g. pSLGP, pSPHCH01, pSWIT01),

which presumably are not involved in the degradation of organic compounds, although the relevant annotations suggest that plasmids pSLPG and pSPHCH01 carry several genes, which are related to the resistance against toxic metals such as Cu or Hg. Unfortunately, there is some confusion in the annotation of the genes encoding the rep genes in this group. Thus, these genes have been annotated as repA in the case of plasmids pCHQ1, pLA1 click here and pSLGP, but as repB for plasmids pISP0, pSWIT01 and pSPHCH01. This differentiation is not reflected by the phylogenetic trees obtained in the course of the sequence comparisons and thus should be avoided (see e.g. Fig. 1). The coexistence of plasmids pSWIT01 and pSWIT02

in S. wittichii RW1 suggests that also the plasmids belonging to the ‘Mega-RPA-group’ (pSWIT02) and ‘Mega-Rep3-group’ (pSWIT01) represent different incompatibility groups within the sphingomonads. The sequence comparisons also suggested that the smaller plasmids in general code for Rep proteins which either belong to the HTH-36 superfamily or the RPA superfamily (Table 1). [But it should be kept in mind that Pfam 10134 (=RPA superfamily) and Pfam 01051(=Rep_3 superfamily) define closely related sequences.] The dendrogram also suggested that pISP2 and pUT1, pISP3 and pSY2, and pISP4 and pYAN-2, respectively, carry closely related Copanlisib mouse Rep proteins. As plasmids pISP2, pISP3 and pISP4 are able to coexist in Sphingomonas sp. MM-1, this might indicate that these groups represent three additional ‘incompatibility groups’ within the sphingomonads which might mainly enclose smaller plasmids. The identification of Rep proteins belonging to the RepA_C-, Rep_3- and RPA-superfamilies N-acetylglucosamine-1-phosphate transferase clearly demonstrated that the plasmids from sphingomonads are closely related to plasmids from other bacterial groups. Thus, RepA proteins belonging to the RepA_C family

have previously been described for plasmids from the incompatibility group IncW. The members of this incompatibility group (e.g. plasmids R388 or pSa) are known as broad-host-range plasmids and have already been isolated from Alphaproteobacteria (Fernández-Lopez et al., 2006). Similarly, Rep proteins belonging to the Rep_3 family have been identified in broad-host-range plasmids belonging to the IncN family (such as e.g. plasmid R46). Furthermore, a recent ‘metagenomic’ survey of rep genes obtained from activated sludge communities demonstrated that these three types of rep genes are rather prevalent among the rep genes observed in these complex communities (Sentchilo et al., 2013). The analysis of the large ‘megaplasmids’ pNL1 and pCAR3 had demonstrated that on these plasmids, parA and parB genes are located in close proximity to the repA genes (Romine et al., 1999; Shintani et al.