Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray

Bacterial transcriptional networks are built on a hierarchy of regulators, on top of which lie the components of the RNA polymerase (in particular the sigma factors) and the global control elements, which play a pivotal role. We have designed a genome-wide oligonucleotide-based DNA microarray for Pseudomonas putida KT2440. In combination with real-time reverse transcription polymerase chain reaction (RT-PCR), we have used it to analyse the expression pattern of the genes encoding the RNA polymerase subunits (the core enzyme and the 24 sigma factors), and various proteins involved in global regulation (Crc, Lrp, Fur, Anr, Fis, CsrA, IHF, HupA, HupB, HupN, BipA and several MvaT-like proteins), during the shift from exponential growth in rich medium into starvation and stress brought about by the entry into stationary phase. Expression of the genes encoding the RNA polymerase core and the vegetative sigma factor decreased in stationary phase, while that of sigma(S) increased. Data obtained for sigma(N), sigma(H), FliA and for the 19 extracytoplasmic function (ECF)-like sigma factors suggested that their mRNA levels change little upon entry into stationary phase. Expression of Crc, BipA, Fis, HupB, HupN and the MvaT-like protein PP3693 decreased in stationary phase, while that of HupA and the MvaT-like protein PP3765 increased significantly. Expression of IHF was indicative of post-transcriptional control. These results provide the first global study of the expression of the transcriptional machinery through the exponential stationary-phase shift in P. putida.

Energetics and surface properties of Pseudomonas putida DOT-T1E in a two-phase fermentation system with 1-decanol as second phase

The solvent-tolerant strain Pseudomonas putida DOT-T1E was grown in batch fermentations in a 5-liter bioreactor in the presence and absence of 10% (vol/vol) of the organic solvent 1-decanol. The growth behavior and cellular energetics, such as the cellular ATP content and the energy charge, as well as the cell surface hydrophobicity and charge, were measured in cells growing in the presence and absence of 1-decanol. Although the cells growing in the presence of 1-decanol showed an about 10% reduced growth rate and a 48% reduced growth yield, no significant differences were measured either in the ATP and potassium contents or in the energy charge, indicating that the cells adapted completely at the levels of membrane permeability and energetics. Although the bacteria needed additional energy for adaptation to the presence of the solvent, they were able to maintain or activate electron transport phosphorylation, allowing homeostasis of the ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities and more negative cell surface charges were observed in cells grown in the presence of 1-decanol. Both reactions occurred within about 10 min after the addition of the solvent and were significantly different after killing of the cells with toxic concentrations of HgCl2. This adaptation of the surface properties of the bacterium to the presence of solvents seems to be very similar to previously observed reactions on the level of lipopolysaccharides, with which bacteria adapt to environmental stresses, such as heat shock, antibiotics, or low oxygen content. The results give clear physiological indications that the process with P. putida DOT-T1E as the biocatalyst and 1-decanol as the solvent is a stable system for two-phase biotransformations that will allow the production of fine chemicals in economically sound amounts.

Inducible uptake and metabolism of glucose by the phosphorylative pathway in Pseudomonas putida CSV86

Pseudomonas putida CSV86 utilizes glucose, naphthalene, methylnaphthalene, benzyl alcohol and benzoate as the sole source of carbon and energy. Compared with glucose, cells grew faster on aromatic compounds as well as on organic acids. The organism failed to grow on gluconate, 2-ketogluconate, fructose and mannitol. Whole-cell oxygen uptake, enzyme activity and metabolic studies suggest that in strain CSV86 glucose utilization is exclusively by the intracellular phosphorylative pathway, while in Stenotrophomonas maltophilia CSV89 and P. putida KT2442 glucose is metabolized by both direct oxidative and indirect phosphorylative pathways. Cells grown on glucose showed five- to sixfold higher activity of glucose-6-phosphate dehydrogenase compared with cells grown on aromatic compounds or organic acids as the carbon source. Study of [14C]glucose uptake by whole cells indicates that the glucose is taken up by active transport. Metabolic and transport studies clearly demonstrate that glucose metabolism is suppressed when strain CSV86 is grown on aromatic compounds or organic acids.

Bacterial endophyte-enhanced phytoremediation of the organochlorine herbicide 2,4-dichlorophenoxyacetic acid

2,4-Dichlorophenoxyacetic acid is a selective systemic herbicide for the control of broad-leaved weeds, which is widely used throughout the world. The persistence of its residues and its potential to migrate in the soil make it necessary to reduce its concentrations in contaminated soil and groundwater. The nature of this compound makes it particularly toxic to the broad-leaved plants, such as the poplar (Populus) and willow (Salix), which are often used in phytoremediation projects. We describe the inoculation of a model plant, the pea (Pisum sativum), with a genetically tagged bacterial endophyte that naturally possesses the ability to degrade 2,4-dichlorophenoxyacetic acid. The results showed that this strain actively colonized inoculated plants internally (and in the rhizosphere). Inoculated plants showed a higher capacity for 2,4-dichlorophenoxyacetic acid removal from soil and showed no 2,4-dichlorophenoxyacetic acid accumulation in their aerial tissues. This demonstrates the usefulness of bacterial endophytes to enhance the phytoremediation of herbicide-contaminated substrates and reduce levels of toxic herbicide residues in crop plants.

Characterization of a HMT2-like enzyme for sulfide oxidation fromPseudomonas putida

The open reading frame pp0053, which has a high homology with the sequence of mitochondrial sulfide dehydrogenase (HMT2) conferring cadmium tolerance in fission yeast, was amplified from Pseudomonas putida KT2440 and expressed in Escherichia coli JM109(DE3). The isolated and purified PP0053-Hisshowed absorption spectra typical of a flavin adenine dinucleotide (FAD)–binding protein. The PP0053-Hiscatalyzed a transfer of sulfide-sulfur to the thiophilic acceptor, cyanide, which decreased the Kmvalue of the enzyme for sulfide oxidation and elevated the sulfide-dependent quinone reduction. Reaction of the enzyme with cyanide elicited a dose-dependent formation of a charge transfer band, and the FAD-cyanide adduct was supposed to work for a sulfur transfer. The pp0053 deletion from P. putida KT2440 led to activity declines of the intracellular catalase and ubiquinone-H2oxidase. The sulfide-quinone oxidoreductase activity in P. putida KT2440 was attributable to the presence of pp0053, and the activity showed a close relevance to enzymatic activities related to sulfur assimilation.Key words: HMT2-like enzyme, pp0053, Pseudomonas putida, sulfide oxidation.

Extracytoplasmic storage as the nickel resistance mechanism in a natural isolate of Pseudomonas putida S4

Metal resistances in microbes are important to study not only to understand metal homeostasis but also to use such organisms further in environmental bioremediation. Nickel (Ni2+) is an important micronutrient, which at higher concentration becomes toxic. Many Ni2+-resistant organisms are known, which resist metal by active efflux. Pseudomonas putida S4, a natural isolate from India, is reported to show a multi-metal resistance profile. In the present study, the Ni2+-resistance mechanism in strain S4 was examined. Wild-type cells gradually accumulated Ni2+ but kept it preferentially in the periplasmic space in a bound form. In Ni2+-sensitive mutants, periplasmic storage was disturbed and more metal accumulated cytoplasmically, producing toxicity. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis analysis of periplasmic proteins revealed a band of approximately 18 kDa, which appeared only in Ni2+-exposed wild-type cells, and which was absent from cells not exposed to Ni2+ as well as from Ni2+-sensitive mutants. On the basis of these observations, we propose a Ni2+-resistance mechanism in P. putida S4 based on sequestration of metal in the periplasmic space. This is the first study of sequestration-based Ni2+ resistance.

Involvement of coenzyme M during aerobic biodegradation of vinyl chloride and ethene by Pseudomonas putida strain AJ and Ochrobactrum sp. strain TD

The involvement of coenzyme M in aerobic biodegradation of vinyl chloride and ethene in Pseudomonas putida strain AJ and Ochrobactrum sp. strain TD was demonstrated using PCR, hybridization, and enzyme assays. The results of this study extend the range of eubacteria known to use epoxyalkane:coenzyme M transferase.

A double mutant of Pseudomonas putida JLR11 deficient in the synthesis of the nitroreductase PnrA and assimilatory nitrite reductase NasB is impaired for growth on 2,4,6-trinitrotoluene (TNT)

Pseudomonas putida JLR11 can grow on 2,4,6-trinitrotoluene (TNT) as the sole nitrogen source. We created nasB (nitrite reductase), pnrA (nitroaromatic reductase) and pnrA nasB mutants and tested their growth with TNT as the sole N source. The nasB and pnrA mutants grew at a reduced rate on TNT, whereas the double nasB pnrA mutant did not. This suggests that P. putida JLR11 carries out multiple enzymatic attacks on TNT-releasing nitrite and/or ammonium. The PnrA nitroreductase plays a key role in the reduction of TNT to 2,6-dinitro-4-hydroxylaminotoluene and the subsequent release of ammonium for growth.

Measurement of the Growth of a Floc Forming Bacterium Pseudomonas putida CP1

Pseudomonas putida CP1 formed clumps of cells when grown on mono-chlorophenols but not on phenol or glucose. An increase in cell numbers for the organism grown on mono-chlorophenols was accompanied by a decrease in the dry weight. The change in shape of the bacterium from rod shape to coccus shape coupled with a reduction in cell size when the organism was grown under nutritional stress was found. This result together with cell aggregation affected the measurement of growth parameters in the system by conventional methods (optical density measurements, dry weight measurements and the plate count technique). Monitoring growth of Pseudomonas putida CP1 by a direct microscopic count technique was found to be more representative than conventional methods including optical density measurements, dry weight measurements and the plate count technique when grown on phenolics.

Preferential utilization of aromatic compounds over glucose by Pseudomonas putida CSV86

Pseudomonas putida CSV86, a naphthalene-degrading organism, exhibited diauxic growth on aromatic compounds plus glucose, with utilization of aromatics in the first log phase and of glucose in the second log phase. Glucose supplementation did not suppress the activity of degrading enzymes, which were induced upon addition of aromatic compounds. The induction was inhibited by chloramphenicol, suggesting that de novo protein synthesis was essential. Cells showed cometabolism of aromatic compounds and organic acids; however, organic acids suppressed glucose utilization.

Biodegradability of end-groups of the biocide polyhexamethylene biguanide (PHMB) assessed using model compounds

Polyhexamethylene biguanide (PHMB), a biocide used in a wide variety of disinfection and preservation applications, is a polydisperse mixture in which the end-groups may be any combination of amine, guanidine and cyanoguanidine. Using PHMB model compounds (1,6-diaminohexane; 1,6-diguanidinohexane; 1,6-di(cyanoguanidino)hexane; 4-guanidinobutyric acid), we have determined the biodegradation characteristics of each end-group in several strains of bacteria isolated for their ability to utilise PHMB as a sole source of nitrogen. Bacteria were screened for growth at the expense of each model compound (at non-inhibitory concentrations) as sole nitrogen source. None of the isolated bacteria was capable of utilising a cyanoguanidine end-group as growth substrate, whereas several bacteria were shown to utilise amine or guanidine end-groups. In particular, a strain of Pseudomonas putida was capable of extensive growth with 1,6-diguanidinohexane as a sole nitrogen source, with complete removal of guanidine groups from culture medium within 2 days, and with concomitant formation of unsubstituted urea, which in turn was also utilised by the organism. We conclude that whilst amine and guanidine end-groups in PHMB are likely to be susceptible to biodegradation, cyanoguanidine end-groups are likely to be recalcitrant.

A two-partner secretion system is involved in seed and root colonization and iron uptake by Pseudomonas putida KT2440

We describe the first two-partner secretion system known to play a role in mutualistic plant-bacterial interactions, identified in the soil and rhizosphere-colonizing bacterium Pseudomonas putida KT2440. The genes coding for the two components of the system are organized in an operon, which we have named hlpBA. HlpA is a secreted protein that has similarities with iron-regulated haemolysins, while HlpB would be responsible for the activation and transport of HlpA across the outer membrane. Mutations in this novel two-partner secretion system result in reduced capacity to colonize corn seeds. When introduced in the rhizosphere, hlpA and hlpB mutants show no competitive disadvantage, but the number of cells attached to the root surface is reduced with respect to the wild type, suggesting this protein plays a role directly in the bacterial cell-root surface interaction. Under iron-limiting conditions, the presence of a truncated HlpA causes reduced viability and high levels of siderophore release. These data further strengthen our previous observations indicating the importance of iron acquisition for attachment of P. putida KT2440 to plant surfaces.

The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes

The effect of archetypal environmental stresses on expression of the catabolic xyl genes of the TOL plasmid pWW0 of the m-xylene degrading strain Pseudomonas putida mt-2 has been investigated. To this end, a subgenomic DNA chip was employed which included structural and regulatory DNA sequences of the TOL pathway along with selected descriptors of specific physiological conditions. Cells were separately exposed to m-xylene under various oxygen tensions, temperatures and nitrogen sources as well as situations of DNA damage, oxidative stress, carbon and iron starvation, respiratory chain damage, and contact with arsenic, but at doses which did not cause a gross effect on growth or cell viability. The incidence of each stress class was categorized through the corresponding descriptors in the chip in respect to the relative output of xyl transcripts. While most of the stresses downregulated the m-xylene biodegradation-related genes, some uncouplers of the respiratory chain (azide) and small doses of arsenate appeared to stimulate their expression. The replacement of NH4+ by NO3- as N source augmented expression of the TOL cistrons also. We subsequently subjected P. putida mt-2 cells to the multiple abiotic stress brought about by exposure to crude tar from the 2002 oil spill of the Prestige tanker, which embraces a complex mixture of hydrocarbons. The resulting expression profile of xyl genes and stress-responding markers over time suggested that adaptation to external insults precedes any significant expression of the catabolic genes. The consequences of this hierarchy of responses for microbial biodegradation in situ are discussed.

Biodegradation of p-nitrophenol by P. putida

A strain of Pseudomonas putida was found capable of metabolizing p-nitrophenol (PNP) as a sole source of carbon, nitrogen and energy. To explore the applicability of this strain for bioremediation for controlling environmental PNP pollution, its degradation potential at 300 and 500 ppm was examined in a medium devoid of carbon and nitrogen source (minimal medium). At A600, 0.5 OD inoculum, the strain metabolized 300 and 500 ppm within 36 and 72 h, respectively. The degradation was accompanied by release of stoichiometric amount of nitrite. Effect of glucose and nitrogen on PNP degradation under similar conditions revealed that (i) glucose (0.4 g/l) at 20 and 50 ppm PNP did not accelerate the rate of PNP degradation, while glucose (0.4 g/l) at 300 ppm PNP inhibited its degradation, (ii) nitrogen supplement viz. sodium nitrate and ammonium sulphate (0.04 and 0.4 g/l) in minimal medium with PNP (300 ppm) showed no effect on PNP degradation, while glutamate alone (0.04 and 0.4 g/l) showed mere rise in biomass (from 0.5 to 1.6 OD units), and (iii) acidic pH (4.0-6.5) did not support PNP degradation, while alkaline pH (7.5-9.5) significantly enhanced the rate of PNP degradation. The complete degradation of PNP at high concentration (300 ppm) was confirmed by HPTLC analysis. In order to probe root cause of higher PNP degradation, preliminary studies on genetic analysis of P. putida were undertaken, which revealed the prevalence of a degradative plasmid of approximately 15 kb, while cured derivatives of P. putida (PNP-) did not show ability to degrade PNP. Further conjugal transfer of PNP+ phenotype from P. putida to standard strain of E. coli Nova blue (PNP-) confirmed the degradative type of plasmid.

Polyhydroxyalkanoate copolymers from forest biomass

The potential for the use of woody biomass in poly-beta-hydroxyalkanoate (PHA) biosynthesis is reviewed. Based on previously cited work indicating incorporation of xylose or levulinic acid (LA) into PHAs by several bacterial strains, we have initiated a study for exploring bioconversion of forest resources to technically relevant copolymers. Initially, PHA was synthesized in shake-flask cultures of Burkholderia cepacia grown on 2.2% (w/v) xylose, periodically amended with varying concentrations of levulinic acid [0.07-0.67% (w/v)]. Yields of poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) [P(3HB-co-3HV)] from 1.3 to 4.2 g/l were obtained and could be modulated to contain from 1.0 to 61 mol% 3-hydroxyvalerate (3HV), as determined by 1H and 13C NMR analyses. No evidence for either the 3HB or 4HV monomers was found. Characterization of these P(3HB-co-3HV) samples, which ranged in molecular mass (viscometric, Mv) from 511-919 kDa, by differential scanning calorimetry and thermogravimetric analyses (TGA) provided data which were in agreement for previously reported P(3HB-co-3HV) copolymers. For these samples, it was noted that melting temperature (Tm) and glass transition temperature (Tg) decreased as a function of 3HVcontent, with Tm demonstrating a pseudoeutectic profile as a function of mol% 3HV content. In order to extend these findings to the use of hemicellulosic process streams as an inexpensive carbon source, a detoxification procedure involving sequential overliming and activated charcoal treatments was developed. Two such detoxified process hydrolysates (NREL CF: aspen and CESF: maple) were each fermented with appropriate LA supplementation. For the NREL CF hydrolysate-based cultures amended with 0.25-0.5% LA, P(3HB-co-3HV) yields, PHA contents (PHA as percent of dry biomass), and mol% 3HV compositions of 2.0 g/l, 40% (w/w), and 16-52 mol% were obtained, respectively. Similarly, the CESF hydrolysate-based shake-flask cultures yielded 1.6 g/l PHA, 39% (w/w) PHA contents, and 4-67 mol% 3HV compositions. These data are comparable to copolymer yields and cellular contents reported for hexose plus levulinic acid-based shake-flask cultures, as reported using Alcaligenes eutrophus and Pseudomonas putida. However, our findings presage a conceivable alternative, forestry-based biorefinery approach for the production of value-added biodegradable PHA polymers. Specifically, this review describes the current and potential utilization of lignocellulosic process streams as platform precursors to PHA polymers including hemicellulosic hydrolysates, residual cellulose-derived levulinic acid, tall oil fatty acids (Kraft pulping residual), and lignin-derived aromatics.

Identification and expression of the cym, cmt, and tod catabolic genes from Pseudomonas putida KL47: expression of the regulatory todST genes as a factor for catabolic adaptation

Pseudomonas putida KL47 is a natural isolate that assimilates benzene, 1-alkylbenzene (C(1)-C(4)), biphenyl, p-cumate, and p-cymene. The genetic background of strain KL47 underlying the broad range of growth substrates was examined. It was found that the cym and cmt operons are constitutively expressed due to a lack of the cymR gene, and the tod operon is still inducible by toluene and biphenyl. The entire array of gene clusters responsible for the catabolism of toluene and p-cymene/p-cumate has been cloned in a cosmid vector, pLAFR3, and were named pEK6 and pEK27, respectively. The two inserts overlap one another and the nucleotide sequence (42,505 bp) comprising the cym, cmt, and tod operons and its flanking genes in KL47 are almost identical (>99%) to those of P. putida F1. In the cloned DNA fragment, two genes with unknown functions, labeled cymZ and cmtR, were newly identified and show high sequence homology to dienelactone hydrolase and CymR proteins, respectively. The cmtR gene was identified in the place of the cmtI gene of previous annotation. Western blot analysis showed that, in strains F1 and KL47, the todT gene is not expressed during growth on Luria Bertani medium. In minimal basal salt medium, expression of the todT gene is inducible by toluene, but not by biphenyl in strain F1; however, it is constantly expressed in strain KL47, indicating that high levels of expression of the todST genes with one amino acid substitution in TodS might provide strain KL47 with a means of adaptation of the tod catabolic operon to various aromatic hydrocarbons.

Culturability of stream bacteria assessed at the assemblage and population levels

Lotic bacterial communities can be examined at multiple levels: from the assemblage level to populations of individual species. In stream environments, as in many other systems, the percentage of bacteria that are culturable is quite low. In this study, the culturability of the overall bacterial assemblage, as well as the culturability of three common species (Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida), was determined in samples collected from four streams on three dates. Colony hybridization (colonies were grown on modified nutrient agar) and fluorescent in situ hybridization were used to calculate the percentage of cells of a given species that were culturable. Approximately half of the overall assemblage was estimated to be viable but nonculturable cells (VBNC). The culturability of two of the species was low (0.29% for A. calcoaceticus and 0.46% for P. putida), whereas the value for B. cepacia (2.48%) exceeded the overall assemblage level culturability (0.90%). Overall, both bacterial assemblages and populations were dominated by VBNC. These results show quantitatively that not all members of a species that has culturable representatives are culturable when retrieved from natural populations, likely because of interspecific phenotypic and genotypic variability. Thus, the large pool of nonculturable cells includes representatives of species that are, under some circumstances, culturable.

Propane and n-butane oxidation by Pseudomonas putida GPo1

Propane and n-butane inhibit methyl tertiary butyl ether oxidation by n-alkane-grown Pseudomonas putida GPo1. Here we demonstrate that these gases are oxidized by this strain and support cell growth. Both gases induced alkane hydroxylase activity and appear to be oxidized by the same enzyme system used for the oxidation of n-octane.

Enhanced exopolymer production and chromium stabilization in Pseudomonas putida unsaturated biofilms

Chromium-contaminated soils threaten surface and groundwater quality at many industrial sites. In vadose zones, indigenous bacteria can reduce Cr(VI) to Cr(III), but the subsequent fate of Cr(III) and the roles of bacterial biofilms are relatively unknown. To investigate, we cultured Pseudomonas putida, a model organism for vadose zone bioremediation, as unsaturated biofilms on membranes overlaying iron-deficient solid media either containing molecular dichromate from potassium dichromate (Cr-only treatment) or with deposits of solid, dichromate-coated hematite (Fe+Cr treatment) to simulate vadose zone conditions. Controls included iron-deficient solid medium and an Fe-only treatment using solid hematite deposits. Under iron-deficient conditions, chromium exposure resulted in lower cell yield and lower amounts of cellular protein and carbohydrate, but providing iron in the form of hematite overcame these toxic effects of Cr. For the Cr and Fe+Cr treatments, Cr(VI) was completely reduced to Cr(III) that accumulated on biofilm cells and extracellular polymeric substances (EPSs). Chromium exposure resulted in elevated extracellular carbohydrates, protein, DNA, and EPS sugars that were relatively enriched in N-acetyl-glucosamine, rhamnose, glucose, and mannose. The proportions of EPS protein and carbohydrate relative to intracellular pools suggested Cr toxicity-mediated cell lysis as the origin. However, DNA accumulated extracellularly in amounts far greater than expected from cell lysis, and Cr was liberated when extracted EPS was treated with DNase. These results demonstrate that Cr accumulation in unsaturated biofilms occurs with enzymatic reduction of Cr(VI), cellular lysis, cellular association, and extracellular DNA binding of Cr(III), which altogether can facilitate localized biotic stabilization of Cr in contaminated vadose zones.

Involvement of cyclopropane fatty acids in the response of Pseudomonas putida KT2440 to freeze-drying

Pseudomonas putida KT2440, a saprophytic soil bacterium that colonizes the plant root, is a suitable microorganism for the removal of pollutants and a stable host for foreign genes used in biotransformation processes. Because of its potential use in agriculture and industry, we investigated the conditions for the optimal preservation of the strain and its derivatives for long-term storage. The highest survival rates were achieved with cells that had reached the stationary phase and which had been subjected to freeze-drying in the presence of disaccharides (trehalose, maltose, and lactose) as lyoprotectants. Using fluorescence polarization techniques, we show that cell membranes of KT2440 were more rigid in the stationary phase than in the exponential phase of growth. This is consistent with the fact that cells grown in the stationary phase exhibited a higher proportion of C17:cyclopropane as a fatty acid than cells in the exponential phase. Mutants for the cfaB gene, which encodes the main C17:cyclopropane synthase, and for the cfaA gene, which encodes a minor C17:cyclopropane synthase, were constructed. These mutants were more sensitive to freeze-drying than wild-type cells, particularly the mutant with a knockout in the cfaB gene that produced less than 2% of the amount of C17:cyclopropane produced by the parental strain.

Transcriptional activation of quinoline degradation operons of Pseudomonas putida 86 by the AraC/XylS-type regulator OxoS and cross-regulation of the PqorM promoter by XylS

The quinoline-degradative gene cluster (oxoO, open reading frames 1 to 6 [ORF1 to -6], qorMSL, ORF7 to -9, oxoR) of Pseudomonas putida 86 consists of several overlapping operons controlled in response to quinoline by the master promoter PoxoO and internal promoters Porf3, PqorM, and PoxoR. ORF7 to -9, presumed to be important for maturation of the molybdenum hydroxylase quinoline 2-oxidoreductase, are also weakly transcribed independently of quinoline. Expression of the oxoS gene, located upstream of oxoO, is not influenced by the carbon source. OxoS shows 26% amino acid sequence identity to XylS, the transcriptional regulator of the meta pathway promoter Pm of TOL plasmid pWW0, and is required for quinoline-dependent transcription from PoxoO, Porf3, PqorM, and PoxoR. 5' deletion analysis of PoxoO and PqorM suggested that a 5'-TGCPuCT-N3-GGGATA-3' motif, which resembles the distal 5'-TGCA-N6-GGNTA-3' half-site of the tandem XylS binding site, is essential for oxoS-dependent transcriptional activation. PqorM, which shows similarity to the tandem XylS recognition site of Pm, was cross-activated by the xylS gene product in response to benzoate. The distal half-site of PqorM is necessary, but probably not sufficient, for transcriptional activation by XylS. Despite conservation in PoxoO of a distal 5'-TGCA-N6-GGNTA-3' sequence, cross-activation of PoxoO by XylS and benzoate was not observed. The oxoS gene product in the presence of quinoline weakly stimulated transcription from the Pm promoter. Involvement of an XylS-type protein in the regulation of genes encoding synthesis of a molybdenum hydroxylase is without precedent and may reflect the evolutionary origin of this pathway in the metabolism of aromatic compounds.

Impact of the microscale distribution of a Pseudomonas strain introduced into soil on potential contacts with indigenous bacteria

Soil bioaugmentation is a promising approach in soil bioremediation and agriculture. Nevertheless, our knowledge of the fate and activity of introduced bacteria in soil and thus of their impact on the soil environment is still limited. The microscale spatial distribution of introduced bacteria has rarely been studied, although it determines the encounter probability between introduced cells and any components of the soil ecosystem and thus plays a role in the ecology of introduced bacteria. For example, conjugal gene transfer from introduced bacteria to indigenous bacteria requires cell-to-cell contact, the probability of which depends on their spatial distribution. To quantitatively characterize the microscale distribution of an introduced bacterial population and its dynamics, a gfp-tagged derivative of Pseudomonas putida KT2440 was introduced by percolation in repacked soil columns. Initially, the introduced population was less widely spread at the microscale level than two model indigenous functional communities: the 2,4-dichlorophenoxyacetic acid degraders and the nitrifiers (each at 10(6) CFU g(-1) soil). When the soil was percolated with a substrate metabolizable by P. putida or incubated for 1 month, the microscale distribution of introduced bacteria was modified towards a more widely dispersed distribution. The quantitative data indicate that the microscale spatial distribution of an introduced strain may strongly limit its contacts with the members of an indigenous bacterial community. This could constitute an explanation to the low number of indigenous transconjugants found most of time when a plasmid-donor strain is introduced into soil.

Engineering of solvent-tolerant Pseudomonas putida S12 for bioproduction of phenol from glucose

Efficient bioconversion of glucose to phenol via the central metabolite tyrosine was achieved in the solvent-tolerant strain Pseudomonas putida S12. The tpl gene from Pantoea agglomerans, encoding tyrosine phenol lyase, was introduced into P. putida S12 to enable phenol production. Tyrosine availability was a bottleneck for efficient production. The production host was optimized by overexpressing the aroF-1 gene, which codes for the first enzyme in the tyrosine biosynthetic pathway, and by random mutagenesis procedures involving selection with the toxic antimetabolites m-fluoro-dl-phenylalanine and m-fluoro-l-tyrosine. High-throughput screening of analogue-resistant mutants obtained in this way yielded a P. putida S12 derivative capable of producing 1.5 mM phenol in a shake flask culture with a yield of 6.7% (mol/mol). In a fed-batch process, the productivity was limited by accumulation of 5 mM phenol in the medium. This toxicity was overcome by use of octanol as an extractant for phenol in a biphasic medium-octanol system. This approach resulted in accumulation of 58 mM phenol in the octanol phase, and there was a twofold increase in the overall production compared to a single-phase fed batch.

Continuous aerobic phenol degradation by defined mixed immobilized culture in packed bed reactors

A defined mixed culture of Pseudomonas putida, Commamonas testosteroni and Candida tropicalis was immobilized by adsorption on polyurethane foam, cocoa-fibers, expanded slate and sintered glass. Packed bed reactors were used for long-term continuous phenol biodegradations. Loading experiments were done to study the impact of the following parameters: (1) hydraulic retention time, (2) dissolved oxygen concentration, and (3) elimination of the oxygen limitation. After the acclimation period (approximately 10 d), the loading test with the individual packings showed the following maximum degradation rates: sintered glass 34, polyurethane foam 12, expanded slate 11.5, and cocoa-fibers 7.7 kg m(-3) d(-1). All these values were reached at a removal efficiency >99 % and with oxygen in excess. Under these conditions, the pH of the diluted unbuffered medium in the reactor effluent was 3.2-4.0 and no incompletely oxidized metabolic intermediates were found. The free cell concentration in the effluent increased after the phenol overloading time period.

Tailor-made olefinic medium-chain-length poly[(R)-3-hydroxyalkanoates] byPseudomonas putida GPo1: Batch versus chemostat production

Functionalized medium-chain-length polyhydroxyalkanoates (mclPHAs) have gained much interest in research on biopolymers because of their ease of chemical modification. Tailored olefinic mclPHA production from mixtures of octanoic acid and 10-undecenoic acid was investigated in batch and dual (C,N) nutrient limited chemostat cultures of Pseudomonas putida GPo1 (ATCC 29347). In a batch culture, where P. putida GPo1 was grown on a mixture of octanoic acid (58 mol%) and 10-undecenoic acid (42 mol%), it was found that the fraction of aliphatic monomers was slightly lower in mclPHA produced during exponential growth than during late stationary phase. Thus, the total monomeric composition changed over time indicating different kinetics for the two carbon substrates. Chemostat experiments showed that the dual (C,N) nutrient limited growth regime (DNLGR) for 10-undecenoic acid coincided with the one for octanoic acid. Five different chemostats on equimolar mixtures of octanoic acid and 10-undecenoic acid within the DNLGR revealed that the monomeric composition of mclPHA was not a function of the carbon to nitrogen (C(0)/N(0)) ratio in the feed medium but rather of the dilution rate. The fraction of aliphatic monomers in the accumulated mclPHA was slightly lower at high dilution rates and increased towards low dilution rates, again indicating different kinetics for the two carbon substrates in P. putida GPo1.