Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements and antibiotic resistance genes

Abstract

Transposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding genetic context. Here, we present a computational approach that allowed us to identify the boundaries of 6,549 Tn7-like transposons at base pair resolution. We found that 96% of these transposons carry at least one cargo gene. Delineation of distinct communities in a gene-sharing network demonstrates how transposons function as a conduit of genes between phylogenetically distant hosts. Comparative analysis of the cargo genes reveals significant enrichment of mobile genetic elements (MGEs) nested within Tn7-like transposons, such as insertion sequences and toxin-antitoxin modules, genes involved in recombination and anti-MGE defense, and in antibiotic resistance. More unexpectedly, cargo also includes genes encoding central carbon metabolism enzymes. Twenty-two Tn7-like transposons carry both an anti-MGE defense system and antibiotic resistance genes, illustrating how bacteria can overcome these combined pressures upon acquisition of a single transposon. This work substantially expands the distribution of Tn7-like transposons, defines their evolutionary relationships and provides a large-scale functional classification of prokaryotic genes mobilized by transposition.

DIVE: a reference-free statistical approach to diversity-generating & mobile genetic element discovery

“…In addition, we found a unique RA cluster in ICE Vch Ban8 in a different location, overlapping a known transposase. Furthermore, when we aligned the corresponding set of targets to a transposable element (TE) database (TnCentral), we found alignment rates of 10% (bowtie2), consistent with the fact that cargo genes mobilize via transposons [37]. Only targets derived from RAs aligning to ICE Vch Ban8, a variant lacking annotation information on the database, produced an alignment rate of 0.02%.…”

Structures of the holo CRISPR RNA-guided transposon integration complex

“…Screened grids were imaged using a Titan Krios (300 kV, ThermoFisher) equipped with a BioQuantum energy filter (Gatan) and K3 direct electron detector (Gatan). 15,740 micrographs were collected using Leginon ( 7 ) at the 81,000X magnification (1.067 Å/pixel) using image shift, with the nominal defocus from -0.8 μm to -2.5 μm. Each movie was collected with 2 seconds of exposure with a total dose of 49.91 electrons/Å 2 , fractionated into 50 frames.…”

“…One of the most remarkable aspects of CAST function is the precision of programmable insertions: DNA cargo is inserted in a single orientation and within a narrow window from the protospacer. These features appear to be generally conserved across CAST families (3,(5)(6)(7), and are likely a consequence of transpososome architecture (i.e. the nucleoprotein complex containing all CAST components).…”

Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

“…Tn7 and its related target-site selective transposons, encoding multiple proteins with roles in transposition, have been mainly discovered in Proteobacteria [39][40][41]. However, if the criteria used in the family de nition were relaxed to the presence of the DDE transposase component (TnsB) and at least one other component, the size of the Tn7 family remarkably increased, including the members carrying a CRISPR-cas system for target site selection [42] as well as members in the new clades [43]. The host taxa of Tn7-related elements now include Actinobacteria, Deinococcus-Thermus, and Cyanobacteria [43].…”

“…However, if the criteria used in the family de nition were relaxed to the presence of the DDE transposase component (TnsB) and at least one other component, the size of the Tn7 family remarkably increased, including the members carrying a CRISPR-cas system for target site selection [42] as well as members in the new clades [43]. The host taxa of Tn7-related elements now include Actinobacteria, Deinococcus-Thermus, and Cyanobacteria [43]. There are only three relevant pieces of literature on the movements of SEs and GInts [21,22,26].…”