Prebiotic synthesis of 5-substituted uracils: a bridge between the RNA world and the DNA-protein world

Science ◽  
1995 ◽  
Vol 268 (5211) ◽  
pp. 702-705 ◽  
Author(s):  
M. Robertson ◽  
S. Miller
Keyword(s):  
Rna World ◽  
Prebiotic Synthesis ◽  
Protein World ◽  
Substituted Uracils

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 Between the ‘RNA World’ and the ‘Protein World’

Structure ◽  
1995 ◽  
Vol 3 (9) ◽  
pp. 969-970
Author(s):  
Thomas R Cech
Keyword(s):  
Rna World ◽  
Protein World

scholarly journals The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

2019 ◽  
Vol 20 (21) ◽  
pp. 5507 ◽  
Author(s):  
Vladimir Kubyshkin ◽  
Nediljko Budisa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Rna World ◽  
Protein Biosynthesis ◽  
Second Phase ◽  
Nucleotide Biosynthesis ◽  
The Core ◽  
Protein World ◽  
Α Helix

A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.

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 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 A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides

2019 ◽  
Author(s):  
Seohyun Chris Kim ◽  
Lijun Zhou ◽  
Wen Zhang ◽  
Derek K. O’Flaherty ◽  
Valeria Rondo-Brovetto ◽  
...  
Keyword(s):  
Rna Synthesis ◽  
Rna World ◽  
Random Sequence ◽  
Prebiotic Synthesis ◽  
Primer Extension ◽  
Complex Mixtures ◽  
Essential Step ◽  
Simultaneous Synthesis ◽  
The Difference ◽  
Chimeric Oligonucleotides

AbstractThe abiotic synthesis of ribonucleotides is thought to have been an essential step towards the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2′-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2′-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabino-nucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2′-deoxy- or arabino-nucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

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