Phelan, et al. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols[J]. Chemistry & Biology, 2015, 22(8):1018.