Life | June 2016 - Browse Articles

1452 KiB

Open AccessArticle

The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

by Paul G. Higgs

Life 2016, 6(2), 24; https://doi.org/10.3390/life6020024 - 08 Jun 2016

Cited by 41 | Viewed by 7035

Abstract

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that [...] Read more.

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction. Full article

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

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1225 KiB

Open AccessReview

Probing Saltern Brines with an Oxygen Electrode: What Can We Learn about the Community Metabolism in Hypersaline Systems?

by Aharon Oren

Life 2016, 6(2), 23; https://doi.org/10.3390/life6020023 - 08 Jun 2016

Cited by 7 | Viewed by 5790

Abstract

We have explored the use of optical oxygen electrodes to study oxygenic photosynthesis and heterotrophic activities in crystallizer brines of the salterns in Eilat, Israel. Monitoring oxygen uptake rates in the dark enables the identification of organic substrates that are preferentially used by [...] Read more.

We have explored the use of optical oxygen electrodes to study oxygenic photosynthesis and heterotrophic activities in crystallizer brines of the salterns in Eilat, Israel. Monitoring oxygen uptake rates in the dark enables the identification of organic substrates that are preferentially used by the community. Addition of glycerol (the osmotic solute synthesized by Dunaliella) or dihydroxyacetone (produced from glycerol by Salinibacter) enhanced respiration rates. Pyruvate, produced from glycerol or from some sugars by certain halophilic Archaea also stimulated community respiration. Fumarate had a sparing effect on respiration, possibly as many halophilic Archaea can use fumarate as a terminal electron acceptor in respiration. Calculating the photosynthetic activity of Dunaliella by monitoring oxygen concentration changes during light/dark incubations is not straightforward as light also affects respiration of some halophilic Archaea and Bacteria due to action of light-driven proton pumps. When illuminated, community respiration of brine samples in which oxygenic photosynthesis was inhibited by DCMU decreased by ~40%. This effect was interpreted as the result of competition between two energy yielding systems: the bacteriorhodopsin proton pump and the respiratory chain of the prokaryotes. These findings have important implications for the interpretation of other published data on photosynthetic and respiratory activities in hypersaline environments. Full article

(This article belongs to the Special Issue Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016)

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836 KiB

Open AccessArticle

Effects of Low-Temperature Plasma-Sterilization on Mars Analog Soil Samples Mixed with Deinococcus radiodurans

by Janosch Schirmack, Marcel Fiebrandt, Katharina Stapelmann and Dirk Schulze-Makuch

Life 2016, 6(2), 22; https://doi.org/10.3390/life6020022 - 26 May 2016

Cited by 2 | Viewed by 5689

Abstract

We used Ar plasma-sterilization at a temperature below 80 °C to examine its effects on the viability of microorganisms when intermixed with tested soil. Due to a relatively low temperature, this method is not thought to affect the properties of a soil, particularly [...] Read more.

We used Ar plasma-sterilization at a temperature below 80 °C to examine its effects on the viability of microorganisms when intermixed with tested soil. Due to a relatively low temperature, this method is not thought to affect the properties of a soil, particularly its organic component, to a significant degree. The method has previously been shown to work well on spacecraft parts. The selected microorganism for this test was Deinococcus radiodurans R1, which is known for its remarkable resistance to radiation effects. Our results showed a reduction in microbial counts after applying a low temperature plasma, but not to a degree suitable for a sterilization of the soil. Even an increase of the treatment duration from 1.5 to 45 min did not achieve satisfying results, but only resulted in in a mean cell reduction rate of 75% compared to the untreated control samples. Full article

(This article belongs to the Section Microbiology)

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6415 KiB

Open AccessEssay

A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond

by Bruce Damer

Life 2016, 6(2), 21; https://doi.org/10.3390/life6020021 - 25 May 2016

Cited by 35 | Viewed by 17499

Abstract

Charles Darwin’s original intuition that life began in a “warm little pond” has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and [...] Read more.

Charles Darwin’s original intuition that life began in a “warm little pond” has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwin’s original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed on similar land masses rising out of Earth’s first oceans. I will report on a field trip to the living and ancient stromatolite fossil localities of Western Australia, which provided key insights into how life may have emerged in Archaean, fluctuating fresh water hydrothermal pools, geological evidence for which has recently been discovered. Laboratory experimentation and fieldwork are providing mounting evidence that such sites have properties that are conducive to polymerization reactions and generation of membrane-bounded protocells. I will build on the previously developed coupled phases scenario, unifying the chemical and geological frameworks and proposing that a hydrogel of stable, communally supported protocells will emerge as a candidate Woese progenote, the distant common ancestor of microbial communities so abundant in the earliest fossil record. Full article

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

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165 KiB

Open AccessEditorial

The Landscape of the Emergence of Life

by Sohan Jheeta

Life 2016, 6(2), 20; https://doi.org/10.3390/life6020020 - 16 May 2016

Cited by 3 | Viewed by 4664

Abstract

Is it unrealistic to presuppose that all of the steps that could lead to the formation of life could occur in one setting?[...] Full article

(This article belongs to the Special Issue The Landscape of the Emergence of Life)

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Open AccessEditorial

Hans Georg Trüper (1936–2016) and His Contributions to Halophile Research

by Aharon Oren

Life 2016, 6(2), 19; https://doi.org/10.3390/life6020019 - 12 May 2016

Cited by 1 | Viewed by 5704

Abstract

Prof. Hans Georg Trüper, one of the most important scientists in the field of halophile research, passed away on 9 March 2016 at the age of 79. I here present a brief obituary with special emphasis on Prof. Trüper’s contributions to our understanding [...] Read more.

Prof. Hans Georg Trüper, one of the most important scientists in the field of halophile research, passed away on 9 March 2016 at the age of 79. I here present a brief obituary with special emphasis on Prof. Trüper’s contributions to our understanding of the halophilic prokaryotes and their adaptations to life in hypersaline environments. He has pioneered the study of the halophilic anoxygenic phototrophic sulfur bacteria of the Ectothiorhodospira—Halorhodospira group. Some of the species he and his group isolated from hypersaline and haloalkaline environments have become model organisms for the study of the mechanisms of haloadaptation: the functions of three major organic compounds – glycine betaine, ectoine, and trehalose – known to serve as “compatible solutes” in halophilic members of the Bacteria domain, were discovered during studies of these anoxygenic phototrophs. Prof. Trüper’s studies of hypersaline alkaline environments in Egypt also led to the isolation of the first known extremely halophilic archaeon (Natronomonas pharaonis). The guest editors dedicate this special volume of Life to the memory of Prof. Hans Georg Trüper. Full article

(This article belongs to the Special Issue Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016)

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2736 KiB

Open AccessReview

Molecular Asymmetry in Prebiotic Chemistry: An Account from Meteorites

by Sandra Pizzarello

Life 2016, 6(2), 18; https://doi.org/10.3390/life6020018 - 13 Apr 2016

Cited by 19 | Viewed by 5392

Abstract

Carbonaceous Chondrite (CC) meteorites are fragments of asteroids, solar planetesimals that never became large enough to separate matter by their density, like terrestrial planets. CC contains various amounts of organic carbon and carry a record of chemical evolution as it came to be [...] Read more.

Carbonaceous Chondrite (CC) meteorites are fragments of asteroids, solar planetesimals that never became large enough to separate matter by their density, like terrestrial planets. CC contains various amounts of organic carbon and carry a record of chemical evolution as it came to be in the Solar System, at the time the Earth was formed and before the origins of life. We review this record as it pertains to the chiral asymmetry determined for several organic compounds in CC, which reaches a broad molecular distribution and enantiomeric excesses of up to 50%–60%. Because homochirality is an indispensable attribute of extant polymers and these meteoritic enantiomeric excesses are still, to date, the only case of chiral asymmetry in organic molecules measured outside the biosphere, the possibility of an exogenous delivery of primed prebiotic compounds to early Earth from meteorites is often proposed. Whether this exogenous delivery held a chiral advantage in molecular evolution remains an open question, as many others regarding the origins of life are. Full article

(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)

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2846 KiB

Open AccessReview

Prebiotic Lipidic Amphiphiles and Condensing Agents on the Early Earth

by Michele Fiore and Peter Strazewski

Life 2016, 6(2), 17; https://doi.org/10.3390/life6020017 - 28 Mar 2016

Cited by 34 | Viewed by 10992

Abstract

It is still uncertain how the first minimal cellular systems evolved to the complexity required for life to begin, but it is obvious that the role of amphiphilic compounds in the origin of life is one of huge relevance. Over the last four [...] Read more.

It is still uncertain how the first minimal cellular systems evolved to the complexity required for life to begin, but it is obvious that the role of amphiphilic compounds in the origin of life is one of huge relevance. Over the last four decades a number of studies have demonstrated how amphiphilic molecules can be synthesized under plausibly prebiotic conditions. The majority of these experiments also gave evidence for the ability of so formed amphiphiles to assemble in closed membranes of vesicles that, in principle, could have compartmented first biological processes on early Earth, including the emergence of self-replicating systems. For a competitive selection of the best performing molecular replicators to become operative, some kind of bounded units capable of harboring them are indispensable. Without the competition between dynamic populations of different compartments, life itself could not be distinguished from an otherwise disparate array or network of molecular interactions. In this review, we describe experiments that demonstrate how different prebiotically-available building blocks can become precursors of phospholipids that form vesicles. We discuss the experimental conditions that resemble plausibly those of the early Earth (or elsewhere) and consider the analytical methods that were used to characterize synthetic products. Two brief sections focus on phosphorylating agents, catalysts and coupling agents with particular attention given to their geochemical context. In Section 5, we describe how condensing agents such as cyanamide and urea can promote the abiotic synthesis of phospholipids. We conclude the review by reflecting on future studies of phospholipid compartments, particularly, on evolvable chemical systems that include giant vesicles composed of different lipidic amphiphiles. Full article

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

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788 KiB

Open AccessReview

Multiple Layers of Stress-Induced Regulation in tRNA Biology

by Hsiao-Yun Huang and Anita K. Hopper

Life 2016, 6(2), 16; https://doi.org/10.3390/life6020016 - 23 Mar 2016

Cited by 54 | Viewed by 11461

Abstract

tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple [...] Read more.

tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple layers of regulatory mechanisms in each step of tRNA biogenesis. For example, tRNA 3′ trailer processing is altered upon nutrient stress; tRNA modification is reprogrammed under various stresses; nuclear accumulation of tRNAs occurs upon nutrient deprivation; tRNA halves accumulate upon oxidative stress. Here we address how environmental stresses can affect nearly every step of tRNA biology and we describe the possible regulatory mechanisms that influence the function or expression of tRNAs under stress conditions. Full article

(This article belongs to the Special Issue Evolution of tRNA)

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794 KiB

Open AccessArticle

tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World

by Savio T. De Farias, Thais G. Rêgo and Marco V. José

Life 2016, 6(2), 15; https://doi.org/10.3390/life6020015 - 23 Mar 2016

Cited by 26 | Viewed by 7480

Abstract

Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA) and the peptidyl transferase center (rRNA), proto-tRNAs were at the core [...] Read more.

Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA) and the peptidyl transferase center (rRNA), proto-tRNAs were at the core of a proto-translation system, and the anticodon and operational codes then arose in tRNAs molecules. Metabolic pathways emerged from evolutionary pressures of the decoding systems. The transitions from the RNA world to the ribonucleoprotein world to modern biological systems were driven by three kinds of tRNAs transitions, to wit, tRNAs leading to both mRNA and rRNA. Full article

(This article belongs to the Special Issue Evolution of tRNA)

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