Benzoate degradation via the ortho pathway in Alcaligenes eutrophus is perturbed by succinate

A Functional Tricarboxylic Acid Cycle Operates during Growth of Bordetella pertussis on Amino Acid Mixtures as Sole Carbon Substrates

It has been claimed that citrate synthase, aconitase and isocitrate dehydrogenase activities are non-functional in Bordetella pertussis and that this might explain why this bacterium’s growth is sometimes associated with accumulation of polyhydroxybutyrate (PHB) and/or free fatty acids. However, the sequenced genome includes the entire citric acid pathway genes. Furthermore, these genes were expressed and the corresponding enzyme activities detected at high levels for the pathway when grown on a defined medium imitating the amino acid content of complex media often used for growth of this pathogenic microorganism. In addition, no significant PHB or fatty acids could be detected. Analysis of the carbon balance and stoichiometric flux analysis based on specific rates of amino acid consumption, and estimated biomass requirements coherent with the observed growth rate, clearly indicate that a fully functional tricarboxylic acid cycle operates in contrast to previous reports.

Benzoate degradation by Rhodococcus opacus 1CP after dormancy: Characterization of dioxygenases involved in the process

The process of benzoate degradation by strain Rhodococcus opacus 1CP after a five-year dormancy was investigated and its peculiarities were revealed. The strain was shown to be capable of growth on benzoate at a concentration of up to 10 g L(-1). The substrate specificity of benzoate dioxygenase (BDO) during the culture growth on a medium with a low (200-250 mg L(-1)) and high (4 g L(-1)) concentration of benzoate was assessed. BDO of R. opacus 1CP was shown to be an extremely narrow specificity enzyme. Out of 31 substituted benzoates, only with one, 3-chlorobenzoate, its activity was higher than 9% of that of benzoate. Two dioxygenases, catechol 1,2-dioxygenase (Cat 1,2-DO) and protocatechuate 3,4-dioxygenase (PCA 3,4-DO), were identified in a cell-free extract, purified and characterized. The substrate specificity of Cat 1,2-DO isolated from cells of strain 1CP after the dormancy was found to differ significantly from that of Cat 1,2-DO isolated earlier from cells of this strain grown on benzoate. By its substrate specificity, the described Cat 1,2-DO was close to the Cat 1,2-DO from strain 1CP grown on 4-methylbenzoate. Neither activity nor inhibition by protocatechuate was observed during the reaction of Cat 1,2-DO with catechol, and catechol had no inhibitory effect on the reaction of PCA 3,4-DO with protocatechuate.

Isolation and preliminary characterization of a o-nitrobenzaldehyde-degrading Alcaligenes sp. ND1

This paper reports the isolation and characterization of a new o-nitrobenzaldehyde (ONBA)-degrading bacterium, Alcaligenes sp. ND1. ND1 degraded almost all ONBA (100 mg L(-1)) in M9 medium within 36 hours. The key enzyme(s) involved in the initial biodegradation was a constitutively intracellular enzyme(s). This bacterium has great potential utility for bioremediation.

Degradation of aromatic compounds by Acinetobacter radioresistens S13: growth characteristics on single substrates and mixtures

Acinetobacter radioresistens S13 is able to grow on phenol or benzoate as the sole carbon and energy source: both these compounds are catabolized through the beta-ketoadipate pathway. Genes encoding the catabolic enzymes for degradation of aromatic compounds are localized on A. radioresistens S13 chromosome and organized in, at least, two distinct sets, one for benzoate degradation and another for phenol catabolism. In the present study, the growth and biodegradation kinetics for benzoate and phenol, and an easily metabolized substrate (acetate) were established. Benzoate was degraded slower and supports a less rapid and efficient growth than either acetate or phenol. A combined transcript-proteomic analysis of some of the major catabolic genes and their products nonetheless has shown that benzoate induces the expression of both benzoate and phenol catabolic operons. This result was confirmed by the fact that benzoate-acclimatized bacteria were rapidly able to degrade phenol too. Finally, the growth and biodegradation kinetics for different mixtures of acetate, benzoate and phenol were determined. Results indicate that a hierarchy of substrate utilization, benzoate > acetate > phenol, occurred: benzoate was the preferred substrate, despite its lower growth and biodegradation parameters. Hypotheses explaining these unusual metabolic features of A. radioresistens S13 are discussed.

Effect of long-term exposure, biogenic substrate presence, and electron acceptor conditions on the biodegradation of multiple substituted benzoates and phenolates

Biodegradation rates of benzoate and related aromatic compounds, 3-nitrobenzoate, 4-chlorobenzoate, 4-chlorophenol, and 2,4-dichlorophenol by unexposed (unacclimated) and long-term exposed (acclimated) biomass were quantified using a modified fed-batch technique. The acclimated biomass was taken after approximately 1-year of operation from three lab-scale sequencing batch reactors (SBR). These reactors were operated under various cycling electron acceptor conditions with a continuous feed of a synthetic wastewater containing biogenic and nonbiogenic chemicals including benzoate, 3-nitrobenzoate, and 4-chlorophenol, but not 4-chlorobenzoate or 2,4-dichlorophenol. The unexposed biomass was taken from a full-scale wastewater treatment plant, which constituted one of the original sources of inoculum for the lab-scale SBRs. The acclimated biomass manifested high removal rates of benzoate and related aromatic compounds with additional removal of structurally similar chemicals (4-chlorobenzoate and 2,4-dichlorophenol). The unacclimated biomass showed no removal of 3-nitrobenzoate, 4-chlorobenzoate or 2,4-dichlorophenol. Addition of biogenic substrates reduced the degradation of most aromatic compounds tested, but it enhanced 2,4-dichlorophenol removal. Biodegradation rates of each aromatic compound with the biomass from the anoxic/aerobic SBR were further determined under anaerobic (absence of aeration and NO3-), anoxic (no aeration, but with surplus NO3-), standard oxygen (DO > 0.2 mg/L), and elevated oxygen (DO > 25 mg/L) conditions. The removal rate of both benzoate and 3-nitrobenzoate decreased under anaerobic condition but not under the anoxic condition; 4-chlorophenol biodegradation, on the other hand, was reduced significantly under both anoxic and anaerobic conditions. The removal rates of aromatic compounds, particularly those of 3-nitrobenzoate and 2,4-dichlorophenol, increased significantly under elevated dissolved oxygen conditions. Our results demonstrated that when the biochemical conditions shifted from oxygen-respiration to nitrate respiration, to anaerobiosis, the biodegradation rates of test aromatic compounds decreased or ceased.

Transcriptional cross-regulation of the catechol and protocatechuate branches of the beta-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene

Transcriptional control of carbon source preferences by Acinetobacter sp. strain ADP1 was assessed with a pobA::lacZ fusion during growth on alternative substrates. The pobA-encoded enzyme catalyzes the first step in the degradation of 4-hydroxybenzoate, a compound consumed rapidly as a sole carbon source. If additional aromatic carbon sources are available, 4-hydroxybenzoate consumption is inhibited by unknown mechanisms. As reported here, during growth on aromatic substrates, pobA was not expressed despite the presence of 4-hydroxybenzoate, an inducer that normally causes the PobR regulator to activate pobA transcription. Growth on organic acids such as succinate, fumarate, and acetate allowed higher levels of pobA expression. In each case, pobA expression increased at the end of the exponential growth phase. Complex transcriptional regulation controlled 4-hydroxybenzoate catabolism in multisubstrate environments. Additional studies focused on the wild-type preference for benzoate consumption prior to 4-hydroxybenzoate consumption. These compounds are degraded via the catechol and protocatechuate branches of the beta-ketoadipate pathway, respectively. Here, mutants were characterized that degraded benzoate and 4-hydroxybenzoate concurrently. These mutants lacked the BenM and CatM transcriptional regulators that normally activate genes for benzoate catabolism. A model is presented in which BenM and CatM prevent pobA expression indirectly during growth on benzoate. These regulators may affect pobA expression by lowering the PcaK-mediated uptake of 4-hydroxybenzoate. Consistent with this model, BenM and CatM bound in vitro to an operator-promoter fragment controlling the expression of several pca genes, including pcaK. These studies provide the first direct evidence of transcriptional cross-regulation between the distinct but analogous branches of the beta-ketoadipate pathway.

The influence of metabolic network structures and energy requirements on xanthan gum yields

The metabolic network of Xanthomonas campestris is complex since a number of cyclic pathways are present making simple stoichiometric yield predictions difficult. The influence of certain pathway configurations and the resulting variations in flux have been examined as regards the maximum yield potential of this bacteria for xanthan gum production. These predictions have been compared with experimental results showing that the strain employed is functioning close to its theoretical maximum as regards yield criteria. The major constraint imposed on the network concerns energy availability which has a more pronounced effect on yield than carbon precursor supply. This can be attributed to the relatively high maintenance requirements determined experimentally and incorporated into the model. While some of this overall energy burden will undoubtedly be associated with incompressible metabolic requirements such as sugar uptake and xanthan efflux mechanisms, future strain improvement strategies will need to attack other non-essential energy-consuming reactions, if yields are to be further increased.

Carbon and energy flux constraints in continuous cultures of Alcaligenes eutrophus grown on phenol

Summary: The growth behaviour of Alcaligenes eutrophus on phenol was investigated in continuous cultures to identify the phenomena limiting both growth efficiency and substrate degradation rates. It was shown that the fixed stoichiometry of the meta pathway of phenol degradation, leading to equimolar quantities of pyruvate and acetate, and the structure of the central pathways, which do not allow gluconeogenesis of acetate during growth on phenol, provoke the accumulation of polyhydroxybutyrate (PHB) under certain growth conditions. Acetate is predominantly used as an energy source and PHB accumulates when the cells are carbon-limited rather than energy-limited. The maximum rates of phenol degradation can be attributed to the expression of the enzymes of the catabolic pathway. This is particularly true of phenol hydroxylase and 2-hydroxymuconate semialdehyde (2-hms) dehydrogenase, whose substrates accumulated to physiologically significant concentrations at high growth rates. Indeed the concentration of 2-hms that accumulated in the medium indicated that this enzyme was substrate-saturated at maximum growth rates. However, the specific activity profiles of other catabolic enzymes associated with phenol degradation were close to the estimated flux through the pathway. This suggests a complex control structure in which several enzymes contribute to the control of pathway flux, as would be expected in a catabolic pathway.