School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan.
J Proteome Res. 2010 Dec 3;9(12):6722-8. doi: 10.1021/pr100868d. Epub 2010 Nov 5.
We have proposed a rapid phylogenetic classification at the strain level by MALDI-TOF MS using ribosomal protein matching profiling. In this study, the S10-spc-alpha operon, encoding half of the ribosomal subunit proteins and highly conserved in eubacterial genomes, was selected for construction of the ribosomal protein database as biomarkers for bacterial identification by MALDI-TOF MS analysis to establish a more reliable phylogenetic classification. Our method revealed that the 14 reliable and reproducible ribosomal subunit proteins with less than m/z 15,000, except for L14, coded in the S10-spc-alpha operon were significantly useful biomarkers for bacterial classification at species and strain levels by MALDI-TOF MS analysis of genus Pseudomonas strains. The obtained phylogenetic tree was consisted with that based on genetic sequence (gyrB). Since S10-spc-alpha operons of genus Pseudomonas strains were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced strains, the ribosomal subunit proteins encoded in S10-spc-alpha operon were suitable biomarkers for construction and correction of the database. MALDI-TOF MS analysis using these 14 selected ribosomal proteins is a rapid, efficient, and versatile bacterial identification method with the validation procedure for the obtained results.
我们提出了一种基于 MALDI-TOF MS 的核糖体蛋白匹配谱快速菌株水平的系统发育分类方法。在这项研究中，选择 S10-spc-alpha 操纵子（编码核糖体亚基蛋白的一半，在真细菌基因组中高度保守）用于构建核糖体蛋白数据库，作为 MALDI-TOF MS 分析鉴定细菌的生物标志物，以建立更可靠的系统发育分类。我们的方法表明，在假单胞菌属菌株的 MALDI-TOF MS 分析中，除 L14 外，S10-spc-alpha 操纵子中编码的 14 种可靠且可重复的小于 15000 m/z 的核糖体亚基蛋白是细菌分类的有用生物标志物，可用于种和株水平的分类。得到的系统发育树与基于遗传序列（gyrB）的系统发育树一致。由于使用基于全基因组测序菌株核苷酸序列设计的特异性引物对假单胞菌属菌株的 S10-spc-alpha 操纵子进行测序，因此 S10-spc-alpha 操纵子中编码的核糖体亚基蛋白适合构建和校正数据库。使用这 14 种选定的核糖体蛋白进行 MALDI-TOF MS 分析是一种快速、高效、通用的细菌鉴定方法，具有验证获得结果的程序。
