Periodic Reporting for period 2 - AbioEvo (Conditions for the emergence of evolution during abiogenesis)
Berichtszeitraum: 2022-12-01 bis 2024-05-31
The origin of life is one of the big unsolved scientific mysteries. Despite competing scenarios, we may have some idea of possible environments and formation of the building blocks of life. However, the process by which these self-organize into cells that evolve remains essentially unknown. Demonstrating an experimental path for the origin of evolution will provide solid scientific ground for the origin of life. Showing that such a path can be gradual will notably enhance the plausibility of origin of life events. Understanding the general principles for the origin of life also provides support for space missions, notably investments in searching for exoplanets which may harbor life.
Abiogenesis, the transition from non-living to living matter, is at the core of the origin of life question. A central hypothesis in origin of life is that of the RNA world, which proposes that RNA predates DNA and protein. Indeed, RNA molecules are capable of carrying sequence information like DNA and perform cataylsis like proteins. However, how RNA systems may self-organize to lead to biological or protobiological systems (a process called abiogenesis) remain unknown. The AbioEvo project aims to test the hypothesis that RNA-catalyzed RNA recombination, if coupled with template-based mechanisms, provides a gradual route for the emergence of evolution by natural selection. It starts from from collective autocatalysis, meaning that collections of RNA molecules can self-reproduce from their fragments. The end of our road is template-based replication, which is the copying of a RNA sequence catalyzed by a RNA. On the way, we propose that recombination allows both self-reproduction and shuffling of other sequences, and can be combined with template-based ligation. To build an evolving system, we will assemble the basic ingredients of reproduction, heredity and variation.
Concretely, we aim to show that mixtures of small RNAs can self-organize into reaction networks capable of evolution, via autocatalysis and evolution. The project decomposes this problem into five steps: (WP1) the study of molecular-level mechanisms to generate and stabilize novel sequences by recombination and templating; (WP2) collective dynamics integrating these mechanisms into the properties of reproduction with heredity, variation, and selection, in order to establish proof-of-concepts of evolutionary modes; (WP3) viability thresholds of recombination-based replicators from increasingly random substrates; (WP4) conditions for open-ended evolution toward template-based replication; (WP5) estimates of thresholds and probabilities of the proposed evolutionary processes. The project would provide first demonstrations of evolution by natural selection in a purely chemical system, gradual and experimentally accessible paths from oligomers to template-based replication, and a method to evaluate prebiotic plausibility from sequence-to-function relationships, kinetics and evolutionary dynamics.
Abiogenesis, the transition from non-living to living matter, is at the core of the origin of life question. A central hypothesis in origin of life is that of the RNA world, which proposes that RNA predates DNA and protein. Indeed, RNA molecules are capable of carrying sequence information like DNA and perform cataylsis like proteins. However, how RNA systems may self-organize to lead to biological or protobiological systems (a process called abiogenesis) remain unknown. The AbioEvo project aims to test the hypothesis that RNA-catalyzed RNA recombination, if coupled with template-based mechanisms, provides a gradual route for the emergence of evolution by natural selection. It starts from from collective autocatalysis, meaning that collections of RNA molecules can self-reproduce from their fragments. The end of our road is template-based replication, which is the copying of a RNA sequence catalyzed by a RNA. On the way, we propose that recombination allows both self-reproduction and shuffling of other sequences, and can be combined with template-based ligation. To build an evolving system, we will assemble the basic ingredients of reproduction, heredity and variation.
Concretely, we aim to show that mixtures of small RNAs can self-organize into reaction networks capable of evolution, via autocatalysis and evolution. The project decomposes this problem into five steps: (WP1) the study of molecular-level mechanisms to generate and stabilize novel sequences by recombination and templating; (WP2) collective dynamics integrating these mechanisms into the properties of reproduction with heredity, variation, and selection, in order to establish proof-of-concepts of evolutionary modes; (WP3) viability thresholds of recombination-based replicators from increasingly random substrates; (WP4) conditions for open-ended evolution toward template-based replication; (WP5) estimates of thresholds and probabilities of the proposed evolutionary processes. The project would provide first demonstrations of evolution by natural selection in a purely chemical system, gradual and experimentally accessible paths from oligomers to template-based replication, and a method to evaluate prebiotic plausibility from sequence-to-function relationships, kinetics and evolutionary dynamics.
The 5 WPs of AbioEvo build up evolutionary properties in RNA reaction networks.
- In WP1, we have shown mechanisms of sequence diversification by recombination and stabilization. This was published by Jeancolas et al. in Chemical Communications (2021) in the case of designed RNA sequences. We now study the same dyanmics using random RNAs. We have also reproduced RNA ligation mechanism already published in the past and now search conditions for a multiple turnover reaction.
- In WP2, we developed a model for heredity in compartmentalized autocatalytic sets. This work is currently deposited as a preprint: Matsubara et al. 2022. We have set up transient compartmentalization using droplet microfluidics. In parallel, we introduced a new idea: using coacervate systems, where compartments self-assemble (instead of being forcefully made) and selection can emerge at the compartment level in response to environmental conditions.
- In WP3, we computed viability conditions for a large category of autocatalytic systems. This work has been published in the Journal of Mathematical Biology by Unterberger & Nghe (2022). We have produced large libraries of diversified RNA self-reproducers, which we submit to serial transfers in order to observe how they evolve. We have also produced a minimized self-reproducer of length 140 nucleotides (article in preparation). We pursue this task with generative models which combine machine learning and structure prediction algorithms.
- In WP4, we are currently developing a computational pipeline that generates complex chemical mixtures and allows us to assess the plausibility of self-reproduction and evolution. The general pipeline is currently under development. Once established, it can be in particular applied to RNA systems
- In WP5, we are developing a model combining RNA recombination and ligation.
- In WP1, we have shown mechanisms of sequence diversification by recombination and stabilization. This was published by Jeancolas et al. in Chemical Communications (2021) in the case of designed RNA sequences. We now study the same dyanmics using random RNAs. We have also reproduced RNA ligation mechanism already published in the past and now search conditions for a multiple turnover reaction.
- In WP2, we developed a model for heredity in compartmentalized autocatalytic sets. This work is currently deposited as a preprint: Matsubara et al. 2022. We have set up transient compartmentalization using droplet microfluidics. In parallel, we introduced a new idea: using coacervate systems, where compartments self-assemble (instead of being forcefully made) and selection can emerge at the compartment level in response to environmental conditions.
- In WP3, we computed viability conditions for a large category of autocatalytic systems. This work has been published in the Journal of Mathematical Biology by Unterberger & Nghe (2022). We have produced large libraries of diversified RNA self-reproducers, which we submit to serial transfers in order to observe how they evolve. We have also produced a minimized self-reproducer of length 140 nucleotides (article in preparation). We pursue this task with generative models which combine machine learning and structure prediction algorithms.
- In WP4, we are currently developing a computational pipeline that generates complex chemical mixtures and allows us to assess the plausibility of self-reproduction and evolution. The general pipeline is currently under development. Once established, it can be in particular applied to RNA systems
- In WP5, we are developing a model combining RNA recombination and ligation.
Our first achievement was to demonstrate that several molecular mechanisms necessary for evolution can be integrated in a same reaction network, purely made of RNA. Indeed, a mixture of fragments can lead to self-reproduction and diversification by recombination. Integrating these mechanisms reveals that different RNA topologies can be form, including non-folded RNAs, hairpins, and circular RNAs. Following up on this, we are currently strongly generalizing recombination as a variation principle, by using highly diversified sequences, and we are testing the degree of RNA fold diversity that can be generated. Reaching particular folds is indeed critical to generate novel catalytic RNAs by chance.
A second achievmenet is to show that many different self-reproducers can be generated in silico, which we tested experimentally. This change the plausibility of origin of life scenarios, as so far we only knew a few autocatalytic RNAs. We have further developed methods to estimate the probability of self-reproduction in the space of RNA sequences, a key question to quantitatively address the probability of the origin of life.
On-going, another important development is to show multiple turn-over template-based ligation with highly diversified sequences. It would represent an important step for origin of life mechanisms as the amplification of sequence information has only been shown in a single highly constrained systems so far.
Expected outcomes at the end of the project:
We will hopefully build an experimentally rooted scenario for the origin of evolution, which explores the possibilities offered by recombination as a primordial mechanism. Important and novel claims expected from the project are:
i. Evolution by natural selection is possible in a prebiotically relevant reaction system;
ii. Open-ended evolution is accessible when coupling recombination, templating and compartmentalization;
iii. Evolution can emerge gradually from autocatalysis in reaction networks;
iv. Relationships between molecular, kinetic and evolutionary parameters, and allow an estimate of the probability of prebiotic transitions.
Overall, the project will unveil dynamical principles and conditions for abiogenesis in the RNA world, with a methodology applicable beyond RNA.
A second achievmenet is to show that many different self-reproducers can be generated in silico, which we tested experimentally. This change the plausibility of origin of life scenarios, as so far we only knew a few autocatalytic RNAs. We have further developed methods to estimate the probability of self-reproduction in the space of RNA sequences, a key question to quantitatively address the probability of the origin of life.
On-going, another important development is to show multiple turn-over template-based ligation with highly diversified sequences. It would represent an important step for origin of life mechanisms as the amplification of sequence information has only been shown in a single highly constrained systems so far.
Expected outcomes at the end of the project:
We will hopefully build an experimentally rooted scenario for the origin of evolution, which explores the possibilities offered by recombination as a primordial mechanism. Important and novel claims expected from the project are:
i. Evolution by natural selection is possible in a prebiotically relevant reaction system;
ii. Open-ended evolution is accessible when coupling recombination, templating and compartmentalization;
iii. Evolution can emerge gradually from autocatalysis in reaction networks;
iv. Relationships between molecular, kinetic and evolutionary parameters, and allow an estimate of the probability of prebiotic transitions.
Overall, the project will unveil dynamical principles and conditions for abiogenesis in the RNA world, with a methodology applicable beyond RNA.