Genomic Signatures of Distributive Conjugal Transfer among Mycobacteria

Abstract

Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis. We have tested popular LGT detection methods on whole-genome sequence data from experimental DCT transconjugants and used the best performing methods to compare genomic signatures of DCT with those of LGT through natural transformation, conjugative plasmids, and mobile genetic elements (MGE). We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT. We used the best performing methods to characterize LGT in Mycobacterium canettii, the mycobacterial species most closely related to Mycobacterium tuberculosis. Patterns of LGT among M. canettii were highly distinctive. Gene flow appeared unidirectional, from lineages with minimal evidence of LGT to isolates with a substantial proportion (6–13%) of sites identified as recombinant. Among M. canettii isolates with evidence of LGT, recombinant fragments were larger and more evenly distributed relative to bacteria that undergo LGT through natural transformation, conjugative plasmids, and MGE. Spatial bias in M. canettii was also unusual in that patterns of recombinant fragment sharing mirrored overall phylogenetic structure. Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.

Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria

“…An M. smegmatis recA donor mutant led to a higher rate of gene conversion in the recipient, likely caused by unrepaired DNA breaks in the donor and, hence, more potential DNA substrates to be transferred (13). For tubercle bacilli, previous genome-based in silico analyses suggested that the analyzed M. canettii strains contained M. canettii J and M. canettii K-derived recombination tracts, thus proposing that these two strains were efficient donors (11). Interestingly, sequence comparison of their recA genes revealed that both strains differ in their intein-encoding and predicted excised RecA sequences from other M. canettii and MTBC strains (SI Appendix, Fig.…”

“…First hints came from putative recombination tracts identified by in silico analyses in genomes of smooth tubercle bacilli of the M. canettii clade (10,11). M. canettii strains are remarkable, rare mycobacteria, which are almost exclusively isolated from patients in the region of the Horn of Africa (35, 36).…”

“…Recent whole genome sequence (WGS) analyses of early branching, smooth tubercle bacilli (STB) of the Mycobacterium canettii clade revealed genome-wide traces of putative interstrain recombination events (10,11), raising questions on the existence and functionality of particular HGT mechanisms in tubercle bacilli. An interesting observation in this respect was made for the nonvirulent, fast-growing model organism Mycobacterium smegmatis, which shows an unconventional conjugal DNA transfer (12,13), distinct from classical plasmid-mediated DNA transfer described for other bacteria (14,15).…”

“…Consequently, this type of HGT was termed distributive conjugal transfer (DCT) (16). Detection of mosaic sequence arrangements in M. canettii genomes (10,11,17,18) raised the issue whether similar molecular mechanisms might be active in tuberculosis-causing mycobacteria and/or in mycobacteria, in general.…”

Virulence Factors and Pathogenicity of Mycobacterium

“…ESX-1 allows cytosolic contact and mediates vacuoles rupture [47]; the protein intervenes in host cell lysis in a contact dependent way, producing gross membrane disruptions [48]. DNA transfer through conjugation is also a function of ESX-1 system [49]; a phenomenon called "distributive conjugal transfer" that describes a genetic exchange between recipient and donor is dependent of ESX-1 in M. smegmatis [50]. espB gene located in the RD1 region has been related with cytotoxicity and their presence in the surface of apoptotic cells for clearance by macrophages through efferocytosis [51].…”