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Was There an RNA World?
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Was There an RNA World?

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 5984

Special Issue Editor

Dr. Ilana Agmon

E-Mail Website
Guest Editor
Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
Interests: origin of life; ribosome structure and function; crystallography

Special Issue Information

Dear Colleagues,

The origin of life is of prime importance in human thinking. In spite of the biological and philosophical quest aimed at answering this question, the current knowledge on the matter is still partial, giving rise to unlimited space for alternative hypotheses. The most widely accepted idea is the “RNA World”, an attractive hypothesis that posits that the emergence of life was based on RNA, which both stored genetic information and performed the catalytic activities. This hypothesis received considerable credibility from the in vitro selection of catalytic RNAs that could carry out a wide range of biological reactions. However, conceptual and experimental difficulties, concerned with various aspects of the RNA World hypothesis, have led to increased support in alternative hypotheses that favor the emergence of life from a mixture of biomolecule classes.

The Special Issue “Was There an RNA World?” aims to hear the present position of the active participants in the intriguing pursuit for a path that could have led, through natural processes, from the inanimate matter into the initial life form. Your opinion on this interesting question on human thinking would be most appreciated.

Dr. Ilana Agmon
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • origin of life
  • RNA world
  • genetic code
  • translation system
  • ribosome evolution
  • tRNA evolution
  • coevolution of RNA and proteins

Published Papers (3 papers)

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14 pages, 1839 KiB  
Hypothesis
Prebiotic Assembly of Cloverleaf tRNA, Its Aminoacylation and the Origin of Coding, Inferred from Acceptor Stem Coding-Triplets
by Ilana Agmon
Int. J. Mol. Sci. 2022, 23(24), 15756; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232415756 - 12 Dec 2022
Cited by 4 | Viewed by 1353
Abstract
tRNA is a key component in life’s most fundamental process, the translation of the instructions contained in mRNA into proteins. Its role had to be executed as soon as the earliest translation emerged, but the questions of the prebiotic tRNA materialization, aminoacylation, and [...] Read more.
tRNA is a key component in life’s most fundamental process, the translation of the instructions contained in mRNA into proteins. Its role had to be executed as soon as the earliest translation emerged, but the questions of the prebiotic tRNA materialization, aminoacylation, and the origin of the coding triplets it carries are still open. Here, these questions are addressed by utilizing a distinct pattern of coding triplets highly conserved in the acceptor stems from the modern bacterial tRNAs of five early-emerging amino acids. Self-assembly of several copies of a short RNA oligonucleotide that carries a related pattern of coding triplets, via a simple and statistically feasible process, is suggested to result in a proto-tRNA model highly compatible with the cloverleaf secondary structure of the modern tRNA. Furthermore, these stem coding triplets evoke the possibility that they were involved in self-aminoacylation of proto-tRNAs prior to the emergence of the earliest synthetases, a process proposed to underlie the formation of the genetic code. Being capable of autonomous materialization and of self-aminoacylation, this verifiable model of the proto-tRNA advent adds principal components to an initial set of molecules and processes that may have led, exclusively through natural means, to the emergence of life. Full article
(This article belongs to the Special Issue Was There an RNA World?)
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15 pages, 737 KiB  
Hypothesis
The Ring World: Eversion of Small Double-Stranded Polynucleotide Circlets at the Origin of DNA Double Helix, RNA Polymerization, Triplet Code, Twenty Amino Acids, and Strand Asymmetry
by Victor Norris and Jacques Demongeot
Int. J. Mol. Sci. 2022, 23(21), 12915; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232112915 - 26 Oct 2022
Cited by 2 | Viewed by 1366
Abstract
It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis [...] Read more.
It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis for a ‘view from here’ that we term the Circlet hypothesis as part of a broader Ring World. To maximize the potential explanatory value of this hypothesis, we speculate boldly about the origins of several of the fundamental characteristics and briefly describe the main methods or treatments applied. The principal prediction of the paper is that the highly constrained, conformational changes will occur preferentially in dsDNA, dsRNA and hybrid RNA-DNA circlets that are below a critical size (e.g., 306 bp) and that these will favor the polymerization of precursors into RNA and DNA. We conclude that the Circlet hypothesis and the Ring World therefore have the attraction of offering the same solution to the fundamental problems probably confronting both the earliest cells and the most recent ones. Full article
(This article belongs to the Special Issue Was There an RNA World?)
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14 pages, 1074 KiB  
Hypothesis
Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets
by Felix Broecker
Int. J. Mol. Sci. 2021, 22(24), 13526; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413526 - 16 Dec 2021
Cited by 3 | Viewed by 2558
Abstract
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and [...] Read more.
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains. Full article
(This article belongs to the Special Issue Was There an RNA World?)
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