Assembly of a Rieske non-heme iron oxygenase multicomponent system from Phenylobacterium immobile E DSM 1986 enables pyrazon cis-dihydroxylation in E. coli

Abstract

Phenylobacterium immobile strain E is a soil bacterium with a striking metabolism relying on xenobiotics, such as the herbicide pyrazon, as sole carbon source instead of more bioavailable molecules. Pyrazon is a heterocyclic aromatic compound of environmental concern and its biodegradation pathway has only been reported in P. immobile. The multicomponent pyrazon oxygenase (PPO), a Rieske non-heme iron oxygenase, incorporates molecular oxygen at the 2,3 position of the pyrazon phenyl moiety as first step of degradation, generating a cis-dihydrodiendiol. The aim of this work was to identify the genes encoding for each one of the PPO components and enable their functional assembly in Escherichia coli. P. immobile strain E genome sequencing revealed genes encoding for RO components, such as ferredoxin-, reductase-, α- and β-subunits of an oxygenase. Though, P. immobile E displays three prominent differences with respect to the ROs currently characterized: (1) an operon-like organization for PPO is absent, (2) all the elements are randomly scattered in its DNA, (3) not only one, but 19 different α-subunits are encoded in its genome. Herein, we report the identification of the PPO components involved in pyrazon cis-dihydroxylation in P. immobile, its appropriate assembly, and its functional reconstitution in E. coli. Our results contributes with the essential missing pieces to complete the overall elucidation of the PPO from P. immobile.

Key points

• Phenylobacterium immobile E DSM 1986 harbors the only described pyrazon oxygenase (PPO).

• We elucidated the genes encoding for all PPO components.

• Heterologous expression of PPO enabled pyrazon dihydroxylation in E. coli JW5510.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11129-w.

Investigation of the microbial degradation of phenazone-type drugs and their metabolites by natural biofilms derived from river water using liquid chromatography/tandem mass spectrometry (LC-MS/MS)

The degradation of the pharmaceuticals phenazone and metamizole, two pyrazolone-derivates in widespread use, using biofilms created by natural organisms from the national park Unteres Odertal, Germany, were investigated. An analytical method based on LC-MS/MS was optimised to determine the substances phenazone and methylaminoantipyrine (MAA), the hydrolysis product of metamizole (also known as dipyrone), as well as their metabolites 1,5-dimethyl-1,2-dehydro-3-pyrazolone (DP), acetaminoantipyrine (AAA), formylaminoantipyrine (FAA) and 4-aminoantipyrine (AA). Performance characteristics of the method were evaluated in terms of recovery, standard deviation, coefficient of variation, method detection limits (MDL) and method quantification limits (MQL). Degradation studies of phenazone and MAA were conducted using a laboratory-scale continuous flow biofilm reactor fed with different nutrient media and with variable hydraulic retention times of 24 and 32 h. MAA was degraded rapidly to FAA and AA, while phenazone was not degraded under the prevailing conditions even after 32 h. By operating the bioreactor in batch mode to study the phenazone degradation potential of the biofilm under limiting nutrient conditions, an elimination rate of 85% phenazone was observed, but because of the slow elimination rate and aerobic conditions, the metabolite DP was not detected. In additional batch experiments using bacterial isolates from the natural biofilm to decompose phenazone, some bacterial strains were able to form DP from phenazone in marginal concentrations over the sampling period of eight weeks. Obviously, the microorganisms need a reasonably long time to adapt their metabolisms to enable the removal of phenazone from water samples.

Behaviour and redox sensitivity of pharmaceutical residues during bank filtration - Investigation of residues of phenazone-type analgesics

The behaviour of residues of phenazone-type pharmaceuticals during bank filtration was investigated at a field site in Berlin, Germany, where bank-filtered water is used for drinking water production. The concentrations of the pharmaceutical residues in the shallow, young bank filtrate (travel times<one month) were correlated to the prevailing hydrochemical conditions at the field site. In addition, their behaviour during passage through an undisturbed sediment core from the lake base at the site (clogging layer) was evaluated in the laboratory. Phenazone, 4-acetylaminoantipyrine (AAA), 4-formylaminoantipyrin (FAA) and 1,5-dimethyl-1,2-dehydro-3-pyrazolone (DP) were eliminated more efficiently under oxic conditions, while 1-acetyl-1-methyl-2-dimethyloxamoyl-2-phenylhydrazide (AMDOPH) was not eliminated at all. The redox conditions and the elimination of the respective pharmaceutical residues displayed strong seasonal variations. Oxic conditions were only encountered close to the shore in winter, when temperatures were low. The column study showed that the elimination is restricted to the uppermost decimetres of the lake base, where oxygen is present. While phenazone elimination is almost complete during aerobic rapid sand filtration in the waterworks, the compounds were found to be more persistent under anoxic field conditions.

Investigation of the behavior and metabolism of pharmaceutical residues during purification of contaminated ground water used for drinking water supply

Residues of phenazone-type pharmaceuticals originating from spills of a former pharmaceutical production plant have recently been detected in ground water in Berlin, Germany. The degradation pathways of phenazone, propyphenazone, and dimethylaminophenazone (DMAA) during water purification were enlightened in batch experiments with groundwater and filter material obtained from operating waterworks. For phenazone and propyphenazone a complete biological transformation into their respective metabolites 1,5-dimethyl-1,2-dehydro-3-pyrazolone (DP) and 4-(2-methylethyl)-1,5-dimethyl-1,2-dehydro-3-pyrazolone (PDP) was observed. Generally, removal of phenazone-type pharmaceutical residues during rapid sand filtration was almost exclusively caused by microorganisms only present in polluted raw water. DMAA applied to fresh filter materials was rapidly degraded into its metabolites 1-acetyl-1-methyl-2-phenylhydrazide (AMPH), acetoaminoantipyrine (AAA), formylaminoantipyrine (FAA), and 1-acetyl-1-methyl-2-dimethyloxamoyl-2-phenylhydrazide (AMDOPH). DMAA, AAA, and FAA were, however, only detected at low levels in a few samples of purified water from an operating water works. Whereas, the metabolites AMDOPH and DP were detected up to 1 microg l(-1). Propyphenazone was rapidly removed and AMPH, phenazone, and PDP were only measured with concentrations in the low ng l(-1) range. The concentrations of the metabolites DP and PDP are even higher in the purified water than in the raw water caused by their formation during degradation of phenazone and propyphenazone. Reduction of filtration velocity on an experimental filter from 5 m h(-1) down to 2 m h(-1) resulted in improved removal of phenazone, propyphenazone and their metabolites DP and PDP, respectively. AMDOPH, however, was highly persistent in all experiments independent from filtration velocities and contact times.

Determination of Polar Drug Residues in Sewage and Surface Water Applying Liquid Chromatography−Tandem Mass Spectrometry

A simple and rapid method is presented for the trace-level analysis of 10 polar pharmaceutical residues in various types of water samples from the aquatic environment. Using this method, the pharmaceuticals and several drug metabolites can be analyzed in drinking and surface waters and in wastewater (treated and untreated sewage) at concentrations down to 0.01 microg/L. Samples are prepared by a simple in situ derivatization enabling the preconcentration of very polar metabolites by automated solid-phase extraction. The analytes were separated by liquid chromatography with tandem mass spectrometric detection and quantified by comparison with an internal standard. Limits of quantification were between 0.01 and 0.02 microg/L for three phenazone-type pharmaceuticals, six of their metabolites, and the antiepileptic drug carbamazepine. Except for dimethylaminophenazone, recoveries for all analytes were between 87 and 117% for raw and purified sewage, groundwater, and surface and drinking water. Investigations of some environmental samples revealed that sewage and surface water treatment causes a slight reduction of the concentrations of some analytes whereas other compounds were persistent during water treatment. Thus, some compounds were detected at the low-microgram per liter level in sewage effluents of wastewater treatment plants in Berlin (Germany) and were also found at high-nanogram per liter concentrations in Berlin surface water samples.

Detection and identification of phenazone-type drugs and their microbial metabolites in ground and drinking water applying solid-phase extraction and gas chromatography with mass spectrometric detection

A new analytical method applying in situ derivatization was developed to enable the extraction of polar drug metabolites from water samples by solid-phase extraction (SPE). An additional derivatization by silylation was used to enhance the sensitivity of analyte detection by gas chromatography-mass spectrometry (GC-MS). Thus, the two metabolites 1,5-di-methyl-1,2-dehydro-3-pyrazolone (DP) and 4-(2-methylethyl)-1,5-dimethyl-1,2-dehydro-3-pyrazolone (PDP), postulated for the degradation of phenazone and propyphenazone, were identified and detected up to the microg/L level in raw and drinking water samples from public water supply.

Bacterial degradation of aminopyrine

1. Four strains of bacteria growing with aminopyrine as sole source of carbon were isolated from soil and were identified as strains of Phenylobacterium immobilis. 2. Strain M13 and strain E, the type species of Phenylobacterium immobilis (DSM 1986), which had been isolated by enrichment with chloridazon (5-amino-4-chloro-2-phenyl-2H-pyridazin-3-one) were used to investigate the bacterial degradation of aminopyrine. 3. Three metabolites were isolated and identified as: 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydro-2,3-dihydroxy-4,6-cyc lohexadien-1-yl)-3H-pyrazol-3-one, 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydroxyphenyl)-3H-pyrazol-3 -one and 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-3H-pyrazol-3-one. 4. An enzyme extract from cells of strain m13 was shown to further metabolize the catechol derivative of aminopyrine, with the formation of 2-pyrone-6-carboxylic acid. 5. Results indicate that the benzene ring of aminopyrine is the principal site of microbial metabolism.