Date Published: November 20, 2009
Publisher: Public Library of Science
Author(s): Nicholas Delihas, Olivier Neyrolles. http://doi.org/10.1371/journal.pone.0007941
Abstract: 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.
Partial Text: Borrelia species are unusual in that they carry a large number of plasmids , . Many of these plasmids encode a heterogeneous group of lipoproteins, some of which are outer cell surface proteins. Several lipoprotein genes are in a state of flux whereby plasmids encode multiple gene copies that vary in sequence and encode fragments of these genes as well . Transposable elements are also present, along with fragmented and degenerate transposase (Tpase) genes. Short repeat sequences are also found, as well as stem loop sequences that are linked to virulence protein genes , complement regulator-acquiring surface protein 1 (CRASP_1) and lipoprotein_1 (part of the paralogous gene family termed PFam60). The recent availability of complete genomic sequences from multiple Borrelia burgdorferi strains as well as different strains of Borrelia garinii and Borrelia afzelii (see http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi) allows for a detailed phylogenetic comparison between strains, which has heretofore not been available.
The functions of stem loops that are downstream of lipoprotein genes are not known. But the BBU29805_G01 and BBU29805_E23 3′ end stem loops retain the IS605B flanking region DNA motifs in a stable form and thus potentially may function at the DNA level. Homologs to lipoprotein BBU29805_G01 are likely to function at the RNA level as they have non-canonical base-pairs. Lipoprotein_1 gene homologs have lost the IS flanking region stem loop motif and developed elaborate stem loop structures. Stem loops in other prokaryotes are known to function as regulators. For example, MITEs and other inverted repeat elements are found linked to protein genes at either their 3′ or 5′ ends , , , . Some are co-transcribed with the associated protein gene , . These transcribed sequences fold into stem loops and are believed to regulate expression of the adjacent genes , , . By analogy, some of the Borrelia lipoprotein-associated stem loops may also serve as regulators.