The Evolution of Metabolism The Evolution of Metabolism

Chrisantha Fernando

School of Computer Science

Birmingham University

17th November 2005. Systems Biology Group Meeting

Chrisantha Fernando

School of Computer Science

Birmingham University

17th November 2005. Systems Biology Group Meeting

Pre-Enzymatic Metabolic Evolution

Pre-Enzymatic Metabolic Evolution

Part 1. Part 1.

Pathways of supersystem evolutionPathways of supersystem evolution

boundary

template

metabolism M B

B T

M T M B T

Pre-enzymatic and post-enzymatic stages can be distinguished.

BackgroundBackground

All living systems today have metabolism.

All living systems today have metabolism.

An organism without metabolism would be one that did not synthesize any of its constituents, but obtained them all preformed from the environment or from its parent(s).

Heterotrophic theories of the origin of life (Oparin, Haldane, Lancet, Eigen, Kauffman, Farmer, Fox, Szostak) assume such ‘organisms’ were possible.

An organism without metabolism would be one that did not synthesize any of its constituents, but obtained them all preformed from the environment or from its parent(s).

Heterotrophic theories of the origin of life (Oparin, Haldane, Lancet, Eigen, Kauffman, Farmer, Fox, Szostak) assume such ‘organisms’ were possible.

The Problem of 1o Heterotrophy.The Problem of 1o Heterotrophy.

Initial bolus of complex organics from space. Chemical energy used to form organism depletes

this bolus. Low gross primary production of complex organics

(because no autotrophs). Therefore any 1o

heterotroph exists in an ecological transient, and can be saved only by the evolution of an autotroph.

In the long term, [metabolic entities] are rate limiting to non-metabolic entities.

Initial bolus of complex organics from space. Chemical energy used to form organism depletes

this bolus. Low gross primary production of complex organics

(because no autotrophs). Therefore any 1o

heterotroph exists in an ecological transient, and can be saved only by the evolution of an autotroph.

In the long term, [metabolic entities] are rate limiting to non-metabolic entities.

All known cellular life has an autocatalytic metabolism.

All known cellular life has an autocatalytic metabolism.

Remove all metabolites, leaving water and informational macromolecules in place + ATP. The network cannot be re-created from the food materials alone.

All cells possess a distributive autocatalytic network, that cannot be seeded from outside, because some of its seed components cannot be taken up (or synthesized) from the medium.

Remove all metabolites, leaving water and informational macromolecules in place + ATP. The network cannot be re-created from the food materials alone.

All cells possess a distributive autocatalytic network, that cannot be seeded from outside, because some of its seed components cannot be taken up (or synthesized) from the medium.

The Chemoton(T. Ganti 1971)

Benefits of autocatalytic metabolism.

Benefits of autocatalytic metabolism.

During hard times, key metabolites cannot escape, whereas the non-autocatalytic entity could loose its metabolites by reactions running in reverse.

Contemporary metabolic networks are endogenously autocatalytic.

The unit of chemical evolution is the autocatalytic cycle, (existing within a recycling system).

During hard times, key metabolites cannot escape, whereas the non-autocatalytic entity could loose its metabolites by reactions running in reverse.

Contemporary metabolic networks are endogenously autocatalytic.

The unit of chemical evolution is the autocatalytic cycle, (existing within a recycling system).

How likely is it for autocatalytic cycles to arise and persist?

How likely is it for autocatalytic cycles to arise and persist?

Imagine an experiment, C,H,N,O,P,S, heterogeneous environments and flux keeps system away from equilibrium.

Under what circumstances will the system settle down into a boring point attractor (tar) and when will it produce life?

G.A.M. King. Selection of rate coefficients and concentrations of reagents are needed to make anything but the smallest cycle to persist. [The problem of side-reactions/specificity].

Imagine an experiment, C,H,N,O,P,S, heterogeneous environments and flux keeps system away from equilibrium.

Under what circumstances will the system settle down into a boring point attractor (tar) and when will it produce life?

G.A.M. King. Selection of rate coefficients and concentrations of reagents are needed to make anything but the smallest cycle to persist. [The problem of side-reactions/specificity].

Pre-enzymatic symbiosis of autocatalytic particles.

Pre-enzymatic symbiosis of autocatalytic particles.

If symbiosis can reduce the rate of decay of the symbiont (i.e. increase specificity), then even if the growth rate of the symbiont is lower than its components, the coupled cycle has a selective advantage.

But a successful symbiosis is not easy, (“The Good Symbiont”, ECAL 2005).

If symbiosis can reduce the rate of decay of the symbiont (i.e. increase specificity), then even if the growth rate of the symbiont is lower than its components, the coupled cycle has a selective advantage.

But a successful symbiosis is not easy, (“The Good Symbiont”, ECAL 2005).

Modeling Chemical Evolution. Modeling Chemical Evolution.

A model of a heterogenious, interestingly structured, platonic, chemical space which can be explored.

Ensure conservation of mass and energy. Allow niche selection in chemical space. Allow physical niche selection (i.e. selection of

abiotic catalysts, and selection of diffusion limiting lipid membranes).

The system must be capable of discovery of scaffolding/channeling systems that reduce side-reactions.

A model of a heterogenious, interestingly structured, platonic, chemical space which can be explored.

Ensure conservation of mass and energy. Allow niche selection in chemical space. Allow physical niche selection (i.e. selection of

abiotic catalysts, and selection of diffusion limiting lipid membranes).

The system must be capable of discovery of scaffolding/channeling systems that reduce side-reactions.

Possible approaches so far… Possible approaches so far…

Gil Benko. My DPhil Chapter 2.

The problem is to develop a valid model of chemistry in which chemical evolution can be explored.

Then to expose this model to appropriate environments.

Efforts underway in Germany to Ix. Formose cycle metabolism evolution.

Gil Benko. My DPhil Chapter 2.

The problem is to develop a valid model of chemistry in which chemical evolution can be explored.

Then to expose this model to appropriate environments.

Efforts underway in Germany to Ix. Formose cycle metabolism evolution.

Post-Enzymatic Metabolic Evolution

Post-Enzymatic Metabolic Evolution

Part 2. Part 2.

General AssumptionsGeneral Assumptions Assume an underlying (non/minimal-enzymatic)

metabolism in a protocell capable of synthesizing ribozymes.

Since there is no relationship between the catalytic power of a given RNA and the protein for which it encodes, there is no clear path from the RNA to the protein world. Therefore protein cladistics reach a historical limit.

Evolution of metabolism is by genetic assimilation of underlying chemical pathways.

Several evolutionary motifs have been proposed.

Assume an underlying (non/minimal-enzymatic) metabolism in a protocell capable of synthesizing ribozymes.

Since there is no relationship between the catalytic power of a given RNA and the protein for which it encodes, there is no clear path from the RNA to the protein world. Therefore protein cladistics reach a historical limit.

Evolution of metabolism is by genetic assimilation of underlying chemical pathways.

Several evolutionary motifs have been proposed.

i) Horowitz’s Retro-extensioni) Horowitz’s Retro-extension

A

B

C

D

Necessarily heterotrophic protocell

ABC

D

A

B

C

ABC

D

Evolved enzymatic reaction

Assume D is the most complex

AB

CD

The final stage of innovationThe final stage of innovation

Horowitz’s assumptions and their consequences.

Horowitz’s assumptions and their consequences.

D is indeed available at an early stage. C,B, and A are available in excess in the

environment. This is only likely where autotrophs produce them. Therefore, retroevolution may be important when a

heterotroph co-evolves closely with an autotroph. Retroevolution is also likely due to membrane co-

evolution, i.e. where D can no longer enter, and so must be synthesized.

D is indeed available at an early stage. C,B, and A are available in excess in the

environment. This is only likely where autotrophs produce them. Therefore, retroevolution may be important when a

heterotroph co-evolves closely with an autotroph. Retroevolution is also likely due to membrane co-

evolution, i.e. where D can no longer enter, and so must be synthesized.

Wachtershauser’s Operations.Wachtershauser’s Operations.

Loss of pathways. Loss of pathways.

ABCD : AB Using various combinations of the above

primitives, predictions can be made about evolutionary trajectories leading to extant metabolic systems.

However the possible trajectories are underdetermined, so additional assumptions are required.

ABCD : AB Using various combinations of the above

primitives, predictions can be made about evolutionary trajectories leading to extant metabolic systems.

However the possible trajectories are underdetermined, so additional assumptions are required.

Assume Evolutionary Opportunism

Assume Evolutionary Opportunism

Melendez-Hevia et al. Melendez-Hevia et al.

Is there an evolutionary trace of the actual trajectory?

Is there an evolutionary trace of the actual trajectory?

Horowitz (1945) : retroevolution Ancient non-enzymatic pathway: A B C D Progressive depletion of D, then C, then B, then A Selection pressure for enzyme appearance in this order Homologous enzymes will have different mechanisms

Jensen (1976) enzyme recruitment (patchwork) One possible mechanism: ambiguity and progressive evolution of

specificity Homologous enzymes will have related mechanisms Enzyme recruitment from anywhere (opportunism)

Horowitz (1945) : retroevolution Ancient non-enzymatic pathway: A B C D Progressive depletion of D, then C, then B, then A Selection pressure for enzyme appearance in this order Homologous enzymes will have different mechanisms

Jensen (1976) enzyme recruitment (patchwork) One possible mechanism: ambiguity and progressive evolution of

specificity Homologous enzymes will have related mechanisms Enzyme recruitment from anywhere (opportunism)

Light and Kraulis (2004)Light and Kraulis (2004)

Homologous enzyme pairs abound at the minimum path length of one, (i.e. the product of one is the substrate of the other).

But does not corroborate retro-extension because, Only small homology between mpl 2 and 3 pairs. Most enzyme pairs with mpl 1 have similar EC

numbers, hence are functionally related. Retro-extension may still have been important in the

RNA world.

Homologous enzyme pairs abound at the minimum path length of one, (i.e. the product of one is the substrate of the other).

But does not corroborate retro-extension because, Only small homology between mpl 2 and 3 pairs. Most enzyme pairs with mpl 1 have similar EC

numbers, hence are functionally related. Retro-extension may still have been important in the

RNA world.

With 20 promis. Without 20 promis.

Function Similar Function Dissimilar.

But patchwork and retro-extension are not mutually exclusive.

But patchwork and retro-extension are not mutually exclusive.

A broader notion of retroevolution proposes just the (frequent) retrograde appearance of consecutive enzymes, not that they are homologous within a pathway

Pathways retroevolving in parallel can recruit enzymes in a patchwork manner

A broader notion of retroevolution proposes just the (frequent) retrograde appearance of consecutive enzymes, not that they are homologous within a pathway

Pathways retroevolving in parallel can recruit enzymes in a patchwork manner

Why Scale-Free?Why Scale-Free?

- Preferential attachment (Light, Kraulis, Elofsson 2005). Older enzymes are more highly connected

(duplic and diverged enzyme may preserve past reagents).

HGT enzymes are more highly connected (may aid retention?

- Preferential attachment (Light, Kraulis, Elofsson 2005). Older enzymes are more highly connected

(duplic and diverged enzyme may preserve past reagents).

HGT enzymes are more highly connected (may aid retention?

The origin of enzyme species by natural selection

The origin of enzyme species by natural selection

Kacser & Beeby (1984) J. Mol. Evol. A precursor cell containing very few multifunctional

enzymes with low catalytic activities is shown to lead inevitably to descendants with a large number of differentiated monofunctional enzymes with high turnover numbers.

Duplication and divergence and natural selection for faster growth are shown to be the only conditions necessary for such a change to have occurred.

Assumes that increasing the copy number of one enzyme gene decreases numbers of other enzymes.

Kacser & Beeby (1984) J. Mol. Evol. A precursor cell containing very few multifunctional

enzymes with low catalytic activities is shown to lead inevitably to descendants with a large number of differentiated monofunctional enzymes with high turnover numbers.

Duplication and divergence and natural selection for faster growth are shown to be the only conditions necessary for such a change to have occurred.

Assumes that increasing the copy number of one enzyme gene decreases numbers of other enzymes.

From K&BFrom K&B

The thermodynamic constraints within which cells operate do not define the particular kinetic organization that we observe.

A clever student of biochemistry could invent a variety of metabolic maps and associated enzymes which differ substantially from those now.

Pathways existed prior to the arrival of enzymes. Their presence allows the kinetic realization of a particular subset of all thermodynamically possible steps. Another set of enzymes would produce another map.

The thermodynamic constraints within which cells operate do not define the particular kinetic organization that we observe.

A clever student of biochemistry could invent a variety of metabolic maps and associated enzymes which differ substantially from those now.

Pathways existed prior to the arrival of enzymes. Their presence allows the kinetic realization of a particular subset of all thermodynamically possible steps. Another set of enzymes would produce another map.

All these ingredients (and more) must be put together

All these ingredients (and more) must be put together

Supersystem evolution Alternative environments Progressive sequestration Duplication and divergence of enzymes Selection for cell fitness Network complexification

Supersystem evolution Alternative environments Progressive sequestration Duplication and divergence of enzymes Selection for cell fitness Network complexification

What should we do?What should we do?

Make a model of the underlying platonic metabolic pathways, coupled with a model of enzyme evolution, and cell level fitness subject to reasonable environmental conditions.

How in principle could such systems co-evolve? E.g. Pfeiffer et al showed co-evolution of

increasing specific group transfer metabolite co-enzymes with their specific enzymes, in a group-transfer network, selected for growth rate.

Make a model of the underlying platonic metabolic pathways, coupled with a model of enzyme evolution, and cell level fitness subject to reasonable environmental conditions.

How in principle could such systems co-evolve? E.g. Pfeiffer et al showed co-evolution of

increasing specific group transfer metabolite co-enzymes with their specific enzymes, in a group-transfer network, selected for growth rate.

Biasing Assumptions.Biasing Assumptions. 1. They assumed that initially ALL enzymes were present capable of catalysing all possible metabolic

group transfers. A more reasonable possibility is that no genetically encoded enzymes are present (only non-encoded catalysts), but that there is an inherent rate of underlying group transfer reactions. In the model there is no underlying metabolic thermodynamics or kinetics.

2. Enzyme kinetics were capable of being arbitrarily uniformly mutated, with free energies of forward and backward reactions being easy to alter arbitrarily by mutation. Is this reasonable? Could an enzyme really be so flexible in its functional response to mutation?

3. They assume that enzyme concentrations cannot be influenced by end products, that enzymes cannot be inhibited or activated by normal substrates. Not so bad for a first attempt.

4. They assume that enzymes specificity is for acceptor and donor groups, but that there is no evolution of enzyme specificity for the catalysed group itself, rather this remains constant throughout. Is this reasonable?

5. Increasing the copy number of one enzyme gene did not decrease the concentrations of other enzymes.

6. They assume that the environment over all evolutionary history consists of 0000000 and 1111111, therefore not properly testing the scenarios would have allowed evolution by retro-extension.

1. They assumed that initially ALL enzymes were present capable of catalysing all possible metabolic group transfers. A more reasonable possibility is that no genetically encoded enzymes are present (only non-encoded catalysts), but that there is an inherent rate of underlying group transfer reactions. In the model there is no underlying metabolic thermodynamics or kinetics.

2. Enzyme kinetics were capable of being arbitrarily uniformly mutated, with free energies of forward and backward reactions being easy to alter arbitrarily by mutation. Is this reasonable? Could an enzyme really be so flexible in its functional response to mutation?

3. They assume that enzyme concentrations cannot be influenced by end products, that enzymes cannot be inhibited or activated by normal substrates. Not so bad for a first attempt.

4. They assume that enzymes specificity is for acceptor and donor groups, but that there is no evolution of enzyme specificity for the catalysed group itself, rather this remains constant throughout. Is this reasonable?

5. Increasing the copy number of one enzyme gene did not decrease the concentrations of other enzymes.

6. They assume that the environment over all evolutionary history consists of 0000000 and 1111111, therefore not properly testing the scenarios would have allowed evolution by retro-extension.