Helicase-like SWI/SNF polypeptides are present in organisms belonging to distant kingdoms from bacteria to humans, indicating that these proteins perform a very basic and ubiquitous form of nucleic acid management. Existing studies associate the activity of SWI/SNF proteins almost exclusively with the remodeling of DNA and protein-DNA complexes. The bacterial SWI/SNF representative RapA has been previously established as an integral element of the E. coli RNA polymerase transcriptional apparatus. In this proposal, we present multiple, independent lines of evidence indicating that RNA is the primary substrate of RapA. We demonstrate the formation of highly stable RapA-RNA intermediates in functional in vitro transcription reactions and present other, independent lines of evidence (including the possible destabilizing effect of RapA on putative non-canonical DNA-RNA complexes, which is consistent with recent studies indicating similar roles for eukaryotic SWI/SNF proteins in DNA triplex displacement) to further support this conclusion. We propose to further study this novel role of RapA in RNA management. During the first stage of the project (years 1 and 2) we propose to focus on determination of the role of RapA in the remodeling of post-termination DNA-RNA polymerase-RNA ternary complexes (Sukhodolets et al., 2001, Genes Dev 15:3330-3341). Taken together, our preliminary studies indicate that RapA may promote RNA release from nonproductive DNA-RNA polymerase-RNA transcription complexes, and we propose to test this model against alternative models. During the course of these experiments, genetically modified forms of RapA incapable of ATP hydrolysis will be used as negative controls. During the second stage of the project (years 2 and 3), we propose to map the nucleic acid template-recognition motifs in RapA as well as its RNA polymerase-recognition subdomains using biochemical and genetic techniques. Furthermore, we propose to carry out an in vivo study of the genetic interactors of rapA in E. coli. Identification of RNA as the primary substrate for a SWI/SNF protein is a novel finding; further studies with RapA could deepen our understanding of the functions of all SWI/SNF proteins. Mutations in human SWI/SNF genes have been conclusively linked to cancer. Studies with RapA could eventually produce a better understanding of how and why mutations in SWI/SNF genes trigger the development of cancer. ? ? A basic study of the RNA-remodeling activity by the bacterial SWI/SNF protein RapA. Mutations in eukaryotic homologs of RapA have been conclusively linked to cancer. ? ? ?
