Paper presentation

Submitted by:

Shweta Kumari

Roll no: 21

M.Sc Bioinformatics

4th semester

Session: 2014-16

Submitted to:

Dr. Durg Vijay Singh

Bioinformatics Programme

Centre for Biological Science

Paper presentation

Title:

The incoherent Fees Forward Loop Accelerates the Response-time of the gal

System Escherichia coli.

Authors:

U. Alon, S. Mangan, S. Itzkovitz and A. Zaslaver

Published in:

J. Mol. Biol. (2006) 356, 1073-1081

Doi: 10.1016/j.jmb.2005.12.003

Content • Network motif

• Three-node patterns

• Feed Forward Loop

• Coherent and Incoherent type FFL

• Combination of C1FFL & I1FFL

• Incoherent type 1-FFL

• I1-FFL: response acceleration

• I1-FFL: gal system

•Materials and Methods

• Results

• References

Introduction

Complex gene regulation networks are made of simple recurring gene circuits.

1st identified in E.Coli.

Present in yeast, Bacilus subtilus, Drosophila and Humans.

Network motif

Fig: Feed-forward loops in the E. coli transcription network. Blue nodes participate in FFLs

Three-node patterns

13 possible 3-node patterns

Coherent and Incoherent type FFL

Two cascaded transcription factor jointly regulate a gene.

8 type of FFL ( +vely & –vely regulation for each interaction)

Coherent FFL

Incoherent FFL

activation inhibition

Coherent and Incoherent type FFL

Fig: The eight FFL types and their relative abundance in the transcription networks of E. coli and S. cerevisiae.

Relative abundance is the fraction of each type relative to the total number of FFLs in the network (138 in E.

coli and 56 in S. cerevisiae in the networks presently studied). The coherent FFL types are denoted C1 through

C4, and the incoherent types I1 through I4.

Coherent and Incoherent type FFL

Two types are more common:

a. C1FFL: three positive

interactions, both X and Y

activate Z.

b. I1FFL: two positive and one

negative interaction, X activate

both Z and Y and Y repress the

expression of Z.

Combination of C1FFL & I1FFL Gene regulation system for sporulation in Bacillus subtilis.

Two Incoherent 1FFL and two Coherent 1 FFL

X and Y regulate several genes, viz., Z1, …Zn

Multi-output FFL.

Incoherent type 1-FFL

2nd common type FFL

X positively regulate Y and Z, and Y repress Z

expression

X and Y act in opposite sign to control Z

Example:

100 different gene in E.coli

One-third of total no in FFL in yeast

Micro-RNA in human

Incoherent type 1-FFL

I1-FFL: response acceleration

Expression of output gene Z has a shorter response time

•Signal Sx appears.

•X is activated and rapidly

binds its downstream

promoters.

•Y and Z production starts

when Y concentration crosses

the repression threshold.

• Z production stops.

The gal system allows

E.coli to grow in galactose

medium.

Expression of gal gene is

inhibited in the presence of

glucose.

I1-FFL: gal system

Fig: Two parallel antagonistic paths

Figure 2: The galactose and lactose systems of E. coli. (a) The I1-FFL in the galactose system. CRP activates galS and galETK (denoted galE

throughout). galS represses galE and its own promoter. The inducers are cAMP for CRP and galactose/d-fucose for GalS. d-Fucose is a non-metabolizable

inducer. (b) A partial map of the interactions in the galactose system. Continuous lines represent transcription interactions, and broken lines represent non-

transcriptional interactions (see the text). (c) The lactose system, in which lacZYA (denoted lacZ throughout) is regulated by CRP and lacI. The inducer

IPTG is used to deactivate LacI and therefore to allow full expression of the lacZ promoter. Here, AND-gates mean binding of the activator AND NOT the

repressor to the promoter region of the target gene.

I1-FFL: gal system

Plasmids and strains

MG1655

Growth medium

M1C, M1G

Culture and measurements

Agar plates

Data analysis

GFP reading

Transcription network databases

EcoCyc

RegulonDB

Materials and Methods

Results

Incoherent type-1 FFLs in the transcription network of both E.coli and yeast.

Many cases of FFL using cases of FFL using genes as nodes, and reported several

hundred new FFLs, including many I1-FFLs.

galE is regulated in an I1-FFL by CRP and GalS.

galS promoter has undetectable activity when bacteria are grown on glucose.

Its promoter activity increases to easily detectable values, once cells are grown on

a non-glucose medium, such as on mannose as a carbon source.

The galE promoter has a significant basal activity level in glucose.

Results

The galE promoter is activated upon

depletion of glucose.

The galE promoter is activated when

glucose is depleted from the medium.

galE promoter activity increases

with increasing D-fucose levels

Figure 3. Dynamics of the galE promoter with different levels

of the inducer D-fucose.

Results

The response of galE promoter is

accelerated.

The galE promoter activity is

enhanced upon depletion of glucose

from the medium, resulting in an

increase of expression.

The normalized dynamics of the

galE promoter without inducer shows

an overshoot, and is accelerated.

The lac operon shows no acceleration.

The dynamics of the lacZ promoter

under the same conditions shows that

the lacZ promoter does not show

accelerated dynamics.

Figure 4. The expression of the galE promoter normalized relative

to steady state.

Results

Accelerated response is dependent on the repressor binding site in the galE

promoter

The dynamics of a mutant galE reporter plasmid in which the main binding

site of galS/galR was deleted.

Mutated promoter loses its responsiveness to D-fucose, but not to glucose

The normalized dynamics of this promoter shows no acceleration following

the depletion of glucose

Its dynamics has a response time of about one cell generation.

Figure : Response time of the I1-FFL is shorter than simple regulation that reaches same steady-state level. The normalized response time of

simple regulation is ln 2 ~ 0.7. (Simple regulation - dashed line, I1-FFL - full line).

Results

Discussion

Incoherent type-1 FFLs in the transcription network of both E.coli and yeast.

Response acceleration by the I1-FFL is due to the fact that at early times, CRP

strongly activates the galE promoter, resulting in rapid production.

The response time, defined as the time to reach 50% of the steady-state level, is about

one-third of the cell generation time.

Text Book

Uri Alon, An Introduction to Systems Biology: Design Principles of Biological

Circuits, 2/e, CRC Press, (2006).

Literature References

Shai S. Shen-Orr, Ron Milo, Shmoolik Mangan & Uri Alon, Network motifs in

the transcriptional regulation network of Escherichia coli, Nature Genetics,

(2002), 31, 64–69.

Mangan and U. Alon, Structure and function of the feed-forward loop network

motif, PNAS, (2003), 100, 11980–11985.

R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon. Network

motifs: simple building blocks of complex networks. Science, 298 (2002), pp.

824–827.

S. Mangan, A. Zaslaver, U. Alon. The coherent feedforward loop serves as a sign-

sensitive delay element in transcription networks. J. Mol. Biol., 334 (2003), pp.

197–204.

References