Optimality in Carbon Metabolism

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Optimalityin CarbonMetabolism
Ron Milo
Department of Plant SciencesWeizmann Institute
of Science
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What limits maximal growth rates?
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What governs the efficiency of photosynthesis
and carbon fixation?
Why is Rubisco slow and non specific?
What governs maximal growth rates?
Design principles in photosynthesis wavelengths
used and saturation
Synthetic carbon fixation pathways for higher
efficiency
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Are there simplifying principles to the structure
of the central carbohydrate metabolism network?
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An illustrative example the Pentose Phosphate
cycle

• Converts between 5 and 6 carbon sugars
• e.g Ribose-5P is used for making nucleotides
• e.g Fructose-6P is used for building the cell
  wall
• Was analyzed as an optimization problem
  (Meléndez-Hevia Isodoro 1994)
• We use this as a starting point

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The Pentose Phosphate Pathway defined as a game

• Goal
• Turn 6 Pentoses into 5 Hexoses
• Rules
• Transfer 2-3 carbons between two molecules
• Never leave a molecule with 1-2 carbons
• Optimization function
• Minimize the number of steps (simplicity)

?
E. Meléndez-Hevia et al. (Journal of theoretical
Biology 1994)
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Serious, take 5 minutes and six 5 carbons and try
it out
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Solution to Pentose Phosphate game in 7 steps
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Solution to Pentose Phosphate game in 7 steps

• Corresponds to natural pathway
• Doesn't explain why the rules exist
• Supports the idea of simplicity

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Are there simplifying principles to the structure
of the central carbohydrate metabolism network?
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We develop a method to find shortest path from A
to B
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But what are the steps allowed in biochemistry?
?
?
?
?
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Arren Bar-Even
Elad Noor
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All possible reaction types are explored
aldehyde dehydrogenase (CoA) pyruvate ?
acetyl-CoA CO2
isomerase (keto to enol) pyruvate ? enolpyruvate
kinase (carboxyl) pyruvate ? pyruvate-P
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EC numbers define 30 possible enzymatic reaction
families
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EC numbers define 30 possible enzymatic reaction
families
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EC rules were encoded into commands
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Optimization function finds minimal number of
steps between any two metabolites

• The shortest path can be found efficiently using
  a customized BFS (breadth first search)

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Are all pairs of metabolites connected by
shortest possible paths? (as allowed by
biochemistry rules)
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Are all pairs of metabolites connected by
shortest possible paths? (as allowed by
biochemistry rules)

• Some pairs are connected by shortest possible
  paths
• Other pairs can be connected in less steps via
  shortcuts

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Are all pairs of metabolites connected by
shortest possible paths? (as allowed by
biochemistry rules)

• Some pairs are connected by possible shortest
  paths
• Other pairs can be connected in less steps via
  shortcuts
• Cluster together pairs that connect via shortest
  paths
• Define these as minimality modules

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minimality modules are defined to contain
shortest paths
A
A
Only metabolites connected by shortest possible
paths are contained in an minimality module
B
B
C
C
D
D
E
E
F
F
Existing reactions (in organism)
Possible EC reactions (biochemistry)
Minimality modules
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Example possible shortcut in glycolysis break it
into modules
GLU
DHAP
GAP
GAP ? 3PG (EC 1.2) is biochemically feasible
(exists in plants), but is not part of E. coli
central metabolism Therefore glycolysis is not as
short as possible and breaks down into minimality
modules
BPG
3PG
2PG
PYR
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Central carbon metabolism network breaks down to
minimality modules
Noor et al, submitted
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Biomass precursors are key metabolites
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• Design principle minimal number of enzymatic
  steps connecting every pair of consecutive
  precursors ?
• central carbon metabolism is a minimal walk
  between the 13 biomass precursors

Make things as simple as possible but not
simpler
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Can carbon fixation metabolism be enhanced?
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Carbon is assimilated into plants by the Calvin
cycle
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RUBISCO the central carboxylating enzyme

• Estimated 4x1010 kg of this enzyme present on
  Earth
• 5 kg per person on Earth
• Most abundant protein on earth ! (?)
• slow enzyme - maximal rate of carboxylation
  only
• 2-3 per sec in C3
• 3-5 per sec in C4
• 8-12 per sec in cyanobacteria

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Non specific enzyme O2 can be incorporated as a
wrong substrate instead of CO2
Photorespiration can have important metabolic
roles (e.g. Ort Baker, 2002 Rachmilevitch,
2004)
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So maybe it can be made better?

• higher catalytic rate,
• better substrate specificity
• or both

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Rubisco shows empirical kinetic rates tradeoff
kC
easier CO2 addition ? harder hydration cleavage
kcat
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Correlations indicate related energy barriers
kC
easier CO2 addition ? harder hydration cleavage
kcat
easier CO2 addition ? easier O2 addition
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Correlations indicate related energy barriers
kC
easier CO2 addition ? harder hydration cleavage
kcat
easier CO2 addition ? easier O2 addition

• Outlier Rhodospirillum rubrum
• (form I Rubisco).

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Rubisco shows empirical kinetic rates tradeoff
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We test carbon fixation rate at every kinetic
rate (for each CO2 environment)
medium carbon concentrating mechanism CO280 µM
Savir et al, in preparation
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Rubiscos nearly optimal to their environments
(rather than slow and non-specific)
Savir et al, in preparation
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Can we find better ways to achieve carbon
fixation?
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There are several alternative carbon fixation
pathways
Bar-Even et al, under review
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We systematically explore all possible synthetic
carbon fixation pathways
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Metabolic networks optimization synthesis a
grand challenge for synthetic biology

• Future directions
• Compare alternative pathways solutions in
  different organisms
• Try to implement alternative carbon fixation
  in-vitro/in-vivo
• Couple synthetic carbon fixation to energy
  sources ? fuel production from sunlight/wind
• or at least learn something about the logic of
  evolution,
• and how evolution is smarter than you are
  (Orgels law)

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