Article Figures & Data
Figures
- Fig. 1.
Structure of the backbones of class 1 integrons. Each integron is bounded by 25-bp inverted repeats, designated IRi and IRt (vertical bars labeled i and t), and includes the 5′-CS (medium line), which begins with IRi, contains the intI1 gene, and ends at the vertical arrow in the attI1 site (narrow open box). This arrow marks the position of integrated cassettes, which are not shown. Parts of the 3′-CS (narrow line) and the tnimodule (thick line) are found to the right of the vertical arrow. Insertion sequences are shown as open boxes. (a) Tn402(also called In16 or Tn5090) includes the completetni module that contains a full set of transposition genes (tniA, -B, and -Q), a resolvase gene (tniR), and a res site (solid box). Tn402 contains an array of three cassettes,dfrB3, orfD, and qacE. (b) In5 includes the 3′-CS, containing qacEΔ1, a truncated version of the qacE cassette, thesul1 sulfonamide resistance determinant, orf5 and orf6, and part of the tni module. In5 has a single cassette,aacA(IIa). (c) In4 includes two copies of very short regions of the IRt end of the tni module separated by a complete copy of IS6100 and a partial copy consisting of the last 321 bp of IS6100 (Δ). The cassette array isaacC1-orfE-aadA2-cmlA1.
- Fig. 2.
Map of Tn1403 and In28. (a) Tn1403. The region shown represents Tn1403, with vertical bars representing the inverted repeats, and In28 is shown as a thicker line ending in bars labeled i and t. The extents of the fragments cloned in various plasmids are shown below. Previously sequenced sections are represented by lines: 1, Huovinen and Jacoby (22); 2, Vézina and Levesque (53); and the extent of the sequence obtained here is indicated by a dotted line. (b) Expanded map of In28. Each cassette is indicated by an open box and adjacent filled box that represents the 59-base element (59-be). Other features are as in Fig. 1. Restriction enzyme sites: B, BamHI; Bg,BglII; E, EcoRI; H,HindIII; P, PstI; S, SalI; Sa, SacI; Sp, SphI; X,XhoI.
- Fig. 3.
Sequence surrounding In28. The Tn1403sequences flanking In28 have been joined together (bases 195 to 73 of GenBank accession no. M59035 plus bases 6357 to 6452 of AF313472) to reconstitute the res site, and the 5 bp duplicated by insertion of In28 are boxed. This sequence is aligned with theres regions of Tn501 (bases 4750 to 4532 in Z00027), Tn1721 (bases 359 to 160 in K01724), and Tn1696 (bases 3562 to 3669 and 12005 to 12116 in U12338) and the extents of the three components of the res site, determined experimentally for Tn1721 by Hall and Halford (21) and Rogowsky et al. (44), are indicated. The 5-bp duplication in Tn1696 is also boxed.
- Fig. 4.
Backbone structures of In4-like class 1 integrons and of Tn610. The structures shown are (a) integrons for which the complete sequence is available and both terminal IRs are present; (b) completely sequenced integrons that lack one of the terminal IRs; (c) integrons for which the sequence does not extend far enough to determine if one or both terminal IRs are present; and (d) Tn610. Features shown are as in Fig. 1, and (IS26) indicates that IS26 is found adjacent to the boundary shown. The sources for the sequences used are: In4, GenBank accession no. U12338; In28, AF313472; pHCM1,http://www.sanger.ac.uk/Projects/S_typhi/; DT104, AF071555 andAF261826; In1, M95287 and AF117344; pCG4, AF164956; pACM1, U90945 andAF107205 plus standard 3′-CS (predicted to be present from available restriction maps); A. baumannii In, AJ289190; Tn610, X53653.
- Fig. 5.
Locations of resolvase genes adjacent to class 1 integrons. Integrons (a) found in transposons and (b) found in plasmids. Open bars labeled i and t indicate the outer IRi and IRt ends of the integron. (−) indicates that the outer IRt is not present, and (?) indicates that the sequence of this region has not been determined. The genes encoding resolvases or resolvase-like proteins are shown by thick arrows and are labeled tnpR for transposon genes,resP for plasmid genes, and res for the DT104 gene, whose origin is not known. Other genes and open reading frames are shown by thin arrows. The res sites (solid boxes) are shown only where their locations and extents have been determined experimentally or can be deduced by comparison with an experimentally determined res site (21, 30, 44). The sources of the sequences are: Tn1403/In28, AF313472 and M59035; Tn1696/In4, U12338; Tn1412/In32, L36547; Tn21/In2, AF071413; R46/In1, M95287; pVS1/In0, U10456and U49101; pSa/In6, U303471; pMG7, S78872; pCG4, AF164956; and DT104,AF071555 and AF261826.
Tables
- Table 1.
Plasmids
Plasmid Description Relevant phenotypea Reference R388::Tn1403 AprCbr Smr Spr SurKmr Tcr Tra+ G. A. Jacoby pRMH105 10.0-kb SalI-EcoRV fragment of pKM101 (R46) Apr 19 pRMH518 6.4-kbBamHI-BglII fragment of R388::Tn1403 in pUC19 Apr This work pRMH519 5.5-kb SacI-BglII fragment of pRMH518 in pUC19 Apr SmrSpr This work pRMH527 1.5-kbSacI-SalI fragment of pRMH519 in pUC19 Apr Smr Spr This work pRMH534 10.0-kb HindIII fragment of R388::Tn1403 in pUC19 AprSmr This work pRMH547 3.0-kb BamHI fragment of R388::Tn1403 in pACYC184 Cmr This work ↵a Ap, ampicillin; Cb, carbenicillin; Cm, chloramphenicol; Km, kanamycin; Sm, streptomycin; Sp, spectinomycin; Su, sulfonamide; Tc, tetracycline.
