Team:Rice/Model

Motivation

Existing RNA thermometers are designed to switch at around 37°C and do not exhibit significant conformational changes between 25°C and 30°C. As most plants cannot be expected to grow at 37°C, it was necessary to design thermometers that experienced conformational changes between 25°C and 30°C. We chose to design thermometers by finding optimal candidates using a genetic algorithm and RNA folding software, as the complexity of RNA folding thermodynamics otherwise makes it difficult to manually mutate existing thermometers to meet our performance criteria or devise them de novo. As the figures below show, A. thaliana grows best between 18–23°C and P. putida is typically grown in lab at 30°C. Along with the need for heterologous gene expression only at higher, stress-inducing temperatures to mediate a stress-mitigating response, we reasoned the need to design RNA thermometers that are optimized to melt at 30°C.

How RNA Thermometers Regulate Translation

In essence, RNA thermometers are a form of temperature dependent translational regulation. At low temperatures, there is a higher probability of more base pairs forming what is known as a "stem-loop structure". At higher temperatures, the thermometers "melt", meaning there is a decreased likelihood of base pairs forming.