Biology Reference
In-Depth Information
Chapter 5
Analyzing the Structure, Function and
Information Flow in Signaling Networks
using Quantitative Cellular Signatures
Meghana M. Kulkarni
1
and Norbert Perrimon
1
,
2
1
Department of Genetics,
2
Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
Chapter Outline
The Concept of Linear Cassettes and Modularity in Signal
Transduction
Quantitative RNAi Signatures or Phenoprints to Infer Context
Dependent Information Flow Through Cellular Signaling
Networks
89
Genetic Dissection of Signal Transduction Pathways
92
100
Systems Approaches to Identify the 'Parts' of Cellular Signaling
Networks
Direction of Information Flow from Gene Expression
Signatures
94
100
RNA Interference (RNAi)
94
Direction of Information Flow from Phosphorylation
Signatures
Protein
e
Protein Interactions
97
103
Transcriptional Profiling
99
Concluding Remarks
106
References
106
THE CONCEPT OF LINEAR CASSETTES
AND MODULARITY IN SIGNAL
TRANSDUCTION
Cells communicate and respond to conditions in their local
environment through signaling, a process consisting of
a series of regulated steps that help propagate information
across the external plasma membrane to the cell interior,
and often to the nucleus, to regulate diverse cellular
processes such as growth, proliferation, differentiation and
apoptosis. The set of molecules recruited by a specific
signal defines what is commonly referred to as a signal
transduction pathway. Dissection of biological responses to
similar families of ligands in various cell types and
organisms revealed that these ligands regulate the activity
of similar sets of downstream genes, a finding that led to the
concept of 'evolutionarily conserved signal transduction
cassettes' or modules
[1]
. A characteristic feature of these
modules is the occurrence of a tight internal link between
their individual components, and few, but well-defined
connections to the rest of the system in which they operate.
The concept of modules gained further acceptance when it
became clear that these characteristic chains of events were
iterated in the same pattern in different cellular and
developmental situations. The extent of signaling modu-
larity was underscored by studies of signal transduction in
simple genetic model organisms, where signaling tends to
be simpler than in more complex mammals (see below)
[2]
.
The methodologies used to recognize and characterize
these pathways relied mostly on the similarity in visible
mutant phenotypes or screens in sensitized genetic back-
grounds (see
Box 5.1
for definition). The resounding
conclusion from these studies was that of elegant
simplicity: it is common for loss-of-function mutations (see
Box 5.1
for definition) in different genes that constitute
a specific pathway to result in identical phenotypes. For
example, in the context of JAK/STAT signaling, mutations
in the activating extracellular ligand (Unpaired/Upd), in the
effector tyrosine kinase (Hopscotch/JAK), or in the effector
transcription factor (STAT92E/Marelle) caused identical
loss-of-function phenotypes, a feature consistent with
linearity of the pathway
[3]
(
Figure 5.1
A). Furthermore,
gain-of-function phenotypes (see
Box 5.1
for definition)
had strikingly opposite developmental phenotypes and
could usually be reverted completely by removing the
activity of a more downstream component of the pathway.
