利用马铃薯晚疫病菌全基因组测序结果, 结合计算机技术和生物信息学的方法, 对马铃薯晚疫病菌的蛋白进行分析, 为明确该病原菌与寄主互作的分子机制奠定基础。文章应用信号肽预测软件SignalP v3.0和PSORT, 跨膜螺旋结构预测软件TMHMM-2.0和THUMBUP, GPI锚定位点预测软件big-PI Predictor, 亚细胞器中蛋白定位分布预测软件TargetP v1.01, 对已经公布的马铃薯晚疫病菌全基因组22 658个蛋白质氨基酸序列进行分析。结果发现, 晚疫病菌全基因组编码蛋白中有671个为潜在的分泌型蛋白, 占编码蛋白总数的3.0%。其中有45个分泌蛋白有功能方面的描述, 其功能涉及细胞代谢、信号转导等方面; 此外, 还有一些与激发子类似的分泌蛋白, 它们可能与晚疫病菌的毒性有关。
Based on the Phytophthora infestans genome sequence, we used bioinformatics and computer-based prediction algorithms to predict the secreted proteins of P. infestans in detail, which would help us to elucidate the molecular mechanism underlying the interaction between the host plants and the P. infestans. In this study, the signal peptide prediction algorithms SignalP v3.0 and PSORT, transmembrane helix prediction algorithms TMHMM-2.0 and THUMBUP, GPI-anchoring site prediction algorithm big-PI Predictor, and subcellular protein location distribution algorithm TargetP v1.01 were used to analyze the 22658 protein sequences of P. infestans published. Our results suggested that there might be 671 secreted proteins, accounting for 3.0% of the total proteins. Among them, the functions of the 45 secreted proteins had been described previously. Their functions involved cellular metabolism and signal transduction etc. In addition, some of the secreted proteins were functionally similar to elicitin, which were likely to be associated with the virulence of P. infestans.
[1] Duncan JM. Phytophthora—an abiding threat to our crops. Microbiol Today, 1999, 26(99): 114-116.
[2] Kamoun S. Molecular genetics of pathogenic oomycetes. Eukaryotic Cell, 2003, 2(2): 191-199.
[3] Margulis L, Schwartz KV. Five Kingdoms-An Illustrated Guide to the Phyla of Life on Earth. San Francisco: Free-man, 1982.
[4] Erwin DC, Ribeiro OK. Phytophthora: Diseases World-wide. St. Paul: APS Press, 1996.
[5] Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. A kingdom-level phylogeny of eukaryotes based on com-bined protein data. Science, 2000, 290(5493): 972-977.
[6] Sogin ML, Silberman JD. Evolution of the protists and protistan parasites from the perspective of molecular systematic. Int J Parasitol, 1998, 28(1): 11-20.
[7] Sansome E, Brasier CM. Diploidy and chromosomal structural hybridity in Phytophthora infestans. Na-ture, 1973, 241(5388): 344-345.
[8] Blobel G, Sabatini DD. Ribosome-membrane interaction in eukaryotic cells. Biomembranes, 1971, 2(2): 193-195.
[9] Martoglio B, Dobberstein B. Signal sequence: more than just greasy peptides. Trends Cell Biol, 1998, 8(10): 410-415.
[10] Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M. Interrelating different types of genomic data from pro-teome to secretome: 'oming in on function. Genome Res, 2001, 11(9): 1463-1468.
[11] Nimchuk Z, Eulgem T, Holt BF III, Dangl JL. Recognition and response in the plant immune system. Annu Rev Genet, 2003, 37(1): 579-609.
[12] Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering, 1997, 10(1): 1-6.
[13] Möller S, Croning MDR, Apweiler R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 2001, 17(7): 646-653.
[14] Zhou HY, Zhou YQ. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Sci, 2003, 12(7): 1547-1555.
[15] Nakai K. Protein sorting signals and prediction of subcellular localization. Adv Protein Chem, 2000, 54(9): 277-344.
[16] Eisenhaber B, Bork P, Eisenhaber F. Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transami-dase. Protein Engineering, 1998, 11(12): 1155-1161.
[17] Eisenhaber B, Bork P, Eisenhaber F. Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol, 1999, 292(3): 741-758.
[18] Barash S, Wang W, Shi YG. Human secretory signal pep-tide description by hidden Markov model and generation of a strong artificial signal peptide for secreted protein expression. Biochem Biophys Res Cammun, 2002, 294(4): 835-842.
[19] Lee SA, Wormsley S, Kamoun S, Lee AFS, Joiner K, Wong B. An analysis of the Candida albicans genome database for soluble secreted proteins using computer-based prediction algorithms. Yeast, 2003, 20(7): 595-610.
[20] Tjalsma H, Bolhuis A, Jongbloed JDH, Bron S, van Dijl JM. Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microb Mol Biol Rev, 2000, 64(3): 515-547.
[21] 周晓罡, 李成云, 赵之伟, 苏源, 李进斌, 杨静, 刘林, 业艳芬, 张绍松. 粗糙脉孢菌基因组分泌蛋白的初步分析. 遗传, 2006, 28(2): 200-207.
[22] 范成明, 李成云, 赵明富, 何月秋. 根癌土壤杆菌C58 Cereon中分泌蛋白信号肽分泌. 微生物学报, 2005, 45(4): 561-566.
[23] 吴红芝, 李成云, 朱有勇, 毕玉芬. 秀丽小杆线虫分泌蛋白组的计算机分析. 遗传, 2006, 28(4): 470-478.
[24] 吴毅歆, 熊国如, 袁远, 罗灯涛, 何月秋. 水稻基因组中分泌蛋白的初步分析. 分子植物育种, 2008, 6(5): 1011-1014.
[25] 于钦亮, 马莉, 刘林, 杨静, 苏源, 王云月, 朱有勇, 李成云. 禾谷镰刀菌基因组中含寄主靶向模体分泌蛋白功能的初步分析. 生物技术通报, 2008, (1): 160-165.
[26] Bhattacharjee S, Hiller NL, Liolios K, Win J, Kanneganti TD, Young C, Kamoun S, Haldar K. The malarial host-targeting signal is conserved in the Irish po
