Origins of Life and Evolution of Biospheres最新文献

{"title":"Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions.","authors":"Thora R Maltais,&nbsp;David VanderVelde,&nbsp;Douglas E LaRowe,&nbsp;Aaron D Goldman,&nbsp;Laura M Barge","doi":"10.1007/s11084-019-09590-9","DOIUrl":"https://doi.org/10.1007/s11084-019-09590-9","url":null,"abstract":"<p><p>Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09590-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37578965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symphony in C: Carbon and the Evolution of (Almost) Everything by Robert M. Hazen, W.W. Norton & Company, 2019","authors":"P. Bahn","doi":"10.1007/s11084-020-09592-y","DOIUrl":"https://doi.org/10.1007/s11084-020-09592-y","url":null,"abstract":"","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2020-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77659663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Membranes Composed of Lipopeptides and Liponucleobases Inspired Protolife Evolution.","authors":"Gordon D Sproul","doi":"10.1007/s11084-019-09587-4","DOIUrl":"10.1007/s11084-019-09587-4","url":null,"abstract":"<p><p>Amino acids and peptides have been demonstrated to form lipoamino acids and lipopeptides under presumed prebiotic conditions, and readily form liposomes. Of the common nucleobases, adenine forms a liponucleobase even below 100 °C. Adenine as well as other nucleobases can also be derivatized with ethylene carbonate (and likely other similar compounds) onto which fatty acids can be attached. The fatty acid tails along with appropriately functionalized nucleobases provide some solubility of liponucleobases in membranes. Such membranes would provide a structure in which three of biology's major components are closely associated and available for chemical interactions. Nucleobase-to-nucleobase interactions would ensure that the liponucleobases would have a uniquely different head-group relationship than other amphiphiles within a membrane, likely forming rafts due their π-π interactions and providing surface discontinuities that could serve as catalytic sites. The π-π bond distance in aromatic compounds is typically 0.34 nm, commensurate with that of the amine to carboxylate distance in alpha amino acids. This would have provided opportunity for hydrogen bonding between amino acids and the distal primary amines or tautomeric carbonyl/hydroxyl groups of two π-bonded nucleobases. Such bonding would weaken the covalent linkages within the amino acids, making them susceptible to forming peptide bonds with an adjacent amino acid, likely a lipoamino acid or lipopeptide. Were this second lipoamino acid bound to a third π-bonded nucleobase, it could result in orientation, destabilization and peptide formation. The stacked triplet of nucleobases might constitute the primordial codon triplet from which peptides were synthesized: primordial translation.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09587-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37496477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Imidazolium-Catalyzed Synthesis of an Imidazolium Catalyst.","authors":"Arthur L Weber, Andro C Rios","doi":"10.1007/s11084-019-09589-2","DOIUrl":"10.1007/s11084-019-09589-2","url":null,"abstract":"<p><p>The chemistry of imidazolium-catalyzed imidazolium synthesis was studied as part of an effort to develop a plausible prebiotic synthesis of a small catalytic molecule capable of catalyzing its own synthesis. Specifically, we investigated the one-pot 1-ethyl-3-methylimidazolium acetate (EMIM-Ac) catalyzed synthesis of 1,3-dibutyl-4,5-difuryl-imidazolium acetate (DBDFIM-Ac) from furfural, n-butylamine, formaldehyde, and acetic acid at 80 °C. Liu et al. (2012) had previously demonstrated the first reaction of the synthetic process, the EMIM-Ac catalyzed benzoin condensation of furfural that yields furoin. Our early studies established the second reaction of the synthetic process, the multicomponent reaction of furoin, n-butylamine, formaldehyde, and acetic acid that yields the imidazolium salt, DBDFIM-Ac. Studies of the complete two-reaction process that uses furfural for the synthesis of DBDFIM-Ac showed that the highest yield of DBDFIM-Ac was obtained when the mole ratio of n-butylamine, formaldehyde, and acetic acid relative to furfural was respectively (0.5:0.25:0.25:1.0-furfural), or one-half of the stoichiometric ratio (1.0:0.5:0.5:1.0-furfural). A time course study of the process showed transient formation of furoin, the obligatory reaction intermediate. DBDFIM-Ac and the imidazolium side product, 1,3-dibutyl-4,5-trifuryl-imidazolium acetate (DBTFIM-Ac), were stable under the reaction conditions. Imidazolium products (DBDFIM and DBTFIM) and the furoin intermediate were not formed in control reactions (80 °C, 24 h) in which EMIM catalyst was either absent or replaced with an equal volume of acetonitrile or DMF. The imidazolium product, DBDFIM-Ac, was shown to catalyze the synthesis of structurally similar 1,3-dipentyl-4,5-difuryl-imidazolium acetate (DPDFIM-Ac) from furfural, n-pentylamine, formaldehyde, and acetic acid at 80 °C.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09589-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74685396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carbonyl Sulfide as a Prebiotic Activation Agent for Stereo- and Sequence-Selective, Amyloid-Templated Peptide Elongation.","authors":"Radoslaw Bomba, Saroj K Rout, Matthias Bütikofer, Witek Kwiatkowski, Roland Riek, Jason Greenwald","doi":"10.1007/s11084-019-09586-5","DOIUrl":"10.1007/s11084-019-09586-5","url":null,"abstract":"<p><p>Prebiotic chemical replication is a commonly assumed precursor to and prerequisite for life and as such is the one of the goals of our research. We have previously reported on the role that short peptide amyloids could have played in a template-based chemical elongation. Here we take a step closer to the goal by reproducing amyloid-templated peptide elongation with carbonyl sulfide (COS) in place of the less-prebiotically relevant carbonyldiimidazole (CDI) used in the earlier study. Our investigation shows that the sequence-selectivity and stereoselectivity of the amyloid-templated reaction is similar for both activation chemistries. Notably, the amyloid protects the peptides from some of the side-reactions that take place with the COS-activation.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09586-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37463716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Oligomerization of Glucose Under Plausible Prebiotic Conditions.","authors":"Zhao Li, Li Li, Kristin R McKenna, Merranda Schmidt, Pamela Pollet, Leslie Gelbaum, Facundo M Fernández, Ramanarayanan Krishnamurthy, Charles L Liotta","doi":"10.1007/s11084-019-09588-3","DOIUrl":"10.1007/s11084-019-09588-3","url":null,"abstract":"<p><p>The prebiotic origin of polysaccharides, the largest class of biopolymers by mass in extant biology, has seldom been investigated experimentally. Herein, we report on the acid-catalyzed condensation of aqueous solutions of glucose, a model monosaccharide, under plausible prebiotic conditions employing a wet-dry (night-day) protocol with 0.01 M HCl at 50 °C. This protocol leads to the formation of oligosaccharides containing up to eight monomeric units identified by high resolution mass spectrometry. The regio- and stereochemistry of the oligomeric acetal linkages, as well as the quantitative analysis of glucose conversion, are elucidated by combining ¹H, ¹³C and 2D NMR spectroscopy. Ten out of eleven possible acetal linkages, including α- and β- anomers, have been identified with the α- and β- 1,6-acetals being the dominant linkages observed. In addition, the acid-catalyzed oligomerization of several glucose disaccharides such as cellobiose, maltose, and gentiobiose are presented along with an accompanying comparison with the corresponding oligomerization of glucose.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09588-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76857120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spontaneous Resolution and Super-coiling in Xerogels of the Products of Photo-Induced Formose Reaction.","authors":"Sergey V Stovbun, Anatoly M Zanin, Mikhail V Shashkov, Aleksey A Skoblin, Dmitry V Zlenko, Vsevolod A Tverdislov, Marya G Mikhaleva, Oxana P Taran, Valentin N Parmon","doi":"10.1007/s11084-019-09583-8","DOIUrl":"10.1007/s11084-019-09583-8","url":null,"abstract":"<p><p>This work addresses the supramolecular self-organization in the xerogels of formose reaction products. The UV-induced formose reaction was held in over-saturated formaldehyde solutions at 70^∘C without a catalyst. The solutions of the obtained carbohydrates were dried on a glass slide, and the obtained xerogels demonstrated a prominent optical activity, while the initial solutions were optically inactive. The xerogels contained highly elongated crystalline elements of a helical structure as well as the isometric ones. Thus xerogel formation was accompanied by a spontaneous resolution of enantiomers and separation of different-shaped supramolecular structures. The thick helices were twisted of thinner ones, while the latter were twisted of elementary structures having a diameter much smaller than 400 nm. Similar structural hierarchy is typical of biological macromolecules (DNA, proteins, and cellulose). Summarizing the obtained results, we proposed a hypothetical mechanism explaining the amplification of the initial enantiomeric excess, as well as chiral and chemical purification of the substances which were essential for the evolution of Life to start.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09583-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80931375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report.","authors":"Carlos Mariscal, Ana Barahona, Nathanael Aubert-Kato, Arsev Umur Aydinoglu, Stuart Bartlett, María Luz Cárdenas, Kuhan Chandru, Carol Cleland, Benjamin T Cocanougher, Nathaniel Comfort, Athel Cornish-Bowden, Terrence Deacon, Tom Froese, Donato Giovannelli, John Hernlund, Piet Hut, Jun Kimura, Marie-Christine Maurel, Nancy Merino, Alvaro Moreno, Mayuko Nakagawa, Juli Peretó, Nathaniel Virgo, Olaf Witkowski, H James Cleaves","doi":"10.1007/s11084-019-09580-x","DOIUrl":"10.1007/s11084-019-09580-x","url":null,"abstract":"<p><p>In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the \"bottom up\" approach) and (4) how to infer the nature of the last universal common ancestor (the \"top down\" approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a\" circularity\" approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09580-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83289938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis of Nucleic Acid Bases by Metal Ferrite Nanoparticles from a Single Carbon Atom Precursor Molecule: Formamide.","authors":"Mohammad Asif Iqubal, Rachana Sharma, Kamaluddin, Sohan Jheeta","doi":"10.1007/s11084-019-09585-6","DOIUrl":"10.1007/s11084-019-09585-6","url":null,"abstract":"<p><p>The synthesis of prebiotic molecules from simple precursors is believed to be a crucial scheme in order to study the origin of life processes. The present study describes the one-pot synthesis of purine and pyrimidine nucleic acid bases in the presence of pre-biologically significant binary metal oxide nanoparticles, metal ferrites, namely NiFe₂O₄, CoFe₂O₄, CuFe₂O₄, ZnFe₂O₄ and MnFe₂O₄. The products identified are cytosine, isocytosine, 4(3H)-pyrimidinone, adenine, hypoxanthine and purine. The ability of isocytosine (a constitutional isomer of cytosine) to recognize cytosine and guanine through normal and reversed Watson-Crick pairing respectively, demonstrates an important storyline for the genesis of ancient nucleic acids. The relevance of other synthesized nucleic acid bases with respect to the origin of life is also discussed. The divalent metal ions in iron oxide make it an appropriate catalytic system because it demonstrates excellent catalytic performance for the nucleic acid bases synthesis with significantly high yield, as compared to pure iron oxide and some other minerals like silica, alumina, manganese oxides and double metal cyanide complexes.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09585-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80908813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interactions of Amino Acids and Aminoxazole Derivatives: Cocrystal Formation and Prebiotic Implications Enabled by Computational Analysis.","authors":"Nieves Lavado, Juan García de la Concepción, Reyes Babiano, Pedro Cintas, Mark E Light","doi":"10.1007/s11084-019-09582-9","DOIUrl":"10.1007/s11084-019-09582-9","url":null,"abstract":"<p><p>In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids. To this end, a bis-aminoxazoline derivative, generated from dihydroxyacetone and cyanamide, gives rise to stable co-crystal forms with dicarboxylic amino acids (Asp and Glu), while ionic interactions owing to proton transfer are inferred from spectroscopic data in aqueous solution. The structure of a 1:2 aminoxazoline: aspartic acid complex, discussed in detail, was elucidated by X-ray diffractometry. Optimized geometries of such ionic structures with bulk aqueous solvation were assessed by DFT calculations, which disclose preferential arrangements that validate the experimental data. Peripherally, we were able to detect in a few cases amino acid dimerization (i.e. dipeptide formation) after prolonged incubation with the bis-aminoxazole derivative. A mechanistic simulation aided by computation provides some predictive conclusions for future explorations and catalytic design.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-019-09582-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75053904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}