scholarly journals Prebiotic Sugar Formation Under Nonaqueous Conditions and Mechanochemical Acceleration

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 52 ◽  
Author(s):  
Saskia Lamour ◽  
Sebastian Pallmann ◽  
Maren Haas ◽  
Oliver Trapp
Keyword(s):  
Ball Mill ◽  
Carbon Sources ◽  
Prebiotic Synthesis ◽  
Building Blocks ◽  
Decomposition Products ◽  
Meteorite Impacts ◽  
Carbon Chains ◽  
Catalytically Active ◽  
Physical Forces ◽  
Mechanic Energy

Monosaccharides represent one of the major building blocks of life. One of the plausible prebiotic synthesis routes is the formose network, which generates sugars from C1 and C2 carbon sources in basic aqueous solution. We report on the feasibility of the formation of monosaccharides under physical forces simulated in a ball mill starting from formaldehyde, glycolaldehyde, DL-glyceraldehyde as prebiotically available substrates using catalytically active, basic minerals. We investigated the influence of the mechanic energy input on our model system using calcium hydroxide in an oscillatory ball mill. We show that the synthesis of monosaccharides is kinetically accelerated under mechanochemical conditions. The resulting sugar mixture contains monosaccharides with straight and branched carbon chains as well as decomposition products. In comparison to the sugar formation in water, the monosaccharides formed under mechanochemical conditions are more stable and selectively synthesized. Our results imply the possibility of a prebiotic monosaccharide origin in geochemical environments scant or devoid of water promoted by mechanochemical forces such as meteorite impacts or lithospheric activity.

scholarly journals A Case of Adaptive Laboratory Evolution (ALE): Biodegradation of Furfural by Pseudomonas pseudoalcaligenes CECT 5344

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 499 ◽  
Author(s):  
M. Isabel Igeño ◽  
Daniel Macias ◽  
Rafael Blasco
Keyword(s):  
Carbon Sources ◽  
Value Added ◽  
Cost Effective ◽  
Building Blocks ◽  
Yeast Fermentation ◽  
Adaptive Laboratory Evolution ◽  
Pseudomonas Pseudoalcaligenes ◽  
Hydroxymethyl Furfural ◽  
Double Recombination ◽  
Lag Period

Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a nitrogen source at alkaline pH. Genome sequencing of this strain allowed the detection of genes related to the utilization of furfurals as a carbon and energy source. Furfural and 5-(hydroxymethyl) furfural (HMF) are byproducts of sugars production during the hydrolysis of lignocellulosic biomass. Since they inhibit the yeast fermentation to obtain bioethanol from sugars, the biodegradation of these compounds has attracted certain scientific interest. P. pseudoalcaligenes was able to use furfuryl alcohol, furfural and furoic acid as carbon sources, but after a lag period of several days. Once adapted, the evolved strain (R1D) did not show any more prolonged lag phases. The transcriptomic analysis (RNA-seq) of R1D revealed a non-conservative punctual mutation (L261R) in BN5_2307, a member of the AraC family of activators, modifying the charge of the HTH region of the protein. The inactivation of the mutated gene in the evolved strain by double recombination reverted to the original phenotype. Although the bacterium did not assimilate HMF, it transformed it into value-added building blocks for the chemical industry. These results could be used to improve the production of cost-effective second-generation biofuels from agricultural wastes.

scholarly journals DNA-mediated engineering of multicomponent enzyme crystals

2015 ◽  
Vol 112 (15) ◽  
pp. 4564-4569 ◽  
Author(s):  
Jeffrey D. Brodin ◽  
Evelyn Auyeung ◽  
Chad A. Mirkin
Keyword(s):  
Gold Nanoparticles ◽  
Protein Interactions ◽  
Building Blocks ◽  
Inorganic Nanoparticles ◽  
Protein Protein Interactions ◽  
Dna Interactions ◽  
Interparticle Interactions ◽  
Crystalline Materials ◽  
Catalytically Active ◽  
Surface Chemistries

The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein–protein interactions for DNA–DNA interactions to direct the assembly of two nucleic-acid–functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA–DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials.

Hybrid Zeolitic Imidazolate Frameworks with Catalytically Active TO4 Building Blocks

2010 ◽  
Vol 123 (2) ◽  
pp. 470-473 ◽  
Author(s):  
Fei Wang ◽  
Zi-Sheng Liu ◽  
Hui Yang ◽  
Yan-Xi Tan ◽  
Jian Zhang
Keyword(s):  
Building Blocks ◽  
Zeolitic Imidazolate Frameworks ◽  
Catalytically Active

scholarly journals Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization

2020 ◽  
Author(s):  
Wen Zhang ◽  
Seohyun Chris Kim ◽  
Chun Pong Tam ◽  
Victor S. Lelyveld ◽  
Saikat Bala ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Prebiotic Synthesis ◽  
Building Blocks ◽  
Primer Extension ◽  
Structural Interpretation ◽  
Structural Distortions ◽  
Noncanonical Nucleotides ◽  
Directed Polymerization

ABSTRACTThe prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3’-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer ten-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

Prebiotic synthesis at impact craters: the role of Fe-clays and iron meteorites

2019 ◽  
Vol 55 (71) ◽  
pp. 10563-10566 ◽  
Author(s):  
Adam Pastorek ◽  
Jana Hrnčířová ◽  
Luboš Jankovič ◽  
Lukáš Nejdl ◽  
Svatopluk Civiš ◽  
...  
Keyword(s):  
Amino Acids ◽  
Prebiotic Synthesis ◽  
Building Blocks ◽  
Impact Craters ◽  
Iron Meteorites ◽  
Post Impact

Iron-rich smectites formed by reprocessing of basalts due to the residual post-impact heat could catalyze the synthesis and accumulation of important prebiotic building blocks such as nucleobases, amino acids and urea.

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level – merging models and mechanisms from advanced computations and experiments

2016 ◽  
Vol 18 (30) ◽  
pp. 20047-20066 ◽  
Author(s):  
Judit E. Šponer ◽  
Rafał Szabla ◽  
Robert W. Góra ◽  
A. Marco Saitta ◽  
Fabio Pietrucci ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Prebiotic Synthesis ◽  
Building Blocks ◽  
Atomic Level ◽  
Computational Studies

Main directions for future computational studies on the origin of the first nucleic acids is outlined.

scholarly journals Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization

2020 ◽  
Author(s):  
Wen Zhang ◽  
Seohyun Chris Kim ◽  
Chun Pong Tam ◽  
Victor S Lelyveld ◽  
Saikat Bala ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Prebiotic Synthesis ◽  
Building Blocks ◽  
Primer Extension ◽  
Structural Interpretation ◽  
Structural Distortions ◽  
Noncanonical Nucleotides ◽  
Directed Polymerization

Abstract The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3′-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

scholarly journals Organic Wastes as Feedstocks for Non-Conventional Yeast-Based Bioprocesses

2019 ◽  
Vol 7 (8) ◽  
pp. 229 ◽  
Author(s):  
Diem T. Hoang Do ◽  
Chrispian W. Theron ◽  
Patrick Fickers
Keyword(s):  
Carbon Sources ◽  
Value Added ◽  
Building Blocks ◽  
Organic Wastes ◽  
Cell Factory ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Alternative Feedstocks ◽  
Global Population ◽  
By Products

Non-conventional yeasts are efficient cell factories for the synthesis of value-added compounds such as recombinant proteins, intracellular metabolites, and/or metabolic by-products. Most bioprocess, however, are still designed to use pure, ideal sugars, especially glucose. In the quest for the development of more sustainable processes amid concerns over the future availability of resources for the ever-growing global population, the utilization of organic wastes or industrial by-products as feedstocks to support cell growth is a crucial approach. Indeed, vast amounts of industrial and commercial waste simultaneously represent an environmental burden and an important reservoir for recyclable or reusable material. These alternative feedstocks can provide microbial cell factories with the required metabolic building blocks and energy to synthesize value-added compounds, further representing a potential means of reduction of process costs as well. This review highlights recent strategies in this regard, encompassing knowledge on catabolic pathways and metabolic engineering solutions developed to endow cells with the required metabolic capabilities, and the connection of these to the synthesis of value-added compounds. This review focuses primarily, but not exclusively, on Yarrowia lipolytica as a yeast cell factory, owing to its broad range of naturally metabolizable carbon sources, together with its popularity as a non-conventional yeast.

L'effet d'acides gras saturés et insaturés sur la croissance et la fructification de quelques espèces du genre Ceratocystis

1980 ◽  
Vol 58 (24) ◽  
pp. 2543-2548 ◽  
Author(s):  
Y. Dalpé ◽  
Ch. Montant
Keyword(s):  
Palmitic Acid ◽  
Linolenic Acid ◽  
Mycelial Growth ◽  
Carbon Sources ◽  
Capric Acid ◽  
Carbon Chains ◽  
Fungitoxic Effect

The mycelial growth of Ceratocystis ips, C. capillifera, C. piceae, and C. ulmi is inhibited by capric acid, and the fungitoxic effect of saturated acids decreases with the length of even numbered carbon chains (C 12:00, C20:0). Palmitic acid does not interfere with glucose for mycelial growth. A competition for the utilization of carbon sources seems to occur when both glucose and linoleic or linolenic acid are present in the medium. In all cases, oleic, linoleic, and linolenic acids are good carbon sources and trigger the differentiation of several fruit bodies.

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