Computational Science and Engineering
Gene Expression and Gene Regulation
Yang Cao
Department of Computer Science
http://courses.cs.vt.edu/~cs6404
Summary
Computational Science and Engineering
•
Gene Expression
• Translation
• Transcription
• A biochemical Model
•
Gene Regulation
• Repressor
• Activator
• Feedback Control
• Models for gene regulation network
DNA Structure and Base Pair
Computational Science and Engineering
Gene Expression
Computational Science and Engineering
Gene is just a small part of DNA. The gene expression
follows the process of:
DNA RNA Protein
Gene expression shows big
difference between prokaryotic
and eukaryotic cells. Most of the
models of gene networks
proposed in literature are for
prokaryotic cells.
Transcription
Computational Science and Engineering
Transcription from DNA to RNA is based on the base pair.
However RNA doesn’t have “T”, instead it has “U”,
which pairs with “A” just as “T” does.
DNA RNA
The Process of Transcription
Computational Science and Engineering
1. Binding
2. Initiation
3. Elongation
4. Termination
Initiation figure
Transcription (Continue)
Computational Science and Engineering
•
•
•
Transcription is carried out by the enzyme RNA
Polymerase (RNAP)
Several types of RNA are produced
• mRNAs
• rRNAs
• tRNAs
• Small RNAs (can regulate transcription)
Transcription occurs only on one strand of DNA
RNA Processing
Computational Science and Engineering
•
•
In Prokaryotic cells, mRNA can be immediately
translated by ribosomes.
In Eukaryotic cells, RNA has to be processed and then
transported to cytoplasm.
Translation: From RNA to Protein
Computational Science and Engineering
•
•
•
An mRNA sequence is decoded in sets of three
nucleotides, called codon.
Amino acids are specified by codons (not one by one).
Amino acids and codons are connected by tRNAs.
tRNA
Translation: From RNA to Protein
Computational Science and Engineering
•
Genetic Code is universal
AUG = Met
Translation: From RNA to Protein
Computational Science and Engineering
•
•
•
•
RNA message is decoded by Ribosomes
Initiation starts at binding site (prokaryotic) or “AUG”
Elongation
Termination
A Model for Prokaryotic Gene Expression
Computational Science and Engineering
1.
2.
Transcription Initiation (the binding and initiation)
P+RNAP → P • RNAP
k1 = 108 M -1s −1
P • RNAP → P+RNAP
k2 = 10 s −1
P • RNAP → TrRNAP
k3 = 1s −1
Elongation (RBS is available before elongation terminates
TrRNAP → RBS + P + ElRNAP
3.
4.
k4 = 1s −1
Translation Initiation
Ribosome +RBS → RibRBS
k5 = 108 M -1s −1
RibRBS → Ribosome +RBS
k6 = 2.25s −1
RibRBS → ElRib +RBS
k7 = 0.5s −1
RBS → decay
k8 = 0.3s −1
Elongation
ElRib → Protein
Protein → decay
k9 = 0.015s −1
k10 = 6.42 × 10−5 s −1
Simulation Results
Computational Science and Engineering
Kierzek, A. M. et al. J. Biol. Chem. 2001;276:8165-8172
Some Further Discussion
Computational Science and Engineering
•
The elongation process
TrRNAP → RBS + P + ElRNAP
RibRBS → ElRib +RBS
ElRib
→ Protein
•
A more detailed model for that
P • RNAP → TrRNAP 0
TrRNAPn → TrRNAPn +1
TrRNAPN → RBS + P + ElRNAP
RNAP
Promoter
0
…
A
C
n
n+1
…
G
N
Model Difference
Computational Science and Engineering
1. From Exponential distribution to Gamma distribution
A0 → A1 → L → AN −1 → AN
N
t = ∑ ti ,
where ti p E ( a ), then t p Γ( a, N ) ≈
N
a
i =1
2. RNAP collision may happen (Dr. Kim pointed out this
should never happen in the real cell)
RNAP
Promoter
…
…
A
C
n
n+1
T
G
G
N
Promoter
RNAP
Modeling for Eukaryotic Gene Expression?
Computational Science and Engineering
Summary
Computational Science and Engineering
•
Gene Expression
• Translation
• Transcription
• A biochemical Model
•
Gene Regulation
• Repressor
• Activator
• Feedback Control
• Models for gene regulation network
Some History: Lac Operon
Computational Science and Engineering
.
During
World War II, Monod was
testing the effects of combinations
of sugars as nutrient sources for E.
coli. He found that bacteria grown
with two different sugars often
displayed two phases of growth.
For example, if glucose and
lactose were both provided,
glucose would be metabolized first
(growth phase I, see Figure 2) and
then lactose (growth phase II). But
why was there a delay between
the two growth phases?
Discovered by Francois Jacob and Jacques Monod, They got
Nobel Prize in Physiology or Medicine in 1965
Gene Regulation
Computational Science and Engineering
•
Repressor (negative feedback)
Gene Regulation
Computational Science and Engineering
•
Activator (positive feedback)
Regulation Reactions in Gene Models
Computational Science and Engineering
Gene expression becomes interesting when regulation system
Is added into it.
Add the following reaction set
O + R → O −R
O −R → O + R
I + R → I−R
I−R → I + R
into the initiation of transcription
O
P+RNAP → P • RNAP
or written as:
P+RNAP+ O → P • RNAP+ O
Feedback Control
Computational Science and Engineering
d(k)
+
-
Target System
u(k)
x(k+1)=Ax (k)+Bu(k)
y(k)=Cx(k)
Feedback Gain
y(k)
x(k)
K
Closed Loop System
Control Law
Characteristic Equation
Trp Corespressor: A negative feedback system
Computational Science and Engineering
Positive Feedback Regulation System
Computational Science and Engineering
Gardner TS, Cantor CR, Collins JJ, Construction of a genetic toggle switch in
Escherichia coli, NATURE 403 (6767): 339-342 JAN 20 2000
Simple Regulation in Biology – Circuits?
Computational Science and Engineering
A
RNAp
B
OR
OA
promoter
OB
A
B
OA
OB
g2
Ap
N
R
AND
promoter
g1
Yes! Circuits!
Computational Science and Engineering
Kitano H, Funahashi A, Matsuoka Y, et al., Using process diagrams for the graphical representation
of biological networks, NATURE BIOTECHNOLOGY 23 (8): 961-966 AUG 2005
A Gene Network Example
Computational Science and Engineering
Lamda Phage
Lambda-phage affected E. Coli
Computational Science and Engineering
Lambda-phage affected E. Coli
Computational Science and Engineering
Lysis
Lysogeny
Stochastic
effects play an
important role
in
lytic/lysogenic
decision
network
Arkin et al.
1997, 1998
Highlight the lambda phage regulation
Computational Science and Engineering
N
cI
PR
cro
PRM
PL
cI
Cro
If cI wins, PR and PL are repressed and the cell enters lysogeny
If Cro wins, PRM is repressed and the cells enters the lytic cycle
A close up on the right promoter- operator region
Computational Science and Engineering
PRM
cI must bind to OR1 to repress rightwards transcription
Computational Science and Engineering
PRM
cI represses PR – shuts off cro
cI activates PRM – expression of cI
cI must bind to the left operators to prevent left transcription
Computational Science and Engineering
OL
1
2
3
N
cI
PL
cI represses PL – shuts off N
PRM
Cro must bind to OR3 to repress expression of repressor by PRM
Computational Science and Engineering
PRM
Cro represses PRM – shuts off cI expression
PRE
Lambda-phage affected E. Coli
Computational Science and Engineering
Another Gene Network
Computational Science and Engineering
Heat Shock Response Model
El-Samad H, Kurata H, Doyle JC, et al.
Surviving heat shock: Control strategies for robustness and performance
PNAS 102 (8): 2736-2741 FEB 22 2005
Death
Loss of Protein
Function
Unfolded
Proteins
Folded
Proteins
Cell
Computational Science and Engineering
Aggregates
Temp
cell
Temp
environ
Computational Science and Engineering
σ 32 mRNA
Heat
Translation
Initiation codon
Translational Induction of heat shock transcription factor σ32 : evidence of
a built-in thermosensor. Morita et. al, Genes & Dev. 1999
σ 32
rpoH
σ70
σ mRNA
RNAP
Heat
Computational Science and Engineering
unfolded
folded
Molecular
σ
Modules
σ DNAK
σ
RNAP
DNAK
ftsH
σ
RNAP
DnaK FtsH Lon
aggregate
Lon
degradation
Negative Feedback in Heat Shock Response (HSR)
Computational Science and Engineering
DNAK
σ
RNAP
σ RNAP
DnaK FtsH
σ DNAK
Interesting Feedback in Gene Regulation
Computational Science and Engineering
Computational Science and Engineering
24000
600
DNAK
Total σ32
450
300
150
Wild Type
No Feedforward
Low S32 Flux
Constitutive S32 Deg
No DnaK interaction
6
8000
0
1E+0
8
6
Free σ32
4
Unfolded
2
0
50
Time
60
70
0
50
60
Time
70
Computational Science and Engineering
Thanks! Questions?
Plato is my friend, Aristotle
is my friend, but my best
friend is truth --- Newton