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.

Understanding Life: A Bioinformatics Perspective

2016 ◽  
Vol 25 (2) ◽  
pp. 231-245 ◽  
Author(s):  
Natalia Szostak ◽  
Szymon Wasik ◽  
Jacek Blazewicz
Keyword(s):  
Origin Of Life ◽  
Rna World ◽  
Origins Of Life ◽  
Life Itself ◽  
Wet Lab ◽  
The Origin Of Life ◽  
To Come ◽  
World Hypothesis ◽  
Definition Of ◽  
Rna World Hypothesis

According to some hypotheses, from a statistical perspective the origin of life seems to be a highly improbable event. Although there is no rigid definition of life itself, life as it is, is a fact. One of the most recognized hypotheses for the origins of life is the RNA world hypothesis. Laboratory experiments have been conducted to prove some assumptions of the RNA world hypothesis. However, despite some success in the ‘wet-lab’, we are still far from a complete explanation. Bioinformatics, supported by biomathematics, appears to provide the perfect tools to model and test various scenarios of the origins of life where wet-lab experiments cannot reflect the true complexity of the problem. Bioinformatics simulations of early pre-living systems may give us clues to the mechanisms of evolution. Whether or not this approach succeeds is still an open question. However, it seems likely that linking efforts and knowledge from the various fields of science into a holistic bioinformatics perspective offers the opportunity to come one step closer to a solution to the question of the origin of life, which is one of the greatest mysteries of humankind. This paper illustrates some recent advancements in this area and points out possible directions for further research.

scholarly journals Prebiotic chemistry: a new modus operandi

2011 ◽  
Vol 366 (1580) ◽  
pp. 2870-2877 ◽  
Author(s):  
Matthew W. Powner ◽  
John D. Sutherland
Keyword(s):  
Origin Of Life ◽  
Early Life ◽  
Rna World ◽  
Origins Of Life ◽  
Geochemical Conditions ◽  
Systems Chemistry ◽  
Novel Approach ◽  
Sequential Addition ◽  
World Hypothesis ◽  
Emergence Of Life

A variety of macromolecules and small molecules—(oligo)nucleotides, proteins, lipids and metabolites—are collectively considered essential to early life. However, previous schemes for the origin of life—e.g. the ‘RNA world’ hypothesis—have tended to assume the initial emergence of life based on one such molecular class followed by the sequential addition of the others, rather than the emergence of life based on a mixture of all the classes of molecules. This view is in part due to the perceived implausibility of multi-component reaction chemistry producing such a mixture. The concept of systems chemistry challenges such preconceptions by suggesting the possibility of molecular synergism in complex mixtures. If a systems chemistry method to make mixtures of all the classes of molecules considered essential for early life were to be discovered, the significant conceptual difficulties associated with pure RNA, protein, lipid or metabolism ‘worlds’ would be alleviated. Knowledge of the geochemical conditions conducive to the chemical origins of life is crucial, but cannot be inferred from a planetary sciences approach alone. Instead, insights from the organic reactivity of analytically accessible chemical subsystems can inform the search for the relevant geochemical conditions. If the common set of conditions under which these subsystems work productively, and compatibly, matches plausible geochemistry, an origins of life scenario can be inferred. Using chemical clues from multiple subsystems in this way is akin to triangulation, and constitutes a novel approach to discover the circumstances surrounding the transition from chemistry to biology. Here, we exemplify this strategy by finding common conditions under which chemical subsystems generate nucleotides and lipids in a compatible and potentially synergistic way. The conditions hint at a post-meteoritic impact origin of life scenario.

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 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 Non-enzymatic primer extension with strand displacement

2019 ◽  
Author(s):  
Lijun Zhou ◽  
Seohyun Chris Kim ◽  
Katherine H. Ho ◽  
Derek K. O’Flaherty ◽  
Constantin Giurgiu ◽  
...  
Keyword(s):  
Rna World ◽  
Genetic Material ◽  
Kinetic Studies ◽  
Single Step ◽  
Primer Extension ◽  
Branch Migration ◽  
Strand Displacement ◽  
World Hypothesis ◽  
Self Replication ◽  
Rna World Hypothesis

AbstractNon-enzymatic RNA self-replication is integral to the ‘RNA World’ hypothesis. Despite considerable progress in non-enzymatic template copying, true replication remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible solution to this problem in which short ‘invader’ oligonucleotides unwind an RNA duplex through a toehold/branch migration mechanism, allowing non-enzymatic primer extension on a template that was previously occupied by its complementary strand. Kinetic studies of single-step reactions suggest that following invader binding, branch migration results in a 2:3 partition of the template between open and closed states. Finally, we demonstrate continued primer extension with strand displacement by employing activated 3′-aminonucleotides, a more reactive proxy for ribonucleotides. Our study suggests that complete cycles of non-enzymatic replication of the primordial genetic material may have been catalyzed by short RNA oligonucleotides.

Borate and the Origin of RNA: A Model for the Precursors to Life

Elements ◽  
2017 ◽  
Vol 13 (4) ◽  
pp. 261-265 ◽  
Author(s):  
Yoshihiro Furukawa ◽  
Takeshi Kakegawa
Keyword(s):  
Origin Of Life ◽  
Chemical Evolution ◽  
Ribonucleic Acid ◽  
Rna World ◽  
Critical Role ◽  
Formose Reaction ◽  
Strong Affinity ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Rna World Hypothesis

According to the RNA World hypothesis, ribonucleic acid (RNA) played a critical role in the origin of life. However, ribose, an essential component of RNA, is easily degraded: finding a way to stabilize it is critical to the viability of the hypothesis. Borate has been experimentally shown to have a strong affinity for ribose, and, thus, could have protected ribose from degradation in the formose reaction, a potential process for prebiotic ribose formation. Accumulation of borate on Hadean Earth (prior to ~4,000 Ma) might have been a key step in the chemical evolution of the biotic sugar. Proto-arcs are suggested as a geological setting sufficiently rich in borate to stabilize ribose during the Hadean.

scholarly journals Origins of Life and the RNA World: Evolution of RNA-Replicase Recognition

2004 ◽  
Vol 213 ◽  
pp. 321-324 ◽  
Author(s):  
Laura Guogas ◽  
James Hogle ◽  
Lee Gehrke
Keyword(s):  
Origin Of Life ◽  
Protein Complex ◽  
Rna Viruses ◽  
Rna World ◽  
Rna Virus ◽  
Genetic Material ◽  
Virus Family ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Rna World Hypothesis

Central to understanding the origin of life is the elucidation of the first replication mechanism. The RNA World hypothesis suggests that the first self-replicating molecules were RNAs and that DNA later superceded RNA as the genetic material. RNA viruses were not subjected to the same evolutionary pressures as cellular organisms; consequently, they likely possess remnants of earlier replication strategies. Our laboratory investigates how members of the RNA virus family Bromoviridae can have structurally distinct 3' end tags yet are specifically recognized by conserved replication enzymes. This work addresses the idea that 3' tRNA tails were functionally replaced in some viruses by an RNA-protein complex. These viruses may serve as a timeline for the transition from the RNA world to DNA and protein based life.

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.

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.

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