Systems Biology
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The search for the syntax of biological information, that is, the study of the
dynamic networks of interacting biological elements.
The aim is to obtain, integrate and analyze complex data from multiple
experimental sources using interdisciplinary tools.
Some typical technology platforms are:
• Transcriptomics:whole cell or tissue gene expression measurements.
• Proteomics:complete identification of proteins and protein expression patterns of a cell or
tissue
• Metabolomics :identification and measurement of all small-molecules metabolites within a
cell or tissue
• Glycomics:identification of the entirety of all carbohydrates in a cell or tissue.
• Interactomics:encompasses interactions between all molecules within a cell
• Fluxomics:which deals with the dynamic changes of molecules within a cell over
time
Illustrative example of the interaction and contrast between a traditional
approach and a Systems Biology approach
Systems Biology is characterized by:
Integration of the levels of biological organization and complexity addressed and
Interaction between experimentation and predictive modeling
Integrated Genomic and Proteomic
Analyses of a Systematically Perturbed
Metabolic Network
Trey Ideker, Vesteinn Thorsson, Jeffrey A. Ranish,
Rowan Christmas, Jeremy Buhler, Jimmy K. Eng,
Roger Bumgarner, David R. Goodlett, Ruedi Aebersold, Leroy Hood
The Integrated Approach
Microarrays
DATA
Global Quantification and
Measurement
Of Protein
Two Hybrid System
Integration and Assimilation
Into BIOLOGICAL MODELS
The Strategy
If possible, define an initial model of
the molecular interactions governing
pathway function.
A)
Define all of the genes in the
genome and the subset of
genes, proteins, and other small
molecules constituting the
pathway of interest.
Design additional perturbation
experiments
D) Formulate new hypotheses
to explain observations not
predicted by the model.
C) Integrate the observed
B) Perturb each pathway
component through a series of
genetic or environmental
manipulations
Detect and quantify the
corresponding global cellular
response
mRNA and protein responses
with the current, pathwayspecific model and with the
global network of proteinprotein, protein-DNA, and other
known physical interactions.
A)
Define all of the genes in the genome and the
subset of genes, proteins, and other small molecules
constituting the pathway of interest.
A) BASICS of Galactose Utilization(GAL) pathway in
Saccharomyces cerevisiae
• Controlled by an operon-like system.
• It converts Galactose to Glocose-6-phosphate.
• It produces the enzymes essential for galactose
breakdown to glucose.
• In the absence of galactose ENZYMES ARE NOT
PRODUCED.
• In the presence of galactose STRUCTURAL
GENES(GAL 1, GAL 7, GAL 10) ARE ACTIVATED.
• The above enzymes are regulated by Gal 4 and Gal 80
regulatory genes.
REGULATION of Galactose Utilization GAL) pathway in
Saccharomyces cerevisiae
GALACTOSE INDUCTION LOOP
Galactose
Gal3p
GAL2
GAL3
Gal 80p
GAL80
Gal 4p
GAL7
GAL10
GAL1
B) Perturb each pathway component through a series of
genetic or environmental manipulations
B) Application of 20 perturbations to the GAL pathway
• Wild type and nine genetically altered strains were examined. These
were:
 Transport(gal∆2)
 Enzymatic(gal∆1, gal∆5, gal∆7, gal∆10)
 Regulatory(gal∆3, gal∆4, gal∆6, gal∆80)
• The strains were perturbed environmentally by growth in presence
(+gal) or absence(-gal) of galactose.
• Global changes in mRNA of 6200 nuclear yeast genes were seen.
• Identified 997 genes whose mRNA level significantly differed from
control.
• These were then divided into 16 clusters in which each cluster
represented genes with similar expression responses over all
perturbations.
PERTURBATION
MATRIX
RESULTS
Comparison of Northern vs. microarray analysis
Medium-gray representing no change, darker or lighter shades representing increasing or
decreasing amounts of expression respectively,
Are the observed changes in mRNA expression
also reflected at the level of protein abundance?
Wt+gal
Wt-gal
Protein extracts
Protein extracts
Labeled with
isotopically heavy and
normal ICAT reagents
Combined and
digested with trypsin
RESULTS:
As a whole, protein-abundance
ratios were moderately correlated with
their mRNA counterparts.
30 proteins showed clear changes
in abundance between wt+gal and wtgal conditions.
Fractionated by
Multidimensional
chromatography
Analyzed by
MS/MS
mRNA of 15 did not change
significantly in response to
perturbation.
 Many ribosomal-protein genes
increased three-to five fold in mRNA
but not in protein abundance.
C) Integrate the observed mRNA and protein responses with
the current, pathway-specific model and with the global network
of protein-protein, protein-DNA, and other known physical
interactions.
C) Can we attribute the observed mRNA and protein changes to
underlying regulatory interactions in the cell?
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They assembled a catalogue of previously observed physical interaction
in yeast by COMBINING:
a)
b)
2709 protein-protein interactions
317 protein-DNA interactions
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Out of the total genes above they observed 348 genes that were affected
in mRNA or protein expression by at least one perturbation and also
involved in two or more interactions with the affected genes….
348 Genes along with their 362 associated interactions
as a PHYSICAL INTERACTION NETWORK
POSSIBILITIES
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A protein DNA interaction may be responsible for directly transmitting an expression
change from a transcription factor to a highly co-related target gene.
e.g. Mcm1
Far1and Mig1
Fbp1
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Two genes may be under control of a common transcription factor which is the 3rd
gene. C
(A,B)
e.g. GAL enzymes regulated by Gnc4
Class of gluconeogenic genes controlled by Sip4
(Fbp1, Pck1, Ic11)
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Scanning of network for indirect effects, such as a change in one gene transmitted to
the other through a protein-protein interaction with a signaling protein.
e.g. Gcr2-Gcr1
Tpi1
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Gal4p directly regulates genes in several processes of other networks through novel
protein DNA interaction.
e.g. Cluster 1,2,3 contained genes with Gal4 binding sites
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The above genes were involved in glycogen accumulation, protein metabolism and
others with unknown function
Tree comparing gene-expression changes resulting
from different perturbations to the GAL pathway.
D) How do the observed responses Of GAL genes compare to
their predicted behavior?
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In general the results were same as predicted.
D) Formulate new hypotheses to explain
observations not predicted by the model.
New Observations, Hypotheses, and possible tests
OBSERVATIONS
1)
Decrease in GAL-gene expression in
EXAMPLE
HYPOTHESES
Dependent on levels of
Gal-1-P or a derivative
response to gal7D+gal or gal10D+gal
SYSTEMS-LEVEL TESTS
Examine EP of a
gal1Dgal10D+gal double
deletion strain, in which Gal-1-
metabolite
P levels are reduced
2)
3)
Effect of gal80D-gal: slow growth and
widespread changes in metabolic-gene
expression
GAL5 and GAL6 mRNA levels are
unaffected by galactose addition or by
deletion of GAL3, 4, or 80
Stress-related, caused
by de-repression of
either the GAL
Examine EP of a gal4Dgal80Dgal double deletion, in which
the GAL enzymes and
enzymes or transporter
transporter are not expressed
Caused by differences
in strains and/or media
between this and
Obtain EPs for identical strains
and media as in previous
studies
previous studies
Contd….
OBSERVATIONS
EXAMPLE
HYPOTHESES
SYSTEMS-LEVEL TESTS
5)
Expression levels of genes in many
other metabolic pathways respond to
perturbations of the GAL pathway
Each affected
pathway depends on
galactose, specific
GAL genes, or on the
total amount of
available energy
Examine EPs of yeast
growing in carbon sources
other than galactose, e.g. 2%
glucose
6)
In wt+gal vs. wt-gal, approx. 15 genes
change in protein but not mRNA
abundance.
These genes are
regulated at the level
of protein translation
or degradation
Compare global translation
state of proteins between +
vs. - gal, using method of [Q.
Zong et al. Proc Natl Acad
Sci U.S.A. 96, 10632-6.
(1999)]
7)
Nine genes w/ predicted Gal4p-binding
sites have EPs that are similar to those
of known GAL genes
Gal4p regulates
transcription of these
genes via proteinDNA interactions
Verify predicted interactions
by global chromatin immunoprecipitation experiments [B.
Ren et al., Science 290,
2306-9. (2000)]
Tree comparing gene-expression changes resulting
from different perturbations to the GAL pathway.
Refinements in the GAL Pathway
Model of galactose utilization. Yeast metabolize galactose through a series of steps involving the GAL2
transporter and enzymes produced by GAL1, GAL7, GAL10, and GAL5. These genes are transcriptionally
regulated by a mechanism consisting primarily of GAL4, GAL80, and GAL3. GAL6 produces another
regulatory factor thought to repress the GAL enzymes in a manner similar to GAL80. Dotted interactions
denote model refinements supported by this study.
References
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http://www.bbsrc.ac.uk/science/spotlight/systems_biology.html
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