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Sarah Maurer
One of the key steps in the origins of life was the formation of a membrane to separate protocells from their environment. These membranes are proposed to have been formed out of single chain amphiphiles, which are less stable than the dialkyl lipids used to form modern membranes. This lack of stability, specifically for decanoate, is often used to refute ocean locations for the origins of life. This review addresses the formation of membranes in hydrothermal-vent like conditions, as well as other environmental constraints...
November 14, 2017: Life
Samuel H A von der Dunk, Enrico Sandro Colizzi, Paulien Hogeweg
Molecules that replicate in trans are vulnerable to evolutionary extinction because they decrease the catalysis of replication to become more available as a template for replication. This problem can be alleviated with higher-level selection that clusters molecules of the same phenotype, favouring those groups that contain more catalysis. Here, we study a simple replicator model with implicit higher-level selection through space. We ask whether the functionality of such system can be enhanced when molecules reproduce through complementary replication, representing RNA-like replicators...
November 2, 2017: Life
Andrew S Tupper, Kevin Shi, Paul G Higgs
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3'-5' bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture...
October 31, 2017: Life
Sarah J Berkemer, Anne Hoffmann, Cameron R A Murray, Peter F Stadler
Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny...
October 31, 2017: Life
Frédéric Foucher, Keyron Hickman-Lewis, Frances Westall, André Brack
In this study, we attempt to illustrate the competition that constitutes the main challenge of astrobiology, namely the competition between the probability of extraterrestrial life and its detectability. To illustrate this fact, we propose a simple statistical approach based on our knowledge of the Universe and the Milky Way, the Solar System, and the evolution of life on Earth permitting us to obtain the order of magnitude of the distance between Earth and bodies inhabited by more or less evolved past or present life forms, and the consequences of this probability for the detection of associated biosignatures...
October 26, 2017: Life
Cole Mathis, Sanjay N Ramprasad, Sara Imari Walker, Niles Lehman
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system...
October 16, 2017: Life
Kunio Kawamura
Although studies about the origin of life are a frontier in science and a number of effective approaches have been developed, drawbacks still exist. Examples include: (1) simulation of chemical evolution experiments (which were demonstrated for the first time by Stanley Miller); (2) approaches tracing back the most primitive life-like systems (on the basis of investigations of present organisms); and (3) constructive approaches for making life-like systems (on the basis of molecular biology), such as in vitro construction of the RNA world...
October 2, 2017: Life
J Baz Jackson
We have recently criticised the natural pH gradient hypothesis which purports to explain how the difference in pH between fluid issuing from ancient alkali vents and the more acidic Hadean ocean could have driven molecular machines that catalyse reactions that are useful in prebiotic and autotrophic chemistry. In this article, we temporarily suspend our earlier criticism while we consider difficulties for primitive organisms to have managed their energy supply and to have left the vents and become free-living...
September 15, 2017: Life
Brian R Francis, Kevin Watkins, Jan Kubelka
The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process...
August 28, 2017: Life
David A Baum, Niles Lehman
The information contained in life exists in two forms, analog and digital. Analog information is manifest mainly in the differing concentrations of chemicals that get passed from generation to generation and can vary from cell to cell. Digital information is encoded in linear polymers such as DNA and RNA, whose side chains come in discrete chemical forms. Here, we argue that the analog form of information preceded the digital. Acceptance of this dichotomy, and this progression, can help direct future studies on how life originated and initially complexified on the primordial Earth, as well as expected trajectories for other, independent origins of complex life...
August 25, 2017: Life
Satoshi Akanuma
Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth's early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms...
August 6, 2017: Life
Megha Karki, Clémentine Gibard, Subhendu Bhowmik, Ramanarayanan Krishnamurthy
Phosphorylation under plausible prebiotic conditions continues to be one of the defining issues for the role of phosphorus in the origins of life processes. In this review, we cover the reactions of alternative forms of phosphate, specifically the nitrogenous versions of phosphate (and other forms of reduced phosphorus species) from a prebiotic, synthetic organic and biochemistry perspective. The ease with which such amidophosphates or phosphoramidate derivatives phosphorylate a wide variety of substrates suggests that alternative forms of phosphate could have played a role in overcoming the "phosphorylation in water problem"...
July 29, 2017: Life
Christian Fernández-García, Adam J Coggins, Matthew W Powner
The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer...
July 13, 2017: Life
Mario Alberto Martínez-Núñez, Zuemy Rodríguez-Escamilla, Katya Rodríguez-Vázquez, Ernesto Pérez-Rueda
The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database...
July 13, 2017: Life
Maheen Gull, Brian J Cafferty, Nicholas V Hud, Matthew A Pasek
Phosphorylation reactions of glycerol were studied using different inorganic phosphates such as sodium phosphate, trimetaphosphate (a condensed phosphate), and struvite. The reactions were carried out in two non-aqueous solvents: formamide and a eutectic solvent consisting of choline-chloride and glycerol in a ratio of 1:2.5. The glycerol reacted in formamide and in the eutectic solvent with phosphate to yield its phosphorylated derivatives in the presence of silicates such as quartz sand and kaolinite clay...
June 29, 2017: Life
Helen Greenwood Hansma
Organelles without membranes are found in all types of cells and typically contain RNA and protein. RNA and protein are the constituents of ribosomes, one of the most ancient cellular structures. It is reasonable to propose that organelles without membranes preceded protocells and other membrane-bound structures at the origins of life. Such membraneless organelles would be well sheltered in the spaces between mica sheets, which have many advantages as a site for the origins of life.
June 20, 2017: Life
Sohan Jheeta
This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3-4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and "from RNA to DNA", i...
June 16, 2017: Life
Takuma Hashimoto, Takekazu Kunieda
Genomic DNA stores all genetic information and is indispensable for maintenance of normal cellular activity and propagation. Radiation causes severe DNA lesions, including double-strand breaks, and leads to genome instability and even lethality. Regardless of the toxicity of radiation, some organisms exhibit extraordinary tolerance against radiation. These organisms are supposed to possess special mechanisms to mitigate radiation-induced DNA damages. Extensive study using radiotolerant bacteria suggested that effective protection of proteins and enhanced DNA repair system play important roles in tolerability against high-dose radiation...
June 15, 2017: Life
Georges Feller
Psychrophiles thrive permanently in the various cold environments on Earth. Their unsuspected ability to remain metabolically active in the most extreme low temperature conditions provides insights into a possible cold step in the origin of life. More specifically, metabolically active psychrophilic bacteria have been observed at -20 °C in the ice eutectic phase (i.e., the liquid veins between sea ice crystals). In the context of the RNA world hypothesis, this ice eutectic phase would have provided stability to the RNA molecules and confinement of the molecules in order to react and replicate...
June 11, 2017: Life
Adolfo Saiardi
Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should look retrospectively to phosphate-rich molecules present in today's cells. Overlooked by origin of life studies until now, inositol and the inositol phosphates, of which some species possess more phosphate groups that carbon atoms, represent ideal molecules to consider in this context...
June 5, 2017: Life
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