Selection dynamics in transient compartmentalization

Blokhuis, Alex; Lacoste, David; Nghe, Philippe; Peliti, Luca

doi:10.1101/258269

Cited by 5 publications

(9 citation statements)

References 24 publications

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“…This follows closely the corresponding steps in Ref. [9]. However, the dynamics of the maturation step is different and is described by the following equations: where m ( t ) and y ( t ) are respectively the self-replicating and the parasitic species populations at time t , while α and γ are their respective replication rates.…”

Section: Methodssupporting

confidence: 62%

“…Replicases can make copies of themselves and of other parasite molecules, while the parasites can only be copied by the replicases. This is a different case from that discussed in [9], where both the molecules of interests (in that case, the ribozymes) and the parasites could be replicated by externally provided enzymes. In further contrast, in the present case there is no externally applied selection.…”

Section: Methodsmentioning

confidence: 95%

“…In the inoculation step, as in Ref. [9], one chooses a number n of molecules from the pool, where n is Poisson distributed with average λ . The resulting inoculum then contains m replicases and y = n − m parasites, which are distributed according to a Binomial distribution of parameter x , where x is the initial fraction of replicases in the pool.…”

Section: Methodsmentioning

confidence: 99%

“…Building on this work and on a recent experiment inspired by it [7], we have recently explored alternative scenarios that are also able to maintain information in replicating systems [8,9]. We have proposed a transient compartmentalization dynamics with no cell division, which should be achievable when only prebiotic chemistry is available.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper, we extend the framework of Ref. [9] to the case of transient compartmentalization of self-replicating molecules. The main new element in this extension is that the selective pressures acting on this system are not externally imposed, as in our previous work, but stem from the system intrinsic dynamics acting as a form of natural selection.…”

Section: Introductionmentioning

confidence: 99%

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Survival of self-replicating molecules under transient compartmentalization with natural selection

Laurent

Peliti²,

Lacoste

2019

Preprint

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The problem of the emergence and survival of self-replicating molecules in origin-of-life 1 scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of 2 compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple 3 system composed of a self-replicating molecule (a replicase) and a parasite molecule that needs the 4 replicase for copying itself, we show that transient (rather than permanent) compartmentalization 5 is sufficient to the task. We also exhibit a regime in which the concentrations of the two kinds of 6 molecules undergo sustained oscillations. Our model should be relevant not only for origin-of-life 7 scenarios but also for describing directed evolution experiments, which increasingly rely on transient 8 compartmentalization with pooling and natural selection.9

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Section: Methodssupporting

confidence: 62%

Section: Methodsmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Survival of self-replicating molecules under transient compartmentalization with natural selection

Laurent

Peliti²,

Lacoste

2019

Preprint

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Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation

Lai

Liu

Chen

2021

Proc. Natl. Acad. Sci. U.S.A.

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Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here, we examine the effect of encapsulation inside model protocells on the self-aminoacylation activity of tens of thousands of RNA sequences using a high-throughput sequencing assay. We find that encapsulation of these ribozymes generally increases their activity, giving encapsulated sequences an advantage over nonencapsulated sequences in an amphiphile-rich environment. In addition, highly active ribozymes benefit disproportionately more from encapsulation. The asymmetry in fitness gain broadens the distribution of fitness in the system. Consistent with Fisher’s fundamental theorem of natural selection, encapsulation therefore leads to faster adaptation when the RNAs are encapsulated inside a protocell during in vitro selection. Thus, protocells would not only provide a compartmentalization function but also promote activity and evolutionary adaptation during the origin of life.

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Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes

Babajanyan

Wolf²,

Khachatryan³

et al. 2022

Preprint

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There are two fundamentally distinct but inextricably linked types of biological evolutionary units, reproducers and replicators. Reproducers are cells and organelles that reproduce via various forms of division and maintain the physical continuity of compartments and their content. Replicators are genetic elements (GE), including genomes of cellular organisms and various autonomous elements, that both cooperate with reproducers and rely on the latter for replication. All known cells and organisms comprise a union between replicators and reproducers. We explore a model in which cells emerged via symbiosis between primordial metabolic reproducers (protocells) which evolved, on short time scales, via a primitive form of selection and random drift, and mutualist replicators. Mathematical modeling identifies the conditions, under which GE-carrying protocells can outcompete GE-less ones, taking into account that, from the earliest stages of evolution, replicators split into mutualists and parasites. Analysis of the model shows that, for the GE-containing protocells to win the competition and to be fixed in evolution, it is essential that the replication rate of the GE is coordinated with the rate of protocell division. At the early stages of evolution, random, high-variance cell division is advantageous compared to symmetrical division because the former provides for the emergence of protocells containing only mutualists, preventing takeover by parasites. These findings illuminate the likely order of key events on the evolutionary route from protocells to cells that involved the origin of genomes, symmetrical cell division and anti-parasite defense systems.

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Selection dynamics in transient compartmentalization

Cited by 5 publications

References 24 publications

Survival of self-replicating molecules under transient compartmentalization with natural selection

Survival of self-replicating molecules under transient compartmentalization with natural selection

Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation

Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes

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