A synthetic replicator system undergoing Darwinian-like evolution

Published in Chemistry
A synthetic replicator system undergoing Darwinian-like evolution
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The bigger picture

Darwinian evolution is an incredibly creative force in the realm of living organisms. It has given rise to a remarkable array of species and allows them to adapt to changes in their environment [1]. So far Darwinian evolution has primarily acted on biological organisms.

Yet, Darwinian principles are not limited to complete organisms; they have been applied in directed evolution to develop new enzymes with new activities [2] and in nucleic acid systems [3]. However, the concept of evolution in fully synthetic chemical systems remains largely unexplored, yet would represent a revolutionary step in achieving the transition from chemistry to biology [4].

 Where did this project begin?

The Otto lab has developed a series of self-replicating macrocycles using disulfide-based dynamic combinatorial chemistry [5]. In this method, the oxidation of thiol building blocks can be mediated through either exposure to oxygen from the air or another oxidizing agent. The “golden” standard has been to ensure the presence of sufficient thiol monomers for the thiol-disulfide exchange reactions, which are crucial for the growth of self-replicators.

During the preparation of a dynamic combinatorial library (DCL), I unintentionally added an excess of oxidizing agent, which I only realized when I examined the UPLC chromatograms. I discovered some unexpected peaks, such as the 12mer-18mers, and observed the emergence of a new type of 3mer self-replicator instead of the anticipated 6mer.

This finding led me to speculate that evolutionary dynamics could potentially be observable in systems containing these two self-replicators, based on a selection pressure exerted by the oxidation level of the environment, which prompted me to explore whether and how such evolution can occur.

Small changes have large effects

Upon further investigation of the two replicators, we made an intriguing discovery regarding their growth characteristics. Surprisingly, we found that the 3mer replicator thrived only at high oxidation levels, specifically above 98%. Conversely, even a small amount of thiol inhibited its growth. On the other hand, the 6mer replicator failed to grow at such high oxidation levels. While these observations were clear, uncovering the mechanisms behind them proved to be an exceedingly challenging task.

Self-replication rate at different oxidation level

The system itself is highly complex, consisting of over a dozen macrocycles and multiple phases, including solutions, precursor aggregates, and fibers. Altering the oxidation level brings about changes across all these components, resulting in phase transition-like transformations of the two replicators. The oxidation level directly impacts the quantities of 12-18mer and 1mer, which we employed as reference points to gain insights into the system.

We observed that 12-18mer molecules readily attach themselves to the fibers of the 3mer replicators, serving as a source of sustenance for their growth through radical-mediated exchange reactions. On the other hand, monomer molecules and associated small rings exhibit a greater tendency for attaching to the fibers of the 6mer replicators, facilitating their self-replication through thiol-disulfide exchange reactions. These observations provided valuable clues for understanding the intricate dynamics at play within the system.

Oxidation level determines the self-replication pathway

The replicators can help each other

Self-replication does not necessarily imply the generation of identical copies exclusively. Indeed, we found that also errors (mutations) occurred upon replication. At high oxidation levels, the 6mer replicator can give rise to 3mer replicator. Conversely, at low oxidation levels, the 3mer replicator can cross-catalyze the formation of 6mer replicator. These cross-catalytic behaviors bear a resemblance to mutations as we know them from nucleic acids, where errors during self-replication can be inherited.

This discovery highlights the expanded structural possibilities within our system. Beyond the structure occupied at a particular time, new environmental conditions have the potential to trigger the formation of an alternative form. This phenomenon is important for the occurrence of evolution.

 Light makes evolution easier

In the above experiments, we controlled the oxidation level by adding varying amounts of an oxidizing agent. But we needed a more flexible approach to manipulate the system. Photoredox catalysis was previously employed to expedite the self-replicating process by enhancing the oxidation of thiol compounds [6]. However, the strength of photocatalysis at that time was insufficient to ensure a high enough oxidation level.

 We now utilized a more potent photocatalytic cofactor and tuned the catalytic efficiency by regulating the intensity of light. Additionally, to mimic natural selection, we constructed a continuous stirred-tank reactor. In such reactor replicators persist only when they have a sufficiently high self-replicating rate (at least as high as the rate at which they are flown out). Under strong or weak light irradiation, 3mer and 6mer replicators prevailed, respectively. These findings were consistent with the outcomes observed in the batch experiments. Furthermore, we discovered that manipulating the light wavelength allows us to achieve similar selection effects. Light serves as a driving force propelling the system towards new adaptations. Importantly, the replicators not only passively adapted to the oxidation levels but also actively alter them through photocatalysis, akin to the eco-evolutionary dynamics observed in nature.

Light-driven eco-evolutionary dynamics of the replicators

Summary and Outlook

A fully synthetic chemical system has been developed, capable of exhibiting rudimentary Darwinian evolution, marking an important step towards unleashing the power of Darwinian evolution in the chemical world, and creating fully synthetic, but living matter. Although at present the evolutionary dynamics only involve a minimal number of heritable states (changes in the size of the replicator ring), we are optimistic that, with further modifications, more, and increasingly complex structures and properties can be accessed. Thus, a new Darwinian world populated with chemical replicators is emerging.

References:

  1. De Duve, C. The onset of selection. Nature. 433, 581-582, (2005).
  2. Arnold, F. H. Directed evolution: bringing new chemistry to life. Angew. Chem. Int. Ed. 57, 4143-4148, (2018).
  3. Mills, D. R., Peterson, R. L., Spiegelman, S. An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc. Natl. Acad. Sci. U.S.A. 58, 217-224, (1967).
  4. Pross, A. What is life?: How chemistry becomes biology. (Oxford University Press, 2016).
  5. Otto, S. An approach to the de novo synthesis of life. Acc. Chem. Res. 55, 145-155, (2021).
  6. Santiago, G. M., Liu, K., Browne, W. R., Otto, S. Emergence of light-driven protometabolism on recruitment of a photocatalytic cofactor by a self-replicator. Nat. Chem. 12, 603-607, (2020).

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