Translational Control of Gene Expression Krystal Joan Annand - PowerPoint PPT Presentation

Engineering a Toggle Switch in Yeast Using Translational Control of Gene Expression Krystal Joan Annand Brychan Cromwell Lisa Dryburgh Joseph Hoare Justyna Kucia Stephen Lam Christina McLeman Ben Porter Margaret-Ann Seger Liz Threlkeld

Aims • Design and construct a toggle switch. • Regulation of switch at translational level is potentially faster. • Use yeast as a model organism to increase the parts available in the Registry of Parts. • Use mathematical modelling to optimise the system.

AYE SWITCH – How It Works DNA Cu2+ galactose mRNA Transcription MS2 stem loops Bbox Translation Protein N-peptide - GFP MS2 - CFP

Characterisation of the Promoters The CUP1 Promoter Dose Response of CUP1 Fluorescence units  The CUP1 promoter shows a clear dose response indicating that it can be regulated. Timed Induction of CUP1 Fluorescence units Copper Concentration ( μ M)  The CUP1 promoter is rapidly fully induced. Time / minutes

Characterisation of the Promoters The GAL1 Promoter Dose Response of GAL1 Fluorescence units  The GAL1 showed a high sensitivity to the inducing agent. Timed Induction of GAL1 Galactose Concentration (w/v) Fluorescence units  Expression induction is linear over time and the response is immediate. Time / minutes

Further Characterisation of GAL1 Decay of GFP Fluorescence units Time / minutes  This confirms that GFP is a very stable protein and the decay is mainly caused by cell division.

Characterising CUP1p-[MS2-CFP]  CUP1p-[MS2-CFP] did not function as expected.  To determine the reason we checked: - the sequence of CFP; - the ‘Regulatory elements’ in CUP1p -[MS2-CFP] using cassette replacement experiments. MS2 - CFP

Checking the Sequence of CFP  Confirmation that sequence of CFP is correct by cassette replacement experiment. Yeast cells under Yeast cells fluorescent conditions

Checking the Regulatory Elements • Replacing the CUP1 promoter with a different version that is known to work. • Replacing the fusion protein with a different set of proteins.

Results  CFP could not be detected in either experiment.  The Bbox sequence or the translational fusion of MS2 coat protein appears to block protein expression. Bbox

Characterising Translational Repression • The translational repression was characterised by trans expression of the MS2 protein. N-peptide GFP MS2-protein C-Ub-URA3 MET17 promoter GAL1 promoter 5000 GFP Fluorescence 4000 3000 High Met = high GFP Low Met = low GFP 2000 1000 0 0 100 200 300 400 500 600 700 Methionine (micro molar)

How the Switch was Modeled DNA GAL1 promoter MET17 promoter u mRNA Proteins N-peptide - GFP MS2 - CFP

Importance of Hill Coefficients Determines the type of switch - analogue/digital n → ∞ n = 4 n = 2 n = 1 Promoter Activity Repressor Concentration

Solving the Equations for the Steady State Stable Fixed Point (CFP dominates) Unstable Fixed Point GFP Stable Fixed Point (GFP dominates) CFP

Bifurcation Diagram Bifurcation GFP Point Stable C = a dimensionless function of our parameters

Our Parameters Parameter Parameter Value Value Parameter Value (converted to number of (converted to number of (converted to number of molecules, N) molecules, N) molecules, N) 1.34 x 10 -1 s -1 5 x 10 3 5 x 10 3 K 1 K 1 λ 1 4.16 x 10 -2 s -1 1 x 10 4 1 x 10 4 K 2 K 2 λ 2 5.84 x 10 -2 s -1 5 x 10 3 5 x 10 3 K 3 K 3 λ 3 4.18 x 10 -2 s -1 1 x 10 5 1 x 10 5 K 4 K 4 λ 4 8.85 x 10 -5 s -1 8.85 x 10 -5 s -1 9.26 x 10 -4 s -1 T T μ 1 2.5 x 10 -4 s -1 n 1 n 1 2 2 μ 2 2.45 x 10 -4 s -1 n 2 n 2 1 - 3 1 - 3 μ 3 2.5 x 10 -4 s -1 n 3 n 3 4 4 μ 4 n 4 n 4 1 1

Calculating n 2 More Precisely • Based on a graph of MS2 binding curves in a paper by Witherell et al (1990) we could calculate the Fraction of MS2 bound to stem loops value for the Hill coefficient of the CFP/MS2 stem loop association (n 2 ). • We reproduced the graph in MATLAB and using MATLABs curve fitting tool we fit the Hill function for activators to the curve. MS2 concentration (Molar) Fraction of MS2 bound to stem loops • The R 2 value was 0.998, suggesting a very good fit to the curve. • The result gave n 2 = 2.6 ± 0.3. MS2 concentration (Molar)

Do We Get a Switch? We can get a switch but only under certain circumstances. For example, from a state of high galactose and high methionine in which GFP dominates, we can switch to a CFP dominated state if we actively remove the galactose and methionine from the system. High Galactose + No No Galactose + No Galactose + Methionine = High Galactose High No Methionine competition between + Methionine = Methionine = = CFP wins proteins! GFP wins no proteins

Robustness of the Switch Parameter Value Range 1.34 x 10 -1 1.34 x 10 -1 ± 2 λ 1 4.16 x 10 -2 4.16 x 10 -2 ± 2 λ 2 5.84 x 10 -2 5.84 x 10 -2 ± 2 λ 3 4.18 x 10 -2 4.18 x 10 -2 ± 2 λ 4 9.26 x 10 -4 9.26 x 10 -4 ± 2 μ 1 2.5 x 10 -4 2.5 x 10 -4 ± 2 μ 2 2.45 x 10 -4 2.45 x 10 -4 ± 2 μ 3 2.5 x 10 -4 2.5 x 10 -4 ± 2 μ 4 5 x 10 3 5.0 x 10 3 ± 2 K 1 1 x 10 4 1.0 x 10 4 ± 2 K 2 K 3 5 x 10 3 5.0 x 10 3 ± 2 1 x 10 5 1.0 x 10 5 ± 2 K 4

Robustness of the Switch

Robustness of the Switch Parameter Value Range Change 1.34 x 10 2 1.34 x 10 2 ± 2 increase by 10 3 λ 1 4.16 x 10 2 4.16 x 10 2 ± 2 increase by 10 4 λ 2 5.84 x 10 2 5.84 x 10 2 ± 2 increase by 10 4 λ 3 4.18 x 10 2 4.18 x 10 2 ± 2 increase by 10 4 λ 4 9.26 x 10 -7 9.26 x 10 -7 ± 2 decrease by 10 3 μ 1 2.5 x 10 -7 2.5 x 10 -7 ± 2 decrease by 10 3 μ 2 2.45 x 10 -7 2.45 x 10 -7 ± 2 decrease by 10 3 μ 3 2.5 x 10 -7 2.5 x 10 -7 ± 2 decrease by 10 3 μ 4 5.0 x 10 4 5.0 x 10 4 ± 2 increase by 10 1 K 1 1.0 x 10 4 1.0 x 10 4 ± 2 K 2 5.0 x 10 5 ± 2 5.0 x 10 5 increase by 10 2 K 3 1.0 x 10 4 ± 2 1.0 x 10 4 decrease by 10 1 K 4

Robustness of the Switch

Improving the System - Directed Evolution

Improving the System - Directed Evolution Parameter Original Value Optimal Value Obtained 1.34 x 10 -1 1.34 x 10 2 λ 1 4.16 x 10 -2 4.16 x 10 2 λ 2 5.84 x 10 -2 5.84 x 10 2 λ 3 4.18 x 10 -2 λ 4 4.18 x 10 2 9.26 x 10 -4 9.26 x 10 -4 μ 1 2.5 x 10 -4 2.5 x 10 -4 μ 2 2.45 x 10 -4 2.45 x 10 -4 μ 3 2.5 x 10 -4 2.5 x 10 -4 μ 4 5 x 10 3 K 1 5 x 10 3 1 x 10 4 1 x 10 4 K 2 5 x 10 3 5 x 10 3 K 3 1 x 10 5 1x 10 4 K 4 A reminder of our parameters

Conclusions  Designed, constructed and tested a novel genetic toggle switch regulated at the translational level.  Expressed a novel translational fusion protein.  Demonstrated that translational regulation by coat binding proteins to mRNA stem loops is a viable design.  Submitted, tested and characterised four biobricks to the Registry of Parts. We also tested the biobrick E2050 mOrange .  Found the optimal parameters for switching behaviour which increased our success to 98%.  By modelling directed evolution we successfully found the optimal parameters for a clearly defined switch.  Our overall analysis suggests that a translationally regulated genetic toggle switch is a viable gene circuit/biological machine.

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