SummaryBacterial dehalogenases catalyse the cleavage of carbon-halogen bonds, which is a key step in aerobic mineralization pathways of many halogenated compounds that occur as environmental pollutants. There is a broad range of dehalogenases, which can be classified in different protein superfamilies and have fundamentally different catalytic mechanisms. Identical dehalogenases have repeatedly been detected in organisms that were isolated at different geographical locations, indicating that only a restricted number of sequences are used for a certain dehalogenation reaction in organohalogen-utilizing organisms. At the same time, massive random sequencing of environmental DNA, and microbial genome sequencing projects have shown that there is a large diversity of dehalogenase sequences that is not employed by known catabolic pathways. The corresponding proteins may have novel functions and selectivities that could be valuable for biotransformations in the future. Apparently, traditional enrichment and metagenome approaches explore different segments of sequence space. This is also observed with alkane hydroxylases, a category of proteins that can be detected on basis of conserved sequence motifs and for which a large number of sequences has been found in isolated bacterial cultures and genomic databases. It is likely that ongoing genetic adaptation, with the recruitment of silent sequences into functional catabolic routes and evolution of substrate range by mutations in structural genes, will further enhance the catabolic potential of bacteria toward synthetic organohalogens and ultimately contribute to cleansing the environment of these toxic and recalcitrant chemicals.
Most aerobic biodegradation pathways for hydrocarbons involve iron-containing oxygenases. In iron-limited environments, such as the rhizosphere, this may influence the rate of degradation of hydrocarbon pollutants. We investigated the effects of iron limitation on the degradation of toluene by Pseudomonas putida mt2 and the transconjugant rhizosphere bacterium P. putida WCS358(pWWO), both of which contain the pWWO (TOL) plasmid that harbors the genes for toluene degradation. The results of continuous-culture experiments showed that the activity of the upper-pathway toluene monooxygenase decreased but that the activity of benzyl alcohol dehydrogenase was not affected under iron-limited conditions. In contrast, the activities of three meta-pathway (lower-pathway) enzymes were all found to be reduced when iron concentrations were decreased. Additional experiments in which citrate was used as a growth substrate and the pathways were induced with the gratuitous inducer o-xylene showed that expression of the TOL genes increased the iron requirement in both strains. Growth yields were reduced and substrate affinities decreased under iron-limited conditions, suggesting that iron availability can be an important parameter in the oxidative breakdown of hydrocarbons.Aerobic degradation of aromatic compounds by microorganisms proceeds via several oxidation steps that are catalyzed by oxygenases. Most of these oxygenases contain iron as a cofactor. Iron is also an important element because of its occurrence as a cofactor in various other proteins, including Krebs cycle enzymes, proteins of the respiratory pathway (6, 11), and enzymes involved in the virulence of pathogens (28). Thus, aerobic metabolism of hydrocarbons is expected to impose a specific iron requirement on cells (29).The availability of iron in natural environments is usually very low. In the rhizosphere, for instance, the total concentration of iron is estimated to be 0.1 M, and the concentration of dissolved iron, depending on the pH, can be as low as 10 Ϫ18 M (4). Under these conditions, where competition is strong, iron availability and the efficiency of iron uptake may influence microbial activity. To compete for iron, microorganisms have developed specialized uptake systems for which they produce siderophores that bind extracellular iron; after binding the iron-siderophore complex can be taken up by the organism via high-affinity receptors (for an overview see references 8, 33, and 34). A well-known example is the production and uptake of siderophores by the root-colonizing organism Pseudomonas putida WCS358 (9, 15); these siderophores can increase the levels of iron available to this strain in the rhizosphere (16). The efficiency of the uptake systems is crucially important in the strong competition among microorganisms that colonize plant roots (7).It has been shown that iron-limited conditions can lead to altered utilization patterns for various compounds (30) and that iron availability can alter the composition of plant root exudates (36). Very little...
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