Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134.
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.
Pérez-Pantoja
Danilo
D
Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Center for Advanced Studies in Ecology and Biodiversity, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, Santiago, Chile.
De la Iglesia
Rodrigo
R
Pieper
Dietmar H
DH
González
Bernardo
B
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D020118:Cupriavidus necator / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D025461:Feedback, Physiological; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000502:physiology*; D005798:Genes, Bacterial / Q000502:physiology; D006841:Hydrocarbons, Aromatic / Q000378:metabolism*; D014176:Protein Biosynthesis / Q000502:physiology; D049490:Systems Biology / Q000379:methods*; D014158:Transcription, Genetic / Q000502:physiology
D001426:Bacterial Proteins; D006841:Hydrocarbons, Aromatic