scholarly journals Limited Sequence Diversity Within a Population Supports Prebiotic RNA Reproduction

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 20 ◽  
Author(s):  
Ryo Mizuuchi ◽  
Niles Lehman
Keyword(s):  
Network Formation ◽  
Rna World ◽  
Sequence Diversity ◽  
Small Subset ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Prebiotic Environments ◽  
Primordial Earth ◽  
Autocatalytic Networks ◽  
Limited Sequence

The origins of life require the emergence of informational polymers capable of reproduction. In the RNA world on the primordial Earth, reproducible RNA molecules would have arisen from a mixture of compositionally biased, poorly available, short RNA sequences in prebiotic environments. However, it remains unclear what level of sequence diversity within a small subset of population is required to initiate RNA reproduction by prebiotic mechanisms. Here, using a simulation for template-directed recombination and ligation, we explore the effect of sequence diversity in a given population for the onset of RNA reproduction. We show that RNA reproduction is improbable in low and high diversity of finite populations; however, it could robustly occur in an intermediate sequence diversity. The intermediate range broadens toward higher diversity as population size increases. We also found that emergent reproducible RNAs likely form autocatalytic networks and collectively reproduce by catalyzing the formation of each other, allowing the expansion of information capacity. These results highlight the potential of abiotic RNAs, neither abundant nor diverse, to kick-start autocatalytic reproduction through spontaneous network formation.

scholarly journals Parsimonious scenario for the emergence of viroid-like repliconsde novo

2019 ◽  
Author(s):  
Pablo Catalán ◽  
Santiago F. Elena ◽  
José A. Cuesta ◽  
Susanna Manrubia
Keyword(s):  
De Novo ◽  
Rna World ◽  
Circular Rna ◽  
Biochemical Properties ◽  
Circular Rnas ◽  
Sequence Motifs ◽  
Rna Sequences ◽  
Specific Sequence ◽  
Evolutionary Pathway ◽  
Rna Molecules

AbstractViroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or severalde novoindependent evolutionary origins in plants. Here we discuss the plausibility ofde novoemergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluate the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules,e.g.RNA polymerases, RNases and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.

scholarly journals Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 425 ◽  
Author(s):  
Pablo Catalán ◽  
Santiago F. Elena ◽  
José A. Cuesta ◽  
Susanna Manrubia
Keyword(s):  
De Novo ◽  
Rna World ◽  
Circular Rna ◽  
Biochemical Properties ◽  
Circular Rnas ◽  
Sequence Motifs ◽  
Rna Sequences ◽  
Specific Sequence ◽  
Evolutionary Pathway ◽  
Rna Molecules

Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluated the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g., RNA polymerases, RNases, and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.

scholarly journals The RNA origin of transfer RNA aminoacylation and beyond

2011 ◽  
Vol 366 (1580) ◽  
pp. 2959-2964 ◽  
Author(s):  
Hiroaki Suga ◽  
Gosuke Hayashi ◽  
Naohiro Terasaka
Keyword(s):  
Amino Acids ◽  
Evolutionary History ◽  
Transfer Rna ◽  
Translation System ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Rna Catalysts ◽  
Modern System ◽  
History Of

Aminoacylation of tRNA is an essential event in the translation system. Although in the modern system protein enzymes play the sole role in tRNA aminoacylation, in the primitive translation system RNA molecules could have catalysed aminoacylation onto tRNA or tRNA-like molecules. Even though such RNA enzymes so far are not identified from known organisms, in vitro selection has generated such RNA catalysts from a pool of random RNA sequences. Among them, a set of RNA sequences, referred to as flexizymes (Fxs), discovered in our laboratory are able to charge amino acids onto tRNAs. Significantly, Fxs allow us to charge a wide variety of amino acids, including those that are non-proteinogenic, onto tRNAs bearing any desired anticodons, and thus enable us to reprogramme the genetic code at our will. This article summarizes the evolutionary history of Fxs and also the most recent advances in manipulating a translation system by integration with Fxs.

scholarly journals Nuclear RNA sequences coding for alpha and beta globins in erythroid cells: evidence for multiple intermediate molecules

Blood ◽  
1979 ◽  
Vol 53 (1) ◽  
pp. 134-141 ◽  
Author(s):  
MG Farace ◽  
E Ullu ◽  
A Fantoni ◽  
GB Rossi ◽  
L Cioe ◽  
...  
Keyword(s):  
Gradient Centrifugation ◽  
Electrophoretic Analysis ◽  
Beta Globin ◽  
Globin Mrna ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Large Size ◽  
Friend Leukemia ◽  
Nuclear Rna ◽  
Putative Precursor

Abstract The poly (A)-containing nuclear RNA from dimethylsulfoxide-induced Friend leukemia cells was fractionated by acrylamide gel electrophoresis in denaturing conditions and analyzed for alpha and beta globin RNA sequences. The results indicate that nuclear RNA contains one species of large-size RNA (0.6 X 10(6) daltons), which is the putative precursor for beta globin mRNA only. In addition, it was shown by electrophoretic analysis that the complex of RNA molecules not resolved by sucrose gradient centrifugation (11S) comprises sequences of decreasing size (0.34, 0.28, and 0.26 X 10(6) daltons), which might be the precursors of alpha and beta globin mRNA.

Chemical evolution toward the origin of life

2007 ◽  
Vol 79 (12) ◽  
pp. 2101-2117 ◽  
Author(s):  
Daniel Fitz ◽  
Hannes Reiner ◽  
Bernd Michael Rode
Keyword(s):  
Chemical Evolution ◽  
Rna World ◽  
Early Stage ◽  
Building Blocks ◽  
Point Of View ◽  
Peptide Formation ◽  
The Origin Of Life ◽  
Life On Earth ◽  
Primordial Earth ◽  
Rna And Dna

Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.

Behaviour of RNA under hydrothermal conditions and the origins of life

2004 ◽  
Vol 3 (4) ◽  
pp. 301-309 ◽  
Author(s):  
Kunio Kawamura
Keyword(s):  
High Temperatures ◽  
Open Systems ◽  
Rna World ◽  
Enzymatic Reaction ◽  
Reaction Rates ◽  
Extensive Literature ◽  
Hydrothermal Conditions ◽  
Phosphodiester Bond ◽  
Rna Molecules ◽  
The Stability

The RNA world hypothesis and the hydrothermal origin of life hypothesis are contradictory to each other. Although it is considered that RNA molecules are too labile to maintain life-like systems at high temperatures and there is extensive literature on nucleic acid hydrolysis, the stability and the chemical evolution of RNA have not been sufficiently analysed from the viewpoint of hydrothermal reactions. Based on our experimental data concerning the stability and the prebiotic formation of RNA at high temperatures, two different aspects seem to be important for evaluating whether RNA molecules are too labile. First, the stability of RNA molecules should be evaluated from the comparison of the rate of formation and the rate of degradation of RNA in open systems. Our prebiotic reaction models of phosphodiester bond formation suggest that at high temperatures the accumulation of RNA may be possible. However, an RNA world entirely consisting of RNA molecules is unlikely to occur because the biologically important interactions are not effective for the bare RNA molecules at high temperatures. Second, since enzymes presently mediate most biological reactions, evaluation of the accumulation of RNA should be based on the comparison between the enzymatic and non-enzymatic reaction rates. Hence, the evaluation of the primitive enzymatic reaction rates at high temperatures has been attempted. There is a large difference between the present enzymatic reaction rates at 25–90 °C and the non-enzymatic reaction rates at high temperatures of 200–300 °C. It is thus possible that prebiotic enzyme-like assemblies could have facilitated the accumulation of RNA molecules at hydrothermal vent temperatures.

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 Accurate detection of m6A RNA modifications in native RNA sequences

2019 ◽  
Author(s):  
Huanle Liu ◽  
Oguzhan Begik ◽  
Morghan C Lucas ◽  
Christopher E. Mason ◽  
Schraga Schwartz ◽  
...  
Keyword(s):  
Rna Modifications ◽  
Rna Sequences ◽  
Single Nucleotide ◽  
Rna Molecules ◽  
Base Calling ◽  
Oxford Nanopore ◽  
Nucleotide Resolution ◽  
The Universe ◽  
Oxford Nanopore Technologies ◽  
Single Nucleotide Resolution

ABSTRACTThe field of epitranscriptomics has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here we show that using Oxford Nanopore Technologies, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Our results open new avenues to investigate the universe of RNA modifications with single nucleotide resolution, in individual RNA molecules.

scholarly journals A convNet based multi label microRNA sub cellular location predictor, by incorporating k-mer positional encoding

2020 ◽  
Author(s):  
Muhammad Nabeel Asim ◽  
Andreas Dengel ◽  
Sheraz Ahmed
Keyword(s):  
Neural Network ◽  
State Of The Art ◽  
Positional Information ◽  
Feature Representation ◽  
Location Prediction ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Evaluation Measures ◽  
Cellular Location ◽  
Mammalian Transcriptome

ABSTRACTMicroRNAs are special RNA sequences containing 22 nucleotides and are capable of regulating almost 60% of highly complex mammalian transcriptome. Presently, there exists very limited approaches capable of visualizing miRNA locations inside cell to reveal the hidden pathways, and mechanisms behind miRNA functionality, transport, and biogenesis. State-of-the-art miRNA sub-cellular location prediction MIRLocatar approach makes use of sequence to sequence model along with pre-train k-mer embeddings. Existing pre-train k-mer embedding generation methodologies focus on the extraction of semantics of k-mers. In RNA sequences, rather than semantics, positional information of nucleotides is more important because distinct positions of four basic nucleotides actually define the functionality of RNA molecules. Considering the dynamicity and importance of nucleotides positions, instead of learning representation on the basis of k-mers semantics, we propose a novel kmerRP2vec feature representation approach that fuses positional information of k-mers to randomly initialized neural k-mer embeddings. Effectiveness of proposed feature representation approach is evaluated with two deep learning based convolutional neural network CNN and recurrent neural network RNN methodologies using 8 evaluation measures. Experimental results on a public benchmark miRNAsubloc dataset prove that proposed kmerRP2vec approach along with a simple CNN model outperforms state-of-the-art MirLocator approach with a significant margin of 18% and 19% in terms of precision and recall.

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