Thiocarbamate herbicide-inducible nonheme haloperoxidase of Rhodococcus erythropolis NI86/21

Functional analysis, diversity, and distribution of carbendazim hydrolases MheI and CbmA, responsible for the initial step in carbendazim degradation

Strains Rhodococcus qingshengii djl-6 and Rhodococcus jialingiae djl-6-2 both harbor the typical carbendazim degradation pathway with the hydrolysis of carbendazim to 2-aminobenzimidazole (2-AB) as the initial step. However, the enzymes involved in this process are still unknown. In this study, the previous reported carbendazim hydrolase MheI was found in strain djl-6, but not in strain djl-6-2, then another carbendazim hydrolase CbmA was obtained by a four-step purification strategy from strain djl-6-2. CbmA was classified as a member of the amidase signature superfamily with conserved catalytic site residues Ser157, Ser181, and Lys82, while MheI was classified as a member of the Abhydrolase superfamily with conserved catalytic site residues Ser77 and His224. The catalytic efficiency (k_cat /K_m ) of MheI (24.0-27.9 μM^-1 min^-1 ) was 200 times more than that of CbmA (0.032-0.21 μM^-1 min^-1 ). The mheI gene (plasmid encoded) was highly conserved (> 99% identity) in the strains from different bacterial genera and its plasmid encoded flanked by mobile genetic elements. The cmbA gene was highly conserved only in strains of the genus Rhodococcus and it was chromosomally encoded. Overall, the function, diversity, and distribution of carbendazim hydrolases MheI and CbmA will provide insights into the microbial degradation of carbendazim.

Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes

Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.

Biogenic Iodine and Iodine-Containing Metabolites

This review is intended as a comprehensive survey of iodinated metabolites possessing carbon–iodine covalent bond, which have been obtained from living organisms. Generally thought to be minor components produced by many different organisms these interesting compounds now number more than 110. Many from isolated and identified iodine-containing metabolites showed high biological activities. Recent research, especially in the marine area, indicates this number will increase in the future. Sources of iodinated metabolites include microorganisms, algae, marine invertebrates, and some animals. Their origin and possible biological significance have also been discussed.

Microbial enzymes involved in lactone compound metabolism and their biotechnological applications

Lactone compounds are widely distributed in nature and play important roles in organisms. These compounds are synthesized and metabolized enzymatically in vivo; however, detailed investigation of these enzymes lags behind that of other common enzymes. In this paper, recent work on the enzymes involved in the metabolism of lactone compounds will be reviewed. In particular, fundamental and application studies on lactonases and Baeyer-Villiger monooxgenases of microbial origin are described.

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

Cloning and expression of a novel esterase gene cpoA from Burkholderia cepacia

AIMS

To screen and clone a novel enzyme with specific activity for the resolution of (R)-beta-acetylmercaptoisobutyrate (RAM) from (R,S)-beta-acetylmercaptoisobutyrate [(R,S)-ester].

METHODS AND RESULTS

A micro-organism that produces a novel esterase was isolated and identified as the bacterium Burkholderia cepacia by using the analysis of cellular fatty acids, Biolog automated microbial identification/characterization system, and 16S rRNA gene sequence analysis. A novel esterase gene was cloned from the chromosomal DNA of B. cepacia and was designated as cpoA. The cpoA encodes a polypeptide of 273 amino acids which shows a strong sequence homology with many bacterial nonhaeme chloroperoxidases. In addition, a typical serine-hydrolase motif, Gly-X-Ser-X-Gly, and the highly conserved catalytic triad, Ser95, Asp224, and His253, were identified in the deduced amino acid sequence of cpoA by multiple sequence alignment.

CONCLUSION

The cpoA cloned from B. cepacia encodes a novel esterase which is highly related to the nonhaeme chloroperoxidases.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report that describes the isolation and cloning of a serine esterase gene from B. cepacia, which is useful in the chiral resolution of (R,S)-ester. The cloned gene will allow additional research on the bifunctionality of the enzyme with esterase and chloroperoxidase activity at the structural and functional levels.

The thiocarbamate-inducible Rhodococcus enzyme ThcF as a member of the family of alpha/beta hydrolases with haloperoxidative side activity

Purified thiocarbamate-inducible ThcF of Rhodococcus erythropolis NI86/21, overexpressed in Escherichia coli, displayed several characteristics of the HASH family of enzymes that groups prokaryotic proteins of the alpha/beta hydrolase superfamily possessing serine-dependent hydrolase and/or haloperoxidase activity. Kinetic analysis of bromination and ester hydrolysis revealed a low affinity of ThcF for model substrates. Sulfoxidation of thiocarbamates was demonstrated but probably represents a side activity due to peroxoacid generation by the enzyme. The thcF-linked thcG gene, encoding a LAL-type regulator, triggers expression of thcF in Rhodococcus. The tandem gene organization thcG-thcF is conserved in the thiocarbamate-degrading strain Rhodococcus sp. B30. It is proposed that HASH enzymes may be involved in the metabolism of plant-derived compounds.

Role of Acinetobacter calcoaceticus 3,4-dihydrocoumarin hydrolase in oxidative stress defence against peroxoacids

The physiological role of a bifunctional enzyme, 3,4-dihydrocoumarin hydrolase (DCH), which is capable of both hydrolysis of ester bonds and organic acid-assisted bromination of organic compounds, was investigated. Purified DCH from Acinetobacter calcoaceticus F46 catalysed dose- and time-dependent degradation of peracetic acid. The gene (dch) was cloned from the chromosomal DNA of the bacterium. The dch ORF was 831 bp long, corresponding to a protein of 272 amino acid residues, and the deduced amino acid sequence showed high similarity to those of bacterial serine esterases and perhydrolases. The dch gene was disrupted by homologous recombination on the A. calcoaceticus genome. The dch disruptant strain was more sensitive to growth inhibition by peracetic acid than the parent strain. On the other hand, the recombinant Escherichia coli cells expressing dch were more resistant to peracetic acid. A putative catalase gene was found immediately downstream of dch, and Northern blot hybridization analysis revealed that they are transcribed as part of a polycistronic mRNA. These results suggested that in vivo DCH detoxifies peroxoacids in conjunction with the catalase, i.e. peroxoacids are first hydrolysed to the corresponding acids and hydrogen peroxide by DCH, and then the resulting hydrogen peroxide is degraded by the catalase.

Gene cloning and characterization of multiple alkane hydroxylase systems in Rhodococcus strains Q15 and NRRL B-16531

The alkane hydroxylase systems of two Rhodococcus strains (NRRL B-16531 and Q15, isolated from different geographical locations) were characterized. Both organisms contained at least four alkane monooxygenase gene homologs (alkB1, alkB2, alkB3, and alkB4). In both strains, the alkB1 and alkB2 homologs were part of alk gene clusters, each encoding two rubredoxins (rubA1 and rubA2; rubA3 and rubA4), a putative TetR transcriptional regulatory protein (alkU1; alkU2), and, in the alkB1 cluster, a rubredoxin reductase (rubB). The alkB3 and alkB4 homologs were found as separate genes which were not part of alk gene clusters. Functional heterologous expression of some of the rhodococcal alk genes (alkB2, rubA2, and rubA4 [NRRL B-16531]; alkB2 and rubB [Q15]) was achieved in Escherichia coli and Pseudomonas expression systems. Pseudomonas recombinants containing rhodococcal alkB2 were able to mineralize and grow on C(12) to C(16) n-alkanes. All rhodococcal alkane monooxygenases possessed the highly conserved eight-histidine motif, including two apparent alkane monooxygenase signature motifs (LQRH[S/A]DHH and NYXEHYG[L/M]), and the six hydrophobic membrane-spanning regions found in all alkane monooxygenases related to the Pseudomonas putida GPo1 alkane monooxygenase. The presence of multiple alkane hydroxylases in the two rhodococcal strains is reminiscent of other multiple-degradative-enzyme systems reported in Rhodococcus.

Reaction mechanism of the Co2+-activated multifunctional bromoperoxidase-esterase from Pseudomonas putida IF-3

The reaction mechanism of the Co2+-activated bromoperoxidase-esterase of Pseudomonas putida IF-3 was studied. Site-directed mutagenesis suggested that the serine residue of the catalytic triad conserved in serine hydrolases participates in the bromination and ester hydrolysis reactions. The enzyme released a trace amount of free peracetic acid depending on the concentration of H2O2, which had been considered the intermediate in the reaction of nonmetal haloperoxidases to oxidize halide ions to hypohalous acid. However, the formation of free peracetic acid could not explain the enzyme activation effect by Co2+ ions which completely depleted the free peracetic acid. In addition, the kcat value of the enzymatic bromination was 900-fold higher than the rate constant of free peracetic acid-mediated bromination. Those results strongly suggested that the peracetic acid-like intermediate formed at the catalytic site is the true intermediate and that the formation of free peracetic acid is only a minor reaction involving the enzyme. We propose the possible reaction mechanism of this multifunctional enzyme based on these findings.

Lactone-ring-cleaving enzymes of microorganisms: their diversity and applications

Microbial lactonohydrolases (lactone-ring-cleaving enzymes) with unique characteristics were found. The Fusarium oxysporum enzyme catalyzes the reversible and stereospecific hydrolysis of aldonate lactones and D-pantolactone (D-PL), and is useful for the optical resolution of racemic PL. The Agrobacterium tumefaciens enzyme hydrolyzes several aromatic lactones, and catalyzes the stereospecific hydrolysis of PL like the Fusarium enzyme, but its selectivity is opposite. The Acinetobacter calcoaceticus enzyme catalyzing the specific hydrolysis of dihydrocoumarin belongs to serine-enzyme family, and is useful for enantioselective hydrolysis of methyl DL-beta-acetylthioisobutyrate and regioselective hydrolysis of methyl cetraxate. This enzyme also catalyzes the bromination of monochlorodimedon when incubated with H(2)O(2) and dihydrocoumarin.

Cloning and biochemical characterization of Co(2+)-activated bromoperoxidase-esterase (perhydrolase) from Pseudomonas putida IF-3 strain

The gene encoding Co(2+)-activated bromoperoxidase (BPO)-esterase (EST), catalyzing the organic acid-assisted bromination of some organic compounds with H2O2 and Br(-) and quite specific hydrolysis of (R)-acetylthioisobutyric acid methyl ester, was cloned from the chromosomal DNA of the Pseudomonas putida IF-3 strain. The bpo-est gene comprises 831 bp and encoded a protein of 30181 Da. The enzyme was expressed at a high level in Escherichia coli and purified to homogeneity by ammonium sulfate fractionation and two-step column chromatographies. The recombinant enzyme required acetic acid, propionic acid, isobutyric acid or n-butyric acid in addition to H2O2 and Br(-) for the brominating reaction and was activated by Co(2+) ions. It catalyzed the bromination of styrene and indene to give the corresponding racemic bromohydrin. Although the enzyme did not release free peracetic acid in the reaction mixture, chemical reaction with peracetic acid could well explain such enzymatic reactions via a peracetic acid intermediate. The results indicated that the enzyme was a novel Co(2+)-activated organic acid-dependent BPO (perhydrolase)-EST, belonging to the non-metal haloperoxidase-hydrolase family.

Nicotinoprotein (NADH-containing) alcohol dehydrogenase from Rhodococcus erythropolis DSM 1069: an efficient catalyst for coenzyme-independent oxidation of a broad spectrum of alcohols and the interconversion of alcohols and aldehydes

Extracts from benzyl-alcohol-grown Rhodococcus erythropolis DSM 1069 showed NAD(P)-independent, N,N-dimethyl-4-nitrosoaniline (NDMA)-dependent alcohol dehydrogenase activity. The enzyme exhibiting this activity was purified to homogeneity and characterized. It appears to be a typical nicotinoprotein as it contains tightly bound NADH acting as cofactor instead of coenzyme. Other characteristics indicate that it is highly similar to the known nicotinoprotein alcohol dehydrogenase (np-ADH) from Amycolatopsis methanolica: it is a homotetramer of 150 kDa; N-terminal amino acid sequencing (22 residues) showed that 77% of these amino acids are identical in the two enzymes; it has optimal activity at pH 7.0; it lacks NAD(P)H-dependent aldehyde reductase activity; it catalyses the oxidation of a broad range of (preferably) primary and secondary alcohols, either aliphatic or aromatic, and formaldehyde, with the concomitant reduction of the artificial electron acceptor NDMA. NDMA could be replaced by an aldehyde, but not formaldehyde, the substrate specificity of the enzyme for the aldehydes reflecting that for the corresponding alcohols. The latter also applied to the low aldehyde dismutase activity displayed by the enzyme. From this, together with the results of the induction studies, it is concluded that np-ADH functions as the main alcohol-oxidizing enzyme in the dissimilation of many, but not all, alcohols by R. erythropolis and may also catalyse coenzyme-independent interconversion of alcohols and aldehydes under certain circumstances. It is anticipated that the enzyme may be of even wider significance since structural data indicate that np-ADH is also present in other (nocardioform) actinomycetes.

3,4-Dihydrocoumarin hydrolase with haloperoxidase activity from Acinetobacter calcoaceticus F46

A novel lactonohydrolase, an enzyme that catalyzes the hydrolysis of 3,4-dihydrocoumarin, was purified 375-fold to apparent homogeneity, with a 22.7% overall recovery, from Acinetobacter calcoaceticus F46, which was isolated as a fluorene-assimilating micro-organism. The molecular mass of the native enzyme, as estimated by high-performance gel-permeation chromatography, is 56 kDa, and the subunit molecular mass is 30 kDa. The enzyme specifically hydrolyzes 3,4-dihydrocoumarin, and the Km and Vmax for 3,4-dihydrocoumarin are 0.806 mM and 4760 U.mg-1, respectively. The N-terminal and internal amino acid sequences of the enzyme show high similarity to those of bacterial non-heme haloperoxidases. The enzyme exhibits brominating activity with monochlorodimedon in the presence of H2O2 and 3, 4-dihydrocoumarin or an organic acid, such as acetate and n-butyrate.

Degradation of pesticides by actinomycetes

Actinomycetes have considerable potential for the biotransformation and biodegradation of pesticides. Members of this group of Gram-positive bacteria have been found to degrade pesticides with widely different chemical structures, including organochlorines, s-triazines, triazinones, carbamates, organophosphates, organophosphonates, acetanilides, and sulfonylureas. A limited number of these xenobiotic pesticides can be mineralized by single isolates, but often consortia of bacteria are required for complete degradation. Cometabolism of pesticides is frequently observed within this group of bacteria. When compared with pesticide degradation by Gram-negative bacteria, much less information about molecular mechanisms involved in biotransformations of pesticides by actinomycetes is available. Progress in this area has been seriously hampered by a lack of suitable molecular genetic tools for most representatives of this major group of soil bacteria. Overcoming this constraint would enable a better exploitation of the biodegradation and biotransformation abilities of actinomycetes for applications such as bioremediation and construction of transgenic herbicide-resistant crops.