Degradative plasmids from sphingomonads

Large plasmids (‘megaplasmids’) are commonly found in members of the Alphaproteobacterial family S phingomonadaceae (‘sphingomonads’). These plasmids contribute to the extraordinary catabolic flexibility of this group of organisms, which degrade a broad range of recalcitrant xenobiotic compounds. The genomes of several sphingomonads have been sequenced during the last years. In the course of these studies, also the sequences of several plasmids have been determined. The analysis of the published information and the sequences deposited in the public databases allowed a first classification of these plasmids into a restricted number of groups according to the proteins involved in the initiation of replication, plasmid partition and conjugation. The sequence comparisons demonstrated that the plasmids from sphingomonads encode for four main groups of replication initiation ( R ep) proteins. These R ep proteins belong to the protein superfamilies R ep A _ C ( P fam 04796), R ep_3 ( P fam 01051), RPA ( P fam 10134) and HTH ‐36 ( P fam 13730). The ‘degradative megaplasmids’ p NL 2, p CAR 3, p SWIT 02, p CHQ 1, p ISP 0, and p ISP 1, which code for genes involved in the degradation of aromatic hydrocarbons, carbazole, dibenzo‐ p ‐dioxin and γ‐hexachlorocyclohexane, carry R ep proteins which either belong to the R ep A _ C ‐ (plasmids p NL 2, p CAR 3, p SWIT 02), R ep‐3‐ (plasmids p CHQ 1, p ISP 0) or RPA‐superfamily (p ISP 1). The classification of these ‘degradative megaplasmids’ into three groups is also supported by sequence comparisons of the proteins involved in plasmid partition ( P ar AB ) and the organization of the three genes on the respective plasmids. All analysed ‘degradative megaplasmids’ carry genes, which might allow a conjugative transfer of the plasmids. Sequence comparisons of these genes suggest the presence of at least two types of transfer functions, which either are closer related to the tra ‐ or vir ‐genes previously described for plasmids from other sources.