title: Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework.
abstract: Horizontal Gene Transfer (HGT) events, initially thought to be rare in Mycobacterium tuberculosis, have recently been shown to be involved in the acquisition of virulence operons in M. tuberculosis. We have developed a new partitioning framework based HGT prediction algorithm, called Grid3M, and applied the same for the prediction of HGTs in Mycobacteria. Validation and testing using simulated and real microbial genomes indicated better performance of Grid3M as compared with other widely used HGT prediction methods. Specific analysis of the genes belonging to dormancy/reactivation regulons across 14 mycobacterial genomes indicated that horizontal acquisition is specifically restricted to important accessory proteins. The results also revealed Burkholderia species to be a probable source of HGT genes belonging to these regulons. The current study provides a basis for similar analyses investigating the functional/evolutionary aspects of HGT genes in other pathogens. A database of Grid3M predicted HGTs in completely sequenced genomes is available at https://metagenomics.atc.tcs.com/Grid3M/.
authors: Bio-sciences R and D Division, TCS Research, Tata Consultancy Services Ltd., Pune 411 013, India.
authors: Varun
authors: V
authors: Mehra
authors: Tarini Shankar
authors: TS
authors: Ghosh
authors: Sharmila S
authors: SS
authors: Mande
mesh_terms: D000465:Algorithms; D019117:Burkholderia / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000472:pathogenicity; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D014376:Tuberculosis / Q000235:genetics* / Q000382:microbiology