Nucleic acids: function and potential for abiogenesis

2017 ◽  
Vol 50 ◽  
Author(s):  
Falk Wachowius ◽  
James Attwater ◽  
Philipp Holliger
Keyword(s):  
Nucleic Acids ◽  
Prebiotic Chemistry ◽  
Molecular Level ◽  
Rna World ◽  
Information Storage ◽  
Molecular Systems ◽  
Rna Molecules ◽  
Functional Potential ◽  
Self Replication ◽  
Uniform Composition

AbstractThe emergence of functional cooperation between the three main classes of biomolecules – nucleic acids, peptides and lipids – defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an ‘RNA world’, notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pKa values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.

scholarly journals Two Dogmas for the Emergence of Biological Systems: Cell Theory and Self-Replication

2018 ◽  
Author(s):  
Francisco Prosdocimi ◽  
Sohan Jheeta ◽  
Sávio Torres de Farias
Keyword(s):  
Nucleic Acids ◽  
Biological System ◽  
Rna World ◽  
World View ◽  
Hard Core ◽  
Cell Theory ◽  
Research Programmes ◽  
Core Concepts ◽  
Life Itself ◽  
Self Replication

A dogma is normally considered as a principle or a belief accepted as an indisputable truth by some individuals and/or groups. Theoretically there can be no dogmas in science, but it has been demonstrated that scientific thought operates by conceptual changes. A dogma therefore can be understood as a concept present at the heart of some contemporary research programmes that need to be altered to overcome paradigms. Here we argue that two ideas relating to emergence of the biological system research need to be re-evaluated. First, is the idea that research programmes about the emergence of the biological system are the same as those of the origin of cells. Cells are strikingly important biological entities, hard core concepts for the entire field of biology. The emergence of the biological system happened much earlier than the origin of cells and thus the First Universal Common Ancestor (FUCA) should be viewed as a great-grandfather to the Last Universal Cellular Ancestor (LUCA); i.e. the latter is the first cellular life form. Second, RNA-world theories are the focus of mainstream research programmes for the origin of life stricto sensu. In the RNA-world view, self-replication of nucleic acids is seen as one of the most relevant events in the pre-biotic world. Without denying the relevance of self-replication, we argue here that the most germane event which occurred in the pre-biotic world was the crosstalk between nucleic acids and peptides. When these two macromolecules started to interact, the singularity that aggregated the complexity required to produce life emerged. Thus, comprehension of the early origins of the translation machinery and the assembly of the genetic code is key. Therefore, the relevance of cell theory and self-replication should be re-evaluated as well as the concept of life itself.

scholarly journals Amplification of RNA by an RNA polymerase ribozyme

2016 ◽  
Vol 113 (35) ◽  
pp. 9786-9791 ◽  
Author(s):  
David P. Horning ◽  
Gerald F. Joyce
Keyword(s):  
Nucleic Acids ◽  
Rna Polymerase ◽  
Genetic Information ◽  
Rna World ◽  
In Vitro Evolution ◽  
Rna Molecules ◽  
Encoded Proteins ◽  
Rna Genes ◽  
Functional Rna

In all extant life, genetic information is stored in nucleic acids that are replicated by polymerase proteins. In the hypothesized RNA world, before the evolution of genetically encoded proteins, ancestral organisms contained RNA genes that were replicated by an RNA polymerase ribozyme. In an effort toward reconstructing RNA-based life in the laboratory, in vitro evolution was used to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template. The improved polymerase ribozyme is able to synthesize a variety of complex structured RNAs, including aptamers, ribozymes, and, in low yield, even tRNA. Furthermore, the polymerase can replicate nucleic acids, amplifying short RNA templates by more than 10,000-fold in an RNA-catalyzed form of the PCR. Thus, the two prerequisites of Darwinian life—the replication of genetic information and its conversion into functional molecules—can now be accomplished with RNA in the complete absence of proteins.

scholarly journals Modified nucleotides may have enhanced early RNA catalysis

2020 ◽  
Vol 117 (15) ◽  
pp. 8236-8242 ◽  
Author(s):  
Steven K. Wolk ◽  
Wesley S. Mayfield ◽  
Amy D. Gelinas ◽  
David Astling ◽  
Jessica Guillot ◽  
...  
Keyword(s):  
Rna World ◽  
Rna Catalysis ◽  
Evolutionary Path ◽  
Rna Molecules ◽  
Catalytic Function ◽  
Short Rnas ◽  
World Hypothesis ◽  
First Moment ◽  
Self Replication ◽  
Rna World Hypothesis

The modern version of the RNA World Hypothesis begins with activated ribonucleotides condensing (nonenzymatically) to make RNA molecules, some of which possess (perhaps slight) catalytic activity. We propose that noncanonical ribonucleotides, which would have been inevitable under prebiotic conditions, might decrease the RNA length required to have useful catalytic function by allowing short RNAs to possess a more versatile collection of folded motifs. We argue that modified versions of the standard bases, some with features that resemble cofactors, could have facilitated that first moment in which early RNA molecules with catalytic capability began their evolutionary path toward self-replication.

scholarly journals The Old and New RNA World

2014 ◽  
Vol 83 (4) ◽  
pp. 441-448
Author(s):  
Zofia Szweykowska-Kulińska
Keyword(s):  
Gene Expression ◽  
Genetic Information ◽  
Environmental Changes ◽  
Rna World ◽  
Chromatin Condensation ◽  
Feedback Regulation ◽  
Information Storage ◽  
Rna Molecules ◽  
Metabolic Reactions ◽  
Almost All

Among the numerous hypotheses offering a scenario for the origin of life on Earth, the one called “The RNA World” has gained the most attention. According to this hypothesis RNA acted as a genetic information storage material, as a catalyst of all metabolic reactions, and as a regulator of all processes in the primordial world. Various experiments show that RNA molecules could have been synthesized abiotically, with the potential to mediate a whole repertoire of metabolic reactions. Ribozymes carrying out aminoacyl-tRNA reactions have been found in SELEX (systematic evolution of ligands by exponential enrichment) approaches and the development of a ribosome from a RNA-built protoribosome is easy to imagine. Transfer RNA aminoacylation, protoribosome origin, and the availability of amino acids on early Earth allowed the genetic code to evolve. Encoded proteins most likely stabilized RNA molecules and were able to create channels across membranes. In the modern cell, DNA replaced RNA as the main depositor of genetic information and proteins carry out almost all metabolic reactions. However, RNA is still playing versatile, crucial roles in the cell. Apart from its classical functions in the cell, a huge small RNA world is controlling gene expression, chromatin condensation, response to environmental cues, and protecting the cell against the invasion of various nucleic acids forms. Long non-coding RNAs act as crucial gene expression regulators. Riboswitches act at the level of transcription, splicing or translation and mediate feedback regulation on biosynthesis and transport of the ligand they sense. Alternative splicing generates genetic variability and increases the protein repertoire in response to developmental or environmental changes. All these regulatory functions are essential in shaping cell plasticity in the changing milieu. Recent discoveries of new, unexpected and important functions of RNA molecules support the hypothesis that we live in a New RNA World.

Significance of strand configuration in self-replicating RNA molecules

1995 ◽  
Vol 350 (1334) ◽  
pp. 345-352 ◽  
Keyword(s):  
Secondary Structure ◽  
Kinetic Theory ◽  
Rna Synthesis ◽  
Rna World ◽  
Base Sequence ◽  
Rna Molecules ◽  
Internal Sequence ◽  
Self Replication ◽  
Annealing Reaction

The kinetic theory of replication has been extended to include dual mechanisms for conversion of self-annealed single-strand RNA to double-strand molecules, which do not replicate. An analysis of experimental results established that the replicate-template annealing reaction during transcription significantly retarded replication in vitro among three RNA variants copied by Qβ replicase. Annealing between complementary RNA strands free in solution had far less significance. The finding that an RNA variant can be replicated in a multiple hairpin configuration, but not as its single, long hairpin conformer, the correlation between stability of strand secondary structure and replicative fitness, and a lack of homology in the internal sequence of RNA variants copied by Qβ replicase support the conclusion that template competence depends on strand configuration, independent of most of the underlying base sequence. Occurrence of self-annealed strands in the Qβ replicase system was attributed to its reliance on RNA-driven strand separation, in the absence of enzyme catalysed strand unwinding. A ‘configuration before sequence’ path to self-replication exhibited a substantially lower combinatorial barrier than standard sequence-dependent evolution. RNA-dependent RNA synthesis in the Qβ system thus displays features of an RNA World and, interestingly, they reveal a rapid path for evolution of the first self-replicating molecule on Earth.

scholarly journals The RNA world and the origin of metabolic enzymes

2014 ◽  
Vol 42 (4) ◽  
pp. 985-988 ◽  
Author(s):  
Markus Ralser
Keyword(s):  
Metal Ions ◽  
Metabolic Network ◽  
Environmental Chemistry ◽  
Rna World ◽  
Chemical Constituents ◽  
Pentose Phosphate ◽  
Rna Molecules ◽  
The Origin Of Life ◽  
Inorganic Molecules ◽  
Self Replication

An RNA world has been placed centre stage for explaining the origin of life. Indeed, RNA is the most plausible molecule able to form both a (self)-replicator and to inherit information, necessities for initiating genetics. However, in parallel with self-replication, the proto-organism had to obtain the ability to catalyse supply of its chemical constituents, including the ribonucleotide metabolites required to replicate RNA. Although the possibility of an RNA-catalysed metabolic network has been considered, it is to be questioned whether RNA molecules, at least on their own, possess the required catalytic capacities. An alternative scenario for the origin of metabolism involves chemical reactions that are based on environmental catalysts. Recently, we described a non-enzymatic glycolysis and pentose phosphate pathway-like reactions catalysed by metal ions [mainly Fe(II)] and phosphate, simple inorganic molecules abundantly found in Archaean sediments. While the RNA world can serve to explain the origin of genetics, the origin of the metabolic network might thus date back to constraints of environmental chemistry. Interestingly, considering a metal-catalysed origin of metabolism gives rise to an attractive hypothesis about how the first enzymes could have formed: simple RNA or (poly)peptide molecules could have bound the metal ions, and thus increased their solubility, concentration and accessibility. In a second step, this would have allowed substrate specificity to evolve.

scholarly journals The origin of life: the first self-replicating molecules were nucleotides

2019 ◽  
Author(s):  
Ken Ohsaka
Keyword(s):  
Origin Of Life ◽  
Clay Minerals ◽  
The Self ◽  
Rna Molecules ◽  
Simulated Environments ◽  
The Origin Of Life ◽  
Prebiotic Earth ◽  
Self Replication

Difficulties to synthesize RNA nucleotides from their subunits in modern labs under simulated environments leads us to propose a possible process for the synthesis by cross complimentary self-replication with help of clay minerals, which might be operated on prebiotic Earth. Clay minerals are known to be good catalysts and certainly existed on prebiotic Earth. The self-replication of RNA nucleotides (monomers) may be considered as the origin of potential self-replication of some extant RNA polymers, and also the reason for homochirality of RNA molecules.

scholarly journals De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 346
Author(s):  
Kevin G Devine ◽  
Sohan Jheeta
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
De Novo ◽  
Chemical Properties ◽  
Amino Acid Sequences ◽  
Information Storage ◽  
Heterocyclic Base ◽  
Dna And Rna ◽  
Phosphate Backbone ◽  
Physical And Chemical

Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?

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