Repression of Pseudomonas putida phenanthrene-degrading activity by plant root extracts and exudates

The phenanthrene-degrading activity (PDA) of Pseudomonas putida ATCC 17484 was repressed after incubation with plant root extracts of oat (Avena sativa), osage orange (Maclura pomifera), hybrid willow (Salix alba x matsudana), kou (Cordia subcordata) and milo (Thespesia populnea) and plant root exudates of oat (Avena sativa) and hybrid poplar (Populus deltoides x nigra DN34). Total organic carbon content of root extracts ranged from 103 to 395 mg l(-1). Characterization of root extracts identified acetate (not detectable to 8.0 mg l(-1)), amino acids (1.7-17.3 mg l(-1)) and glucose (1.6-14.0 mg l(-1)), indicating a complex mixture of substrates. Repression was also observed after exposure to potential root-derived substrates, including organic acids, glucose (carbohydrate) and glutamate (amino acid). Carbon source regulation (e.g. catabolite repression) was apparently responsible for the observed repression of P. putida PDA by root extracts. However, we showed that P. putida grows on root extracts and exudates as sole carbon and energy sources. Enhanced growth on root products may compensate for partial repression, because larger microbial populations are conducive to faster degradation rates. This would explain the commonly reported increase in phenanthrene removal in the rhizosphere.     

Role of indoleacetic acid-lysine synthetase in regulation of indoleacetic acid pool size and virulence of Pseudomonas syringae subsp. savastanoi.

The phytopathogen Pseudomonas syringae subsp. savastanoi incites the production of galls on olive and oleander plants. Gall formation is dependent upon the bacterial synthesis of the phytohormone indole-3-acetic acid (IAA). Strains isolated from oleander galls are capable of further metabolizing IAA to an amino acid conjugate, 3-indoleacetyl-epsilon-L-lysine (IAA-lysine); bacterial olive gall isolates lack this activity. In this study, the cloned gene for IAA-lysine synthetase (iaaL+) was introduced into strains isolated from olive and oleander galls to determine its effect on the regulation of IAA pool size and virulence. IAA-lysine was synthesized by isolates from olive galls when iaaL+ was introduced by conjugation, but the amount of IAA which accumulated in culture by the transconjugant was reduced by one-third. When the iaaL+ locus of an oleander gall isolate was inactivated by Tn5 mutagenesis, the resulting mutant did not convert IAA to IAA-lysine; however, it accumulated fivefold more IAA in culture than the wild type did. When inoculated into oleander plants, the iaaL mutant did not cause typical gall symptoms, nor did it replicate within host tissue similarly to the wild type.     

Engineering adipic acid metabolism in Pseudomonas putida

Bio-upcycling of plastics is an upcoming alternative approach for the valorization of diverse polymer waste streams that are too contaminated for traditional recycling technologies. Adipic acid and other medium-chain-length dicarboxylates are key components of many plastics including polyamides, polyesters, and polyurethanes. This study endows Pseudomonas putida KT2440 with efficient metabolism of these dicarboxylates. The dcaAKIJP genes from Acinetobacter baylyi, encoding initial uptake and activation steps for dicarboxylates, were heterologously expressed. Genomic integration of these dca genes proved to be a key factor in efficient and reliable expression. In spite of this, adaptive laboratory evolution was needed to connect these initial steps to the native metabolism of P. putida, thereby enabling growth on adipate as sole carbon source. Genome sequencing of evolved strains revealed a central role of a paa gene cluster, which encodes parts of the phenylacetate metabolic degradation pathway with parallels to adipate metabolism. Fast growth required the additional disruption of the regulator-encoding psrA, which upregulates redundant β-oxidation genes. This knowledge enabled the rational reverse engineering of a strain that can not only use adipate, but also other medium-chain-length dicarboxylates like suberate and sebacate. The reverse engineered strain grows on adipate with a rate of 0.35 ± 0.01 h⁻¹, reaching a final biomass yield of 0.27 ± 0.00 g_CDW g_adipate⁻¹. In a nitrogen-limited medium this strain produced polyhydroxyalkanoates from adipate up to 25% of its CDW. This proves its applicability for the upcycling of mixtures of polymers made from fossile resources into biodegradable counterparts.     

The solvent-tolerant Pseudomonas putida S12 as host for the production of cinnamic acid from glucose

A Pseudomonas putida S12 strain was constructed that efficiently produced the fine chemical cinnamic acid from glucose or glycerol via the central metabolite phenylalanine. The gene encoding phenylalanine ammonia lyase from the yeast Rhodosporidium toruloides was introduced. Phenylalanine availability was the main bottleneck in cinnamic acid production, which could not be overcome by the overexpressing enzymes of the phenylalanine biosynthesis pathway. A successful approach in abolishing this limitation was the generation of a bank of random mutants and selection on the toxic phenylalanine anti-metabolite m-fluoro-phenylalanine. Following high-throughput screening, a mutant strain was obtained that, under optimised culture conditions, accumulated over 5 mM of cinnamic acid with a yield (Cmol%) of 6.7%.     

Octanoic acid uptake in Pseudomonas putida U

Pseudomonas putida U grown in a chemically defined medium containing octanoic acid as the sole carbon source accumulated a homopolymer of poly(3-hydroxyoctanoate) as intracellular reserve material, and metabolized the polymer during the late exponential phase of growth. Kinetic measurement of the uptake of [1-¹⁴C]octanoic acid by cells at 34°C in 85 mM phosphate buffer, pH 7.0 showed linear uptake for at least 2 min and the calculated K_m and V_max were 100 μM and 9 nmol min⁻¹ respectively. This transport system is constitutive, energy-dependent, and is strongly inhibited by structural analogs of octanoic acid, by various fatty acids with a carbon length higher than C₅ and by certain phenyl derivatives.     

Competitiveness in root colonization by Pseudomonas putida requires the rpoS gene

The rpoS gene in Pseudomonas putida was essential for plant root colonization under competitive conditions from other microbes. The RpoS- mutant survived less well than the wild-type strain in culture medium, and unlike the wild-type, failed to colonize the roots in a peat matrix containing an established diverse microflora. The RpoS-deficient P. putida isolate was generated by insertion of a glucuronidase-npt cassette into the rpoS gene. The RpoS mutant had dose-dependent increased sensitivity to oxidative stress and produced Mn-superoxide dismutase activity earlier than the parent. While extracts from wild-type P. putida stationary-phase cells contained three isozymes of catalase (CatA, CatB, and CatC), the sigma38-deficient P. putida lacked CatB. These results are consistent with previous findings that CatB is induced in stationary-phase.     

Transport of 14C-lableled indoleacetic acid in Vicia root segments

IAA transport in Vicia root segments was investigated for comparisonwith that in intact roots. Lanolin paste (1-mm-wide ring) oragar blocks (3?3?1.5mm), both containing IAA-2-¹⁴C were appliedto the surface or a cut end of the root segments, respectively;transported ¹⁴C was collected in receiver agar blocks placedon the cut end of the segments. When lanolin paste was appliedto 5-mm segments, basipetal transport of IAA predominated overacropetal transport. When agar blocks were applied to 1- and2-mm segments, the same was true; in longer segments (3 and5 mm long), however, basipetal movement occurred predominantlyat first but was surpassed by acropetal movement after 2–3hr. Among the segments tested (regions 2–4, 4–6and 8–10 mm from the tip), the most apical one showedthe distinctest predominancy of basipetal movement. The velocitiesof the acropetal and basipetal movement of the ¹⁴C were estimatedat 3–3.8 and 8–12 mm/hr, respectively. Autoradiographicstudy and the experiment in which wire was inserted longitudinallythrough the central part of the segments showed that basipetalmovement occurred mainly through the outer part of the rootsand acropetal movement mainly through the central cylinder.The present results were compatible with those obtained previouslywith intact roots. Some properties of polar movement, such asits specificity, inhibition by TIBA, and dependency on terneprature are described. (Received March 22, 1978; )     

Structure and function of the Pseudomonas putida integration host factor.

Integration host factor (IHF) is a DNA-binding and -bending protein that has been found in a number of gram-negative bacteria. Here we describe the cloning, sequencing, and functional analysis of the genes coding for the two subunits of IHF from Pseudomonas putida. Both the ihfA and ihfB genes of P. putida code for 100-amino-acid-residue polypeptides that are 1 and 6 residues longer than the Escherichia coli IHF subunits, respectively. The P. putida ihfA and ihfB genes can effectively complement E. coli ihf mutants, suggesting that the P. putida IHF subunits can form functional heterodimers with the IHF subunits of E. coli. Analysis of the amino acid differences between the E. coli and P. putida protein sequences suggests that in the evolution of IHF, amino acid changes were mainly restricted to the N-terminal domains and to the extreme C termini. These changes do not interfere with dimer formation or with DNA recognition. We constructed a P. putida mutant strain carrying an ihfA gene knockout and demonstrated that IHF is essential for the expression of the P(U) promoter of the xyl operon of the upper pathway of toluene degradation. It was further shown that the ihfA P. putida mutant strain carrying the TOL plasmid was defective in the degradation of the aromatic model compound benzyl alcohol, proving the unique role of IHF in xyl operon promoter regulation.     

Involvement of plasmid deoxyribonucleic acid in indoleacetic acid synthesis in Pseudomonas savastanoi.

Olive (or oleander) knot is a plant disease incited by Pseudomonas savastanoi. Disease symptoms consist of tumorous outgrowths induced in the plant by bacterial production of indole-3-acetic acid (IAA). Synthesis of IAA occurs by the following reactions: L-tryptophan leads to indoleacetamide leads to indoleacetic acid, catalyzed by tryptophan 2-monooxygenase and indoleacetamide hydrolase, respectively. Whereas the enzymology of IAA synthesis is well characterized, nothing is known about the genetics of the system. We devised a positive selection for the presence of tryptophan 2-monooxygenase based on its capacity to use as a substrate the toxic tryptophan analogue 5-methyltryptophan. Efficient curing of the bacterium of tryptophan 2-monoxygenase, indoleacetamide hydrolase, and IAA production was obtained by acridine orange treatment. Further, loss of capacity to produce IAA by curing was correlated with loss of a plasmid of 34 X 10(6) molecular weight. This plasmid, here called pIAA1, when reintroduced into Iaa- mutants by transformation, restored tryptophan 2-monooxygenase and indoleacetamide hydrolase activities and production of IAA.     

Myo-inositol transport system in Pseudomonas putida.

The kinetic features of the myo-inositol transport system in Pseudomonas putida are reported. The system is sensitive to osmotic shock, is not operative in membrane vesicles, and does not involved substrate phosphorylation. Line-weaver-Burk plots indicate the presence of two different systems, whose Kt are 5 micrometer and 0.43 mM and whose V max are 7.9 and 27 nml/mg per min, respectively. Transport activity of glucose-grown cells is very low. myo-Inositol-grown cells lose the high-affinity system upon osmotic shock; concentrated shock fluid possesses myo-inositol-binding activity. The system is very specific for the myo-configuration of the cyclitol.     

Effect of indoleacetic acid on the metabolic activity oftaraxacum root segments

Inoubation of thin slioes ofTaraxacum root segments in 3-indoleaoetic acid solutions enhanced the level of total proteins, RNA, DNA and a number of enzymes reaching an optimum at 0.01 mg 1^-1. It has been shown that the auxin promotes the synthesis of DNA, again with an optimum promotion at 0.01 mg 1^-1 IAA. This work was carried out at the Department of Botany, University of Sheffield, Sheffield, England. The author wishes to thank Dr. A. Booth for taking a keen interest in this work.     

Utilization of the plant hormone indole-3-acetic acid for growth by Pseudomonas putida strain 1290

We have isolated from plant surfaces several bacteria with the ability to catabolize indole-3-acetic acid (IAA). One of them, isolate 1290, was able to utilize IAA as a sole source of carbon, nitrogen, and energy. The strain was identified by its 16S rRNA sequence as Pseudomonas putida. Activity of the enzyme catechol 1,2-dioxygenase was induced during growth on IAA, suggesting that catechol is an intermediate of the IAA catabolic pathway. This was in agreement with the observation that the oxygen uptake by IAA-grown P. putida 1290 cells was elevated in response to the addition of catechol. The inability of a catR mutant of P. putida 1290 to grow at the expense of IAA also suggests a central role for catechol as an intermediate in IAA metabolism. Besides being able to destroy IAA, strain 1290 was also capable of producing IAA in media supplemented with tryptophan. In root elongation assays, P. putida strain 1290 completely abolished the inhibitory effect of exogenous IAA on the elongation of radish roots. In fact, coinoculation of roots with P. putida 1290 and 1 mM concentration of IAA had a positive effect on root development. In coinoculation experiments on radish roots, strain 1290 was only partially able to alleviate the inhibitory effect of bacteria that in culture overproduce IAA. Our findings imply a biological role for strain 1290 as a sink or recycler of IAA in its association with plants and plant-associated bacteria.     

LapF,the second largest Pseudomonas putida protein,contributes to plant root colonization and determines biofilm architecture

We have investigated the role of LapF, one of the two largest proteins encoded in the genome of Pseudomonas putida KT2440, in bacterial colonization of solid surfaces. LapF is 6310 amino acids long, and is localized on the cell surface. The C‐terminal region of the protein is essential for its secretion, which presumably requires the ABC transporter encoded by an operon (lapHIJ) adjacent to the lapF gene. Although the initial attachment stages are not different between the wild type and a lapF mutant, microcolony formation and subsequent development of a mature biofilm is impaired in the mutant. This is consistent with the expression pattern of lapF; activation of its promoter takes place at late stages of growth and is regulated by the alternative sigma factor RpoS. A lapF mutant is also affected in individual and competitive plant root colonization. In these assays, mixed microcolonies formed by cells of both the wild‐type and the mutant strains could be observed but microcolonies of the mutant alone were not found. These data and the localization of the protein at discrete spots in areas of contact between cells in biofilms suggest that LapF determines the establishment of cell–cell interactions during sessile growth.     

Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1

We report the complete sequence of the 5.7-Mbp genome of Pseudomonas putida BIRD-1, a metabolically versatile plant growth-promoting rhizobacterium that is highly tolerant to desiccation and capable of solubilizing inorganic phosphate and iron and of synthesizing phytohormones that stimulate seed germination and plant growth.     

Catalase activity and the survival of Pseudomonas putida, a root colonizer, upon treatment with peracetic acid

Peracetic acid is used as a sterilant in several industrial settings. Cells of a plant-colonizing bacterium, Pseudomonas putida in liquid suspension, were more sensitive to killing by peracetic acid when they lacked a major catalase activity, catalase A. Low doses of peracetic acid induced promoter activity of the gene encoding catalase A and increased total catalase specific activity in cell extracts. Microbes present in native agricultural soils rapidly degraded the active oxygen species present in peracetic acid. The simultaneous release of oxygen was consistent with a role for catalase in degrading the hydrogen peroxide that is part of the peracetic acid-equilibrium mixture. Amendment of sterilized soils with wild-type P. putida restored the rate of degradation of peracetic acid to a higher level than was observed in the soils amended with the catalase A-deficient mutant. The association of the bacteria with the plant roots resulted in protection of the wild-type as well as the catalase-deficient mutant from killing by peracetic acid. No differential recovery of the wild-type and catalase A mutant of P. putida was observed from roots after the growth matrix containing the plants was flushed with peracetic acid.     

Minimizing loss of indoleacetic acid during purification of plant extracts

Summary Published methods for isolation of 3-indoleacetic acid (IAA) were found to give low yields due to losses at specific steps. Loss during extraction was minimized by grinding tissue under a nitrogen atmosphere, using 0.02% sodium diethyldithiocarbamate in 80% ethanol as the extractant. When ethereal solutions of IAA were concentrated in vacuo, the hormone was lost, presumably by sublimation. This significant source of loss was eliminated by concentration at atmospheric pressure. Oxidative losses during application of extracts to chromatograms were reduced by prior application of an antioxidant to the origin of chromatograms. These precautions permitted development of a method where 10–50 g of IAA could be recovered from soybean leaves with approximately 60% yield.