Identification of naphthalene carboxylase subunits of the sulfate-reducing culture N47

Abstract

Expanding industrialization and the associated usage and production of mineral oil products has caused a worldwide spread of polycyclic aromatic hydrocarbons. These pollutants accumulate and persist under anoxic conditions but little is known about the biochemical reactions catalyzing their anaerobic degradation. Recently, carboxylation of naphthalene was demonstrated for the sulfate-reducing culture N47. Proteogenomic studies on N47 allowed the identification of a gene cluster with products suggested to be involved in the initial reaction of naphthalene degradation. Here, we performed comparative proteomic studies with N47 proteins extracted from naphthalene versus 2-methylnapththalene-grown cells on blue native PAGE. The analysis led to the identification of subunits of the naphthalene carboxylase of N47. Moreover, we show that the identified subunits are encoded in an operon structure within the previously mentioned naphthalene carboxylase gene cluster. These findings were supported by a pull-down experiment revealing in vitro interaction partners of a heterologously produced GST-tagged naphthalene carboxylase subunit. Based on these lines of evidence, naphthalene carboxylase is proposed to be a complex of about 750 kDa. Naphthalene carboxylase can be seen as a prototype of a new enzyme family of UbiD like de-/carboxylases catalyzing the anaerobic activation of non-substituted polycyclic aromatic hydrocarbons.

Enzymes involved in phthalate degradation in sulphate‐reducing bacteria

“…However, no other gene typical of anaerobic phthalate degradation was identified in the near genomic environment. Notably, naphthalene degradation is initiated by naphthalene carboxylation, catalysed by a further UbiD-like enzyme present in sulphate-reducing bacteria during growth with aromatics (Koelschbach et al, 2019). No other clearly significant homologue of PCD (amino acid sequence identity ≥65%) was identified in the genomes of other strictly anaerobic bacteria that are known to have the enzyme inventory of the benzoyl-CoA degradation pathway.…”

Identification of a Fully Dechlorinated Product of Chlordecone in Soil Microcosms and Enrichment Cultures

“…However, the chlorinated indenes (9C) are more chlorinated than the carboxylated indenes (10C), which is confusing if the carboxyl substituent remained from the parent compound. Perhaps, multiple separate and parallel pathways to the various sets of products are operating (Figure S1) as previously proposed; a carboxylation reaction following formation of pentachloroindene is also a possibility, akin to naphthalene carboxylation in anaerobic environments …”

Anaerobic biodegradation of phenanthrene by a newly isolated nitrate‐dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses

“…Genes encoding candidate enzymes capable of degrading phenanthrene under denitrifying conditions were noted in the assembled genome based on functional genes for anaerobic benzene, the benzene series, naphthalene and phenanthrene biodegradation. Homologues of genes known to mediate carboxylation of phenol, benzene naphthalene and phenanthrene ( ubiD ) (Bergmann et al ., 2011b; Atashgahi et al ., 2018; Koelschbach et al ., 2019; Kraiselburd et al ., 2019), benzene, phenol and naphthalene ( ppcD ) (Abu Laban et al ., 2010; DiDonato Jr. et al ., 2010; Bergmann et al ., 2011b) were present in the PheN1 genome (Table S1). Homologues of genes encoding enzymes that may be associated with the methylation of phenanthrene, the fumarate addition to 2‐methylphenanthrene and the sequential β‐oxidation of phenanthyl‐2‐methyl‐succine were also present in the genome.…”