Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function.

The oxygenases have attracted considerable attention in enzyme-mediated bioremediation of xenobiotic compounds due to their high specificity, cost-effectiveness, and targeted field applications. Here, we performed a functional metagenomics approach to cope with culturability limitations to isolate a novel extradiol dioxygenase. Fosmid clone harboring dioxygenase gene was sequenced and analyzed by bioinformatics tools. One ring-cleaving dioxygenase RW4-MPC (metapyrocatechase) was purified and characterized to examine its degradation efficiency. The RW4-MPC was significantly active in the temperature and pH range of 5 to 40 °C, and 7-10, respectively, with an optimum temperature of 25 °C and pH 8. To gain insight into observed differential activity, Small-Angle X-ray Scattering (SAXS) data of the protein samples were analyzed, which brought forth that the RW4-MPC molecules form tight globular tetramers in solution. This native association was stable till 35 °C, and protein started to associate at higher temperatures, explaining heat-induced loss of function. Similarly, RW4-MPC aggregated or lost globular profile below pH 7 or at pH 10, respectively. The kinetic parameters showed the six folds high catalytic efficiency of RW4-MPC towards 2,3-dihydroxy biphenyl than catechol and its derivatives. RW4-MPC molecules showed remarkable retention of functionality in hypersaline conditions with more than 70% activity in a buffer having 3 M NaCl concentration. In concordance, SAXS data analysis showed retention of functional shape profile in hypersaline conditions. The halotolerant and oxygen insensitive nature of this enzyme makes it a potential candidate for bioremediation.

Catechol 2,3-dioxygenase from a new phenolic compound degrader Thauera sp. K11: purification and biochemical characterization.

Catechol 2,3-dioxygenase (C23O) from a new phenolic compound degrader Thauera sp. K11 was purified and characterized. The native form of the enzyme was determined as a homotetramer with a molecular weight of 140 kDa, and its isoelectric point was close to 6.4. One iron per enzyme subunit was detected using atom absorption spectroscopy, and the effective size of C23O in its dilute solution (0.2 g L-1 , pH 8.0) was 14.5 nm. The optimal pH and temperature were 8.4 and 45 °C, respectively. The addition of Mg2+ , Cu2+ , Fe2+ , and Mn2+ could improve the enzyme activity, while Ag+ was found to be a strong inhibitor. C23O was stable in alkali conditions (pH 7.6-11.0) and thermostable below 50 °C. The final purified C23O had a sheet content of 53%, consistent with the theoretical value. This showed that the purified catechol 2,3-dioxygenase folded with a reasonable secondary structure.

Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium.

Study of enzymes in halophiles will help to understand the mechanism of aromatic hydrocarbons degradation in saline environment. In this study, two novel catechol 2,3-dioxygenases (C23O1 and C23O2) were cloned and overexpressed from a halophilic bacterial consortium enriched from an oil-contaminated saline soil. Phylogenetic analysis indicated that the novel C23Os and their relatives formed a new branch in subfamily I.2.A of extradiol dioxygenases and the sequence differences were further analyzed by amino acid sequence alignment. Two enzymes with the halotolerant feature were active over a range of 0-30% salinity and they performed more stable at high salinity than in the absence of salt. Surface electrostatic potential and amino acids composition calculation suggested high acidic residues content, accounting for their tolerance to high salinity. Moreover, two enzymes were further characterized. The enzymes activity both increased in the presence of Fe(3+), Fe(2+), Cu(2+) and Al(3+) and showed no significant inhibition by other tested metal ions. The optimal temperatures for the C23Os were 40 °C and 60 °C and their best substrates were catechol and 4-methylcatechol respectively. As the firstly isolated and characterized catechol dioxygenases from halophiles, the two halotolerant C23Os presented novel characteristics suggesting their potential application in aromatic hydrocarbons biodegradation.

Activity of a carboxyl-terminal truncated form of catechol 2,3-dioxygenase from Planococcus sp. S5.

Catechol 2,3-dioxygenases (C23Os, E.C.1.13.12.2) are two domain enzymes that catalyze degradation of monoaromatic hydrocarbons. The catalytically active C-domain of all known C23Os comprises ferrous ion ligands as well as residues forming active site pocket. The aim of this work was to examine and discuss the effect of nonsense mutation at position 289 on the activity of catechol 2,3-dioxygenase from Planococcus strain. Although the mutant C23O showed the same optimal temperature for activity as the wild-type protein (35 °C), it exhibited activity slightly more tolerant to alkaline pH. Mutant enzyme exhibited also higher affinity to catechol as a substrate. Its K(m) (66.17 µM) was approximately 30% lower than that of wild-type enzyme. Interestingly, removal of the C-terminal residues resulted in 1.5- to 1.8-fold (P < 0.05) increase in the activity of C23OB61 against 4-methylcatechol and 4-chlorocatechol, respectively, while towards catechol the activity of the protein dropped to about 80% of that of the wild-type enzyme. The results obtained may facilitate the engineering of the C23O for application in the bioremediation of polluted areas.

Isolation, identification and characterization of a novel Ralstonia sp. FD-1, capable of degrading 4-fluoroaniline.

A gram-negative strain, designated as FD-1, isolated from aerobic activated sludge was capable of metabolizing 4-fluoroaniline (4-FA) as its sole carbon and nitrogen source and energy supply. According to the Biolog GNIII detection method 17 of 71 carbon substrates were easily utilized, while 12 of 23 substrates did not inhibit strain FD-1. The 16S rDNA sequence from strain FD-1 was 99 % similar to Ralstonia sp., suggesting that it belonged to the genus Ralstonia. The optimal conditions for growth and 4-FA degradation were pH 7 and 30 °C. The tolerance to 4-FA were 1,250 mg/L, while the tolerance to salinity was 15 g/L. Catechol 2,3-dioxygenase activity was detected and degradation intermediates were analyzed by liquid chromatography mass spectrometry leading to a proposed degradation pathway and suggesting that extradiol cleavage was involved in 4-FA degradation. This is the first report on the degradation of 4-FA by a bacterium from the Ralstonia genus.

Bacterial degradation of pyrene in minimal salt medium mediated by catechol dioxygenases: enzyme purification and molecular size determination.

In vitro degradation of pyrene was studied in MSM by three bacterial strains individually, designated as BP10, NJ2 and P2. Among these strains, NJ2 was the highest degrader (60%) of pyrene, followed by BP10 (44%) and the least was P2 (42%) in MSM with pyrene (50 µg ml(-1)) in 8 days. During pyrene degradation, catechol 1,2 dioxygenase (C12O) activity was induced by 13 folds in BP10 and 17 folds in P2 as compared to catechol 2,3 dioxygenase (C23O). However, in NJ2, C23O activity was augmented 1.3 times more than C12O. This clearly indicated that C12O played a major role in pyrene degradation by BP10 and P2, while in NJ2, C23O contributed more to degradation process than C12O. Molecular weight of highly inducible C12O was determined as ~64 kDa by size exclusion chromatography and as ~32 kDa on denaturing SDS PAGE in BP10 which indicated dimeric nature of the enzyme.

Characterization of catechol 2,3-dioxygenase from Planococcus sp. strain S5 induced by high phenol concentration.

This study aimed at characterization of a new catechol 2,3-dioxygenase isolated from a Gram-positive bacterium able to utilize phenol as the sole carbon and energy source. Planococcus sp. strain S5 grown on 1 or 2 mM phenol showed activity of both a catechol 1,2- and catechol 2,3-dioxygenase while at a higher concentrations of phenol only catechol 2,3-dioxygenase activity was observed. The enzyme was optimally active at 60°C and pH 8.0. Kinetic studies showed that the K(m) and V(max) of the enzyme were 42.70 µM and 329.96 mU, respectively. The catechol 2,3-dioxygenase showed the following relative meta-cleavage activities for various catechols tested: catechol (100%), 3-methylcatechol (13.67%), 4-methylcatechol (106.33%) and 4-chlorocatechol (203.80%). The high reactivity of this enzyme towards 4-chlorocatechol is different from that observed for other catechol 2,3-dioxygenases. Nucleotide sequencing and homology search revealed that the gene encoding the S5 catechol 2,3-dioxygenase shared the greatest homology with the known genes encoding isoenzymes from Gram-negative Pseudomonas strains.

Enzymes of naphthalene metabolism by Pseudomonas fluorescens 26K strain.

The ability of Pseudomonas fluorescens 26K strain to utilize naphthalene at concentrations up to 600 mg/liter as the sole source of carbon and energy in mineral liquid media was shown. Using HPLC, TLC, and mass-spectrometry, the intermediates of naphthalene transformation by this strain were identified as naphthalene cis-1,2-dihydrodiol, salicylaldehyde, salicylate, catechol, 2-hydroxymuconic semialdehyde, and 1-naphthol. Catechol 2,3-dioxygenase (a homotetramer with native molecular mass 125 kDa) and NAD+-dependent homohexameric naphthalene cis-1,2-dihydrodiol dehydrogenase with native molecular mass 160 kDa were purified from crude extract of the strain and characterized. NAD+-dependent homodimeric salicylaldehyde dehydrogenase with molecular mass 110 kDa was purified and characterized for the first time. Based on the data, a pathway of naphthalene degradation by P. fluorescens 26K is suggested.

Quantification of catechol dioxygenase gene expression in soil during degradation of 2,4-dichlorophenol.

The tfdC and C23O genes encode two catechol dioxygenases that catalyse ortho and meta cleavage of a key metabolite (chlorocatechol) of 2,4-dichlorophenol (2,4-DCP) metabolism, respectively. Primers were designed and a real-time PCR assay was developed to assess the abundance and expression of both tfdC and C23O genes in a soil amended with 2,4-DCP over a 21-day period. tfdC, the gene encoding the ortho cleaving dioxygenase, was significantly more abundant than the meta cleaving dioxygenase gene (C23O) throughout the experiment. The highest levels of tfdC were observed 2 days after amendment of soil with 2,4-DCP, at which stage the rate of 2,4-DCP degradation was at its maximum. In contrast, C230 copy numbers declined initially and peaked when degradation had slowed considerably. mRNA of the two chlorocatechol dioxygenase genes was not detected on day 0, but both genes were expressed after this time point. tfdC was expressed at a significantly higher level than C23O in 2,4-DCP-amended soil throughout the course of the microcosm, indicating the dominance of the ortho metabolic pathway. Phylogenetic analysis revealed a wide diversity of chlorocatechol dioxygenase genes in the 2,4-DCP-exposed soil examined.

Thermal effects on the activity and structural conformation of catechol 2,3-dioxygenase from Pseudomonas putida SH1.

A bacterium, Pseudomonas putida SH1, which can catabolize phenol, naphthalene, or cresol as the sole carbon and energy source, was isolated from a petroleum-contaminated site in Taiwan. The catechol 2,3-dioxygenase (C23O) was purified from this bacterial strain when grown on naphthalene as the sole carbon and energy source. The enzyme is composed of four identical subunits with a native molecular weight of 128 +/- 5 kD. Small-angle neutron scattering (SANS) techniques were employed to study the thermal effects on the structural conformation of this enzyme in solution. The SANS measurements revealed distinct changes in the size of the enzyme between 50 and 80 degrees C, and the size was not restored during the subsequent cooling. The enzyme started to denature at 55 degrees C, and the structure was destroyed by the time the temperature reached 80 degrees C, at which the enzyme had become more than twice the original size. The optimal catalytic temperature of the enzyme was at 50 degrees C. The half-life of the activity at this temperature was 45 min. The enzyme activity increases starting from 25 degrees C and reaches its maximum at 50 degrees C, below which no obvious change in the size of the enzyme is found. Noticeable enlargement of the enzyme is revealed when the enzymatic activity starts to fall. By combination of SANS measurement and biochemical properties of the enzyme, this study demonstrates the correlation of enzyme size in solution and catalytic activity upon a heat treatment. In addition, for a protein composed of multiple subunits, the shape of the enzyme and the dissociation of the enzyme subunits in a thermal cycle were also demonstrated by SANS methodology.

Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation.

The extradiol dioxygenase diversity of a site highly contaminated with aliphatic and aromatic hydrocarbons under air-sparging treatment was assessed by functional screening of a fosmid library in Escherichia coli with catechol as substrate. The 235 positive clones from inserts of DNA extracted from contaminated soil were equivalent to one extradiol dioxygenase-encoding gene per 3.6 Mb of DNA screened, indicating a strong selection for genes encoding this function. Three subfamilies were identified as being predominant, with 72, 55 and 43 fosmid inserts carrying genes, related to those encoding TbuE of Ralstonia pickettii PK01 (EXDO-D), IpbC of Pseudomonas sp. JR1 (EXDO-K2) or DbtC of Burkholderia sp. DBT1 (EXDO-Dbt), respectively, whereas genes encoding enzymes related to XylE of Pseudomonas putida mt-2 were not observed. Genes encoding oxygenases related to isopropylbenzene dioxygenases were usually colocalized with genes encoding EXDO-K2 dioxygenases. Functional analysis of representative proteins indicated a subcluster of EXDO-D proteins to show exceptional high affinity towards different catecholic substrates. Based on V(max)/K(m) specificity constants, a task-sharing between different extradiol dioxygenases in the community of the contaminated site can be supposed, attaining a complementary and community-balanced catalytic power against diverse catecholic derivatives, as necessary for effective degradation of mixtures of aromatics.

Purification and characterization of alkylcatechol 2,3-dioxygenase from butylphenol degradation pathway of Pseudomonas putida MT4.

Alkylcatechol 2,3-dioxygenase was purified from the cell extract of recombinant Escherichia coli JM109 harboring the alkylcatechol 2,3-dioxygenase gene (bupB) cloned from the butylphenol-degrading bacterium Pseudomonas putida MT4. The purified enzyme (BupB) showed relative meta-cleavage activities for the following catechols: catechol (100%), 4-methylcatechol (572%), 4-n-butylcatechol (185%), 4-n-hexylcatechol (53%), 4-n-heptylcatechol (45%), 4-n-nonylcatechol (10%), 4-tert-butylcatechol (0%), and 3-methylcatechol (33%). The kinetic parameters, namely, K(m) and V(max), for catechol, 4-methylcatechol, and 4-n-butylcatechol, were 23.4, 8.4, and 6.5 microM and 25.8, 76.9, and 18.0 U mg(-1), respectively. These results suggest that BupB has broad substrate specificity for 4-n-alkylcatechols.

Purification and characterization of catechol 2,3-dioxygenase from the aniline degradation pathway of Acinetobacter sp. YAA and its mutant enzyme, which resists substrate inhibition.

Catechol 2,3-dioxygenase (C23O), a key enzyme in the meta-cleavage pathway of catechol metabolism, was purified from cell extract of recombinant Escherichia coli JM109 harboring the C23O gene (atdB) cloned from an aniline-degrading bacterium Acinetobacter sp. YAA. SDS-polyacrylamide gel electrophoresis and gel filtration chromatography analysis suggested that the enzyme (AtdB) has a molecular mass of 35 kDa as a monomer and forms a tetrameric structure. It showed relative meta-cleavage activities for the following catechols tested: catechol (100%), 3-methylcatechol (19%), 4-methylcatechol (57%), 4-chlorocatechol (46%), and 2,3-dihydroxybiphenyl (5%). To elevate the activity, a DNA self-shuffling experiment was carried out using the atdB gene. One mutant enzyme, named AtdBE286K, was obtained. It had one amino acid substitution, E286K, and showed 2.4-fold higher C23O activity than the wild-type enzyme at 100 microM. Kinetic analysis of these enzymes revealed that the wild-type enzyme suffered from substrate inhibition at >2 microM, while the mutant enzyme loosened substrate inhibition.