Regulation of phenolic catabolism in Rhizobium leguminosarum biovar trifolii

Benzoate metabolism intermediate benzoyl coenzyme A affects gentisate pathway regulation in Comamonas testosteroni

A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in Azoarcus evansii (R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the Comamonas testosteroni strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (box genes) and gentisate (gen genes) pathways were identified. Genetic disruption revealed that the gen genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated gen gene regulation in the CNB-1 strain. The PgenA promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present. In vivo studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate PgenA promoter, while transcription of genA was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail.

A product analog bound form of 3-oxoadipate-enol-lactonase (PcaD) reveals a multifunctional role for the divergent cap domain

Lactones are a class of structurally diverse molecules that serve essential roles in biological processes ranging from quorum sensing to the aerobic catabolism of aromatic compounds. Not surprisingly, enzymes involved in the bioprocessing of lactones are often targeted for protein engineering studies with the potential, for example, of optimized bioremediation of aromatic pollutants. The enol-lactone hydrolase (ELH) represents one such class of targeted enzymes and catalyzes the conversion of 3-oxoadipate-enol-lactone into the linear β-ketoadipate. To define the structural details that govern ELH catalysis and assess the impact of divergent features predicted by sequence analysis, we report the first structural characterization of an ELH (PcaD) from Burkholderia xenovorans LB400 in complex with the product analog levulinic acid. The overall dimeric structure of PcaD reveals an α-helical cap domain positioned atop a core α/β-hydrolase domain. Despite the localization of the conserved catalytic triad to the core domain, levulinic acid is bound largely within the region of the active site defined by the cap domain, suggesting a key role for this divergent substructure in mediating product release. Furthermore, the architecture of the cap domain results in an unusually deep active-site pocket with topological features to restrict binding to small or kinked substrates. The evolutionary basis for this substrate selectivity is discussed with respect to the homologous dienelactone hydrolase. Overall, the PcaD costructure provides a detailed insight into the intimate role of the cap domain in influencing all aspects of substrate binding, turnover, and product release.

Application of p-Toluidine in Chromogenic Detection of Catechol and Protocatechuate, Diphenolic Intermediates in Catabolism of Aromatic Compounds

In the presence of p-toluidine and iron, protocatechuate and catechols yield color. Inclusion of p-toluidine in media facilitates the screening of microbial strains for alterations affecting aromatic catabolism. Such strains include mutants affected in the expression of oxygenases and Escherichia coli colonies carrying cloned or subcloned aromatic catabolic genes which encode enzymes giving rise to protocatechuate or catechol. The diphenolic detection system can also be applied to the creation of vectors relying on insertion of cloned DNA into one of the latter marker genes.

Characterization of phenol degradation by Rhizobium sp. CCNWTB 701 isolated from Astragalus chrysopteru in mining tailing region

To screen high strength phenol degrading bacteria, we selected 108 rhizobial strains isolated from nodules of eight wild legumes species in the mining tailing region of Shaanxi province, northwest of China, and cultivated them in a basal salt (BS) medium supplemented with different phenol concentrations as a sole carbon source. The results showed that some of the strains could use phenol as sole carbon source. In order to study the characteristics of phenol degradation, the strain CCNWTB701 isolated from Astragalus chrysopteru was used as well, due to the fact that it was very efficient in phenol degradation. The phenol degradation was around 99.5 and 78.3%, with an initial concentration of 900 and 1000 mg/l phenol in 62 and 66 h, respectively. Kinetic studies indicated that the strain had a high KS (743.1 microM) and an extremely high KSI (10,469 microM) in Haldane's model. The phylogenetic analysis based on 16S rRNA gene sequences showed that CCNWTB701 belonged to the Rhizobium genus, and it was closely related to Rhizobium mongolense and Rhizobium gallicum.

Binding site determinants for the LysR-type transcriptional regulator PcaQ in the legume endosymbiont Sinorhizobium meliloti

LysR-type transcriptional regulators represent one of the largest groups of prokaryotic regulators described to date. In the gram-negative legume endosymbiont Sinorhizobium meliloti, enzymes involved in the protocatechuate branch of the beta-ketoadipate pathway are encoded within the pcaDCHGB operon, which is subject to regulation by the LysR-type protein PcaQ. In this work, purified PcaQ was shown to bind strongly (equilibrium dissociation constant, 0.54 nM) to a region at positions -78 to -45 upstream of the pcaD transcriptional start site. Within this region, we defined a PcaQ binding site with dyad symmetry that is required for regulation of pcaD expression in vivo and for binding of PcaQ in vitro. We also demonstrated that PcaQ participates in negative autoregulation by monitoring expression of pcaQ via a transcriptional fusion to lacZ. Although pcaQ homologues are present in many alpha-proteobacteria, this work describes the first reported purification of this regulator, as well as characterization of its binding site, which is conserved in Agrobacterium tumefaciens, Rhizobium leguminosarum, Rhizobium etli, and Mesorhizobium loti.

Characterization of phenol and trichloroethene degradation by the rhizobium Ralstonia taiwanensis

Ralstonia taiwanensis is a root nodule bacterium originally isolated from Mimosa sp. in southern Taiwan. Some strains of R. taiwanensis demonstrated the ability to grow on medium containing phenol as the sole carbon source, especially strain TJ86, which was able to survive and grow at phenol concentrations of up to 900 mg/l. The dependence of the phenol degradation rate on the phenol concentration can be described by Haldane's model with a low KS (the apparent half-saturation constant) of 5.46 microM and an extremely high KSI (the apparent inhibition constant) 9075 microM. The optimal phenol degradation rate was 61 micromol/min/g cell, which occurred at a phenol concentration of 228 microM. The phenol-limited growth kinetics of TJ86 by Andrews's model also followed a similar trend to that of phenol degradation, indicating the close links between phenol degradation and cell growth. Strain TJ86 also achieved 100 and 40% degradation for soil samples amended with 500 and 1000 microg phenol/g soil (dry weight) within 9 days, respectively. Moreover, strain TJ86 cometabolically degraded trichloroethene (TCE) after being cultivated with media containing phenol or m-cresol as the carbon substrate. The sequence of the large-subunit phenol hydroxylase (LmPH) gene obtained from TJ86 displayed high homology to that of other phenol-utilizing bacteria. Results from kinetic and phylogenetic analyses suggest that strain TJ86 most likely belongs to group I phenol-degrading bacteria which are considered to be efficient TCE degraders. It is proposed that the symbiotic relationship between rhizobia R. taiwanensis and its host plant Mimosa sp. may have the potential for rhizoremediation of aquatic and soil environments contaminated by phenol and TCE.

Microbial transformations of p-coumaric acid by Bacillus megaterium and Curvularia lunata

p-Coumaric acid (1) is an abundant phenolic natural product that exhibits both chemoprotectant and antioxidant properties. Microbial transformation screening studies showed that 1 was converted to 4-vinylphenol (4), 4-hydroxybenzoic acid (2), caffeic acid (5), protocatechuic acid (6), and other unidentified metabolites over 144 h. 4-Vinylphenol (4) and its dimer, (2R,2S)-4-(2,3-dihydro-5-hyroxy-2-benzofuranyl) phenol (11), were produced by Bacillus megaterium, and 5-[(E)-2-carboxyethenyl]-2,3-dihydro-2-(4-hydroxyphenyl)-3-benzofurancarboxylic acid (15) and 4-hydroxybenzoic acid (2) were produced by Curvularia lunata. On the basis of deuterium-labeling experiments, B. megaterium catalyzes the nonoxidative enzymatic tautomerization of 1 to a vinylogous beta-keto acid intermediate that decarboxylates to 4. The presence of peroxidase and laccase activities in C. lunata extracts suggests that these enzymes may be involved in one-electron, p-coumaric acid dimerization in this organism.

Physiological characterization of Pseudomonas putida DOT-T1E tolerance to p-hydroxybenzoate

Pseudomonas putida DOT-T1E was isolated as a toluene-tolerant strain. We show that it is also able to grow on high concentrations (up to 17 g/liter [123 mM]) of p-hydroxybenzoate (4HBA). Tolerance to this aromatic carboxylic acid (up to 30 g/liter [217 mM]) is improved by preexposing the cells to low 4HBA concentrations; the adaptation process is caused by the substrate itself rather than by products resulting from its metabolism. The mechanisms of 4HBA tolerance seem to involve increased rigidity of the cell membrane as a result of a decrease in the cis/trans ratio of unsaturated fatty acids. In addition, energy-dependent efflux systems seem to operate in the exclusion of 4HBA from the cell membranes.

Positive selection for mutations affecting bioconversion of aromatic compounds in Agrobacterium tumefaciens: analysis of spontaneous mutations in the protocatechuate 3,4-dioxygenase gene

A positive selection method for mutations affecting bioconversion of aromatic compounds was applied to a mutant strain of Agrobacterium tumefaciens A348. The nucleotide sequence of the A348 pcaHGB genes, which encode protocatechuate 3,4-dioxygenase (PcaHG) and beta-carboxy-cis,cis-muconate cycloisomerase (PcaB) for the first two steps in catabolism of the diphenolic protocatechuate, was determined. An omega element was introduced into the pcaB gene of A348, creating strain ADO2077. In the presence of phenolic compounds that can serve as carbon sources, growth of ADO2077 is inhibited due to accumulation of the tricarboxylate intermediate. The toxic effect, previously described for Acinetobacter sp., affords a powerful selection for suppressor mutations in genes required for upstream catabolic steps. By monitoring loss of the marker in pcaB, it was possible to determine that the formation of deletions was minimal compared to results obtained with Acinetobacter sp. Thus, the tricarboxylic acid trick in and of itself does not appear to select for large deletion mutations. The power of the selection was demonstrated by targeting the pcaHG genes of A. tumefaciens for spontaneous mutation. Sixteen strains carrying putative second-site mutations in pcaH or -G were subjected to sequence analysis. All single-site events, their mutations revealed no particular bias toward multibase deletions or unusual patterns: five (-1) frameshifts, one (+1) frameshift, one tandem duplication of 88 bp, one deletion of 92 bp, one nonsense mutation, and seven missense mutations. PcaHG is considered to be the prototypical ferric intradiol dioxygenase. The missense mutations served to corroborate the significance of active site amino acid residues deduced from crystal structures of PcaHG from Pseudomonas putida and Acinetobacter sp. as well as of residues in other parts of the enzyme.

Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage

Aromatic compound degradation in six bacteria representing an ecologically important marine taxon of the alpha-proteobacteria was investigated. Initial screens suggested that isolates in the Roseobacter lineage can degrade aromatic compounds via the beta-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. Six Roseobacter isolates were screened for the presence of protocatechuate 3,4-dioxygenase, a key enzyme in the beta-ketoadipate pathway. All six isolates were capable of growth on at least three of the eight aromatic monomers presented (anthranilate, benzoate, p-hydroxybenzoate, salicylate, vanillate, ferulate, protocatechuate, and coumarate). Four of the Roseobacter group isolates had inducible protocatechuate 3, 4-dioxygenase activity in cell extracts when grown on p-hydroxybenzoate. The pcaGH genes encoding this ring cleavage enzyme were cloned and sequenced from two isolates, Sagittula stellata E-37 and isolate Y3F, and in both cases the genes could be expressed in Escherichia coli to yield dioxygenase activity. Additional genes involved in the protocatechuate branch of the beta-ketoadipate pathway (pcaC, pcaQ, and pobA) were found to cluster with pcaGH in these two isolates. Pairwise sequence analysis of the pca genes revealed greater similarity between the two Roseobacter group isolates than between genes from either Roseobacter strain and soil bacteria. A degenerate PCR primer set targeting a conserved region within PcaH successfully amplified a fragment of pcaH from two additional Roseobacter group isolates, and Southern hybridization indicated the presence of pcaH in the remaining two isolates. This evidence of protocatechuate 3, 4-dioxygenase and the beta-ketoadipate pathway was found in all six Roseobacter isolates, suggesting widespread abilities to degrade aromatic compounds in this marine lineage.

Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) catalyzes the ring cleavage step in the catabolism of aromatic compounds through the protocatechuate branch of the beta-ketoadipate pathway. A protocatechuate 3,4-dioxygenase was purified from Streptomyces sp. strain 2065 grown in p-hydroxybenzoate, and the N-terminal sequences of the beta- and alpha-subunits were obtained. PCR amplification was used for the cloning of the corresponding genes, and DNA sequencing of the flanking regions showed that the pcaGH genes belonged to a 6. 5-kb protocatechuate catabolic gene cluster; at least seven genes in the order pcaIJFHGBL appear to be transcribed unidirectionally. Analysis of the cluster revealed the presence of a pcaL homologue which encodes a fused gamma-carboxymuconolactone decarboxylase/beta-ketoadipate enol-lactone hydrolase previously identified in the pca gene cluster from Rhodococcus opacus 1CP. The pcaIJ genes encoded proteins with a striking similarity to succinyl-coenzyme A (CoA):3-oxoacid CoA transferases of eukaryotes and contained an indel which is strikingly similar between high-G+C gram-positive bacteria and eukaryotes.

The beta-ketoadipate pathway and the biology of self-identity

The beta-ketoadipate pathway is a chromosomally encoded convergent pathway for aromatic compound degradation that is widely distributed in soil bacteria and fungi. One branch converts protocatechuate, derived from phenolic compounds including p-cresol, 4-hydroxybenzoate and numerous lignin monomers, to beta-ketoadipate. The other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates. Enzyme studies and amino acid sequence data indicate that the pathway is highly conserved in diverse bacteria, including Pseudomonas putida, Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Rhodococcus erythropolis, and many others. The catechol branch of the beta-ketoadipate pathway appears to be the evolutionary precursor for portions of the plasmid-borne ortho-pathways for chlorocatechol degradation. However, accumulating evidence points to an independent and convergent evolutionary origin for the eukaryotic beta-ketoadipate pathway. In the face of enzyme conservation, the beta-ketoadipate pathway exhibits many permutations in different bacterial groups with respect to enzyme distribution (isozymes, points of branch convergence), regulation (inducing metabolites, regulatory proteins), and gene organization. Diversity is also evident in the behavioral responses of different bacteria to beta-ketoadipate pathway-associated aromatic compounds. The presence and versatility of transport systems encoded by beta-ketoadipate pathway regulons is just beginning to be explored in various microbial groups. It appears that in the course of evolution, natural selection has caused the beta-ketoadipate pathway to assume a characteristic set of features or identity in different bacteria. Presumably such identities have been shaped to optimally serve the diverse lifestyles of bacteria.

Conservation of PcaQ, a transcriptional activator of pca genes for catabolism of phenolic compounds, in Agrobacterium tumefaciens and Rhizobium species

In Agrobacterium tumefaciens A348, control of five genes for catabolism of the phenolic compound protocatechuate to beta-ketoadipate is exerted by the gene pcaQ. The product of pcaQ is a transcriptional activator which is distinct from regulators of the beta-ketoadipate pathway characterized in other bacterial groups. An investigation of whether pcaQ is present and conserved in related Rhizobium species employed Southern hybridization and an agrobacterial pcaD::LacZ promoter probe plasmid. These studies revealed that homologs of the activator are widespread among members of the family Rhizobiaceae, being present in Rhizobium leguminosarum, Rhizobium fredii, Rhizobium meliloti, Rhizobium etli, and Rhizobium tropici.

Characterization of PcaQ, a LysR-type transcriptional activator required for catabolism of phenolic compounds, from Agrobacterium tumefaciens

Previous work demonstrated that catabolism of the phenolic compounds p-hydroxybenzoate and protocatechuate via the beta-ketoadipate pathway in Agrobacterium tumefaciens is mediated by a regulatory gene, pcaQ, that acts in trans to elicit expression of many of the enzymes encoded by the pca genes. There was evidence that five pca structural genes are organized in a polycistronic operon transcribed in the order pcaDCHGB. The pcaQ gene is upstream of this operon. The activator encoded by pcaQ was novel in having the metabolite beta-carboxy-cis,cis-muconate as a coinducer. This communication reports the nucleotide sequence of pcaQ and identifies its deduced polypeptide product as a member of the LysR family of regulatory molecules. PcaQ has a calculated molecular weight of 33,546, which is consistent with the size of LysR relatives. Like many other LysR members, PcaQ serves as an activator at the level of transcription, it has a conserved amino-terminal domain, and its gene is transcribed divergently from the operon that it regulates and is subject to negative autoregulation. Studies of coinducer specificity identified an unstable pathway metabolite, gamma-carboxymuconolactone, as a second coinducer. Analysis of expression from a pcaD::lacZ promoter probe plasmid revealed that PcaQ and the coinducer exert their effect on a 133-nucleotide region upstream of pcaD. The nucleotide sequence of this region in a mutant strain constitutive for enzymes encoded by the pcaDCHGB operon identified nucleotides likely to be involved in the pcaDCHGB promoter and substantiated the inclusion of five pca structural genes in the operon.

Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens

The protocatechuate branch of the beta-ketoadipate pathway comprises the last six enzymatic steps in the catabolism of diverse phenolic compounds to citric acid cycle intermediates. In this paper, the regulation and tight supraoperonic clustering of the protocatechuate (pca) genes from Agrobacterium tumefaciens A348 are elucidated. A previous study found that the pcaD gene is controlled by an adjacent regulatory gene, pcaQ, which encodes an activator. The activator responded to beta-carboxy-cis,cis-muconate and was shown to control the synthesis of at least three genes (pcaD and pcaHG). In this work, eight genes required for the catabolism of protocatechuate were localized within a 13.5-kb SalI region of DNA. Isolation and characterization of transposon Tn5 mutant strains facilitated the localization of pca genes. Five structural genes were found to respond to the tricarboxylic acid and to be contiguous in an operon transcribed in the order pcaDCHGB. These genes encode enzymes beta-ketoadipate enol-lactone hydrolase, gamma-carboxymuconolactone decarboxylase, protocatechuate 3,4-dioxygenase (pcaHG), and beta-carboxy-cis,cis-muconate lactonizing enzyme, respectively. Approximately 4 kb from the pcaD gene are the pcaIJ genes, which encode beta-ketoadipate succinyl-coenzyme A transferase for the next-to-last step of the pathway. The pcaIJ genes are transcribed divergently from the pcaDCHGB operon and are expressed in response to beta-ketoadipate. The pattern of induction of pca genes by beta-carboxy-cis,cis-muconate and beta-ketoadipate in A. tumefaciens is similar to that observed in Rhizobium leguminosarum bv. trifolii and is distinct from induction patterns for the genes from other microbial groups.

Cloning of Protocatechuate 3,4-Dioxygenase Genes from Bradyrhizobium japonicum USDA110

A heterologous gene probe encoding the α and β subunits of the Pseudomonas cepacia protocatechuate 3,4-dioxygenase (PCD) was used to detect its homolog in the genome of Bradyrhizobium japonicum USDA110. Three cosmid clones carrying a 2.2-kb Bam HI insert showed high levels of PCD activity. Sac I digestion of one of the genomic clones, pBjG17, produced a 2.5-kb insert DNA that complemented a PCD mutant of P. cepacia.

Positive regulation of phenolic catabolism in Agrobacterium tumefaciens by the pcaQ gene in response to beta-carboxy-cis,cis-muconate

An Escherichia coli system for generating a commercially unavailable catabolite in vivo was developed and was used to facilitate molecular genetic studies of phenolic catabolism. Introduction of the plasmid-borne Acinetobacter pcaHG genes, encoding the 3,4-dioxygenase which acts on protocatechuate, into E. coli resulted in bioconversion of exogenously supplied protocatechuate into beta-carboxy-cis,cis-muconate. This compound has been shown to be an inducer of the protocatechuate (pca) genes required for catabolism of protocatechuate to tricarboxylic acid cycle intermediates in Rhizobium leguminosarum biovar trifolii. The E. coli bioconversion system was used to explore regulation of the pca genes in a related bacterium, Agrobacterium tumefaciens. The pcaD gene, which encodes beta-ketoadipate enol-lactone hydrolase, from A. tumefaciens A348 was cloned and was shown to be adjacent to a regulatory region which responds strongly to beta-carboxy-cis,cis-muconate in E. coli. Site-specific insertional mutagenesis of the regulatory region eliminated expression of the pcaD gene in E. coli. When the mutation was incorporated into the A. tumefaciens chromosome, it eliminated expression of the pcaD gene and at least three other pca genes as well. The regulatory region was shown to activate gene expression in trans. The novel regulatory gene was termed pcaQ to differentiate it from pca regulatory genes identified in other microbes, which bind different metabolites.

Characterization of the genes encoding beta-ketoadipate: succinyl-coenzyme A transferase in Pseudomonas putida

beta-Ketoadipate:succinyl-coenzyme A transferase (beta-ketoadipate:succinyl-CoA transferase) (EC 2.8.3.6) carries out the penultimate step in the conversion of benzoate and 4-hydroxybenzoate to tricarboxylic acid cycle intermediates in bacteria utilizing the beta-ketoadipate pathway. This report describes the characterization of a DNA fragment from Pseudomonas putida that encodes this enzyme. The fragment complemented mutants defective in the synthesis of the CoA transferase, and two proteins of sizes appropriate to encode the two nonidentical subunits of the enzyme were produced in Escherichia coli when the fragment was placed under the control of a phage T7 promoter. DNA sequence analysis revealed two open reading frames, designated pcaI and pcaJ, that were separated by 8 bp, suggesting that they may comprise an operon. A comparison of the deduced amino acid sequence of the P. putida CoA transferase genes with the sequences of two other bacterial CoA transferases and that of succinyl-CoA:3-ketoacid CoA transferase from pig heart suggests that the homodimeric structure of the mammalian enzyme may have resulted from a gene fusion of the bacterial alpha and beta subunit genes during evolution. Conserved functional groups important to the catalytic activity of CoA transferases were also identified.