Gene Expression Talk publish version - Virginia Techcourses.cs.vt.edu/~cs6404/CS6404_Gene Expression Talk.pdf · Computational Science and Engineering Gene Expression Gene is just

Computational Science and Engineering

Gene Expression and Gene Regulation

Yang Cao

Department of Computer Science

http://courses.cs.vt.edu/~cs6404


Summary

• Gene Expression• Translation• Transcription • A biochemical Model

• Gene Regulation• Repressor• Activator• Feedback Control• Models for gene regulation network


DNA Structure and Base Pair


Gene Expression

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

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

1. Binding

2. Initiation

3. Elongation

4. Termination

Initiation figure


Transcription (Continue)

• 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

• 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

• 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



• Genetic Code is universal

AUG = Met



• RNA message is decoded by Ribosomes• Initiation starts at binding site (prokaryotic) or “AUG”• Elongation • Termination


A Model for Prokaryotic Gene Expression

1. Transcription Initiation (the binding and initiation)

2. Elongation (RBS is available before elongation terminates

3. Translation Initiation

4. Elongation

RNAPP RNAPP +→•

RNAPPRNAPP •→+

RNAPTr RNAPP →•

ElRNAPPRBSTrRNAP ++→

RibRBSRBS Ribosome →+

RBS RibosomeRibRBS +→

RBS ElRibRibRBS +→

decayRBS →

Protein ElRib →

decayProtein →

1-18

1 M10−

= sk

1

2 10−

= sk

1

3 1 −= sk

1

4 1 −= sk

1-18

5 M10 −= sk

1

6 25.2 −= sk

1

7 5.0 −= sk

1

8 3.0 −= sk

1

9 015.0 −= sk

15

10 1042.6 −−×= sk


Simulation Results

Kierzek, A. M. et al. J. Biol. Chem. 2001;276:8165-8172


Some Further Discussion

ElRNAPPRBSTrRNAP ++→

• The elongation process

• A more detailed model for that

RBS ElRibRibRBS +→

Protein ElRib →

1nn TrRNAPTrRNAP+

→

0TrRNAPP →• RNAP

ElRNAPPRBSTrRNAPN ++→

…A C

n n+1

G

N

RNAP

…Promoter

0


Model Difference

1. From Exponential distribution to Gamma distribution

2. RNAP collision may happen (Dr. Kim pointed out this should never happen in the real cell)

…A C

n n+1

G

N

RNAP

…Promoter

PromoterT G

RNAP

NNAAAA →→→→

−110 L

a

N

i

N

i

iNataEttt ≈Γ=∑

=

),( then,)( e wher,1

pp


Modeling for Eukaryotic Gene Expression?


Summary

• Gene Expression• Translation• Transcription • A biochemical Model

• Gene Regulation• Repressor• Activator• Feedback Control• Models for gene regulation network


Some History: Lac Operon

.

Discovered by Francois Jacob and Jacques Monod, They got

Nobel Prize in Physiology or Medicine in 1965

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?


Gene Regulation

• Repressor (negative feedback)


Gene Regulation

• Activator (positive feedback)


Regulation Reactions in Gene Models

Gene expression becomes interesting when regulation system

Is added into it.

Add the following reaction set

into the initiation of transcription

or written as: RNAPP

ORNAPP •→+

ORNAPPORNAPP +•→++

RIRI

RIRI

RORO

RORO

+→

→+

+→

→+

−

−

−

−


Feedback Control

K

x(k+1)=Ax(k)+Bu(k)y(k)=Cx(k)

u(k)

x(k)

y(k)Target System

Feedback Gain

-

+

d(k)

Control Law

Closed Loop System

Characteristic Equation


Trp Corespressor: A negative feedback system


Positive Feedback Regulation System

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?

RNApA

OBpromoterOA

g2

ORB

RNAp

BA

OBpromoterOA

g1

AND


Yes! Circuits!

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

Lamda Phage


Lambda-phage affected E. Coli



Stochastic effects play an important role

in lytic/lysogenic

decision network

Arkin et al. 1997, 1998

Lysis

Lysogeny


Highlight the lambda phage regulation

cI

PL

PRN cro

PRM

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

PRM

Computational Science and EngineeringcI must bind to OR1 to repress rightwards transcription

cI represses PR – shuts off cro

cI activates PRM – expression of cI

PRM

Computational Science and EngineeringcI must bind to the left operators to prevent left transcription

N

PL

cI

PRM

OL

321

cI represses PL – shuts off N

Computational Science and EngineeringCro must bind to OR3 to repress expression of repressor by PRM

Cro represses PRM – shuts off cI expression

PRMPRE




Another Gene Network

Heat Shock Response Model

El-Samad H, Kurata H, Doyle JC, et al.

Surviving heat shock: Control strategies for robustness and performancePNAS 102 (8): 2736-2741 FEB 22 2005


Temp

environ

Temp

cellFolded

Proteins

Unfolded

ProteinsAggregates

Loss of Protein

Function

CellDeath


32σ mRNA

32σ

TranslationHeat

Translational Induction of heat shock transcription factor σσσσσσσσ3232 : evidence of

a built-in thermosensor. Morita et. al, Genes & Dev. 1999

Initiation codon


σ70

RNAP

σ

RNAP

DNAK

Lon

ftsH

RNAP

DNAK

σ

σ

σ mRNA

DnaK

rpoH

FtsH Lon

Heat

Molecular

Modules

degradation

foldedunfolded

aggregate

σ


Negative Feedback in Heat Shock Response (HSR)

σ DNAKσ

RNAP

RNAP

σ

DnaK FtsH

DNAK


Interesting Feedback in Gene Regulation


Time50 60 70

6

Time

Wild TypeNo FeedforwardLow S32 FluxConstitutive S32 DegNo DnaK interaction

8000

24000

0

1E+0

50 60 700

2

4

6

8

0

150

300

450

600

Free σ32

Total σ32DNAK

Unfolded


Thanks! Questions? Plato is my friend, Aristotle

is my friend, but my best

friend is truth --- Newton

Gene Expression Talk publish version - Virginia Techcourses.cs.vt.edu/~cs6404/CS6404_Gene Expression Talk.pdf · Computational Science and Engineering Gene Expression Gene is just

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