The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins.
The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins.
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铜绿假单胞菌膜相关蛋白的研究概况
DOI：
10.3390/cells9112421
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发表时间：
2020-11-05
期刊：
影响因子：
6
通讯作者：
Di Silvestre D
中科院分区：
文献类型：
--
作者：
Motta S;Vecchietti D;Martorana AM;Brunetti P;Bertoni G;Polissi A;Mauri P;Di Silvestre D
背景：铜绿假单胞菌细胞膜相关蛋白在感染机制中发挥相关作用。它们可以促进细菌细胞对抗生素的耐药性，并参与与宿主细胞的相互作用。因此，有助于阐明这些关键分子成分的研究对于寻找替代疗法非常重要。方法：用不同方法提取蛋白质和多肽，并用多维蛋白质鉴定技术(MudPIT)进行分析。蛋白质组学数据用Discoverer2.1软件和多元统计软件进行线性判别分析(LDA)，免疫表位数据库(IEDB)资源用于预测实验鉴定的多肽和蛋白质的抗原性和免疫原性。结果：29个MudPIT运行组合可鉴定出10,611个多肽和2539个不同的蛋白质。随着丰富特定蛋白质结构域的提取方法的应用，约15%的鉴定多肽被归类为跨内膜、内膜暴露、跨外膜和外膜暴露。在这种情况下，9个外膜蛋白(OPRE、OprI、OprF、OprD、PagL、OprG、PA1053、PAL和PA0833)被预测为高度抗原性。因此，对它们进行了进一步的处理，并预测了T细胞(MHC Class I和Class II)和B细胞的表位靶点。结论：本研究代表了铜绿假单胞菌膜相关蛋白质组最广泛的特征之一。我们的方法的可行性可能会促进其他细菌物种的研究，这些细菌的包膜暴露蛋白结构域仍然未知。此外，通过结合实验蛋白质组数据和反向疫苗学对蛋白质组进行逐步优先排序，可能有助于减少疫苗开发中需要测试的蛋白质数量。
Background: Pseudomonas aeruginosa cell envelope-associated proteins play a relevant role in infection mechanisms. They can contribute to the antibiotic resistance of the bacterial cells and be involved in the interaction with host cells. Thus, studies contributing to elucidating these key molecular elements are of great importance to find alternative therapeutics. Methods: Proteins and peptides were extracted by different methods and analyzed by Multidimensional Protein Identification Technology (MudPIT) approach. Proteomic data were processed by Discoverer2.1 software and multivariate statistics, i.e., Linear Discriminant Analysis (LDA), while the Immune Epitope Database (IEDB) resources were used to predict antigenicity and immunogenicity of experimental identified peptides and proteins. Results: The combination of 29 MudPIT runs allowed the identification of 10,611 peptides and 2539 distinct proteins. Following application of extraction methods enriching specific protein domains, about 15% of total identified peptides were classified in trans inner-membrane, inner-membrane exposed, trans outer-membrane and outer-membrane exposed. In this scenario, nine outer membrane proteins (OprE, OprI, OprF, OprD, PagL, OprG, PA1053, PAL and PA0833) were predicted to be highly antigenic. Thus, they were further processed and epitopes target of T cells (MHC Class I and Class II) and B cells were predicted. Conclusion: The present study represents one of the widest characterizations of the P. aeruginosa membrane-associated proteome. The feasibility of our method may facilitates the investigation of other bacterial species whose envelope exposed protein domains are still unknown. Besides, the stepwise prioritization of proteome, by combining experimental proteomic data and reverse vaccinology, may be useful for reducing the number of proteins to be tested in vaccine development.
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MHC I类的性质提出了增强免疫原性的肽。
影响因子：
4.3
作者：
Calis JJ;Maybeno M;Greenbaum JA;Weiskopf D;De Silva AD;Sette A;Keşmir C;Peters B
通讯作者：
Peters B
影响因子：
2.8
作者：
Berisio R;Vitagliano L
通讯作者：
Vitagliano L
影响因子：
4.4
作者：
Gong, Q.;Ruan, M. D.;Guo, J. Z.
通讯作者：
Guo, J. Z.
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
3.4
作者：
Imperi, Francesco;Ciccosanti, Fabiola;Fimia, Gian Maria
通讯作者：
Fimia, Gian Maria