Regulation of pathways degrading aromatic substrates in Pseudomonas putida. Enzymic response to binary mixtures of substrates

Molecular Signatures of Dissolved Organic Matter Generated from the Photodissolution of Microplastics in Sunlit Seawater

Plastics are accumulating on Earth, including at sea. The photodegradation of microplastics floating in seawater produces dissolved organic matter (DOM), indicating that sunlight can photodissolve microplastics at the sea surface. To characterize the chemistry of DOM produced as microplastics photodissolve, three microplastics that occur in surface waters, polyethylene (PE), polypropylene (PP), and expanded polystyrene (EPS), were incubated floating on seawater in both the light and the dark. We present the molecular signatures of the DOM produced during these incubations, as determined via ultrahigh-resolution mass spectrometry. Zero to 12 products were identified in the dark, whereas 319-705 photoproducts were identified in the light. Photoproduced DOM included oxygen atoms, indicating that soluble, oxygen-containing organics were formed as plastics photodegrade. PP and PE plastics have hydrogen-to-carbon (H/C) ratios of 2 and generated DOM with average H/C values of 1.7 ± 0.1 to 1.8 ± 0.1, whereas EPS, which has an H/C of 1, generated DOM with an average H/C of 0.9 ± 0.2, indicating the stoichiometry of photoproduced DOM was related to the stoichiometry of the photodegrading polymer. The photodissolution of plastics produced hundreds of photoproducts with varying elemental stoichiometries, indicating that a single abiotic process (photochemistry) can generate hundreds of different chemicals from stoichiometrically monotonous polymers.

Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134

Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.

Repression of the glucose-inducible outer-membrane protein OprB during utilization of aromatic compounds and organic acids in Pseudomonas putida CSV86

Pseudomonas putida CSV86 shows preferential utilization of aromatic compounds over glucose. Protein analysis and [¹⁴C]glucose-binding studies of the outer membrane fraction of cells grown on different carbon sources revealed a 40 kDa protein that was transcriptionally induced by glucose and repressed by aromatics and succinate. Based on 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry analysis, the 40 kDa protein closely resembled the porin B of P. putida KT2440 and carbohydrate-selective porin OprB of various Pseudomonas strains. The purified native protein (i) was estimated to be a homotrimer of 125 kDa with a subunit molecular mass of 40 kDa, (ii) displayed heat modifiability of electrophoretic mobility, (iii) showed channel conductance of 166 pS in 1 M KCl, (iv) permeated various sugars (mono-, di- and tri-saccharides), organic acids, amino acids and aromatic compounds, and (v) harboured a glucose-specific and saturable binding site with a dissociation constant of 1.3 µM. These results identify the glucose-inducible outer-membrane protein of P. putida CSV86 as a carbohydrate-selective protein OprB. Besides modulation of intracellular glucose-metabolizing enzymes and specific glucose-binding periplasmic space protein, the repression of OprB by aromatics and organic acids, even in the presence of glucose, also contributes significantly to the strain's ability to utilize aromatics and organic acids over glucose.

Benzoate catabolite repression of the phthalate degradation pathway in Rhodococcus sp. strain DK17

Rhodococcus sp. strain DK17 exhibits a catabolite repression-like response when provided simultaneously with benzoate and phthalate as carbon and energy sources. Benzoate in the medium is depleted to detection limits before the utilization of phthalate begins. The transcription of the genes encoding benzoate and phthalate dioxygenase paralleled the substrate utilization profile. Two mutant strains with defective benzoate dioxygenases were unable to utilize phthalate in the presence of benzoate, although they grew normally on phthalate in the absence of benzoate.

Acetate utilization is inhibited by benzoate in Alcaligenes eutrophus: evidence for transcriptional control of the expression of acoE coding for acetyl coenzyme A synthetase

During batch growth of Alcaligenes eutrophus on benzoate-acetate mixtures, benzoate was the preferred substrate, with acetate consumption being delayed until the rate of benzoate consumption had diminished. This effect was attributed to a transcriptional control of the synthesis of acetyl coenzyme A (acetyl-CoA) synthetase, an enzyme necessary for the entry of acetate into the central metabolic pathways, rather than to a biochemical modulation of the activity of this enzyme. Analysis of a 2.4-kb mRNA transcript hybridizing with the A. eutrophus acoE gene confirmed this repression effect. In a benzoate-limited chemostat culture, derepression was observed, with no increase in the level of expression following an acetate pulse. Benzoate itself was not the signal triggering the repression of acetyl-CoA synthetase. This role was played by catechol, which transiently accumulated in the medium when high specific rates of benzoate consumption were reached. The lack of rapid inactivation of the functional acetyl-CoA synthetase after synthesis has been stopped enables A. eutrophus to retain the capacity to metabolize acetate for prolonged periods while conserving minimal protein expenditure.

The induction and repression of benzene and catechol oxidizing capacity of Pseudomonas putida ML2 studied in perturbed chemostat culture

The oxidation of catechol, an intermediate in benzene catabolism, was studied using transient variations in dissolved oxygen tension (DOT) when a succinate limited steady state culture of Pseudomonas putida ML2 was perturbed with a pulse of another substrate. A model was developed and tested for the effect of fluctuations in oxidizing enzyme activity on DOT. It was found that the rate of induction of catechol oxidizing enzymes was independent of dilution rate up to a relative growth rate (mu/mumax) of 0.75. Only at higher dilution rates was catabolite repression observed.

Microbial metabolism of mandelate: a microcosm of diversity

This review highlights the diversity of prokaryotic and eukaryotic microorganisms that can metabolise mandelate and it describes how a wide range of compounds related to mandelate is formed in many environments. The chief aspects that are summarised include the various pathways whereby mandelate and its structural analogues are converted into catechol or protocatechuate, the properties of the enzymes that are involved in the pathways, and the regulation and genetics of the pathways. The review incorporates the idea that the study of peripheral metabolic pathways is particularly useful for illuminating evolutionary speculations and it concludes with a list of questions that need to be answered.

Induction of phenol-metabolizing enzymes in Trichosporon cutaneum

Some aspects of the induction of enzymes participating in the metabolism of phenol and resorcinol in Trichosporon cutaneum were studied using intact cells and cell-free preparations. Activities of phenol hydroxylase (1.14.13.7), catechol 1,2-oxygenase (1.13, 11.1), cis-cis-muconate cyclase (5.5.1.-), delactonizing enzyme(s) and maleolylacetate reductase were 50-400 times higher in fully induced cells than in noninduced cells. In addition to phenol and resorcinol, also catechol, cresols and fluorophenols could induce phenol hydroxylase. The induction was severely inhibited by phenol concentrations higher than 1 mM. Using optimum inducer concentrations (0.01-0.10 mM), it took more than 8 h to obtain full induction, whether in proliferating or in nonproliferating cells. Phenol hydroxylase, catechol 1,2-oxygenase and cis, cis-muconate cyclase were induced simultaneously. The synthesis of the de-lactonizing activity was delayed in relation to these three preceeding enzymes of the pathway. High glucose concentration (over 15 mM) inhibited completely the induction of phenol oxidation by nonproliferating cells. It also inhibited phenol oxidation by pre-induced cells. Among the NADPH-generating enzymes, the activity of iso-citrate dehydrogenase was elevated in cells grown on phenol and resorcinol instead of glucose.

Regulation of the enzymes converting L-mandelate into benzoate in bacterium N.C.I.B. 8250

l-Mandelate is oxidized to benzoate by the enzymes l-mandelate dehydrogenase, phenylglyoxylate carboxy-lyase and benzaldehyde dehydrogenase I. Conditions have been established for measuring these three enzymes as well as benzyl alcohol dehydrogenase, benzaldehyde dehydrogenase II and catechol 1,2-oxygenase in a single cell-free extract prepared from bacterium N.C.I.B. 8250. The kinetics of induction of all these enzymes have been measured under a variety of conditions. l-Mandelate dehydrogenase, phenylglyoxylate carboxy-lyase and benzaldehyde dehydrogenase I appear to be co-ordinately regulated because (a) their differential rates of synthesis are proportional to one another under various conditions of induction and repression, (b) they are specifically and gratuitously induced by thiophenoxyacetate and a number of other compounds, and (c) mutant strains have been isolated that lack all three enzymes. Phenylglyoxylate is the primary inducer of the regulon as mutant strains lacking phenylglyoxylate carboxy-lyase form the other two enzymes in the presence of l-mandelate or phenylglyoxylate, whereas in mutant strains devoid of l-mandelate dehydrogenase activity only phenylglyoxylate induces phenylglyoxylate carboxy-lyase and benzaldehyde dehydrogenase I.

Evidence for induced synthesis of an active transport factor for mandelate in Pseudomonas putida

1. At low concentrations of mandelate there is a lag before induction of the mandelate regulon begins at a sub-maximum rate. Cells preinduced with a saturating concentration of inducer do not exhibit this lag when they are transferred to sub-maximum inducer concentrations and are able to maintain a high rate of induction under these conditions. 2. Chloramphenicol was used to show that a protein is synthesized during the lag period that is probably responsible for the maintenance effects observed in batch and continuous cultures. 3. Direct measurements appear to show that induced cells possess an active transport factor for mandelate, sensitive to dinitrophenol, and this is presumably responsible for the maintenance effect. Mandelate is accumulated unchanged against a concentration gradient from media containing low concentrations. At higher external concentrations no accumulation occurs and only a rapid equilibration is noted. Uninduced cells merely equilibrate mandelate.