Post-initiation mechanisms, like those regulating the ethanolamine utilization (eut) genes in E. faecalis, are incompletely understood representing a critical gap in knowledge. The long-term goal of this research is to determine how ethanolamine (EA) utilization is regulated in E. faecalis. The objective of this application is to elucidate the post-initiation regulatory mechanisms that control gene expression. The central hypothesis is that the AmiR and NasR Transcriptional Antiterminator Regulators' (ANTARs) RNA substrates are the central regulatory feature of the system and control gene expression by three interrelated mechanisms. The central hypothesis will be tested in three aims.
Aim 1 will elucidate the molecular details of how EutV, the ANTAR in the eut system, interacts with its RNA substrates to control gene expression. There is evidence that EutV binds a dual hairpin RNA structure with specific features. To further understand the structure of this complex, biophysical approaches will be employed, including resolution of three-dimensional structures of the protein-RNA complex by X-ray crystallography.
In Aim 2, the mechanism by which the AdoCbl riboswitch regulates gene expression will be uncovered. The novel, working hypothesis is that a dual hairpin substrate just downstream of the riboswitch binds and sequesters active EutV, preventing induction by EA alone. AdoCbl binding to the riboswitch causes a conformational change that prevents EutV sequestration, allowing for induction when both EA and AdoCbl are present. The model will be assessed by quantifying in vivo levels of protein and RNA, measuring binding constants, and by mutational analysis of the sRNA. Finally, in silico analysis will investigate how broadly this mechanism applies to microbial systems.
Aim 3 will identify how eut gene expression is turned off. Our working hypothesis is that bacterial microcompartment (BMC) formation sequesters one or more of the crucial ingredients for gene expression - EA, AdoCbl and/or EutV/EutW. By characterizing the dynamics of gene expression and BMC formation with fluorescent markers and transmission electron microscopy (TEM), the hypothesis will be tested. The research in this proposal will further the understanding of how the eut genes are regulated, contributing knowledge to the field of prokaryotic gene regulation and to the identification of potential antimicrobial targets. Specifically, the significance of this contribution will be the uncovering of novel mechanisms by which ANTARs, riboswitches, and BMCs control gene expression. The proposed research is innovative because these new mechanisms will challenge the status quo and expand the field's thinking on how RNA structural features and BMCs can operate.
The research proposed in this application will lead to greater understanding of how regulatory RNAs in a human bacterial pathogen control gene expression. Such knowledge is relevant to public health because it will contribute to efforts focused on exploiting these regulatory mechanisms as potential antimicrobial targets.
