Tianjin Institute of Health & Environmental Medicine, Tianjin, People's Republic of China.
Virulence. 2013 Aug 15;4(6):473-82. doi: 10.4161/viru.25730. Epub 2013 Jul 15.
In the process of host-pathogen interactions, bacterial pathogens always employ some special genes, e.g., virulence factors (VFs) to interact with host and cause damage or diseases to host. A number of VFs have been identified in bacterial pathogens that confer upon bacterial pathogens the ability to cause various types of damage or diseases. However, it has been clarified that some of the identified VFs are also encoded in the genomes of nonpathogenic bacteria, and this finding gives rise to considerable controversy about the definition of virulence factor. Here 1988 virulence factors of 51 sequenced pathogenic bacterial genomes from the virulence factor database (VFDB) were collected, and an orthologous comparison to a non-pathogenic bacteria protein database was conducted using the reciprocal-best-BLAST-hits approach. Six hundred and twenty pathogen-specific VFs and 1368 common VFs (present in both pathogens and nonpathogens) were identified, which account for 31.19% and 68.81% of the total VFs, respectively. The distribution of pathogen-specific VFs and common VFs in pathogenicity islands (PAIs) was systematically investigated, and pathogen-specific VFs were more likely to be located in PAIs than common VFs. The function of the two classes of VFs were also analyzed and compared in depth. Our results indicated that most but not all T3SS proteins are pathogen-specific. T3SS effector proteins tended to be distributed in pathogen-specific VFs, whereas T3SS translocation proteins, apparatus proteins, and chaperones were inclined to be distributed in common VFs. We also observed that exotoxins were located in both pathogen-specific and common VFs. In addition, the architecture of the two classes of VFs was compared, and the results indicated that common VFs had a higher domain number and lower domain coverage value, revealed that common VFs tend to be more complex and less compact proteins.
在宿主-病原体相互作用的过程中，细菌病原体总是利用一些特殊的基因，例如毒力因子（Virulence Factors，VFs）与宿主相互作用，导致宿主损伤或疾病。已经在细菌病原体中鉴定出许多 VFs，这些 VFs 赋予了细菌病原体引起各种类型损伤或疾病的能力。然而，已经阐明，一些已鉴定的 VFs 也编码在非致病性细菌的基因组中，这一发现引起了关于毒力因子定义的相当大的争议。在这里，我们从毒力因子数据库（VFDB）中收集了 51 个测序的致病性细菌基因组的 1988 个毒力因子，并使用相互最佳 BLAST 命中方法对非致病性细菌蛋白质数据库进行了同源比较。鉴定出 620 个病原体特异性 VFs 和 1368 个共同 VFs（存在于病原体和非病原体中），分别占总 VFs 的 31.19%和 68.81%。系统地研究了病原体特异性 VFs 和共同 VFs 在致病性岛（Pathogenicity Islands，PAIs）中的分布，结果表明病原体特异性 VFs 比共同 VFs 更有可能位于 PAIs 中。我们还深入分析和比较了这两类 VFs 的功能。我们的结果表明，大多数但不是所有的 T3SS 蛋白都是病原体特异性的。T3SS 效应蛋白倾向于分布在病原体特异性 VFs 中，而 T3SS 易位蛋白、装置蛋白和伴侣蛋白则倾向于分布在共同 VFs 中。我们还观察到外毒素位于病原体特异性和共同 VFs 中。此外，比较了这两类 VFs 的结构，结果表明共同 VFs 具有更高的结构域数量和更低的结构域覆盖率值，表明共同 VFs 倾向于更复杂和不紧凑的蛋白质。
