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Gene repression and activation. www.biochemweb.org. Gene transcription. Gene expression = production - degradation Production depends on many factors type of promoter (activator or repressor) single transcription factor (TF) - PowerPoint PPT Presentation
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Gene repression and activation
www.biochemweb.org
Gene transcriptionGene 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
Gene transcriptionGene expression = production - degradation
gene expression
(or the amount/number of mRNA molecules)
production (or transcription) rate
linear degradation rate
)()()( ttpt )(t
)(tp
)(t
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).
0
TF
TFtp )(
0
0
Michaelis-Menten model of gene regulation
TF
TFtp
)(
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
)()(
)()( t
tTF
tTFt
)( TF
TF
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
)()(
)()( t
ts
tst
)( s
s
TF as a repressor Repressor TF decreases the transcription rate of gene g:
)(
1)(
tTFtp
)()(
1)( t
tTFt
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)
hTFtp
1
)(
h
h
TF
TFtp
)(
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.
22
22
11
11)(
TF
TF
TF
TFtp
22
2
11
11)(
TF
TF
TF
TFtp
Multiple Transcription Factors
OR gate: two TFS compete for binding to the promoter region)
For activator
For repressor
hh
h
a vVuU
uUvVuUf
TFTFfTFTFftp
)/()/(1
)/(),,,(
),,,(),,,()( 11222211
hhr vVuUvVuUf
)/()/(1
1),,,(
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
)()()( ttt p
Post-translational modification
)()( * tt ationphosphoryl
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)
*2
*
1
* '
pm
p
m
p
K
k
K
k
dt
d
Negative AutoregulationSynthetic 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
Negative Autoregulation
)()()( ttt p
)()(
1)( t
tt
h
Positive Autoregulation
)()()( ttt p
)()(
)( tt
th
h
Positive autoregulation with multiple regulators
SUM gate: effect from the sensor and autoregulator is additive
)(
)(
)(
)()(
22
11 t
t
ts
tstp
)()()( ttpt
)()()( ttt p
Positive autoregulation with multiple regulators
AND gate: effect from the sensor and autoregulator is multiplicative
)(
)(
)(
)()(
21 t
t
ts
tstp
)()()( ttpt
)()()( ttt p
Tasks
• Model and simulate in matlab the following scenario:
• Initially there is no signal, and as a result
Transcriptional time delay
)()(
1)( t
tt
h
)()()( ttt p
