University of Groningen
Steps towards de-novo life
Monreal Santiago, Guillermo
DOI:
10.33612/diss.121581426
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Publication date: 2020
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Monreal Santiago, G. (2020). Steps towards de-novo life: compartmentalization and feedback mechanisms in synthetic self-replicating systems. University of Groningen. https://doi.org/10.33612/diss.121581426
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English summary
In this thesis, we aimed to implement some of the fundamental properties of life in a synthetic system, with the ultimate goal of making what we call de-novo life. The approach we took follows the definition of life provided by Ganti in 1971. This definition states that a minimal version of life should contain subsystems ca-pable of self-replication, compartmentalization and metabolism. Chapter 1 dis-cusses these properties and their relevance for life, and reviews previous progress towards their implementation.
Chapter 2is focused on the self-replication mechanism of peptide-based
fi-bres that emerge from a dynamic combinatorial library. Our group has previ-ously established how those fibres self-replicate through a combination of me-chanical fragmentation and templated growth, using small disulfide macrocycles as precursors. In this chapter, we study the growth step in detail, using HS-AFM (high speed atomic force microscopy) to directly visualize it. These results show that growth is based on a new mechanism of supramolecular polymerization, in which the small macrocycles accumulate on the side of the self-replicating fi-bres and form aggregates from which they diffuse towards the fibre end. We also study the aggregation of those macrocycles separately from the fibres as an off-pathway state that does not contribute to fibre growth, and discuss how this mechanism could be part of the formation of other supramolecular polymers and autocatalytic structures.
Chapter 3 treats compartmentalization. In it, we use complex coacervates
(droplets based on polyelectrolyte complexation) to encapsulate the self- repli-cating fibres discussed in the previous section. We first study the uptake of re-plicators and precursors by the coacervates, which is practically complete in both cases due to their high charge. Secondly, we study their diffusion between coac-ervates, proving that small macrocycles can move in and out of the coacervate phase much faster than the fibres. This is a very convenient result for de-novo life: in this system, the molecules containing the information are retained in the compartment, while their precursors can be exchanged with the environment. Fi-nally, we show how encapsulation in coacervates affects the library and changes the stability of the different disulfide macrocycles: a trimer replicator is formed in the coacervate phase, in contrast to the hexamer that dominates the library in bulk solution.
The results of Chapter 4 are the first example of a synthetic system that is both able to self-replicate and use external energy to catalyse the formation of its own precursors. In that chapter, we discover that the peptide-based replicators that we described above are able to recruit dyes that produce singlet oxygen. This re-cruitment changes the properties of the dyes, either increasing their absorbance or shifting it to different wavelengths. We design conditions where this process increases the photocatalytic efficiency of the dyes in presence of replicators,
English summary
ing to enhanced photooxidation. This photooxidation yields the precursors of the replicator as a product, which increases the replication rate as well. This critical first step allows for future research where the replicators could catalyse the for-mation of other compounds or be selected based on their capacity to trigger this protometabolic reaction.
The recruitment of photocatalytic cofactors described in Chapter 4 combines two sources of positive feedback in one system: self-replication and photooxida-tion enhancement. But the results of that chapter also indicate that the second one can be transformed into negative feedback: by choosing a different wavelength for irradiation, replicators can inhibit photooxidation instead of enhancing it. In
Chapter 5, we confirm this effect experimentally, and use it to design a
chemi-cal oscillator. We then use a kinetic model to simulate this design, confirming that the proposed combination of self-replication, negative feedback, and out-of-equilibrium conditions (through constant inflow of a reducing agent, which transforms the replicator back to monomers) can theoretically lead to oscillations. However, the oscillations found in the part of the parameter space that was ex-plored by the model were always damped, and they required a strong inhibition - possibly stronger than what the system can show at the moment. In order to im-plement this oscillator design experimentally, new photosensitizers would need to be explored.
Finally, Chapter 6 takes a step back and puts the results of these thesis in the context of synthesizing de-novo life. The author reflects on what has been achieved and what are the next steps for this system, and shows his personal view of the future of the field.
