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Proteomics for the Investigation of Mycobacteria

Bespyatykh JA, Shitikov EA, Ilina EN

Acta Naturae, 2017;9(1):15-25.
PMID: 28461970

The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is widespread in Russia. Considering that the proteome is a set of all the proteins in the cell, post-translational modifications of mycobacterium proteins are also described.
Application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the study of Helicobacter pylori

Ilina EN, Borovskaya AD, Serebryakova MV, Chelysheva VV, Momynaliev KT, Maier T, et al.

Rapid Commun Mass Spectrom, 2010 Feb;24(3):328-34.
PMID: 20049887 DOI: 10.1002/rcm.4394

The characteristics of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability. Accurate tools for species identification and epidemiological characterization could help the scientific community to better understand the transmission pathways and virulence mechanisms of these bacteria. Seventeen clinical as well as two laboratory strains of H. pylori were analyzed by the MALDI Biotyper method for rapid species identification. Mass spectra collected were found containing 7-13 significant peaks per sample, and only six protein signals were identical for more than half of the strains. Four of them could be assigned to ribosomal proteins RL32, RL33, RL34, and RL36. The reproducible peak with m/z 6948 was identified as a histidine-rich metal-binding polypeptide by tandem mass spectrometry (MS/MS). In spite of the evident protein heterogeneity of H. pylori the mass spectra collected for a particular strain under several cultivations were highly reproducible. Moreover, all clinical strains were perfectly identified as H. pylori species through comparative analysis using the MALDI Biotyper software (Bruker Daltonics, Germany) by pattern matching against a database containing mass spectra from different microbial strains (n = 3287) including H. pylori 26695 and J99. The results of this study allow the conclusion that the MALDI-TOF direct bacterial profiling is suited for H. pylori identification and could be supported by mass spectra fragmentation of the observed polypeptide if necessary.
Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads

Konanov DN, Babenko VV, Belova AM, Madan AG, Boldyreva DI, Glushenko OE, et al.

Bioinformatics, 2023 Nov 20.
PMID: 37982752 DOI: 10.1093/bioinformatics/btad702

MOTIVATION: The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole genome methylome profiling. However, we found that there are no methylation motifs detection algorithms which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all H. pylori methylation sites de novo even using the iterative manually controlled approach implemented in the most up-to-date methylation analysis tool Nanodisco.
RESULTS: We present Snapper, a new highly-sensitive approach to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper does not require manual control during the enrichment process and has enrichment sensitivity higher than MEME coupled with Tombo or Nanodisco instruments that was demonstrated on H. pylori strain J99 studied earlier by the PacBio technology and on four external datasets representing different bacterial species. We used Snapper to characterize the total methylome of a new H.pylori strain A45. At least four methylation sites that have not been described for H. pylori earlier were revealed. We experimentally confirmed the presence of a new CCAG-specific methyltransferase and inferred a gene encoding a new CCAAK-specific methyltransferase.
AVAILABILITY: Snapper is implemented using Python and freely available as a pip package named 'snapper-ont'. Also, Snapper and the demo dataset are available in Zenodo (10.5281/zenodo.10117651).
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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