Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of the utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study, we integrated whole-genome sequencing and mass spectrometry (GeLC–MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach, we identified 59 peptides containing single amino acid variants, which covered ∼9% of all coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here, we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e., large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.

中文翻译：

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结核分枝杆菌临床分离株菌株变异的蛋白质组学研究。

结核分枝杆菌由大量显示独特毒力特征的不同菌株组成。全基因组测序揭示了临床分离的结核分枝杆菌之间的大量遗传多样性，阐明这种遗传多样性编码的表型变异对充分了解结核分枝杆菌的生物学和致病性至关重要。在这项研究中，我们整合了全基因组测序和质谱（GeLC–MS / MS），以揭示两种临床结核分枝杆菌的蛋白质组中的菌株特异性特征。拉丁美洲-地中海分离株。使用这种方法，我们鉴定了59个含有单个氨基酸变体的肽，这些肽覆盖了全基因组测序检测到的所有编码非同义单核苷酸变体的约9％。此外，我们确定了29种不同的肽，它们映射到结核分枝杆菌H37Rv参考蛋白质组中不存在的假设蛋白质。在这里，我们为该蛋白在临床结核分枝杆菌SAWC3651分离物中的表达提供了证据。菌株特异性数据库能够确认这两种临床结核分枝杆菌的基因组差异（即，差异较大的基因组区域和非同义的单核苷酸变体）分离并允许在蛋白质组水平上进行菌株分化。我们的结果为临床微生物蛋白质组学的发展做出了贡献，并可以增进我们对临床结核分枝杆菌分离株表型变异的了解。