Integrated Multi-Omic Analysis of Mycobacterium tuberculosis H37Ra Redefines Virulence Attributes

Abstract

H37Ra is a virulence attenuated strain of Mycobacterium tuberculosis widely employed as a model to investigate virulence mechanisms. Comparative high-throughput studies have earlier correlated its avirulence to the presence of specific mutations or absence of certain proteins. However, a recent sequencing study of H37Ra, has disproved several genomic differences earlier reported to be associated with virulence. This warrants further investigations on the H37Ra proteome as well. In this study, we carried out an integrated analysis of the genome, transcriptome, and proteome of H37Ra. In addition to confirming single nucleotide variations (SNVs) and insertion-deletions that were reported earlier, our study provides novel insights into the mutation spectrum in the promoter regions of 7 genes. We also provide transcriptional and proteomic evidence for 3,900 genes representing ~80% of the total predicted gene count including 408 proteins that have not been identified previously. We identified 9 genes whose coding potential was hitherto reported to be absent in H37Ra. These include 2 putative virulence factors belonging to ESAT-6 like family of proteins. Furthermore, proteogenomic analysis enabled us to identify 63 novel proteins coding genes and correct 25 existing gene models in H37Ra genome. A majority of these were found to be conserved in the virulent strain H37Rv as well as in other mycobacterial species suggesting that the differences in the virulent and avirulent strains of M. tuberculosis are not entirely dependent on the expression of certain proteins or their absence but may possibly be ascertained to functional changes.

Modern clinical Mycobacterium tuberculosis strains leverage type I IFN pathway for a pro-inflammatory response in the host

“…Previous studies have implicated an important role of the Mtb ESX-1 secretion system in cytosolic egress of ligands and activation of the cytosolic surveillance pathway resulting in type I IFN activation ( 5-10 ). However, we did not observe any difference between the IFN inducing abilities of H 37 Ra or H 37 Rv despite the reported differences in the levels of the Esx-1 proteins ( 24 ). Further, comparable expression of ESAT6 in our clinical Mtb strains (L1 and L3) (Fig.…”

Global Proteome Profiling Reveals Drug-Resistant Traits in Elizabethkingia meningoseptica: An Opportunistic Nosocomial Pathogen

“…Sample preparation for mass spectrometry was done using two parallel approaches, in-gel and in-solution trypsin digestion, followed by basic reverse-phase liquid chromatography (bRPLC) following the published protocol (Datta et al, 2016;Pinto et al, 2018). Briefly, the protocol followed was: For in-gel digestion, 300 lg of the protein was resolved on 10% SDS-PAGE (sodium dodecyl sulfate-pulsed-field gel electrophoresis) gel and stained with colloidal Coomassie blue.…”

Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling

“…Systems biology and integrative biology offer several approaches to identify molecular mechanisms operating behind biological processes in unprecedented detail. Integrated approaches such as Proteogenomics can provide macro-resolution snapshots to facilitate understanding of intricate molecular mechanisms in cancers [25,26] and infectious diseases [27,28]. Applying integrated approaches in the context of immunology can, therefore, offer unique insights into mechanisms of innate and adaptive immunity.…”