Sugiyama Naoyuki, Miyake Satomi, Lin Miao-Hsia, Wakabayashi Masaki, Marusawa Hiroyuki, Nishiumi Shin, Yoshida Masaru, Ishihama Yasushi
Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Genes Cells. 2019 Feb;24(2):139-150. doi: 10.1111/gtc.12662. Epub 2019 Jan 20.
Helicobacter pylori, a pathogen of various gastric diseases, has many genome sequence variants. Thus, the pathogenesis and infection mechanisms of the H. pylori-driven gastric diseases have not been elucidated. Here, we carried out a large-scale proteome analysis to profile the heterogeneity of the proteome expression of 7 H. pylori strains by using an LC/MS/MS-based proteomics approach combined with a customized database consisting of nonredundant tryptic peptide sequences derived from full genome sequences of 52 H. pylori strains. The nonredundant peptide database enabled us to identify more peptides in the database search of MS/MS data compared with a simply merged protein database. Using this approach, we carried out proteome analysis of genome-unknown strains of H. pylori at as large a scale as genome-known ones. Clustering of the H. pylori strains using proteome profiling slightly differed from the genome profiling and more clearly divided the strains into two groups based on the isolated area. Furthermore, we identified phosphorylated proteins and sites of the H. pylori strains and obtained the phosphorylation motifs located in the N-terminus that are commonly observed in bacteria.
幽门螺杆菌是多种胃部疾病的病原体，有许多基因组序列变体。因此，幽门螺杆菌引发胃部疾病的发病机制和感染机制尚未阐明。在此，我们采用基于液相色谱/串联质谱的蛋白质组学方法，并结合一个由来自52株幽门螺杆菌全基因组序列的非冗余胰蛋白酶肽序列组成的定制数据库，对7株幽门螺杆菌菌株的蛋白质组表达异质性进行了大规模蛋白质组分析。与简单合并的蛋白质数据库相比，非冗余肽数据库使我们能够在MS/MS数据的数据库搜索中鉴定出更多肽段。使用这种方法，我们对幽门螺杆菌基因组未知菌株进行了与基因组已知菌株一样大规模的蛋白质组分析。利用蛋白质组图谱对幽门螺杆菌菌株进行聚类与基因组图谱略有不同，并且更清楚地根据分离区域将菌株分为两组。此外，我们鉴定了幽门螺杆菌菌株的磷酸化蛋白和位点，并获得了位于细菌中常见的N端的磷酸化基序。
