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361 results on '"Amador-Noguez, Daniel"'

5. Near-equilibrium glycolysis supports metabolic homeostasis and energy yield

Author

Park, Junyoung O, Tanner, Lukas B, Wei, Monica H, Khana, Daven B, Jacobson, Tyler B, Zhang, Zheyun, Rubin, Sara A, Li, Sophia Hsin-Jung, Higgins, Meytal B, Stevenson, David M, Amador-Noguez, Daniel, and Rabinowitz, Joshua D

Subjects
Biological Sciences, Industrial Biotechnology, Affordable and Clean Energy, Animals, Cell Line, Clostridium acetobutylicum, Clostridium cellulolyticum, Energy Metabolism, Escherichia coli, Glucose, Glycolysis, Homeostasis, Mice, Nitrogen, bcl-2-Associated X Protein, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Biochemistry & Molecular Biology, Biochemistry and cell biology, Medicinal and biomolecular chemistry
Abstract

Glycolysis plays a central role in producing ATP and biomass. Its control principles, however, remain incompletely understood. Here, we develop a method that combines 2H and 13C tracers to determine glycolytic thermodynamics. Using this method, we show that, in conditions and organisms with relatively slow fluxes, multiple steps in glycolysis are near to equilibrium, reflecting spare enzyme capacity. In Escherichia coli, nitrogen or phosphorus upshift rapidly increases the thermodynamic driving force, deploying the spare enzyme capacity to increase flux. Similarly, respiration inhibition in mammalian cells rapidly increases both glycolytic flux and the thermodynamic driving force. The thermodynamic shift allows flux to increase with only small metabolite concentration changes. Finally, we find that the cellulose-degrading anaerobe Clostridium cellulolyticum exhibits slow, near-equilibrium glycolysis due to the use of pyrophosphate rather than ATP for fructose-bisphosphate production, resulting in enhanced per-glucose ATP yield. Thus, near-equilibrium steps of glycolysis promote both rapid flux adaptation and energy efficiency.

Published
2019

8. A metabolic pathway for catabolizing levulinic acid in bacteria

Author

Rand, Jacqueline M, Pisithkul, Tippapha, Clark, Ryan L, Thiede, Joshua M, Mehrer, Christopher R, Agnew, Daniel E, Campbell, Candace E, Markley, Andrew L, Price, Morgan N, Ray, Jayashree, Wetmore, Kelly M, Suh, Yumi, Arkin, Adam P, Deutschbauer, Adam M, Amador-Noguez, Daniel, and Pfleger, Brian F

Subjects
Biological Sciences, Industrial Biotechnology, Biotechnology, Genetics, Affordable and Clean Energy, Bacteria, Bacterial Proteins, Base Sequence, Biomass, CRISPR-Cas Systems, Carbon, DNA Transposable Elements, Escherichia coli, Gene Expression Regulation, Bacterial, Gene Knockdown Techniques, Genes, Bacterial, Levulinic Acids, Metabolic Engineering, Metabolic Networks and Pathways, Operon, Propionates, Pseudomonas putida, Microbiology, Medical Microbiology
Abstract

Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. This discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.

Published
2017

15. ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism

Author

Rashan, Edrees H., primary, Bartlett, Abigail K., additional, Khana, Daven B., additional, Zhang, Jingying, additional, Jain, Raghav, additional, Smith, Andrew J., additional, Baker, Zakery N., additional, Cook, Taylor, additional, Caldwell, Alana, additional, Chevalier, Autumn R., additional, Pfleger, Brian F., additional, Yuan, Peng, additional, Amador-Noguez, Daniel, additional, Simcox, Judith A., additional, and Pagliarini, David J., additional

Published
2024
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16. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

Author

Park, Junyoung O, Rubin, Sara A, Xu, Yi-Fan, Amador-Noguez, Daniel, Fan, Jing, Shlomi, Tomer, and Rabinowitz, Joshua D

Subjects
Animals, Cell Line, Enzymes, Escherichia coli, Mice, Saccharomyces cerevisiae, Thermodynamics, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Biochemistry & Molecular Biology
Abstract

In metabolism, available free energy is limited and must be divided across pathway steps to maintain a negative ΔG throughout. For each reaction, ΔG is log proportional both to a concentration ratio (reaction quotient to equilibrium constant) and to a flux ratio (backward to forward flux). Here we use isotope labeling to measure absolute metabolite concentrations and fluxes in Escherichia coli, yeast and a mammalian cell line. We then integrate this information to obtain a unified set of concentrations and ΔG for each organism. In glycolysis, we find that free energy is partitioned so as to mitigate unproductive backward fluxes associated with ΔG near zero. Across metabolism, we observe that absolute metabolite concentrations and ΔG are substantially conserved and that most substrate (but not inhibitor) concentrations exceed the associated enzyme binding site dissociation constant (Km or Ki). The observed conservation of metabolite concentrations is consistent with an evolutionary drive to utilize enzymes efficiently given thermodynamic and osmotic constraints.

Published
2016

29. Systematic Analysis of Metabolic Bottlenecks in the Methylerythritol 4-Phosphate (MEP) Pathway of Zymomonas mobilis

Author

Khana, Daven B., primary, Tatli, Mehmet, additional, Rivera Vazquez, Julio, additional, Weraduwage, Sarathi M., additional, Stern, Noah, additional, Hebert, Alexander S., additional, Angelica Trujillo, Edna, additional, Stevenson, David M., additional, Coon, Joshua J., additional, Sharky, Thomas D., additional, and Amador-Noguez, Daniel, additional

Published
2023
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31. Listeria monocytogenes GlmR Is an Accessory Uridyltransferase Essential for Cytosolic Survival and Virulence

Author

Pensinger, Daniel A., primary, Gutierrez, Kimberly V., additional, Smith, Hans B., additional, Vincent, William J. B., additional, Stevenson, David S., additional, Black, Katherine A., additional, Perez-Medina, Krizia M., additional, Dillard, Joseph P., additional, Rhee, Kyu Y., additional, Amador-Noguez, Daniel, additional, Huynh, TuAnh N., additional, and Sauer, John-Demian, additional

Published
2023
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38. Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway

Author

Gambacorta, Francesca V., primary, Wagner, Ellen R., additional, Jacobson, Tyler B., additional, Tremaine, Mary, additional, Muehlbauer, Laura K., additional, McGee, Mick A., additional, Baerwald, Justin J., additional, Wrobel, Russell L., additional, Wolters, John F., additional, Place, Mike, additional, Dietrich, Joshua J., additional, Xie, Dan, additional, Serate, Jose, additional, Gajbhiye, Shabda, additional, Liu, Lisa, additional, Vang-Smith, Maikayeng, additional, Coon, Joshua J., additional, Zhang, Yaoping, additional, Gasch, Audrey P., additional, Amador-Noguez, Daniel, additional, Hittinger, Chris Todd, additional, Sato, Trey K., additional, and Pfleger, Brian F., additional

Published
2022
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41. Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels

Author

Lynd, Lee R., primary, Beckham, Gregg T., additional, Guss, Adam M., additional, Jayakody, Lahiru N., additional, Karp, Eric M., additional, Maranas, Costas, additional, McCormick, Robert L., additional, Amador-Noguez, Daniel, additional, Bomble, Yannick J., additional, Davison, Brian H., additional, Foster, Charles, additional, Himmel, Michael E., additional, Holwerda, Evert K., additional, Laser, Mark S., additional, Ng, Chiam Yu, additional, Olson, Daniel G., additional, Román-Leshkov, Yuriy, additional, Trinh, Cong T., additional, Tuskan, Gerald A., additional, Upadhayay, Vikas, additional, Vardon, Derek R., additional, Wang, Lin, additional, and Wyman, Charles E., additional

Published
2022
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43. Listeria monocytogenes GlmR is an accessory uridyltransferase essential for cytosolic survival and virulence

Author

Pensinger, Daniel A., primary, Gutierrez, Kimberly V., additional, Smith, Hans B., additional, Vincent, William J.B., additional, Stevenson, David S., additional, Black, Katherine A., additional, Perez-Medina, Krizia M., additional, Dillard, Joseph P., additional, Rhee, Kyu Y., additional, Amador-Noguez, Daniel, additional, Huynh, TuAnh N, additional, and Sauer, John-Demian, additional

Published
2021
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47. Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13 C-Tracer Analysis

Author

Lawson, Christopher E., primary, Mundinger, Aniela B., additional, Koch, Hanna, additional, Jacobson, Tyler B., additional, Weathersby, Coty A., additional, Jetten, Mike S. M., additional, Pabst, Martin, additional, Amador-Noguez, Daniel, additional, Noguera, Daniel R., additional, McMahon, Katherine, additional, and Lücker, Sebastian, additional

Published
2021
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49. Investigating the chemolithoautotrophic and formate metabolism of nitrospira moscoviensis by constraint-based metabolic modeling and 13C-tracer analysis

Author

Lawson, Christopher E. (author), Mundinger, Aniela B. (author), Koch, Hanna (author), Jacobson, Tyler B. (author), Weathersby, Coty A. (author), Jetten, Mike S.M. (author), Pabst, M. (author), Amador-Noguez, Daniel (author), Noguera, Daniel R. (author), Lawson, Christopher E. (author), Mundinger, Aniela B. (author), Koch, Hanna (author), Jacobson, Tyler B. (author), Weathersby, Coty A. (author), Jetten, Mike S.M. (author), Pabst, M. (author), Amador-Noguez, Daniel (author), and Noguera, Daniel R. (author)

Abstract

Nitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple organic compounds to fuel their energy metabolism, the metabolic networks controlling their autotrophic and mixotrophic growth remain poorly understood. Here, we reconstructed a genome-scale metabolic model for Nitrospira moscoviensis (iNmo686) and used flux balance analysis to evaluate the metabolic networks controlling autotrophic and formatotrophic growth on nitrite and formate, respectively. Subsequently, proteomic analysis and [13C]bicarbonate and [13C]formate tracer experiments coupled to metabolomic analysis were performed to experimentally validate model predictions. Our findings corroborate that N. moscoviensis uses the reductive tricarboxylic acid cycle for CO2 fixation, and we also show that N. moscoviensis can indirectly use formate as a carbon source by oxidizing it first to CO2 followed by reassimilation, rather than direct incorporation via the reductive glycine pathway. Our study offers the first measurements of Nitrospira's in vivo central carbon metabolism and provides a quantitative tool that can be used for understanding and predicting their metabolic processes. IMPORTANCE Nitrospira spp. are globally abundant nitrifying bacteria in soil and aquatic ecosystems and in wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge. Here, we provide the first constraint-based metabolic model of Nitrospira moscoviensis representing the ubiquitous Nitrospira linea, BT/Environmental Biotechnology

Published
2021
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50. Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum

Author

Amador-Noguez, Daniel, Feng, Xiao-Jiang, Fan, Jing, Roquet, Nathaniel, Rabitz, Herschel, and Rabinowitz, Joshua D.

Subjects
Tracers (Biology) -- Research, Clostridium -- Physiological aspects, Microbial metabolism -- Research, Biological sciences
Abstract

Obligatory anaerobic bacteria are major contributors to the overall metabolism of soil and the human gut. The metabolic pathways of these bacteria remain, however, poorly understood. Using isotope tracers, mass spectrometry, and quantitative flux modeling, here we directly map the metabolic pathways of Clostridium acetobutylicum, a soil bacterium whose major fermentation products include the biofuels butanol and hydrogen. While genome annotation suggests the absence of most tricarboxylic acid (TCA) cycle enzymes, our results demonstrate that this bacterium has a complete, albeit bifurcated, TCA cycle; oxaloacetate flows to succinate both through citrate/[alpha]-ketoglutarate and via malate/fumarate. Our investigations also yielded insights into the pathways utilized for glucose catabolism and amino acid biosynthesis and revealed that the organism's one-carbon metabolism is distinct from that of model microbes, involving reversible pyruvate decarboxylation and the use of pyruvate as the one-carbon donor for biosynthetic reactions. This study represents the first in vivo characterization of the TCA cycle and central metabolism of C. acetobutylicum. Our results establish a role for the full TCA cycle in an obligatory anaerobic organism and demonstrate the importance of complementing genome annotation with isotope tracer studies for determining the metabolic pathways of diverse microbes. doi: 10.1128/JB.00490-10

Published
2010

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