Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains

• Published in: Journal of proteomics 2019-02, Vol.192, p.18-26
• Main Authors: Bespyatykh, Julia, Smolyakov, Alexander, Guliaev, Andrei, Shitikov, Egor, Arapidi, Georgij, Butenko, Ivan, Dogonadze, Marine, Manicheva, Olga, Ilina, Elena, Zgoda, Victor, Govorun, Vadim
• Format: Article
• Language: English
• Subjects: Beijing B0/W148; Label-free proteomic analysis; Mycobacterium tuberculosis; Proteogenomic; Proteome; proteomics; Tuberculosis
• ISSN: 1874-3919; 1876-7737
• DOI: 10.1016/j.jprot.2018.07.002

Nowadays proteomics is one of the major instruments for editing and correcting annotation of genomic information. The correct genome annotation is necessary for omics studies of clinically relevant pathogens like Mycobacterium tuberculosis as well as for the progress in drug design and in silico biology. Here, we focused on the proteogenomic analysis of W-148 strain belonging to the Beijing B0/W148 cluster. This cluster, also known as a “successful” clone possesses unique pathogenic properties and has a unique genome organization. Taking into account high similarity of cluster strains at the genomic level we analyzed MS/MS dataset obtained for 63 clinical isolates of Beijing B0/W148. Based on H37Rv and W-148 annotations we identified 2546 proteins representing more than 60% of total proteome. A set of peptides (n = 404) specific for W-148 was found when compared with H37Rv. Start sites for 32 genes were corrected based on the combination of LC-MS/MS proteomic data with genomic six-frame translation. Additionally, we have shown the presence of peptides related to 10 genes earlier known as “pseudogenes”. Mycobacterium tuberculosis is one of the most dangerous pathogens. Phylogenetically, it may be divided into major lineages and among them, lineage 2 (predominantly Beijing genotype) one of the most successful lineages with an increasing prevalence in the global population. At the same time, strains of the Beijing B0/W148 cluster, a “successful” clone of Mycobacterium tuberculosis possess even more interesting features. Only one complete genome of this cluster, W-148, present in the NCBI database (CP012090.1) and it demonstrates a number of significant differences from the well-known reference genome H37Rv. For the W-148 strain many genes are annotated as “pseudo” and no attempts were made to correct this. Thereby, in this study, we have conducted a proteomic analysis of the cluster strains and corrected current genome annotation. We hope that the data obtained will help to increase the quality of identifications in proteomic and transcriptomic analysis of M. tuberculosis Beijing B0/W148 cluster strain in subsequent studies. [Display omitted] •The proteogenomic analysis of W-148 Mycobacterium tuberculosis strain belonged to Beijing B0/W148 cluster was done.•Start sites for 32 genes of M. tuberculosis W-148 were corrected.•For 10 genes annotated as “pseudogenes” peptides were identified.