Identification of proteins exhibiting in vitro RNA chaperone activity through gradient profiling in the Lyme disease spirochete, Borrelia burgdorferi

RNA-binding proteins (RBPs) play key roles in regulating gene expression in bacteria. However, relatively few RBPs have been discovered and characterized in Borrelia (Borreliella) burgdorferi, the causative agent of Lyme disease. We utilized gradient profiling to identify putative RBPs that co-sediment with small RNAs (sRNAs) and nascent mRNAs. We employed in vitro and in vivo assays to characterize the RNA chaperone activities of several proteins we identified in the gradient profiling. The previously hypothetical proteins BB0749, BB0713 and BB0796, as well as the chemotaxis-related protein CheY2 and the flagella-associated protein FlgV displayed RNA annealing and/or strand displacement activity. Moreover, in vivo Co-IP assays demonstrated BB0749 binds RNA in B. burgdorferi.