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PubMed1999

[Studies on the metabolism pathway of aniline degradation by Comamonas acidovorans AN3].

All of the enzymes relating to aniline degradation in C. acidovorans AN3 were inducible ones. When growing on aniline as sole carbon, nitrogen and energy sources, the cells of C. acidovorans AN3 contained aniline dioxygenase, catechol-2, 3-dioxygenase, 2-hydromuconic semialdehyde dehydrogenase, 4-oxalocrotonic acid decarboxylase and 4-hydroxy-2-oxovalerate acid aldolase. The Km and Vmax of aniline dioxygenase were 292 mumol/L and 3.57 mumol.mg-1. min-1, respectively. The Km and Vmax of catechol-2, 3-dioxygenase were 16.4 mumol/L and 15.2 mumol.mg-1.min-1, respectively. According to these results, the degradation metabolism pathway of aniline by C. acidovorans AN3 was hypothesised.

Aniline Compounds↗
PubMed2004

Removal of nitriles from synthetic wastewater by acrylonitrile utilizing bacteria.

This study describes the ability of two bacteria strains, isolated from an ABS resin manufacturing wastewater treatment system, to remove high acrylonitrile concentrations. Straight chain aliphatic nitrile compound (propionitrile, allyl cyanide); branch chain aliphatic nitrile compound (isobutyronitrilc) and aromatic nitrile compound (benzonitrile) removal by Comamonas testosteroni and Acidovorax sp. was also investigated. The results are: Comamonas testosteroni and Acidovorax sp. can remove acrylonitrile completely up to 1904.8 mg/L within 66.6 h and 1538.5 mg/L within 143.3 h, respectively. Comamonas testosteroni degraded acrylonitrile faster than Acidovorax sp., and accumulated much more acrylic acid in the medium than Acidovorax sp. The addition of acrylamide to the medium was removed by Comamonas testosteroni and Acidovorax sp. Both strains utilized acrylic acid, a metabolic by-product of acrylonitrile, as a carbon source and ammonium nitrogen, a metabolic by-product of acrylonitrile, as a nitrogen source for growth. Comamonas testosteroni and Acidovorax sp. removed propionitrile completely up to 1352.8 mg/L and 975.7 mg/L within 166.9 h, respectively. With isobutyronitrile as a substrate, more than 97.8% could be removed within 169.8 h by Comamonas testosteroni up to 1352.8 mg/L, and by Acidovorax sp. up to 975.7 mg/L. These two strains could remove allyl cyanide completely up to 775 mg/L within 49.1 h and benzonitrile completely up to 442.7 mg/L within 31.1 h. Because Comamonas testosteroni and Acidovorax sp. have good degrading ability for removing nitrile compounds they are expected to play an important role in the treatment of nitrile compounds.

Acrylonitrile↗
PubMed1999

Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov.

The phylogenetic relationships among members of the family Comamonadaceae and several unclassified strains were studied by direct sequencing of their PCR-amplified 16S rRNA genes. Based on the 16S rRNA gene sequence analysis, members of the family formed a coherent group. The closest relatives are species of the Rubrivivax sub-group: Leptothrix discophora, Ideonella dechloratans and Rubrivivax gelatinosus. The genus Hydrogenophaga formed two subclusters, as did the species of Acidovorax, whereas the five species of the genus [Aquaspirillum] were polyphyletic. Comamonas acidovorans was phylogenetically distant from the type species of Comamonas, Comamonas terrigena. On the basis of this work and previous studies, Comamonas acidovorans is removed from the genus Comamonas and renamed as Delftia acidovorans gen. nov., comb. nov. Descriptions of the new genus Delftia and of the type species Delftia acidovorans, for which the type strain is ATCC 15668T, are presented.

DNA, Bacterial↗
PubMed2001

Insights into the genetic diversity of initial dioxygenases from PAH-degrading bacteria.

Alpha subunit genes of initial polyaromatic hydrocarbon (PAH) dioxygenases were used as targets for the PCR detection of PAH-degrading strains of the genera Pseudomonas, Comamonas and Rhodococcus which were obtained from activated sludge or soil samples. Sequence analysis of PCR products from several Pseudomonas strains showed that alpha subunits (nahAc allele) of this genus are highly conserved. PCR primers for the specific detection of alpha subunit genes of initial PAH dioxygenases from Pseudomonas strains were not suitable for detecting the corresponding genes from the genera Comamonas and Rhodococcus. Southern analysis using a heterologous gene probe derived from the P. putida OUS82 PAH dioxygenase alpha subunit identified segments of the PAH-degradation gene cluster from C. testosteroni strain H. Parts of this gene cluster containing three subunits of the initial PAH dioxygenase were isolated. These three subunits [ferredoxin (pahAb), alpha (pahAc) and beta (pahAd) subunit] were amplified by PCR as one fragment and expressed in Escherichia coli DH5alpha, resulting in an active initial dioxygenase with the ability to transform indole and phenanthrene. The DNA sequence alignment of alpha subunits from C. testosteroni H and various PAH-degrading bacteria permitted the design of new primers and oligonucleotide probes which are useful for the detection of the initial PAH dioxygenases from strains of Pseudomonas, Comamonas and Rhodococcus.

Bacterial Proteins↗
PubMed1999

Bioconversion of pyrimidine by resting cells of quinoline-degrading bacteria.

Nine quinoline-degrading bacterial strains were tested for their ability to hydroxylate pyrimidine. All strains converted pyrimidine to uracil via pyrimidine-4-one in a cometabolic process. Quinoline 2-oxidoreductases (QuinORs) were the catalysts of fortuitous pyrimidine hydroxylation. Whereas in most strains the activity of the QuinOR towards pyrimidine was very low compared to its activity towards quinoline, QuinOR in crude extracts from Comamonas testosteroni 63 showed a specific activity of 64 (mU mg protein)-1 with pyrimidine as substrate, compared to a specific activity of 237 (mU mg protein)-1 towards the intrinsic substrate quinoline. Resting cells of Comamonas testosteroni 63 rapidly converted pyrimidine almost stoichiometrically to uracil, which accumulated in the cell suspension. Using an adsorbent resin, uracil was prepared from the supernatant of Comamonas testosteroni 63 resting cells with a yield of > 98%.

Biodegradation, Environmental↗
PubMed1999

Genetic and biochemical comparison of 2-aminophenol 1,6-dioxygenase of Pseudomonas pseudoalcaligenes JS45 to meta-cleavage dioxygenases: divergent evolution of 2-aminophenol meta-cleavage pathway.

Nitrobenzene is degraded to pyruvate and acetaldehyde by Pseudomonas pseudoalcaligenes JS45 via a reductive pathway, and by Comamonas sp. JS765 via an oxidative pathway. Although the initial reactions in the degradation of nitrobenzene by the two bacteria are totally different, the lower pathways are similar and converge at the level of 4-oxalocrotonate. In order to further investigate the biochemical properties and reveal the evolutionary relationships between the two lower pathways, the genes encoding the 2-aminophenol 1,6-dioxygenase were cloned and sequenced. 2-Aminophenol 1,6-dioxygenase from P. pseudoalcaligenes JS45 and catechol 2,3-dioxygenase from Comamonas sp. JS765 were able to act on both catechol and 2-aminophenol, but catechol was a suicide substrate of 2-aminophenol 1,6-dioxygenase. The activity of 2-aminophenol 1,6-dioxygenase was restored after removal of catechol and incubation with ascorbate and FeCl(2). Both the alpha-subunit (AmnA) and the beta-subunit (AmnB) of the dioxygenase from P. pseudoalcaligenes JS45 show a high degree of identity to the corresponding subunits of the ring-fission dioxygenase from Pseudomonas sp. AP-3: 67% for the alpha-subunit, and 84% for the beta-subunit. Sequence similarity studies suggest that the beta-subunits of both 2-aminophenol 1,6-dioxygenases are distantly related to homoprotocatechuate 2,3-dioxygenase from Escherichia coli strains W and C and then to catechol 2, 3-dioxygenase from Alcaligenes eutrophus. Four active-site-relevant histidines are conserved in AmnB, but not in AmnA. The lack of conserved histidines indicates the absence of an Fe(2+) binding site in AmnA, which explains the previous observations of only approximately one Fe(2+) per two subunits in the 2-aminophenol 1, 6-dioxygenases from P. pseudoalcaligenes JS45. The 2-aminophenol 1, 6-dioxygenase genes are located upstream of the 2-aminomuconic semialdehyde dehydrogenase gene, and a putative member of the YjgF protein family is upstream of the dioxygenase genes. Transcriptional analysis indicates that the YjgF-like protein, 2-aminophenol 1, 6-dioxygenase, and 2-aminomuconic semialdehyde dehydrogenase are coordinately transcribed. A putative ORF similar to part of the RNA helicase genes is downstream of the dehydrogenase gene. Both the novel organization of the genes and the phylogeny of the dioxygenases and dehydrogenase indicate that the 2-aminophenol pathway in P. pseudoalcaligenes JS45 represents an example of a distant divergent evolution of meta-cleavage pathways.

Amino Acid Sequence↗
PubMed2000

Development of a vital fluorescent staining method for monitoring bacterial transport in subsurface environments.

Previous bacterial transport studies have utilized fluorophores which have been shown to adversely affect the physiology of stained cells. This research was undertaken to identify alternative fluorescent stains that do not adversely affect the transport or viability of bacteria. Initial work was performed with a groundwater isolate, Comamonas sp. strain DA001. Potential compounds were first screened to determine staining efficiencies and adverse side effects. 5-(And 6-)-carboxyfluorescein diacetate, succinimidyl ester (CFDA/SE) efficiently stained DA001 without causing undesirable effects on cell adhesion or viability. Members of many other gram-negative and gram-positive bacterial genera were also effectively stained with CFDA/SE. More than 95% of CFDA/SE-stained Comamonas sp. strain DA001 cells incubated in artificial groundwater (under no-growth conditions) remained fluorescent for at least 28 days as determined by epifluorescent microscopy and flow cytometry. No differences in the survival and culturability of CFDA/SE-stained and unstained DA001 cells in groundwater or saturated sediment microcosms were detected. The bright, yellow-green cells were readily distinguished from autofluorescing sediment particles by epifluorescence microscopy. A high throughput method using microplate spectrofluorometry was developed, which had a detection limit of mid-10(5) CFDA-stained cells/ml; the detection limit for flow cytometry was on the order of 1,000 cells/ml. The results of laboratory-scale bacterial transport experiments performed with intact sediment cores and nondividing DA001 cells revealed good agreement between the aqueous cell concentrations determined by the microplate assay and those determined by other enumeration methods. This research indicates that CFDA/SE is very efficient for labeling cells for bacterial transport experiments and that it may be useful for other microbial ecology research as well.

Comamonas↗
PubMed1996

Biodegradation of polychlorinated biphenyls by rhizobia: a novel finding.

Metabolism of simple aromatic compounds in rhizobial strains has been a subject of study for a few decades, due either to the significance of nutritional diversity in the inoculum survival during agricultural applications or to the importance of plant phenolics in the microbe-plant cross-talk and signal-transduction. Here, we report the capability of rhizobial strains to catabolize polychlorinated biphenyls (PCBs). In order to identify the genes in these strains that mediate the catabolism of PCBs we used the bphABC genes from Comamonas testosteroni strain B-356. Our results showed that genomic DNAs from all four rhizobial strains studied hybridized strongly with the Comamonas-derived probe, indicating the presence of a similar genetic system. This is a novel and interesting finding indicating for the first time, perhaps, of a role of rhizobia in recycling of aromatic compounds in nature and, certainly, opening a new avenue to be explored in the field of bioremediation.

Aroclors↗
PubMed2004

Continuous acetonitrile degradation in a packed-bed bioreactor.

A 20-l packed-bed reactor filled with foamed glass beads was tested for the treatment of acetonitrile HPLC wastes. Aeration was provided by recirculating a portion of the reactor liquid phase through an aeration tank, where the dissolved oxygen concentration was kept at 6 mg/l. At a feeding rate of 0.77 g acetonitrile l(-1) reactor day(-1), 99% of the acetonitrile was removed; and 86% of the nitrogen present in acetonitrile was released as NH3, confirming that acetonitrile volatilization was not significant. Increasing the acetonitrile loading resulted in lower removal efficiencies, but a maximum removal capacity of 1.0 g acetonitrile l(-1) reactor day(-1) was achieved at a feeding rate of 1.6 g acetonitrile l(-1) reactor day(-1). The removal capacity of the system was well correlated with the oxygenation capacity, showing that acetonitrile removal was likely to be limited by oxygen supply. Microbial characterization of the biofilm resulted in the isolation of a Comamonas sp. able to mineralize acetonitrile as sole carbon, nitrogen and energy source. This organism was closely related to C. testosteroni (91.2%) and might represent a new species in the Comamonas genus. This study confirms the potential of packed-bed reactors for the treatment of a concentrated mixture of volatile pollutants.

Acetonitriles↗
PubMed1997

D-lysine production from L-lysine by successive chemical racemization and microbial asymmetric degradation.

In order to develop a practical process for D-lysine production from L-lysine, successive chemical racemization and microbial asymmetric degradation were investigated. The racemization of L-lysine proceeded quantitatively at elevated temperatures. A sample of 1000 strains of bacteria, fungi, yeast and actinomyces were screened for the ability to degrade L-lysine asymmetrically. Microorganisms belonging to the Achromobacter, Agrobacterium, Candida, Comamonas, Flavobacterium, Proteus, Providencia, Pseudomonas and Yarrowia genera exhibited a high L-lysine-degrading activity. Comamonas testosteroni IAM 1048 was determined to be the best strain and used as a biocatalyst for eliminating the L isomer. The degradation rate of L-lysine with C. testosteroni IAM 1048 was influenced by pH, temperature and agitation speed. Under the optimal conditions, the L isomer in a 100-g/l mixture of racemic lysine was completely degraded within 72 h, with 47 g D-lysine/l left in the reaction mixture. Crystalline D-lysine, with a chemical purity greater than 99% and optical purity of 99.9% enantiomeric excess, was obtained at a yield of 38% from the reaction mixture by simple purification. An engineering analysis of L-lysine racemization and microbial degradation was carried out to establish the basis of process design for D-lysine production.

Biodegradation, Environmental↗
PubMed1998

The adsorption of substrate-binding domain of PHB depolymerases to the surface of poly(3-hydroxybutyric acid).

The binding characteristic of PHB depolymerase has been studied by using glutathione S-transferase (GST) fusion proteins with substrate-binding domain of three bacterial PHB depolymerases, Alcaligenes faecalis, Comamonas acidovorans and Comamonas testosteroni. Analysis using immuno-gold labeling technique and transmission electron microscopy indicated that a novel GST fusion protein derived from A. Faecalis enzyme adsorbed to the surface of poly(3-hydroxybutyric acid) (P(3HB)) single crystals like other fusion proteins. Comparison of inhibiting degree of P(3HB) powder hydrolysis activity of PHB depolymerase by fusion proteins indicated that three fusion proteins bind to P(3HB) powder in the same degree. The measurement of the surface hydrophobicity of proteins suggests that the interaction of the substrate-binding domain with insoluble P(3HB) may include not only a hydrophobic effect but also molecule-specific contacts.

Acyltransferases↗
PubMed1999

Substrate and binding specificities of bacterial polyhydroxybutyrate depolymerases.

The substrate specificities of three extracellular polyhydroxybutyrate (PHB) depolymerases from Alcaligenes faecalis (PhaZ Afa), Pseudomonas stutzeri (PhaZ Pst), and Comamonas acidovorans (PhaZ Cac), which are grouped into types A and B based on the position of a lipase box sequence in the catalytic domain, were examined for films of 12 different aliphatic polyesters. Each of these PHB depolymerases used was capable of hydrolyzing poly(3-hydroxybutyrate) (P(3HB)), poly(3-hydroxypropionate) (P(3HP)), poly(4-hydroxybutyrate) (P(4HB)), poly(ethylene succinate) (PESU), and poly(ethylene adipate) (PEA) but could not hydrolyze another seven polyesters. In addition, the binding characteristics of substrate binding domains from PhaZ Afa, PhaZ Cac, and PHB depolymerase from Comamonas testosteroni (PhaZ Cte) were studied by using fusions with glutathione S-transferase (GST). All of fusion proteins adsorbed strongly on the surfaces of polyester granules of P(3HB), P(3HP), and poly(2-hydroxypropionate) (P(2HP)) which was not hydrolyzed by the PHB depolymerases used in this study, while they did not bind on Avicel and chitin granules. The adsorption kinetics of the fusion proteins to the surface of P(3HB) and P(2HP) granules were found to obey the Langmuir isotherm. The cross-area per molecule of fusion protein bound to P(3HB) granules was estimated to be 12+/-4 nm2/molecule. It has been suggested that the active sites in catalytic domains of PHB depolymerases have a similar conformational structure, and that several amino acids in substrate-binding domains of PHB depolymerases interact specifically with the surface of polyesters.

Adsorption↗