Functional Significance of RNA Secondary Structure in an RNA Thermometer From Bradyrhizobium Japonicum
Open Access
- Author:
- Bormes, Katie
- Area of Honors:
- Chemistry
- Degree:
- Bachelor of Science
- Document Type:
- Thesis
- Thesis Supervisors:
- Philip C Bevilacqua, Thesis Supervisor
Przemyslaw Maslak, Thesis Honors Advisor - Keywords:
- ROSE elements
RNA
Secondary Structure - Abstract:
- Through unique chemical and structural properties, mRNA is able to regulate the expression of genes via sensory RNAs within the 5’ untranslated region (5’ UTR). These RNAs are able to change their secondary structure when in the presence of various stimuli, such as temperature. Temperature is an important physical property highly monitored in a variety of bacteria through the expression of heat shock proteins and virulence factors. These genes are regulated through a class of noncoding temperature sensitive RNAs called RNA thermometers (RNATs). At low temperatures, the secondary structure of the RNA thermometer blocks the ribosome from binding to the 5’ UTR; however, as temperature increases the RNA undergoes a conformational change that allows the ribosome to bind and initiate translation. One subclass of RNATs are ROSE (Repression Of heat Shock Expression) elements. ROSE elements are short RNA sequences that contain two to four hairpin loops and are associated with expression of small heat shock proteins. Bradyrhizobium japonicum is a nitrogen fixing bacteria that contains a ROSE element that encodes for a heat-shock protein. The entire 5’UTR is predicted to form three additional hairpins upstream of the RNAT. The influence of the surrounding hairpins on the RNAT are not understood. This project is aimed at determining the effect of the neighboring hairpins on the known RNAT. Through UV thermal denaturation experiments, it was concluded that the upstream hairpins do not affect the stability of the RNAT. Thus, we hypothesized that the upstream stem-loops may be necessary for proper folding of the RNAT. Using computational and experimental studies we concluded that the function of the upstream hairpins is to ensure proper folding of the RNAT.