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9 pages, 2361 KiB

Open AccessArticle

Prebiotic Route to Thymine from Formamide—A Combined Experimental–Theoretical Study

by Lukáš Petera, Klaudia Mrazikova, Lukas Nejdl, Kristyna Zemankova, Marketa Vaculovicova, Adam Pastorek, Svatopluk Civis, Petr Kubelik, Alan Heays, Giuseppe Cassone, Jiri Sponer, Martin Ferus and Judit Sponer

Molecules 2021, 26(8), 2248; https://doi.org/10.3390/molecules26082248 - 13 Apr 2021

Cited by 1 | Viewed by 2919

Abstract

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to [...] Read more.

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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18 pages, 25100 KiB

Open AccessArticle

Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo

by Federica De Lise, Roberta Iacono, Andrea Strazzulli, Rosa Giglio, Nicola Curci, Luisa Maurelli, Rosario Avino, Antonio Carandente, Stefano Caliro, Alessandra Tortora, Fabio Lorenzini, Paola Di Donato, Marco Moracci and Beatrice Cobucci-Ponzano

Molecules 2021, 26(7), 1861; https://doi.org/10.3390/molecules26071861 - 25 Mar 2021

Cited by 3 | Viewed by 2516

Abstract

Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed “recoding”. In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and [...] Read more.

Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed “recoding”. In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for −1 programmed frameshifting that allow the expression of a fully functional α-l-fucosidase in the crenarchaeon Saccharolobus solfataricus, in which several functional interrupted genes have been identified. Increasing evidence suggests that the flexibility of the genetic code decoding could provide an evolutionary advantage in extreme conditions, therefore, the identification and study of interrupted genes in extremophilic Archaea could be important from an astrobiological point of view, providing new information on the origin and evolution of the genetic code and on the limits of life on Earth. In order to shed some light on the mechanism of programmed −1 frameshifting in Archaea, here we report, for the first time, on the analysis of the transcription of this recoded archaeal α-l-fucosidase and of its full-length mutant in different growth conditions in vivo. We found that only the wild type mRNA significantly increased in S. solfataricus after cold shock and in cells grown in minimal medium containing hydrolyzed xyloglucan as carbon source. Our results indicated that the increased level of fucA mRNA cannot be explained by transcript up-regulation alone. A different mechanism related to translation efficiency is discussed. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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12 pages, 3543 KiB

Open AccessArticle

Shock Processing of Amino Acids Leading to Complex Structures—Implications to the Origin of Life

by Surendra V. Singh, Jayaram Vishakantaiah, Jaya K. Meka, Vijayan Sivaprahasam, Vijayanand Chandrasekaran, Rebecca Thombre, Vijay Thiruvenkatam, Ambresh Mallya, Balabhadrapatruni N. Rajasekhar, Mariyappan Muruganantham, Akshay Datey, Hugh Hill, Anil Bhardwaj, Gopalan Jagadeesh, Kalidevapura P. J. Reddy, Nigel J. Mason and Bhalamurugan Sivaraman

Molecules 2020, 25(23), 5634; https://doi.org/10.3390/molecules25235634 - 30 Nov 2020

Cited by 17 | Viewed by 4348

Abstract

The building blocks of life, amino acids, are believed to have been synthesized in the extreme conditions that prevail in space, starting from simple molecules containing hydrogen, carbon, oxygen and nitrogen. However, the fate and role of amino acids when they are subjected [...] Read more.

The building blocks of life, amino acids, are believed to have been synthesized in the extreme conditions that prevail in space, starting from simple molecules containing hydrogen, carbon, oxygen and nitrogen. However, the fate and role of amino acids when they are subjected to similar processes largely remain unexplored. Here we report, for the first time, that shock processed amino acids tend to form complex agglomerate structures. Such structures are formed on timescales of about 2 ms due to impact induced shock heating and subsequent cooling. This discovery suggests that the building blocks of life could have self-assembled not just on Earth but on other planetary bodies as a result of impact events. Our study also provides further experimental evidence for the ‘threads’ observed in meteorites being due to assemblages of (bio)molecules arising from impact-induced shocks. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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23 pages, 8252 KiB

Open AccessFeature PaperArticle

Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia

by Roberta Iacono, Beatrice Cobucci-Ponzano, Federica De Lise, Nicola Curci, Luisa Maurelli, Marco Moracci and Andrea Strazzulli

Molecules 2020, 25(17), 4023; https://doi.org/10.3390/molecules25174023 - 3 Sep 2020

Cited by 13 | Viewed by 3880

Abstract

Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which [...] Read more.

Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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20 pages, 4720 KiB

Open AccessFeature PaperArticle

The Role of State-of-the-Art Quantum-Chemical Calculations in Astrochemistry: Formation Route and Spectroscopy of Ethanimine as a Paradigmatic Case

by Carmen Baiano, Jacopo Lupi, Nicola Tasinato, Cristina Puzzarini and Vincenzo Barone

Molecules 2020, 25(12), 2873; https://doi.org/10.3390/molecules25122873 - 22 Jun 2020

Cited by 22 | Viewed by 4615

Abstract

The gas-phase formation and spectroscopic characteristics of ethanimine have been re-investigated as a paradigmatic case illustrating the accuracy of state-of-the-art quantum-chemical (QC) methodologies in the field of astrochemistry. According to our computations, the reaction between the amidogen, NH, and ethyl, C₂H [...] Read more.

The gas-phase formation and spectroscopic characteristics of ethanimine have been re-investigated as a paradigmatic case illustrating the accuracy of state-of-the-art quantum-chemical (QC) methodologies in the field of astrochemistry. According to our computations, the reaction between the amidogen, NH, and ethyl, C₂H₅, radicals is very fast, close to the gas-kinetics limit. Although the main reaction channel under conditions typical of the interstellar medium leads to methanimine and the methyl radical, the predicted amount of the two E,Z stereoisomers of ethanimine is around 10%. State-of-the-art QC and kinetic models lead to a [E−CH₃CHNH]/[Z−CH₃CHNH] ratio of ca. 1.4, slightly higher than the previous computations, but still far from the value determined from astronomical observations (ca. 3). An accurate computational characterization of the molecular structure, energetics, and spectroscopic properties of the E and Z isomers of ethanimine combined with millimeter-wave measurements up to 300 GHz, allows for predicting the rotational spectrum of both isomers up to 500 GHz, thus opening the way toward new astronomical observations. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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11 pages, 1731 KiB

Open AccessArticle

Monitoring the Reactivity of Formamide on Amorphous SiO₂ by In-Situ UV-Raman Spectroscopy and DFT Modeling

by Matteo Signorile, Stefano Pantaleone, Nadia Balucani, Francesca Bonino, Gianmario Martra and Piero Ugliengo

Molecules 2020, 25(10), 2274; https://doi.org/10.3390/molecules25102274 - 12 May 2020

Cited by 5 | Viewed by 4155

Abstract

Formamide has been recognized in the literature as a key species in the formation of the complex molecules of life, such as nucleobases. Furthermore, several studies reported the impact of mineral phases as catalysts for its decomposition/polymerization processes, increasing the conversion and also [...] Read more.

Formamide has been recognized in the literature as a key species in the formation of the complex molecules of life, such as nucleobases. Furthermore, several studies reported the impact of mineral phases as catalysts for its decomposition/polymerization processes, increasing the conversion and also favoring the formation of specific products. Despite the progresses in the field, in situ studies on these mineral-catalyzed processes are missing. In this work, we present an in situ UV-Raman characterization of the chemical evolution of formamide over amorphous SiO₂ samples, selected as a prototype of silicate minerals. The experiments were carried out after reaction of formamide at 160 °C on amorphous SiO₂ (Aerosil OX50) either pristine or pre-calcined at 450 °C, to remove a large fraction of surface silanol groups. Our measurements, interpreted on the basis of density functional B3LYP-D3 calculations, allow to assign the spectra bands in terms of specific complex organic molecules, namely, diaminomaleonitrile (DAMN), 5-aminoimidazole (AI), and purine, showing the role of the mineral surface on the formation of relevant prebiotic molecules. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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Review

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14 pages, 950 KiB

Open AccessReview

Gravitational Influence on Human Living Systems and the Evolution of Species on Earth

by Konstantinos Adamopoulos, Dimitrios Koutsouris, Apostolos Zaravinos and George I. Lambrou

Molecules 2021, 26(9), 2784; https://doi.org/10.3390/molecules26092784 - 8 May 2021

Cited by 21 | Viewed by 4914

Abstract

Gravity constituted the only constant environmental parameter, during the evolutionary period of living matter on Earth. However, whether gravity has affected the evolution of species, and its impact is still ongoing. The topic has not been investigated in depth, as this would require [...] Read more.

Gravity constituted the only constant environmental parameter, during the evolutionary period of living matter on Earth. However, whether gravity has affected the evolution of species, and its impact is still ongoing. The topic has not been investigated in depth, as this would require frequent and long-term experimentations in space or an environment of altered gravity. In addition, each organism should be studied throughout numerous generations to determine the profound biological changes in evolution. Here, we review the significant abnormalities presented in the cardiovascular, immune, vestibular and musculoskeletal systems, due to altered gravity conditions. We also review the impact that gravity played in the anatomy of snakes and amphibians, during their evolution. Overall, it appears that gravity does not only curve the space–time continuum but the biological continuum, as well. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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18 pages, 3053 KiB

Open AccessReview

On the Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters Since the Prebiotic World

by Patrizio Campitelli and Marcello Crucianelli

Molecules 2020, 25(13), 3073; https://doi.org/10.3390/molecules25133073 - 6 Jul 2020

Cited by 3 | Viewed by 2920

Abstract

For a long time the biological role of vanadium was not known, while now the possibility of using its derivatives as potential therapeutic agents has given rise to investigations on their probable side effects. Vanadium compounds may inhibit different biochemical processes and lead [...] Read more.

For a long time the biological role of vanadium was not known, while now the possibility of using its derivatives as potential therapeutic agents has given rise to investigations on their probable side effects. Vanadium compounds may inhibit different biochemical processes and lead to a variety of toxic effects and serious diseases. But, on the other hand, vanadium is an essential element for life. In recent years, increasing evidence has been acquired on the possible roles of vanadium in the higher forms of life. Despite several biochemical and physiological functions that have been suggested for vanadium and notwithstanding the amount of the knowledge so far accumulated, it still does not have a clearly defined role in the higher forms of life. What functions could vanadium or its very stable oxidovanadium(IV) derivatives have had in the prebiotic world and in the origins of life? In this review, we have briefly tried to highlight the most useful aspects that can be taken into consideration to give an answer to this still unresolved question and to show the high versatility of the oxidovanadium(IV) group to act as promoter of several oxidation reactions when coordinated with a variety of ligands, including diketones like acylpyrazolones. Full article

(This article belongs to the Special Issue From Molecules to Origin of Life: The Astrobiology Network)

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