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Metabolic network
reconstruction
“Metabolism
is not boring”
Systems Biology Paradigm:
components -> networks -> computational models -> phenotypes
Palsson,BO; Systems Biology, Cambridge University Press 2006
Building a genome-scale
metabolic network model
Model construction:
– Metabolic enzymes
– Enzyme specificities
Inputs:
– Cell objective (e.g.
growth, etc.)
– Metabolite uptake rates
– Genetic or expression
changes
Predicts:
– Growth rate
– Pathway usage
– Perturbation effects
RECONSTRUCTIONS ARE 2D
GENOME ANNOTATIONS AND
KNOWLEDGE BASES
Links and nodes
Network Reconstruction are 2D
genome annotations
Nature Biotechnology, 22:1218(2004)
Sequence assembly and bottom-up
reconstruction are ‘similar’ processes
Bottom-up Network Reconstructions
are knowledge bases:
Nature Reviews Microbiology, Feb 2009
STEP 1: DEFINING AN INITIAL
COMPONENT LIST
Automated Generation of Draft Reconstruction
Obtain Genome
Annotation
Identify Candidate
Metabolic Functions
Obtain candidate
metabolic reactions
Assemble Draft
Reconstruction.
Look for EC numbers, GO terms,
Comparative genomics
Issues
associated
with
automated
extraction of
content
Nat Rev Microbiol. 2009 Feb;7(2):129-43
STEP 2: CURATION AND ADDING
CONTENT TO A RECONSTRUCTION
The manual curation process
Defining Metabolic Reactions
hslJ
ldhA
ydbH
Nat Rev Genet. 2006 Feb;7(2):130-41.
Nat Rev Genet. 2006 Feb;7(2):130-41.
Gene, Protein,
Reaction
Associations
(GPRs) and
data mapping
The
process
of
forming
GPRs
Nat Rev Microbiol. 2009
Feb;7(2):129-43
Sources of data
for curation
Nat Rev Microbiol. 2009 Feb;7(2):129-43
Current Knowledge Status for Organisms
SKI =
No. Abstracts
No. Genes
E. coli
55.1
Human
48.5
S. aureus
16-17
Mouse
15.6
H. pylori
13
S. cerevisiae
10.6
20
EMBO Reports. 6(5): 397-9 2005
Lysine Biosynthesis: Gap analysis
Example of Integrated Reconstruction Process :
Non-Gene
• Genome annotation reveals incomplete pathway for lysine biosynthesis
Associated
• Gap analysis indicates no other routes for lysine production
Reactions
• Growth physiology data indicates no auxotrophic requirement for lysine
• Three additional reactions will be included into the model to complete pathway
• These reactions represent hypotheses for future investigation
Gene Associated Reactions
Knowledge gaps
Ubiquinone 10 Biosynthesis
Coq2
?
?
Coq3
•physiological data suggest these
reactions, not all genes are
identified
•Some reaction are biochemically
not well-defined
?
Coq6
?
Score:
Coq7
Coq3
Confidence Score:
Sources of Evidence
Increasing Confidence
• Biochemical
Enzyme has been tested biochemically.
• Genetic
Gene overexpression and purification,
gene deletions.
• Sequence
There is significant sequence similarity to
another gene with known function.
• Physiological
There is physiological data to support
inclusion in the model.
• Modeling
Reaction is included to improve simulation
results.
Kinetic Assay
Overexpression
86% Homology
Grows on Ascorbate
Challenge--Orphan Reactions:
Reactions without a known gene.
EC classification of
enzymes
• Several reactions
are known to
happen, but their
associated genes
are unknown
A large number of metabolic enzymes
have no known genetic basis
• Many known metabolic
reactions with EC numbers
are orphan.
• Can be probably be found by
a combined experimental –
computational strategy.
• Combination of gene
neighborhood, mRNA coexpression data and expts
like phenotype profiling and
metabolomics measurements.
• Distribution of
enzymatic activities
in orphans reactions
BMC Bioinformatics 8:244 (2007)
STEP 3: GENOME-SCALE MODELS AND
VALIDATION
From a reconstruction to a
model
• Add boundaries
• Describe network mathematically
The Process of metabolic reconstruction and validation
Procedure to generate a biomass
function
Nat Rev Microbiol. 2009 Feb;7(2):129-43
Computations: Functional
states
STEP 4: EVALUATION AND ITERATIVE
VALIDATION
An Example:
The process
used for
reconstructing
the human
metabolic
network
Mol Biosyst. 2007 Sep;3(9):598-603.
Nat Rev Genet. 2006 Feb;7(2):130-41.
USES OF RECONSTRUCTIONS
Applications of
Genome-Scale
metabolic
Reconstructions
Molec. Sys. Biol, 5:320, 2009
AVAILABLE RECONSTRUCTIONS
Growth in Available Reconstructions and
their use is exponential
Kim et al. Current Opinion in Biotechnology, Volume 23, Issue 4, 2012
Expanding scope in omics data types
NEW HORIZONS IN METABOLIC NETWORK
RECONSTRUCTION
A view of a metabolic network
Inclusion of protein structure
Science 325:1544 (2009).
Brunk et al. BMC Sys Bio (2016).
Chang, et al. Science (2013).
Environmental applications
Nat Rev Micro, 9: 39 (2011)
Multiple cells/organs
Nature Biotech 28:1279 (2010)
Host-Pathogen
Mol Sys Biol 6:422 (2010)
Microbial interactions
Lewis, et al. Nat Rev Microb, 2012
More cellular processes
Nat Rev Micro 7:129 (2009)
Metabolic Reconstruction
• Assume genes are
expressed at sufficient
quantity
• Protein / mRNA synthesis
costs are in the biomass
objective function
Lerman, et al. Nat Communications, 2012
Metabolic + TR/TR
• All enzymes must be produced
• Biomass objective includes fewer components
Lerman, et al. Nat Communications, 2012
Integrating transcription/translation
with metabolism
• 3-step process
• Formulation of transcription & translation reactions for metabolic
genes
• Formulation of metabolic reactions with enzymes explicitly represented
• “Merging” of the networks
Thiele et al., plos one, 2012
ME does
stuff
• Predicts
proteome
• Finds motifs
• Finds gene
functions