Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237

Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Spain.
Tuberculosis (Edinburgh, Scotland) (Impact Factor: 2.71). 03/2011; 91(2):117-26. DOI: 10.1016/
Source: PubMed


The capacity of infection and the ability of Mycobacterium tuberculosis strains belonging to the Beijing family to spread rapidly probably result from genetic advantages and unidentified mechanisms of virulence not yet thoroughly investigated. Among the mechanisms proposed to be responsible for the varying virulence phenotypes of M. tuberculosis strains we find IS6110 insertions, genetic reorganizations and deletions, which have strong influences on fitness. Beijing family is one of the lineages with the highest number of copies of IS6110. By studying genetic markers characteristic for this lineage, here we have characterized the clinical isolate M. tuberculosis GC1237 strain responsible for important epidemic outbreaks in the Gran Canary Island. We have identified and analyzed each point of insertion of IS6110 using a bacterial artificial chromosome (BAC) library of this strain, in addition to the use of other approximations. Nineteen copies of IS6110 have been localized in GC1237 genome of which, four copies of IS6110 can act as a promoter and we have focused in the characterization of one copy located 31 bp upstream of the essential gene Rv2179c and compared to the reference strain H37Rv.

Download full-text


Available from: Isabel Otal, Feb 06, 2014
  • Source
    • "In the framework of an ongoing project on structural and functional properties of mycobacterial cell wall components (Correale et al., 2013; Squeglia et al., 2013), we show here that deletion of a single gene in the genome of Mycobacterium marinum (MMAR_3223), a widely used model organism for M. tuberculosis (Bouley et al., 2001; Broussard and Ennis, 2007), affects mycobacterial cell surface properties in vitro and virulence in vivo in the zebrafish model. MMAR_3223 has been shown to be upregulated inside granulomas during long-term frog infection by M. marinum (Chan et al., 2002), whereas its ortholog in M. tuberculosis, rv2179c, is essential for mycobacterial growth (Sassetti et al., 2003) and upregulated in the hyper virulent Beijing strains of M. tuberculosis during macrophage infections (Alonso et al., 2011). However, the exact role played by this gene in mycobacterial pathogenicity is hitherto unknown. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The cell-envelope of Mycobacterium tuberculosis plays a key role in bacterial virulence and antibiotic resistance. Little is known about the molecular mechanisms of regulation of cell-envelope formation. Here, we elucidate functional and structural properties of RNase AS, which modulates M. tuberculosis cell-envelope properties and strongly impacts bacterial virulence in vivo. The structure of RNase AS reveals a resemblance to RNase T from Escherichia coli, an RNase of the DEDD family involved in RNA maturation. We show that RNase AS acts as a 3'-5'-exoribonuclease that specifically hydrolyzes adenylate-containing RNA sequences. Also, crystal structures of complexes with AMP and UMP reveal the structural basis for the observed enzyme specificity. Notably, RNase AS shows a mechanism of substrate recruitment, based on the recognition of the hydrogen bond donor NH2 group of adenine. Our work opens a field for the design of drugs able to reduce bacterial virulence in vivo.
    Preview · Article · Apr 2014 · Structure
  • Source
    • "On the other hand unique locations were observed in papA4 and Rv2957 genes (N4 strain), interrupting mez and PPE49 genes (CAM22 strain) and in the intergenic region of Rv1542c:Rv1543 (W4 strain) (Additional file 1: Table S5). We corroborated the uniqueness of these sites, after analyzing the literature [10,11,13,16-18,20,22-24,27-35], as was the case for the copy located upstream of Rv2180c gene in GC1237 [10] (Figure 1 and Figure 2). The data suggests that although IS6110 has preferential genomic regions, its insertion is sufficiently random that could generate differences among strains of the same family. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Mycobacterium tuberculosis Beijing strains are characterized by a large number of IS6110 copies, suggesting the potential implication of this element in the virulence and capacity for rapid dissemination characteristic of this family. This work studies the insetion points of IS6110 in high-copy clinical isolates specifically focusing on the Beijing genotype. In the present work we mapped the insertion points of IS6110 in all the Beijing strains available in the literature and in the DNA sequence databases. We generated a representative primer collection of the IS6110 locations, which was used to analyse 61 high-copy clinical isolates. A total of 440 points of insertion were identified and analysis of their flanking regions determined the exact location, the direct repeats (DRs), the orientation and the distance to neighboring genes of each copy of IS6110. We identified specific points of insertion in Beijing strains that enabled us to obtain a dendrogram that groups the Beijing genotype. This work presents a detailed analysis of locations of IS6110 in high-copy clinical isolates, showing points of insertion present with high frequency in the Beijing family and absent in other strains.
    Full-text · Article · Jun 2013 · BMC Genomics
  • Source
    • "Whole-genome SNP discovery and phylogeny of MTBC strains The genomes of three M. tuberculosis strains—GC1237, R34- 990172, and W4—were sequenced at high coverage rates (673, 4113, and 3863, respectively) to obtain a better sampling of the East Asian clade, which includes the fast disseminating Beijing strains (Bifani et al. 2002; von Groll et al. 2010). The GC1237 strain is pan-susceptible to all first-line anti-tuberculosis drugs (rifampin, isoniazid, streptomycin, ethombutol, and pyrazinamide) and is responsible for an ongoing epidemic in the Gran Canaries Island (Caminero et al. 2001; Alonso et al. 2011). We compared these three strains with 21 others publicly available (Supplemental Table S1). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.
    Full-text · Article · Feb 2012 · Genome Research
Show more