To separate these plasmids and to transfer them to a nonpathogenic host, in vitro transposition was performed with transposon EZ::TN
gene. This resulted in the selection of three recombinant LBH589 chemical structure plasmids in E. coli NM522: pIGMS31KAN, pIGMS32KAN, and pIGRKKAN (Table 1). Purified DNA of these plasmids served as the templates for DNA sequencing reactions. The position of the transposon insertion site in the individual plasmids is shown in Fig. 1. The full nucleotide sequences of plasmids pIGMS31 (2520 bp), pIGRK (2348 bp), and pIGMS32 (9294 bp) were determined. Interestingly, the plasmids pIGMS31 and pIGRK were found to have a very low GC content (32.7% and 33.4%, respectively; Fig. 1), well below that of pIGMS32 (55.2%) or the total DNA of K. pneumoniae (57%; Fouts et al., 2008; Wu et al., 2009), which suggested the relatively recent acquisition of these replicons Everolimus concentration by HGT. Detailed sequence analysis identified a number of putative functional genetic modules in the plasmids: (1) a replication system (REP; in pIGRK, pIGMS31), (2) a system for mobilization
for conjugal transfer (MOB; in pIGMS31, pIGMS32), (3) a toxin–antitoxin system (TA) encoding a ParE family toxin (in pIGMS32; Jiang et al., 2002), and (4) a phenotypic module responsible for bacteriocin (cloacin) production (in pIGMS32; Fig. 1). Comparative sequence analysis (NCBI database) revealed that pIGMS32 is identical to a recently reported plasmid pCKO3 from Citrobacter koseri ATCC BAA-895 (accession no. CP000823). Moreover, it shows significant similarity to other ColE1-like plasmids, such as CloDF13 (Nijkamp et al., 1986), and to a much larger plasmid 15S (23.7 kb) from K. pneumoniae strain 15 (Gootz et al., 2009; Fig. 1c). The core region of 15S is 100% identical to pIGMS32, but the structure of this plasmid has been affected by insertions and deletions generated by two transposons containing antibiotic resistance genes (Fig. 1c). This analysis also identified plasmids related to pIGMS31 and pIGRK, containing homologous
REP or MOB systems see more (Fig. 1a and b), which indicated recombinational shuffling of the plasmid-encoded genetic modules. Comparative sequence analysis revealed that plasmids pIGMS31 and pIGRK carry related replication systems. Their predicted replication initiation proteins (ReppIGMS31 and ReppIGRK) exhibit 35% identity at the amino acid sequence level. ReppIGMS31 also shows local similarities (c. 45% identity) to Rep proteins encoded by plasmids residing in Pectobacterium atrosepticum, Salmonella enterica, and E. coli (all Gammaproteobacteria), while ReppIGRK is most similar (58% identity) to a replication protein of pHW126 from Rahnella genomospecies 3 (strain WMR126; Rozhon et al., 2010).