The document summarizes a research paper that studied the incoherent feed forward loop (I1-FFL) network motif in the galactose system of E. coli. It found that the I1-FFL accelerates the response time of the galE gene to depletion of glucose by allowing initial rapid expression from CRP activation before repression by GalS occurs. The galE promoter dynamics showed an accelerated response and overshoot not seen in the simple lacZ promoter regulation. Deletion of the GalS binding site eliminated this accelerated response, demonstrating it is dependent on the I1-FFL structure.

1. 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

2. 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

3. 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

4. Introduction

5.  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

6. Three-node patterns
 13 possible 3-node patterns

7. 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

8. 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.

9. 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.

10. 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.

11. 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

12. Incoherent type 1-FFL

13. 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.

14.  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

15. 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

16.  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

17. 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.

18. 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.

19. 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.

20. 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.

21. 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

22. 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.

23. 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