The new class II transposon Tn163 is plasmid-borne in two unrelated Rhizobium leguminosarum biovar viciae strains

Capture of a novel, antibiotic resistance encoding, mobile genetic element from Escherichia coli using a new entrapment vector

AIMS

Antimicrobial resistance genes (ARGs) are often associated with mobile genetic elements (MGEs), which facilitate their movement within and between bacterial populations. Detection of mobility is therefore important to understand the dynamics of MGE dissemination and their associated genes, especially in resistant clinical isolates that often have multiple ARGs associated with MGEs. Therefore, this study aimed to develop an entrapment vector to capture active MGEs and ARGs in clinical isolates of Escherichia coli.

METHODS AND RESULTS

We engineered an entrapment vector, called pBACpAK, to capture MGEs in clinical E. coli isolates. It contains a cI-tetA positive selection cartridge in which the cI gene encodes a repressor that inhibits the expression of tetA. Therefore, any disruption of cI, for example, by insertion of a MGE, will allow tetA to be expressed and result in a selectable tetracycline-resistant phenotype. The pBACpAK was introduced into clinical E. coli isolates and grown on tetracycline-containing agar to select for clones with the insertion of MGEs into the entrapment vector. Several insertion sequences were detected within pBACpAK, including IS26, IS903B and ISSbo1. A novel translocatable unit (TU), containing IS26 and dfrA8 was also captured, and dfrA8 was shown to confer trimethoprim resistance when it was cloned into E. coli DH5α.

CONCLUSIONS

The entrapment vector, pBACpAK was developed and shown to be able to capture MGEs and their associated ARGs from clinical E. coli isolates. We have captured, for the first time, a TU encoding antibiotic resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first time that a TU and associated resistance gene has been captured from clinical E. coli isolates using an entrapment vector. The pBACpAK has the potential to be used not only as a tool to capture MGEs in clinical E. coli isolates, but also to study dynamics, frequency and potentiators of mobility for MGEs.

Conjugative transfer of a derivative of the IncP-1α plasmid RP4 and establishment of transconjugants in the indigenous bacterial community of poplar plants

The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 10(5) to 9 × 10(6) CFU g(-1) fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas.

Influence of Bovine Slurry Deposition on the Structure of Nodulating Rhizobium leguminosarum bv. viciae Soil Populations in a Natural Habitat

The population of nodulating R. leguminosarum bv. viciae in soil from a grass-covered valley area which had been used for bovine slurry deposition over a period of 5 years was analyzed. For these studies, a rapid and reproducible method based on enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to identify Rhizobium strains which had infected pea nodules. Soil samples were taken from different areas and further analyzed in plant tests to determine the impact of the application of slurry (polluted or nonpolluted), the slope position (summit or toe), and exposure (north or south). After comparison of all PCR fingerprint patterns, 24 strain groups were defined. Some strain groups from the nonpolluted soil were suppressed in the polluted samples, and new strain groups were detected in the slurry-polluted soil. After analyzing relationships between the strain groups, we determined the influences of local factors on the nodulating R. leguminosarum bv. viciae population. We show that one of those local parameters, slope position, had significantly greater impact on the composition of the Rhizobium population than the presence of slurry.

Nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria

Arabidopsis thaliana mutants prors1-1 and -2 were identified on the basis of a decrease in effective photosystem II quantum yield. Mutations were localized to the 5'-untranslated region of the nuclear gene PROLYL-tRNA SYNTHETASE1 (PRORS1), which acts in both plastids and mitochondria. In prors1-1 and -2, PRORS1 expression is reduced, along with protein synthesis in both organelles. PRORS1 null alleles (prors1-3 and -4) result in embryo sac and embryo development arrest. In mutants with the leaky prors1-1 and -2 alleles, transcription of nuclear genes for proteins involved in photosynthetic light reactions is downregulated, whereas genes for other chloroplast proteins are upregulated. Downregulation of nuclear photosynthetic genes is not associated with a marked increase in the level of reactive oxygen species in leaves and persists in the dark, suggesting that the transcriptional response is light and photooxidative stress independent. The mrpl11 and prpl11 mutants are impaired in the mitochondrial and plastid ribosomal L11 proteins, respectively. The prpl11 mrpl11 double mutant, but neither of the single mutants, resulted in strong downregulation of nuclear photosynthetic genes, like that seen in leaky mutants for PRORS1, implying that, when organellar translation is perturbed, signals derived from both types of organelles cooperate in the regulation of nuclear photosynthetic gene expression.

Coordination of plastid and nuclear gene expression

The coordinated expression of genes distributed between the nuclear and plastid genomes is essential for the assembly of functional chloroplasts. Although the nucleus has a pre-eminent role in controlling chloroplast biogenesis, there is considerable evidence that the expression of nuclear genes encoding photosynthesis-related proteins is regulated by signals from plastids. Perturbation of several plastid-located processes, by inhibitors or in mutants, leads to decreased transcription of a set of nuclear photosynthesis-related genes. Characterization of arabidopsis gun (genomes uncoupled) mutants, which express nuclear genes in the presence of norflurazon or lincomycin, has provided evidence for two separate signalling pathways, one involving tetrapyrrole biosynthesis intermediates and the other requiring plastid protein synthesis. In addition, perturbation of photosynthetic electron transfer produces at least two different redox signals, as part of the acclimation to altered light conditions. The recognition of multiple plastid signals requires a reconsideration of the mechanisms of regulation of transcription of nuclear genes encoding photosynthesis-related proteins.

Role of tfxE, but not tfxG, in trifolitoxin resistance

Eight genes, tfxABCDEFG and tfuA, confer production of trifolitoxin (TFX), a ribosomally synthesized, posttranslationally modified peptide antibiotic, in TFX-sensitive alpha-proteobacteria. An in-frame deletion in tfxE significantly reduced a strain's resistance to TFX in comparison to that of an otherwise identical construct containing wild-type tfxE. The deletion of tfxG had no effect on TFX resistance. Nevertheless, RNase protection assays showed that tfxE and tfxG are transcribed, showing that the tfxDEFG mRNA was produced on the same transcript. Examination of the role of tfxG in TFX production showed that the tfxG mutant expressed slightly less TFX activity and produced only one TFX isomer while four are produced by the wild-type strain. Thus, tfxE plays an important role in TFX resistance while tfxG is important in optimal TFX production through the production of TFX isomers.

Transposon targeting determined by resolvase

The Mu-related transposon Tn5090, also called Tn402, was observed to be highly selective for targets clustered in or close to recombination sites of serine-type recombinases in plasmids R388 and RP1. Transposition to the par area of RP1 responded strongly to a deletion in the gene of resolvase ParA. A search in sequence databanks revealed further insertions of Tn5090/Tn402 close to different genes of resolvases. These results imply that the target selection of Tn5090 depends on a property that is shared among several serine recombinases.

Isolation and characterization of IS1416 from Pseudomonas glumae, a new member of the IS3 family

Isolation and characterization of four different insertion sequence (IS) elements from Pseudomonas glumae MAFF 302744 through transposition into the entrapment vector pSHI1063 are described. One of the elements, IS1416, was further characterized. IS1416 is 1322 bp long and carries 29-bp terminal inverted repeats flanked by a 3-bp direct duplication. IS1416 contains three open reading frames (ORFs), which are designated ORFA1, ORFA2, and ORFB, on one strand. Both DNA sequence of IS1416 and the deduced amino acid sequences of its ORFs strongly suggest that IS1416 is a member of the IS3 family, and is closely related to IS401 from Pseudomonas cepacia and IS51 from Pseudomonas syringae. To our knowledge, IS1416 is the first IS element isolated from P. glumae. The gene organization and possible regulation of transposition functions of IS1416 are also discussed.

ISRf1, a transposable insertion sequence from Sinorhizobium fredii

Sinorhizobium fredii strain HH103, a nitrogen-fixing bacterial symbiont of plants, contains an insertion sequence (IS) that can transpose into plasmid pMUS248 and activate a promoterless TcR gene that is normally not expressed. We have cloned and characterized this element, which we designate ISRf1. The IS is 1002 bp in length, contains a single 513-bp open reading frame (ORF), is flanked by imperfect 36-bp terminal inverted repeats, and creates 5-bp target duplications. Two copies of ISRf1 are present in the genome of HH103, but it is absent from 12 other Sinorhizobium and Rhizobium strains. The element transposes at a frequency of 2.7 x 10(-6) per generation per cell.

Structure and evolution of NGRRS-1, a complex, repeated element in the genome of Rhizobium sp. strain NGR234

Much of the remarkable ability of Rhizobium sp. strain NGR234 to nodulate at least 110 genera of legumes, as well as the nonlegume Parasponia andersonii, stems from the more than 80 different Nod factors it secretes. Except for nodE, nodG, and nodPQ, which are on the chromosome, most Nod factor biosynthesis genes are dispersed over the 536,165-bp symbiotic plasmid, pNGR234a. Mosaic sequences and insertion sequences (ISs) comprise 18% of pNGR234a. Many of them are clustered, and these IS islands divide the replicon into large blocks of functionally related genes. At 6 kb, NGRRS-1 is a striking example: there is one copy on pNGR234a and three others on the chromosome. DNA sequence comparisons of two NGRRS-1 elements identified three types of IS, NGRIS-2, NGRIS-4, and NGRIS-10. Here we show that all four copies of NGRRS-1 probably originated from transposition of NGRIS-4 into a more ancient IS-like sequence, NGRIS-10. Remarkably, all nine copies of NGRIS-4 have transposed into other ISs. It is unclear whether the accumulation of potentially mutagenic sequences in large clusters is due to the nature of the IS involved or to some selection process. Nevertheless, a direct consequence of the preferential targeting of transposons into such IS islands is to minimize the likelihood of disrupting vital functions.

Identification of cultivar-specific leghaemoglobin components in Pisum sativum

The components of leghaemoglobin (Lb) from twelve different Pisum sativum L. cvs and three near-isogenic foliar mutants were investigated by anion-exchange high-performance liquid chromatography (HPLC). Five different Lb component profiles could he found. The number of components varied from four to six dependent on cultivar used. An Lb pattern composed of four Lb components could be detected in thirteen P. sativum cultivars and lines. Ten of them showed an identical profile. In nodules of each cultivar, the two known major components, LbI and LbV, but also LbIV, could be detected. Additionally, cultivar-specific Lb components could be identified, each representing up to 10%, of total Lb. One of these components, LbIII, has been described previously, but three new Lb components (LbII, LbVI, and LbVII) were found. The presence of all Lb components detected by HPLC was confirmed by analytical isoelectric focusing. Further, it was shown that age-dependent changes in the relative concentrations of LbI and LbV are common in P. sativum and that these variations are independent of breeding lines and cultivars.

Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651

This paper reports the discovery and characterization of Tn5041, a novel-type transposon vehicle for dissemination of mercury resistance in natural bacterial populations. Tn5041 (14876 bp), identified in a Pseudomonas strain from a mercury mine, is a Tn3 family mercury resistance transposon far outside the Tn21 subgroup. As in other Tn3 family transposons, Tn5041 duplicates 5 bp of the target sequence following insertion. Tn5041 apparently acquired its mer operon as a single-ended relic of a transposon belonging to the classical mercury resistance transposons of the Tn21 subgroup. The putative transposase and the 47 bp terminal inverted repeats of Tn5041 are closely related to those of the toluene degradative transposon Tn4651 and fall into a distinct subgroup on the fringe of the Tn3 family. The amino acid sequence of the putative resolvase of Tn5041 resembles site-specific recombinases of the integrase family. Besides the mer operon and putative transposition genes, Tn5041 contains a 4 kb region that accommodates a number of apparently defective genes and mobile elements.