Life | June 2018 - Browse Articles

15 pages, 694 KiB

Open AccessReview

Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA

by Raffaele Saladino, Judit E. Šponer, Jiří Šponer, Giovanna Costanzo, Samanta Pino and Ernesto Di Mauro

Life 2018, 8(2), 24; https://doi.org/10.3390/life8020024 - 20 Jun 2018

Cited by 13 | Viewed by 5678

Abstract

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously [...] Read more.

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry of Biomolecules)

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16 pages, 21646 KiB

Open AccessArticle

Integrity of the DNA and Cellular Ultrastructure of Cryptoendolithic Fungi in Space or Mars Conditions: A 1.5-Year Study at the International Space Station

by Silvano Onofri, Laura Selbmann, Claudia Pacelli, Jean Pierre De Vera, Gerda Horneck, John E. Hallsworth and Laura Zucconi

Life 2018, 8(2), 23; https://doi.org/10.3390/life8020023 - 19 Jun 2018

Cited by 17 | Viewed by 6951

Abstract

The black fungi Cryomyces antarcticus and Cryomyces minteri are highly melanized and are resilient to cold, ultra-violet, ionizing radiation and other extreme conditions. These microorganisms were isolated from cryptoendolithic microbial communities in the McMurdo Dry Valleys (Antarctica) and studied in Low Earth Orbit [...] Read more.

The black fungi Cryomyces antarcticus and Cryomyces minteri are highly melanized and are resilient to cold, ultra-violet, ionizing radiation and other extreme conditions. These microorganisms were isolated from cryptoendolithic microbial communities in the McMurdo Dry Valleys (Antarctica) and studied in Low Earth Orbit (LEO), using the EXPOSE-E facility on the International Space Station (ISS). Previously, it was demonstrated that C. antarcticus and C. minteri survive the hostile conditions of space (vacuum, temperature fluctuations, and the full spectrum of extraterrestrial solar electromagnetic radiation), as well as Mars conditions that were simulated in space for a 1.5-year period. Here, we qualitatively and quantitatively characterize damage to DNA and cellular ultrastructure in desiccated cells of these two species, within the frame of the same experiment. The DNA and cells of C. antarcticus exhibited a higher resistance than those of C. minteri. This is presumably attributable to the thicker (melanized) cell wall of the former. Generally, DNA was readily detected (by PCR) regardless of exposure conditions or fungal species, but the C. minteri DNA had been more-extensively mutated. We discuss the implications for using DNA, when properly shielded, as a biosignature of recently extinct or extant life. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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14 pages, 2132 KiB

Open AccessArticle

Big Sound and Extreme Fungi—Xerophilic, Halotolerant Aspergilli and Penicillia with Low Optimal Temperature as Invaders of Historic Pipe Organs

by Katja Sterflinger, Christian Voitl, Ksenija Lopandic, Guadalupe Piñar and Hakim Tafer

Life 2018, 8(2), 22; https://doi.org/10.3390/life8020022 - 14 Jun 2018

Cited by 16 | Viewed by 5881

Abstract

Recent investigations have shown that xerophilic fungi may pose a biodeterioration risk by threatening objects of cultural heritage including many types of materials, including wood, paint layers, organic glues or leather and even metal. Historic—and also new built—pipe organs combine all those materials. [...] Read more.

Recent investigations have shown that xerophilic fungi may pose a biodeterioration risk by threatening objects of cultural heritage including many types of materials, including wood, paint layers, organic glues or leather and even metal. Historic—and also new built—pipe organs combine all those materials. In this study, halotolerant aspergilli and penicillia with low optimal temperatures were shown to be the most frequent invaders of pipe organs. The fungi form white mycelia on the organic components of the organs with a clear preference for the bolus paint of the wooden pipes, the leather-made hinges of the stop actions and all parts fixed by organic glue. Physiological tests showed that the strains isolated from the instruments all show a halotolerant behavior, although none was halophilic. The optimum growth temperature is below 20 °C, thus the fungi are perfectly adapted to the cool and relatively dry conditions in the churches and organs respectively. The de-novo genome sequences analyses of the strains are currently ongoing and will reveal the genomic basis for the halotolerant behavior of the fungi. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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14 pages, 373 KiB

Open AccessArticle

Homochirality through Photon-Induced Denaturing of RNA/DNA at the Origin of Life

by Karo Michaelian

Life 2018, 8(2), 21; https://doi.org/10.3390/life8020021 - 6 Jun 2018

Cited by 10 | Viewed by 6755

Abstract

Since a racemic mixture of chiral nucleotides frustrates the enzymeless extension of RNA and DNA, the origin of homochirality must be intimately connected with the origin of life. Homochirality theories have elected to presume abiotic mechanisms for prebiotic enantiomer enrichment and post amplification, [...] Read more.

Since a racemic mixture of chiral nucleotides frustrates the enzymeless extension of RNA and DNA, the origin of homochirality must be intimately connected with the origin of life. Homochirality theories have elected to presume abiotic mechanisms for prebiotic enantiomer enrichment and post amplification, but none, so far, has been generally accepted. Here I present a novel hypothesis for the procurement of homochirality from an asymmetry in right- over left-circularly polarized photon-induced denaturing of RNA and DNA at the Archean ocean surface as temperatures descended below that of RNA and DNA melting. This asymmetry is attributed to the small excess of right-handed circularly polarized submarine light during the afternoon, when surface water temperatures were highest and thus most conducive to photon-induced denaturing, and to a negative circular dichroism band extending from 230 to 270 nm for small oligos of RNA and DNA. Because D-nucleic acids have greater affinity for L-tryptophan due to stereochemistry, and because D-RNA/DNA+L-tryptophan complexes have an increased negative circular dichroism band between 230 and 270 nm, the homochirality of tryptophan can also be explained by this hypothesis. A numerical model is presented, demonstrating the efficacy of such a mechanism in procuring homochirality of RNA or DNA from an original racemic solution in as little as 270 Archean years. Full article

(This article belongs to the Special Issue The Origin of Chirality in Life (Chiral Symmetry Breaking))

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Circular dichroism of the 20 base pair oligo B-form duplex 3′-GCGGCGACTGGTGAGTACGC (M.W. 12,306 g mol−1) at neutral pH and room temperature taken from Figure 3a of [<a href="#B60-life-08-00021" class="html-bibr">60</a>] (black line with triangles). Circular dichroism of the 11 base pair hairpin B-form duplex 3′-TTTCGCGAAAT (M.W. 6839 g mol−1) (blue line with crosses, left y-scale) at neutral pH and room temperature adapted from Figure 5a of [<a href="#B61-life-08-00021" class="html-bibr">61</a>]. Circular dichroism of adenosine with tryptophan in the ratio 1:2 taken from Figure 3a of Arcaya et al. [<a href="#B62-life-08-00021" class="html-bibr">62</a>] (red line with circles: the CD spectrum for adenosine+tryptophan is plotted divided by 4 for convenience of scale. Arcaya et al. state that the CD spectrum of DNA+tryptophan is similar to the average of the CD spectra of the individual nucleosides with tryptophan [<a href="#B62-life-08-00021" class="html-bibr">62</a>]). Short oligo (25 bp) absorption spectrum taken from [<a href="#B47-life-08-00021" class="html-bibr">47</a>] normalized to a peak value of one (black dotted line, right y-scale). Note that, at wavelengths shorter than 220 nm, the absorption spectrum is not reliable due to the reduced output of the deuterium light used [<a href="#B47-life-08-00021" class="html-bibr">47</a>]. Solar Archean spectrum at Earth’s surface [<a href="#B40-life-08-00021" class="html-bibr">40</a>] normalized to a peak value of one (red dashed line, right y-scale). Full article ">Figure 2
Circular dichroism spectra of the 20 bp oligo 3′-GCGGCGACTGGTGAGTACGC, the 11 bp oligo 3′-TTTCGCGAAAT, and adenosine+tryptophan convoluted with a short oligo (25 bp) absorption spectrum and the wavelength-dependent intensity of the light reaching Earth’s surface during the Archean (see <a href="#life-08-00021-f001" class="html-fig">Figure 1</a>). Adenosine+tryptophan is plotted at 1/4 of its real amplitude for convenience of scale. The average CD values, integrated over the region 200 to 300 nm are −0.279, −1.06 and −13.37 (220 to 300 nm) for 3′-GCGGCGACTGGTGAGTACGC, 3′-TTTCGCGAAAT and adenosine+tryptophan respectively. Full article ">Figure 3
Chirality Ci as a function of the number of Archean days i for the two oligos and DNA+Tryptophan as calculated through Equation (<a href="#FD5-life-08-00021" class="html-disp-formula">5</a>). (a) The three smooth curves to the right were calculated assuming denaturation probability is simply proportional to the number of photons absorbed, but that complete denaturing occurs only in the afternoon, and a 5% excess of right-hand circularly polarized submarine light at the ocean surface during the afternoon. (b) These three curves to the left include in the calculation a stochastic photon absorption probability (±2% with respect to nominal values given by Equation (<a href="#FD2-life-08-00021" class="html-disp-formula">2</a>)) and an energy threshold for denaturation related to the complementary strand binding energy (see text). Full article ">

11 pages, 894 KiB

Open AccessTechnical Note

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R

by Dominic J. Bennett, Hannes Hettling, Daniele Silvestro, Alexander Zizka, Christine D. Bacon, Søren Faurby, Rutger A. Vos and Alexandre Antonelli

Life 2018, 8(2), 20; https://doi.org/10.3390/life8020020 - 5 Jun 2018

Cited by 23 | Viewed by 8805

Abstract

The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data [...] Read more.

The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate and test our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: Palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis. Full article

(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)

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The phylotaR pipeline identifies all sequences in GenBank associated with a user-specified taxonomic identity (a). The pipeline then performs all-vs.-all BLAST across all the sequences to identify orthologous clusters (b). These searches are constrained to run within taxonomic groups up to a user-determined limit (default 50,000 sequences and 100,000 nodes). To generate higher taxonomic level clusters, an additional BLAST search is performed of the most connected sequences within clusters (i.e., the seed sequences) from the lower-level clusters. The clusters of overlapping seed sequences are then merged into larger clusters (c). All clusters, merged and non-merged, are then reported for inspection by the user. For more details on the pipeline, see <a href="#app2-life-08-00020" class="html-app">Appendix A</a>. Full article ">Figure 2
Initiating the phylotaR pipeline in R for primates (TaxID: 9443). Full article ">Figure 3
Presence/absence of tribes and genera for palms (a) and primates (b), respectively, across the top ten best clusters. X-axis numbers are unique cluster Ids. For more details on each of these clusters, see <a href="#app1-life-08-00020" class="html-app">Tables S4a and S4b</a>. Full article ">Figure 4
Tribe- and genus-level trees for palms (a) and primates (b). Roots were determined manually by rooting with Strepsirrhini and Calamoideae for primates and palms respectively. Branch lengths have been removed. Support calculated from 100 rapid bootstraps: *** >0.95, ** >0.75 and * >0.50. Complete tree construction methods are in <a href="#app3-life-08-00020" class="html-app">Appendix B</a>. For tree comparisons with published trees for palms [<a href="#B37-life-08-00020" class="html-bibr">37</a>] and primates [<a href="#B38-life-08-00020" class="html-bibr">38</a>], see <a href="#app1-life-08-00020" class="html-app">Figures S4 and S5</a>. Full article ">

15 pages, 2410 KiB

Open AccessArticle

Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities

by Claudia Coleine, Laura Zucconi, Silvano Onofri, Nuttapon Pombubpa, Jason E. Stajich and Laura Selbmann

Life 2018, 8(2), 19; https://doi.org/10.3390/life8020019 - 2 Jun 2018

Cited by 36 | Viewed by 6496

Abstract

Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent [...] Read more.

Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors. Sandstone rocks were collected in Victoria Land, Antarctica along an altitudinal gradient from 834 to 3100 m a.s.l.; differently sun-exposed rocks were selected to test the influence of this parameter on endolithic settlement. Metabarcoding targeting the fungal internal transcribed spacer region 1 (ITS1) was used to catalogue the species found in these communities. Functional profile of guilds found in the samples was associated to species using FUNGuild and variation in functional groups compared across sunlight exposure and altitude. Results revealed clear dominance of lichenized and stress-tolerant fungi in endolithic communities. The main variations in composition and abundance of functional groups among sites correlated to sun exposure, but not to altitude. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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Localities visited in the McMurdo Dry Valleys (Southern Victoria Land), showing different sun exposition: (A,B) Battleship Promontory North and South, respectively; (C,D) University Valley North and South, respectively; (E,F) Siegfried Peak North and South, respectively; (G,H) Finger Mt. North and South, respectively. Full article ">Figure 2
Spearman’s correlation coefficients between fungal richness of each functional group along an altitudinal gradient. p > 0.05 in LIC, SAP and SAP + PP panels; p < 0.05 in RIF + BY panel. Full article ">Figure 3
Spearman’s correlation coefficients between fungal biodiversity (Shannon’s index) of each functional group along an altitudinal gradient. p > 0.05 in all four panels. Full article ">Figure 4
Non-metric multidimensional scaling (NMDS) ordination plots for each functional fungal group of Antarctic endolithic communities differently sun exposed (blue lines: south sun exposition; red lines: north sun exposition), based on square-root transformed abundance data. Full article ">Figure 5
Venn diagram of the four functional groups of fungi showing the distribution of OTUs between north and south exposition. The abbreviations represent functional groups. Both the percentages of OTUs that were shared and found exclusively in each sun exposure are indicated. Full article ">

31 pages, 1809 KiB

Open AccessReview

Data-Driven Astrochemistry: One Step Further within the Origin of Life Puzzle

by Alexander Ruf, Louis L. S. D’Hendecourt and Philippe Schmitt-Kopplin

Life 2018, 8(2), 18; https://doi.org/10.3390/life8020018 - 1 Jun 2018

Cited by 29 | Viewed by 10539

Abstract

Astrochemistry, meteoritics and chemical analytics represent a manifold scientific field, including various disciplines. In this review, clarifications on astrochemistry, comet chemistry, laboratory astrophysics and meteoritic research with respect to organic and metalorganic chemistry will be given. The seemingly large number of observed astrochemical [...] Read more.

Astrochemistry, meteoritics and chemical analytics represent a manifold scientific field, including various disciplines. In this review, clarifications on astrochemistry, comet chemistry, laboratory astrophysics and meteoritic research with respect to organic and metalorganic chemistry will be given. The seemingly large number of observed astrochemical molecules necessarily requires explanations on molecular complexity and chemical evolution, which will be discussed. Special emphasis should be placed on data-driven analytical methods including ultrahigh-resolving instruments and their interplay with quantum chemical computations. These methods enable remarkable insights into the complex chemical spaces that exist in meteorites and maximize the level of information on the huge astrochemical molecular diversity. In addition, they allow one to study even yet undescribed chemistry as the one involving organomagnesium compounds in meteorites. Both targeted and non-targeted analytical strategies will be explained and may touch upon epistemological problems. In addition, implications of (metal)organic matter toward prebiotic chemistry leading to the emergence of life will be discussed. The precise description of astrochemical organic and metalorganic matter as seeds for life and their interactions within various astrophysical environments may appear essential to further study questions regarding the emergence of life on a most fundamental level that is within the molecular world and its self-organization properties. Full article

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

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14 pages, 2928 KiB

Open AccessArticle

Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions

by David J. Martínez-Cano, Gil Bor, Andrés Moya and Luis Delaye

Life 2018, 8(2), 17; https://doi.org/10.3390/life8020017 - 29 May 2018

Cited by 3 | Viewed by 5068

Abstract

The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the [...] Read more.

The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola. We provide statistical evidence indicating pairs of genes in B. aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis. In contrast, pairs of genes in B. aphidicola not showing correlated gene loss tend to have orthologs in E. coli known to have aggravating epistasis. These results suggest that during the process of genome reduction in B. aphidicola by gene loss, positive or alleviating epistasis facilitates correlated gene losses while negative or aggravating epistasis impairs correlated gene losses. We interpret this as evidence that the reduced proteome of B. aphidicola contains less pathway redundancy and more compensatory interactions, mimicking the situation of E. coli when grown under environmental constrains. Full article

(This article belongs to the Special Issue Evolution of Mutualistic Symbiosis)

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Graphical abstract

15 pages, 2082 KiB

Open AccessArticle

Molecular Evolution in a Peptide-Vesicle System

by Christian Mayer, Ulrich Schreiber, María J. Dávila, Oliver J. Schmitz, Amela Bronja, Martin Meyer, Julia Klein and Sven W. Meckelmann

Life 2018, 8(2), 16; https://doi.org/10.3390/life8020016 - 24 May 2018

Cited by 31 | Viewed by 14259

Abstract

Based on a new model of a possible origin of life, we propose an efficient and stable system undergoing structural reproduction, self-optimization, and molecular evolution. This system is being formed under realistic conditions by the interaction of two cyclic processes, one of which [...] Read more.

Based on a new model of a possible origin of life, we propose an efficient and stable system undergoing structural reproduction, self-optimization, and molecular evolution. This system is being formed under realistic conditions by the interaction of two cyclic processes, one of which offers vesicles as the structural environment, with the other supplying peptides from a variety of amino acids as versatile building blocks. We demonstrate that structures growing in a combination of both cycles have the potential to support their own existence, to undergo chemical and structural evolution, and to develop unpredicted functional properties. The key mechanism is the mutual stabilization of the peptides by the vesicles and of the vesicles by the peptides together with a constant production and selection of both. The development of the proposed system over time would not only represent one of the principles of life, but could also be a model for the formation of self-evolving structures ultimately leading to the first living cell. The experiment yields clear evidence for a vesicle-induced accumulation of membrane-interacting peptide which could be identified by liquid chromatography combined with high-resolution mass spectroscopy. We found that the selected peptide has an immediate effect on the vesicles, leading to (i) reduced vesicle size, (ii) increased vesicle membrane permeability, and (iii) improved thermal vesicle stability. Full article

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

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14 pages, 1065 KiB

Open AccessReview

Fungal Diversity in Lichens: From Extremotolerance to Interactions with Algae

by Lucia Muggia and Martin Grube

Life 2018, 8(2), 15; https://doi.org/10.3390/life8020015 - 22 May 2018

Cited by 73 | Viewed by 13147

Abstract

Lichen symbioses develop long-living thallus structures even in the harshest environments on Earth. These structures are also habitats for many other microscopic organisms, including other fungi, which vary in their specificity and interaction with the whole symbiotic system. This contribution reviews the recent [...] Read more.

Lichen symbioses develop long-living thallus structures even in the harshest environments on Earth. These structures are also habitats for many other microscopic organisms, including other fungi, which vary in their specificity and interaction with the whole symbiotic system. This contribution reviews the recent progress regarding the understanding of the lichen-inhabiting fungi that are achieved by multiphasic approaches (culturing, microscopy, and sequencing). The lichen mycobiome comprises a more or less specific pool of species that can develop symptoms on their hosts, a generalist environmental pool, and a pool of transient species. Typically, the fungal classes Dothideomycetes, Eurotiomycetes, Leotiomycetes, Sordariomycetes, and Tremellomycetes predominate the associated fungal communities. While symptomatic lichenicolous fungi belong to lichen-forming lineages, many of the other fungi that are found have close relatives that are known from different ecological niches, including both plant and animal pathogens, and rock colonizers. A significant fraction of yet unnamed melanized (‘black’) fungi belong to the classes Chaethothyriomycetes and Dothideomycetes. These lineages tolerate the stressful conditions and harsh environments that affect their hosts, and therefore are interpreted as extremotolerant fungi. Some of these taxa can also form lichen-like associations with the algae of the lichen system when they are enforced to symbiosis by co-culturing assays. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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21 pages, 3709 KiB

Open AccessReview

Insights into Abiotically-Generated Amino Acid Enantiomeric Excesses Found in Meteorites

by Aaron S. Burton and Eve L. Berger

Life 2018, 8(2), 14; https://doi.org/10.3390/life8020014 - 12 May 2018

Cited by 43 | Viewed by 10793

Abstract

Biology exhibits homochirality, in that only one of two possible molecular configurations (called enantiomers) is used in both proteins and nucleic acids. The origin of this phenomenon is currently unknown, as nearly all known abiotic mechanisms for generating these compounds result in equal [...] Read more.

Biology exhibits homochirality, in that only one of two possible molecular configurations (called enantiomers) is used in both proteins and nucleic acids. The origin of this phenomenon is currently unknown, as nearly all known abiotic mechanisms for generating these compounds result in equal (racemic) mixtures of both enantiomers. However, analyses of primitive meteorites have revealed that a number of amino acids of extraterrestrial origin are present in enantiomeric excess, suggesting that there was an abiotic route to synthesize amino acids in a non-racemic manner. Here we review the amino acid contents of a range of meteorites, describe mechanisms for amino acid formation and their potential to produce amino acid enantiomeric excesses, and identify processes that could have amplified enantiomeric excesses. Full article

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

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15 pages, 3249 KiB

Open AccessArticle

Caveats to Exogenous Organic Delivery from Ablation, Dilution, and Thermal Degradation

by Chris Mehta, Anthony Perez, Glenn Thompson and Matthew A. Pasek

Life 2018, 8(2), 13; https://doi.org/10.3390/life8020013 - 12 May 2018

Cited by 16 | Viewed by 5441

Abstract

A hypothesis in prebiotic chemistry argues that organics were delivered to the early Earth in abundance by meteoritic sources. This study tests that hypothesis by measuring how the transfer of organic matter to the surface of Earth is affected by energy-dissipation processes such [...] Read more.

A hypothesis in prebiotic chemistry argues that organics were delivered to the early Earth in abundance by meteoritic sources. This study tests that hypothesis by measuring how the transfer of organic matter to the surface of Earth is affected by energy-dissipation processes such as ablation and airbursts. Exogenous delivery has been relied upon as a source of primordial material, but it must stand to reason that other avenues (i.e., hydrothermal vents, electric discharge) played a bigger role in the formation of life as we know it on Earth if exogenous material was unable to deliver significant quantities of organics. For this study, we look at various properties of meteors such as initial velocity and mass of the object, and atmospheric composition to see how meteors with different initial velocities and masses ablate. We find that large meteors do not slow down fast enough and thus impact the surface, vaporizing their components; fast meteors with low masses are vaporized during entry; and meteors with low velocities and high initial masses reach the surface. For those objects that survive to reach the surface, about 60 to >99% of the mass is lost by ablation. Large meteors that fragment are also shown to spread out over increasingly larger areas with increasing mass, and small meteors (~1 mm) are subjected to intense thermal heating, potentially degrading intrinsic organics. These findings are generally true across most atmospheric compositions. These findings provide several caveats to extraterrestrial delivery models that—while a viable point source of organics—likely did not supply as much prebiotic material as an effective endogenous production route. Full article

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

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The final mass of a meteorite vs. its initial mass and velocity, under present atmospheric conditions. Normalized mass is the final mass of the object divided by its initial mass. Full article ">Figure 2
As per <a href="#life-08-00013-f001" class="html-fig">Figure 1</a>, for a thin N2 atmosphere (0.5 atm at the surface). Full article ">Figure 3
As per <a href="#life-08-00013-f001" class="html-fig">Figure 1</a>, with a CO2 atmosphere (3 atm at the surface). Full article ">Figure 4
Relationship between the total mass of a single meteorite recovered, and the area over which all the fragments were recovered (the strewn field). The regression line has a slope of log A = 1.25 log M − 0.23 (R2 = 0.47) where A is the radial area and M is the mass. This is not to say that the mass is the direct control on strewn field area, as other factors (angle of entry, meteoroid structural integrity prior to entry) likely play as large of roles in strewn field sizes. Some of this information is not known for these strewn fields as many are meteorite finds. However, that there is a relationship between mass and area is suggestive that the mass controls a portion of the area over which a meteorite is distributed. Full article ">Figure 5
T-t-r (Temperature, time and radius) profile predicted for meteors in contact with a 1000 K surface. This model assumes a total meteor radius of 1 mm, and the dashed lines provide the temperature from the center (0 mm) to the exterior (1 mm) as a function of time. Full article ">Figure 6
The timescale it takes to degrade valine as a function of temperature. The black line is the time required to degrade 50% of the material (a chemical half life), and the red line corresponds to the time required to degrade 99% of the valine. Full article ">Figure 7
Schematic showing that higher velocity objects may vaporize as they travel through the atmosphere, and larger objects vaporize when they impact the surface. Full article ">

22 pages, 1845 KiB

Open AccessArticle

Comet Pond II: Synergistic Intersection of Concentrated Extraterrestrial Materials and Planetary Environments to Form Procreative Darwinian Ponds

by Benton C. Clark and Vera M. Kolb

Life 2018, 8(2), 12; https://doi.org/10.3390/life8020012 - 11 May 2018

Cited by 12 | Viewed by 5918

Abstract

In the “comet pond” model, a rare combination of circumstances enables the entry and landing of pristine organic material onto a planetary surface with the creation of a pond by a soft impact and melting of entrained ices. Formation of the constituents of [...] Read more.

In the “comet pond” model, a rare combination of circumstances enables the entry and landing of pristine organic material onto a planetary surface with the creation of a pond by a soft impact and melting of entrained ices. Formation of the constituents of the comet in the cold interstellar medium and our circumstellar disk results in multiple constituents at disequilibrium which undergo rapid chemical reactions in the warmer, liquid environment. The planetary surface also provides minerals and atmospheric gases which chemically interact with the pond’s organic- and trace-element-rich constituents. Pond physical morphology and the heterogeneities imposed by gravitational forces (bottom sludge; surface scum) and weather result in a highly heterogeneous variety of macro- and microenvironments. Wet/dry, freeze/thaw, and natural chromatography processes further promote certain reaction sequences. Evaporation concentrates organics less volatile than water. Freezing concentrates all soluble organics into a residual liquid phase, including CH₃OH, HCN, etc. The pond’s evolutionary processes culminate in the creation of a Macrobiont with the metabolically equivalent capabilities of energy transduction and replication of RNA (or its progenitor informational macromolecule), from which smaller organisms can emerge. Planet-wide dispersal of microorganisms is achieved through wind transport, groundwater, and/or spillover from the pond into surface hydrologic networks. Full article

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

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A cometary nucleus or primitive carbonaceous planetoid accomplishes a rare entry event which allows the survival of pristine organic material and ices upon landing on the surface of a planetary body, such as Earth. (Credit: Lockheed Martin). Full article ">Figure 2
Following a relatively low-velocity landing, the ices melt to form a pond with a residual organic-rich central mound as well as bottom sludge, plus liquid with solutes and colloidal particulates, and surface scum. The pond interacts with surface minerals and atmospheric gases to create ideal conditions for diverse prebiotic syntheses. (credit: Lockheed Martin). Full article ">Figure 3
Comet pond phases (a) Schematic of early pond configuration, with satellite pond (s). (b) Gravitational force results in floating scum and sunken sludge (graded bed). (c) In a hot dry climate, evaporation will precipitate salts and form hydrogels. (d) In a cold climate, or at night, ice forms and freeze/thaw cycling can occur. (e) The Macrobiont forms (a consortium of living entities, see text). (f) Escape from the pond can occur via multiple paths, into the air or planetary hydrological network. Full article ">Figure 3 Cont.
Comet pond phases (a) Schematic of early pond configuration, with satellite pond (s). (b) Gravitational force results in floating scum and sunken sludge (graded bed). (c) In a hot dry climate, evaporation will precipitate salts and form hydrogels. (d) In a cold climate, or at night, ice forms and freeze/thaw cycling can occur. (e) The Macrobiont forms (a consortium of living entities, see text). (f) Escape from the pond can occur via multiple paths, into the air or planetary hydrological network. Full article ">

15 pages, 5358 KiB

Open AccessArticle

Amphiphilic Compounds Assemble into Membranous Vesicles in Hydrothermal Hot Spring Water but Not in Seawater

by Daniel Milshteyn, Bruce Damer, Jeff Havig and David Deamer

Life 2018, 8(2), 11; https://doi.org/10.3390/life8020011 - 10 May 2018

Cited by 60 | Viewed by 9305

Abstract

There is a general assumption that amphiphilic compounds, such as fatty acids, readily form membranous vesicles when dispersed in aqueous phases. However, from earlier studies, it is known that vesicle stability depends strongly on pH, temperature, chain length, ionic concentration and the presence [...] Read more.

There is a general assumption that amphiphilic compounds, such as fatty acids, readily form membranous vesicles when dispersed in aqueous phases. However, from earlier studies, it is known that vesicle stability depends strongly on pH, temperature, chain length, ionic concentration and the presence or absence of divalent cations. To test how robust simple amphiphilic compounds are in terms of their ability to assemble into stable vesicles, we chose to study 10- and 12-carbon monocarboxylic acids and a mixture of the latter with its monoglyceride. These were dispersed in hydrothermal water samples drawn directly from hot springs in Yellowstone National Park at two pH ranges, and the results were compared with sea water under the same conditions. We found that the pure acids could form membranous vesicles in hydrothermal pool water, but that a mixture of dodecanoic acid and glycerol monododecanoate was less temperature-sensitive and assembled into relatively stable membranes at both acidic and alkaline pH ranges. Furthermore, the vesicles were able to encapsulate nucleic acids and pyranine, a fluorescent anionic dye. None of the amphiphiles that were tested formed stable vesicles in sea water because the high ionic concentrations disrupted membrane stability. Full article

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

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19 pages, 2429 KiB

Open AccessReview

Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research

by Richard J. Gillams and Tony Z. Jia

Life 2018, 8(2), 10; https://doi.org/10.3390/life8020010 - 8 May 2018

Cited by 30 | Viewed by 8171

Abstract

An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers [...] Read more.

An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers. Full article

(This article belongs to the Special Issue Water–Rock Interactions and Life)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
The snapshot time step from molecular dynamics simulations of ethanol layer assembly (into two distinct layers: a thin, ordered monolayer with the thickness of exactly one ethanol molecule, and a second larger less-ordered layer above the monolayer, separated by a gap) on a calcite surface, along with the ethanol spatial density profile associated with it. Reprinted with permission from Pasarín, I. S., Yang, M., Bovet, N., Glyvradal, M., Nielsen, M. M., Bohr, J., Feidenhans’l, R., and Stipp, S. L. S. 2012. “Molecular Ordering of Ethanol at the Calcite Surface.” Langmuir 28 (5):2545–50. [<a href="#B45-life-08-00010" class="html-bibr">45</a>] Copyright 2011 American Chemical Society. Full article ">Figure 2
Atomic force microscope images of a structured DNA microarray self-assembled on a mica (general) surface. Reprinted with permission from Sun, X., Ko, S. H., Zhang, C., Ribbe, A. E., and Mao, C., 2009. “Surface-Mediated DNA Self-Assembly.” J. Am. Chem. Soc. 131 (37):13248-9. [<a href="#B80-life-08-00010" class="html-bibr">80</a>] Copyright 2009 American Chemical Society. Full article ">Figure 3
Atomic force microscope images of the assembly dynamics of SMA (an amyloidogenic light chain variable domain peptide with 114 residues) nanofibrils on a mica surface over time (A–E) show 12–16 h of incubation with image size of 1 µm × 1 µm, while (F) shows 6 days of incubation with image size of 5 µm × 5 µm). It appears that longer incubation times result in longer nanofibrils, such as in (F), as compared to shorter incubation times, such as in (A–E). Reprinted with permission from Zhu, M., Souillac, P. O., Ionescu-Zanetti, C., Carter, S. A., and Fink, A. L. 2002. “Surface-catalyzed Amyloid Fibril Formation.” J. Biol. Chem. 277(52):50914-22. [<a href="#B112-life-08-00010" class="html-bibr">112</a>] Copyright 2002 American Society for Biochemistry and Molecular Biology. Full article ">Figure 4
Transmission electron microscope images of calcium carbonate minerals at different nutrient concentrations and incubation times grown on a self-assembled short peptide nanostructure (Ac-VHVEVS-CONH2), suggesting that mineral growth can be effected by simple peptide self-assemblies. Reprinted with permission from Murai, K., Kinoshita, T., Nagata, K., and Higuchi, M. 2016. “Mineralization of Calcium Carbonate on Multifunctional Peptide Assembly Acting as Mineral Source Supplier and Template.” Langmuir 32 (36):9351–59. [<a href="#B157-life-08-00010" class="html-bibr">157</a>] Copyright 2016 American Chemical Society. Full article ">Figure 5
Synergistic cyclical model of mineral-templated self-assembling systems promoting mineralization. Simple precursors of biomolecules adsorbed onto a mineral surface react and produce biomolecules such as nucleotides or amino acids. Then, some of these adsorbed molecules polymerize into polymers (such as peptides or nucleic acids). Given the optimal conditions and mineral surfaces, biopolymers produced then self-assemble into supramolecular structures such as amyloid fibers or primitive nucleic acid “origamis”. Although not shown in the figure, at any stage in the adsorption, polymerization, and self-assembly pathway (which are all reversible reactions), each molecule can also desorb off of the mineral surface. However, certain self-assembled supramolecular structures (whether on or off the mineral surface) have the ability to promote the formation of new minerals, such as peptide nanostructures catalyzing the formation of hydroxyapatite, similar to modern-day biomineralization processes. The newly produced mineral surfaces could then catalyze and template the synthesis, polymerization, and/or assembly of the same structures that allowed its own mineralization, leading to a synergistic cyclical positive feedback loop by which primitive self-assemblies could have affected the mineral composition of early Earth, and vice-versa. Full article ">

15 pages, 16733 KiB

Open AccessArticle

Cystobasidium alpinum sp. nov. and Rhodosporidiobolus oreadorum sp. nov. from European Cold Environments and Arctic Region

by Benedetta Turchetti, Laura Selbmann, Nina Gunde-Cimerman, Pietro Buzzini, José Paulo Sampaio and Polona Zalar

Life 2018, 8(2), 9; https://doi.org/10.3390/life8020009 - 5 May 2018

Cited by 17 | Viewed by 7020

Abstract

Over 80% of the Earth’s environments are permanently or periodically exposed to temperatures below 5 °C. Cold habitats harbour a wide diversity of psychrophilic and psychrotolerant yeasts. During ecological studies of yeast communities carried out in cold ecosystem in the Italian Alps, Svalbard [...] Read more.

Over 80% of the Earth’s environments are permanently or periodically exposed to temperatures below 5 °C. Cold habitats harbour a wide diversity of psychrophilic and psychrotolerant yeasts. During ecological studies of yeast communities carried out in cold ecosystem in the Italian Alps, Svalbard (Norway, Arctic region), and Portugal, 23 yeast strains that could not be assigned to any known fungal taxa were isolated. In particular, two of them were first identified as Rhodotorula sp., showing the highest degree of D1/D2 sequence identity with Cystobasidum laryngis accounted to only 97% with the type strain (C. laryngis CBS 2221). The other 21 strains, exhibiting identical D1/D2 sequences, had low identity (97%) with Rhodosporidiobolus lusitaniae and Rhodosporidiobolus colostri. Similarly, ITS sequences of the type strains of the most closely related species (93–94%). In a 2-genes multilocus D1/D2 and ITS ML phylogenetic tree, the studied strains pooled in two well separated and supported groups. In order to classify the new 23 isolates based on phylogenetic evidences, we propose the description of two novel species Cystobasidium alpinum sp. nov. and Rhodosporidiobolus oreadorum sp. nov. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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