A novel family of potentially mobile DNA elements encoding site‐specific gene‐integration functions: integrons

Abstract

A family of novel mobile DNA elements is described, examples of which are found at several independent locations and encode a variety of antibiotic resistance genes. The complete elements consist of two conserved segments separated by a segment of variable length and sequence which includes inserted antibiotic resistance genes. The conserved segment located 3' to the inserted resistance genes was sequenced from Tn21 and R46, and the sequences are identical over a region of 2026 bases, which includes the sulphonamide resistance gene sull, and two further open reading frames of unknown function. The complete sequences of both the 3' and 5' conserved regions of the DNA element have been determined. A 59-base sequence element, found at the junctions of inserted DNA sequences and the conserved 3' segment, is also present at this location in the R46 sequence. A copy of one half of this 59-base element is found at the end of the sull gene, suggesting that sull, though part of the conserved region, was also originally inserted into an ancestral element by site-specific integration. Inverted or direct terminal repeats or short target site duplications, both of which are characteristics of class I and class II transposons, are not found at the outer boundaries of the elements described here. Furthermore, the conserved regions do not encode any proteins related to known transposition proteins, except the DNA integrase encoded by the 5' conserved region which is implicated in the gene insertion process. Mobilization of this element has not been observed experimentally; mobility is implied from the identification of the element in at least four independent locations, in Tn21, R46 (IncN), R388 (IncW) and Tn1696. The definitive features of these novel elements are (i) that they include site-specific integration functions (the integrase and the insertion site); (ii) that they are able to acquire various gene units and act as an expression cassette by supplying the promoter for the inserted genes. As a consequence of acquiring different inserted genes, the element exists in a variety of forms which differ in the number and nature of the inserted genes. This family of elements appears formally distinct from other known mobile DNA elements and we propose the name DNA integration elements, or integrons.

Why are bacteria refractory to antimicrobials?

“…Sci. 5 (1), 2009 Hogan, Kolter resistance genes, have also contributed to the problem of antibiotic resistance in bacteria [24]. Indeed, integrons that contain up to eight different antibiotic resistance cassettes have been found in multidrug resistant clinical isolates [25].…”

MOLECULAR DETECTION OF ANTIBIOTIC-RESISTANCE DETERMINANTS INESCHERICHIA COLIISOLATED FROM THE ENDANGERED AUSTRALIAN SEA LION (NEOPHOCA CINEREA)

“…Integrons encode for integrase genes (int) that enable insertion of gene cassettes at a recombination site (attI) and subsequent expression at an adjacent promotor (P c ) (Hall and Collis 1995;Collis et al 1998). Integrons can be classified into classes I, II, and III, with class I being most common in clinical pathogens (Stokes and Hall 1989). Class I integrons integrate within transposons or plasmids, a feature that has further facilitated their spread within and between species of bacteria (Gillings et al 2008).…”

Characterization of the nonenzymatic chloramphenicol resistance (cmlA) gene of the In4 integron of Tn1696: similarity of the product to transmembrane transport proteins

“…orfl is contained within cmlA, while orJ2 overlaps the C-terminal region of cmlA and the junction between the cmlA cassette and the N-terminal region of orf4. ORF4 is characteristic of the 3'-conserved segment (55). Sequencing of the sull gene region of TnJ696 (data not shown) indicates 100% identity with the sull gene of plasmid R388 (56).…”

“…Alternative promoters for the sull gene of R46 have been located on the 3'-conserved segment (19). At the 3' end of the gene cassettes, putative stem-loop structures potentially involved in site-specific recombination are observed (59-bp elements) (20,30,52,55). The requirement for these elements in cis for site-specific recombination has been demonstrated by Martinez and de la Cruz (31).…”

“…Stokes and Hall (55) have defined the elements borne on these multiresistance plasmids and transposons as integrons, a novel family of potentially mobile DNA elements which are composed of two conserved segments between which discrete units, ordinarily antibiotic resistance genes, have been integrated as gene cassettes. The 5'-conserved segment encodes a site-specific recombinase (Int) showing active-site residue similarity with the phage integrases (31,41,55). The 3'-conserved segment encodes a sulfonamide-resistant dihydropteroate synthase (Sull [56]) and two open reading frames (ORFs) of unknown phenotype, ORF4 and ORF5 (see Fig.…”