Computational and Genetic Exploration of RNA-binding FinO-domain Structures.

Evolving research on small RNAs (sRNAs) in bacteria implicates sRNAs as a key effector of gene regulation. While some sRNAs are able to act independently, many are dependent on an RNA-binding protein, such as the well-established Hfq in Escherichia coli. Another family of RNA-binding proteins is the FinO family, including ProQ and FinO in E. coli, NMB1681 in N. meningitidis, and Lpp1663 in L. pneumophila. Structures for these proteins have been solved through both NMR and X-ray diffraction, in addition to computational predictions. While many structural elements are common across all structures, there are interesting differences in regions that have been implicated by genetic experiments to be important for RNA binding. In order to investigate the structure and function relationships of these proteins, we have analyzed the available models for FinO family proteins to compare intriguing structural features, including the position and predicted contacts of a universally conserved arginine that plays a critical role in RNA binding. Finally, we are probing predicted interactions from structural models with the use of site-directed mutagenesis and our laboratory's bacterial three-hybrid (B3H) assay. Together, this work is generating insights into the most relevant structural conformations for in vivo RNA binding by FinO proteins and the ways in which the structure of E. coli ProQ is both similar and distinct from orthologous FinO domain proteins.