Physical mapping of TOL plasmids pWWO and pND2 and various R plasmid-TOL derivatives from Pseudomonas spp

Genetic Rearrangement of Plasmids: In Vivo Recombination between a Dehalogenation Plasmid and Multiple-Resistance Plasmid RP4 in Pseudomonas sp

When Moraxella plasmid pUO1 encoding haloacetate dehalogenase and mercury resistance coexisted with IncP-1 plasmid RP4 in Pseudomonas sp., genetic exchange between the plasmids often occurred, probably by site-specific recombination. The recombinant plasmids obtained were classified into four groups on the basis of phenotype. Representative plasmids for each group were analyzed for DNA composition and function, and the mechanism for the formation of these plasmids was sought. They were inherited stably in Escherichia coli and a Pseudomonas sp.

Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly

The persistence of chloroaromatic compounds can be caused by various bottlenecks, such as incomplete degradative pathways or inappropriate regulation of these pathways. Patchwork assembly of existing pathways in novel combinations provides a general route for the development of strains degrading chloroaromatics. The recruitment of known complementary enzyme sequences in a suitable host organism by conjugative transfer of genes might generate a functioning hybrid pathway for the mineralization of some chloroaromatics not degraded by the parent organisms. The rational combination uses (a) peripheral, funneling degradation sequences originating from aromatics-degrading strains to fulfill the conversion of the respective analogous chloroaromatic compound to chlorocatechols as the central intermediates; (b) a central chlorocatechol degradation sequence, the so-called modified ortho pathway, which brings about elimination of chlorine substituents; and (c) steps of the 3-oxoadipate pathway to reach the tricarboxylic acid cycle. The genetic organization of these pathway segments has been well characterized. The specificity of enzymes of the xylene, benzene, biphenyl, and chlorocatechol pathways and the specificity of the induction systems for the chlorinated substrates are analyzed in various organisms to illustrate eventual bottlenecks and to provide alternatives that are effective in the conversion of the "new" substrate. Hybrid pathways are investigated in "new" strains degrading chlorinated benzoates, toluenes, benzenes, and biphenyls. Problems occurring after the conjugative DNA transfer and the "natural" solution of these are examined, such as the prevention of misrouting into the meta pathway, to give a functioning hybrid pathway. Some examples clearly indicate that patchwork assembly also happens in nature.

Localization and functional analysis of structural and regulatory dehalogenase genes carried on DEH from Pseudomonas putida PP3

Pseudomonas putida PP3 expressed two dehalogenases, DehI and DehII. The DehI gene (dehI) was located on a mobile DNA element (DEH) which inserted at high frequencies into target plasmids from its chromosomal location. From a recombinant TOL plasmid (pWW0) containing a 6.0-kb DEH element inserted into the plasmid's 5.6-kb EcoRI-G restriction endonuclease fragment, an 11.6-kb EcoRI fragment was cloned. Subcloning analysis and insertion mutagenesis produced a structural map of the DEH element and located the dehalogenase functions. The gene dehI was transcribed from a regulated promoter on DEH which was expressed in P. putida and Escherichia coli. The direction of transcription of dehI was determined, and it was also found to be under positive control, activated by an adjacent regulatory gene (dehRI). Expression of dehI in clones containing the intact DEH supported good growth on 2-monochloropropionate (2MCPA). Subclones lacking dehRI expressed dehI at levels which allowed only slow growth on 2MCPA, even when dehI expression was initiated from vector promoters. Expression of dehI in P. putida containing the intact DEH element required rpoN, suggesting that it was omega 54 dependent. The intact DEH element transferred to P. putida on a suicide plasmid donor pAWT34 (pBR325 replicon), and dehI was stably inherited, without vector DNA sequences, in transformants selected on 2MCPA. This indicated that the cloned DEH element contained functions associated with recombination.

The dehalogenase gene dehI from Pseudomonas putida PP3 is carried on an unusual mobile genetic element designated DEH

As a result of the production of two dehalogenases (DehI and DehII), Pseudomonas putida PP3 utilized halogenated alkanoic acids, such as 2-monochloropropionic acid (2MCPA), as sole sources of carbon and energy. The DehI gene (dehI) was carried on a mobile genetic element (DEH) located on the chromosome of strain PP3. DEH recombined with target plasmid DNAs at high frequencies (e.g. 3.8 x 10(-4) per RP4.5 plasmid transferred). The regulated expression of dehI was detected in P. putida, Pseudomonas aeruginosa, and Escherichia coli strains containing derivative plasmids of RP4.5 and pWW0 recombined with DEH. Movement of DEH from the unstable RP4 derivatives pNJ5000 and pMR5 resulted in the insertion of DEH into the chromosome of RecA+ strains of P. putida but not in RecA+ nor RecA- strains of E. coli. Rescue of DEH from the chromosome of P. putida KT2441 onto plasmid RP4 involved recombination at a frequency (2.7 x 10(-4) per RP4 plasmid transferred) comparable to that observed in strain PP3. The DEH element was not classified as a conventional transposon because it did not move as a discrete DNA fragment: dehI-containing inserts in plasmid DNA targets varied in size between 6 and 13 kb. In addition, DEH exhibited a marked preference for insertion into a specific site on the plasmid pWW0, but its transposition, independent of host recombinational systems, remains to be demonstrated. However, the transposonlike characteristics of DEH included the conservation of restriction endonuclease sites, high-frequency recombination with different target replicons (plasmid and chromosomal DNA), and promiscuous insertion into plasmid RP4-based replicons. Therefore, it is proposed that DEH is an unusual mobile genetic element.

Genetic analysis of chromosomal operons involved in degradation of aromatic hydrocarbons in Pseudomonas putida TMB

The catabolic pathway for the degradation of aromatic hydrocarbons encoded by Pseudomonas putida TMB differs from the TOL plasmid-encoded pathway as far as regulation of the upper pathway is concerned. We found, by analyzing Tn5-induced mutants and by Southern blot hybridization with appropriate probes derived from the TOL plasmid pWW0, that the catabolic genes of strain TMB were located on the bacterial chromosome and not on the 84-kb plasmid harbored by this strain. The catabolic genes of TMB and pWW0 had sequence homology, as shown by Southern blot hybridization, but differed significantly in their restriction patterns. The analysis of the mutants suggests that a regulatory mechanism similar to that present in pWW0 coexists in TMB with a second mode of regulation which is epistatic on the former and that the chromosomal region carrying the catabolic genes is prone to rearrangements and deletions.

Molecular relationship of chromosomal genes encoding biphenyl/polychlorinated biphenyl catabolism: some soil bacteria possess a highly conserved bph operon

All the genes we examined that encoded biphenyl/polychlorinated biphenyl (PCB) degradation were chromosomal, unlike many other degradation-encoding genes, which are plasmid borne. The molecular relationship of genes coding for biphenyl/PCB catabolism in various biphenyl/PCB-degrading Pseudomonas, Achromobacter, Alcaligenes, Moraxella, and Arthrobacter strains was investigated. Among 15 strains tested, 5 Pseudomonas strains and one Alcaligenes strain possessed the bphABC gene cluster on the XhoI 7.2-kilobase fragment corresponding to that of Pseudomonas pseudoalcaligenes KF707. More importantly, the restriction profiles of these XhoI 7.2-kilobase fragments containing bphABC genes were very similar, if not identical, despite the dissimilarity of the flanking chromosomal regions. Three other strains also possessed bphABC genes homologous with those of KF707, and five other strains showed weak or no significant genetic homology with bphABC of KF707. The immunological cross-reactivity of 2,3-dihydroxybiphenyl dioxygenases from various strains corresponded well to the DNA homology. On the other hand, the bphC gene of another PCB-degrading strain, Pseudomonas paucimobilis Q1, lacked genetic as well as immunological homology with any of the other 15 biphenyl/PCB degraders tested. The existence of the nearly identical chromosomal genes among various strains may suggest that a segment containing the bphABC genes has a mechanism for transferring the gene from one strain to another.

In vivo generation of R68.45-pPGH1 hybrid plasmids conferring a Phl+ (meta pathway) phenotype

Plasmid pPGH1 originating from Pseudomonas putida strain H carries all the genes required for the degradation of phenol (or cresols) via the meta cleavage pathway. Besides mobilization of pPGH1 by a plasmid of the incompatibility group P-1, hybrid plasmids conferring the Phl+ phenotype could be selected, when R68.45 was the conjugative plasmid. The hybrids contain the complete R68.45 and part of pPGH1. Integration of Phl-DNA of pPGH1 into R68.45 occurred exclusively via the IS21 region of R68.45.

Identification and characterization of Tn4653, a transposon covering the toluene transposon Tn4651 on TOL plasmid pWW0

A Pseudomonas TOL plasmid pWW0 possesses toluene degradative pathway (xyl) genes. Unstable maintenance of a pWW0 derivative in Escherichia coli allowed us to identify two transposable elements each carrying all the xyl genes. One element corresponded to a 56 kb transposon, Tn4651, which we had previously characterized. The other element newly identified in this study was 70 kb long, and this element, designated Tn4653, completely included Tn4651. Genetic analysis of Tn4653 demonstrated that its transposition involves two steps, i.e. cointegrate formation and its subsequent resolution. The former step required a trans-acting factor, transposase, which was encoded in a 3.0 kb fragment at one end of Tn4653, and the latter step was inferred to be mediated by the factors necessary for resolution of the Tn4651-mediated cointegrate. The transposase functions were not interchangeable between the two transposons.

Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWW0

Toluene degrading (xyl) genes on a Pseudomonas TOL plasmid pWW0 are located within a 39-kb DNA portion. The 56-kb region including these xyl genes and its 17-kb derivative with a deletion of the internal 39-kb portion transposed to various sites on target replicons such as pACYC184 and R388 in Escherichia coli recA strains. Thus the 56- and 17-kb regions were designated Tn4651 and Tn4652, respectively. Genetic analysis of Tn4652 demonstrated that its transposition occurs by a two-step process, namely, cointegrate formation and its subsequent resolution. The presence in cis of DNA sequences of no more than 150 bp at both ends of Tn4652 was prerequisite for cointegrate formation, and this step was mediated by a trans-acting factor, transposase, which was encoded in a 3.0-kb segment at one end of the transposon. Cointegrate resolution took place site-specifically within a 200-bp fragment, which was situated 10 kb away from the transposase gene. Based on the stability of cointegrates formed by various mini-Tn4652 derivatives, it was shown that the cointegrate resolution requires two trans-acting factors encoded within 1.0- and 1.2-kb fragments that encompass the recombination site involved in the resolution.

Chromosomal location of TOL plasmid DNA in Pseudomonas putida

The soil isolate Pseudomonas putida MW1000 can grow on toluene and other hydrocarbons; in this respect it is similar to strains of Pseudomonas which carry the TOL plasmid. By conjugation experiments, the genes conferring these growth abilities have been shown to be located on the bacterial chromosome, linked to vil and catB. A 56-kilobase segment of the bacterial chromosome of MW strains carrying the TOL genes can transpose to the IncP-1 plasmid R18-18. Physical analysis of these TOL R18-18 hybrids has shown that the TOL segment is almost identical to the same region found in the TOL plasmid pWW0.

Spontaneous deletion of a 20-kilobase DNA segment carrying genes specifying isopropylbenzene metabolism in Pseudomonas putida RE204

The genes encoding isopropylbenzene metabolism in Pseudomonas putida RE204 are readily lost in two ways: by loss (curing) of plasmid pRE4 which specifies the catabolic pathway and by deletion from pRE4 of an approximately 20-kilobase segment of DNA carrying the catabolic genes. The presence of DNA sequences at the ends of the catabolic gene region sharing homology with one another suggests that the deletions result from recombination events between these homologous sequences.

Gene order of the TOL catabolic plasmid upper pathway operon and oxidation of both toluene and benzyl alcohol by the xylA product

TOL plasmid pWW0 specifies enzymes for the oxidative catabolism of toluene and xylenes. The upper pathway converts the aromatic hydrocarbons to aromatic carboxylic acids via corresponding alcohols and aldehydes and involves three enzymes: xylene oxygenase, benzyl alcohol dehydrogenase, and benzaldehyde dehydrogenase. The synthesis of these enzymes is positively regulated by the product of xylR. Determination of upper pathway enzyme levels in bacteria carrying Tn5 insertion mutant derivatives of plasmid pWW0-161 has shown that the genes for upper pathway enzymes are organized in an operon with the following order: promoter-xylC (benzaldehyde dehydrogenase gene[s])-xylA (xylene oxygenase gene[s])-xylB (benzyl alcohol dehydrogenase gene). Subcloning of the upper pathway genes in a lambda pL promoter-containing vector and analysis of their expression in Escherichia coli K-12 confirmed this order. Two distinct enzymes were found to attack benzyl alcohol, namely, xylene oxygenase and benzyl alcohol dehydrogenase; and their catalytic activities were additive in the conversion of benzyl alcohol to benzaldehyde. The fact that benzyl alcohol is both a product and a substrate of xylene oxygenase indicates that this enzyme has a relaxed substrate specificity.

Identification of cis-diols as intermediates in the oxidation of aromatic acids by a strain of Pseudomonas putida that contains a TOL plasmid

Pseudomonas putida BG1 was isolated from soil by enrichment with p-toluate and selection for growth with p-xylene. Other hydrocarbons that served as growth substrates were toluene, m-xylene, 3-ethyltoluene, and 1,2,4-trimethylbenzene. The enzymes responsible for growth on these substrates are encoded by a large plasmid with properties similar to those of TOL plasmids isolated from other strains of Pseudomonas. Treatment of P. putida BG1 with nitrosoguanidine led to the isolation of a mutant strain which, when grown with fructose, oxidized both p-xylene and p-toluate to (-)-cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylic acid (cis-p-toluate diol). The structure of the diol was determined by conventional chemical techniques including identification of the products formed by acid-catalyzed dehydration and characterization of a methyl ester derivative. The cis-relative stereochemistry of the hydroxyl groups was determined by the isolation and characterization of an isopropylidene derivative. p-Xylene-grown cells contained an inducible NAD+-dependent dehydrogenase which formed catechols from cis-p-toluate diol and the analogous acid diols formed from the other hydrocarbon substrates listed above. The catechols were converted to meta ring fission products by an inducible catechol-2,3-dioxygenase which was partially purified from p-xylene-grown cells of P. putida BG1.

Construction of bacterial strains with novel degradative capabilities for chloroaromatics

Biodegradation of most naturally occurring compounds is relatively fast, since microorganisms have evolved appropriate enzyme systems. However, biodegradation is less likely in the case of man-made compounds like haloaromatics, which have structural features rarely or never encountered in natural products. One strategy to develop new metabolic activities for novel compounds by strains of microorganisms is by the alteration of their existing genetic information. The present paper summarizes results of studies where the degradation capabilities of bacteria were expanded by genetic material from external sources either by natural exchange or by cloning procedures.

Molecular relationships between pseudomonas INC P-9 degradative plasmids TOL, NAH, and SAL

We have examined the extent to which the degradative plasmids SAL, NAH, and TOL of the Inc P-9 incompatibility group share common DNA sequences. The homology we observe using 32P-labeled SAL and NAH DNA probes can be assigned to six regions of the TOL (pWWO) restriction endonuclease cleavage map. At least three of these regions are probably related to transfer and replication functions, whereas a fourth region is related to the common metacleavage pathway. Restriction endonuclease maps of the SAL and NAH plasmids are derived and the relationships between these plasmids discussed.

Characterization by molecular cloning of insertion mutants in TOL catabolic functions

A physical and genetic map of the Tol catabolic region of pWWO (TOL) was obtained by restriction endonuclease analysis of several DNA insertion mutants (xylA, xylA xylS, xylS, and xylR) of R plasmid--TOL derivatives. In two cases, the inserted DNA was shown from restriction, DNA hybridization, or heteroduplex analysis of cloned Hind III fragments to originate from within pWWO fragment Hind III-E. The effect of these DNA insertions on Tol catabolic activity and on structural alterations to the TOL plasmid is discussed.