Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101

Biochemical characterization and structure prediction of the Cerrado soil CRB2(1) metagenomic dioxygenase

Dioxygenases are enzymes involved in the conversion of polyconic aromatic hydroxycarbons (PAHs), attracting significant biotechnological interest for the conversion of recalcitrant organic compounds. Furthermore, few studies show that dioxygenases can take on the function of resistance genes in clones. This enzymatic versatility opens up new opportunities for elucidating the mechanisms of microbial resistance, as well as its biotechnological application. In this work, a Cerrado soil dioxygenase named CRB2(1) was biochemically characterized. The enzyme was shown to have optimal activity at pH 7; a temperature of 30 °C; and using iron ions as a cofactor for substrate cleavage. The kinetic catalytic parameters of CRB2(1) were Vmax = 0.02281 µM/min and KM = 97.6. Its predicted three-dimensional structure obtained using the Modeller software v9.22 based on the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) (PDB ID 3BU7, resolution 2.80 Å, residues 17-374) revealed substrate binding to the cupin domain, where the active site is located. The analyzed substrates interact directly with the iron ion, coordinated by three histidine residues. Changing the iron ion charge modifies the binding between the active site and the substrates. Currently, there is a demand for enzymes that have biotechnological activities of interest. Metagenomics allows analyzing the biotechnological potential of several organisms at the same time, based on sequence and functional activity analyses.

Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review

Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.

Complete Genome Sequence of Rhodococcus erythropolis JCM 2895, an Antibiotic Protein-Producing Strain

The complete genome sequence of Rhodococcus erythropolis JCM 2895, an antibiotic protein-producing strain, was determined. It consists of a 6,455,263-bp chromosome, one linear plasmid (pR09L01 [227,989 bp]), and three circular plasmids (pR09C01 [79,600 bp], pREC01 [5,420 bp], and pREC02 [5,444 bp]).

A Review of Soil Contaminated with Dioxins and Biodegradation Technologies: Current Status and Future Prospects

This article provides a comprehensive assessment of dioxins contaminating the soil and evaluates the bioremediation technology currently being widely used, and also offers recommendations for future prospects. Soil pollution containing dioxins is extremely toxic and hazardous to human health and the environment. Dioxin concentrations in soils around the world are caused by a variety of sources and outcomes, but the main sources are from the consequences of war and human activities. Bioremediation technology (bioaugmentation, biostimulation, and phytoremediation) is considered an optimal and environmentally friendly technology, with the goal of applying native microbial communities and using plant species with a high biomass to treat contaminated dioxins in soil. The powerful bioremediation system is the growth of microorganisms that contribute to the increased mutualistic and competitive relationships between different strains of microorganisms. Although biological treatment technology can thoroughly treat contaminated dioxins in soil with high efficiency, the amount of gas generated and Cl radicals dispersed after the treatment process remains high. Further research on the subject is required to provide stricter control over the outputs noted in this study.

Unraveling metabolic flexibility of rhodococci in PCB transformation

Even though the genetic attributes suggest presence of multiple degradation pathways, most of rhodococci are known to transform PCBs only via regular biphenyl (bph) pathway. Using GC-MS analysis, we monitored products formed during transformation of 2,4,4'-trichlorobiphenyl (PCB-28), 2,2',5,5'-tetrachlorobiphenyl (PCB-52) and 2,4,3'-trichlorobiphenyl (PCB-25) by previously characterized PCB-degrading rhodococci Z6, T6, R2, and Z57, with the aim to explore their metabolic pleiotropy in PCB transformations. A striking number of different transformation products (TPs) carrying a phenyl ring as a substituent, both those generated as a part of the bph pathway and an array of unexpected TPs, implied a curious transformation ability. We hypothesized that studied rhodococcal isolates, besides the regular one, use at least two alternative pathways for PCB transformation, including the pathway leading to acetophenone formation (via 3,4 (4,5) dioxygenase attack on the molecule), and a third sideway pathway that includes stepwise oxidative decarboxylation of the aliphatic side chain of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate. Structure of the identified chlorinated benzoic acids and acetophenones allowed us to hypothesize that the first two pathways were the outcome of a ring-hydroxylating dioxygenase with the ability to attack both the 2,3 (5,6) and the 3,4 (4,5) positions of the biphenyl ring as well as dechlorination activity at both, -ortho and -para positions. We propose that several TPs produced by the bph pathway could have caused the triggering of the third sideway pathway. In conclusion, this study proposed ability of rhodococci to use different strategies in PCB transformation, which allows them to circumvent potential negative aspect of TPs on the overall transformation pathway.

Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.

Comparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits

The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.

Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence

The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.

Genes and novel sRNAs involved in PAHs degradation in marine bacteria Rhodococcus sp. P14 revealed by the genome and transcriptome analysis

Rhodococcus sp. P14 is able to degrade various polycyclic aromatic hydrocarbons (PAHs). In this study, 6 ring-hydroxylating dioxygenases and 24 monooxygenases genes related to PAHs degradation were identified in its genome. Moreover, various genes, like serine hydrolase, hydratase, alcohol dehydrogenase, protocatechuate 3,4-dioxygenase, β-ketoadipate CoA transferase and β-Ketoadipyl CoA thiolase, which were supposed to be involved in PAHs degradation were also identified. Based on the genome analysis, the proposed PAHs degradation pathway was constructed in P14 strain, which showed that PAHs was degraded into the acetyl CoA and succinyl CoA, then mineralized to CO₂ via the TCA cycle. Furthermore, several genes, including cytochrome P450 (RS16725; RS16695; RS12220), catalase (RS15825), dehydrogenase (RS15755; RS18420) and hydrolase (RS16460; RS24665), showed increased expression level during PAHs degradation according to the transcriptome data. In addition, 12 novel sRNAs which were supposed to have the regulation function in PAHs degradation were identified. This study gives us the outlook of PAHs degradation pathway in Rhodococcus sp. P14. Moreover, it first demonstrates that sRNAs may harbor the regulation function in PAHs degradation.

Superior performance and mechanism of chlorobenzene degradation by a novel bacterium

A newly isolated strain was identified as Ochrobactrum sp. by 16S rRNA sequence analysis and named as ZJUTCB-1.

Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations

Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups.

Cometabolic Degradation of Dibenzofuran and Dibenzothiophene by a Naphthalene-Degrading Comamonas sp. JB

Comamonas sp. JB was used to investigate the cometabolic degradation of dibenzofuran (DBF) and dibenzothiophene (DBT) with naphthalene as the primary substrate. Dehydrogenase and ATPase activity of the growing system with the presence of DBF and DBT were decreased when compared to only naphthalene in the growing system, indicating that the presence of DBF and DBT inhibited the metabolic activity of strain JB. The pathways and enzymes involved in the cometabolic degradation were tested. Examination of metabolites elucidated that strain JB cometabolically degraded DBF to 1,2-dihydroxydibenzofuran, subsequently to 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid, and finally to catechol. Meanwhile, strain JB cometabolically degraded DBT to 1,2-dihydroxydibenzothiophene and subsequently to the ring cleavage product. A series of naphthalene-degrading enzymes including naphthalene dioxygenase, 1,2-dihydroxynaphthalene dioxygenase, salicylaldehyde dehydrogenase, salicylate hydroxylase, and catechol 2,3-oxygenase have been detected, confirming that naphthalene was the real inducer of expression the degradation enzymes and metabolic pathways were controlled by naphthalene-degrading enzymes.

Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation

The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.

Complete Genome Sequence of Rhodococcus sp. Strain IcdP1 Shows Diverse Catabolic Potential

The complete genome sequence of Rhodococcus sp. strain IcdP1 is presented here. This organism was shown to degrade a broad range of high-molecular-weight polycyclic aromatic hydrocarbons and organochlorine pesticides. The sequence data can be used to predict genes for xenobiotic biodegradation and metabolism.

Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose

In the present study, by applying comparative quantitative proteomics, we investigated the metabolic adaptation of Arthrobacter phenanthrenivorans Sphe3 when using phenanthrene, phthalate, glucose or glucose plus phenanthrene as sole carbon and energy sources. More than a third of the total Sphe3 proteins, with function prediction within the genome, were identified with confidence. Proteomic analysis data and annotated genomic information coincide, allowing us to clarify the phenanthrene catabolic pathway. We confirmed the implication of several proteins in aromatic substrate degradation by identifying those mediating the initial ring-hydroxylation and ring cleavage of phenanthrene to phthalate, phthalate degradation, as well as ortho- and meta-protocatechuate catabolism. Repression of catabolic genes by glucose was observed by both proteomic and transcriptional analyses. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in substrate and amino acid metabolism, stress response, detoxification and membrane and cell wall metabolism. Uptake and transport associated proteins differ in the substrates used, indicating the use of different uptake mechanisms for transport of each compound in the Sphe3 cells. Our results also suggest the activation of a glyoxylate shunt in the presence of aromatic compounds, based on the up-regulation of the key enzymes of this pathway.

BIOLOGICAL SIGNIFICANCE

A. phenanthrenivorans Sphe3, isolated from a creosote contaminated soil in Greece, can grow on phenanthrene as the sole source of carbon and energy. To explore the phenanthrene catabolic pathway by determining the key proteins involved in this pathway, as well as the global changes in proteins due to the adaptive response of Sphe3 cells grown on different substrates, we applied a gel-free quantitative proteomic analysis using nanoLC-MS/MS. To our knowledge this is the first study of comparative global proteomic changes occurring in the Sphe3 cells under exposure in different nutritional environments. The extended proteomic changes observed in Sphe3 grown on different substrates provide an insight in the complex interactions occurring in the presence of aromatic compounds and could serve as a basis for further investigations intended to elucidate the general regulatory mechanism by which Sphe3 adapts to such xenobiotic environments. This may light the way for more efficient engineering of bacteria towards more effective bioremediation applications.

An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases

Bacterial aromatic ring-hydroxylating oxygenases (RHOs) are multicomponent enzyme systems which have potential utility in bioremediation of aromatic compounds in the environment. To cope with the enormous diversity of aromatic compounds in the environment, this enzyme family has evolved remarkably exhibiting broad substrate specificity. RHOs are multicomponent enzymes comprising of a homo- or hetero-multimeric terminal oxygenase and one or more electron transport (ET) protein(s). The present study attempts in depicting the evolutionary scenarios that might have occurred during the evolution of RHOs, by analyzing a set of available sequences including those obtained from complete genomes. A modified classification scheme identifying four new RHO types has been suggested on the basis of their evolutionary and functional behaviours, in relation to structural configuration of substrates and preferred oxygenation site(s). The present scheme emphasizes on the fact that the phylogenetic affiliation of RHOs is distributed among four distinct 'Similarity classes', independent of the constituent ET components. Similar combination of RHO components that was previously considered to be equivalent and classified together [Kweon et al., BMC Biochemistry 9, 11 (2008)] were found here in distinct similarity classes indicating the role of substrate-binding terminal oxygenase in guiding the evolution of RHOs irrespective of the nature of constituent ET components. Finally, a model for evolution of the multicomponent RHO enzyme system has been proposed, beginning from genesis of the terminal oxygenase components followed by recruitment of constituent ET components, finally evolving into various 'extant' RHO types.

Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter

Genetic and functional diversity of Citrobacter spp. for their abilities to degrade aromatic compounds was evaluated to develop mixed cultures or a consortium for bioremediation technology. Thirty Citrobacter strains isolated from various effluent treatment plants were found to degrade a range of aromatic compounds: phenol, benzoate, hydroxy benzoic acid and biotransform mono-chlorophenols and di-chlorophenol within 24 to 48 h of incubation at 30 °C. Sequence similarity and phylogeny of the ARHD gene transcripts (730 nucleotides) depicted their diversity within 9 Citrobacter strains: HPC255, HPC369, HPC560, HPC570, HPC784, HPC1196, HPC1216, HPC1276 and HPC1299. Here, the degree of associations varied up to 84% with (i) ARHD α-sub unit (SU), (ii) LSU of Phenylpropionate dioxygenase (PDO), (iii) Phenol hydroxylase α-SU, (iv) Benzoate 1,2-dioxygenase, α-SU, (v) Naphthalene dioxygenase LSU, etc. This study has provided basic information, which can be used to develop a consortium of bacteria with mutually beneficial characteristics.

Bacteria-mediated PAH degradation in soil and sediment

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the natural environment and easily accumulate in soil and sediment due to their low solubility and high hydrophobicity, rendering them less available for biological degradation. However, microbial degradation is a promising mechanism which is responsible for the ecological recovery of PAH-contaminated soil and sediment for removing these recalcitrant compounds compared with chemical degradation of PAHs. The goal of this review is to provide an outline of the current knowledge of biodegradation of PAHs in related aspects. Over 102 publications related to PAH biodegradation in soil and sediment are compiled, discussed, and analyzed. This review aims to discuss PAH degradation under various redox potential conditions, the factors affecting the biodegradation rates, degrading bacteria, the relevant genes in molecular monitoring methods, and some recent-year bioremediation field studies. The comprehensive understanding of the bioremediation kinetics and molecular means will be helpful for optimizing and monitoring the process, and overcoming its limitations in practical projects.

New vector system for random, single-step integration of multiple copies of DNA into the Rhodococcus genome

We designed a new vector system for creating a random mutant library with multiple integrations of DNA fragments into the Rhodococcus genome in a single step. For this, we cotransformed two vectors into Rhodococcus by electroporation: pTip-istAB-sacB regulates the expression of the transposase (IstA) and its helper protein (IstB) under the influence of a thiostrepton-inducible promoter, and pRTSK-sacB provides the transposable-marker DNA. Both are multicopy vectors that are stable in the host cells; transposition of the transposable-marker DNA occurs only after the induction of IstA/IstB expression. With the addition of thiostrepton, all cultured cells harboring the two vectors, irrespective of the volume, can be mutated by random insertion of the transposable-marker DNA into their genome. Among the generated mutants examined, 30% showed multiple (two to five) insertion copies. The multiple integrated DNA copies were stable in the genome for more than 80 generations of serial growth without the addition of any selective antibiotics. This system can also be used for integrating various copy numbers of stably maintained protein expression cassettes in the host cell genome to modulate the expression level of biologically active recombinant proteins. We successfully applied this system to integrate multiple copies of expression cassettes for proline iminopeptidase and vitamin D(3) hydroxylase into the Rhodococcus genome and verified that the clones containing double or multiple copies of the integrated cassettes produced higher levels and showed higher enzymatic activities of the target protein than clones with only a single copy of integration.

Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations

The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest soil. The bacterial community structure of soil suspensions amended with 1 microg/g of either DF or DD was analyzed by 16S rRNA and functional gene sequencing. To analyze the functional genes in the communities, we targeted a gene sequence that functions as the binding site of Rieske iron sulfur center common to ring-hydroxylating dioxygenases (RHDs) for monocyclic, bicyclic, and tricyclic aromatic compounds. The gene fragments were polymerase chain reaction-amplified from DNAs extracted from soil suspensions spiked with either DF or DD, cloned, and sequenced (70 clones). Bacterial community analysis based on 16S rRNA genes revealed that specific 16S rRNA gene sequences, in particular, phylotypes within alpha-Proteobacteria, increased in the soil suspension amended with DF or DD. RHD gene-based functional community analysis showed that, in addition to two groups of RHD genes that were also detected in unamended soil suspensions, another two groups of RHD genes, each of which is specific to DF- and DD-amended soil, respectively, emerged to a great extent. The DD-specific genotype is phylogenetically distant from any known RHDs. These results strongly suggest that soil microbial community potentially harbors a wide array of organisms having diverse RHDs including those previously unknown, and that they could quickly respond to an impact of contamination of hazardous chemicals by changing the microbial community and gene diversity.

Biodegradation potential of the genus Rhodococcus

A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.

Two angular dioxygenases contribute to the metabolic versatility of dibenzofuran-degrading Rhodococcus sp. strain HA01

Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% +/- 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.