Dataset Information

Integrated multi-omic analysis of M. tuberculosis H37Ra redefines virulence attributes

ABSTRACT: M. tuberculosis H37Ra, an avirulent tubercle bacillus, is a commonly used model to investigate virulence attenuation in M. tuberculosis. 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 and insertion-deletions that were reported earlier, our study provides novel insights into the mutation spectrum in the promoter regions of 7 genes. In all, we provide protein coding evidence for 3,199 proteins representing ~79% of the total predicted gene count. Transcriptome analysis revealed the expression of 3,945 high-confidence transcripts including several transcripts mapping to the genome that were previously thought to be non-coding. 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 sp. suggesting that 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mycobacterium Tuberculosis H37ra

SUBMITTER: Keshava Prasad T. S.

LAB HEAD: T. S. Keshava Prasad

PROVIDER: PXD008555 | Pride | 2018-10-22

REPOSITORIES: Pride

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Publications

Integrated Multi-Omic Analysis of <i>Mycobacterium tuberculosis</i> H37Ra Redefines Virulence Attributes.

Pinto Sneha M SM Verma Renu R Advani Jayshree J Chatterjee Oishi O Patil Arun H AH Kapoor Saketh S Subbannayya Yashwanth Y Raja Remya R Gandotra Sheetal S Prasad T S Keshava TSK

Frontiers in microbiology 20180619

H37Ra is a virulence attenuated strain of <i>Mycobacterium tuberculosis</i> 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 st ...[more]

PMID: 29971057

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Project description:The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specific cell wall components and attenuation both ex vivo and in vivo. Using antibodies against the native protein in ChIP-seq experiments (chromatin immunoprecipitation followed by high-throughput sequencing) we demonstrated that PhoP binds to at least 35 loci on the M. tuberculosis genome. The PhoP regulon comprises several transcriptional regulators as well as genes for polyketide synthases and PE/PPE proteins. Integration of ChIP-seq results with high-resolution transcriptomic analysis (RNA-seq) revealed that PhoP controls 30 genes directly, whilst regulatory cascades are responsible for signal amplification and downstream effects. The most prominent site of PhoP regulation was located in the intergenic region between rv2395 and PE_PGRS41, where the mcr7 gene codes for a small non-coding RNA (ncRNA). Northern blot experiments confirmed the absence of Mcr7 in the M. tuberculosis phoP mutant as well as low-level expression of the ncRNA in M. tuberculosis complex members other than M. tuberculosis. By means of genetic and proteomic analyses we demonstrated that Mcr7 modulates translation of the tatC mRNA thereby impacting the activity of the Twin Arginine Translocation (Tat) protein secretion apparatus. As a result, secretion of the immunodominant Ag85 complex and the beta-lactamase BlaC is affected, among others. Mcr7, the first ncRNA of M. tuberculosis whose function has been established, therefore represents a missing link between the PhoPR two-component system and the downstream functions necessary for successful infection of the host. ChiP-Seq: M. tuberculosis H37Rv (GC1237) cultures grown in vitro to exponential phase. Two wild type samples plus one isogenic phoP mutant as control

Dataset Information

Integrated multi-omic analysis of M. tuberculosis H37Ra redefines virulence attributes

Publications

Integrated Multi-Omic Analysis of <i>Mycobacterium tuberculosis</i> H37Ra Redefines Virulence Attributes.

Similar Datasets

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