Vavilov Institute of General Genetics, Moscow, Russia.
Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
Genome Biol Evol. 2017 Apr 1;9(4):887-899. doi: 10.1093/gbe/evx053.
Mycobacterium tuberculosis is divided into several distinct lineages, and various genetic markers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an M. tuberculosis classification approach based on functional polymorphisms in virulence genes. An M. tuberculosis virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin-antitoxin systems. Another catalog of 1,573 M. tuberculosis isolates of different lineages has been developed. The developed SNP-calling program has identified 3,563 nonsynonymous SNPs. The constructed SNP-based phylogeny reflected the evolutionary relationship between lineages and detected new sublineages. SNP analysis of sublineage F15/LAM4/KZN revealed four lineage-specific mutations in cyp125, mce3B, vapC25, and vapB34. The Ural lineage has been divided into two geographical clusters based on different SNPs in virulence genes. A new sublineage, B0/N-90, was detected inside the Beijing-B0/W-148 by SNPs in irtB, mce3F and vapC46. We have found 27 members of B0/N-90 among the 227 available genomes of the Beijing-B0/W-148 sublineage. Whole-genome sequencing of strain B9741, isolated from an HIV-positive patient, was demonstrated to belong to the new B0/N-90 group. A primer set for PCR detection of B0/N-90 lineage-specific mutations has been developed. The prospective use of mce3 mutant genes as genetically engineered vaccine is discussed.
结核分枝杆菌分为几个不同的谱系，通常使用 IS 元件、VNTR 和 SNPs 等遗传标记来鉴定谱系。我们提出了一种基于毒力基因功能多态性的结核分枝杆菌分类方法。建立了结核分枝杆菌毒力基因目录，包括来自各种蛋白质组的 319 个基因，如蛋白酶、细胞壁蛋白、脂肪酸和脂质代谢蛋白、σ 因子、毒素-抗毒素系统。还开发了不同谱系的 1573 株结核分枝杆菌的另一个目录。开发的 SNP 调用程序已经鉴定出 3563 个非同义 SNP。构建的 SNP 系统发育反映了谱系之间的进化关系，并检测到新的亚谱系。对 F15/LAM4/KZN 亚谱系的 SNP 分析显示，cyp125、mce3B、vapC25 和 vapB34 四个谱系特异性突变。根据毒力基因中的不同 SNP，将 Ural 谱系分为两个地理群。通过irtB、mce3F 和 vapC46 中的 SNP，在 Beijing-B0/W-148 中检测到一个新的亚谱系 B0/N-90。在 227 个可用的 Beijing-B0/W-148 亚谱系基因组中，我们发现了 27 个 B0/N-90 成员。从 HIV 阳性患者中分离出的菌株 B9741 的全基因组测序证明属于新的 B0/N-90 组。已经开发了用于检测 B0/N-90 谱系特异性突变的 PCR 检测引物组。讨论了 mce3 突变基因作为基因工程疫苗的潜在用途。
