Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134

Abstract

Cupriavidus necator JMP134 is a model for chloroaromatics biodegradation, capable of mineralizing 2,4-D, halobenzoates, chlorophenols and nitrophenols, among other aromatic compounds. We performed the metabolic reconstruction of aromatics degradation, linking the catabolic abilities predicted in silico from the complete genome sequence with the range of compounds that support growth of this bacterium. Of the 140 aromatic compounds tested, 60 serve as a sole carbon and energy source for this strain, strongly correlating with those catabolic abilities predicted from genomic data. Almost all the main ring-cleavage pathways for aromatic compounds are found in C. necator: the beta-ketoadipate pathway, with its catechol, chlorocatechol, methylcatechol and protocatechuate ortho ring-cleavage branches; the (methyl)catechol meta ring-cleavage pathway; the gentisate pathway; the homogentisate pathway; the 2,3-dihydroxyphenylpropionate pathway; the (chloro)hydroxyquinol pathway; the (amino)hydroquinone pathway; the phenylacetyl-CoA pathway; the 2-aminobenzoyl-CoA pathway; the benzoyl-CoA pathway and the 3-hydroxyanthranilate pathway. A broad spectrum of peripheral reactions channel substituted aromatics into these ring cleavage pathways. Gene redundancy seems to play a significant role in the catabolic potential of this bacterium. The literature on the biochemistry and genetics of aromatic compounds degradation is reviewed based on the genomic data. The findings on aromatic compounds biodegradation in C. necator reviewed here can easily be extrapolated to other environmentally relevant bacteria, whose genomes also possess a significant proportion of catabolic genes.

Coenzyme A-dependent Aerobic Metabolism of Benzoate via Epoxide Formation

“…For comparison, 7% of the species harbor benzoate 1,2-dioxygenase benABC and cis-diol dehydrogenase benD genes characteristic for the classical benzoate pathway involving ring-cleaving dioxygenases. Some species contain even both options (1.3%) (supplemental Table S1), which might be required for high turnover of benzoate or if reduced oxygen tension is present, as has been suggested for Burkholderia xenovorans LB400 (6,25). These percentages indicate that the new pathway is not a minor route.…”

Nitroaromatic Compounds, from Synthesis to Biodegradation

“…10). While genome sequencing of JMP134 has led to the identification of possible genes encoding the enzymes of the 3-nitrophenol degradation pathway, they have yet to be verified experimentally (150).…”

“…Removal of the second nitro group is predicted to occur in the later steps of the pathway. The recently completed genome sequence of C. necator JMP134 (150) should aid in the identification of the genes and enzymes for the catabolism of 2,6-dinitrophenol.…”

Desulfitobacterium contributes to the microbial transformation of 2,4,5‐T by methanogenic enrichment cultures from a Vietnamese active landfill

“…Daubaras et al ., 1996; Schlömann, 2002; Pérez‐Pantoja et al ., 2008; Xu et al ., 2013). Degradation starts with an oxygenase‐catalysed cleavage of the ether bond (e.g.…”