Synthetic Biology - Parts - RNA Regulators

From Keaslingwiki

Researchers

James Carothers, Jonathan Goler

Project Description

Darwinian evolution has resulted in naturally-occurring metabolic pathways with mechanisms that enable cells to conserve the chemical substrates needed for growth and replication, prevent the accumulation of toxic intermediates and respond to changes in the internal or external environment. Our goal is to combine rational design and directed evolution to engineer RNA-based controls that can be tailored to any biochemical pathway or problem, not just those for which the components already exist in nature.

We are working to understand how steady-state mRNA levels can be manipulated with secondary structure elements that either protect or target protein-encoding messages for degradation by cellular enzymes. In addition, we are attempting to employ catalytic RNAs (ribozymes) and ligand-binding RNA structures (aptamers) to couple fluctuations in intracellular conditions to dynamic changes in gene expression. Synthetic ribozymes and aptamers with novel substrates and ligands can be generated in the laboratory with in vitro selection, alleviating the need to limit ourselves to pre-existing biological molecules as the source of functional structures. Toward this end we are devising improved in vitro selection methods.

Relevant Publications

Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol. 2006 Aug;24(8):1027-32. [[1]]

Pfleger BF, Fawzi NJ, Keasling JD. Optimization of DsRed production in Escherichia coli: effect of ribosome binding site sequestration on translation efficiency. Biotechnol Bioeng. 2005 Dec 5;92(5):553-8. [[2]]

Funding Resources

Synthetic Biology Engineering Research Center (SynBERC)- A National Science Foundation Engineering Research Center

National Science Foundation Grant no. BES9906405.