The Experts below are selected from a list of 19863 Experts worldwide ranked by ideXlab platform
Eric S. Boyd - One of the best experts on this subject based on the ideXlab platform.
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microbial Substrate Preference dictated by energy demand rather than supply
Nature Geoscience, 2017Co-Authors: Maximiliano J. Amenabar, Eric S. Boyd, Eric E. Roden, Everett L. Shock, John W. PetersAbstract:Growth Substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of Substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and fourfold more energy per mole of electrons transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eightfold greater than when provided S°/Fe3+ or H2/Fe3+, indicating that the H2/S° redox couple is preferred. Indeed, cells provided with all three growth Substrates (H2, Fe3+ and S°) grew preferentially by reduction of S° with H2. We conclude that Substrate Preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different Substrates, rather than Substrate energy supply. Microbes are expected to prefer Substrates with the highest energy yield. Laboratory experiments demonstrate that a metabolically flexible archaeon exhibits Preference for and greater growth from lower energy Substrates.
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Microbial Substrate Preference dictated by energy demand rather than supply
Nature geoscience, 2017Co-Authors: Maximiliano J. Amenabar, Eric E. Roden, Everett L. Shock, John W. Peters, Eric S. BoydAbstract:Growth Substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of Substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and four-fold more energy per mol electron transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eight-fold greater than when provided S°/Fe3+ or H2/Fe3+, indicating the H2/S° redox couple is preferred. Indeed, cells provided with all three growth Substrates (H2, Fe3+, and S°) grew preferentially by reduction of S° with H2. We conclude that Substrate Preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different Substrates, rather than Substrate energy supply.
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Substrate Preference uptake kinetics and bioenergetics in a facultatively autotrophic thermoacidophilic crenarchaeote
FEMS Microbiology Ecology, 2016Co-Authors: Matthew R Urschel, Eric S. Boyd, Trinity L Hamilton, Eric E. RodenAbstract:Facultative autotrophs are abundant components of communities inhabiting geothermal springs. However, the influence of uptake kinetics and energetics on Preference for Substrates is not well understood in this group of organisms. Here, we report the isolation of a facultatively autotrophic crenarchaeote, strain CP80, from Cinder Pool (CP, 88.7°C, pH 4.0), Yellowstone National Park. The 16S rRNA gene sequence from CP80 is 98.8% identical to that from Thermoproteus uzonensis and is identical to the most abundant sequence identified in CP sediments. Strain CP80 reduces elemental sulfur (S8°) and demonstrates hydrogen (H2)-dependent autotrophic growth. H2-dependent autotrophic activity is suppressed by amendment with formate at a concentration in the range of 20 to 40 μM, similar to the affinity constant determined for formate utilization. Synthesis of a cell during growth with low concentrations of formate required 0.5 μJ compared to 2.5 μJ during autotrophic growth with H2. These results, coupled to data indicating greater C assimilation efficiency when grown with formate as compared to carbon dioxide, are consistent with preferential use of formate for energetic reasons. Collectively, these results provide new insights into the kinetic and energetic factors that influence the physiology and ecology of facultative autotrophs in high temperature acidic environments.
Eric E. Roden - One of the best experts on this subject based on the ideXlab platform.
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microbial Substrate Preference dictated by energy demand rather than supply
Nature Geoscience, 2017Co-Authors: Maximiliano J. Amenabar, Eric S. Boyd, Eric E. Roden, Everett L. Shock, John W. PetersAbstract:Growth Substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of Substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and fourfold more energy per mole of electrons transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eightfold greater than when provided S°/Fe3+ or H2/Fe3+, indicating that the H2/S° redox couple is preferred. Indeed, cells provided with all three growth Substrates (H2, Fe3+ and S°) grew preferentially by reduction of S° with H2. We conclude that Substrate Preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different Substrates, rather than Substrate energy supply. Microbes are expected to prefer Substrates with the highest energy yield. Laboratory experiments demonstrate that a metabolically flexible archaeon exhibits Preference for and greater growth from lower energy Substrates.
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Microbial Substrate Preference dictated by energy demand rather than supply
Nature geoscience, 2017Co-Authors: Maximiliano J. Amenabar, Eric E. Roden, Everett L. Shock, John W. Peters, Eric S. BoydAbstract:Growth Substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of Substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and four-fold more energy per mol electron transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eight-fold greater than when provided S°/Fe3+ or H2/Fe3+, indicating the H2/S° redox couple is preferred. Indeed, cells provided with all three growth Substrates (H2, Fe3+, and S°) grew preferentially by reduction of S° with H2. We conclude that Substrate Preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different Substrates, rather than Substrate energy supply.
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Substrate Preference uptake kinetics and bioenergetics in a facultatively autotrophic thermoacidophilic crenarchaeote
FEMS Microbiology Ecology, 2016Co-Authors: Matthew R Urschel, Eric S. Boyd, Trinity L Hamilton, Eric E. RodenAbstract:Facultative autotrophs are abundant components of communities inhabiting geothermal springs. However, the influence of uptake kinetics and energetics on Preference for Substrates is not well understood in this group of organisms. Here, we report the isolation of a facultatively autotrophic crenarchaeote, strain CP80, from Cinder Pool (CP, 88.7°C, pH 4.0), Yellowstone National Park. The 16S rRNA gene sequence from CP80 is 98.8% identical to that from Thermoproteus uzonensis and is identical to the most abundant sequence identified in CP sediments. Strain CP80 reduces elemental sulfur (S8°) and demonstrates hydrogen (H2)-dependent autotrophic growth. H2-dependent autotrophic activity is suppressed by amendment with formate at a concentration in the range of 20 to 40 μM, similar to the affinity constant determined for formate utilization. Synthesis of a cell during growth with low concentrations of formate required 0.5 μJ compared to 2.5 μJ during autotrophic growth with H2. These results, coupled to data indicating greater C assimilation efficiency when grown with formate as compared to carbon dioxide, are consistent with preferential use of formate for energetic reasons. Collectively, these results provide new insights into the kinetic and energetic factors that influence the physiology and ecology of facultative autotrophs in high temperature acidic environments.
Satoru Funamoto - One of the best experts on this subject based on the ideXlab platform.
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glycosylation status of nicastrin influences catalytic activity and Substrate Preference of γ secretase
Biochemical and Biophysical Research Communications, 2018Co-Authors: Mohammad Moniruzzaman, Mika Nobuhara, Seiko Ishihara, Hidekazu Higashide, Satoru FunamotoAbstract:Abstract γ-Secretase complex, the assembly of nicastrin (NCT), Presenilin (PS), Presenilin Enhancer-2 (PEN-2) and Anterior pharynx defective 1 (Aph-1), catalyzes the cleavage of amyloid precursor protein to generate amyloid-β protein (Aβ), the main culprit of Alzheimer's disease. NCT becomes matured through complex glycosylation and play important role in γ-secretase activity by interacting with catalytic subunit PS. However, the role of NCT glycosylation on γ-secretase activity and Substrate specificity is still unknown. The purpose of this study is to investigate the effect of NCT glycosylation on γ-secretase activity and Substrate specificity in a group of glycosylation mutant lectin resistant CHO (Lec) cells. CHO Lec-1 cells lack glycosyltransferase-I, GnT-I, thus N-glycan on NCT are all oligomannose type, whereas CHO Lec-2 cells synthesize NCT containing sialic acid deficient oligosaccharides due to the impairment of cytidine 5′-monophosphate-sialic acid transporter. Here, we reported that mutant CHO Lec-1 and Lec-2 reduced γ-secretase activity in both cell-based and biochemical assays, and that CHO Lec-1 preferentially reduced Aβ generation. Endogenous level of γ-secretase complex, subcellular distribution of γ-secretase subunits and the level of functional γ-secretase complex remained unchanged in mutants. Interestingly, Coimmunoprecipitation study revealed that mutant γ-secretase could recognize Substrate as well as parental γ-secretase. Our data suggests that thorough glycosylation of NCT is critical for enzymatic activity and Substrate Preference of γ-secretase.
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Substrate ectodomain is critical for Substrate Preference and inhibition of γ-secretase
Nature communications, 2013Co-Authors: Satoru Funamoto, Toru Sasaki, Seiko Ishihara, Mika Nobuhara, Masaki Nakano, Miho Watanabe-takahashi, Takashi Saito, Nobuto Kakuda, Tomohiro Miyasaka, Kiyotaka NishikawaAbstract:Understanding the Substrate recognition mechanism of γ-secretase is a key step for establishing Substrate-specific inhibition of amyloid β-protein (Aβ) production. However, it is widely believed that γ-secretase is a promiscuous protease and that its Substrate-specific inhibition is elusive. Here we show that γ-secretase distinguishes the ectodomain length of Substrates and preferentially captures and cleaves Substrates containing a short ectodomain. We also show that a subset of peptides containing the CDCYCxxxxCxCxSC motif binds to the amino terminus of C99 and inhibits Aβ production in a Substrate-specific manner. Interestingly, these peptides suppress β-secretase-dependent cleavage of APP, but not that of sialyltransferase 1. Most importantly, intraperitoneal administration of peptides into mice results in a significant reduction in cerebral Aβ levels. This report provides direct evidence of the Substrate Preference of γ-secretase and its mechanism. Our results demonstrate that the ectodomain of C99 is a potent target for Substrate-specific anti-Aβ therapeutics to combat Alzheimer's disease.
Yong Q Chen - One of the best experts on this subject based on the ideXlab platform.
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molecular mechanism of Substrate Preference for ω 3 fatty acid desaturase from mortierella alpina by mutational analysis and molecular docking
Applied Microbiology and Biotechnology, 2018Co-Authors: Chunchi Rong, Haiqin Chen, Mingxuan Wang, Jianxin Zhao, Hao Zhang, Wei Chen, Yong Q ChenAbstract:The ω-3 fatty acid desaturase (ω3Des) is a key enzyme in the biosynthesis of polyunsaturated fatty acids (PUFAs). However, the enzyme exhibits a significant Preference towards different fatty acid Substrates. To examine the molecular mechanism of its Substrate specificity, a series of site-directed mutants were constructed based on the membrane topology model and functionally characterised by heterologous expression in Saccharomyces cerevisiae. Our results revealed that the W106F and V137T mutations markedly decreased the enzyme activity which indicated that these two residues were associated with Substrate recognition. In contrast, the A44S, M156I and W291M mutations showed significant increments (30 to 40%) of the conversion rate for AA Substrate desaturation, which suggests that these residues play a pivotal role in desaturation of longer chain-length Substrates. Through homology modelling of 3-dimensional structures and molecular docking of FADS15, we propose that the critical residues that bind to the CoA groups may affect Substrate localisation and govern Substrate Preference and chain-length specificity. Our work increases the understanding of the structure-function relationships of the microbial membrane-bound desaturases. The growing knowledge of the molecular mechanism will also aid in the efficient production of value-added fatty acids.
Tom L Blundell - One of the best experts on this subject based on the ideXlab platform.
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Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate.
mBio, 2019Co-Authors: Vitor Mendes, Michal Blaszczyk, Nupur Verma, Marcio Vinicius Bertacine Dias, Marta Acebrón-garcía-de-eulate, Tom L BlundellAbstract:ABSTRACT Trehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential in Mycobacterium tuberculosis, with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Here, we report the first mycobacterial OtsA structures from Mycobacterium thermoresistibile in both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of Substrate Preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme, and map a new allosteric site. IMPORTANCE Mycobacterial infections are a significant source of mortality worldwide, causing millions of deaths annually. Trehalose is a multipurpose disaccharide that plays a fundamental structural role in these organisms as a component of mycolic acids, a molecular hallmark of the cell envelope of mycobacteria. Here, we describe the first mycobacterial OtsA structures. We show mechanisms of Substrate Preference and show that OtsA is regulated allosterically by 2-oxoglutarate and 2-phosphoglycerate at an interfacial site. These results identify a new allosteric site and provide insight on the regulation of trehalose synthesis through the OtsAB pathway in mycobacteria.
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mycobacterial otsa structures reveal an allosteric site regulated by 2 oxoglutarate and 2 phosphoglycerate and the mechanism for Substrate Preference
bioRxiv, 2019Co-Authors: Vitor Mendes, Michal Blaszczyk, Marta Acebrongarciadeeulate, Nupur Verma, Marcio Vinicius Bertacine Dias, Tom L BlundellAbstract:Trehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential in M. tuberculosis, with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Herein, we report here the first mycobacterial OtsA structures from M. thermoresistibile in both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of Substrate Preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme and map a new allosteric site.
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Mycobacterial OtsA structures unveil Substrate Preference mechanism and allosteric regulation by 2-oxoglutarate and 2-phosphoglycerate
2019Co-Authors: Vitor Mendes, Michal Blaszczyk, Nupur Verma, Marcio Vinicius Bertacine Dias, Marta Acebrón-garcía-de-eulate, Tom L BlundellAbstract:AbstractTrehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential inM. tuberculosis, with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Herein, we report the first mycobacterial OtsA structures fromM. thermoresistibilein both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of Substrate Preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme and map a new allosteric site.
