The intent of this review is to provide an outline of the microbial degradation of polycyclic aromatic hydrocarbons. A catabolically diverse microbial community, consisting of bacteria, fungi and algae, metabolizes aromatic compounds. Molecular oxygen is essential for the initial hydroxylation of polycyclic aromatic hydrocarbons by microorganisms. In contrast to bacteria, filamentous fungi use hydroxylation as a prelude to detoxification rather than to catabolism and assimilation. The biochemical principles underlying the degradation of polycyclic aromatic hydrocarbons are examined in some detail. The pathways of polycyclic aromatic hydrocarbon catabolism are discussed. Studies are presented on the relationship between the chemical structure of the polycyclic aromatic hydrocarbon and the rate of polycyclic aromatic hydrocarbon biodegradation in aquatic and terrestrial ecosystems.

Biodegradation of polycyclic aromatic hydrocarbons

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.

/pdf/complete-genome-sequence-and-comparative-analysis-of-the-4xl8ywmhap.pdf

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

Aromatic compounds are both common growth substrates for microorganisms and prominent environmental pollutants. The crucial step in their degradation is overcoming the resonance energy that stabilizes the ring structure. The classical strategy for degradation comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen. Here, we describe three alternative strategies used by microorganisms to degrade aromatic compounds. All three of these methods involve the use of CoA thioesters and ring cleavage by hydrolysis. However, these strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.

/pdf/microbial-degradation-of-aromatic-compounds-from-one-1uyafyshep.pdf

Microbial degradation of aromatic compounds — from one strategy to four

The beta-ketoadipate pathway is a chromosomally encoded convergent pathway for aromatic compound degradation that is widely distributed in soil bacteria and fungi. One branch converts protocatechuate, derived from phenolic compounds including p-cresol, 4-hydroxybenzoate and numerous lignin monomers, to beta-ketoadipate. The other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates. Enzyme studies and amino acid sequence data indicate that the pathway is highly conserved in diverse bacteria, including Pseudomonas putida, Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Rhodococcus erythropolis, and many others. The catechol branch of the beta-ketoadipate pathway appears to be the evolutionary precursor for portions of the plasmid-borne ortho-pathways for chlorocatechol degradation. However, accumulating evidence points to an independent and convergent evolutionary origin for the eukaryotic beta-ketoadipate pathway. In the face of enzyme conservation, the beta-ketoadipate pathway exhibits many permutations in different bacterial groups with respect to enzyme distribution (isozymes, points of branch convergence), regulation (inducing metabolites, regulatory proteins), and gene organization. Diversity is also evident in the behavioral responses of different bacteria to beta-ketoadipate pathway-associated aromatic compounds. The presence and versatility of transport systems encoded by beta-ketoadipate pathway regulons is just beginning to be explored in various microbial groups. It appears that in the course of evolution, natural selection has caused the beta-ketoadipate pathway to assume a characteristic set of features or identity in different bacteria. Presumably such identities have been shaped to optimally serve the diverse lifestyles of bacteria.

THE β-KETOADIPATE PATHWAY AND THE BIOLOGY OF SELF-IDENTITY

Publisher Summary This chapter discusses the catabolism of aromatic compounds by micro-organisms, and reviews (1) enzymic degradations of di- and trihydroxy phenols, (2) reactions converting aromatic compounds into ring-fission substrates, and (3) regulation of catabolic reaction sequences. Ortho-Fission pathways of catechol and protocatechuate as well as meta-fission pathways of catechols are discussed. Important information relating to meta fission has emerged from studies of the microbial degradation of steroids, and an outline of some of these reactions is also given. The enzymic hydroxylation of phenylalanine has been extensively investigated. The system resembles p-hydroxybenzoate hydroxylase except that the natural cofactor is dihydrobiopterin and not FAD. Pteridines resemble flavins in chemical structure and in their enzymic reactions, but they serve only as electron carriers for hydroxylations and not in the normal electron-transport systems. In both the mammalian and pseudomonad systems, hydroxylation of phenylalanine proceeds by a mechanism, which has been termed the “NIH shift”. The chapter also discusses the bacterial metabolism of gentisates, metabolism of thymol, the oxidation of phenylpropanoid structures arising from Lignins, degradation of α-conidendrin, and regulation of ortho-fission pathways.

Catabolism of aromatic compounds by micro-organisms.

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Catabolism of aromatic compounds by micro-organisms.