fumarates and naphthalene

In spite of their chemical inertness, hydrocarbons are degraded by microorganisms in the complete absence of oxygen. As all known aerobic hydrocarbon degradation pathways start with oxygen-dependent reactions, hydrocarbon catabolism in anaerobes must be initiated by novel biochemical reactions. In recent years, the enzymes catalyzing oxygen-independent activation of several hydrocarbons have been identified. Surprisingly, a variety of reactions seems to be employed to overcome the activation barrier of different hydrocarbons. This review presents the current understanding on some of these reactions and the associated degradation pathways: oxygen-independent hydroxylation as employed in ethylbenzene metabolism, fumarate addition to methyl or methylene carbons in toluene or alkane degradation, and only recently discovered reactions such as methylation of naphthalene or anaerobic methane oxidation via reverse methanogenesis.

Topics: Anaerobiosis; Fumarates; Hydrocarbons; Hydroxylation; Methane; Methylation; Naphthalenes; Oxidation-Reduction

Bacterial chemotaxis enables motile cells to move along chemical gradients and to swim toward optimal places for biodegradation. However, its potentially positive effects on subsurface remediation rely on the efficiency of bacterial movement in porous media, which is often restricted by high deposition rates and adhesion to soil surfaces. In well-controlled column systems, we assessed the influence of the chemo-effectors naphthalene, salicylate, fumarate, and acetate on deposition of chemotactic, naphthalene-degrading Pseudomonas putida G7 in selected porous environments (sand, forest soil, and clay aggregates). Our data showed that the presence of naphthalene in the pore water decreased deposition of strain 67 (but not of a derivative strain, P. putida 67.C1 (pHG100), nonchemotactic to naphthalene) by 50% in sand-filled columns, as calculated by the relative adhesion efficiency (at). Similar effects were observed with P. putida G7 strain for the other chemoeffectors. Deposition, however, depended on the chemoeffector's chemical structure, its interaction with the column packing material, and concomitantly its pore-water concentration. As the presence of the chemoeffectors had no influence on the physicochemical surface properties of the bacteria, we suggest that chemotactic sensing, combined with changed swimming modes, is likely to influence the deposition of bacteria in the subsurface, provided that the chemoeffector is dissolved at sufficient concentration in the pore water.

Topics: Acetates; Chemotaxis; Fumarates; Naphthalenes; Pseudomonas putida; Salicylic Acid; Water Microbiology

Prior research revealed that Polaromonas naphthalenivorans CJ2 carries and expresses genes encoding the gentisate metabolic pathway for naphthalene. These metabolic genes are split into two clusters, comprising nagRAaGHAbAcAdBFCQEDJI'-orf1-tnpA and nagR2-orf2I''KL (C. O. Jeon, M. Park, H. Ro, W. Park, and E. L. Madsen, Appl. Environ. Microbiol. 72:1086-1095, 2006). BLAST homology searches of sequences in GenBank indicated that the orf2 gene from the small cluster likely encoded a salicylate 5-hydroxylase, presumed to catalyze the conversion of salicylate into gentisate. Here, we report physiological and genetic evidence that orf2 does not encode salicylate 5-hydroxylase. Instead, we have found that orf2 encodes 3-hydroxybenzoate 6-hydroxylase, the enzyme which catalyzes the NADH-dependent conversion of 3-hydroxybenzoate into gentisate. Accordingly, we have renamed orf2 nagX. After expression in Escherichia coli, the NagX enzyme had an approximate molecular mass of 43 kDa, as estimated by gel filtration, and was probably a monomeric protein. The enzyme was able to convert 3-hydroxybenzoate into gentisate without salicylate 5-hydroxylase activity. Like other 3-hydroxybenzoate 6-hydroxylases, NagX utilized both NADH and NADPH as electron donors and exhibited a yellowish color, indicative of a bound flavin adenine dinucleotide. An engineered mutant of P. naphthalenivorans CJ2 defective in nagX failed to grow on 3-hydroxybenzoate but grew normally on naphthalene. These results indicate that the previously described small catabolic cluster in strain CJ2 may be multifunctional and is essential for the degradation of 3-hydroxybenzoate. Because nagX and an adjacent MarR-type regulatory gene are both closely related to homologues in Azoarcus species, this study raises questions about horizontal gene transfer events that contribute to operon evolution.

Topics: Bacterial Proteins; Comamonadaceae; Dicarboxylic Acids; Electrophoresis, Polyacrylamide Gel; Fumarates; Gene Deletion; Gentisates; Hydroxybenzoates; Mixed Function Oxygenases; Models, Genetic; Molecular Structure; Mutation; Naphthalenes; Pimelic Acids; Pyruvates; Recombinant Proteins