Transcriptomic profile of the most successful Mycobacterium tuberculosis strain in Aragon, the MtZ strain, during exponential and stationary growth phases

Abstract

The Mycobacterium tuberculosis Zaragoza (MtZ) strain has produced the largest outbreak in Aragon Community, Spain, as it started in the 90s and continues today, contributing with more than 240 cases of tuberculosis, around 10% of the TB cases. Previous studies were carried out to identify the reasons for its successful spread capacity among the population. Some single nucleotide polymorphisms (SNPs) in genes considered as virulence factors were found, as well as an oversecretion of PE_PGRS factors. Different copies of IS 6110 have been localized, and a transcriptomic study was carried out to study how the different IS 6110 copies could affect the adjacent gene expression. In this work, we analyzed the transcriptomic profile of the MtZ, strain trying to delve into the mechanisms behind its success. We found that ESX-1 system is upregulated during both exponential and stationary growth phases in vitro , as well as the virulence pathways of cholesterol degradation and peptidoglycan biosynthesis. In addition, MtZ has the iron uptake genes downregulated in exponential growth phase (mycobactin biosynthesis and IrtAB transporters), while the iron storage could be upregulated. The desA3 gene transcription was interrupted by the insertion of an IS 6110 copy. This gene codes for a stearoyl-coenzyme A (CoA) Δ9 desaturase involved in the production of oleic acid, which is necessary for the metabolism of the bacteria. In spite of this, although MtZ strain has an initial long lag phase growing in liquid media, it is capable of achieving normal growth, suggesting the existence of an alternative route for obtaining oleic acid. IMPORTANCE Aragon Community suffered, during the first years of the beginning of this century, a large outbreak caused by the MtZ strain, producing more than 240 cases to date. MtZ strain and the outbreak have been previously studied from an epidemiological and molecular point of view. In this work, we analyzed the transcriptomic profile of the strain for better understanding of its success among our population. We have discovered that MtZ has some upregulated virulence pathways, such as the ESX-1 system, the cholesterol degradation pathway or the peptidoglycan biosynthesis. Interestingly, MtZ has downregulated the uptake of iron. Another special feature of MtZ strain is the interruption of desA3 gene, essential for producing oleic acid. Although the strain takes a long time to grow in the initial culture media, eventually it is able to reach normal optical densities, suggestive of the presence of another route for obtaining oleic acid in Mycobacterium tuberculosis .

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis

“…The disruptions in protein secretion processes can potentially impact the physiology of the bacterium, thus the secF mutation is considered to be related to drug resistance in MTB [ 28 ]. The desA3 gene is associated with the biosynthesis of oleic acids, which is essential for the formation of the cell wall of actively replicating bacteria [ 29 , 30 ]. The mutation of these genes may highly affect their function, which results in drug-resistant events in MTB.…”