scholarly journals Metals enable a non-enzymatic acetyl CoA pathway

2017 ◽  
Author(s):  
Sreejith J. Varma ◽  
Kamila B. Muchowska ◽  
Paul Chatelain ◽  
Joseph Moran
Keyword(s):  
Carbon Fixation ◽  
Acid Synthesis ◽  
Last Universal Common Ancestor ◽  
Amino Acid Synthesis ◽  
Evolutionary Origins ◽  
Universal Common Ancestor ◽  
Wide Range ◽  
Biological Conversion ◽  
Acetyl Coa Pathway ◽  
Late Invention

The evolutionary origins of carbon fixation, the biological conversion of CO2to metabolites, remain unclear. Phylogenetics indicates that the AcCoA pathway, the reductive fixation of CO2to acetyl and pyruvate, was a key biosynthetic route used by the Last Universal Common Ancestor (LUCA) to build its biochemistry. However, debate exists over whether CO2fixation is a relatively late invention of pre-LUCA evolution or whether it dates back to prebiotic chemistry. Here we show that zero-valent forms of the transition metals known to act as co-factors in the AcCoA pathway (Fe0, Ni0, Co0) fix CO2on their surface in a manner closely resembling the biological pathway, producing acetate and pyruvate in near mM concentrations following cleavage from the surface. The reaction is robust over a wide range of temperatures and pressures with acetate and pyruvate constituting the major products in solution at 1 bar of CO2and 30 °g;C. The discovered conditions also promote 7 of the 11 steps of the rTCA cycle and amino acid synthesis, providing a stunning direct connection between simple inorganic chemistry and ancient CO2-fixation pathways. The results strongly sup-port the notion that CO2-fixation pathways are an outgrowth of spontaneous geochemistry.

scholarly journals Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Tomonari Sumi ◽  
Kouji Harada
Keyword(s):  
Carbon Metabolism ◽  
Carbon Fixation ◽  
Citrate Synthase ◽  
Tricarboxylic Acid Cycle ◽  
Necessary Condition ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Biomass Components ◽  
Kinetics Of ◽  
Reductive Tricarboxylic Acid Cycle

AbstractThe origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood–Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.

scholarly journals Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Nicolas Barraud ◽  
Sylvie Létoffé ◽  
Christophe Beloin ◽  
Joelle Vinh ◽  
Giovanni Chiappetta ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Redox Homeostasis ◽  
Acid Synthesis ◽  
Amino Acid Synthesis ◽  
Physiological Basis ◽  
Proteomic Approach ◽  
Wide Range ◽  
Range Of Functions ◽  
Cysteine Thiols

AbstractCommunities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen, and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG, and GltD altered important biofilm properties, including motility, biofilm maturation, or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.

scholarly journals Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress

2020 ◽  
Author(s):  
Nicolas Barraud ◽  
Sylvie Létoffé ◽  
Christophe Beloin ◽  
Joelle Vinh ◽  
Giovanni Chiappetta ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Redox Homeostasis ◽  
Acid Synthesis ◽  
Amino Acid Synthesis ◽  
Physiological Basis ◽  
Proteomic Approach ◽  
Wide Range ◽  
Range Of Functions ◽  
Cysteine Thiols

SUMMARYCommunities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG and GltD altered important biofilm properties, including motility, biofilm maturation or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.

Changes in ribulose-1,5-bisphosphate carboxylase/oxygenase and phosphoenolpyruvate carboxylase activities and 14CO2 fixation during the rooting of strawberry shoots in vitro

1994 ◽  
Vol 74 (4) ◽  
pp. 827-831 ◽  
Author(s):  
Chafik Hdider ◽  
Yves Desjardins
Keyword(s):  
Phosphoenolpyruvate Carboxylase ◽  
Time Course ◽  
Carbon Fixation ◽  
Acid Synthesis ◽  
Rubisco Activity ◽  
Amino Acid Synthesis ◽  
Bisphosphate Carboxylase ◽  
Rooting Medium ◽  
Rapid Incorporation

The potential for carbon fixation was investigated in in vitro strawberry (Fragaria × ananassa Duch. Kent) shoots 5, 10 and 28 d after transfer to a rooting medium. The activities of ribulose-1,5-bisphosphate carboxylase (Rubisco) and phosphoenolpyruvate carboxylase (PEPC) and the time course of 14CO2 fixation were investigated. Five days after transfer, Rubisco activity was low but was increased two-fold after 28 d. In contrast PEPC activity was highest at 5 d and declined to about 0.4-fold by day 28. The rate of 14CO2 fixation was similar at 5, 10 and 28 d after transfer. However, a more rapid incorporation of 14CO2 into amino acids was observed at 5 than at 10 or 28 d after transfer. These results suggest that strawberry shoots undergo a progressive transition from heterotrophic to autotrophic carbon fixation during their rooting and that PEPC plays an important role in sustaining carbon fixation and amino acid synthesis during the first few days after their transfer to rooting medium. Key words: In vitro culture, phosphoenolpyruvate carboxylase, ribulose-1,5-bisphosphate carboxylase

scholarly journals A hydrogen dependent geochemical analogue of primordial carbon and energy metabolism

2019 ◽  
Author(s):  
Martina Preiner ◽  
Kensuke Igarashi ◽  
Kamila B. Muchowska ◽  
Mingquan Yu ◽  
Sreejith J. Varma ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Hydrogen Gas ◽  
Last Universal Common Ancestor ◽  
Acetyl Coa ◽  
Universal Common Ancestor ◽  
Acetyl Coa Pathway ◽  
Aqueous Conditions ◽  
Metal Cofactors ◽  
Alkaline Hydrothermal Vents ◽  
Electrochemical Potentials

AbstractHydrogen gas, H2, is generated in alkaline hydrothermal vents from reactions of iron containing minerals with water during a geological process called serpentinization. It has been a source of electrons and energy since there was liquid water on the early Earth, and it fuelled early anaerobic ecosystems in the Earth’s crust1–3. H2is the electron donor for the most ancient route of biological CO2fixation, the acetyl-CoA (or Wood-Ljungdahl) pathway, which unlike any other autotrophic pathway simultaneously supplies three key requirements for life: reduced carbon in the form of acetyl groups, electrons in the form of reduced ferredoxin, and ion gradients for energy conservation in the form of ATP4,5. The pathway is linear, not cyclic, it releases energy rather than requiring energy input, its enzymes are replete with primordial metal cofactors6,7, it traces to the last universal common ancestor8and abiotic, geochemical organic syntheses resembling segments of the pathway occur in hydrothermal vents today9,10. Laboratory simulations of the acetyl-CoA pathway’s reactions include the nonenzymatic synthesis of thioesters from CO and methylsulfide11, the synthesis of acetate12and pyruvate13from CO2using native iron or external electrochemical potentials14as the electron source. However, a full abiotic analogue of the acetyl-CoA pathway from H2and CO2as it occurs in life has not been reported to date. Here we show that three hydrothermal minerals — awaruite (Ni3Fe), magnetite (Fe3O4) and greigite (Fe3S4) — catalyse the fixation of CO2with H2at 100 °C under alkaline aqueous conditions. The product spectrum includes formate (100 mM), acetate (100 μM), pyruvate (10 μM), methanol (100 μM), and methane. With these simple catalysts, the overall exergonic reaction of the acetyl-CoA pathway is facile, shedding light on both the geochemical origin of microbial metabolism and on the nature of abiotic formate and methane synthesis in modern hydrothermal vents.

Influence of increased nutrient supply on Microcystis aeruginosa at cellular and proteomic levels

2020 ◽  
Vol 85 ◽  
pp. 47-58
Author(s):  
Y Jiang ◽  
Y Liu
Keyword(s):  
Microcystis Aeruginosa ◽  
Regulatory Protein ◽  
Acid Synthesis ◽  
Nutrient Supply ◽  
Nitrogen Supply ◽  
Nitrogen And Phosphorus ◽  
Comprehensive Description ◽  
Amino Acid Synthesis ◽  
High Nutrient ◽  
Proteomic Responses

Various studies have observed that increased nutrient supply promotes the growth of bloom-forming cyanobacteria, but only a limited number of studies have investigated the influence of increased nutrient supply on bloom-forming cyanobacteria at the proteomic level. We investigated the cellular and proteomic responses of Microcystis aeruginosa to elevated nitrogen and phosphorus supply. Increased supply of both nutrients significantly promoted the growth of M. aeruginosa and the synthesis of chlorophyll a, protein, and microcystins. The release of microcystins and the synthesis of polysaccharides negatively correlated with the growth of M. aeruginosa under high nutrient levels. Overexpressed proteins related to photosynthesis, and amino acid synthesis, were responsible for the stimulatory effects of increased nutrient supply in M. aeruginosa. Increased nitrogen supply directly promoted cyanobacterial growth by inducing the overexpression of the cell division regulatory protein FtsZ. NtcA, that regulates gene transcription related to both nitrogen assimilation and microcystin synthesis, was overexpressed under the high nitrogen condition, which consequently induced overexpression of 2 microcystin synthetases (McyC and McyF) and promoted microcystin synthesis. Elevated nitrogen supply induced the overexpression of proteins involved in gas vesicle organization (GvpC and GvpW), which may increase the buoyancy of M. aeruginosa. Increased phosphorus level indirectly affected growth and the synthesis of cellular substances in M. aeruginosa through the mediation of differentially expressed proteins related to carbon and phosphorus metabolism. This study provides a comprehensive description of changes in the proteome of M. aeruginosa in response to an increased supply of 2 key nutrients.

O-AcylTEMPOs, a Modified and Fundamental, but Unexplored Carboxylic Derivative: Recent Progress in Synthetic Applications

2019 ◽  
Vol 23 (19) ◽  
pp. 2102-2121
Author(s):  
Hiroyuki Kawafuchi ◽  
Lijian Ma ◽  
Md Imran Hossain ◽  
Tsutomu Inokuchi
Keyword(s):  
Organic Synthesis ◽  
Recent Progress ◽  
Knoevenagel Condensation ◽  
Acid Synthesis ◽  
Amino Acid Synthesis ◽  
Electrophilic Amination ◽  
Weinreb Amides ◽  
Anionic Species ◽  
Diastereoselective Addition ◽  
Carbonyl Function

O-Acylated 2,2,6,6-tetramethylpiperidine-N-oxyls (abbr. O-AcylTEMPOs) are easily available and stable carboxylic derivatives, but their utility in organic synthesis is unexplored in contrast to analogues, such as the N-methoxy-N-methylamides, known as Weinreb amides. Especially, the O–N unit of the O-acylTEMPOs dictates a fairly electronwithdrawing character for the carbonyl function. This enhances the reactivity and stability of the resulting enolate ions. Accordingly, O-acylTEMPOs allow various transformations and this review encompasses seven topics: (1) Reactivity of O-acylTEMPOs towards nucleophiles and chemoselective transformations, (2) Reactivity of anionic species derived from O-acylTEMPOs, (3) E-Selective Knoevenagel condensation of acetoacetylTEMPOs and synthesis of furans, (4) Electrocyclization of 2,4-dienones derived from acetoacetic derivatives and 2-substituted enals, (5) Diastereoselective addition of amide anion to O-(2-alkenoyl)TEMPOs and β-amino acid synthesis, (6) Thermolysis of O-acylTEMPOs, and (7) Applications for Umpolung reactions using O-benzoylTEMPOs, useful for the electrophilic amination of alkenes and alkynes.

scholarly journals Petasis vs. Strecker Amino Acid Synthesis: Convergence, Divergence and Opportunities in Organic Synthesis

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1707
Author(s):  
Wayiza Masamba
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Organic Synthesis ◽  
Acid Synthesis ◽  
Physical Sciences ◽  
Amino Acid Synthesis

α-Amino acids find widespread applications in various areas of life and physical sciences. Their syntheses are carried out by a multitude of protocols, of which Petasis and Strecker reactions have emerged as the most straightforward and most widely used. Both reactions are three-component reactions using the same starting materials, except the nucleophilic species. The differences and similarities between these two important reactions are highlighted in this review.

scholarly journals Enzymatic cascade systems for D-amino acid synthesis: progress and perspectives

2021 ◽  
Author(s):  
Anwen Fan ◽  
Jiarui Li ◽  
Yangqing Yu ◽  
Danping Zhang ◽  
Yao Nie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acid Synthesis ◽  
Amino Acid Synthesis ◽  
Cascade Systems
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