Development of a biophysical modelof translational coupling

Tian TianSalis Lab

Year 7 Fall RetreatSeptember 23, 2012

Metabolic Engineering

… … …E1

En

E2

Many proteins work together to manufacture products

E1: E2…En = a: b…n

Translational Coupling to Coordinate Protein Expression

Translational coupling

Upstream Downstream

Intergenic region

Examples:

F(Upstream gene expression)

Escherichia. coli

Escherichia. coli

Salmonella Typhimurium

Translational Coupling No Coupling

Down-stream

geneexpression

Objectives Develop a biophysical model of translational coupling that

can predict the downstream mRNA translation initiation rate;

Engineer metabolic pathway with optimal stoichiometries to coordinate protein expression and improve the pathway function.

Mechanism of Translational Coupling

Ribosome

Upstream gene Downstream gene

Upstream gene Downstream gene

Mechanism of Translational CouplingRibosome

Upstream Gene Downstream Gene

De novo initiation

Mechanism of Translational CouplingRibosome

Upstream Gene Downstream Gene

Re - initiation

Low upstream TIR

High upstream TIR

Medium upstream TIR

Hairpin is never unfolded

Hairpin is always unfolded

Hairpin is unfolded 50% of time

High Fcoupling

Ribosome-assisted Unfolding of mRNA Hairpins

Medium Fcoupling

Low Fcoupling

Medium downstream TIR

High downstream TIR

Low downstream TIR

Translational Coupling Calculator

Coming Soon !