Nakano Y, Shibata Y, Kawada M, Kojima M, Fukamachi H, Shibata Y, Okano S, Matsushima K, Abiko Y, Yamashita Y
Department of Preventive Dentistry, Kyushu University Faculty of Dental Science, Fukuoka, Japan.
Oral Microbiol Immunol. 2005 Dec;20(6):344-8. doi: 10.1111/j.1399-302X.2005.00235.x.
An online database of proteomes for two-dimensional electrophoresis (2DE) gel data was constructed and it is now freely accessible through a web-based interface. Proteins from three oral bacteria, Streptococcus mutans UA159, Actinobacillus actinomycetemcomitans HK1651, and Porphyromonas gingivalis W83, whose genome databases are freely available, were separated by 2DE, and protein spots were analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and identified. About 1000 spots from the gels of P. gingivalis W83 were extracted and analyzed by MALDI-TOF, and 330 proteins were identified. In addition, 160 of 240 spots of A. actinomycetemcomitans and 158 of 356 spots of S. mutans were identified. Information such as spot coordinates on the gels, protein names (predicted functions), molecular weights, isoelectroric points, and links to online databases, including Oral Pathogen Sequence Databases of the Los Alamos National Laboratory Bioscience Division (ORALGEN) and National Center for Biotechnology Information (NCBI) or The Institute Genomic Research (TIGR), were stored in tables accessible through the relational database management system MySQL on an Apache web server. To test for functionality of this database system, responses of S. mutans to environmental changes were analyzed using the database and 21 spots on the gel were identified as proteins whose expression had been increased or decreased by environmental pH change without in-gel trypsin digestion, protein extraction, or MALDI-TOF/TOF-MS (mass spectrometer) analysis. The identified proteins are agreement with those reported in previous papers on acid tolerance of S. mutans, demonstrating the usefulness of the system. This database is available at http://www.myamagu.dent.kyushu-u.ac.jp/~bioinformatics/index.html or http://www.bipos.mascat.nihon-u.ac.jp/index.html.
构建了一个用于二维电泳（2DE）凝胶数据的蛋白质组在线数据库，现在可通过基于网络的界面免费访问。从三种口腔细菌变形链球菌UA159、伴放线放线杆菌HK1651和牙龈卟啉单胞菌W83中提取蛋白质，这些细菌的基因组数据库可免费获取，通过二维电泳分离蛋白质，并用基质辅助激光解吸/电离飞行时间（MALDI-TOF）分析蛋白质斑点并进行鉴定。从牙龈卟啉单胞菌W83的凝胶中提取了约1000个斑点，用MALDI-TOF进行分析，鉴定出330种蛋白质。此外，伴放线放线杆菌240个斑点中的160个以及变形链球菌356个斑点中的158个也得到了鉴定。凝胶上斑点坐标、蛋白质名称（预测功能）、分子量、等电点以及与在线数据库的链接等信息，包括洛斯阿拉莫斯国家实验室生物科学部的口腔病原体序列数据库（ORALGEN）、国家生物技术信息中心（NCBI）或基因组研究所（TIGR），都存储在可通过Apache网络服务器上的关系数据库管理系统MySQL访问的表格中。为测试该数据库系统的功能，利用该数据库分析了变形链球菌对环境变化的反应，在未进行凝胶内胰蛋白酶消化、蛋白质提取或MALDI-TOF/TOF-MS（质谱仪）分析的情况下，鉴定出凝胶上21个斑点为其表达因环境pH变化而增加或减少的蛋白质。鉴定出的蛋白质与先前关于变形链球菌耐酸性的论文中报道的蛋白质一致，证明了该系统的实用性。该数据库可在http://www.myamagu.dent.kyushu-u.ac.jp/~bioinformatics/index.html或http://www.bipos.mascat.nihon-u.ac.jp/index.html获取。
