Alcaligenes eutrophus JMP134 "2,4-dichlorophenoxyacetate monooxygenase" is an alpha-ketoglutarate-dependent dioxygenase

Niche-specification of aerobic 2,4-dichlorophenoxyacetic acid biodegradation by tfd-carrying bacteria in the rice paddy ecosystem

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfd-mediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D.

Synthesizing Laboratory and Field Experiments to Quantify Dominant Transformation Mechanisms of 2,4-Dichlorophenoxyacetic Acid (2,4-D) in Aquatic Environments

Laboratory studies used to assess the environmental fate of organic chemicals such as pesticides fail to replicate environmental conditions, resulting in large errors in predicted transformation rates. We combine laboratory and field data to identify the dominant loss processes of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in lakes for the first time. Microbial and photochemical degradation are individually assessed using laboratory-based microcosms and irradiation studies, respectively. Field campaigns are conducted in six lakes to quantify 2,4-D loss following large-scale herbicide treatments. Irradiation studies show that 2,4-D undergoes direct photodegradation, but modeling efforts demonstrated that this process is negligible under environmental conditions. Microcosms constructed using field inocula show that sediment microbial communities are responsible for degradation of 2,4-D in lakes. Attempts to quantify transformation products are unsuccessful in both laboratory and field studies, suggesting that their persistence is not a major concern. The synthesis of laboratory and field experiments is used to demonstrate best practices in designing laboratory persistence studies and in using those results to mechanistically predict contaminant fate in complex aquatic environments.

Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides

Oxygenases, which catalyze the reductive activation of O₂ and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.

Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions

Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.

Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants

The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.

A novel environmental fate of graphene oxide: Biodegradation by a bacterium Labrys sp. WJW to support growth

Graphene oxide (GO) is a new type of nanomaterial with unique physicochemical properties and diverse applications, whereas it poses potential risk to human and environment. By screening from natural soil exposed to GO in the laboratory, we successfully obtained a novel bacterium, Labrys sp. WJW, which was able to use GO as the sole carbon source for growth. Within 8 days, cell numbers increased 16.76 ± 3.21 folds using 100 mg/L GO as the carbon source by qPCR analysis. The bacterial biodegradation which resulted in formation of holes and functional group changes of GO was proved by Raman spectroscopy, atomic force microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy analyses. Aromatic intermediates with structures of benzoic acid and phenol were identified using gas chromatograph-mass spectrometry and liquid chromatography/time-of-flight/mass spectrometry. Combination of genomic and proteomic analyses were performed to explore the proteins associated with GO degradation. A total of 644 proteins were significantly shifted. Bioinformatics analysis indicated that part of the up-regulated proteins were related to oxidation, ring cleavage and intermediates transmembrane processes, and GO was supposed to be degraded to benzoate and further degraded for downstream processes. This study enriches our understanding and provides new insights into the environmental fate of GO.

Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH

Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH. The genome has an intricate organization of the chlorophenoxy-herbicide catabolic genes sdpA, rdpA, and cadABCD that encode the (R)- and (S)-enantiomer-specific 2,4-dichlorophenoxypropionate dioxygenases and four subunits of a Rieske non-heme iron oxygenase involved in 2-methyl-chlorophenoxyacetic acid degradation, respectively. Several major genomic rearrangements are proposed to help understand the evolution and mobility of these important genes and their genetic context. Single-strain mobilomic sequence analysis uncovered plasmids and insertion sequence-associated circular intermediates in this environmentally important bacterium and enabled the description of evolutionary models for pesticide degradation in strain MH and related organisms. The mobilome presented a complex mosaic of mobile genetic elements including four plasmids and several circular intermediate DNA molecules of insertion-sequence elements and transposons that are central to the evolution of xenobiotics degradation. Furthermore, two individual chromosomally integrated prophages were shown to excise and form free circular DNA molecules. This approach holds great potential for improving the understanding of genome plasticity, evolution, and microbial ecology.

2-Oxoglutarate-Dependent Oxygenases

2-Oxoglutarate (2OG)-dependent oxygenases (2OGXs) catalyze a remarkably diverse range of oxidative reactions. In animals, these comprise hydroxylations and N-demethylations proceeding via hydroxylation; in plants and microbes, they catalyze a wider range including ring formations, rearrangements, desaturations, and halogenations. The catalytic flexibility of 2OGXs is reflected in their biological functions. After pioneering work identified the roles of 2OGXs in collagen biosynthesis, research revealed they also function in plant and animal development, transcriptional regulation, nucleic acid modification/repair, fatty acid metabolism, and secondary metabolite biosynthesis, including of medicinally important antibiotics. In plants, 2OGXs are important agrochemical targets and catalyze herbicide degradation. Human 2OGXs, particularly those regulating transcription, are current therapeutic targets for anemia and cancer. Here, we give an overview of the biochemistry of 2OGXs, providing examples linking to biological function, and outline how knowledge of their enzymology is being exploited in medicine, agrochemistry, and biocatalysis.

Role of CadC and CadD in the 2,4-dichlorophenoxyacetic acid oxygenase system of Sphingomonas agrestis 58-1

In the present study, we confirm that 2,4-dichlorophenoxyacetic acid (2,4-D) oxygenase from Sphingomonas agrestis 58-1 belongs to the family of Rieske non-heme iron aromatic ring-hydroxylating oxygenases, which comprise a core enzyme (oxygenase), ferredoxin, and oxidoreductase. It has previously been shown that cadAB genes are necessary for the conversion of 2,4-D to 2,4-dichlorophenol; however, the respective roles of ferredoxin and oxidoreductase in the 2,4-D oxygenase system from S. agrestis 58-1 remain unknown. Using nucleotide sequence analysis of the plasmid pCADAB1 from Sphingomonas sp. ERG5, which degrades 4-chloro-2-methylphenoxyacetic acid and 2,4-D, Nielsen et al. identified orf95, upstream of cadA, and orf98, downstream of cadB, which were predicted and designated as cadD (oxidoreductase) and cadC (ferredoxin), respectively (Nielsen et al., PLoS One, 8, e83346, 2013). These designations were the result of sequence analysis; therefore, we constructed an expression system of CadABC and CadABCD in Escherichia coli and assayed their enzyme activities. Our findings indicate that CadC is essential for the activity of 2,4-D oxygenase and CadD promotes CadABC activity in recombinant E. coli cells.

Mathematical basis of improved protein subfamily classification by a HMM-based sequence filter

Informative phylogenetic analysis is dependent on the presence of curated and annotated sequences. This may be complemented by the simultaneous availability of empirical data pertaining to their in vivo function. Confounding sequences, with their similarity to more than one functional cluster, can therefore, render any categorization ambiguous, subjective, and imprecise. Here, I analyze and discuss the development of a mathematical expression that can characterize a potential confounding protein sequence. Specifically, statistical descriptors of combinatorially arranged profile HMM scores are computed and evaluated. The resultant data is then incorporated into an index of sequence suitability. The sequence may then be recommended as either suitable for inclusion or be excluded all together. The index is independent of experimental data and, can, be computed from the primary structure of the protein sequence. This can be utilized to trim previously grouped sequences and can either finalize the composition of training set or reduce the search space of sequences to be tested.

2,4-Dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading gene cluster in the soybean root-nodulating bacterium Bradyrhizobium elkanii USDA94

Herbicides 2,4-dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading Bradyrhizobium strains possess tfdAα and/or cadABC as degrading genes. It has been reported that root-nodulating bacteria belonging to Bradyrhizobium elkanii also have tfdAα and cadA like genes but lack the ability to degrade these herbicides and that the cadA genes in 2,4-D-degrading and non-degrading Bradyrhizobium are phylogenetically different. In this study, we identified cadRABCK in the genome of a type strain of soybean root-nodulating B. elkanii USDA94 and demonstrated that the strain could degrade the herbicides when cadABCK was forcibly expressed. cadABCK-cloned Escherichia coli also showed the degrading ability. Because co-spiked phenoxyacetic acid (PAA) could induce the degradation of 2,4-D in B. elkanii USDA94, the lack of degrading ability in this strain was supposed to be due to the low inducing potential of the herbicides for the degrading gene cluster. On the other hand, tfdAα from B. elkanii USDA94 showed little potential to degrade the herbicides, but it did for 4-chlorophenoxyacetic acid and PAA. The 2,4-D-degrading ability of the cad cluster and the inducing ability of PAA were confirmed by preparing cadA deletion mutant. This is the first study to demonstrate that the cad cluster in the typical root-nodulating bacterium indeed have the potential to degrade the herbicides, suggesting that degrading genes for anthropogenic compounds could be found in ordinary non-degrading bacteria.

Evidence for the importance of litter as a co-substrate for MCPA dissipation in an agricultural soil

Environmental controls of 2-methyl-4-chlorophenoxyacetic acid (MCPA) degradation are poorly understood. We investigated whether microbial MCPA degraders are stimulated by (maize) litter and whether this process depends on concentrations of MCPA and litter. In a microcosm experiment, different amounts of litter (0, 10 and 20 g kg(-1)) were added to soils exposed to three levels of the herbicide (0, 5 and 30 mg kg(-1)). The treated soils were incubated at 20 °C for 6 weeks, and samples were taken after 1, 3 and 6 weeks of incubation. In soils with 5 mg kg(-1) MCPA, about 50 % of the MCPA was dissipated within 1 week of the incubation. Almost complete dissipation of the herbicide had occurred by the end of the incubation with no differences between the three litter amendments. At the higher concentration (30 mg kg(-1)), MCPA endured longer in the soil, with only 31 % of the initial amount being removed at the end of the experiment in the absence of litter. Litter addition greatly increased the dissipation rate with 70 and 80 % of the herbicide being dissipated in the 10 and 20 g kg(-1) litter treatments, respectively. Signs of toxic effects of MCPA on soil bacteria were observed from related phospholipid fatty acid (PLFA) analyses, while fungi showed higher tolerance to the increased MCPA levels. The abundance of bacterial tfdA genes in soil increased with the co-occurrence of litter and high MCPA concentration, indicating the importance of substrate availability in fostering MCPA-degrading bacteria and thereby improving the potential for removal of MCPA in the environment.

Cytochrome P450 3A Enzymes Catalyze the O6-Demethylation of Thebaine, a Key Step in Endogenous Mammalian Morphine Biosynthesis

Morphine, first characterized in opium from the poppy Papaver somniferum, is one of the strongest known analgesics. Endogenous morphine has been identified in several mammalian cells and tissues. The synthetic pathway of morphine in the opium poppy has been elucidated. The presence of common intermediates in plants and mammals suggests that biosynthesis occurs through similar pathways (beginning with the amino acid L-tyrosine), and the pathway has been completely delineated in plants. Some of the enzymes in the mammalian pathway have been identified and characterized. Two of the latter steps in the morphine biosynthesis pathway are demethylation of thebaine at the O(3)- and the O(6)-positions, the latter of which has been difficult to demonstrate. The plant enzymes responsible for both the O(3)-demethylation and the O(6)-demethylation are members of the Fe(II)/α-ketoglutarate-dependent dioxygenase family. Previous studies showed that human cytochrome P450 (P450) 2D6 can catalyze thebaine O(3)-demethylation. We report that demethylation of thebaine at the O(6)-position is selectively catalyzed by human P450s 3A4 and 3A5, with the latter being more efficient, and rat P450 3A2. Our results do not support O(6)-demethylation of thebaine by an Fe(II)/α-ketoglutarate-dependent dioxygenase. In rat brain microsomes, O(6)-demethylation was inhibited by ketoconazole, but not sulfaphenazole, suggesting that P450 3A enzymes are responsible for this activity in the brain. An alternate pathway to morphine, oripavine O(6)-demethylation, was not detected. The major enzymatic steps in mammalian morphine synthesis have now been identified.

Isolation and 2,4-D-degrading characteristics of Cupriavidus campinensis BJ71

An indigenous bacterial strain capable of utilizing 2,4-dichlorophenoxyacetic acid as the sole carbon and energy source was isolated from a soil used for grown wheat with a long-term history of herbicide use in Beijing, China. The strain BJ71 was identified as Cupriavidus campinensis based on its 16S rRNA sequence analysis and morphological, physiological, and biochemical characteristics. The degradation characteristics of strain BJ71 were evaluated. The optimal conditions for 2,4-D degradation were as follows: pH 7.0, 30 °C, 3% (v/v) inoculum size, and an initial 2,4-D concentration of 350 mg L(-1). Up to 99.57% of the 2,4-D was degraded under optimal conditions after 6 days of incubation. Strain BJ71 was also able to degrade quizalofop and fluroxypyr. This is the first report of a 2,4-D-degrader containing tfdA gene that can utilize these two herbicides. In a biodegradation experiment, 87.13% and 42.53% of 2,4-D (initial concentration, 350 mg kg(-1)) was degraded in non-sterile and sterilized soil inoculated with BJ71, respectively, after 14 days. The 2,4-D degradation was more rapid in a soil microcosm including BJ71 than in a soil microcosm without BJ71. These results indicate that strain BJ71 is a potential candidate for the bioremediation of soil contaminated with the herbicide 2,4-D.

Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71

2,4-Dichlorophenoxyacetic acid (2,4-D)/α-ketoglutarate (α-KG) dioxygenase (TfdA) is an Fe(II)-dependent enzyme that catalyzes the first step in degradation of the herbicide 2,4-D. Previous studies focused on the tfdA gene in Ralstonia eutropha JMP134 isolated in Australia. In this study, a new tfdA gene was cloned from Cupriavidus campinensis BJ71, an effective degrading bacteria from China, based on the iCOnsensus-DEgenerate Hybrid Oligonucleotide Primers (iCODEHOPs) protocol, combined with high-efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR). The open reading frame of 861 bp encoded a putative 287 amino acid protein with a theoretical molecular mass of 32.32 kDa. The gene was overexpressed in Escherichia coli BL21 (DE3) and the purified TfdA showed optimal activity at pH 6.75 and 30 °C. This enzyme was more thermostable and it could use 3-hydrocinnamic acid as substrate, with a similar enzyme activity compared with 2,4-D. TfdA and its variants were created as maltose-binding protein (MBP) tagged fusion proteins to examine the roles of putative substrate-binding residues. The MBP-N110A, MBP-V198A and MBP-R207K proteins showed decreased k cat and increased Km, and MBP-R278A was inactive, suggesting these residues may affect 2,4-D binding or catalysis.

16S rRNA gene phylogeny and tfdA gene analysis of 2,4-D-degrading bacteria isolated in China

Twenty-two 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterial isolates were collected from agricultural soils at three sites in China. Sequence analysis of the 16S rRNA genes indicated that the isolates were phylogenetically grouped into four categories: Ochrobactrum anthropi, in the Alpha- class of the phylum Proteobacteria (3 out of 22 isolates), Cupriavidus sp., of the Betaproteobacteria (3 out of 22), Pseudomonas sp. and Stenotrophomonas sp., which are Gammaproteobacteria (7 out of 22), and Bacillus sp., of the phylum Firmicutes (9 out of 22). Primers were designed to amplify the conserved domain of tfdA, which is known to be involved in the degradation of 2,4-D. Results showed that the tfdA genes of all 22 strains were most similar to that of Cupriavidus necator JMP134, which belongs to the 2,4-D/α-ketoglutarate dioxygenase TfdA protein family, indicating that the JMP134-type tfdA gene is likely to be almost universal among the 2,4-D-degrading bacteria isolated from China. Degradation abilities of these 22 strains were investigated in assays using 2,4-D as the sole source of carbon and energy. Thirteen strains degraded >60 % of the available 2,4-D (500 mg l(-1)) over a 1-week incubation period, while a further nine Bacillus sp. strains degraded 50-81 % of the available 2,4-D. None of these nine strains degraded other selected herbicides, such as mecoprop, 2-methyl-4-chlorophenoxyacetic acid, quizalofop, and fluroxypyr. This is the first report of 2,4-D-degradation by Bacilli.

Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas

The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads.

Evolutions of microbial degradation pathways for parent xenobiotic and for its metabolites follow different schemes

BACKGROUND AND PURPOSES

The pathways used by microorganisms for the metabolism of every xenobiotic substrate are specific. The catabolism of a xenobiotic goes through a series of intermediate steps and lower intermediates (metabolites) appear in sequence. The structure of the metabolites can be similar to the parents due to kinship. The purposes of this study were to examine if the degradation pathways that were developed for a parent xenobiotic are effective to degrade the parent's lower metabolites, and if the reverse is true.

MATERIALS AND METHODS

The xenobiotic substrates, 2,4-dichlorophenoxyacetic acid (2,4-D, the parent xenobiotic) and its metabolite 2,4-dichlorophenol (2,4-DCP), were independently subjected to acclimation and degradation tests by the biomasses of mixed-culture activated sludge and a pure culture of Arthrobacter sp.

RESULTS

Activated sludge and Arthrobacter sp. that were acclimated to 2,4-D effectively degraded 2,4-D and the lower metabolites of 2,4-D, typically 2,4-DCP. During the degradation of 2,4-D, accumulations of the lower metabolites of 2,4-D were not found. The degradation pathways acquired from acclimation to 2,4-D are effective for all the metabolites of 2,4-D. However, pathways acquired from acclimation to 2,4-DCP are not effective in the degradation of the parent 2,4-D.

CONCLUSIONS

Microorganisms acclimated to 2,4-D evolve their degradation pathways by a scheme that is different from the scheme the microorganisms employ when they are acclimated to the metabolites of 2,4-D.

Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases

BACKGROUND

The 2-oxoglutarate dependent superfamily is a diverse group of non-haem dioxygenases, and is present in prokaryotes, eukaryotes, and archaea. The enzymes differ in substrate preference and reaction chemistry, a factor that precludes their classification by homology studies and electronic annotation schemes alone. In this work, I propose and explore the rationale of using substrates to classify structurally similar alpha-ketoglutarate dependent enzymes.

FINDINGS

Differential catalysis in phylogenetic clades of 2-OG dependent enzymes, is determined by the interactions of a subset of active-site amino acids. Identifying these with existing computational methods is challenging and not feasible for all proteins. A clustering protocol based on validated mechanisms of catalysis of known molecules, in tandem with group specific hidden markov model profiles is able to differentiate and sequester these enzymes. Access to this repository is by a web server that compares user defined unknown sequences to these pre-defined profiles and outputs a list of predicted catalytic domains. The server is free and is accessible at the following URL (http://comp-biol.theacms.in/H2OGpred.html).

CONCLUSIONS

The proposed stratification is a novel attempt at classifying and predicting 2-oxoglutarate dependent function. In addition, the server will provide researchers with a tool to compare their data to a comprehensive list of HMM profiles of catalytic domains. This work, will aid efforts by investigators to screen and characterize putative 2-OG dependent sequences. The profile database will be updated at regular intervals.

Degradation of 2,4-dichlorophenoxyacetic acid by a halotolerant strain of Penicillium chrysogenum: antibiotic production

The extensive use of pesticides in agriculture has prompted intensive research on chemical and biological methods in order to protect contamination of water and soil resources. In this paper the degradation of the pesticide 2,4-dichlorophenoxyacetic acid by a Penicillium chrysogenum strain previously isolated from a salt mine was studied in batch cultures. Co-degradation of 2,4-dichlorophenoxyacetic acid with additives such as sugar and intermediates of pesticide metabolism was also investigated. Penicillium chrysogenum in solid medium was able to grow at concentrations up to 1000 mg/L of 2,4-dichlorophenoxyacetic acid (2,4-D) with sucrose. Meanwhile, supplementation of the solid medium with glucose and lactose led to fungal growth at concentrations up to 500 mg/L of herbicide. Batch cultures of 2,4-D at 100 mg/L were developed under aerobic conditions with the addition of glucose, lactose and sucrose, showing sucrose as the best additional carbon source. The 2,4-D removal was quantified by liquid chromatography. The fungus was able to use 2,4-D as the sole carbon and energy source under 0%, 2% and 5.9% NaCl. The greatest 2,4-D degradation efficiency was found using alpha-ketoglutarate and ascorbic acid as co-substrates under 2% NaCl at pH 7. Penicillin production was evaluated in submerged cultures by bioassay, and higher amounts of beta-lactam antibiotic were produced when the herbicide was alone. Taking into account the ability of P. chrysogenum CLONA2 to degrade aromatic compounds, this strain could be an interesting tool for 2,4-D herbicide remediation in saline environments.

Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: implications for lipid-based stable isotope probing methods

Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [(13)C]2,4-D, [(13)C]glucose, or mixtures of both substrates alternatively labeled with (13)C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the (13)C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.

The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid (PAA) herbicide. Earthworms represent the dominant macrofauna and enhance microbial activities in many soils. Thus, the effect of the model earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) on microbial MCPA degradation was assessed in soil columns with agricultural soil. MCPA degradation was quicker in soil with earthworms than without earthworms. Quantitative PCR was inhibition-corrected per nucleic acid extract and indicated that copy numbers of tfdA-like and cadA genes (both encoding oxygenases initiating aerobic PAA degradation) in soil with earthworms were up to three and four times higher than without earthworms, respectively. tfdA-like and 16S rRNA gene transcript copy numbers in soil with earthworms were two and six times higher than without earthworms, respectively. Most probable numbers (MPNs) of MCPA degraders approximated 4 × 10(5) g(dw)(-1) in soil before incubation and in soil treated without earthworms, whereas MPNs of earthworm-treated soils were approximately 150 × higher. The aerobic capacity of soil to degrade MCPA was higher in earthworm-treated soils than in earthworm-untreated soils. Burrow walls and 0-5 cm depth bulk soil displayed higher capacities to degrade MCPA than did soil from 5-10 cm depth bulk soil, expression of tfdA-like genes in burrow walls was five times higher than in bulk soil and MCPA degraders were abundant in burrow walls (MPNs of 5 × 10(7) g(dw)(-1)). The collective data indicate that earthworms stimulate abundance and activity of MCPA degraders endogenous to soil by their burrowing activities and might thus be advantageous for enhancing PAA degradation in soil.

Evidence for Acquisition in Nature of a Chromosomal 2,4-Dichlorophenoxyacetic Acid/(alpha)-Ketoglutarate Dioxygenase Gene by Different Burkholderia spp

We characterized the gene required to initiate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the soil bacterium Burkholderia sp. strain TFD6, which hybridized to the tfdA gene of the canonical 2,4-D catabolic plasmid pJP4 under low-stringency conditions. Cleavage of the ether bond of 2,4-D by cell extracts of TFD6 proceeded by an (alpha)-ketoglutarate-dependent reaction, characteristic of TfdA (F. Fukumori and R. P. Hausinger, J. Bacteriol. 175:2083-2086, 1993). The TFD6 tfdA gene was identified in a recombinant plasmid which complemented a tfdA transposon mutant of TFD6 created by chromosomal insertion of Tn5. The plasmid also expressed TfdA activity in Escherichia coli DH5(alpha), as evidenced by enzyme assays with cell extracts. Sequence analysis of the tfdA gene and flanking regions from strain TFD6 showed 99.5% similarity to a tfdA gene cloned from the chromosome of a different Burkholderia species (strain RASC) isolated from a widely separated geographical area. This chromosomal gene has 77.2% sequence identity to tfdA from plasmid pJP4 (Y. Suwa, W. E. Holben, and L. J. Forney, abstr. Q-403, in Abstracts of the 94th General Meeting of the American Society for Microbiology 1994.). The tfdA homologs cloned from strains TFD6 and RASC are the first chromosomally encoded 2,4-D catabolic genes to be reported. The occurrence of highly similar tfdA genes in different bacterial species suggests that this chromosomal gene can be horizontally transferred.

Purification and Properties of Component B of 2,4,5-Trichlorophenoxyacetate Oxygenase from Pseudomonas cepacia AC1100

Pseudomonas cepacia AC1100 degrades 2,4,5-trichlorophenoxyacetate (2,4,5-T), an herbicide and chlorinated aromatic compound. Although some progress has been made in understanding 2,4,5-T degradation by AC1100 by molecular analysis, little is known about the biochemistry involved. Enzymatic activity converting 2,4,5-T to 2,4,5-trichlorophenol in the presence of NADH and O(inf2) was detected in cell extracts of AC1100. Phenyl agarose chromatography of the ammonium sulfate-fractionated cell extracts yielded no active single fractions, but the mixing of two fractions, named component A and component B, resulted in the recovery of enzyme activity. Component B was further purified to homogeneity by hydroxyapatite and DEAE chromatographies. Component B had a native molecular weight of 140,000, and it was composed of two 49-kDa (alpha)-subunits and two 24-kDa (beta)-subunits. Component B was red, and its spectrum in the visible region had maxima at 430 and 560 nm (shoulder), whereas upon reduction it had maxima at 420 (shoulder) and 530 nm. Each mole of (alpha)(beta) heterodimer contained 2.9 mol of iron and 2.1 mol of labile sulfide. These properties suggest strong similarities between component B and the terminal oxygenase components of the aromatic ring-hydroxylating dioxygenases. Component A was highly purified but not to homogeneity. The reconstituted 2,4,5-T oxygenase, consisting of components A and B, converted 2,4,5-T quantitatively into 2,4,5-trichlorophenol and glyoxylate with the coconsumption of NADH and O(inf2).

The biomass yielding process of xenobiotic degradation

Yields of activated sludge and an Arthrobacter sp. biomass on organic xenobiotic 2,4-dichlorophenoxyacetic acid (2,4-D) and on the intermediates of selected 2,4-D metabolism pathways were measured. Activated sludge yield on 2,4-D was lower by approximately 24-45% compared to the combined yields produced separately by the lower intermediates. For activated sludge, cell synthesis only consumed 33% of the electrons generated from 2,4-D oxidation, while the other 67% were used for energy. The high energy consumption, which was the primary cause of low activated sludge yield from 2,4-D degradation, occurred mainly in the catabolism of 2,4-D. The degrader sludge supplied this catabolism energy demand with the ATP contained in the biomass. As a result, the sludge's ATP contents suffered a deficit that was not fully remunerated after 2,4-D was degraded. Metabolism of the lower intermediates provided materials for further biomass growth and refilled part of the energy initially consumed.

Abundance of novel and diverse tfdA-like genes, encoding putative phenoxyalkanoic acid herbicide-degrading dioxygenases, in soil

Phenoxyalkanoic acid (PAA) herbicides are widely used in agriculture. Biotic degradation of such herbicides occurs in soils and is initiated by alpha-ketoglutarate- and Fe2+-dependent dioxygenases encoded by tfdA-like genes (i.e., tfdA and tfdAalpha). Novel primers and quantitative kinetic PCR (qPCR) assays were developed to analyze the diversity and abundance of tfdA-like genes in soil. Five primer sets targeting tfdA-like genes were designed and evaluated. Primer sets 3 to 5 specifically amplified tfdA-like genes from soil, and a total of 437 sequences were retrieved. Coverages of gene libraries were 62 to 100%, up to 122 genotypes were detected, and up to 389 genotypes were predicted to occur in the gene libraries as indicated by the richness estimator Chao1. Phylogenetic analysis of in silico-translated tfdA-like genes indicated that soil tfdA-like genes were related to those of group 2 and 3 Bradyrhizobium spp., Sphingomonas spp., and uncultured soil bacteria. Soil-derived tfdA-like genes were assigned to 11 clusters, 4 of which were composed of novel sequences from this study, indicating that soil harbors novel and diverse tfdA-like genes. Correlation analysis of 16S rRNA and tfdA-like gene similarity indicated that any two bacteria with D>20% of group 2 tfdA-like gene-derived protein sequences belong to different species. Thus, data indicate that the soil analyzed harbors at least 48 novel bacterial species containing group 2 tfdA-like genes. Novel qPCR assays were established to quantify such new tfdA-like genes. Copy numbers of tfdA-like genes were 1.0x10(6) to 65x10(6) per gram (dry weight) soil in four different soils, indicating that hitherto-unknown, diverse tfdA-like genes are abundant in soils.

Expression of tfdA genes in aquatic microbial communities during acclimation to 2,4-dichlorophenoxyacetic acid

The role of gene expression during acclimation of aquatic microbial communities was examined by relating transcription of tfdA to the degradation of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). The tfdA gene encodes for a 2,4-D/2-oxoglutarate dioxygenase that transforms 2,4-D to 2,4-dichlorophenol. Transcription of tfdA, the abundance of tfdA genes and 2,4-D degrading populations, and the rate of 2,4-D disappearance were followed in laboratory incubations of two pond water samples that were exposed to 0.11 mM 2,4-D. Both communities responded to 2,4-D exposure by induction of tfdA transcription but the dynamics of transcript abundance and the homology to the tfdA riboprobe suggested different populations of 2,4-D degraders in the two ponds. In one community, where tfdA transcripts were highly homologous to the tfdA gene of Ralstonia eutropha JMP134, transcription of tfdA was transient and dropped while 2,4-D degradation continued. In the other freshwater community, where tfdA genes with a lower similarity to the tfdA gene of strain JMP134 were transcribed, transcript levels remained high although 2,4-D degradation had ceased. Restriction fragment length polymorphism analysis of tfdA amplicons similarly demonstrated the presence of different tfdA loci in the two freshwater communities, and this difference in populations of tfdA genes probably explains the observed difference in dynamics of catabolic gene transcription.

Analysis of genes encoding the 2,4-dichlorophenoxyacetic acid-degrading enzyme from Sphingomonas agrestis 58-1

A 2,4-dichlorophenoxy acetic acid (2,4-D)-degrading bacterium, strain 58-1, was newly isolated from soil samples collected in the Fukuoka Prefecture, Japan, and grown on an enrichment culture medium containing 2,4-D as the sole carbon source. Phylogenic analysis identified strain 58-1 as Sphingomonas agrestis. In 2,4-D degraders, classes I, II, and III inherit the tfdA, cadA, and tfdAalpha genes, respectively, and the results from degenerate-PCR indicated that this strain belongs to the class II degraders. A clone that includes the cadA gene homolog of S. agrestis 58-1 was screened from a library by using the PCR amplified fragment as a DNA probe. The cloned fragment was sequenced and found to consist of 5043 nucleotides and include 3 open reading frames (orfs). The orf1, orf2, and orf3 genes encode polypeptides consisting of 412, 448, and 177 amino acids, respectively. The Orf2 product shares a high degree of sequence similarity (92%) with the large subunit of 2,4-D oxygenase from the Bradyrhizobium sp. strain HW13, which belongs to the class III 2,4-D degraders, while the orf3 product shared 63% sequence similarity with the small subunit of 2,4-D oxygenase from the strain HW13. The results of the functional expression analysis using various deletion mutants in Escherichia coli revealed that the expression of both orf2 and orf3 genes, but not orf1, is essential for the conversion of 2,4-D to 2,4-DCP. From these results, we conclude the first isolation of 2,4-D oxygenase genes from a class II 2,4-D degrader.

TaqMan probe-based real-time PCR assay for detection and discrimination of class I, II, and III tfdA genes in soils treated with phenoxy acid herbicides

Separate quantification of three classes of tfdA genes was performed using TaqMan quantitative real-time PCR for 13 different soils subsequent to mineralization of three phenoxy acids. Class III tfdA genes were found to be involved in mineralization more often than class I and II tfdA genes.

Bacterial diversity in soil enrichment cultures amended with 2 (2-methyl-4-chlorophenoxy) propionic acid (mecoprop)

Summary The tfdA gene encodes for an alpha-ketoglutarate-dependent dioxygenase enzyme which catalyses the first step of the degradation of phenoxyalkanoic acid herbicides such as 2 (2-methyl-4-chlorophenoxy) propionic acid (mecoprop). The bacterial diversity of soil enrichment cultures containing mecoprop was examined by Denaturing Gradient Gel Electrophoresis (DGGE) and clone libraries of both 16S rRNA genes and tfdA genes. The 16S rRNA gene sequences were diverse and clustered with either the Beta- or Gammaproteobacteria. The 16S rRNA gene sequence from a bacterial strain isolated from an enrichment culture, grown on R-mecoprop, which represented a dominant band in the DGGE profiles, had a high 16S rRNA sequence identity (100%) to Burkholderia glathei. This is the first report that B. glathei is implicated in mecoprop degradation. PCR amplification of the tfdA genes detected class III tfdA genes only, and no class I or class II tfdA sequences were detected. To understand the genes involved the degradation of specific mecoprop (R-) and (S-) enantiomers, oligonucleotide probes targeting the tfdA, rdpA, sdpA and cadA genes were hybridized to DNA extracted from enrichment cultures grown on either R-mecoprop or (R/S) racemic mecoprop. Strong hybridization signals were obtained with sdpA and tfdA probes using DNA extracted from cultures grown on racemic mecoprop. A strong hybridization signal was also obtained with the rdpA probe with DNA extracted from the cultures grown on R-mecoprop. This suggests the rdpA gene is involved in R-mecoprop degradation while tfdA, sdpA and cadA genes are involved in the degradation of both R- and S-mecoprop.

Tracing 2,4-D metabolism in Cupriavidus necator JMP134 with 13C-labelling technique and fatty acid profiling

The use of stable isotope probing of fatty acid methyl esters (FAME-SIP) is a powerful tool to study the microorganisms involved in xenobiotic biodegradation in soil. Nevertheless, it is important to determine how representative these molecules are of microorganisms both qualitatively and quantitatively. Using Cupriavidus necator JMP134 as a simple experimental model, we showed that the (13)C-labelling technique can be used both at a global (here defined as cellular, medium and CO(2)) and molecular level to study the metabolism of 2,4-Dichlorophenoxyacetic acid (2,4-D). Although isotopic fractionation among substrate, biomass and FAME were observed, this technique could be used when using a highly (13)C-labelled substrate. Global (13)C analyses gave similar results to those obtained with traditional (14)C-labelling methods. After 10 days of incubation 59% of ring-C was mineralized and about 30% remained in the liquid medium. A maximum of 11% was incorporated into the biomass after 3 days. The assimilation yield of chain-C into the biomass was about half that of ring-C, suggesting a preferential use of chain-C for energy acquisition. Molecular analysis of the lipid fraction evidenced that the incorporation of the labelled 2,4-D did not correspond to a bioaccumulation of pesticide residues but to the metabolism of the 2,4-D carbons for FAME synthesis. Provided the labelling is located on the benzenic ring, the assessment of (13)C-FAME is a robust method to quantify the incorporation of (13)C into the whole microbial biomass. However, the variability of the (13)C incorporation among FAME due to physiological processes has to be considered in complex biological systems. The coupling of bulk and molecular studies with a simple model as C. necator JMP134 is a good approach for testing FAME-SIP.

Molecular and population analyses of a recombination event in the catabolic plasmid pJP4

Cupriavidus necator JMP134(pJP4) harbors a catabolic plasmid, pJP4, which confers the ability to grow on chloroaromatic compounds. Repeated growth on 3-chlorobenzoate (3-CB) results in selection of a recombinant strain, which degrades 3-CB better but no longer grows on 2,4-dichlorophenoxyacetate (2,4-D). We have previously proposed that this phenotype is due to a double homologous recombination event between inverted repeats of the multicopies of this plasmid within the cell. One recombinant form of this plasmid (pJP4-F3) explains this phenotype, since it harbors two copies of the chlorocatechol degradation tfd gene clusters, which are essential to grow on 3-CB, but has lost the tfdA gene, encoding the first step in degradation of 2,4-D. The other recombinant plasmid (pJP4-FM) should harbor two copies of the tfdA gene but no copies of the tfd gene clusters. A molecular analysis using a multiplex PCR approach to distinguish the wild-type plasmid pJP4 from its two recombinant forms, was carried out. Expected PCR products confirming this recombination model were found and sequenced. Few recombinant plasmid forms in cultures grown in several carbon sources were detected. Kinetic studies indicated that cells containing the recombinant plasmid pJP4-FM were not selectable by sole carbon source growth pressure, whereas those cells harboring recombinant plasmid pJP4-F3 were selected upon growth on 3-CB. After 12 days of repeated growth on 3-CB, the complete plasmid population in C. necator JMP134 apparently corresponds to this form. However, wild-type plasmid forms could be recovered after growing this culture on 2,4-D, indicating that different plasmid forms can be found in C. necator JMP134 at the population level.