scholarly journals The Way forward for the Origin of Life: Prions and Prion-Like Molecules First Hypothesis

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 872
Author(s):  
Sohan Jheeta ◽  
Elias Chatzitheodoridis ◽  
Kevin Devine ◽  
Janice Block
Keyword(s):  
Chemical Evolution ◽  
Rna World ◽  
Rna Virus ◽  
Evolutionary Process ◽  
Life Forms ◽  
Evolutionary Processes ◽  
Genetic Encoding ◽  
Universal Common Ancestor ◽  
Long Line ◽  
Virus Genomes

In this paper the hypothesis that prions and prion-like molecules could have initiated the chemical evolutionary process which led to the eventual emergence of life is reappraised. The prions first hypothesis is a specific application of the protein-first hypothesis which asserts that protein-based chemical evolution preceded the evolution of genetic encoding processes. This genetics-first hypothesis asserts that an “RNA-world era” came before protein-based chemical evolution and rests on a singular premise that molecules such as RNA, acetyl-CoA, and NAD are relics of a long line of chemical evolutionary processes preceding the Last Universal Common Ancestor (LUCA). Nevertheless, we assert that prions and prion-like molecules may also be relics of chemical evolutionary processes preceding LUCA. To support this assertion is the observation that prions and prion-like molecules are involved in a plethora of activities in contemporary biology in both complex (eukaryotes) and primitive life forms. Furthermore, a literature survey reveals that small RNA virus genomes harbor information about prions (and amyloids). If, as has been presumed by proponents of the genetics-first hypotheses, small viruses were present during an RNA world era and were involved in some of the earliest evolutionary processes, this places prions and prion-like molecules potentially at the heart of the chemical evolutionary process whose eventual outcome was life. We deliberate on the case for prions and prion-like molecules as the frontier molecules at the dawn of evolution of living systems.

Buds of the tree: the highway to the last universal common ancestor

2016 ◽  
Vol 16 (2) ◽  
pp. 105-113 ◽  
Author(s):  
Savio Torres de Farias ◽  
Francisco Prosdocimi
Keyword(s):  
Origin Of Life ◽  
Common Ancestor ◽  
Rna World ◽  
Biological Activities ◽  
Ribosomal Subunit ◽  
Life Forms ◽  
Point Of View ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
The Origin Of Life

AbstractThe last universal common ancestor (LUCA) has been considered as the branching point on which Bacteria, Archaea and Eukaryotes have diverged. However, the increased information relating to viruses’ genomes and the perception that many virus genes do not have homologs in other organisms opened a new discussion. Based on these facts, there has emerged the idea of an early LUCA that should be moved further into the past to include viruses, implicating that life should have originated before the appearance of cellular life forms. Another point of view from advocates of the RNA-world suggests that the origin of life happened a long time before organisms were capable of organizing themselves into cellular entities. Relevant data about the origin of ribosomes indicate that the catalytic unit of the large ribosomal subunit is what should actually be considered as the turning point that separated chemistry from biology. Other researchers seem to think that a tRNA was probably some sort of a strange attractor on which life has originated. Here we propose a theoretical synthesis that tries to provide a crosstalk among the theories and define important points on which the origin of life could have been originated and made more complex, taking into account gradualist assumptions. Thus, discussions involving the origin of biological activities in the RNA-world might lead into a world of progenotes on which viruses have been taken part until the appearance of the very first cells. Along this route of complexification, we identified some key points on which researchers may consider life as an emerging principle.

scholarly journals Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 154
Author(s):  
Tony Z. Jia ◽  
Melina Caudan ◽  
Irena Mamajanov
Keyword(s):  
Chemical Evolution ◽  
Evolutionary Dynamics ◽  
Evolutionary Process ◽  
Origins Of Life ◽  
Droplet Microfluidics ◽  
Modern Life ◽  
Chemical Systems ◽  
Universal Common Ancestor ◽  
Associated Functions ◽  
Organismic Evolution

Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.

Getting Beyond the Apemen

2021 ◽  
pp. 1-18
Author(s):  
Lesley Newson ◽  
Peter J. Richerson
Keyword(s):  
At Risk ◽  
Natural Selection ◽  
Human Evolution ◽  
Evolutionary Process ◽  
Adult Males ◽  
Evolutionary Processes ◽  
Complex Information ◽  
History Of ◽  
Evolution By Natural Selection

This introductory chapter explains why a new story of human evolution is needed, and also lays the foundations of the story told in this book. One of the reasons we need a new story is that previous stories have concentrated on what our male ancestors were doing. Since survival is most at risk in the first years of life, it makes much more sense to concentrate on children and their mothers than on adult males. A brief account of the history of ideas in evolution by natural selection and human evolution provides readers with a background in evolutionary processes. Humans are a product of evolution, but we are not like other animals, because we are connected and readily share complex information. We are unique and our evolution was the result of a unique evolutionary process. To understand ourselves in evolutionary terms, it’s necessary to consider two intertwined evolutionary processes—genes and culture.

scholarly journals A functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ahmad Ibrahim ◽  
Jelke Fros ◽  
Andre Bertran ◽  
Ferdyansyah Sechan ◽  
Valerie Odon ◽  
...  
Keyword(s):  
Rna Virus ◽  
Plant Viruses ◽  
Tobacco Plants ◽  
Protein Coding ◽  
Antiviral Responses ◽  
Fold Reduction ◽  
Analogous Process ◽  
Systemic Spread ◽  
Functional Investigation ◽  
Virus Genomes

AbstractFrequencies of CpG and UpA dinucleotides in most plant RNA virus genomes show degrees of suppression comparable to those of vertebrate RNA viruses. While pathways that target CpG and UpAs in HIV-1 and echovirus 7 genomes and restrict their replication have been partly characterised, whether an analogous process drives dinucleotide underrepresentation in plant viruses remains undetermined. We examined replication phenotypes of compositionally modified mutants of potato virus Y (PVY) in which CpG or UpA frequencies were maximised in non-structural genes (including helicase and polymerase encoding domains) while retaining protein coding. PYV mutants with increased CpG dinucleotide frequencies showed a dose-dependent reduction in systemic spread and pathogenicity and up to 1000-fold attenuated replication kinetics in distal sites on agroinfiltration of tobacco plants (Nicotiana benthamiana). Even more extraordinarily, comparably modified UpA-high mutants displayed no pathology and over a million-fold reduction in replication. Tobacco plants with knockdown of RDP6 displayed similar attenuation of CpG- and UpA-high mutants suggesting that restriction occurred independently of the plant siRNA antiviral responses. Despite the evolutionary gulf between plant and vertebrate genomes and encoded antiviral strategies, these findings point towards the existence of novel virus restriction pathways in plants functionally analogous to innate defence components in vertebrate cells.

scholarly journals The Role of Elision in Evolutionary Processes

Languages ◽  
2019 ◽  
Vol 4 (1) ◽  
pp. 12
Author(s):  
María Azofra Sierra
Keyword(s):  
Language Change ◽  
Evolutionary Process ◽  
Category Membership ◽  
Evolutionary Processes ◽  
Linguistic Change ◽  
Specific Meaning ◽  
Theoretical Overview

Changes by elision—as well as those due to processes of adfunctionalization or refunctionalization—must be taken into account as explanatory mechanisms of linguistic change. In this paper, we study the role of elision in the theoretical overview of explanatory theories of language change by focusing on the evolutionary process of the Spanish adverb aparte. We analyze the consequences of the elision of an initial construction for the development of new functions as an exceptive or additive adverb, and as an additive connector with a specific meaning, conditioned by the evolution of the entire construction. We find that, in this case, the ellipsis of a verbal element has led to important modifications of the preserved item (aparte), not only at the semantic-pragmatic and functional levels but also in its category membership.

scholarly journals Extensive Recombination-Induced Disruption of Genetic Interactions Is Highly Deleterious but Can Be Partially Reversed by Small Numbers of Secondary Recombination Events

2014 ◽  
Vol 88 (14) ◽  
pp. 7843-7851 ◽  
Author(s):  
Adérito L. Monjane ◽  
Darren P. Martin ◽  
Francisco Lakay ◽  
Brejnev M. Muhire ◽  
Daniel Pande ◽  
...  
Keyword(s):  
Genetic Material ◽  
Evolutionary Process ◽  
Virus Genome ◽  
Maize Streak Virus ◽  
Genetic Interactions ◽  
Streak Virus ◽  
Fitness Costs ◽  
A Genome ◽  
Virus Genomes ◽  
Recombination Breakpoints

ABSTRACTAlthough homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own “lethally recombinant.” Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains.IMPORTANCERecombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.

scholarly journals Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes

2020 ◽  
Vol 16 (1) ◽  
pp. 516-531
Author(s):  
Byungil Kim ◽  
Sarah Arcos ◽  
Katherine Rothamel ◽  
Manuel Ascano
Keyword(s):  
Solid Phase ◽  
Rna Virus ◽  
Ribonucleoprotein Complexes ◽  
Virus Genomes

scholarly journals Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam

2017 ◽  
Vol 3 (2) ◽  
Author(s):  
Bas B. Oude Munnink ◽  
My V.T. Phan ◽  
Peter Simmonds ◽  
Marion P.G. Koopmans ◽  
Paul Kellam ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rna Virus ◽  
Amino Acid Identity ◽  
Nucleotide Composition ◽  
Composition Analysis ◽  
Fecal Samples ◽  
Acid Identity ◽  
Single Location ◽  
Human Viruses ◽  
Virus Genomes

Abstract Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus (husavirus) are viruses in the order Picornavirales recently described in porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs) also includes fish stool-associated RNA virus (fisavirus) as well as members detected in insects (Drosophila subobscura and Anopheles sinensis) and parasites (Ascaris suum). As part of an agnostic deep sequencing survey of animal and human viruses in Vietnam, we detected three husaviruses in human fecal samples, two of which share 97–98% amino acid identity to Dutch husavirus strains and one highly divergent husavirus with only 25% amino acid identity to known husaviruses. In addition, the current study found forty-seven complete posavirus genomes from pigs, ten novel rat stool-associated RNA virus genomes (tentatively named rasavirus), and sixteen novel bat stool-associated RNA virus genomes (tentatively named basavirus). The five expected Picornavirales protein domains (helicase, 3C-protease, RNA-dependent RNA polymerase, and two Picornavirus capsid domain) were found to be encoded by all PPLV genomes. In addition, a nucleotide composition analysis revealed that the PPLVs shared compositional properties with arthropod viruses and predicted non-mammalian hosts for all PPLV lineages. The study adds seventy-six genomes to the twenty-nine PPLV genomes currently available and greatly extends our sequence knowledge of this group of viruses within the Picornavirales order.

scholarly journals Marine RNA Virus Quasispecies Are Distributed throughout the Oceans

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Marli Vlok ◽  
Andrew S. Lang ◽  
Curtis A. Suttle
Keyword(s):  
Amino Acid ◽  
Rna Viruses ◽  
Rna Virus ◽  
Purifying Selection ◽  
Amino Acid Sequences ◽  
Metagenomic Data ◽  
Spatial And Temporal Patterns ◽  
Data Set ◽  
Virus Diversity ◽  
Virus Genomes

ABSTRACTRNA viruses, particularly genetically diverse members of thePicornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, andHeterosigma akashiwoRNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans.IMPORTANCEVery little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, theMarnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.

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