Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Abstract

Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed 38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb DNA form was assembled from the sequences of clones carrying genes belonging to a novel EDO subfamily. This plasmid-like DNA form, designated pSKYE1, possessed genes for DNA replication and stable maintenance as well as a small set of genes for phenol degradation; the encoded enzymes, phenol hydroxylase and EDO, are capable of the detoxification of aromatic compounds. This gene set was found in 20 of the 38 analyzed clones, suggesting that this 'detoxification apparatus' may be widespread in the environment.

Isolation of a diphenylamine-degrading bacterium and characterization of its metabolic capacities, bioremediation and bioaugmentation potential

“…4). The low degradation capacity of the DPA-degrading bacterium against OPP could be of cometabolic nature and could be linked with the activity of monooxygenases or dioxygenases with relaxed substrate specificity that could attack one of the two aromatic rings adding one or two atoms of oxygen then converted by dehydrogenases in hydroxylated groups (Suenaga et al 2009). The capacity of the P. putida strain DPA1 to degrade, even at a slower rate, the fungicide OPP which is also used in the fruitpackaging industry and its residues could co-occur with DPA in the wastewaters constituting a desirable asset for its The degradation of DPA by the isolated strain in a range of pH and temperatures pH and temperature are among the main factors influencing the degradation ability of inoculants in full-scale applications Awasthi et al 2000), and optimization of such conditions is crucial for the efficiency of the process.…”

A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site

“…There are several uncharacterized close homologs (80 to 100% inferred aa identity) of the pDCA RepA gene product in draft genome sequences from Ochrobactrum, Paracoccus, Agrobacterium, Sphingobium, and Mesorhizobium strains. The closest homolog to the pDCA RepA protein that is known to be plasmid associated is RepA from the aromatic hydrocarbon catabolic plasmid pSKYE1 (88% inferred aa identity), derived from an uncultured bacterium (47). The closest homolog that is experimentally characterized is RepA from the tartrate catabolic plasmid pTAR, from Agrobacterium tumefaciens (34% inferred aa identity).…”

Characterization of Biphenyl Dioxygenase Sequences and Activities Encoded by the Metagenomes of Highly Polychlorobiphenyl-Contaminated Soils

“…Of course, the possibility that minor sequence differences were due to PCR errors cannot be ruled out. However, the detection of similar microheterogeneities and of comparable frequencies of nonsense and frameshift mutations in metagenomic studies involving not PCR, but direct cloning of environmental DNA (36,38), suggests that all or a major fraction of the apparent sequence diversity was of natural origin. Unequivocal consensus sequences could be determined for clusters I and II, as the bias toward one specific nucleotide or amino acid, respectively, was always very strong.…”