Analysis of the nucleotide sequence of a cryptic plasmid from Yersinia pestis strains in the Central-Caucasian high-mountain plague focus

An analysis of a 5.4-kb cryptic plasmid detected in the course of whole-genome sequencing of the Yersinia pestis medieval biovar strain isolated in the Russian Central-Caucasian high-mountain plague focus was performed. The identification of the nucleotide sequence of this cryptic plasmid and its structural and functional analysis revealed that it contained eight open reading frames, among which the following genes were identified: the rep gene of a replication protein, the virB6 gene of a type IV secretion system inner membrane protein, the virB5 gene of the type IV secretion system minor pilin, and a number of genes probably associated with secretion and transport. A general analysis of the pCKF plasmid DNA showed that the adenine content was 28.34%, the cytosine content was 20.5%, the guanine content was 17.87%, and that of thymine was 33.28%, while the total G+C content appeared to be 38.38%. The G+C content of the chromosome of the Y. pestis strain C-627 is 47.6%, which indicates that the pCKF plasmid was obtained from a microorganism phylogenetically distant from the Yersinia bacteria and any other bacteria from the Enterobacteriaceae family. A comparison of the amino acid sequences of hypothetical proteins encoded by pCKF plasmid with analogous proteins encoded by other bacteria was carried out. The possible contribution of the pCKF plasmid to the maintenance of the most ancient known phylogenetic line of Y. pestis medieval biovar, 2.MED0, was discussed.