Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199

The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, f rom Sphingomonas aromaticivorans F199 has been determined. A total of 186 o pen reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compou nds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with differe nt pathways appears to have evolved in response to similarities in biochemi cal mechanisms required for the degradation of intermediates in different p athways. A putative efflux pump and several hypothetical membrane-associate d proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall . Several genes associated with integration and recombination, including tw o group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision ev ents with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes as sociated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes .