PXD008555

PXD008555 is an original dataset announced via ProteomeXchange.

Title	Integrated multi-omic analysis of M. tuberculosis H37Ra redefines virulence attributes
Description	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.
HostingRepository	PRIDE
AnnounceDate	2018-10-22
AnnouncementXML	Submission_2018-10-22_09:19:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Mycobacterium tuberculosis H37Ra; NCBI TaxID: 419947;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-22 06:59:01	ID requested
⏵ 1	2018-10-22 09:19:18	announced

Pinto SM, Verma R, Advani J, Chatterjee O, Patil AH, Kapoor S, Subbannayya Y, Raja R, Gandotra S, Prasad TSK, H37Ra Redefines Virulence Attributes. Front Microbiol, 9():1314(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Tuberculosis, Next-Generation sequencing, Orbitrap, genome annotation, virulence attenuation

T. S. Keshava Prasad
contact affiliation	Institute of Bioinformatics, 7th floor, Discover Building, International Tech Park, Bangalore, India
contact email	keshav@ibioinformatics.org
lab head
Keshava Prasad T. S.
contact affiliation	Institute of Bioinformatics, Bangalore, Karnataka, India.
contact email	keshav@ibioinformatics.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008555
     1. Label: PRIDE project
     2. Name: Integrated multi-omic analysis of M. tuberculosis H37Ra redefines virulence attributes