Nouwens Amanda S, Walsh Bradley J, Cordwell Stuart J
Australian Proteome Analysis Facility, Sydney, Australia 2109.
Adv Biochem Eng Biotechnol. 2003;83:117-40. doi: 10.1007/3-540-36459-5_5.
The recent completion of the Pseudomonas Genome Project, in conjunction with the Pseudomonas Community Annotation Project (PseudoCAP) has fast-tracked our ability to apply the tools encompassed under the term 'proteomics' to this pathogen. Such global approaches will allow the research community to answer long-standing questions regarding the ability of Pseudomonas aeruginosa to survive diverse habitats, its high intrinsic resistance to antibiotics and its pathogenic nature towards humans. Proteomics provides an array of tools capable of confirming the expression of Open Reading Frames (ORF), the relative levels of their expression, the environmental conditions required for this expression and the sub-cellular location of the encoded gene-products. Since proteins are important cellular effectors, the biological questions we pose can be defined in terms of changes in protein expression detectable by separation to purity using two-dimensional gel electrophoresis (2-DGE) and relation to gene sequences via mass spectrometry. As such, we can compare strains with well-characterized phenotypic differences, growth under a variety of stresses, protein interactions and complexes and aid in defining proteins of unknown function. While the complete genome has only recently been finished, a number of studies have already utilized this information and examined various protein gene-products using proteomics. This review summarizes the application of proteomics to P. aeruginosa and highlights potential areas of future research, including overcoming the traditional technical limitations associated with 2-DGE. More focused approaches that target sub-cellular fractions ('sub-proteomes') prior to 2-DGE can provide further functional information. A review of current and previous proteomic projects on P. aeruginosa is presented, as well as theoretical considerations of the importance of sub-proteomic approaches to enhance these investigations.
假单胞菌基因组计划的近期完成，连同假单胞菌群体注释计划（PseudoCAP），加快了我们将“蛋白质组学”一词所涵盖的工具应用于这种病原体的能力。这种全局性方法将使研究界能够回答一些长期存在的问题，这些问题涉及铜绿假单胞菌在不同生境中生存的能力、其对抗生素的高度固有抗性以及其对人类的致病特性。蛋白质组学提供了一系列工具，能够确认开放阅读框（ORF）的表达、它们的相对表达水平、这种表达所需的环境条件以及编码基因产物的亚细胞定位。由于蛋白质是重要的细胞效应物，我们提出的生物学问题可以根据通过二维凝胶电泳（2-DGE）分离至纯后可检测到的蛋白质表达变化以及通过质谱与基因序列的关系来定义。因此，我们可以比较具有明确表型差异的菌株、在各种应激条件下的生长情况、蛋白质相互作用和复合物，并有助于确定未知功能的蛋白质。虽然完整基因组直到最近才完成，但已有多项研究利用了这些信息，并使用蛋白质组学研究了各种蛋白质基因产物。本综述总结了蛋白质组学在铜绿假单胞菌中的应用，并突出了未来研究的潜在领域，包括克服与二维凝胶电泳相关的传统技术局限性。在二维凝胶电泳之前针对亚细胞组分（“亚蛋白质组”）的更具针对性的方法可以提供更多功能信息。本文介绍了当前和以往关于铜绿假单胞菌的蛋白质组学项目综述，以及亚蛋白质组学方法对加强这些研究的重要性的理论思考。
