The metabolism problem: ingredients of an emerging theory

Eörs Szathmáry & Chrisantha Fernando

Collegium Budapest Eötvös University Budapest

Thanks to Günter!

Pathways of supersystem evolution

boundary

template

metabolism M B

B T

M T M B T

INFRABIOLOGICAL SYSTEMS

General background to the talk

The problems of phylogenetic reconstruction (top-down)

• LUCA was too advanced • Reconstructions (e.g. Delaye et al. OLEB in press)

cannot reach deep enough• The fact that metabolic enzymes are not well

conserved does not mean that they were not there!• Scaffolds (pre-RNA, primitive metabolic

reactions) may have disappeared without leaving a trace behind!!!

• A more synthetic approach is needed• General evolutionary mechanisms must be sought

Benner’s hypothetical ribo-organism (1999)

Membrane? Cofactors?

This raises a lot of questions

• How could such a metabolic network build up? • Did the environment change or not during the

process? • What was the nature of the non-enzymatic

reactions producing (some of) these metabolites? • Is an autotrophic, non-enzymatic metabolism

feasible? • What are the constraints on metabolic evolution in

the context of supersystem evolution?

Some elementary considerations

O L

Environment 1 Environment 2

Organic synthesis

Life

•Autotrophy impossible

•Enzymatic pathways are likely to be radically new inventions

L

O

•Autotrophy possible

•Enzymatic pathways may resemble non-enzymatic ones

Further complication of supersystem organization

• The example of the Template/Boundary system: progressive distinction from the environment

Metabolites pass freely Metabolites are hindered

evolution

Progressive sequestration

• Initially only templates are kept in• They can evolve catalytic properties• Carriers and channels can also evolve• Membrane permeability can become progressively

restrictive• Finally, only a very limited sample of molecules

can come in• Inner and outer environments differentiate• Membrane and metabolism coevolve gradually

Evolution of metabolism: primitive heterotrophy with pathway innovation

A

B

C

D

Necessarily heterotrophic protocell

ABC

D

A

B

C

ABC

D

Evolved enzymatic reaction

Assume D is the most complex

The final stage of innovation

AB

CD

This could be a heterotroph or autotroph (depending on the nature of A)

Evolution of metabolism: primitive autotrophy with pathway retention

A

B

C

D

A

B

C

D

a

b

c

d

a

b

c

DRetroevolution is also likely because of membrane coevolution

Reversible versus irreversible: the control of leakage

A C

Unfavourable:

Vulnerable to depletion in A

A C

B D

Favourable:

Resistant to depletion in A

Two contrasting modes of enzymatic pathway evolution

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)

What evidence is there for the two mechanisms?

• New data using the whole armamentarium of bioinformatics

• It is about the evolution of PROTEIN enzymatic pathways

• Could be strongly suggestive for RIBOZYME-aided metabolism (the RNA world)

The example of biotin metabolism

Light and Kraulis (2004) BMC Bioinformatics

Homology: strict cutoff in PSI-BLAST

Enzymes as edges: the whole E.coli network is analyzed

Minimal path length

The most promiscuous 20 compounds

Frequency: the number of edges where is shows up

Homology versus minimal path length

With the 20 Without the 20

Different types of homologous enzyme pairs

Mechanistically similar

Mechanistically different

A statistical analysis

Functionally similar Functionally dissimilar

Conclusion

• There is some evidence for retroevolution

• BUT the dominant mode seems to fit the patchwork mechanism

• Same mechanisms might worrk for an RNA world!

Patchwork and retroevolution can be made compatible

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

• Pathways retroevolving in parallel can recruit enzymes in a pacthwork manner

Evolution of catalytic proteins or on the origin of enzyme species by means of

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.

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

• The division of labour for enzymes!

Evolution of connectivity: Pfeiffer et al. (2005) PloS Biology

• Enzymes are initially specific for the group transferred but not for the substrates

• Metabolism is based on group transfer reactions between metabolites

• Without group transfer (D) only unimolecular reactions

An emerging group transfer network

the frequency, P(k), of metabolites participating in k reactionsis given by k-c, where c is a constant coefficient

Hubs (127126 for group 1) emerge as consequence of selection for growth rate

An emerging network without group transfer

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