Table 1.
Paracoccus spp. strains used in this study.
Table 2.
Transposable elements of Paracoccus spp. identified in this study.
Figure 1.
Genetic organization of the insertion sequences (A, B, C, D, E) and composite transposon Tn6097 (F) of Paracoccus spp. identified in this study.
The families and names of the identified ISs are shown on the panel. Inverted repeats (IRL – left IR; IRR – right IR) flanking ISs are marked by black arrowheads. Predicted coding regions are represented by arrows indicating the direction of transcription. Gray arrows indicate TPase genes and white arrows indicate additional ORFs present within the ISs and within the core of Tn6097. Two of the ORFs of Tn6097 (ORF2 and ORF13) are truncated (the disruptions are most probably remnants of the ancient ISPfe2 transposition events that led to the formation of Tn6097 in its native host). The predicted genetic modules of the transposon are indicated.
Figure 2.
Genetic organization of the Tn3 family transposons captured in Paracoccus spp. using trap plasmids.
The cryptic transposon Tn3434a (A), Tn5393 carrying streptomycin resistance genes (B) and the composite element TnPpa1 flanked by two identical copies of Tn3434 (C). Predicted coding regions are represented by arrows indicating the direction of transcription. Gray arrows indicate TPase genes (tnpA) and additional genes (including resolvase genes – tnpR) are indicated by white arrows. Inverted repeats (IRs) flanking transposons are marked by black arrowheads (IRL – left IR; IRR – right IR) and res sites are shown by black squares. Plots of the G+C content of the Tn3434a and Tn5393 sequences are shown in panels A and B (the average value is given on the right).
Figure 3.
Schematic overview of five ways in which transposition can deliver promoters to the transcriptionally silent tetA (tetracycline resistance) gene of the trap plasmid pCM132TC.
The location of promoters in the plasmids pCM132TC::TE, conferring a Tcr phenotype, are appropriately indicated: an outwardly oriented promoter in the terminal parts of a TE (A), a hybrid promoter composed of a −35 hexamer (delivered by the TE) and a −10 hexamer located in close proximity to the target site of transposition (B), the promoter of a TPase gene (C), a promoter present in the core region of a composite transposon (D), and a promoter derived from another plasmid delivered by the generation of transient co-integrates resulting from replicative transposition (E). DNA fragments used in the localization of the promoters are shown as open thin boxes below each panel. The activity of promoters (tested in Paracoccus spp.) accompanying the presence of the DNA fragments is indicated on the right: (+) promoter activity, (−) lack of promoter activity.
Figure 4.
Deletions within the trap plasmid pMEC1 generated in P. versutus UW400 upon transposition of ISPve1.
The range of the deletion within four individual derivatives of pMEC1 is shown by curved gray lines.
Figure 5.
The distribution of TEs (identified in our studies) in the genomes of strains of Paracoccus spp.
A specific DNA probe (fragment of a TPase gene amplified by PCR and DIG-labeled) was prepared for each TE and used in dot blot hybridization analysis with total DNA isolated from the Paracoccus spp. strains.
Figure 6.
Distribution of IS-families identified in Paracoccus spp., among other genera of the class Alphaproteobacteria (ISfinder database).
The Paracoccus spp. elements are members of 10 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380, IS1634, ISAs1). Each IS-family is represented by a different color on the three dimensional histogram. The family IS1634 unique to the genus Paracoccus is shown in red.