Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

Abstract

Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a metaanalysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3′ region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability.

Heterogeneous and Flexible Transmission of mcr-1 in Hospital-Associated Escherichia coli

“…Furthermore, IS Kpn26 was adjacent to mcr-1 in isolates ZJ148 and ZJ1653, and several other IS elements such as IS 2 , IS 609 , IS 683 , IS 1294 , IS 150 , and IS Sen6 were found in the mcr-1 -positive contigs but not in locations immediately proximal to mcr-1 . Whether these IS elements could contribute to the mobilization of mcr-1 remains unknown, but their presence would enhance the transmission of mcr-1 and facilitate its close association with other antibiotic resistance genes as seen in isolates ZJ134, ZJ33, ZJ487, ZJ26, and ZJ71 ( 41 , 54 , 55 ).…”

Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli

“…For instance, a recent study reported the contamination by 1.3 kb IS2 in a pDNA vaccine candidate, with pVAX1 as the backbone, between the kanamycin resistance cassette and BGH polyA signal [35]. The frequency at which such undesirable events could be triggered relies on the presence of switch sites of GC and AT skews (ssGCs and ssATs) in pDNA, as well as on the time, cell density and mode of cultivation [36]. Complete sequencing of the plasmids from the master cell bank and from the conditions assessed in this work demonstrated that DOT availability did not altered plasmid sequence fidelity.…”

Structural and Functional Disparities within the Human Gut Virome in terms of Genome Topology and Representative Genome Selection

“…GC-skew is known to be a non-trivial property that on occasion reflect the presence of certain genomic features. For example, a change of polarity (the sign) of GC-skew indicates such features as the origin of replication [36] and the site of mobile genetic element insertion [37]. The consistently higher mean GC-skew that we observe in circular viruses compared to linear viruses may have a role in structural configuration given that GC-skew in this case is a property that discriminates between two topological classes.…”