Riboswitch-based gene regulation of manganese ion transporters

University Of California-San Diego, La Jolla CA

Investigators

Abstract

Metal ions are important components of biomolecules in cells and help those molecules perform chemical reactions for cell survival. In excess, however, metals can be toxic to cells. Organisms evolved ways to regulate metal ion quantity to keep it at a healthy level. This is achieved by controlling metal ion import and export based on its current amount within the cell. One of the ways by which bacteria sense the current cellular content of metals is with RNA “switches” that bind the metal and turn production of metal ion transporters ON or OFF. This project aims to understand the details of how the signal from RNA-metal ion interaction is propagated into the part of a messenger RNA from which the transporter protein is produced. The gained knowledge will be useful for engineering new RNA-based biosensors, for sensing metal ions in water, as an example. This project will engage and support community college students as they navigate applying to transfer to a four-year university and getting involved in research once transferred. Multiple activities scheduled around the transfer application cycle will provide students with information, as well as networking and paid research opportunities. Riboswitches are non-coding gene regulatory RNAs, which adopt intricate folds that are “switched” when a ligand in the cell binds to the RNA “aptamer”. Although riboswitches were discovered ~20 years ago, the details of signal transduction from the aptamer to the expression platform, where the gene regulatory decision is made, are still not well understood. This project will expand our understanding of how riboswitches rearrange their structure during transcription in response to a ligand, getting to the heart of how they execute gene regulatory decisions. In Aim 1, we will map the co-transcriptional folding pathway of example manganese (Mn)-sensing riboswitches in E. coli. In Aim 2, we will expand our studies to other members of the large Mn-sensing family of riboswitches, which share some of the key aptamer elements but diverge in other aptamer components and the expression platform. This analysis will uncover general principles as well as distinct features of how these riboswitches regulate genes upon binding a metal ion ligand within their native environments. To accomplish these goals, we will employ a multidisciplinary suite of experimental tools from in vitro probing of RNA structure during transcription to reading out gene expression outputs in bacterial cells. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.