On the origin and evolution of some genetic systems

Eörs Szathmáry

Collegium Budapest AND Eötvös University

John Maynard Smith (1920-2004)

• Educated in Eaton• The influence of J.B.S.

Haldane• Aeroplane engineer• Sequence space• Evolution of sex• Game theory• Animal signalling• Balsan, Kyoto,

Crafoord prizes

The major transitions (1995)

***

*

* These transitions are regarded to be ‘difficult’

Difficulty of a transition

• Selection limited (special environment)

• Pre-emption: first come selective overkill

• Variation-limited: improbable series of rare variations (genetic code, eukaryotic nucleocytoplasm, etc.)

Difficult transitions are ‘unique’

• Operational definition: all organisms sharing the trait go back to a common ancestor after the transition

• These unique transitions are usually irreversible (no cell without a genetic code, no bacterium derived from a eukaryote can be found today)

Units of evolution

hereditary traits affecting survival and/or reproduction

1. multiplication

2. heredity

3. variation

Gánti’s chemoton model (1974)

ALL THREE SUBSYSTEMS ARE AUTOCATALYTIC

template copying

metabolism

membrane growth

The latest edition: OUP 2003

• After several editions in Hungarian

• Two previous books (the Principles and Contra Crick) plus one essay

• Essays appreciating the biological and philosophical importance

Pathways of supersystem evolution

boundary

template

metabolism M B

B T

M T M B T

INFRABIOLOGICAL SYSTEMS

What about replication?

• Replication from a chemical point of view always rests on autocatalysis

• The basic form is

A + X 2 A + Y

• very important for biology

• Much more general than DNA

The formose ‘reaction’

formaldehyde

glycolaldehyde

autocatalysis

Butlerow, 1861

Replication in the formose reaction

• Replication is non-informational• Autocatalysis – YES• Heredity – NO• Good for metabolism• Not good for genetics• Butlerow was born on the 15th Sept, 1829• He was regarded as one of the best lecturers of his

time. His lectures were lucid and thorough, yet his language was colourful. Local society often preferred his lectures to the theatre

Primitive ancestry of the reverse citric acid cycle

• Was proposed by Günter Wächtershäuser (1990)

• Coupled to CO2 fixation and pyrite formation around deep-sea hydrothermal vents

The main problem of the origin of life is metabolite channelling

• Enzymes speed up reactions relative to the unwanted reactions

• Spontaneous decay reactions abound

• Maintenance, not only reproduction, requires autocatalysis

dx/ dt = k x – d x = 0

All network models neglecting side reactions are seriously incomplete

• E.g. protein networks

• In model assumptions, a reaction is either good or neutral for the system – but the number of harmful transformations is in fact much higher

• Did life emerge from a chemical canyon?

Chemical evolution was a race between tar formation and life

formation

Chemical networks

Life Tar

What fraction of planets would end up with just tar?

Another case: von Kiedrowski’s replicators

Von Kiedrowski’s replicator

• Theory with experiment• J. Mol. Evol., forthcoming

Does temperature cycling work?

Elongation taxes the system badly

Classification of replicators

Limited heredity

Unlimited heredity

Holistic formose

Modular Von Kiedrowski

genes

Limited (number of individuals) > (number of types)

Unlimited (# of individuals) << (# of types)

A crucial insight: Eigen’s paradox (1971)

• Early replication must have been error-prone

• Error threshold sets the limit of maximal genome size to <100 nucleotides

• Not enough for several genes• Unlinked genes will compete• Genome collapses• Resolution???

Simplified error threshold

x + y = 1

Molecular hypercycle (Eigen, 1971)

autocatalysis

heterocatalytic aid

Parasites in the hypercycle (JMS)

parasite

short circuit

“Hypercyles spring to life”…

• Cellular automaton simulation on a 2D surface

• Reaction-diffusion

• Emergence of mesoscopic structure

• Conducive to resistance against parasites

• Good-bye to the well-stirred flow reactor

…but then die if modelled in more detail

• Are not resistant to short-circuits

• Collapse if the adhesive surface is patchy (the mesoscopic structure collapses)

• Only compartmentation saves them

Hairpin Ribozyme

aaacaGAGAAGUcaACCAg|||||

A G AA

AUGGUcCAUUAUAUG

A C A

GUG

CACG|||

uu

1

10

20 30

40

50

5’

3’

H1

loop A

H2 H3 H4

loop BaaacaGAGAAGUcaACCAg

|||||A G A

A

AUGGUcCAUUAUAUG

A C A

GUG

CACG|||

uu

1

10

20 30

40

50

5’

3’

H1

loop A

H2 H3 H4

loop B

N = 50

39/50 (78%) of the positions were mutated, we used 142 mutants

Error rates and the origin of replicators

Nature 420, 360-363 (2002).

Replicase RNA

Other RNA

Increase in efficiency• Target efficiency:

the acceptance of help

• Replicase efficiency: how much help it gives

• Copying fidelity

• Trade-off among all three traits: worst case

The dynamics becomes interesting on the rocks!

Evolving population

• Molecules interact with their neighbours• Have limited diffusion on the surface

Error rate Replicase activity

The stochastic corrector model for compartmentation

Szathmáry, E. & Demeter L. (1987) Group selection of early replicators and the origin of life. J. theor Biol. 128, 463-486.

Grey, D., Hutson, V. & Szathmáry, E. (1995) A re-examination of the stochastic corrector model. Proc. R. Soc. Lond. B 262, 29-35.

Dynamics of the SC model

• Independently reassorting genes• Selection for optimal gene composition between

compartments• Competition among genes within the same

compartment• Stochasticity in replication and fission generates

variation on which natural selection acts• A stationary compartment population emerges

Group selection of early replicators

• Many more compartments than templates within any compartment

• No migration (fusion) between compartments

• Each compartment has only one parent• Group selection is very efficient• Selection for replication synchrony Chromosomes!