Role of the DNA Mismatch Repair Gene MutS4 in Driving the Evolution of Mycobacterium yongonense Type I via Homologous Recombination

Abstract

We recently showed that Mycobacterium yongonense could be divided into two genotypes: Type I, in which the rpoB gene has been transferred from Mycobacterium parascrofulaceum, and Type II, in which the rpoB gene has not been transferred. Comparative genome analysis of three M. yongonense Type I, two M. yongonense Type II and M. parascrofulaceum type strains were performed in this study to gain insight into gene transfer from M. parascrofulaceum into M. yongonense Type I strains. We found two genome regions transferred from M. parascrofulaceum: one contained 3 consecutive genes, including the rpoBC operon, and the other contained 57 consecutive genes that had been transferred into M. yongonense Type I genomes via homologous recombination. Further comparison between the M. yongonense Type I and II genomes revealed that Type I, but not Type II has a distinct DNA mismatch repair gene (MutS4 subfamily) that was possibly transferred via non-homologous recombination from other actinomycetes. We hypothesized that it could facilitate homologous recombination from the M. parascrofulaceum to the M. yongonense Type I genomes. We therefore generated recombinant Mycobacterium smegmatis containing a MutS4 operon of M. yongonense. We found that the M. tuberculosis rpoB fragment with a rifampin resistance-conferring mutation was more frequently inserted into recombinant M. smegmatis than the wild type, suggesting that MutS4 is a driving force in the gene transfer from M. parascrofulaceum to M. yongonense Type I strains via homologous recombination. In conclusion, our data indicated that MutS4 in M. yongonense Type I genomes may drive gene transfer from M. parascrofulaceum via homologous recombination, resulting in division of M. yongonense into two genotypes, Type I and II.

Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania

“…The pronounced difference in a number of unshared genes among the M. yongonense genomes highlights the possibility of extensive HGT from outside the cell in these genomes. Evidence of HGT among NTM members has been described previously (Kim et al, 2016(Kim et al, , 2017Fedrizzi et al, 2017;Kim et al, 2013b).…”

“…The substantial difference between the M. yongonense RT 955-2015 rpoB sequence and that of M. parascrofulaceum and M. yongonense 05-1390, while showing high similarity to M. intracellulare and its closely related species (M. chimaera DSM 44623, M. paraintracellulare KCTC 290849), is additional evidence that the RT 955-2015 strain belongs to the Type II genotype group. Kim et al used genome-based phylogenetic analysis to classify M. yongonense species into two distinct genotypes (Type I genotype and Type II genotype) (Kim et al, 2016), and demonstrated that Type I genotype has laterally acquired rpoB from M. parascrofulaceum while Type II genotype possess the M. intracellulare rpoB gene (Kim et al, 2016(Kim et al, , 2017. Kim (Kim et al, 2016).…”

“…More recently the same authors have provided additional evidence that the entire M. yongonense Type I rpoBC operon resulted from a distantly related species of M. parascrofulaceum (Kim et al, 2017). The authors also revealed that members of M. yongonense Type I genotype harbour a unique DNA mismatch repair gene MutS4 family, that potentially serves as a putative driving force for the suggested HGT between the M. parascrofulaceum and M. yongonense Type I genomes through homologous recombination events (Kim et al, 2017). The occurrence of NTM in Tanzania has been reported frequently (Hoza et al, 2016a,b;Mfinanga et al, 2014;Kilale et al, 2016;Mnyambwa et al, 2017a), but characterization of the isolates has relied on suboptimal typing methods that have potentially hindered accurate species identification.…”

“…Kim et al have suggested two distinct genotypes of M. yongonense based on the rpoB sequence, specifically M. yongonense Type I genotype with the rpoB gene acquired through horizontal gene transfer (HGT) from M. parascrofulaceum and M. yongonense Type II genotype with the M. intracellulare rpoB gene (Kim et al, 2016). More recently the same authors have provided additional evidence that the entire M. yongonense Type I rpoBC operon resulted from a distantly related species of M. parascrofulaceum (Kim et al, 2017). The authors also revealed that members of M. yongonense Type I genotype harbour a unique DNA mismatch repair gene MutS4 family, that potentially serves as a putative driving force for the suggested HGT between the M. parascrofulaceum and M. yongonense Type I genomes through homologous recombination events (Kim et al, 2017).…”

Development of a Live Recombinant BCG Expressing Human Immunodeficiency Virus Type 1 (HIV-1) Gag Using a pMyong2 Vector System: Potential Use As a Novel HIV-1 Vaccine

“…We have recently identified a novel human pathogenic member of the M. avium complex, Mycobacterium yongonense ( 32 ). By conducting a genome analysis of M. yongonense DSM 45126 T ( 33 – 37 ), we also introduced a novel Mycobacterium–Escherichia coli shuttle vector system using the mycobacterial replicon of pMyong2, which is a linear plasmid within its genome that can lead to increased heterologous gene expression in recombinant M. smegmatis (rSmeg) and rBCG compared to that using the conventional pAL5000 vector system which was originated from M. fortuitum ( 38 , 39 ). Furthermore, we showed that rSmeg expressing HIV-1 p24 Gag using a pMyong2 vector system led to the enhanced immune responses against HIV-1 p24 Gag in mice, compared to rSmeg in the pAL5000 vector system or using an integrative plasmid, pMV306 system, suggesting the feasibility of the pMyong2 vector system in rSmeg vaccine application ( 40 ).…”