scholarly journals The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors

2021 ◽  
Vol 9 (2) ◽  
pp. 458 ◽  
Author(s):  
Jessica L. E. Wimmer ◽  
Andrey do Nascimento Vieira ◽  
Joana C. Xavier ◽  
Karl Kleinermanns ◽  
William F. Martin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Reaction Network ◽  
High Energy ◽  
Hydrothermal Systems ◽  
Aqueous Environment ◽  
The Core ◽  
Autotrophic Metabolism ◽  
Far From Equilibrium ◽  
Hydrolysis Of

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems.

Dipeptidase PEPDA is required for the conidiation pattern shift in Metarhizium acridum

2021 ◽  
Author(s):  
Juan Li ◽  
Xueling Su ◽  
Yueqing Cao ◽  
Yuxian Xia
Keyword(s):  
Amino Acids ◽  
Filamentous Fungi ◽  
Pathogenic Fungus ◽  
Digital Gene Expression ◽  
Hyphal Growth ◽  
Metarhizium Acridum ◽  
Key Enzyme ◽  
Hydrolysis Of ◽  
Microcycle Conidiation

Filamentous fungi conduct two types of conidiation, typical conidiation from mycelia and microcycle conidiation (MC). Fungal conidiation can shift between the two patterns, which involved a large number of genes in the regulation of this process. In this study, we investigated the role of a dipeptidase gene pepdA in conidiation pattern shift in Metarhizium acridum , which is upregulated in MC pattern compared to typical conidiation. Results showed that disruption of the pepdA resulted in a shift of conidiation pattern from MC to typical conidiation. Metabolomic analyses of amino acids showed that the levels of 19 amino acids significantly changed in Δ pepdA mutant. The defect of MC in Δ pepdA can be rescued when nonpolar amino acids, α-alanine, β-alanine or proline, were added into s ucrose y east extract a gar (SYA) medium. Digital gene expression profiling analysis revealed that PEPDA mediated transcription of sets of genes which were involved in hyphal growth and development, sporulation, cell division, and amino acid metabolism. Our results demonstrated that PEPDA played important roles in the regulation of MC by manipulating the levels of amino acids in M. acridum . IMPORTANCE Conidia, as the asexual propagules in many fungi, are start and end of fungal lifecycle. In entomopathogenic fungi, conidia are the infective form essential for their pathogenicity. Filamentous fungi conduct two types of conidiation, typical conidiation from mycelia and microcycle conidiation. The mechanisms of the shift between the two conidiation patterns remain to be elucidated. In this study, we demonstrated that the dipeptidase PEPDA, a key enzyme from the insect-pathogenic fungus Metarhizium acridum for the hydrolysis of dipeptides, is associated with a shift of conidiation pattern. The conidiation pattern of the Δ pepdA mutant was restored when supplemented with the nonpolar amino acids rather than polar amino acids. Therefore, this report highlights that the dipeptidase PEPDA regulates MC by manipulating the levels of amino acids in M. acridum.

Conservation of structure in ATP-depleted proximal tubules: role of calcium, polyphosphoinositides, and glycine

1993 ◽  
Vol 265 (5) ◽  
pp. F605-F623 ◽  
Author(s):  
R. Garza-Quintero ◽  
J. M. Weinberg ◽  
J. Ortega-Lopez ◽  
J. A. Davis ◽  
M. A. Venkatachalam
Keyword(s):  
Amino Acids ◽  
Phospholipase C ◽  
Cell Structure ◽  
Proximal Tubules ◽  
Atp Depletion ◽  
The Other ◽  
Antimycin A ◽  
Phospholipid Hydrolysis ◽  
Hydrolysis Of

Increases of intracellular free Ca2+ (Caf) may mediate phospholipid hydrolysis and disintegration in energy-compromised cells; on the other hand, glycine and related amino acids preserve structure. We have examined the effects of increased Caf on phospholipids and structure in ATP-depleted cells, as well as how these actions may be modified by glycine. Incubation of isolated proximal tubules with antimycin A led to ATP depletion, delayed increases of Caf to micromolar levels, polyphosphoinositide (PPI) hydrolysis by phospholipase C, and generalized disintegration of cell structure. Glycine inhibited PPI hydrolysis and preserved cell structure in entirety but did not apparently modify the Caf increases. When overwhelming increases of Caf were induced by the additional presence of a Ca2+ ionophore, glycine did not inhibit either the hydrolysis of PPI or disruption of mitochondria and microvilli. However, the cells remained integrated and unbroken. Incubation in low-Ca2+ medium prevented Caf increases, inhibited PPI hydrolysis, and preserved the structure of mitochondria and microvilli. Nevertheless, there was lethal damage by disintegration of all other membranes. This damage was prevented specifically and completely by glycine. Thus compartments of cells were shown to be differentially susceptible to injury from increased Caf or lack of glycine. Although damage by either factor occurs by distinct mechanisms, glycine also appears to have effects that suppress the deleterious effects of Ca2+ so long as Caf increases are not overwhelming. Our results also suggest that the PPI have a major structural role, which may be compromised by Caf increase during ATP depletion.

Energy Conservation via Thioesters in a Non-Enzymatic Metabolism-like Reaction Network

2019 ◽  
Author(s):  
Elodie Chevallot-Beroux ◽  
Jan Gorges ◽  
Joseph Moran
Keyword(s):  
Prebiotic Chemistry ◽  
Reaction Network ◽  
Biochemical Networks ◽  
Biochemical Evolution ◽  
Top Down ◽  
The Core ◽  
Energy Flows ◽  
Oxidative Breakdown ◽  
Intermediary Role

<p><b>Life’s catabolic processes capture chemical energy from the oxidative breakdown of metabolites. In the catabolic pathways at the core of biochemistry, the oxidation of </b>α-<b>ketoacids or aldehydes is coupled to the synthesis of thioesters, whose energy-releasing hydrolysis is in turn coupled to the production of adenosine 5’-triphosphate (ATP). How these processes became linked before life emerged, and thus how the framework for modern bioenergetics was established, is a major problem for understanding the origins of biochemistry. The structure of biochemical networks suggests that the intermediary role of thioesters in biological energy flows, and their central role in biosynthesis, is a consequence of their entry into metabolism at the earliest stage of biochemical evolution. However, how thioesters could have become embedded within a metabolic network before the advent of enzymes remains unclear. Here we demonstrate non-enzymatic oxidant- or light-driven thioester synthesis from biological </b>α-<b>ketoacids and show it can be integrated within an iron-promoted metabolism-like reaction network. The thioesters obtained are those predicted to be pivotal in computational reconstructions of primitive biochemical networks (acetyl, malonyl, malyl and succinyl thioesters), demonstrating a rare convergence between top-down and bottom-up approaches to the origins of metabolism. The diversity and simplicity of conditions that form thioesters from core metabolites suggests the energetic link between thioester synthesis and catabolism was in place at the earliest stage of prebiotic chemistry, constraining the path for the later evolution of life’s phosphorus-based energy currencies.</b></p>

Inverted Turbo-Jet Engine for Hypersonic Propulsion

2005 ◽  
Author(s):  
Yoshiharu Tsujikawa ◽  
Ken-Ichi Kaneko ◽  
Shusuke Tokumoto
Keyword(s):  
High Energy ◽  
Brayton Cycle ◽  
Jet Engine ◽  
Hypersonic Propulsion ◽  
The Core ◽  
Mode Of Operation ◽  
High Energy Efficiency ◽  
Engine Components ◽  
Power Generation Systems

This paper concerns to the inverted turbo-jet engine intended for operation in the range of Mach numbers from 0 to 6. In the present engine configuration, which is based on the inverted Brayton cycle, the sequence of the core-engine components was arranged in the order: turbine - heat exchanger - compressor - combustor. It should also be noted that the inverted Brayton cycle has also been considered for application to stationary power generation systems in the role of a bottoming cycle. An improved version of the inverted turbo-jet engine (ITE), has also been proposed in the present paper, incorporates an additional combustor installed between the inlet and the turbine. At low speeds this additional burner allows a heat input upstream of the initial turbine to augment thrust. The fuel-rich mode of operation is expected to be beneficial, as speed increases. In summary, the inverted turbojet engine can produce sufficient thrust compared to another engine concepts and it reveals high energy efficiency over the wide speed of range.

scholarly journals Molecular and Physiological Role of the Trehalose-Hydrolyzing α-Glucosidase from Thermus thermophilus HB27

2008 ◽  
Vol 190 (7) ◽  
pp. 2298-2305 ◽  
Author(s):  
Susana Alarico ◽  
Milton S. da Costa ◽  
Nuno Empadinhas
Keyword(s):  
Amino Acids ◽  
Minimal Medium ◽  
Thermus Thermophilus ◽  
Physiological Role ◽  
Hydrolytic Activity ◽  
Recombinant Enzyme ◽  
New Feature ◽  
Hydrolysis Of ◽  
Reciprocal Replacement

ABSTRACT Trehalose supports the growth of Thermus thermophilus strain HB27, but the absence of obvious genes for the hydrolysis of this disaccharide in the genome led us to search for enzymes for such a purpose. We expressed a putative α-glucosidase gene (TTC0107), characterized the recombinant enzyme, and found that the preferred substrate was α,α-1,1-trehalose, a new feature among α-glucosidases. The enzyme could also hydrolyze the disaccharides kojibiose and sucrose (α-1,2 linkage), nigerose and turanose (α-1,3), leucrose (α-1,5), isomaltose and palatinose (α-1,6), and maltose (α-1,4) to a lesser extent. Trehalose was not, however, a substrate for the highly homologous α-glucosidase from T. thermophilus strain GK24. The reciprocal replacement of a peptide containing eight amino acids in the α-glucosidases from strains HB27 (LGEHNLPP) and GK24 (EPTAYHTL) reduced the ability of the former to hydrolyze trehalose and provided trehalose-hydrolytic activity to the latter, showing that LGEHNLPP is necessary for trehalose recognition. Furthermore, disruption of the α-glucosidase gene significantly affected the growth of T. thermophilus HB27 in minimal medium supplemented with trehalose, isomaltose, sucrose, or palatinose, to a lesser extent with maltose, but not with cellobiose (not a substrate for the α-glucosidase), indicating that the α-glucosidase is important for the assimilation of those four disaccharides but that it is also implicated in maltose catabolism.

scholarly journals Energy Conservation via Thioesters in a Non-Enzymatic Metabolism-like Reaction Network

2019 ◽  
Author(s):  
Elodie Chevallot-Beroux ◽  
Jan Gorges ◽  
Joseph Moran
Keyword(s):  
Prebiotic Chemistry ◽  
Reaction Network ◽  
Biochemical Networks ◽  
Biochemical Evolution ◽  
Top Down ◽  
The Core ◽  
Energy Flows ◽  
Oxidative Breakdown ◽  
Intermediary Role

<p><b>Life’s catabolic processes capture chemical energy from the oxidative breakdown of metabolites. In the catabolic pathways at the core of biochemistry, the oxidation of </b>α-<b>ketoacids or aldehydes is coupled to the synthesis of thioesters, whose energy-releasing hydrolysis is in turn coupled to the production of adenosine 5’-triphosphate (ATP). How these processes became linked before life emerged, and thus how the framework for modern bioenergetics was established, is a major problem for understanding the origins of biochemistry. The structure of biochemical networks suggests that the intermediary role of thioesters in biological energy flows, and their central role in biosynthesis, is a consequence of their entry into metabolism at the earliest stage of biochemical evolution. However, how thioesters could have become embedded within a metabolic network before the advent of enzymes remains unclear. Here we demonstrate non-enzymatic oxidant- or light-driven thioester synthesis from biological </b>α-<b>ketoacids and show it can be integrated within an iron-promoted metabolism-like reaction network. The thioesters obtained are those predicted to be pivotal in computational reconstructions of primitive biochemical networks (acetyl, malonyl, malyl and succinyl thioesters), demonstrating a rare convergence between top-down and bottom-up approaches to the origins of metabolism. The diversity and simplicity of conditions that form thioesters from core metabolites suggests the energetic link between thioester synthesis and catabolism was in place at the earliest stage of prebiotic chemistry, constraining the path for the later evolution of life’s phosphorus-based energy currencies.</b></p>

Thioester Synthesis by Geoelectrochemical CO2 Fixation on Ni Sulfides

2020 ◽  
Author(s):  
Norio Kitadai ◽  
Ruhei Nakamura ◽  
Masahiro Yamamoto ◽  
Satoshi Okada ◽  
Wataru Takahagi ◽  
...  
Keyword(s):  
Origin Of Life ◽  
Nickel Sulfide ◽  
Co2 Fixation ◽  
Hydrothermal Systems ◽  
Co Dehydrogenase ◽  
Enzymatic Process ◽  
Electrochemical Condition ◽  
Autotrophic Metabolism ◽  
Co2 Electroreduction

<i></i>Thioester synthesis via CO2 fixation by CO dehydrogenase/acetyl-CoA synthase is among the most ancient autotrophic metabolism often suggested to have a prebiotic root. Here we demonstrate that, under an electrochemical condition realizable in early ocean hydrothermal systems, nickel sulfide (NiS) gradually reduces to Ni0, thereby drastically enhancing its capability of driving nonenzymatic CO2 fixation. It catalyzes CO2 electroreduction to CO, concentrates CO on the surface Ni0 sites, and promotes CO condensation to a thioester in the presence of methanethiol. Even greater CO-to-thioester reaction efficiency is realized with NiS coprecipitating with FeS or CoS. Considering the central role of Ni in the enzymatic process mentioned above, our demonstrated thioester synthesis by the partially electroreduced NiS could have a direct implication to the autotrophic origin of life.<br>

Heat-initiated prebiotic formation of peptides from glycine/aspartic acid and glycine/valine in aqueous environment and clay suspension

2009 ◽  
Vol 8 (2) ◽  
pp. 107-115 ◽  
Author(s):  
Chandra Kala Pant ◽  
Hem Lata ◽  
Hari Datt Pathak ◽  
Mohan Singh Mehata
Keyword(s):  
Amino Acids ◽  
Aspartic Acid ◽  
Cyclic Peptides ◽  
Divalent Cations ◽  
Reaction System ◽  
Montmorillonite Clay ◽  
Aqueous Environment ◽  
Clay Suspension ◽  
Peptide Formation

AbstractThe effect of heat on the reaction system of glycine/aspartic acid and glycine/valine in the aqueous environment as well as in montmorillonite clay suspension with or without divalent cations (Ca2+, Mg2+ and Ni2+) has been investigated at 85°C±5°C for varying periods under prebiotic drying and wetting conditions. The resulting products were analysed and characterized by chromatographic and spectroscopic methods. Peptide formation appears to depend on the duration of heat effect, nature of reactant amino acids and, to some extent, on montmorillonite clay incorporated with divalent cations. In the glycine/aspartic acid system, oligomerization of glycine was limited up to trimer level (Gly)3 along with the formation of glycyl-aspartic acid, while linear and cyclic peptides of aspartic acid were not formed, whereas the glycine/valine system preferentially elongated homo-oligopeptide of glycine up to pentamer level (Gly)5 along with formation of hetero-peptides (Gly-Val and Val-Gly). These studies are relevant in the context of the prebiotic origin of proteins and the role of clay and metal ions in condensation and oligomerization of amino acids. The length of the bio-oligomer chain depends upon the reaction conditions. However, condensation into even a small length seems significant, as the same process would have taken millions of years in the primitive era of the Earth, leading to the first proteins.

Structure and composition of the alkali-insoluble cell wall fraction of Coprinus macrorhizus var. microsporus

1980 ◽  
Vol 58 (2) ◽  
pp. 147-153 ◽  
Author(s):  
Carey B. Bottom ◽  
Donald J. Siehr
Keyword(s):  
Amino Acids ◽  
Cell Wall ◽  
Acid Hydrolysis ◽  
Cell Walls ◽  
Cell Wall Fraction ◽  
Enzymic Hydrolysis ◽  
Methylation Analysis ◽  
Partial Acid Hydrolysis ◽  
The Core ◽  
Hydrolysis Of

The alkali-insoluble (R-) fraction from the cell walls of Coprinus macrorhizus var. microsporus is a highly branched glucan, containing α-(1 → 4), β-(1 → 3), and β-(1 → 6) linkages as shown by methylation, partial acid hydrolysis, and enzymic hydrolysis. The α-(1 → 4)-linked segments are joined by occasional β-(1 → 3) links as suggested by the identification of 2-O-α-glucopyranosyl erythritol in the hydrolysate of the reduced, periodate-oxidized glucan. Hydrolysis of the permethylated glucan gave nearly equimolar amounts of 2,4-di- and 2,3-di-O-methyl-D-glucose. Methylation analysis of the residue from enzymic hydrolysis, the "CORE-fraction," indicated the presence of glucose residues in this fraction linked through positions O1, O3, O4, and O6. Hydrolysates of the R-fraction contained mannose, glucosamine, and amino acids in addition to glucose.

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