Life | September 2017 - Browse Articles

1042 KiB

Open AccessReview

Ancient Living Organisms Escaping from, or Imprisoned in, the Vents?

by J. Baz Jackson

Life 2017, 7(3), 36; https://doi.org/10.3390/life7030036 - 15 Sep 2017

Cited by 7 | Viewed by 5217

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 [...] Read more.

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. We point out that it may have been impossible for organisms to have acquired membrane-located proton (or sodium ion) pumps to replace the natural pH gradient, and independently to have driven essential molecular machines such as the ATP synthase. The volumes of the ocean and of the vent fluids were too large for a membrane-located pump to have generated a significant ion concentration gradient. Our arguments apply to three of the four concurrent models employed by the proponents of the natural pH gradient hypothesis. A fourth model is exempt from these arguments but has other intrinsic difficulties that we briefly consider. We conclude that ancient organisms utilising a natural pH gradient would have been imprisoned in the vents, unable to escape and become free-living. Full article

(This article belongs to the Special Issue Hydrothermal Vents or Hydrothermal Fields: Challenging Paradigms)

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5154 KiB

Open AccessArticle

Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (β-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids

by Brian R. Francis, Kevin Watkins and Jan Kubelka

Life 2017, 7(3), 35; https://doi.org/10.3390/life7030035 - 28 Aug 2017

Cited by 18 | Viewed by 6787

Abstract

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 [...] Read more.

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. If so, what was the original polymer from which RNA and DNA evolved? In most syntheses of simpler RNA or DNA analogs, the D-ribose phosphate polymer backbone is altered and the purine and pyrimidine bases are retained for hydrogen bonding between complementary base pairs. However, the bases are themselves products of complex biosynthetic pathways and hence they too may have evolved from simpler polymer side chains that had the ability to form hydrogen bonds. We hypothesize that the earliest evolutionary predecessor of nucleic acids was the simple linear polyester, poly (β-D-malic acid), for which the carboxyl side chains could form double hydrogen bonds. In this study, we show that in accord with this hypothesis a closely related polyester, poly (β-L-malic acid), uses carboxyl side chains to form robust intramolecular double hydrogen bonds in moderately acidic solution. Full article

(This article belongs to the Section Hypotheses in the Life Sciences)

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204 KiB

Open AccessHypothesis

Life’s Late Digital Revolution and Why It Matters for the Study of the Origins of Life

by David A. Baum and Niles Lehman

Life 2017, 7(3), 34; https://doi.org/10.3390/life7030034 - 25 Aug 2017

Cited by 5 | Viewed by 6311

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Origin of Life)

1428 KiB

Open AccessReview

Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere

by Satoshi Akanuma

Life 2017, 7(3), 33; https://doi.org/10.3390/life7030033 - 06 Aug 2017

Cited by 21 | Viewed by 7911

Abstract

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 [...] Read more.

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. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth’s surface temperature gradually decreased over time, from Archean to present. Full article

(This article belongs to the Special Issue Hydrothermal Vents or Hydrothermal Fields: Challenging Paradigms)

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14310 KiB

Open AccessReview

Nitrogenous Derivatives of Phosphorus and the Origins of Life: Plausible Prebiotic Phosphorylating Agents in Water

by Megha Karki, Clémentine Gibard, Subhendu Bhowmik and Ramanarayanan Krishnamurthy

Life 2017, 7(3), 32; https://doi.org/10.3390/life7030032 - 29 Jul 2017

Cited by 40 | Viewed by 11248

Abstract

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 [...] Read more.

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”. We submit that serious consideration should be given to the search for primordial sources of nitrogenous versions of phosphate and other versions of phosphorus. Full article

(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)

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3126 KiB

Open AccessReview

A Chemist’s Perspective on the Role of Phosphorus at the Origins of Life

by Christian Fernández-García, Adam J. Coggins and Matthew W. Powner

Life 2017, 7(3), 31; https://doi.org/10.3390/life7030031 - 13 Jul 2017

Cited by 49 | Viewed by 10241

Abstract

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 [...] Read more.

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. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid–base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth. Full article

(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)

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2180 KiB

Open AccessArticle

Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms

by Mario Alberto Martínez-Núñez, Zuemy Rodríguez-Escamilla, Katya Rodríguez-Vázquez and Ernesto Pérez-Rueda

Life 2017, 7(3), 30; https://doi.org/10.3390/life7030030 - 13 Jul 2017

Cited by 7 | Viewed by 5194

Abstract

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 [...] Read more.

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. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea. Full article

(This article belongs to the Special Issue Extremophiles and the Origin of Life)

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1105 KiB

Open AccessArticle

Silicate-Promoted Phosphorylation of Glycerol in Non-Aqueous Solvents: A Prebiotically Plausible Route to Organophosphates

by Maheen Gull, Brian J. Cafferty, Nicholas V. Hud and Matthew A. Pasek

Life 2017, 7(3), 29; https://doi.org/10.3390/life7030029 - 29 Jun 2017

Cited by 22 | Viewed by 6515

Abstract

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 [...] Read more.

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. The reactions were carried out by heating glycerol with a phosphate source at 85 °C for one week and were analyzed by ³¹P-nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). The yield of the phosphorylated glycerol was improved by the presence of silicates, and reached 90% in some experiments. Our findings further support the proposal that non-aqueous solvents are advantageous for the prebiotic synthesis of biomolecules, and suggest that silicates may have aided in the formation of organophosphates on the prebiotic earth. Full article

(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)

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