SELF-REPLICATION: Even peptides do it

By Stuart A. Kauffman


This article originally appeared in Nature 382 August 8, 1996.
Copyright 1996 by Nature.

On page 525 of this issue [1], David Lee and colleagues describe what appears to be the first case of a self-replicating peptide, a result that may prove to be either a mere chemical curiosity, or seminal.

The authors show that a 32-amino-acid peptide, folded into an alpha-helix and having a structure based on a region of the yeast transcription factor GCN4, can autocatalyse its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution (see Fig. 1 on page 525).

The design of this replicator was based on a protein found in nature, an alpha-helical coiled coil. Reasoning that a given alpha-helical subunit of the entire structure could be seen as a complementary binding surface, acting cooperatively to organize other participating peptide subunits in the coiling, the authors hoped that a similar 'template' function could be found in smaller fragments. The ligation, or joining, site was constructed so as to lie on the solvent-exposed surface of the alpha-helical structure of their 32-amino-acid sequence.

Lee et al. established autocatalysis by showing that by increasing initial concentrations of the 32-amino-acid template, with constant concentrations of the 15- and 17-amino-acid substrates, a marked increase was produced in the initial rates of template production. The increase correlates with the square root of the initial template concentration, as seen in self-ligating polynucleotide systems [2,3]. The reaction is region- and chemically selective, yielding less that 15% side products, and proceeds through the major autocatalytic pathway open to the system.

Do these results reflect a rare chemical quirk in the repertoire of peptides and polypeptides, or might they hint at a route to self-reproducing molecular systems on a basis for wider than Watson-Crick base-pairing in polynucleotides? At this stage, we cannot know, but the way is now open to investigate.

The first step, beyond independent verification of the reaction system, is to construct self-reproducing cross-catalytic systems of two peptides, A and B, here A catalyses the formation of B from B's two fragment substrates, and B does the same for A. Such a system would be collectively autocatalytic--no molecule would catalyse its own formation, but the system would collectively catalyse its own formation from 'food' sources--where, the two A fragments and the two B fragments. If collectively autocatalytic peptide sets with two catalytic components can be constructed, can systems with three, four or hundreds of cross-coupled catalysts be created?

Such experiments are important. A free-living cell, prokaryote or eukaryote, is in fact a collectively autocatalytic system--virtually no molecule, including DNA, catalyses its own formation. Most of the cell's catalysts are proteins, so if collective autocatalysis in complex peptide systems is possible, we would have a new model for self-reproducing systems.

A host of experimental and theoretical questions about such systems present themselves. If such systems can be created, is it possible in general to constrain the side reactions enough for the autocatalytic system to increase in concentration as the fragment 'fuel' is added? Would such an increase be aided by confining reactions to a surface, or within a small volume? Are there means other than thioester promotion to drive the synthesis of peptide bonds? Even if such systems can be designed using clever synthetic chemistry, is the spontaneous formation of collective autocatalytic sets of peptides rare or common as a function of the diversity of the peptides, and of the regions of sequence space they are derived from? Can such autocatalytic systems be constructed or spontaneously assembled from mixed polymer systems consisting of DNA, RNA, peptides and perhaps other polymers and their building blocks? Can such systems evolve to 'neighbouring' autocatalytic systems while retaining 'catalytic closure', and could current life have evolved from one?

The new autocatalytic ligation-reaction system is merely exergonic: left to its own devices, the system will simply run to equilibrium. Can an autocatalytic system be created that carries out thermodynamic work cycles whereby the system sustains displacement from equilibrium, performs coordinated work and achieves such coordination by controlling, constraining and 'correcting' unwanted side reactions (as in DNA editing and repair; P. W. Anderson, personal communication and ref. 4) to enhance its own rate of reproduction?

The dominant view of life assumes that self-replication must be based on something akin to Watson-Crick base pairing. The 'RNA world' model of the origins of life conforms to this view. But years of careful effort to find an enzyme-free polynucleotide system able to undergo replication cycles by sequentially and correctly adding the proper nucleotide to the newly synthesized strand have not yet succeeded [5,6].

A polynucleotide system based on a ribozyme polymerase able sequentially to add the correct nucleotides (and thus copy itself) might work. In contrast, the simple and successful reproducing molecular systems described by Lee et al. [1] and by von Kiedrowski [2] which uses a single-stranded DNA hexamer and its two trimer fragments) are based on a polymer catalysing its own formation from two fragments. Both show that autocatalytic systems based on specific ligation reactions are possible. Because a variety of polymers and small molecules can catalyse such reactions, these results may prove seminal: the creation or spontaneous formation of simple or collectively autocatalytic sets may occur far more readily than we thought. Given the emerging field of 'molecular diversity', with its capacity to synthesize high-diversity DNA, RNA and peptide libraries [7], these questions are now open to detailed scrutiny.

References

[1.] Lee, D. H., Granja, J. R., Martinez, J. A., Severin K., and Ghadiri, M. R. Nature 382 525-528 (1996). [return to text]

[2.] von Kiedrowski, G. Agnew. Chem. 25 932-935 (1986).

[3.] von Kiedrowski, G., Wiotzka, B., Hielbing, J., Matzan, M. and Jordan, S. Agnew, Chem. 30 423-426 (1991).

[4.] Hopfield, J. J. Proc. Natl Acad. Sci. USA 71 4135-4139 (1974).

[5.] Joyce, G. F., and Orgel, L. E. J. Mol. Biol. 188 433-437 (1986).

[6.] Joyce, G. F. Cold Spring Harb. Symp. Quant. Biol. 52 (1987).

[7.] Scott, J. K., and Smith, G. P. Science 249 386-389 (1990).