Enzymes involved in phthalate degradation in sulphate‐reducing bacteria

Abstract

Summary The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o‐phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here, we demonstrate a previously overseen growth of the δ‐proteobacterium Desulfosarcina cetonica with phthalate/sulphate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short‐lived phthaloyl‐CoA by an ATP‐dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl‐CoA by an UbiD‐like phthaloyl‐CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulphate‐reducing Desulfobacula toluolica, strain NaphS2, and other δ‐proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl‐CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl‐CoA, the possibly most unstable CoA ester in biology.

Microbial degradation of phthalates: biochemistry and environmental implications

“…Further, a Pelotomaculum isopthalicum species has been described that grows with all three phthalate isomers in syntrophic association with a methanogen (Qiu et al ., ). In a recent study, the previously overseen capacity of the sulfate‐reducing, benzoate‐degrading Desulfosarcina cetonica to use phthalate as carbon and together with sulfate as energy source was reported (Geiger et al ., ). A differential proteome analysis identified a gene cluster that was induced in D. cetonica cells grown with phthalate versus benzoate.…”

“…Similar as in denitrifying bacteria, phthaloyl‐CoA accumulated only to submicromolar concentrations as a result of its rapid decay by intramolecular hydrolysis. In the coupled assays with enriched PCD, the ready formation of benzoyl‐CoA from ATP, CoA and PA was demonstrated (Geiger et al ., ).…”

“…As a consequence, succinyl‐CoA is not available to significant amounts to serve as CoA donor for phthalate activation. Indeed, the cellular succinyl‐CoA concentrations in D. cetonica grown with phthalate are several orders of magnitude lower than in denitrifying bacteria (Geiger et al ., ).…”

“…A phthalate degradation gene cluster highly similar to that of D. cetonica was identified in Desulfobacula toluolica , a sulfate‐reducing δ‐proteobacterium known to degrade several monocyclic aromatic compounds (Wöhlbrand et al ., ), leaving little doubt that this organism has the capacity to growth with phthalate and sulfate. However, no complete phthalate catabolic gene cluster was found in other known aromatic compound degrading strictly anaerobic bacteria (Geiger et al ., ). A number of putative δ‐proteobacterial PCD encoding genes (amino acid sequence identity ≥66%) are present in the metagenomes of a shallow sediment‐hosted perennially suboxic/oxic aquifer (Anantharaman et al ., ), suggesting that phthalate degradation capacity is present in many so far unknown δ‐proteobacteria.…”

The class II benzoyl‐coenzyme A reductase complex from the sulfate‐reducing Desulfosarcina cetonica

“…Desulfosarcina cetonica strain 480 (DSMZ 7267) was anaerobically cultivated in a 200 L fermenter at 30 C in a mineral salt medium with benzoate (1-5 mM) as sole carbon source and sulfate (20-25 mM) as electron acceptor, similar as described recently (Geiger et al, 2019). Cells were harvested by centrifugation (20 000g) in the exponential growth phase.…”