Microbial degradation of pyridine: a complete pathway deciphered in Arthrobacter sp. 68b

Vida Časaitė, Rūta Stanislauskienė, Justas Vaitekūnas, Daiva Tauraitė, Rasa Rutkienė, Renata Gasparavičiūtė, Rolandas Meškys
Applied and Environmental Microbiology 2020 May 29
Pyridine and its derivatives constitute majority of heterocyclic aromatic compounds that occur largely as a result of human activities and contribute to the environmental pollution. It is known, that they can be degraded by various bacteria in the environment, however, the degradation of unsubstituted pyridine has not yet been completely resolved. In this study we present data on the pyridine catabolic pathway in Arthrobacter sp. 68b at the level of genes, enzymes and metabolites. The pyr genes cluster, responsible for degradation of pyridine, was identified in a catabolic plasmid p2MP. The pathway of pyridine metabolism consisted of four enzymatic steps and ended by formation of succinic acid. The first step in the degradation of pyridine proceeds through a direct ring cleavage catalyzed by a two-component flavin-dependent monooxygenase system, encoded by pyrA and pyrE genes. The genes pyrB , pyrC , and pyrD were found to encode ( Z )- N -(4-oxobut-1-enyl)formamide dehydrogenase, amidohydrolase, and succinate semialdehyde dehydrogenase, respectively. These enzymes participate in the subsequent steps of pyridine degradation. The metabolites of these enzymatic reactions were identified that allowed us to reconstruct the entire catabolic pathway of pyridine in Arthrobacter sp. 68b. Importance The biodegradation pathway of pyridine, a notorious toxicant, is relatively unexplored, as no genetic data related to this process has ever been presented. In this paper, we describe the plasmid-born pyr gene cluster, which encodes the complete set of genes responsible for degradation of pyridine. A key enzyme, the monooxygenase PyrA, which is responsible for the first step of the catabolic pathway, performs an oxidative cleavage of the pyridine ring without typical activation steps, such as reduction or hydroxylation of heterocycle. This work provides new insights into the metabolism of N -heterocyclic compounds in nature.

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