Department of Pathogenobiology, Norman Bethune Medical College of Jilin University, Changchun 130021, Jilin Province, China.
World J Gastroenterol. 2013 Aug 14;19(30):5006-10. doi: 10.3748/wjg.v19.i30.5006.
To apply a new, integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori (H. pylori).
A genomic barcode imaging method (converting frequency matrices to grey-scale levels) was designed to visually distinguish origin-specific genomic regions in H. pylori. The complete genome sequences of the six H. pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned, and compared to the genome barcodes of Escherichia coli (E. coli) O157:H7 strain EDL933 and a random nucleotide sequence. The following criteria were applied to identify potential pathogenicity islands (PAIs): (1) barcode distance distinct from that of the general background; (2) length greater than 10000 continuous base pairs; and (3) containing genes with known virulence-related functions (as determined by PfamScan and Blast2GO).
Comparison of the barcode images generated for the 26695, HPAG1, J99, Shi470, G27 and P12 H. pylori genomes with those for the E. coli and random sequence controls revealed that H. pylori genomes contained fewer anomalous regions. Among the H. pylori-specific continuous anomalous regions (longer than 20 kbp in each strain's genome), two fit the criteria for identifying candidate PAIs. The bioinformatic-based functional analyses revealed that one of the two anomalous regions was the known pathogenicity island cag-PAI, this finding also served as proof-of-principle for the utility of the genomic barcoding approach for identifying PAIs, and characterized the other as a novel PAI, which was designated as tfs3-PAI. Furthermore, the cag-PAI and tfs3-PAI harbored genes encoding type IV secretion system proteins and were predicted to have potential for functional synergy.
Genomic barcode imaging represents an effective bioinformatic-based approach for scanning bacterial genomes, such as H. pylori, to identify candidate PAIs.
应用一种新的细菌基因组可视化综合技术，鉴定幽门螺杆菌（H. pylori）中新型的致病性岛。
设计了一种基因组条码成像方法（将频率矩阵转换为灰度级），用于在 H. pylori 中直观地区分特定起源的基因组区域。扫描了国家生物技术信息中心公布的 6 株 H. pylori 菌株的全基因组序列，并与大肠杆菌（E. coli）O157:H7 菌株 EDL933 和随机核苷酸序列的基因组条码进行比较。应用以下标准鉴定潜在的致病性岛（PAIs）：（1）条码距离与一般背景不同；（2）长度大于 10000 个连续碱基对；（3）包含已知与毒力相关功能的基因（由 PfamScan 和 Blast2GO 确定）。
与大肠杆菌和随机序列对照的条码图像比较显示，26695、HPAG1、J99、Shi470、G27 和 P12 株 H. pylori 基因组生成的条码图像显示，H. pylori 基因组中异常区域较少。在各菌株基因组中长于 20 kbp 的 H. pylori 特异性连续异常区域中，有两个符合鉴定候选 PAIs 的标准。基于生物信息学的功能分析表明，其中一个异常区域是已知的致病性岛 cag-PAI，这一发现也证明了基因组条码方法用于鉴定 PAIs 的有效性，并将另一个异常区域确定为新型 PAI，命名为 tfs3-PAI。此外，cag-PAI 和 tfs3-PAI 含有编码 IV 型分泌系统蛋白的基因，预计具有潜在的功能协同作用。
基因组条码成像代表了一种有效的基于生物信息学的方法，用于扫描 H. pylori 等细菌基因组，以鉴定候选 PAIs。
