Transient compartmentalization of RNA replicators prevents extinction due to parasites

Matsumura, Shigeyoshi; Kun, András István; Ryckelynck, Michaël; Coldren, Faith; Szilágyi, András; Jossinet, Fabrice; Rick, Christian; Nghe, Philippe; Szathmáry, Eörs; Griffiths, Andrew D.

doi:10.1126/science.aag1582

Cited by 126 publications

(159 citation statements)

References 40 publications

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“…RNA can be copied and compartments selected based on the activity of the ribozymes within the compartment (e.g. (Matsumura et al, 2016)). We envision the four setups as follows: case (a) and (b) are straightforward.…”

Section: The Coding Coenzyme Handle Hypothesismentioning

confidence: 99%

The evolution of the genetic code: Impasses and challenges

Kun

Radványi

2018

Biosystems

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The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. The stereochemical, the coding coenzyme handle, the coevolution, the four-column theory, the error minimization and the frozen accident hypotheses are discussed. The integration of these hypotheses can account for the origin of the genetic code. But experiments are badly needed. Thus we suggest a host of experiments that could (in)validate some of the models. We focus especially on the coding coenzyme handle hypothesis (CCH). The CCH suggests that amino acids attached to RNA handles enhanced catalytic activities of ribozymes. Alternatively, amino acids without handles or with a handle consisting of a single adenine, like in contemporary coenzymes could have been employed. All three scenarios can be tested in in vitro compartmentalized systems.

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Section: The Coding Coenzyme Handle Hypothesismentioning

confidence: 99%

The evolution of the genetic code: Impasses and challenges

Kun

Radványi

2018

Biosystems

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“…The resulting polymers are significantly shorter than that of the ribozyme and will therefore replicate much faster. Based on the experiments of [17], we estimated Λ to be in a range from 10 to about 470, as explained in the Supplemental Materials [18]. In contrast, if the replicase makes errors but keeps overall the length of the polymers unchanged, then the replication time is essentially unaffected.…”

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Selection dynamics in transient compartmentalization

Blokhuis

Lacoste

Nghe

et al. 2018

Preprint

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Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Motivated by this experiment, we show that a broad class of selection dynamics is able to achieve this goal. We identify two key parameters, the relative amplification of non-active replicators (parasites) and the size of compartments. Since the basic ingredients of our model are the competition between a host and its parasite, and the diversity generated by small size compartments, our results are relevant to various phage-bacteria or virus-host ecology problems.

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“…Compartmentalization of biological systems imposed a selective barrier for genetic parasites [19]. Because intracellular replication of genetic parasites consumes resources without providing any functional benefit to the host, cells that host genetic parasites experience a reduction in growth (that is, a fitness cost) compared to parasite-free cells [20,21].…”

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How genetic parasites persist despite the purge of natural selection

Iranzo

Koonin

2018

EPL

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-Genetic parasites, such as transposons, plasmids and viruses, are ubiquitous in cellular life forms. Although the selfish nature of these genetic elements is undeniable, the actual cost that they impose on their host and the mechanisms by which they counteract natural selection remain unclear. We combined mathematical models and comparative genomics to disentangle the roles of selection, horizontal gene transfer, gene duplication and gene loss in the spread and persistence of genetic parasites. By quantifying the mean contribution of transposons, conjugative plasmids, prophages and toxin-antitoxin modules to the fitness of microbial hosts, we provide evidence that these genetic elements are deleterious at evolutionary timescales. Moreover, the transfer rates experienced by selfish genetic elements exceed the minimum rates required for their long-term survival, which fully characterizes these elements as parasites.

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Transient compartmentalization of RNA replicators prevents extinction due to parasites

Cited by 126 publications

References 40 publications

The evolution of the genetic code: Impasses and challenges

The evolution of the genetic code: Impasses and challenges

Selection dynamics in transient compartmentalization

How genetic parasites persist despite the purge of natural selection

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