Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains

Bespyatykh, Julia; Smolyakov, Alexander; Guliaev, Andrei; Shitikov, Egor; Arapidi, Georgij; Butenko, Ivan; Dogonadze, Marine; Manicheva, Olga; Ilina, Elena N.; Zgoda, Victor G.; Govorun, Vadim M.

doi:10.1016/j.jprot.2018.07.002

Cited by 12 publications

(9 citation statements)

References 44 publications

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“…Carrying out of the whole genome sequencing of the RUS_B0 strain allowed us to correct a number of inaccuracies present in the annotation of the W-148, the only previously sequenced member of the Beijing B0/W48 cluster 32 . For example, the peptides AASSLSGGADTLEALGVR and IDLGPDLVAR, previously identified as parts of the of the pseudogene TBPG_RS21255 in W-148 by using H37Rv annotation, do belong to the TrpD anthranilate phosphoribosyltransferase (DPM14_10670) in RUS_B0.…”

Section: Discussionmentioning

confidence: 99%

“…In the RUS_B0 annotation, the corresponding peptides were identified for the DUF3000 domain-containing protein (DPM14_13425). It has been proposed earlier that the TBPG_RS19380/Rv3684 might have an alternative start 32 . In the present study, we confirmed this conclusion, as we identified GSSP SWTDNAIR and new GSSP LIEADAR peptides in our proteomic dataset.…”

Section: Discussionmentioning

confidence: 99%

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System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster

Bespyatykh

Shitikov

Guliaev

et al. 2019

Sci Rep

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Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the “success” of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 394 cluster strains were used to describe the main genetic features of the population. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrated that expression of the whiB6 which contains cluster-specific polymorphism (a151c) increased almost 40 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 was increased by more than 7 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes. In summary, our analysis allowed us to summarize the available results and also to obtain fundamentally new data.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster

Bespyatykh

Shitikov

Guliaev

et al. 2019

Sci Rep

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“…30 While one of the disadvantages of membrane proteomics based on the gel-free approach is the solubilization of membranous proteins, which is because of different optimum condition, 31 the volume of data available for membrane protein repertoire is growing. 32 Several bacterial studies including Mycobacterium tuberculosis, 33 Scheffersomyces stipitis, 34 and Staphylococcus aureus 35 have used a gelfree technique, which further indicates the potential of this method by the identification of a far larger number of proteins. Gel-based and gel-free protein quantification, which are used as complementary approaches, are effective techniques to analyze the regulatory mechanisms utilized by bacteria.…”

Section: Protein Identificationmentioning

confidence: 99%

<p>Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies</p>

Khodadadi

Zeinalzadeh

Taghizadeh

et al. 2020

IDR

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Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.

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“…Proteolytic in-gel digestion was performed in three biological and two technical replicates: 1) sample, fractionated into 6 parts; 2) total load sample as described previously [51]. Peptides were cleaned using C18 Sep-Pak columns (Waters, Milford, USA) [17].…”

Section: Protein Extraction and Trypsin Digestionmentioning

confidence: 99%

“…For protein identification, the proteomic databases for the RUS_B0 (RefSeq: CP030093.1) and reference strain H37Rv (RefSeq: NC_000962.3) genomes were used. Additionally, in proteome searching database peptides containing strain-specific single amino acid polymorphisms were added according to the approach described earlier [51]. The local false discovery rate scoring algorithm with standard experiment-wide protein grouping was used.…”

Section: Protein Identification and Quantitationmentioning

confidence: 99%

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy

et al. 2020

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Tuberculosis, caused by Mycobacterium tuberculosis complex bacteria, remains one of the most pressing health problems. Despite the general trend towards reduction of the disease incidence rate, the situation remains extremely tense due to the distribution of the resistant forms. Most often, these strains emerge through the intra-host microevolution of the pathogen during treatment failure. In the present study, the focus was on three serial clinical isolates of Mycobacterium tuberculosis Beijing B0/W148 cluster from one patient with pulmonary tuberculosis, to evaluate their changes in metabolism during anti-tuberculosis therapy. Using whole genome sequencing (WGS), 9 polymorphisms were determined, which occurred in a stepwise or transient manner during treatment and were linked to the resistance (GyrA D94A; inhA t-8a) or virulence. The effect of the inhA t-8a mutation was confirmed on both proteomic and transcriptomic levels. Additionally, the amount of RpsL protein, which is a target of anti-tuberculosis drugs, was reduced. At the systemic level, profound changes in metabolism, linked to the evolution of the pathogen in the host and the effects of therapy, were documented. An overabundance of the FAS-II system proteins (HtdX, HtdY) and expression changes in the virulence factors have been observed at the RNA and protein levels.

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Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains

Cited by 12 publications

References 44 publications

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster

<p>Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies</p>

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy

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