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.

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 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 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.

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 Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

2017 ◽  
Vol 4 (9) ◽  
pp. 170376
Author(s):  
Nisha Dhar ◽  
Marc S. Weinberg ◽  
Richard E. Michod ◽  
Pierre M. Durand
Keyword(s):  
Molecular Level ◽  
Rna World ◽  
Catalytic Efficiency ◽  
Molecular Size ◽  
Functional Flexibility ◽  
Trade Offs ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Rna World Hypothesis

In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3′ end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.

scholarly journals Toy trains, loaded dice and the origin of life: dimerization on mineral surfaces under periodic drive with Gaussian inputs

2017 ◽  
Vol 4 (11) ◽  
pp. 170141 ◽  
Author(s):  
Rowena Ball ◽  
John Brindley
Keyword(s):  
Origin Of Life ◽  
Chemical Evolution ◽  
Rna World ◽  
Mineral Surfaces ◽  
Dynamical Equations ◽  
Output Fluctuations ◽  
New Information ◽  
The Origin Of Life ◽  
Set Up ◽  
Life On Earth

In a major extension of previous work, we model the putative hydrothermal rock pore setting for the origin of life on Earth as a series of coupled continuous flow units (the toy train ). Perfusing through this train are reactants that set up thermochemical and pH oscillations, and an activated nucleotide that produces monomer and dimer monophosphates. The dynamical equations that model this system are thermally self-consistent. In an innovative step that breaks some new ground, we build stochasticity of the inputs into the model. The computational results infer various constraints and conditions on, and insights into, chemical evolution and the origin of life and its physical setting: long, interconnected porous structures with longitudinal non-uniformity would have been favourable, and the ubiquitous pH dependences of biology may have been established in the prebiotic era. We demonstrate the important role of Gaussian fluctuations of the inputs in driving polymerization, evolution and diversification. In particular, we find that the probability distribution of the resulting output fluctuations is left-skewed and right-weighted (the loaded dice ), which could favour chemical evolution towards a living RNA world. We tentatively name this distribution ‘Goldilocks’. These results also vindicate the general approach of constructing and running a simple model to learn important new information about a complex system.

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 Are Scientific Models of Life Testable? A Lesson from Simpson’s Paradox

Sci ◽  
2020 ◽  
Vol 2 (3) ◽  
pp. 73
Author(s):  
Prasanta S. Bandyopadhyay ◽  
Nolan Grunska ◽  
Don Dcruz ◽  
Mark C. Greenwood
Keyword(s):  
Origin Of Life ◽  
Rna World ◽  
Scientific Models ◽  
Scientific Model ◽  
Simpson’S Paradox ◽  
World Theory ◽  
Life Issues ◽  
The Origin Of Life ◽  
Logical Sense ◽  
Simpson's Paradox

We address the need for a model by considering two competing theories regarding the origin of life: (i) the Metabolism First theory and (ii) the RNA World theory. We discuss two inter-related points. (I) Models are valuable tools in understanding both the processes and intricacies of the origin of life issues. (II) Insights from models also help us to evaluate the core objection to origin of life theories called “the inefficiency objection” commonly raised by proponents of both the Metabolism First theory and the RNA World theory against each other. We use Simpson’s paradox as a tool for challenging this objection. We will use models in various senses ranging from taking them as representations of reality to treating them as theories/accounts that provide heuristics for probing reality. In this paper, we will frequently use models and theories interchangeably. Additionally, we investigate Conway’s Game of Life and contrast it with our Simpson’s Paradox (SP)-based approach to emergence of life issues. Finally, we discuss some of the consequences of our view. A scientific model is testable in three senses: (i) a logical sense, (ii) a nomological sense, and (iii) a current technological sense. The SP-based model is testable in the logical sense. It is also testable nomologically. However, it is not currently feasible to test it.

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