Special Issue "The Origins and Early Evolution of RNA"

Quicklinks

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

Deadline for manuscript submissions: closed (30 September 2014)

Special Issue Editor

Guest Editor
Prof. Dr. Niles Lehman (Website)

Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA
Phone: +1-503-725-8769
Interests: origins of life; RNA; ribozymes; recombination; prebiotic chemistry; systems chemistry, cooperation; in vitro evolution

Special Issue Information

Dear Colleagues,

The notion that molecular systems such as RNA can display a wide range of evolutionary processes in the absence of fully formed cellular life continues to gain support. Understanding how RNA can behave in an abiotic context is a key piece of our picture of how life developed and expanded on the Earth, and by proxy, elsewhere. We can study how RNA behaves in this regard through a combination of in vivo work (with small regulatory RNAs and larger catalytic RNAs alike), experimental work in the laboratory, and through powerful analytical and simulation studies. These efforts will not only grant us a better sense of the early stages of life on this planet but also of how RNA evolved to play a central role in contemporary metabolism. Many key ideas of primitive RNA functionality were developed in the 1970s and 1980s before we had either the experimental systems in place to fully explore these concepts or the appreciation of the extent to which RNAs were important to the cell. In this special issue, some of the recent discoveries and advances in RNA biology, biochemistry, and evolutionary biology are presented.

Prof. Dr. Niles Lehman
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 quarterly 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 600 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • RNA
  • primitive genotypes
  • genetic networks
  • fitness landscapes
  • genetic takeover
  • early evolutionary processes
  • evolvability
  • robustness
  • error threshold
  • quasispecies
  • small RNA-directed gene regulation

Published Papers (18 papers)

View options order results:
result details:
Displaying articles 1-18
Export citation of selected articles as:

Editorial

Jump to: Research, Review, Other

Open AccessEditorial The RNA World: 4,000,000,050 years old
Life 2015, 5(4), 1583-1586; doi:10.3390/life5041583
Received: 13 October 2015 / Accepted: 13 October 2015 / Published: 22 October 2015
Cited by 2 | PDF Full-text (152 KB) | HTML Full-text | XML Full-text
Abstract The RNA World is now some four billion years behind us, but only recently turned 50 as a human hypothesis. [...] Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

Research

Jump to: Editorial, Review, Other

Open AccessArticle From Formamide to RNA, the Path Is Tenuous but Continuous
Life 2015, 5(1), 372-384; doi:10.3390/life5010372
Received: 30 September 2014 / Revised: 20 January 2015 / Accepted: 22 January 2015 / Published: 30 January 2015
Cited by 7 | PDF Full-text (1086 KB) | HTML Full-text | XML Full-text
Abstract
Reactions of formamide (NH2COH) in the presence of catalysts of both terrestrial and meteoritic origin yield, in plausible and variegated conditions, a large panel of precursors of (pre)genetic and (pre)metabolic interest. Formamide chemistry potentially satisfies all of the steps from [...] Read more.
Reactions of formamide (NH2COH) in the presence of catalysts of both terrestrial and meteoritic origin yield, in plausible and variegated conditions, a large panel of precursors of (pre)genetic and (pre)metabolic interest. Formamide chemistry potentially satisfies all of the steps from the very initial precursors to RNA. Water chemistry enters the scene in RNA non-enzymatic synthesis and recombination. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessArticle Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth
Life 2015, 5(1), 65-84; doi:10.3390/life5010065
Received: 16 October 2014 / Accepted: 23 December 2014 / Published: 5 January 2015
Cited by 8 | PDF Full-text (1347 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in [...] Read more.
Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessArticle The Place of RNA in the Origin and Early Evolution of the Genetic Machinery
Life 2014, 4(4), 1050-1091; doi:10.3390/life4041050
Received: 24 October 2014 / Revised: 2 December 2014 / Accepted: 9 December 2014 / Published: 19 December 2014
Cited by 6 | PDF Full-text (1005 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo [...] Read more.
The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessArticle On the Contribution of Protein Spatial Organization to the Physicochemical Interconnection between Proteins and Their Cognate mRNAs
Life 2014, 4(4), 788-799; doi:10.3390/life4040788
Received: 30 September 2014 / Revised: 12 November 2014 / Accepted: 17 November 2014 / Published: 21 November 2014
Cited by 2 | PDF Full-text (996 KB) | HTML Full-text | XML Full-text
Abstract
Early-stage evolutionary development of the universal genetic code remains a fundamental, open problem. One of the possible scenarios suggests that the code evolved in response to direct interactions between peptides and RNA oligonucleotides in the primordial environment. Recently, we have revealed a [...] Read more.
Early-stage evolutionary development of the universal genetic code remains a fundamental, open problem. One of the possible scenarios suggests that the code evolved in response to direct interactions between peptides and RNA oligonucleotides in the primordial environment. Recently, we have revealed a strong matching between base-binding preferences of modern protein sequences and the composition of their cognate mRNA coding sequences. These results point directly at the physicochemical foundation behind the code’s origin, but also support the possibility of direct complementary interactions between proteins and their cognate mRNAs, especially if the two are unstructured. Here, we analyze molecular-surface mapping of knowledge-based amino-acid/nucleobase interaction preferences for a set of complete, high-resolution protein structures and show that the connection between the two biopolymers could remain relevant even for structured, folded proteins. Specifically, protein surface loops are strongly enriched in residues with a high binding propensity for guanine and cytosine, while adenine- and uracil-preferring residues are uniformly distributed throughout protein structures. Moreover, compositional complementarity of cognate protein and mRNA sequences remains strong even after weighting protein sequence profiles by residue solvent exposure. Our results support the possibility that protein/mRNA sequence complementarity may also translate to cognate interactions between structured biopolymers. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessArticle Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids
Life 2014, 4(3), 341-373; doi:10.3390/life4030341
Received: 29 April 2014 / Revised: 23 July 2014 / Accepted: 25 July 2014 / Published: 11 August 2014
Cited by 3 | PDF Full-text (1572 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization [...] Read more.
Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessArticle The Evolution of the Ribosome and the Genetic Code
Life 2014, 4(2), 227-249; doi:10.3390/life4020227
Received: 30 January 2014 / Revised: 23 April 2014 / Accepted: 25 April 2014 / Published: 20 May 2014
Cited by 6 | PDF Full-text (709 KB) | HTML Full-text | XML Full-text
Abstract
The evolution of the genetic code is mapped out starting with the aminoacyl tRNA-synthetases and their interaction with the operational code in the tRNA acceptor arm. Combining this operational code with a metric based on the biosynthesis of amino acids from the [...] Read more.
The evolution of the genetic code is mapped out starting with the aminoacyl tRNA-synthetases and their interaction with the operational code in the tRNA acceptor arm. Combining this operational code with a metric based on the biosynthesis of amino acids from the Citric acid, we come to the conclusion that the earliest genetic code was a Guanine Cytosine (GC) code. This has implications for the likely earliest positively charged amino acids. The progression from this pure GC code to the extant one is traced out in the evolution of the Large Ribosomal Subunit, LSU, and its proteins; in particular those associated with the Peptidyl Transfer Center (PTC) and the nascent peptide exit tunnel. This progression has implications for the earliest encoded peptides and their evolutionary progression into full complex proteins. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

Review

Jump to: Editorial, Research, Other

Open AccessReview Fitness Landscapes of Functional RNAs
Life 2015, 5(3), 1497-1517; doi:10.3390/life5031497
Received: 25 May 2015 / Revised: 26 July 2015 / Accepted: 3 August 2015 / Published: 21 August 2015
Cited by 2 | PDF Full-text (769 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole [...] Read more.
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Open AccessReview The Origin and Evolution of Ribonucleotide Reduction
Life 2015, 5(1), 604-636; doi:10.3390/life5010604
Received: 15 January 2015 / Revised: 4 February 2015 / Accepted: 6 February 2015 / Published: 27 February 2015
Cited by 5 | PDF Full-text (3684 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by [...] Read more.
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessReview Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals
Life 2015, 5(1), 637-650; doi:10.3390/life5010637
Received: 29 September 2014 / Revised: 9 February 2015 / Accepted: 12 February 2015 / Published: 27 February 2015
Cited by 4 | PDF Full-text (837 KB) | HTML Full-text | XML Full-text
Abstract
Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a [...] Read more.
Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the “RNA world”. The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Open AccessReview Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution
Life 2015, 5(1), 321-331; doi:10.3390/life5010321
Received: 12 November 2014 / Revised: 14 January 2015 / Accepted: 21 January 2015 / Published: 26 January 2015
Cited by 4 | PDF Full-text (1095 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70–100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein [...] Read more.
Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70–100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein world. Thus, study of the evolution of tRNA molecules may reveal the processes that led to the establishment of the central dogma: genetic information flows from DNA to RNA to protein. Thanks to the development of DNA sequencers in this century, we have determined a huge number of nucleotide sequences from complete genomes as well as from transcriptomes in many species. Recent analyses of these large data sets have shown that particular tRNA genes, especially in Archaea, are disrupted in unique ways: some tRNA genes contain multiple introns and some are split genes. Even tRNA molecules themselves are fragmented post-transcriptionally in many species. These fragmented small RNAs are known as tRNA-derived fragments (tRFs). In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessReview What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention
Life 2015, 5(1), 294-320; doi:10.3390/life5010294
Received: 24 November 2014 / Accepted: 12 January 2015 / Published: 23 January 2015
Cited by 8 | PDF Full-text (2914 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins [...] Read more.
We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Open AccessReview RNA Synthesis by in Vitro Selected Ribozymes for Recreating an RNA World
Life 2015, 5(1), 247-268; doi:10.3390/life5010247
Received: 2 October 2014 / Revised: 22 December 2014 / Accepted: 13 January 2015 / Published: 20 January 2015
Cited by 4 | PDF Full-text (1124 KB) | HTML Full-text | XML Full-text
Abstract
The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic [...] Read more.
The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme’s possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Open AccessReview How Amino Acids and Peptides Shaped the RNA World
Life 2015, 5(1), 230-246; doi:10.3390/life5010230
Received: 30 November 2014 / Revised: 16 December 2014 / Accepted: 14 January 2015 / Published: 19 January 2015
Cited by 7 | PDF Full-text (738 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA [...] Read more.
The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a “pure RNA ribosome” evolution started out with. Though the oldest center of the ribosome seems “RNA only”, we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the “RNA world” view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Open AccessReview The Stereochemical Basis of the Genetic Code and the (Mostly) Autotrophic Origin of Life
Life 2014, 4(4), 1013-1025; doi:10.3390/life4041013
Received: 23 October 2014 / Revised: 27 November 2014 / Accepted: 11 December 2014 / Published: 16 December 2014
Cited by 3 | PDF Full-text (1051 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Spark-tube experiments and analysis of meteorite contents have led to the widespread notion that abiotic organic molecules were the first life components. However, there is a contradiction between the abundance of simple molecules, such as the amino acids glycine and alanine, observed [...] Read more.
Spark-tube experiments and analysis of meteorite contents have led to the widespread notion that abiotic organic molecules were the first life components. However, there is a contradiction between the abundance of simple molecules, such as the amino acids glycine and alanine, observed in these studies, and the minimal functional complexity that even the least sophisticated living system should require. I will argue that although simple abiotic molecules must have primed proto-metabolic pathways, only Darwinian evolving systems could have generated life. This condition may have been initially fulfilled by both replicating RNAs and autocatalytic reaction chains, such as the reductive citric acid cycle. The interactions between nucleotides and biotic amino acids, which conferred new functionalities to the former, also resulted in the progressive stereochemical recognition of the latter by cognate anticodons. At this point only large enough amino acids would be recognized by the primordial RNA adaptors and could polymerize forming the first peptides. The gene duplication of RNA adaptors was a crucial event. By removing one of the anticodons from the acceptor stem the new RNA adaptor liberated itself from the stereochemical constraint and could be acylated by smaller amino acids. The emergence of messenger RNA and codon capture followed. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Open AccessReview Looked at Life from Both Sides Now
Life 2014, 4(4), 887-902; doi:10.3390/life4040887
Received: 12 October 2014 / Revised: 1 December 2014 / Accepted: 2 December 2014 / Published: 11 December 2014
Cited by 2 | PDF Full-text (1122 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many [...] Read more.
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Open AccessReview RNA Sociology: Group Behavioral Motifs of RNA Consortia
Life 2014, 4(4), 800-818; doi:10.3390/life4040800
Received: 7 October 2014 / Revised: 11 November 2014 / Accepted: 12 November 2014 / Published: 24 November 2014
Cited by 1 | PDF Full-text (551 KB) | HTML Full-text | XML Full-text
Abstract
RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in [...] Read more.
RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in regulatory processes in cellular and non-cellular life. RNA stem loop self-folding and group building do not depend solely on sequence syntax; more important are their contextual (functional) needs. Also, evolutionary processes seem to occur through RNA stem loop consortia that may act as a complement. This means the whole entity functions only if all participating parts are coordinated, although the complementary building parts originally evolved for different functions. If complementary groups, such as rRNAs and tRNAs, are placed together in selective pressure contexts, new evolutionary features may emerge. Evolution initiated by competent agents in natural genome editing clearly contrasts with statistical error replication narratives. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

Other

Jump to: Editorial, Research, Review

Open AccessHypothesis RNA Catalysis, Thermodynamics and the Origin of Life
Life 2014, 4(2), 131-141; doi:10.3390/life4020131
Received: 27 February 2014 / Revised: 28 March 2014 / Accepted: 31 March 2014 / Published: 10 April 2014
Cited by 5 | PDF Full-text (804 KB) | HTML Full-text | XML Full-text
Abstract
The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5ʹ-polyphosphates (or their analogues) as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient [...] Read more.
The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5ʹ-polyphosphates (or their analogues) as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient abundance to supply a growing and evolving population of RNAs is problematic for evolutionary hypotheses because non-enzymatic synthesis and assembly of nucleotide 5ʹ-triphosphates (or other analogously activated phosphodiester species) is inherently difficult. However, nucleotide 2ʹ,3ʹ-cyclic phosphates are also phosphodiesters, and are the natural and abundant products of RNA degradation. These have previously been dismissed as viable substrates for prebiotic RNA synthesis. We propose that the arguments for their dismissal are based on a flawed assumption, and that nucleotide 2ʹ,3ʹ-cyclic phosphates in fact possess several significant, advantageous properties that indeed make them particularly viable substrates for prebiotic RNA synthesis. An RNA World hypothesis based upon the polymerization of nucleotide 2ʹ,3ʹ-cyclic phosphates possesses additional explanatory power in that it accounts for the observed ribozyme “fossil record”, suggests a viable mechanism for substrate transport across lipid vesicle boundaries of primordial proto-cells, circumvents the problems of substrate scarcity and implausible synthetic pathways, provides for a primitive but effective RNA replicase editing mechanism, and definitively explains why RNA, rather than DNA, must have been the original catalyst. Finally, our analysis compels us to propose that a fundamental and universal property that drives the evolution of living systems, as well as pre-biotic replicating molecules (be they composed of RNA or protein), is that they exploit chemical reactions that already possess competing kinetically-preferred and thermodynamically-preferred pathways in a manner that optimizes the balance between the two types of pathways. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
Figures

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Acytota: Neglected Kingdom of Life
Authors:
Edward N. Trifonov 1 and Eduard Kejnovsky 2
Affiliation:
1 Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
2
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, 61265 Brno, Czech Republic
Abstract:
There is a huge variety of RNA- and DNA-containing entities which multiply within and propagate between cells of all kingdoms of life, having no cells of their own. Apart of cellular organisms these entities (viroids, plasmids, mobile elements, viruses and others) are the only ones which have their distinct genetic identities, but not included in any kingdom of life, since all the traditional kingdoms are cellular. We suggest to introduce the distinct category of the acellular organisms, Acytota, as an additional, undeservedly ignored kingdom of life. Acytota are indispensable for cellular life and its evolution. Six traditional kingdoms (Cytota) together with Acytota complete the classification of biological world (Biota), leaving nothing life-like beyond.

Title: The Origin and Evolution of Ribonucleotide Reduction—A Repeated History of Reciprocal Dependencies
Authors:
Daniel Lundin 1, Gustav Berggren 1, David Nord 1, Derek Logan 2 and Britt-Marie Sjöberg 1
Affiliations:
1 Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden
2
Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden
Abstract
: Ribonucleotide reduction is the only pathway for de novo synthesisof deoxyribonucleotides in extant organisms. Ribonucleotide reductase (RNR) catalyses the reaction, which is chemically demanding and involves a carbon-based radical. The mechanism has been deemed unlikely to be catalysed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesised at the transition from RNA to DNA encoded genomes. While it is entirely possible that a different pathway was used, later to be replaced with the extant mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA+protein world and suggest a model for a proto typical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to extant RNRs, the urRNR, which diversified to the extant three classes characterised mainly by how the radical is initially generated. Subsequent to the origin of the three classes, RNRs have undergone further specialisations, and we describe a phylogenetic subclassification of the enzyme family. RNR genes are frequent hosts of selfish genetic elements—introns and inteins—and we observe an interesting organism distribution of classes and subclasses indicating both short and long-range horizontal transfer of RNR genes.

Journal Contact

MDPI AG
Life Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
life@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Life
Back to Top