The analysis of the published information and the sequences deposited in the public databases
allowed a first classification of these plasmids into a Nutlin-3 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 (Rep) proteins. These Rep proteins belong to the protein superfamilies RepA_C (Pfam 04796), Rep_3 (Pfam 01051), RPA (Pfam 10134) and HTH-36 (Pfam 13730). The ‘degradative megaplasmids’ pNL2, pCAR3, pSWIT02, pCHQ1, pISP0, and pISP1, which code for genes involved in the degradation of aromatic hydrocarbons, carbazole, dibenzo-p-dioxin and γ-hexachlorocyclohexane, carry Rep proteins which either belong to the RepA_C- (plasmids
pNL2, pCAR3, pSWIT02), Rep-3- (plasmids pCHQ1, pISP0) or RPA-superfamily (pISP1). The classification of these ‘degradative megaplasmids’ into three groups is also supported by sequence comparisons GSI-IX cell line of the proteins involved in plasmid partition (ParAB) 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. The sphingomonads represent a group of Alphaproteobacteria, Demeclocycline which encompass in our days the genera Novosphingobium, Sphingobium, Sphingomonas, Sphingopyxis, Sphingosinicella, Sphingomicrobium, Sphingorhabdus and Parasphingopyxis. These genera share a number of phenotypic traits, such as the presence of sphingolipids in their outer membranes, the formation of usually yellow-pigmented colonies and a specific pattern of polyamines (Kämpfer et al., 2012; Uchida et al., 2012; Jogler et al., 2013). Sphingomonads have been
intensively studied during the last years because of their pronounced ability to degrade recalcitrant natural and xenobiotic compounds, such as various polycyclic aromatic hydrocarbons (PAHs), nonylphenols, sulphonated naphthalenes, chlorinated dibenzofurans and dibenzodioxins, carbazole, polyethylene glycols and different herbicides and pesticides (Stolz, 2009). It was shown in the last years that many sphingomonads possess (often several) plasmids and especially that rather large plasmids are common in this bacterial group. These large plasmids are commonly designated as ‘megaplasmids’ if their sizes exceed about 100 kbp (Basta et al., 2004, 2005; Aylward et al., 2013). These ‘megaplasmids’ often carry genes coding for degradative pathways, which are often found either on different replicons (as e.g.