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OUP accepted manuscript. Metallomics 2022; 14:6549566. [DOI: 10.1093/mtomcs/mfac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
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Abstract
The efficient use of natural resources is essential for the planet’s sustainability and ensuring food security. Colombia’s large availability of water resources in combination with its climatic characteristics allows for the development of many microalgae species. The use of microalgae can potentially contribute to sustainable production in support of the agri-food sector. The nutritional composition (proteins, carbohydrates, fatty acids, vitamins, pigments, and antioxidants) of microalgae along with the ease of producing high biomass yields make them an excellent choice for human and animal nutrition and agriculture. Several species of microalgae have been studied seeking to develop food supplements for pigs, ruminants, poultry, fish, crustaceans, rabbits, and even bees. Important benefits to animal health, production, and improved bromatological and organoleptic characteristics of milk, meat, and eggs have been observed. Based on the functional properties of some microalgae species, foods and supplements have also been developed for human nutrition. Moreover, because microalgae contain essential nutrients, they can be utilized as biofertilizers by replacing chemical fertilizers, which are detrimental to the environment. In view of the above, the study of microalgae is a promising research area for the development of biotechnology and bioeconomy in Colombia.
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Osumah A, Krishnamurthy R. Diamidophosphate (DAP): A Plausible Prebiotic Phosphorylating Reagent with a Chem to BioChem Potential? Chembiochem 2021; 22:3001-3009. [PMID: 34289217 PMCID: PMC8589086 DOI: 10.1002/cbic.202100274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/20/2021] [Indexed: 11/11/2022]
Abstract
Known since the 1890s, diamidophosphate (DAP) has been investigated within the context of its inorganic chemistry. In 1999 - with the demonstration of DAP's potential as a phosphorylating agent of sugars in aqueous medium - began the exciting phase of research about DAP's role as a plausible prebiotic phosphorylating agent. More recently, in the last five years, there has been a steady increase in the publications that have documented the surprising versatility of DAP enabling the emergence of many classes of biomolecules of life, such as nucleic acids, peptides and protocells. Thus, though in its infancy, DAP seems to be uniquely positioned to play a central role in modelling abiotic- to prebiotic-chemical evolution. In this context, there is a need for systematic investigations for: (a) establishing DAP's likely availability on the early Earth, and (b) developing DAP's potential as a tool for use in synthetic and bioorganic chemistry.
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Affiliation(s)
- Abdulakeem Osumah
- Department of ChemistryThe Scripps Research Institute10550 North Torrey Pines RdLa JollaCA 92037USA
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54
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Boros E, Takács A, Dobosy P, Vörös L. Extreme guanotrophication by phosphorus in contradiction with the productivity of alkaline soda pan ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148300. [PMID: 34174614 DOI: 10.1016/j.scitotenv.2021.148300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Waterbirds as nutrient vectors can cause high phosphorus loading in shallow inland aquatic ecosystems. The main goal of this study was to determine the causal relationships between the characteristic physico-chemical properties of intermittent (temporary) alkaline soda pan (playa) ecosystems and specific (surface and volume-related) P loading of waterbirds by in situ field investigation, estimation as well as laboratory experiments using standard methods. In addition, our aim was to estimate the contribution of groundwater and precipitation to the total phosphorus pool of soda pans in Hungary. The estimated high specific external P loading of waterbirds (mean: 185 mg P/m2/y, 3.32 mg P/L/year) can explain the majority of the hypertrophic TP pool (mean: 5.17 mg/L, 64%) in soda pans, which is mediated by large-bodied herbivorous (e.g. geese and ducks) and medium-bodied omnivorous (e.g. gulls) waterbirds, who are important external nutrient importers and major phosphorus source. The results also confirm the hypothesis that groundwater (3%) and precipitation (5%) together account for a smaller estimated (8% in this study) contribution to the hypertrophic TP pool in soda pans, while the contribution of waterbirds (64% in this study) to the TP is much higher (64-100%). In this study, the remaining part of TP (maximum 28%) pool can be explained by internal P sources. Soda pans are characterized by physical and chemical characteristics coupled with high densities of waterbirds, as biotic mediators of external P sources, which together cause the maintenance of high concentrations of P-forms. The extreme guanotrophication by high P loading of herbivorous waterbirds causing a hypertrophic state is in contradiction with the limited primary production of natural soda pans. This unique phenomenon can be explained by the multiple impact of prevailing extreme physico-chemical drivers (intermittent hydrological cycle, shallow water depth, high turbidity, salinity, alkalinity) and by the specific nutrient cycle of these alkaline soda ecosystems.
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Affiliation(s)
- Emil Boros
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina str. 29., H-1113 Budapest, Hungary.
| | - Anita Takács
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina str. 29., H-1113 Budapest, Hungary
| | - Péter Dobosy
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina str. 29., H-1113 Budapest, Hungary
| | - Lajos Vörös
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3. P.O. Box 35, H-8237 Tihany, Hungary
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55
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Liu Z, Wu LF, Kufner CL, Sasselov DD, Fischer WW, Sutherland JD. Prebiotic photoredox synthesis from carbon dioxide and sulfite. Nat Chem 2021; 13:1126-1132. [PMID: 34635812 PMCID: PMC7611910 DOI: 10.1038/s41557-021-00789-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Carbon dioxide (CO2) is the major carbonaceous component of many planetary atmospheres, which includes the Earth throughout its history. Carbon fixation chemistry-which reduces CO2 to organics, utilizing hydrogen as the stoichiometric reductant-usually requires high pressures and temperatures, and the yields of products of potential use to nascent biology are low. Here we demonstrate an efficient ultraviolet photoredox chemistry between CO2 and sulfite that generates organics and sulfate. The chemistry is initiated by electron photodetachment from sulfite to give sulfite radicals and hydrated electrons, which reduce CO2 to its radical anion. A network of reactions that generates citrate, malate, succinate and tartrate by irradiation of glycolate in the presence of sulfite was also revealed. The simplicity of this carboxysulfitic chemistry and the widespread occurrence and abundance of its feedstocks suggest that it could have readily taken place on the surfaces of rocky planets. The availability of the carboxylate products on early Earth could have driven the development of central carbon metabolism before the advent of biological CO2 fixation.
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Affiliation(s)
- Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Long-Fei Wu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Corinna L Kufner
- Harvard-Smithsonian Center for Astrophysics, Massachusetts, MA, USA
| | | | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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56
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Maguire OR, Smokers IBA, Huck WTS. A physicochemical orthophosphate cycle via a kinetically stable thermodynamically activated intermediate enables mild prebiotic phosphorylations. Nat Commun 2021; 12:5517. [PMID: 34535651 PMCID: PMC8448844 DOI: 10.1038/s41467-021-25555-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/18/2021] [Indexed: 12/02/2022] Open
Abstract
The incorporation of orthophosphate from scarce geochemical sources into the organic compounds essential for life under mild conditions is a fundamental challenge for prebiotic chemistry. Here we report a prebiotic system capable of overcoming this challenge by taking inspiration from extant life's recycling of orthophosphate via its conversion into kinetically stable thermodynamically activated (KSTA) nucleotide triphosphates (e.g. ATP). We separate the activation of orthophosphate from its transfer to organic compounds by, crucially, first accumulating a KSTA phosphoramidate. We use cyanate to activate orthophosphate in aqueous solution under mild conditions and then react it with imidazole to accumulate the KSTA imidazole phosphate. In a paste, imidazole phosphate phosphorylates all the essential building blocks of life. Integration of this chemistry into a wet/dry cycle enables the continuous recycling of orthophosphate and the accretion of phosphorylated compounds. This system functions even at low reagent concentrations due to solutes concentrating during evaporation. Our system demonstrates a general strategy for how to maximise the usage of scarce resources based upon cycles which accumulate and then release activated intermediates.
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Affiliation(s)
- Oliver R Maguire
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands.
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57
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Xu J, Green NJ, Russell DA, Liu Z, Sutherland JD. Prebiotic Photochemical Coproduction of Purine Ribo- and Deoxyribonucleosides. J Am Chem Soc 2021; 143:14482-14486. [PMID: 34469129 PMCID: PMC8607323 DOI: 10.1021/jacs.1c07403] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
The
hypothesis that life on Earth may have started with a heterogeneous
nucleic acid genetic system including both RNA and DNA has attracted
broad interest. The recent finding that two RNA subunits (cytidine,
C, and uridine, U) and two DNA subunits (deoxyadenosine, dA, and deoxyinosine,
dI) can be coproduced in the same reaction network, compatible with
a consistent geological scenario, supports this theory. However, a
prebiotically plausible synthesis of the missing units (purine ribonucleosides
and pyrimidine deoxyribonucleosides) in a unified reaction network
remains elusive. Herein, we disclose a strictly stereoselective and
furanosyl-selective synthesis of purine ribonucleosides (adenosine,
A, and inosine, I) and purine deoxynucleosides (dA and dI), alongside
one another, via a key photochemical reaction of thioanhydroadenosine
with sulfite in alkaline solution (pH 8–10). Mechanistic studies
suggest an unexpected recombination of sulfite and nucleoside alkyl
radicals underpins the formation of the ribo C2′–O bond.
The coproduction of A, I, dA, and dI from a common intermediate, and
under conditions likely to have prevailed in at least some primordial
locales, is suggestive of the potential coexistence of RNA and DNA
building blocks at the dawn of life.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Nicholas J Green
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - David A Russell
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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58
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Rimmer PB, Thompson SJ, Xu J, Russell DA, Green NJ, Ritson DJ, Sutherland JD, Queloz DP. Timescales for Prebiotic Photochemistry Under Realistic Surface Ultraviolet Conditions. ASTROBIOLOGY 2021; 21:1099-1120. [PMID: 34152196 PMCID: PMC8570677 DOI: 10.1089/ast.2020.2335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet (UV) light has long been invoked as a source of energy for prebiotic chemical synthesis, but experimental support does not involve sources of UV light that look like the young Sun. Here we experimentally investigate whether the UV flux available on the surface of early Earth, given a favorable atmosphere, can facilitate a variety of prebiotic chemical syntheses. We construct a solar simulator for the UV light of the faint young Sun on the surface of early Earth, called StarLab. We then attempt a series of reactions testing different aspects of a prebiotic chemical scenario involving hydrogen cyanide (HCN), sulfites, and sulfides under the UV light of StarLab, including hypophosphite oxidation by UV light and hydrogen sulfide, photoreduction of HCN with bisulfite, the photoanomerization of α-thiocytidine, the production of a chemical precursor of a potentially prebiotic activating agent (nitroprusside), the photoreduction of thioanhydrouridine and thioanhydroadenosine, and the oxidation of ethanol (EtOH) by photochemically generated hydroxyl radicals. We compare the output of StarLab to the light of the faint young Sun to constrain the timescales over which these reactions would occur on the surface of early Earth. We predict that hypophosphite oxidation, HCN reduction, and photoproduction of nitroprusside would all operate on the surface of early Earth in a matter of days to weeks. The photoanomerization of α-thiocytidine would take months to complete, and the production of oxidation products from hydroxyl radicals would take years. The photoreduction of thioanhydrouridine with hydrogen sulfide did not succeed even after a long period of irradiation, providing a lower limit on the timescale of several years. The photoreduction of thioanhydroadenosine with bisulfite produced 2'-deoxyriboadenosine (dA) on the timescale of days. This suggests the plausibility of the photoproduction of purine deoxyribonucleotides, such as the photoproduction of simple sugars, proceeds more efficiently in the presence of bisulfite.
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Affiliation(s)
- Paul B. Rimmer
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Address correspondence to: Paul B. Rimmer, Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom
| | | | - Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | | | | | - Didier P. Queloz
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
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59
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Matreux T, Le Vay K, Schmid A, Aikkila P, Belohlavek L, Çalışkanoğlu AZ, Salibi E, Kühnlein A, Springsklee C, Scheu B, Dingwell DB, Braun D, Mutschler H, Mast CB. Heat flows in rock cracks naturally optimize salt compositions for ribozymes. Nat Chem 2021; 13:1038-1045. [PMID: 34446924 DOI: 10.1038/s41557-021-00772-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 07/13/2021] [Indexed: 11/09/2022]
Abstract
Catalytic nucleic acids, such as ribozymes, are central to a variety of origin-of-life scenarios. Typically, they require elevated magnesium concentrations for folding and activity, but their function can be inhibited by high concentrations of monovalent salts. Here we show that geologically plausible high-sodium, low-magnesium solutions derived from leaching basalt (rock and remelted glass) inhibit ribozyme catalysis, but that this activity can be rescued by selective magnesium up-concentration by heat flow across rock fissures. In contrast to up-concentration by dehydration or freezing, this system is so far from equilibrium that it can actively alter the Mg:Na salt ratio to an extent that enables key ribozyme activities, such as self-replication and RNA extension, in otherwise challenging solution conditions. The principle demonstrated here is applicable to a broad range of salt concentrations and compositions, and, as such, highly relevant to various origin-of-life scenarios.
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Affiliation(s)
- T Matreux
- Systems Biophysics, Ludwig Maximilians University Munich, Munich, Germany
| | - K Le Vay
- MPI für Biochemie, Biomimetische Systeme, Martinsried, Germany
| | - A Schmid
- Systems Biophysics, Ludwig Maximilians University Munich, Munich, Germany
| | - P Aikkila
- Systems Biophysics, Ludwig Maximilians University Munich, Munich, Germany
| | - L Belohlavek
- Earth and Environmental Sciences, Ludwig Maximilians University Munich, Munich, Germany
| | - A Z Çalışkanoğlu
- Earth and Environmental Sciences, Ludwig Maximilians University Munich, Munich, Germany
| | - E Salibi
- MPI für Biochemie, Biomimetische Systeme, Martinsried, Germany
| | - A Kühnlein
- Systems Biophysics, Ludwig Maximilians University Munich, Munich, Germany
| | - C Springsklee
- Earth and Environmental Sciences, Ludwig Maximilians University Munich, Munich, Germany
| | - B Scheu
- Earth and Environmental Sciences, Ludwig Maximilians University Munich, Munich, Germany
| | - D B Dingwell
- Earth and Environmental Sciences, Ludwig Maximilians University Munich, Munich, Germany
| | - D Braun
- Systems Biophysics, Ludwig Maximilians University Munich, Munich, Germany
| | | | - C B Mast
- Systems Biophysics, Ludwig Maximilians University Munich, Munich, Germany.
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60
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Kooijman AM, Arens SM, Postema AEL, van Dalen BR, Cammeraat LH. Lime-rich and lime-poor coastal dunes: Natural blowout activity differs with sensitivity to high N deposition through differences in P availability to the vegetation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146461. [PMID: 34030245 DOI: 10.1016/j.scitotenv.2021.146461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
In industrialized countries, biodiversity is threatened by high atmospheric N deposition. In coastal dunes, blowouts can mitigate this through deposition of fresh sand, but lime-rich and lime-poor dunes may differ in blowout activity. We studied natural blowout activity and explanatory factors in 2000 and 2014 in up to 51 sites along the Dutch coast, representative for other parts of Europe. We further analyzed plant and soil characteristics related to P nutrition in seven sites in 2019 and found that blowout activity was intrinsically linked to interactions between the geosphere, pedosphere and biosphere. Blowout activity was higher in lime-rich than in lime-poor dunes, especially in 2014. This difference could not be explained by wind velocity and only partly by position in the landscape, but was associated with pH, critical N load and rabbit density. At high pH, P availability to the vegetation was low. Arbuscular mycorrhizal (AM) plant species thus predominated, which belong to the most characteristic dune plants and may provide rabbit food of better quality than nonmycorrhizal (NM) or ericoid mycorrhizal (ErM) plants. Root biomass was also low at high pH, which may reduce cohesion of the sand and increase blowout activity, especially in areas with high rabbit density. At low pH, P availability increased, which favored NM and ErM rather than AM plants, and root biomass increased, which increased stability of the blowouts. As a restoration measure, (re)activation of blowouts may improve buffer capacity, characteristic biodiversity and conservation status of coastal dune grasslands. However, lime-poor dunes are more vulnerable to acidification, increase in P availability and blowout stabilization than lime-rich dunes. In extremely lime-poor dunes, it may even be better to let vegetation develop towards Dune heathlands, which are also EU priority habitats.
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Affiliation(s)
- A M Kooijman
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, PO Box 94240, 1090 GE Amsterdam, the Netherlands.
| | - S M Arens
- Arens Bureau voor Strand en Duinonderzoek, the Netherlands
| | - A E L Postema
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, PO Box 94240, 1090 GE Amsterdam, the Netherlands
| | - B R van Dalen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, PO Box 94240, 1090 GE Amsterdam, the Netherlands
| | - L H Cammeraat
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, PO Box 94240, 1090 GE Amsterdam, the Netherlands
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61
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Verma S, Ravichandiran V, Ranjan N. Selective, pH sensitive, "turn on" fluorescence sensing of carbonate ions by a benzimidazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 255:119624. [PMID: 33789191 DOI: 10.1016/j.saa.2021.119624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Anions play crucial roles in the sustenance of life on earth in many ways. Selective detection of specific anions is important in developing new diagnostic tools and therapeutics. A pH-sensitive & selective benzimidazole-based fluorescent sensor has been developed for rapid detection of carbonate ions which can detect carbonate ions in low nanomolar concentrations. NMR based experiments indicate direct interaction of benzimidazole imino protons with the carbonate ions leading to 1:1 ligand carbonate ion complexation events. This is one of the first reports of benzimidazole sensing carbonate ions with high selectivity which may have implications in disease prevention and toxicity assessment.
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Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, Near CRPF Base Camp, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow, Uttar Pradesh 226301, India; National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, Near CRPF Base Camp, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow, Uttar Pradesh 226301, India.
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62
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Guo W, Kinghorn AB, Zhang Y, Li Q, Poonam AD, Tanner JA, Shum HC. Non-associative phase separation in an evaporating droplet as a model for prebiotic compartmentalization. Nat Commun 2021; 12:3194. [PMID: 34045455 PMCID: PMC8160217 DOI: 10.1038/s41467-021-23410-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
The synthetic pathways of life’s building blocks are envisaged to be through a series of complex prebiotic reactions and processes. However, the strategy to compartmentalize and concentrate biopolymers under prebiotic conditions remains elusive. Liquid-liquid phase separation is a mechanism by which membraneless organelles form inside cells, and has been hypothesized as a potential mechanism for prebiotic compartmentalization. Associative phase separation of oppositely charged species has been shown to partition RNA, but the strongly negative charge exhibited by RNA suggests that RNA-polycation interactions could inhibit RNA folding and its functioning inside the coacervates. Here, we present a prebiotically plausible pathway for non-associative phase separation within an evaporating all-aqueous sessile droplet. We quantitatively investigate the kinetic pathway of phase separation triggered by the non-uniform evaporation rate, together with the Marangoni flow-driven hydrodynamics inside the sessile droplet. With the ability to undergo liquid-liquid phase separation, the drying droplets provide a robust mechanism for formation of prebiotic membraneless compartments, as demonstrated by localization and storage of nucleic acids, in vitro transcription, as well as a three-fold enhancement of ribozyme activity. The compartmentalization mechanism illustrated in this model system is feasible on wet organophilic silica-rich surfaces during early molecular evolution. Prebiotic compartmentalization could prove essential for the evolution of life. Guo et al. show that liquid-liquid separation in an aqueous two-phase system driven by evaporation may already suffice to facilitate chemical processes required for the RNA world hypothesis.
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Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Yage Zhang
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Qingchuan Li
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China.,School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, Jinan, 250100, China
| | - Aditi Dey Poonam
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China.
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63
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Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT. In search of the RNA world on Mars. GEOBIOLOGY 2021; 19:307-321. [PMID: 33565260 PMCID: PMC8248371 DOI: 10.1111/gbi.12433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 05/17/2023]
Abstract
Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe2+ , Mg2+ , and Mn2+ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg2+ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe2+ and Mn2+ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe2+ or Mn2+ cleave more RNA than Mg2+ ; and (c) alkaline environments with Mg2+ dramatically cleaves more RNA while precipitates were observed for Fe2+ and Mn2+ .
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lin Jin
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - Jack W. Szostak
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - James W. Head
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRIUSA
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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Inner Workings: Making headway with the mysteries of life's origins. Proc Natl Acad Sci U S A 2021; 118:2105383118. [PMID: 33853953 DOI: 10.1073/pnas.2105383118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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65
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A Series of Data-Driven Hypotheses for Inferring Biogeochemical Conditions in Alkaline Lakes and Their Deposits Based on the Behavior of Mg and SiO2. MINERALS 2021. [DOI: 10.3390/min11020106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Alkaline (pH > 8.5) lakes have been common features of Earth’s surface environments throughout its history and are currently among the most biologically productive environments on the planet. The chemistry of alkaline lakes favors the deposition of aluminum-poor magnesian clays (e.g., sepiolite, stevensite, and kerolite) whose chemistry and mineralogy may provide a useful record of the biogeochemistry of the lake waters from which they were precipitated. In this forward-looking review, we present six data-driven, testable hypotheses devoted to furthering our understanding of the biogeochemical conditions in paleolake waters based on the geochemical behavior of Mg and SiO2. In the development of these hypotheses, we bring together a compilation of modern lake water chemistry, recently published and new experimental data, and empirical, thermodynamic, and kinetic relationships developed from these data. We subdivide the hypotheses and supporting evidence into three categories: (1) interpreting paleolake chemistry from mineralogy; (2) interpreting the impact of diatoms on alkaline lake sedimentation; and (3) interpreting depositional mineralogy based on water chemistry. We demonstrate the need for further investigation by discussing evidence both for and against each hypothesis, which, in turn, highlights the gaps in our knowledge and the importance of furthering our understanding of the relevant geological and biological systems. The focused testing of these hypotheses against modern occurrences and the geologic record of alkaline lakes can have profound implications for the interpretation of the paleo-biogeochemistry and paleohabitability of these systems on Earth and beyond.
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Spustova K, Köksal ES, Ainla A, Gözen I. Subcompartmentalization and Pseudo-Division of Model Protocells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005320. [PMID: 33230918 DOI: 10.1002/smll.202005320] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Membrane enclosed intracellular compartments have been exclusively associated with the eukaryotes, represented by the highly compartmentalized last eukaryotic common ancestor. Recent evidence showing the presence of membranous compartments with specific functions in archaea and bacteria makes it conceivable that the last universal common ancestor and its hypothetical precursor, the protocell, may have exhibited compartmentalization. To the authors' knowledge, there are no experimental studies yet that have tested this hypothesis. They report on an autonomous subcompartmentalization mechanism for protocells which results in the transformation of initial subcompartments to daughter protocells. The process is solely determined by the fundamental materials properties and interfacial events, and does not require biological machinery or chemical energy supply. In the light of the authors' findings, it is proposed that similar events may have taken place under early Earth conditions, leading to the development of compartmentalized cells and potentially, primitive division.
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Affiliation(s)
- Karolina Spustova
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Elif Senem Köksal
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Alar Ainla
- International Iberian Nanotechnology Laboratory, Braga, 4715-330, Portugal
| | - Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0315, Norway
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
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67
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Fontecilla-Camps JC. Primordial bioenergy sources: The two facets of adenosine triphosphate. J Inorg Biochem 2020; 216:111347. [PMID: 33450675 DOI: 10.1016/j.jinorgbio.2020.111347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H+ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.
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68
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Kostetsky EY, Uversky VN. On the origin of matrix mechanism in protocells and key problems of molecular biology. J Biomol Struct Dyn 2020; 40:572-583. [PMID: 32820704 DOI: 10.1080/07391102.2020.1809523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The theory of the emergence of the matrix mechanism in protocells on complexes of minerals (apatite, carbonate-apatite, calcite, and quartz) with the reciprocal proportions and with the participation of the gas phase radicals (NH3, CH4, and CO) is considered. The structure of apatite and carbonate-apatite predetermined the formation of a double helix of DNA with the complementary pairs of purine-pyrimidine bases, as well as RNA strands complementary to DNA, and helical protein chains combined into supramolecular structures with RNA. It is proposed that during the Archean Eon, a gradual replacement of the mineral matrix with organic matter took place. The site of the origin of the matrix mechanism is the defect-free and growing defective zone of apatite and carbonate-apatite. The size and specificity of DNA, complementary-bound RNA and protein molecules in supramolecular protein-RNA complexes increased as defects accumulated in the structure of minerals. An increase in the size of RNA transcripts was accompanied by an increase in the number of protein molecules in supramolecular protein-RNA complexes. At the first, anhydrous, stage, the formation of a transcriptional-translational apparatus in the form of a crystalline organic-mineral complex -DNA, RNA and protein, based on the "spiral into spiral" principle of gas phase elements. The appearance of water determined the launch of the transcriptional-translational apparatus and the transformation of the organo-mineral crystalline complex into a liquid-crystalline state. A detailed description of the preparation and launch of the matrix mechanism is given. The following problems are discussed: the origin of ribosomal proteins and the role of super-specific aminoacyl-tRNA synthetase as a true carrier of genetic information; properties of the genetic code and synthesis of protocells without violating the second law of thermodynamics; the origin of biological asymmetry; the appearance of nanobacteria and dark genetic matter of eukaryotic systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Eduard Y Kostetsky
- Department of Biochemistry, Microbiology and Biotechnology, School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
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69
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Mineral Vesicles and Chemical Gardens from Carbonate-Rich Alkaline Brines of Lake Magadi, Kenya. CRYSTALS 2020. [DOI: 10.3390/cryst10060467] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mineral vesicles and chemical gardens are self-organized biomimetic structures that form via abiotic mineral precipitation. These membranous structures are known to catalyze prebiotic reactions but the extreme conditions required for their synthesis has cast doubts on their formation in nature. Apart from model solutions, these structures have been shown to form in serpentinization-driven natural silica-rich water and by fluid-rock interaction of model alkaline solutions with granites. Here, for the first time, we demonstrate that self-assembled hollow mineral vesicles and gardens can be synthesized in natural carbonate-rich soda lake water. We have synthesized these structures by a) pouring saturated metal salt solutions, and b) by immersing metal salt pellets in brines collected from Lake Magadi (Kenya). The resulting structures are analyzed by using SEM coupled with EDX analysis, Raman spectroscopy, and powder X-ray diffraction. Our results suggest that mineral self-assembly could have been a common phenomenon in soda oceans of early Earth and Earth-like planets and moons. The composition of the obtained vesicles and gardens confirms the recent observation that carbonate minerals in soda lakes sequestrate Ca, thus leaving phosphate behind in solution available for biochemical reactions. Our results strengthens the proposal that alkaline brines could be ideal sites for “one-pot” synthesis of prebiotic organic compounds and the origin of life.
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70
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Fialho DM, Roche TP, Hud NV. Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides. Chem Rev 2020; 120:4806-4830. [PMID: 32421316 DOI: 10.1021/acs.chemrev.0c00069] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The origin of nucleotides is a major question in origins-of-life research. Given the central importance of RNA in biology and the influential RNA World hypothesis, a great deal of this research has focused on finding possible prebiotic syntheses of the four canonical nucleotides of coding RNA. However, the use of nucleotides in other roles across the tree of life might be evidence that nucleotides have been used in noncoding roles for even longer than RNA has been used as a genetic polymer. Likewise, it is possible that early life utilized nucleotides other than the extant nucleotides as the monomers of informational polymers. Therefore, finding plausible prebiotic syntheses of potentially ancestral noncanonical nucleotides may be of great importance for understanding the origins and early evolution of life. Experimental investigations into abiotic noncanonical nucleotide synthesis reveal that many noncanonical nucleotides and related glycosides are formed much more easily than the canonical nucleotides. An analysis of the mechanisms by which nucleosides and nucleotides form in the solution phase or in drying-heating reactions from pre-existing sugars and heterocycles suggests that a wide variety of noncanonical nucleotides and related glycosides would have been present on the prebiotic Earth, if any such molecules were present.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
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The Prebiotic Provenance of Semi-Aqueous Solvents. ORIGINS LIFE EVOL B 2020; 50:1-14. [PMID: 32388697 DOI: 10.1007/s11084-020-09595-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
The numerous and varied roles of phosphorylated organic molecules in biochemistry suggest they may have been important to the origin of life. The prominence of phosphorylated molecules presents a conundrum given that phosphorylation is a thermodynamically unfavorable, endergonic process in water, and most natural sources of phosphate are poorly soluble. We recently demonstrated that a semi-aqueous solvent consisting of urea, ammonium formate, and water (UAFW) supports the dissolution of phosphate and the phosphorylation of nucleosides. However, the prebiotic feasibility and robustness of the UAFW system are unclear. Here, we study the UAFW system as a medium in which phosphate minerals are potentially solubilized. Specifically, we conduct a series of chemical experiments alongside thermodynamic models that simulate the formation of ammonium formate from the hydrolysis of hydrogen cyanide, and demonstrate the stability of formamide in such solvents (as an aqueous mixture). The dissolution of hydroxylapatite requires a liquid medium, and we investigate whether a UAFW system is solid or liquid over varied conditions, finding that this characteristic is controlled by the molar ratios of the three components. For liquid UAFW mixtures, we also find the solubility of phosphate is higher when the quantity of ammonium formate is greater than urea. We suggest the urea within the system can lower the activity of water, help create a stable and persistent solution, and may act as a condensing agent/catalyst to improve nucleoside phosphorylation yields.
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Longo A, Damer B. Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond. Life (Basel) 2020; 10:E52. [PMID: 32349245 PMCID: PMC7281141 DOI: 10.3390/life10050052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 01/13/2023] Open
Abstract
Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life's origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have advanced on Titan. These environments will be compared to ancient and modern terrestrial analogs to assess their habitability and biopreservation potential. Origins of life approaches can guide the biosignature detection strategies of the next generation of planetary science missions, which could in turn advance one or both of the leading alternative abiogenesis hypotheses.
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Affiliation(s)
- Alex Longo
- National Aeronautics and Space Administration Headquarters, Washington, DC 20546, USA
- Department of Geology, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bruce Damer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA or
- Digital Space Research, Boulder Creek, CA 95006, USA
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