scholarly journals Life Emerged from [GADV]-Protein World, but Not from RNA World!?

2017 ◽  
Author(s):  
Kenji Ikehara
Keyword(s):  
Amino Acid ◽  
Rna World ◽  
Amino Acid Sequences ◽  
Molecular Systems ◽  
Dna Base ◽  
Protein World ◽  
World Hypothesis ◽  
Life On Earth ◽  
Gadv Hypothesis ◽  
Rna World Hypothesis

All life on Earth uses three integrated molecular systems in which genetic information contained in DNA base sequences is transmitted to ribosomes by RNA and a genetic code, then translated into the amino acid sequences of structural and catalytic proteins. Therefore, the most important point for understanding the origin of life is to determine how such systems could emerge from random processes on the early Earth. In this review, two alternatives are compared: the RNA world hypothesis and the [GADV]-protein world hypothesis. [GADV] refers to four amino acids, Gly [G], Ala [A], Asp [D] and Val [V] that are conserved in the amino acid sequences of many common proteins. Here I will argue that the origins of the three primary processes required for life to begin can be better explained by the GADV hypothesis than the RNA world hypothesis. The GADV hypothesis also incorporates a conversion process by which random polymers can evolve into proteins with ordered sequences.

scholarly journals Life Emerged as the “Protein/Metabolism-First” Theory Expects

2018 ◽  
Author(s):  
Kenji Ikehara
Keyword(s):  
Protein Metabolism ◽  
Rna World ◽  
Order Structure ◽  
Protein World ◽  
Weak Points ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Emergence Of Life ◽  
Gadv Hypothesis ◽  
Rna World Hypothesis

The origin of life has not been solved as yet, in spit of the time passage more than thirty years from publication of RNA world hypothesis by W. Gilbert (1986), which is based on the “gene/replicator--first” theory. On the contrary, I have proposed [GADV]-protein world hypothesis (GADV hypothesis), assuming that life emerged from [GADV]-protein world, which is grounded on the “protein/metabolism-first” theory. However, two weak points of protein world hypothesis, (i) protein cannot be produced without gene, and (ii) protein cannot be self-replicated, have been frequently pointed out by supporters of RNA world hypothesis. Then, I examined whether the two weak points could be overcome by GADV hypothesis or not. From the results, it was confirmed that (i) [GADV]-protein could be pseudo-replicated in the absence of gene owing to protein 0th-order structure or [GADV]-amino acids, and (ii) the replication ability is not always required from the beginning but it is sufficient to acquire it at some time point until the emergence of life. Thus, it was concluded that life emerged as [GADV]-protein world hypothesis, which is grounded on the “protein/metabolism-first” theory, expects.

scholarly journals Transcription and translation in an RNA world

2006 ◽  
Vol 361 (1474) ◽  
pp. 1751-1760 ◽  
Author(s):  
William R Taylor
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Rna World ◽  
Large Subunit ◽  
Trna Synthetase ◽  
Nucleoside Triphosphate ◽  
Amino Acid Binding ◽  
World Hypothesis ◽  
Protein Elongation ◽  
Rna World Hypothesis

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90°C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have ‘poisoned’ the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors.

Template-directed nonenzymatic oligonucleotide synthesis: lessons from synthetic chemistry

2015 ◽  
Vol 87 (2) ◽  
pp. 205-218 ◽  
Author(s):  
Albert C. Fahrenbach
Keyword(s):  
Nucleic Acids ◽  
Organic Molecules ◽  
Rna World ◽  
Significant Development ◽  
Directed Synthesis ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Life On Earth ◽  
And Storage ◽  
Rna World Hypothesis

AbstractThe nonenzymatic synthesis of nucleic acids, in particular, RNA, and the template-directed synthesis of artificial organic molecules, such as macrocycles, catenanes and rotaxanes, have both undergone significant development since the last half of the 20th century. The intersection of these two fields affords insights into how template effects can lead to information copying and storage at the molecular level. Mechanistic examples of model template-directed RNA replication experiments as well as those for totally artificial organic template-directed syntheses will be discussed. The fact that templates typically bind to their reacted products more tightly than their unreacted substrates may be a mechanistic feature necessary to store information in the form of nucleic acids. Understanding the mechanisms of nonenzymatic RNA synthesis is not only essential for testing the RNA world hypothesis in the context of the origin of life on Earth and other planetary bodies, but may one day afford chemists the insights to construct their own artificial molecular replicators.

scholarly journals The difficult case of an RNA-only origin of life

2019 ◽  
Vol 3 (5) ◽  
pp. 469-475 ◽  
Author(s):  
Kristian Le Vay ◽  
Hannes Mutschler
Keyword(s):  
Origin Of Life ◽  
Rna World ◽  
Large Body ◽  
Difficult Case ◽  
Experimental Approaches ◽  
World Hypothesis ◽  
Life On Earth ◽  
Self Replication ◽  
Emergence Of Life ◽  
Rna World Hypothesis

The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of-equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems.

Randomness and Complexity

2018 ◽  
Author(s):  
Steven E. Vigdor
Keyword(s):  
Quantum Mechanics ◽  
Natural Selection ◽  
Rna World ◽  
Biological Evolution ◽  
Variable Theory ◽  
Cosmological Natural Selection ◽  
Einstein Podolsky Rosen ◽  
World Hypothesis ◽  
Rna World Hypothesis

Chapter 7 describes the fundamental role of randomness in quantum mechanics, in generating the first biomolecules, and in biological evolution. Experiments testing the Einstein–Podolsky–Rosen paradox have demonstrated, via Bell’s inequalities, that no local hidden variable theory can provide a viable alternative to quantum mechanics, with its fundamental randomness built in. Randomness presumably plays an equally important role in the chemical assembly of a wide array of polymer molecules to be sampled for their ability to store genetic information and self-replicate, fueling the sort of abiogenesis assumed in the RNA world hypothesis of life’s beginnings. Evidence for random mutations in biological evolution, microevolution of both bacteria and antibodies and macroevolution of the species, is briefly reviewed. The importance of natural selection in guiding the adaptation of species to changing environments is emphasized. A speculative role of cosmological natural selection for black-hole fecundity in the evolution of universes is discussed.

scholarly journals A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids

Symmetry ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 2046
Author(s):  
Dimas A. M. Zaia ◽  
Cássia Thaïs B. V. Zaia
Keyword(s):  
Amino Acids ◽  
Rna World ◽  
High Concentration ◽  
Protein World ◽  
Protein Amino Acids ◽  
Hydrothermal Environment ◽  
World Hypothesis ◽  
Prebiotic Earth ◽  
Hydrothermal Environments ◽  
Selection Of

The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions. Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.

scholarly journals RNA Back and Forth: Looking through Ribozyme and Viroid Motifs

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 283 ◽  
Author(s):  
Marie-Christine Maurel ◽  
Fabrice Leclerc ◽  
Jacques Vergne ◽  
Giuseppe Zaccai
Keyword(s):  
Rna World ◽  
Hammerhead Ribozyme ◽  
Intramolecular Interactions ◽  
Modern World ◽  
Widespread Occurrence ◽  
Living Fossils ◽  
Evolution Of Life ◽  
Catalytically Active ◽  
World Hypothesis ◽  
Rna World Hypothesis

Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the “RNA world” hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the widespread occurrence of HHRs in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitous features of life. Those are the structural and functional versatility of small RNAs, ribozymes, and viroids, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.

The “Strong” RNA World Hypothesis: Fifty Years Old

Astrobiology ◽  
2013 ◽  
Vol 13 (4) ◽  
pp. 391-403 ◽  
Author(s):  
Marc Neveu ◽  
Hyo-Joong Kim ◽  
Steven A. Benner
Keyword(s):  
Rna World ◽  
World Hypothesis ◽  
Rna World Hypothesis

scholarly journals Solvent viscosity facilitates replication and ribozyme catalysis from an RNA duplex in a model prebiotic process

2019 ◽  
Vol 47 (13) ◽  
pp. 6569-6577 ◽  
Author(s):  
Christine He ◽  
Adriana Lozoya-Colinas ◽  
Isaac Gállego ◽  
Martha A Grover ◽  
Nicholas V Hud
Keyword(s):  
Information Transfer ◽  
Rna World ◽  
Hammerhead Ribozyme ◽  
Information Storage ◽  
Additional Challenge ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Synthesis Reactions ◽  
Rna World Hypothesis ◽  
Single Sequence

Abstract The RNA World hypothesis posits that RNA was once responsible for genetic information storage and catalysis. However, a prebiotic mechanism has yet to be reported for the replication of duplex RNA that could have operated before the emergence of polymerase ribozymes. Previously, we showed that a viscous solvent enables information transfer from one strand of long RNA duplex templates, overcoming ‘the strand inhibition problem'. Here, we demonstrate that the same approach allows simultaneous information transfer from both strands of long duplex templates. An additional challenge for the RNA World is that structured RNAs (like those with catalytic activity) function poorly as templates in model prebiotic RNA synthesis reactions, raising the question of how a single sequence could serve as both a catalyst and as a replication template. Here, we show that a viscous solvent also facilitates the transition of a newly synthesized hammerhead ribozyme sequence from its inactive, duplex state to its active, folded state. These results demonstrate how fluctuating environmental conditions can allow a ribozyme sequence to alternate between acting as a template for replication and functioning as a catalyst, and illustrate the potential for temporally changing environments to enable molecular processes necessary for the origin of life.

scholarly journals Expanding the informational chemistries of life: peptide/RNA networks

2017 ◽  
Vol 375 (2109) ◽  
pp. 20160356 ◽  
Author(s):  
Olga Taran ◽  
Chenrui Chen ◽  
Tolulope O. Omosun ◽  
Ming-Chien Hsieh ◽  
Allisandra Rha ◽  
...  
Keyword(s):  
Rna World ◽  
Chemical Information ◽  
Disease States ◽  
Complementary Approach ◽  
The Subject ◽  
Active Research ◽  
World Hypothesis ◽  
Reaction Cascades ◽  
Rna World Hypothesis ◽  
Emergent Behaviours

The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond. This article is part of the themed issue ‘Reconceptualizing the origins of life’.

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