Purification, characterization, and gene analysis of catechol 2,3-dioxygenase from the aniline-assimilating bacterium Pseudomonas species AW-2

Retrospect and prospect of aerobic biodegradation of aniline: Overcome existing bottlenecks and follow future trends

Aniline is a highly bio-toxic industrial product, even at low concentrations, whose related wastewater has been flowing out worldwide on a large scale along with human production. As a green technology, aerobic biological treatment has been widely applied in industrial wastewater and exhibited various characteristics in the field of aniline wastewater. Meanwhile, this technology has shown its potential of synchronous nitrogen removal, but it still consumes energy badly. In the face of resource scarcity, this review comprehensively discusses the existing research in aerobic biodegradation of aniline wastewater to find out the developmental dawn of aerobic biological treatment. Primarily, it put forward the evolution history details of aniline biodegradation from pure culture to mixed culture and then to simultaneous nitrogen removal. On this basis, it presented the existing challenges to further expand the application of aerobic biotechnology, including the confusions of aniline metabolic mechanism, the development of co-degradation of multiple pollutants and the lack of practical experience of bioreactor operation for aniline and nitrogen removal. Additionally, the prospects of the technological shift to meet the needs of an energy-conserving society was described according to existing experiences and feasibility. Including but not limiting to the development of multifunctional bacteria, the reduction of greenhouse gases and the combination of green technologies.

Desulfatiglans anilini Initiates Degradation of Aniline With the Production of Phenylphosphoamidate and 4-Aminobenzoate as Intermediates Through Synthases and Carboxylases From Different Gene Clusters

The anaerobic degradation of aniline was studied in the sulfate-reducing bacterium Desulfatiglans anilini. Our aim was to identify the genes and their proteins that are required for the initial activation of aniline as well as to characterize intermediates of this reaction. Aniline-induced genes were revealed by comparison of the proteomes of D. anilini grown with different substrates (aniline, 4-aminobenzoate, phenol, and benzoate). Most genes encoding proteins that were highly abundant in aniline- or 4-aminobenzoate-grown D. anilini cells but not in phenol- or benzoate-grown cells were located in the putative gene clusters ani (aniline degradation), hcr (4-hydroxybenzoyl-CoA reductase) and phe (phenol degradation). Of these putative gene clusters, only the phe gene cluster has been studied previously. Based on the differential proteome analysis, four candidate genes coding for kinase subunits and carboxylase subunits were suspected to be responsible for the initial conversion of aniline to 4-aminobenzoate. These genes were cloned and overproduced in E. coli. The recombinant proteins were obtained in inclusion bodies but could be refolded successfully. Two subunits of phenylphosphoamidate synthase and two carboxylase subunits converted aniline to 4-aminobenzoate with phenylphosphoamidate as intermediate under consumption of ATP. Only when both carboxylase subunits, one from gene cluster ani and the other from gene cluster phe, were combined, phenylphosphoamidate was converted to 4-aminobenzoate in vitro, with Mn²⁺, K⁺, and FMN as co-factors. Thus, aniline is degraded by the anaerobic bacterium D. anilini only by recruiting genes for the enzymatic machinery from different gene clusters. We conclude, that D. anilini carboxylates aniline to 4-aminobenzoate via phenylphosphoamidate as an energy rich intermediate analogous to the degradation of phenol to 4-hydroxybenzoate via phenylphosphate.

Enhanced biodegradation of crude oil in soil by a developed bacterial consortium and indigenous plant growth promoting bacteria

AIMS

This study aimed to develop an efficient, cost-effective and eco-friendly bacterial consortium to degrade petroleum sludge.

METHODS AND RESULTS

Four bacterial strains belonging to genera Acinetobacter and Pseudomonas were selected to constitute three different consortia based on their initial concentration. The highest degradation rate (78%) of 1% (v/v) crude oil after 4 weeks of incubation was recorded when the concentration of biosurfactant (BS) producing isolate was high. Genes, such as alkB, almA, cyp153, pah-rhdGN, nah, phnAC and cat23 were detected using the polymerase chain reaction method and their induction levels were optimal at pH 7·0. A crude oil sludge was artificially constituted, and its bacterial composition was investigated using 16S rRNA gene amplicon sequencing. The results showed that the soil bacterial community was dominated by plant growth-promoting bacteria (PGPB) after crude oil treatment.

CONCLUSIONS

Our findings indicate the decontamination of the crude oil contaminated soil was more effective in the presence of both the constituted consortium and PGPB compared to the presence of PGPB alone.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study showed that the PGPB (Taibaiella) present in petroleum uncontaminated soil can promote the soil decontamination. The addition of both efficient hydrocarbon-degrading and BS producing bacteria is also necessary to improve the decontamination.

Bacterial degradation of monocyclic aromatic amines

Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.

Cloning and mutagenesis of catechol 2,3-dioxygenase gene from the gram-positive Planococcus sp. strain S5

In this study, the catechol 2,3-dioxygenase gene that encodes a 307- amino-acid protein was cloned from Planococcus sp. S5. The protein was identified to be a member of the superfamily I, subfamily 2A of extradiol dioxygenases. In order to study residues and regions affecting the enzyme's catalytic parameters, the c23o gene was randomly mutated by error-prone PCR. The wild-type enzyme and mutants containing substitutions within either the C-terminal or both domains were functionally produced in Escherichia coli and their activity towards catechol was characterized. The C23OB65 mutant with R296Q substitution showed significant tolerance to acidic pH with an optimum at pH 5.0. In addition, it showed activity more than 1.5 as high as that of the wild type enzyme and its Km was 2.5 times lower. It also showed altered sensitivity to substrate inhibition. The results indicate that residue at position 296 plays a role in determining pH dependence of the enzyme and its activity. Lower activity toward catechol was shown for mutants C23OB58 and C23OB81. Despite lower activity, these mutants showed higher affinity to catechol and were more sensitive to substrate concentration than nonmutated enzyme.

Catabolism of 4-alkylphenols by Acinetobacter sp. OP5: genetic organization of the oph gene cluster and characterization of alkylcatechol 2, 3-dioxygenase

In this study, a specific PCR primer set was successfully designed for alkylcatechol 2, 3-dioxygenase genes and applied to detect the presence of this biomarker in 4-t-octylphenol-degrading Acinetobacter sp. strain OP5. A gene cluster (ophRBA1A2A3A4A5A6CEH) encoding multicomponent phenol hydroxylase and alkylcatechol 2, 3-dioxygenase was then cloned from this strain and showed the highest homology to those involved in the published medium-chain alkylphenol gene clusters. The pure enzyme of recombinant cell harboring ophB showed meta-cleavage activities for 4-methylcatechol (1,435%), 4-ethylcatechol (982%), catechol (100%), 4-t-butylcatechol (16.6%), and 4-t-octylcatechol (3.2%). The results suggest that the developed molecular technique is useful and easy in detection of medium/long-chain alkylphenol degradation gene cluster. In addition, it also provides a better understanding of the distribution of biodegradative genes and pathway for estrogenic-active long-chain alkylphenols in bacteria.

Influence of food colorant and initial COD concentration on the efficiencies of micro-aerobic sequencing batch reactor (micro-aerobic SBR) for casein recovery under non-sterile condition by Lactobacillus casei TISTR 1500

The acid biocoagulants produced from non-sterile lactic acid fermentation by Lactobacillus casei TISTR 1500 were used to settle colloidal protein, mainly casein, at the isoelectric point in dairy effluent prior to secondary treatment. High concentration of azo dye (Ponceau 4R) in the dairy wastewater and the stress of starvation decreased the efficiencies of the micro-aerobic SBR. Consequently, low casein recovery obtained and organic removal suffered a decline. The number of lactic acid bacteria (LAB) also declined from log 7.4 to log 5.30 in the system fed with 400 mg L(-1) of the dye containing wastewater. The recovery of the system, however, showed that 25,000 mg COD L(-1) influent with 200 mg L(-1) of the dye maintained the growth of LAB in the range of log 7.74-8.12, with lactic and acetic production (2597 and 197 mg L(-1)) and 83% protein removal. The results in this study suggested that the inhibitory effects were compensated with high organic content feeding.

Metabolism of azo dyes by Lactobacillus casei TISTR 1500 and effects of various factors on decolorization

Lactobacillus casei TISTR 1500 was isolated from soil of a dairy wastewater treatment plant and selected as the most active azo dye degrader of 19 isolates. Growing cells and freely suspended cells of this strain completely degraded methyl orange, thereby decolorizing the medium. The strain stoichiometrically converted methyl orange to N,N-dimethyl-p-phenylenediamine and 4-aminobenzenesulfonic acid, which were identified by HPLC, GC, and GC-MS analyses. The enzyme activity responsible for the cleavage of the azo bond of methyl orange was localized to the cytoplasm of cells grown on modified MRS medium containing methyl orange. The effect of sugars, oligosaccharides, organic acids, metal ions, pHs, oxygen and temperatures on methyl orange decolorization by freely suspended cells was investigated. The optimal conditions for the decolorization of methyl orange by the Lactobacillus casei TISTR 1500 are incubation at 35 degrees C and pH 6 with sucrose provided as the energy source.

Microbial transformation of aniline derivatives: regioselective biotransformation and detoxification of 2-phenylenediamine by Bacillus cereus strain PDa-1

A bacterial isolate, strain PDa-1, grew well on basal medium supplemented with 2-phenylenediamine, sucrose, and ammonium nitrate and completely transformed 2-phenylenediamine. The isolate was identified as Bacillus cereus. The product formed from 2-phenylenediamine was identified by EI-MS and NMR as 2-aminoacetanilide; whole cells converted 2-phenylenediamine to the product with a 76% molar yield. Whole cells also showed a broad substrate specificity toward 20 of 26 tested arylamines with substituent groups of various size and positions. Especially 2-aminobenzoic acid, 4-aminosalicylic acid, 5-aminosalicylic acid, and 2-aminofluorene were converted completely to the corresponding product with an aminoacetyl group. Cell extracts of strain PDa-1 had a high arylamine N-acetyltransferase activity. The partially purified enzyme converted 2-phenylenediamine to 2-aminoacetanilide. Strain PDa-1 constitutively expressed the enzyme in the absence of 2-phenylenediamine. Effects of 2-phenylenediamine and 2-aminoacetanilide on growth indicated that this enzyme probably plays a role in the detoxification of toxic arylamines in this strain.

Proteome analysis ofPseudomonas sp. K82 biodegradation pathways

Pseudomonas sp. K82 is a soil bacterium that can degrade and use monocyclic aromatic compounds including aniline, 3-methylaniline, 4-methylaniline, benzoate and p-hydroxybenzoate as its sole carbon and energy sources. In order to understand the impact of these aromatic compounds on metabolic pathways in Pseudomonas sp. K82, proteomes obtained from cultures exposed to different substrates were displayed by two-dimensional gel electrophoresis and were compared to search for differentially induced metabolic enzymes. Column separations of active fractions were performed to identify major biodegradation enzymes. More than thirty proteins involved in biodegradation and other types of metabolism were identified by electrospray ionization-quadrupole time of flight mass spectrometry. The proteome analysis suggested that Pseudomonas sp. K82 has three main metabolic pathways to degrade these aromatic compounds and induces specific metabolic pathways for each compound. The catechol 2,3-dioxygenase (CD2,3) pathway was the major pathway and the catechol 1,2-dioxygenase (beta-ketoadipate) pathway was the secondary pathway induced by aniline (aniline analogues) exposure. On the other hand, the catechol 1,2-dioxygenase pathway was the major pathway induced by benzoate exposure. For the degradation of p-hydroxybenzoate, the protocatechuate 4,5-dioxygenase pathway was the major degradation pathway induced. The nuclear magnetic resonance analysis of substrates demonstrated that Pseudomonas sp. K82 metabolizes some aromatic compounds more rapidly than others (benzoate > p-hydroxybenzoate > aniline) and that when combined, p-hydroxybenzoate metabolism is repressed by the presence of benzoate or aniline. These results suggest that proteome analysis can be useful in the high throughput study of bacterial metabolic pathways, including that of biodegradation, and that inter-relationships exist with respect to the metabolic pathways of aromatic compounds in Pseudomonas sp. K82.

Cloning of a gene encoding 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. 10d

Bordetella sp. 10d produces a novel dioxygenase catalyzing the meta-cleavage of 4-amino-3-hydroxybenzoic acid, 4-amino-3-hydroxybenzoate 2,3-dioxygenase (4A3HBA23D). A gene encoding 4A3HBA23D was cloned and named ahdA. The deduced amino acid sequence of ahdA showed 29.2-24.2% identities to those of prokaryotic and eukaryotic 3-hydoxybenzoate 3,4-dioxygenases in reported meta-cleavage dioxygenases. However, no identities were observed in the amino-terminal sequences of the first 29 amino acid residues. An ORF was found downstream of ahdA. The deduced amino acid sequence of the ORF showed identities to those of LysR family regulators involved in protocatechuate metabolism and contained motifs conserved in the regulators. On the basis of these results, the ORF was named ahdR encoding a putative LysR family regulator. The transcription start point of ahdA was localized 414-bp upstream of the start codon of ahdA. Two DNA-binding motifs of LysR family regulators were found upstream of the transcription start point. These observations suggest that a LysR family regulator encoded by ahdR regulates the expression of ahdA.

A novel meta-cleavage dioxygenase that cleaves a carboxyl-group-substituted 2-aminophenol. Purification and characterization of 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. strain 10d

A bacterial strain that grew on 4-amino-3-hydroxybenzoic acid was isolated from farm soil. The isolate, strain 10d, was identified as a species of Bordetella. Cell extracts of Bordetella sp. strain 10d grown on 4-amino-3-hydroxybenzoic acid contained an enzyme that cleaved this substrate. The enzyme was purified to homogeneity with a 110-fold increase in specific activity. The purified enzyme was characterized as a meta-cleavage dioxygenase that catalyzed the ring fission between C2 and C3 of 4-amino-3-hydroxybenzoic acid, with the consumption of 1 mol of O2 per mol of substrate. The enzyme was therefore designated as 4-amino-3-hydroxybenzoate 2,3-dioxygenase. The molecular mass of the native enzyme was 40 kDa based on gel filtration; the enzyme is composed of two identical 21-kDa subunits according to SDS/PAGE. The enzyme showed a high dioxygenase activity only for 4-amino-3-hydroxybenzoic acid. The Km and Vmax values for this substrate were 35 micro m and 12 micro mol.min-1.(mg protein)-1, respectively. Of the 2-aminophenols tested, only 4-aminoresorcinol and 6-amino-m-cresol inhibited the enzyme. The enzyme reported here differs from previously reported extradiol dioxygenases, including 2-aminophenol 1,6-dioxygenase, in molecular mass, subunit structure and catalytic properties.

Immobilization of functionally unstable catechol-2,3-dioxygenase greatly improves operational stability

Thermophilic catechol 2,3-dioxygenase (EC 1.13.11.2) from Bacillus stearothermophilus has been immobilized on highly activated glyoxyl agarose beads. The enzyme could be fully immobilized at 4 degrees C and pH 10.05 with a high retention of activity (around 80%). Enzyme immobilized under these conditions showed little increase in thermostability compared with the soluble enzyme, but further incubation of immobilized enzyme at 25 degrees C and pH 10.05 for 3 h before borohydride reduction resulted in conjugates exhibiting a 100-fold increase in stability (c.f. the free enzyme). The stability of catechol 2,3-dioxygenase immobilized under these conditions was essentially independent of protein concentration whereas free enzyme was rapidly inactivated at low protein concentrations. An apparent stabilization factor of over 700-fold was recorded in the comparison of free and immobilized catechol 2,3-dioxygenases at protein concentrations of 10 µg/ml. Immobilization increased the 'optimum temperature' for activity by 20 degrees C, retained activity at substrate concentrations where the soluble enzyme was fully inactivated and enhanced the resistance to inactivation during catalysis. These results suggest that the immobilization of the enzyme under controlled conditions with the generation of multiple covalent links between the enzyme and matrix both stabilized the quaternary structure of the protein and increased the rigidity of the subunit structures.