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Life
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The RNA World and the Origin of Life
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The RNA World and the Origin of Life

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (30 September 2017) | Viewed by 32724

Special Issue Editor

Prof. Dr. Paul Higgs

E-Mail Website
Guest Editor
Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
Interests: origin of life; RNA structure and evolution; RNA world; mathematical and computational models; phylogenetic methods; molecular evolution; population genetics; biophysics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The RNA World has become a widely-accepted hypothesis for the Origin of Life, and has reached the level of a 'textbook theory'. Nevertheless, many issues related to the RNA World remain to be demonstrated fully in experiments, and important theoretical questions remain as to how RNA-based life could have originated, survived, and evolved. This Special Issue will focus on all questions related to the role of RNA, or similar nucleic-acid like polymers, in the origin of life and the early stages of evolution.

Under what prebiotic conditions could RNA be synthesized and remain stable? Is there a reason RNA was selected as a substrate for genetics and catalysis, rather than any alternative kind of polymer? What are the capabilities of synthetic ribozymes in the laboratory? How does the origin of replicating systems relate to the origin of protocells and metabolism? How complex did the RNA world become before the advent of the genetic code and translation? How can co-operative replicators (such as polymerase ribozymes) overcome the problems of parasitic templates and the limited accuracy of replication? How can simple replicating molecules evolve towards the complex genetic systems that we see in today's prokaryotic cells?

By addressing questions such as these, this Special Issue aims to understand to what extent the RNA World concept stands up as a comprehensive theory for the origin of life.

Prof. Paul Higgs
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA World
  • Ribozymes
  • Polymerases
  • Template-directed synthesis
  • Nucleic Acids
  • Replication
  • Evolution of cooperation
  • Modelling the Origin of Life

Published Papers (6 papers)

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Research

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1201 KiB  
Article
Kin Selection in the RNA World
by Samuel R. Levin and Stuart A. West
Life 2017, 7(4), 53; https://doi.org/10.3390/life7040053 - 05 Dec 2017
Cited by 2 | Viewed by 6330
Abstract
Various steps in the RNA world required cooperation. Why did life’s first inhabitants, from polymerases to synthetases, cooperate? We develop kin selection models of the RNA world to answer these questions. We develop a very simple model of RNA cooperation and then elaborate [...] Read more.
Various steps in the RNA world required cooperation. Why did life’s first inhabitants, from polymerases to synthetases, cooperate? We develop kin selection models of the RNA world to answer these questions. We develop a very simple model of RNA cooperation and then elaborate it to model three relevant issues in RNA biology: (1) whether cooperative RNAs receive the benefits of cooperation; (2) the scale of competition in RNA populations; and (3) explicit replicator diffusion and survival. We show: (1) that RNAs are likely to express partial cooperation; (2) that RNAs will need mechanisms for overcoming local competition; and (3) in a specific example of RNA cooperation, persistence after replication and offspring diffusion allow for cooperation to overcome competition. More generally, we show how kin selection can unify previously disparate answers to the question of RNA world cooperation. Full article
(This article belongs to the Special Issue The RNA World and the Origin of Life)
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6759 KiB  
Article
Evolutionary Conflict Leads to Innovation: Symmetry Breaking in a Spatial Model of RNA-Like Replicators
by Samuel H. A. Von der Dunk, Enrico Sandro Colizzi and Paulien Hogeweg
Life 2017, 7(4), 43; https://doi.org/10.3390/life7040043 - 02 Nov 2017
Cited by 3 | Viewed by 4294
Abstract
Molecules that replicate in trans are vulnerable to evolutionary extinction because they decrease the catalysis of replication to become more available as a template for replication. This problem can be alleviated with higher-level selection that clusters molecules of the same phenotype, favouring those [...] Read more.
Molecules that replicate in trans are vulnerable to evolutionary extinction because they decrease the catalysis of replication to become more available as a template for replication. This problem can be alleviated with higher-level selection that clusters molecules of the same phenotype, favouring those groups that contain more catalysis. Here, we study a simple replicator model with implicit higher-level selection through space. We ask whether the functionality of such system can be enhanced when molecules reproduce through complementary replication, representing RNA-like replicators. For high diffusion, symmetry breaking between complementary strands occurs: one strand becomes a specialised catalyst and the other a specialised template. In ensemble, such replicators can modulate their catalytic activity depending on their environment, thereby mitigating the conflict between levels of selection. In addition, these replicators are more evolvable, facilitating survival in extreme conditions (i.e., for higher diffusion rates). Our model highlights that evolution with implicit higher-level selection—i.e., as a result of local interactions and spatial patterning—is very flexible. For different diffusion rates, different solutions to the selective conflict arise. Our results support an RNA World by showing that complementary replicators may have various ways to evolve more complexity. Full article
(This article belongs to the Special Issue The RNA World and the Origin of Life)
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2417 KiB  
Article
The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture
by Andrew S. Tupper, Kevin Shi and Paul G. Higgs
Life 2017, 7(4), 41; https://doi.org/10.3390/life7040041 - 31 Oct 2017
Cited by 20 | Viewed by 4451
Abstract
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3′-5′ bonds rather than a mixture [...] Read more.
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3′-5′ bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture. We show that template-directed replication can lead to the emergence of all the uniform properties of RNA by the same mechanism. We study a computational model in which nucleotides react via polymerization, hydrolysis, and template-directed ligation. Uniform strands act as templates for ligation of shorter oligomers of the same type, whereas mixed strands do not act as templates. The three uniform properties emerge naturally when the ligation rate is high. If there is an exact symmetry, as with the chase of chirality, the uniform property arises via a symmetry-breaking phase transition. If there is no exact symmetry, as with monomer selection and backbone regioselectivity, the uniform property emerges gradually as the rate of template-directed ligation is increased. Full article
(This article belongs to the Special Issue The RNA World and the Origin of Life)
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2178 KiB  
Article
Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation
by Cole Mathis, Sanjay N. Ramprasad, Sara Imari Walker and Niles Lehman
Life 2017, 7(4), 38; https://doi.org/10.3390/life7040038 - 16 Oct 2017
Cited by 13 | Viewed by 5467
Abstract
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based [...] Read more.
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life. Full article
(This article belongs to the Special Issue The RNA World and the Origin of Life)
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Review

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4103 KiB  
Review
Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems
by András Szilágyi, István Zachar, István Scheuring, Ádám Kun, Balázs Könnyű and Tamás Czárán
Life 2017, 7(4), 48; https://doi.org/10.3390/life7040048 - 27 Nov 2017
Cited by 26 | Viewed by 5431
Abstract
As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up [...] Read more.
As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future. Full article
(This article belongs to the Special Issue The RNA World and the Origin of Life)
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Other

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228 KiB  
Concept Paper
What Does “the RNA World” Mean to “the Origin of Life”?
by Wentao Ma
Life 2017, 7(4), 49; https://doi.org/10.3390/life7040049 - 29 Nov 2017
Cited by 11 | Viewed by 5499
Abstract
Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a [...] Read more.
Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. In the light of those possible scenes included in this scenario, Darwinian evolution may have originated at the molecular level, realized upon a functional RNA. When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. But it was not until the appearance of the “unitary-protocell”, which had all of its RNA genes linked into a chromosome, that Darwinian evolution made its full step towards the cellular level—no longer severely constrained by the low-grade evolution at the molecular level. Self-sustainment did not make sense before protocells emerged. The selection pressure that was favoring the exploration of more and more fundamental raw materials resulted in an evolutionary tendency of life to become more and more self-sustained. New functions for the entities to adapt to environments, including those that are involved in the self-sustainment per se, would bring new burdens to the self-sustainment—the advantage of these functions must overweigh the corresponding disadvantage. Full article
(This article belongs to the Special Issue The RNA World and the Origin of Life)
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