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Background  Plasmids of  Borrelia  species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element  IS605/200  family, as well as degenerate forms of this  IS  element, are prevalent. In  Helicobacter pylori , flanking regions of the  IS605  transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level.    Methodology/Principal Findings  In work reported here, bioinformatics techniques were used to scan  Borrelia  plasmid genomes for  IS605  transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found “free-standing” and phylogenetically conserved without the associated  IS605  transposase gene or the adjacent flanking sequence. Importantly,  IS605  specific stem loop sequences are also found at the 3′ ends of lipoprotein genes (PFam12 and PFam60), however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the  IS605  stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the  IS605  stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place.    Conclusions/Significance  Stem loop sequences specific to the transposable element  IS605  are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in  Borrelia  plasmids. These sequences are evolutionarily conserved and/or structurally developed in an RNA format. The findings show that  IS605  stem loop sequences are multifaceted and are selectively conserved during evolution when the transposable element dissipates.

Stem Loop Sequences Specific to Transposable Element IS605 Are Found Linked to Lipoprotein Genes in Borrelia Plasmids