These four sequence blocks were separated selleck chemicals by a variable to a certain degree among the plasmids 10-mer sequence that was identical for each plasmid. Of note, the same 10-mer sequence could also be found preceding the first 12-mer block. DNA folding simulations for pREN

ori revealed a putative hairpin in the variable region and two identical stem loops in the iteron region (Fig. 3b). Similar secondary structure organizations could also be detected in the oris of all other plasmids (data not shown). While the significance of these structures remains to be investigated, it is important to state that the similarity in secondary structures among the plasmids is clearly driven by sequence conservation (Fig. 3a). The overall architecture of pREN was assessed in comparison with that of other members of the pUCL287 family of plasmids. Interestingly, while the replication backbone of pREN (ori and repA) was highly conserved (data not shown), blastn queries returned only two hits showing identity over the entire plasmid sequence, i.e. pLB925A03 and Nutlin-3a supplier pLJ42. pLB925A03 carries seven orfs on its 8881 bp sequence, consisting of two genes (repA and repB) involved in the replication process, three genes for mobilization and two

unknown genes. pLJ42 (5529 bp in length) encodes a replication (RepA) and three mobilization (MobA, MobB and MobC) proteins. We synchronized all three plasmid annotations so as to start from the first nucleotide of the repA gene in order to perform full-length Bacterial neuraminidase plasmid sequence alignments (Fig. 4). This comparative mapping of plasmids demonstrated that they share a common organization not only in their replication backbone (repA-orf2 operon and the ori regions) but also in the mobilization backbone. The three consecutive mob genes showed a high degree of identity among the plasmids, with the exception of pREN, which, due to the frameshift mutation mentioned earlier, had its mobA gene disrupted in two truncated pseudogenes. This organization of the replication and mobilization elements seems to be unique

within the pUCL287 family. According to our analysis, only pREN and pLJ42 possess the basal backbone for this type of plasmids, because an insertion of approximately 4500 bp was evident downstream of the mob genes for plasmid pLB925A03. Furthermore, the phylogeny of RepA, MobC and MobA was surveyed. MobB was excluded from this analysis because it could be detected in only five other bacteria, as mentioned earlier. In the case of MobA, the two truncated proteins of pREN were also omitted from the phylogenetic trees and therefore all conclusions presented below were based on the MobA sequence of plasmid pLB925A03. RepA of pREN clustered with the respective proteins of other Lactobacillus plasmids (Fig. 5a) and a clear relation of this cluster with several enterococci replication initiation proteins was observed.