Tn2610, a transposon involved in the spread of the carbenicillin-hydrolyzing beta-lactamase gene

Organization of tn2610 containing two transposition modules

Transposon Tn2610, found in a conjugative plasmid from an Escherichia coli isolate recovered at a hospital in Chiba, Japan, in 1975, was completely sequenced. Tn2610 is 23,883 bp long and is bracketed by two transposition modules, a Tn1721-like module and a Tn21-derived module, which correspond, respectively, to the long inverted repeats IRa and IRb previously described for this transposon. Although both tnpA genes are intact, only that in the Tn21-derived module (IRb) functions in the transposition, while that in the Tn1721-derived module (IRa) cannot recognize the 38-bp imperfect repeat at the end of the IRb element. Both tnpR and res are present in IRa, while the tnpR gene of IRb is interrupted by the insertion of an IS26 insertion element. The intervening region, between the res site of the Tn1721 module and IS26, carries multiple integron-associated resistance genes within a Tn21 backbone, including a region identical to that found in the genome of Salmonella enterica serovar Typhimurium DT104. These findings suggest that Tn2610 originated from Tn1721 and Tn21, with extensive recombination events with other elements which have resulted in a complex mosaic structure.

The Tn21 subgroup of bacterial transposable elements

The Tn3 family of transposable elements is probably the most successful group of mobile DNA elements in bacteria: there are many different but related members and they are widely distributed in gram-negative and gram-positive bacteria. The Tn21 subgroup of the Tn3 family contains closely related elements that provide most of the currently known variation in Tn3-like elements in gram-negative bacteria and that are largely responsible for the problem of multiple resistance to antibiotics in these organisms. This paper reviews the structure, the mechanism of transposition, the mode of acquisition of accessory genes, and the evolution of these elements.

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

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.

Organization of complex transposon Tn2610 carrying two copies of tnpA and tnpR

Transposon Tn2610 has two elements of 3.5 kilobase pairs as inverted repeats, one set at each end. This unique terminal element contained the transposition genes tnpA and tnpR. Only the tnpA gene in the left element was functional for transposition, whereas both tnpR genes were active. Possible evolutionary relationships among class II transposable elements are proposed on the basis of the genetic and structural organization of Tn2610.

The Salmonella wien virulence plasmid pZM3 carries Tn1935, a multiresistance transposon containing a composite IS1936-kanamycin resistance element

Tn1935, a 23.5-kb transposon mediating resistance to ampicillin, kanamycin, mercury, spectinomycin, and sulfonamide was isolated from pZM3, an IncFIme virulence plasmid from Salmonella wien. Tn1935 possesses the entire sequence of Tn21 and contains two additional DNA segments of 0.95 and 2.7 kb carrying the ampicillin and kanamycin resistance genes, respectively. The latter is part of a composite element since it is flanked by two IS15-like insertion sequences (IS1936) in direct orientation. IS1936 is about 800 bp long and is closely related to IS15 delta, IS26, IS46, IS140, and IS176. Functional analysis of IS1936-mediated cointegrates shows that both insertion sequences are active and able to form cointegrates at the same frequency. Resolution of the cointegrates requires the presence of the host Rec system. The presence of the composite IS1936-element within Tn1935 supports the hypothesis that multidrug resistance transposons evolved by insertion of antibiotic determinants which are themselves transposable.

The region of the IncN plasmid R46 coding for resistance to beta-lactam antibiotics, streptomycin/spectinomycin and sulphonamides is closely related to antibiotic resistance segments found in IncW plasmids and in Tn21-like transposons

The nucleotide sequence of a 2.5 kb segment of the pKM101 (R46) genome has been determined. The 1.3 kb from a BamHI site at 153 to base 1440 differs by only 2 bases from a part of the published sequence of the aadB (gentamicin resistance) gene region including the coding region for the N-terminal 70 amino acids of the predicted aadB product. The same sequence has been found 5'-to the dhfrII gene of R388 and to the aadA gene of Tn21 (R538-1). Three open reading frames are located in this region, two on the same strand as the resistance genes and one on the complementary strand. The latter predicts a polypeptide of 337 amino acids, whose N-terminal segment is 40% homologous to the predicted product of an open reading frame of 179 amino acids located next to the dhfrI gene of Tn7. The oxa2 (oxacillin resistance) gene predicts a long polypeptide commencing with (the N-terminal) 70 amino acids of the aadB product. A similar arrangement is found in the aadA gene of R538-1. The N-terminal segment of an aadA gene is located 3'- to oxa2, separated by 36 bases. Sequences surrounding the BamHI site are identical to sequences 5'- to the tnpM gene of Tn21 and homology ceases where homology between Tn21 and Tn501 commences. The possibility that this antibiotic resistance segment is a discrete mobile DNA element is discussed.

The genetics and biochemistry of mercury resistance

The ability of bacteria to detoxify mercurial compounds by reduction and volatilization is conferred by mer genes, which are usually plasmid located. The narrow spectrum (Hg2+ detoxifying) Tn501 and R100 determinants have been subjected to molecular genetic and DNA sequence analysis. Biochemical studies on the flavoprotein mercuric reductase have elucidated the mechanism of reduction of Hg2+ to Hg0. The mer genes have been mapped and sequenced and their protein products studied in minicells. Based on the deduced amino acid sequences, these proteins have been assigned a role in a mechanistic scheme for mercury flux in resistant bacteria. The mer genes are inducible, with regulatory control being exerted at the transcriptional level both positively and negatively. Attention is now focusing on broad-spectrum resistance involving detoxification of organomercurials by an additional enzyme, organomercurial lyase. Lyase genes have recently been cloned and sequencing studies are in progress.

Analysis by using DNA probes of the OXA-1 beta-lactamase gene and its transposon

From recombinant clone pTY27, encoding an OXA-1 beta-lactamase gene, we performed subcloning experiments to more precisely delimit the gene. We describe the use as probes of six different restriction fragments known from subcloning experiments to be within the structural gene or part of the transposable element, Tn2603, flanking the OXA-1 determinant. We showed that the OXA-1 structural gene is slightly related to the OXA-2 determinant and also that sequences within Tn2603 are common to all the OXA- and PSE-producing strains tested. For epidemiological purposes, we began nucleotide sequencing of the OXA-1 determinant, and from preliminary sequence data we synthesized an oligonucleotide 15 bases in length, corresponding to a sequence within the OXA-1 gene. This oligonucleotide was found to be specific for the OXA-1 determinant, because it hybridized only to bacteria producing that beta-lactamase.

Genesis of a complex transposon encoding the OXA-1 (type II) beta-lactamase gene

Plasmid R753-1-encoded resistance to ampicillin (by production of OXA-1 [type II] beta-lactamase), streptomycin, and sulfonamide was analyzed functionally and physically. The OXA-1 beta-lactamase gene on R753-1 could not transpose, whereas on some plasmids this gene was capable of transposition as part of transposon Tn2603. By using the nontransposable gene on R753-1 with Tn21 on a separate plasmid, we observed the genesis of a complex transposon with a structure similar to that of Tn2603. This finding confirms our previous hypothesis that Tn2603 has evolved directly from Tn21 through acquisition of the OXA-1 beta-lactamase gene by substitution of DNA segments. Furthermore, the mechanism of mobilization of pACYC184 derivatives by RecA-dependent homologous recombination was demonstrated.

Genetic and biochemical properties of AER-1, a novel carbenicillin-hydrolyzing beta-lactamase from Aeromonas hydrophila

A novel carbenicillin-hydrolyzing beta-lactamase has been discovered in a blood isolate of Aeromonas hydrophila. The enzyme resembles plasmid-determined carbenicillinases in substrate profile but differs in isoelectric point (pI 5.9) and molecular weight (22,000) and has been termed AER-1. No evidence for a plasmid location could be obtained in A. hydrophila, but the AER-1 gene and resistance to chloramphenicol, streptomycin, and sulfonamide could be transferred by mobilization with IncP plasmids to Escherichia coli, where the gene cluster inserted at a unique chromosomal site. The linked resistances are similar to those found on multiresistance beta-lactamase transposons, but since insertion of the A. hydrophila gene cluster was site specific and recA+ dependent, the cluster is not a functional transposon.

Plasmid R46 provides a function that promotes recA-independent deletion, fusion and resolution of replicon

We report that plasmid R46 provides a function which promotes recA-independent deletion, replicon fusion, and resolution of the fusion. R46 belongs to the incompatibility group N and specifies resistance to ampicillin, tetracycline, streptomycin and sulfonamide. Four kinds of deletion derivatives were observed by selection for susceptability to tetracycline from ampicillin-resistant clones. A common region, will be called alpha region thereafter, was postulated to be involved in these deletions. The replicon fusion occurred by a conjugative mobilization of each derivative with plasmid R388. The fusion was suggested to contain both replicons linked at each junction by the sequence in the alpha region in direct orientation. The resolution of the replicon fusion was found between two alpha regions and a consequently generated, parental deletion derivative and an R388 derivative which gained one alpha region. It is possible that the alpha region contains one potential Insertion Sequence (IS) element. These events were also speculated to occur as a consequence of insertion of the potential IS onto the intramolecular or intermolecular target sequence, or reciprocal recombination between two potential IS elements.

Fine structure of transposition genes on Tn2603 and complementation of its tnpA and tnpR mutations by related transposons

The fine structure of the genes tnpA, tnpR and res of Tn2603 required for its own transposition, was determined. The order of the genes was tnpA-tnpR-res from the right end of the right hand side region in Tn2603, the tnpA and tnpR encoded gene products having molecular weights of 110,000 and 21,000, respectively. The 110,000 molecular weight polypeptides was absolutely required for replicon fusion as the first stage of transposition, and named transposase. On the other hand, the 21,000 molecular weight polypeptide was necessary for resolution of the cointegrate as the second stage of transposition, and named resolvase. We also examined the ability of various transposons, assumed to be closely related, to complement the tnpA and tnpR mutations of Tn2603. The results indicated that the mercury resistance transposon, Tn2613, and Tn501, can complement both genes, but TnAs and gamma delta cannot at all. Tn501 had much less efficiency of complementation for tnpA than Tn2613. We have also discovered that the transposition frequency of transposons in the tn2613 family systematically depend on their size of transposon.