Integrated Analysis of RNA-RNA Interactions for the Rational Design of Synthetic Metabolic Regulators

Open Access
Dong, Emily Rae
Area of Honors:
Chemical Engineering
Bachelor of Science
Document Type:
Thesis Supervisors:
  • Howard M Salis, Thesis Supervisor
  • Darrell Velegol, Honors Advisor
  • RNA
  • Regulatory RNA
  • Synthetic Biology
  • Metabolic Engineering
In optimizing metabolic pathways for the production of valuable products from microorganisms, it is often desirable to attain a specific stoichiometry of enzyme expression levels to maximize product yield. Such precision and flexibility is not possible through the current metabolic engineering methods of overexpression and gene knockouts. Instead, a rational, tunable method of controlling protein expression is needed. RNAs not only act as intermediates between the expression of a protein and the DNA that encodes it, but also act as regulators of gene expression in a wide range of organisms. Many regulatory small RNAs work by antisense pairing to a target messenger RNA to either repress or activate the expression of the encoded protein. Using a statistical thermodynamic model, we can predict the change in protein expression resulting from small RNA regulation. However, additional kinetic parameters not currently included in the model may also play a significant role in RNA-RNA interactions. This thesis aims to integrate our understanding of the thermodynamics of these interactions with structure and sequence analysis of both naturally occurring and synthetically designed small RNAs to elucidate important factors affecting RNA-RNA interaction. While work remains to be done in integrating these factors into the existing biophysical model, the results discussed give insight into ways to rationally design fully synthetic small RNAs for applications in metabolic engineering.