A DNA segment encoding the anticodon stem/loop of tRNA determines the specific recombination of integrative-conjugative elements in Acidithiobacillus species

Abstract

Horizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans encodes an integrative-conjugative genetic element (ICEAfe1) inserted in the gene encoding a tRNA. This genetic element is actively excised from the chromosome upon induction of DNA damage. A similar genetic element (ICEAca.2) is also found in an equivalent position in the genome of Acidithiobacillus caldus. The local genomic context of both mobile genetic elements is highly syntenous and the cognate integrases are well conserved. By means of site directed mutagenesis, target site deletions and in vivo integrations assays in the heterologous model Escherichia coli, we assessed the target sequence requirements for site-specific recombination to be catalyzed by these integrases. We determined that each enzyme recognizes a specific small DNA segment encoding the anticodon stem/loop of the tRNA as target site and that specific positions in these regions are well conserved in the target attB sites of orthologous integrases. Also, we demonstrate that the local genetic context of the target sequence is not relevant for the integration to take place. These findings shed new light on the mechanism of site-specific integration of integrative-conjugative elements in members of Acidithiobacillus genus.

Molecular Epidemiology of Photobacterium damselae subsp. damselae Outbreaks in Marine Rainbow Trout Farms Reveals Extensive Horizontal Gene Transfer and High Genetic Diversity

“…This region, in addition to integrase genes and IS elements, also contained several tRNA genes. The role of tRNA genes as target loci for the insertion of horizontally acquired DNA sequences has been extensively documented ( Schmidt and Hensel, 2004 ; Castillo et al, 2017 ). The increasing evidence that Vibrionaceae species are indeed prone to gain foreign DNA by natural transformation ( Sun et al, 2013 ; Antonova and Hammer, 2015 ; Metzger and Blokesch, 2016 ), suggests that some of these variable DNA sequences might have been taken from the environment and inserted into the P. damselae subsp.…”

Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer

“…In 16 of these 18 instances, an integrase or a transposase gene also was present, suggesting that HGT events that occur at the site of a tRNA gene may occur via a different mechanism compared to the majority of HGT events. In fact, Castillo et al [19] described a mobile element in Acidithiobacillus that integrates at the site of a tRNA gene. Thus, tRNA genes may be sites that are specifically targeted by some integrases and recombinases.…”

Transfer RNA function and evolution

“…In addition to their vital role in protein synthesis and synthetic biology applications, tRNAs are also involved in cellular processes beyond translation. These processes include lipid aminoacylation [9] and bacterial conjugation [10]. The contributions to the special issue in this area also focused on the role of tRNA modifications in wobble decoding [11] and bacterial cell death [12].…”

“…Alamos et al found that the acidophilic bacterium Acidithiobacillus ferrooxidans encodes 36 of its 95 tRNAs in an integrative-conjugative genetic element [13]. Indeed, Castillo et al show that the integrases encoded in the conjugative element recognize the anticodon stem loop region in the tRNA gene for active and site-specific recombination [10].…”