Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Abstract

Integrons ensure a rapid and “on demand” response to environmental stresses driving bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. Integrons can be either sedentary and chromosomally located or mobile when they are associated with transposons and plasmids. They are respectively called sedentary chromosomal integrons (SCIs) and mobile integrons (MIs). MIs are key players in the dissemination of antibiotic resistance genes. Here, we used in silico and in vivo approaches to study cassette excision dynamics in MIs and SCIs. We show that the orientation of cassette arrays relative to replication influences attC site folding and cassette excision by placing the recombinogenic strands of attC sites on either the leading or lagging strand template. We also demonstrate that stability of attC sites and their propensity to form recombinogenic structures also regulate cassette excision. We observe that cassette excision dynamics driven by these factors differ between MIs and SCIs. Cassettes with high excision rates are more commonly found on MIs, which favors their dissemination relative to SCIs. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions. These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria.

Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement

“…Since the integrase recognizes the structure of the bottom strand of attC sites ( 6 ), we based our features on the predicted folding of the bottom strand of each mutant using the RNAfold program from the ViennaRNA 2.1.8 package (Supplementary Materials) ( 24 ). Our list included several global features describing attC site folding, such as Gibbs free energy (∆ G ) of the structures, the probability to fold a functional structure (pfold), i.e., a structure with correctly folded integrase binding sites ( 25 , 26 ), and others. It also included a set of characteristics for each particular base, such as the nucleotide present at that position, its pairing probability, and positional entropy.…”

“…Our previous studies have already suggested that attC site recombination frequency depends on numerous properties related to their sequence, structure, and stability ( 6 , 8 , 9 , 11 , 12 , 25 , 26 , 40 , 41 ). Most of these factors apply to both attI × attC and attC × attC recombination reactions.…”

“…Most of these factors apply to both attI × attC and attC × attC recombination reactions. In addition, recombination frequency between two attC sites depends on folding properties of both sites, the distance between them, and their orientation relative to the replication fork ( 26 ). To evaluate synthetic attC sites in a context that does not depend on the partner attC site, in this work, we used attI × attC recombination assays.…”

The Association of Group IIB Intron with Integrons in Hypersaline Environments

“…In attC recombination, replication is not only important for the formation of the folded bs, but also for the resolution of recombination products [32] [33]. However, the presence of single stranded proteins (SSP) hampers the formation of a fully folded attC bs in absence of integron integrase (IntI) [34] [35].…”

Can the legacy of industrial pollution influence antimicrobial resistance in estuarine sediments?

“…In comparison with the number of investigations conducted examining other drivers of antimicrobial resistance (e.g., pharmaceutic compounds and PTEs), there have been relatively minimal studies on the effects of PAH contamination to AMR, and few prediction models exist. However, research has demonstrated that naphthalene and phenanthrene exposure were primarily linked to conjugative transfer of genes mediated by class I integrons (Wang et al 2017); these genetic mechanisms allow bacteria to adapt and evolve rapidly through the acquisition, stockpiling and differential expression of new genes and have been previously correlated with clinical antibiotic resistance (Gillings et al 2008;Deng et al 2015;Loot et al 2017). Genes for PTEs and ARGs have been found in bacterial plasmids and could facilitate the dissemination of these genes under elevated stresses (Li et al 2015a;Zhai et al 2016).…”