Novel plasmid vectors for gene cloning in Pseudomonas

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

Plasmids are important drivers of bacterial evolution, but it is challenging to understand how plasmids persist over the long term because plasmid carriage is costly. Classical models predict that horizontal transfer is necessary for plasmid persistence, but recent work shows that almost half of plasmids are non-transmissible. Here we use a combination of mathematical modelling and experimental evolution to investigate how a costly, non-transmissible plasmid, pNUK73, can be maintained in populations of Pseudomonas aeruginosa. Compensatory adaptation increases plasmid stability by eliminating the cost of plasmid carriage. However, positive selection for plasmid-encoded antibiotic resistance is required to maintain the plasmid by offsetting reductions in plasmid frequency due to segregational loss. Crucially, we show that compensatory adaptation and positive selection reinforce each other’s effects. Our study provides a new understanding of how plasmids persist in bacterial populations, and it helps to explain why resistance can be maintained after antibiotic use is stopped.

Plasmids are important for bacterial evolution but the evolutionary mechanisms behind their maintenance are unclear. Here the authors show that the interplay between compensatory adaptation and positive selection for plasmid-encoded antibiotic resistance determines plasmid persistence in P. aeruginosa.

Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations

Plasmids have a key role in the horizontal transfer of genes among bacteria. Although plasmids are catalysts for bacterial evolution, it is challenging to understand how they can persist in bacterial populations over the long term because of the burden they impose on their hosts (the ‘plasmid paradox'). This paradox is especially perplexing in the case of ‘small' plasmids, which are unable to self-transfer by conjugation. Here, for the first time, we investigate how interactions between co-infecting plasmids influence plasmid persistence. Using an experimental model system based on interactions between a diverse assemblage of ‘large' plasmids and a single small plasmid, pNI105, in the pathogenic bacterium Pseudomonas aeruginosa, we demonstrate that positive epistasis minimizes the cost associated with carrying multiple plasmids over the short term and increases the stability of the small plasmid over a longer time scale. In support of these experimental data, bioinformatic analysis showed that associations between small and large plasmids are more common than would be expected owing to chance alone across a range of families of bacteria; more generally, we find that co-infection with multiple plasmids is more common than would be expected owing to chance across a wide range of bacterial phyla. Collectively, these results suggest that positive epistasis promotes plasmid stability in bacterial populations. These findings pave the way for future mechanistic studies aimed at elucidating the molecular mechanisms of plasmid–plasmid interaction, and evolutionary studies aimed at understanding how the coevolution of plasmids drives the spread of plasmid-encoded traits.

Characterization of pNI10 plasmid in Pseudomonas, and the construction of an improved Escherichia and Pseudomonas shuttle vector, pNUK73

The complete nucleotide sequence of pNI10 (3.75 kb), from which pNI105 and pNI107 were constructed as medium-host-range vectors for Gram-negative bacteria, was determined. A fragment of about 2.1 kb of pNI10 was essential for replication in Escherichia coli and Pseudomonas fluorescens. This fragment encodes a putative origin of replication ( ori) and one putative replication-controlling protein (Rep). An improved version of the medium-host-range plasmid vector pNUK73 (5.13 kb) was constructed with the basic-replicon of pNI10 and pHSG298 (2.68 kb). We show that expression in pseudomonads of the bromoperoxidase gene ( bpo) of Pseudomonas putida, inserted downstream of the lac promoter in pNUK73, resulted in about 30% (13.6 U/l culture) of the enzyme level obtained in E. coli.

Resistance to tellurite as a selection marker for genetic manipulations of Pseudomonas strains

Resistance to the toxic compound potassium tellurite (Telr) has been employed as a selection marker built into a set of transposon vectors and broad-host-range plasmids tailored for genetic manipulations of Pseudomonas strains potentially destined for environmental release. In this study, the activated Telr determinants encoded by the cryptic telAB genes of plasmid RK2 were produced, along with the associated kilA gene, as DNA cassettes compatible with cognate vectors. In one case, the Telr determinants were assembled between the I and O ends of a suicide delivery vector for mini-Tn5 transposons. In another case, the kilA and telAB genes were combined with a minimal replicon derived from a variant of Pseudomonas plasmid pPS10, which is able to replicate in a variety of gram-negative hosts and is endowed with a modular collection of cloning and expression assets. Either in the plasmid or in the transposon vector, the Telr marker was combined with a 12-kb DNA segment of plasmid pWW0 of Pseudomonas putida mt-2 encoding the upper TOL pathway enzymes. This allowed construction of antibiotic resistance-free but selectable P. putida strains with the ability to grow on toluene as the sole carbon source through an ortho-cleavage catabolic pathway.

Purification and characterization of a novel metal-containing nonheme bromoperoxidase from Pseudomonas putida

A novel bromoperoxidase was purified to homogeneity from the bacterium Pseudomonas putida IF-3 strain, which produces the antibiotic pyrrolnitrin. The enzyme had a molecular mass of 68,000 and was composed of two identical subunits (33,000). It was specific for I- and Br- and inactive toward Cl- and F- in the monochlorodimedone assay system. The optimum pH of the enzyme was around 4.2 and it rapidly lost its activity below 3.5, but it was stable over of range pH of 4 to 11. The purified enzyme was activated several fold by incubation with only cobalt ions, and did not contain an organic prosthetic group such as heme, flavin and cobalamin. Analyses of prosthetic metal compounds in the enzyme using plasma atomic emission spectroscopy (ICP-AES) combined with mass-spectroscopy (MS) and trace metal determination by high performance liquid chromatography (HPLC)-spectrometry, revealed that the enzyme contained 0.35 +/- 0.1 mol of cobalt ions, 1.0 +/- 0.2 mol of nickel ions, 0.8 +/- 0.2 mol of zinc ions and 2.0 +/- 0.2 mol of ferric iron per mol of enzyme, assuming the molecular weight of 68,000. There was no trace of vanadium in the enzyme, unlike in some nonheme haloperoxidases. Thus the bromoperoxidase of P. putida is a novel nonheme metal-containing bromoperoxidase.

Novel narrow-host-range vectors for direct cloning of foreign DNA in Pseudomonas

Narrow-host-range vectors, based on an indigenous replicon and containing a multiple cloning site, have been constructed in a Pseudomonas host capable of growth on unusual substrates. The new cloning vectors yield sufficient amounts of DNA for preparative purposes and belong to an incompatibility group different from that of the incP and incQ broad-host-range vectors. One of these vectors, named pDB47F, was used to clone, directly in Pseudomonas, DNA fragments from Agrobacterium, Pseudomonas, and Rhizobium. A clone containing Agrobacterium and KmR gene sequences was transformed with a higher efficiency than an RSF1010-derived vector (by as much as 1250-fold) in four out of five Pseudomonas strains tested. The considerable efficiency obtained with this system makes possible the direct cloning and phenotypic selection of foreign DNA in Pseudomonas.

A variety of catalases and bromoperoxidases in genus Pseudomonas and their characterization

A survey of bromoperoxidase in some Pseudomonas strains revealed that they contain different types of bromoperoxidase, catalase-bromoperoxidase and catalase. Although all Pseudomonas strains exhibited catalase activity, the enzyme isolated from P. pyrrolnitrica was named catalase-bromoperoxidase, because it catalyzed not only a catalase reaction, but also the bromination of monochlorodimedone. Except heme-type catalase-bromoperoxidase, this strain contained four isoenzymes of general nonheme bromoperoxidase, and their molecular weights were about 73,000. On the other hand, P. putida and P. aeruginosa had the usual heme-type catalase, but they differed in molecular weight and pI value. Both strains also had a nonheme bromoperoxidase which catalyzed the bromination of monochlorodimedone and aniline, and the molecular weight of each enzyme was 68,000 for P. putida and 86,000 for P. aeruginosa. Considering the results reported by Van Pée et al. [1] and Weisner et al. [2], regarding the haloperoxidases of Pseudomonas, the genus was revealed to contain a wide variety of bromoperoxidase and catalase.