Enzymatic dehalogenation of 2,2-dichloropropionate

Isolation of novel bacteria able to degrade alpha-halocarboxylic acids by enrichment from environmental samples

In order to isolate novel bacteria able to degrade alpha-halocarboxylic acids a variety of culturing strategies were implemented. Eight pure cultures were obtained and were found to be associated with the Gram negative Proteobacteria and the Gram positive Bacillus and Enterococcus genera. Furthermore, several strains were obtained which were able to degrade the DL-halocarboxylic acids anaerobically. Molecular analysis of the pure cultures led us to conclude that they may possess novel enzymes involved in the biodegradation of the alpha-halocarboxylic acids. These results are the first for nearly 40 years to describe the isolation of Gram positive isolates on an alpha-halocarboxylic acid as the sole source of carbon and energy, which also show the ability to de-toxify the test substrate by releasing chloride.

Comparing the dehalogenase gene pool in cultivated alpha-halocarboxylic acid-degrading bacteria with the environmental metagene pool

Culture-dependent and culture-independent approaches were used to determine the relationship between the dehalogenase gene pool in bacteria enriched and isolated on 2,2-dichloropropionic acid (22DCPA) and the environmental metagene pool (the collective gene pool of both the culturable and uncultured microbes) from which they were isolated. The dehalogenases in the pure-cultures isolates, which were able to degrade 22DCPA, were similar to previously described group I and II dehalogenases. Significantly, the majority of the dehalogenases isolated from activated sludge by degenerate PCR with primers specific for alpha-halocarboxylic acid dehalogenases were not closely related to the dehalogenases in any isolate. Furthermore, the dehalogenases found in the pure cultures predominated in the enrichments but were a minor component of the community used to inoculate the batch cultures. Phylogenetic analysis of the dehalogenase sequences isolated by degenerate PCR showed that the diversity of the group II deh gene was greater than that of the group I deh gene. Direct plating of the activated sludge onto minimal media supplemented with 22DCPA resulted in biomass and DNA from which dehalogenases were amplified. Analysis of the sequences revealed that they were much more closely related to the sequences found in the community used to start the enrichments. However, no pure cultures were obtained with this isolation method, and thus no pure cultures were available for identification. In this study we examined the link between genes found in pure cultures with the metagene pool from which they were isolated. The results show that there is a large bias introduced by culturing, not just in the bacteria isolated but also the degradative genes that they contain. Moreover, our findings serve as a caveat for studies involving the culturing of pure cultures of bacteria and conclusions which are drawn from analysis of these organisms.

Diversity of alpha-halocarboxylic acid dehalogenases in bacteria isolated from a pristine soil after enrichment and selection on the herbicide 2,2-dichloropropionic acid (Dalapon)

Five pure cultures of bacteria (strains DA1-5) able to degrade 2,2-dichloropropionic acid (22DCPA) were isolated for the first time from pristine bulk soil samples. From 16S rDNA analysis, it was concluded that strains DA2, DA3 and DA4 were members of the Bradyrhizobium subgroup (alpha-Proteobacteria), strain DA5 clustered in the Brucella assemblage (alpha-Proteobacteria) and strain DA1 clustered in the beta-Proteobacteria. Biochemical and molecular analysis of the dehalogenases from the isolates showed that these enzymes were quite diverse. Several dehalogenases were closely related to group I and II alpha-halocarboxylic acid dehalogenases, and partial polymerase chain reaction (PCR) products were obtained from isolates DA1, 2, 3 and 4 using degenerate dehalogenase primers. However, no PCR products were obtained from isolate DA5 using either of the group I or II alpha-halocarboxylic acid dehalogenase primers. Isolates DA2 and DA4 contained putative silent dehalogenases. The investigation highlighted the endemic nature of these genes in pristine environments and how diverse these were even from spatially close samples.

Biotransformation of halogenated compounds

As a result of natural production and contamination of the environment by xenobiotic compounds, halogenated substances are widely distributed in the biosphere. Concern arises as a result of the toxic, carcinogenic, and potential teratogenic nature of these substances. The biotransformations of such halogenated substances are reviewed, with particular emphasis on the biocatalytic cleavage of the carbon-halogen bonds. The physiology, biochemistry, and genetics of the biological system involved in the dehalogenation reactions are discussed for three groups of organohalogens: (1) the haloacids, (2) the haloaromatics, and (3) the haloalkanes. Finally, the biotechnological applications of these microbial transformations are discussed. This includes prospects for their future application in biosynthetic processes for the synthesis of halogenated intermediates or novel compounds and also the use of such systems for the detoxification and degradation of environmental pollutants.

The origin of the oxygen incorporated during the dehalogenation/hydroxylation of 4-chlorobenzoate by an Arthrobacter sp

An Arthrobacter sp. has been shown to dehalogenate 4-chlorobenzoate yielding 4-hydroxybenzoate. Experiments with 18O indicate that, in the presence of cell-free extracts, the hydroxyl group which is substituted onto the aromatic nucleus during dehalogenation is derived from water and not from molecular oxygen. Dehalogenation therefore is not catalysed by a mixed-function oxidase; instead a novel aromatic hydroxylase is implicated in the reaction.

2-Haloacid dehalogenase from a 4-chlorobenzoate-degrading Pseudomonas spec. CBS 3

Pseudomonas spec. CBS 3 contains a 2-haloacid dehalogenase induced by chloroacetate. The enzyme was purified about 25-fold to electrophoretic homogeneity by ammonium sulfate fractionation, hydroxyapatite, DEAE-cellulose and gel filtration. The relative molecular masses, as determined by Sephadex G-75 gel filtration and dodecyl sulfate polyacrylamide gel electrophoresis, were 41 000 and 28 000, respectively. The enzyme dehalogenated all monohaloacetates except fluoroacetate. Low activities were found against dichloroacetate and 2,2-dichloropropionate. The enzyme was inactive against trichloroacetate and 3-chloropropionate, it catalysed the stereospecific dehalogenation of L-2-chloropropionate to D-lactate, the rate of dehalogenation being about 20% of the rate of chloroacetate dechlorination. The enzyme activity was not affected by chelating agents and thiol reagents.

Microbial growth on 2-bromobutane

A member of the genus Arthrobacter was isolated which grew at the expense of 2-bromobutane as sole source of carbon and energy. Evidence is presented which suggests that the initial conversion of 2-bromobutane to 2-butanol is a spontaneous chemical hydrolysis and not mediated by the organism. Further evidence from oxygen consumption experiments indicates that 2-bromobutane is oxidized through 2-butanol, methyl ethyl ketone, ethyl acetate to acetate and ethanol. Results of experiments with cells grown on pathway intermediates reveal that the enzymes necessary for the oxidation of 2-butanol, methyl ethyl ketone, ethyl acetate, ethanol and acetaldehyde are not coordinately, but individually induced by their respective substrates.

Bacterial dehalogenation of halogenated alkanes and fatty acids

Sewage samples dehalogenated 1,9-dichloronane, 1-chloroheptane, and 6-bromohexanoate, but an organism able to use 1,9-dichlorononane as the sole carbon source could not be isolated from these samples. Resting cells of Pseudomonas sp. grown on n-undecane, but not cells grown on glycerol, dehalogenated 1,9-dichlorononane in the presence of chloramphenicol. Resting cells of five other n-undecane-utilizing bacteria cleaved the halogen from dichlorononane and 6-bromohexanoate, and four dehalogenated 1-chloroheptane; however, none of these organisms used 1,9-dichlorononane for growth. By contrast, four benzoate-utilizing bacteria removed bromine from 6-bromohexanoate but had little or no activity on the chlorinated hydrocarbons. Incubation of sewage with 1,9-dichlorononane increased its subsequent capacity to dehalogenate 1,9-dichlorononane and 6-bromohexanoate but not 1-chloroheptane. A soil isolate could dehalogenate several dichloralkanes, three halogenated heptanes, and halogen-containing fatty acids. An enzyme preparation from this bacterium released chloride from 1,9-dichlorononane.

Bacterial and spontaneous dehalogenation of organic compounds

Only 3 of more than 500 soil enrichments contained organisms able to use 1,9-dichlorononane as a sole carbon source. One isolate, a strain of Pseudomonas, grew on the compound and released much of the halogen as chloride. Resting cells dehalogenated 1,9-dichlorononane aerobically but not anaerobically. Pseudomonas sp. grew on and resting cells dehalogenated 1,6-dichlorohexane, 1,5-dichloroheptane, 2-bromoheptanoate, and 1-chloro-, 1-bromo-, and 1-iodoheptane, but the bacterium cometabolized but did not grow on 3-chloropropionate. p-Methylbenzyl alcohol, chloride, and p-methylbenzoate were formed when resting cells were incubated with alpha-chloro-p-xylene; the first two products were also formed in the absence of the bacteria. Similarly, o- and m-methylbenzyl alcohols were generated from the corresponding chlorinated xylenes in the presence or absence of Pseudomonas sp. The formation of m- and p-chlorobenzoic acid from m- and p-chlorobenzyl chloride proceeded only in the presence of the cells, but p-chlorobenzyl alcohol was generated from p-chlorobenzyl chloride even in the absence of the bacterium. These results are discussed in terms of possible mechanisms of dehalogenation.

Enzyme evolution in a microbial community growing on the herbicide Dalapon

A seven-membered microbial community capable of utilising the herbicide Dalapon has been isolated by continuous-flow enrichment culture. The composition of this community has remained remarkably stable over thousands of hours in a Dalapon-limited chemostat. During this period, however, one member of the community, Pseudomonas putida, acquired the ability to grow on Dalapon through the evolution of an extant dehalogenase.