PXD017194-1

PXD017194 is an original dataset announced via ProteomeXchange.

Title	Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis
Description	The Mycobacterium tuberculosis (Mtb) complex comprises seven phylogenetically distinct human-adapted lineages exhibiting different geographical distribution and degrees of pathogenicity. Among these, Lineage 1 (L1) has been associated with low virulence whereas Lineage 2 (L2) has been linked to hyper-virulence, enhanced transmission and drug resistance. Here, we conducted multi-layer comparative analyses using whole genome sequencing data combined with quantitative transcriptomic and proteomic profiling of a set of L1 and L2 clinical strains, each grown under two different conditions in vitro. Our data revealed different degrees of correlation between transcript and protein abundances across clinical strains and functional gene categories, indicating variable levels of post-transcriptional regulation in the tested lineages. Contrasting genomic and gene expression data showed that the magnitude of the transcriptional and translational changes was proportional to the phylogenetic distance between strains, with one out of three single nucleotide polymorphisms leading to a transcriptional and/or translational change on average. We devised a new genome-scale transcriptional regulatory model and identified several master transcription factors, strongly linked to the sigma factor network, whose targets were differentially regulated between the two lineages. These differences resulted in a higher basal expression of DosR proteins and a stronger response to nitric oxide (NO) exposure in L2 compared to L1. These patterns are most likely responsible for the shorter NO-induced growth arrest in L2 observed. Given the limited genetic variation between strains, it appears that phenotypic differences in Mtb are substantially driven by differences in the regulation of biochemical networks through master transcriptional regulators.
HostingRepository	PRIDE
AnnounceDate	2026-01-27
AnnouncementXML	Submission_2026-01-27_09:40:29.517.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amir Banaei-Esfahani
SpeciesList	scientific name: Mycobacterium tuberculosis H37Rv; NCBI TaxID: NEWT:83332;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-20 02:56:59	ID requested
⏵ 1	2026-01-27 09:40:30	announced

Dataset with its publication pending

submitter keyword: bacterial pathogen, proteomics, multi-omics,Mycobacterium tuberculosis, infectious diseases, genomics, DIA/SWATH-MS, transcriptional network

Prof. Dr. Ruedi Aebersold
contact affiliation	ETH Zurich
contact email	aebersold@imsb.biol.ethz.ch
lab head
Amir Banaei-Esfahani
contact affiliation	Swiss TPH
contact email	amir.banaei@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD017194

PRIDE project URI

• PRIDE
  1. PXD017194
     1. Label: PRIDE project
     2. Name: Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis