Spatial arrangement of functional domains in OxyS stress response sRNA
- 1Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- 2Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- 3Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
- 4EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
- Corresponding author: peter.podbevsek{at}ki.si
Abstract
Small noncoding RNAs are an important class of regulatory RNAs in bacteria, often regulating responses to changes in environmental conditions. OxyS is a 110 nt, stable, trans-encoded small RNA found in Escherichia coli and is induced by an increased concentration of hydrogen peroxide. OxyS has an important regulatory role in cell stress response, affecting the expression of multiple genes. In this work, we investigated the structure of OxyS and the interaction with fhlA mRNA using nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and unbiased molecular dynamics simulations. We determined the secondary structures of isolated stem–loops and confirmed their structural integrity in OxyS. Unexpectedly, stem–loop SL4 was identified in the region that was predicted to be unstructured. Three-dimensional models of OxyS demonstrate that OxyS adopts an extended structure with four solvent-exposed stem–loops, which are available for interaction with other RNAs and proteins. Furthermore, we provide evidence of base-pairing between OxyS and fhlA mRNA.
Keywords
- Received February 1, 2023.
- Accepted June 18, 2023.
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