1. Gene repression and activation www.biochemweb.org

2. Gene transcription Gene expression = production - degradation Production depends on many factors type of promoter (activator or repressor) single transcription factor (TF) its cooperativity (or number of binding sites) multiple TFs type of gate (AND, OR, SUM) binding strengths of transcription promoter activity Degradation is usually assumed to be a linear process: the amount that decays is proportional to the amount present

3. Gene transcription Gene expression = production - degradation gene expression (or the amount/number of mRNA molecules) production (or transcription) rate linear degradation rate

4. Michaelis-Menten model of gene regulation Activator TF increases the transcription rate of gene g: basal rate of transcription maximum transcription rate half-saturation constant (the ratio of association and dissociation constants of TF binding to a gene’s promoter).

5. Michaelis-Menten model of gene regulation

6. Equation for gene transcription If TF is a function of time, this equation cannot be solved analytically. If TF does not change with time, gene expression will reach steady-state

7. Equation for gene transcription Regulator can be a signal, s(t): like in the case of a sensor that we want to construct in iGEM. If signal s(s)=s does not change with time, gene expression will reach steady-state

8. TF as a repressor Repressor TF decreases the transcription rate of gene g:

9. Cooperativity If more than one binding site for TF exist then for activator and for repressor h is the number of binding sites = cooperativity (or Hill coefficient)

10. Multiple Transcription Factors SUM gate: effect from multiple TFs is additive AND gate: effect from multiple TFs is multiplicative In these two cases, the maximal production rate can only be achieved when both TFs are bound. Also, it could be that a signal is needed to activate the promoter.

11. Multiple Transcription Factors OR gate: two TFS compete for binding to the promoter region) For activator For repressor

12. Translation of protein Protein = production – decay Decay: a linear process but it can be regulated (regulated proteolysis) Production: amount of protein produced by translation is proportional to the amount of mRNA

13. Post-translational modification

14. Michaelis-Menten equation for phosphorylation-dephosphorylation d /dt == rate of phosphorylation k == maximal rate for the forward reaction (phosphorylation) k’ == maximal rate for the reverse reaction (dephosphorylation)

15. Negative Autoregulation Synthetic transcription circuits. (a) Simple transcription unit (open loop). Cells expressing TetR can be induced, by adding aTc to the medium, to produce GFP. (b) Negative autoregulation: the tet promoter controls the production of its repressor, TetR fused to GFP. The TetR–GFP fusion protein represses its own promoter. Rosenfeld et al, J.Mol.Biol.2002

16. Negative Autoregulation

17. Positive Autoregulation

18. Positive autoregulation with multiple regulators SUM gate: effect from the sensor and autoregulator is additive

19. Positive autoregulation with multiple regulators AND gate: effect from the sensor and autoregulator is multiplicative

20. Tasks Model and simulate in matlab the following scenario: Initially there is no signal, and as a result

21. Transcriptional time delay