Dataset Information

Casini2022 - genome scale metabolic model (iMTD22IC) of Methanothermobacter thermautotrophicus Delta H

ABSTRACT: (iMTD22IC) This model is described in these articles: Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G.G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N.D., Aristilde, L., Huson, D., Drager, A., Ley, R., Marcellin, E., Angenent, L.T., Molitor, B. 2023. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. Iscience, 26(10). Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G.G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N.D., Aristilde, L., Huson, D., Drager, A., Ley, R., Marcellin, E., Angenent, L.T., Molitor, B. 2022. An integrated systems-biology platform for power-to-gas technology. bioRxiv, 2022.12.30.522236. Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments, first, with molecular hydrogen and carbon dioxide, and second, with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Transcriptomics and proteomics data sets from these steady-state bioreactors, in combination with the implementation of a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach combining fermentation and omics data with genome-scale modeling to reveal knowledge gaps of archaeal metabolisms and the biotechnological potential of Methanothermobacter spp. as production platform hosts.

SUBMITTER: Isabella Casini

PROVIDER: MODEL2211290001 | BioModels | 2024-01-11

REPOSITORIES: BioModels

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Project description:(iMTD22IC) This model is described in these articles: Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G.G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N.D., Aristilde, L., Huson, D., Drager, A., Ley, R., Marcellin, E., Angenent, L.T., Molitor, B. 2023. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. Iscience, 26(10). Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G.G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N.D., Aristilde, L., Huson, D., Drager, A., Ley, R., Marcellin, E., Angenent, L.T., Molitor, B. 2022. An integrated systems-biology platform for power-to-gas technology. bioRxiv, 2022.12.30.522236. Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments, first, with molecular hydrogen and carbon dioxide, and second, with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Transcriptomics and proteomics data sets from these steady-state bioreactors, in combination with the implementation of a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach combining fermentation and omics data with genome-scale modeling to reveal knowledge gaps of archaeal metabolisms and the biotechnological potential of Methanothermobacter spp. as production platform hosts.

Project description:This model is described in these articles: Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G.G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N.D., Aristilde, L., Huson, D., Drager, A., Ley, R., Marcellin, E., Angenent, L.T., Molitor, B. 2023. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. Iscience, 26(10). Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G.G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N.D., Aristilde, L., Huson, D., Drager, A., Ley, R., Marcellin, E., Angenent, L.T., Molitor, B. 2022. An integrated systems-biology platform for power-to-gas technology. bioRxiv, 2022.12.30.522236. Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments, first, with molecular hydrogen and carbon dioxide, and second, with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Transcriptomics and proteomics data sets from these steady-state bioreactors, in combination with the implementation of a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach combining fermentation and omics data with genome-scale modeling to reveal knowledge gaps of archaeal metabolisms and the biotechnological potential of Methanothermobacter spp. as production platform hosts.

Project description:Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance and gas consumption/production of three wild-type strains and one genetically engineered strain in two independent quadruplicate chemostat bioreactor experiments: 1) with molecular hydrogen and carbon dioxide; and 2) with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. We collected statistically reliable transcriptomics and proteomics data sets from these steady-state bioreactors, which we integrated within our genome-scale metabolic models. The implementation of an pan-model that contains combined reactions from all three microbes allowed us to perform an interspecies comparison of the complete omics data set. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways, such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach using fermentation and omics data with genome-scale modeling for the investigation of lesser studied metabolisms, and the biotechnological potential of Methanothermobacter spp. as production platform hosts.

Project description:Modified atmosphere packaging (MAP) is a common strategy to selectively prevent the growth of certain species of meat spoiling bacteria. While studies on the effectiveness of MAP are still scarce on a putative control over the population of photobacteria detected as meat spoilers, they could develop means to enhance safety and quality of raw meat. This study aims to determine the impact on photobacteria of two modified atmospheres: with high oxygen concentration (red and white meats), and free oxygen MAP (white meats and seafood). We have conducted growth experiments of the two main species found on meat, Photobacterium carnosum (P.) and P. phosphoreum, on a meat simulation media under different gas mixtures of nitrogen, oxygen and carbon dioxide representing air-, high oxygen- and vacuum-like conditions with and without carbon dioxide present. Growth was monitored based on optical density, and samples were taken during exponential growth for a comparative proteomic analysis that allowed the determination of the effects of the different gases and their synergy. Growth under air atmosphere appears optimal particularly for P. carnosum, with enhancement of energy metabolism, respiration, oxygen consuming reactions, and a predicted preference for lipids as carbon source. However, all the other atmospheres show some degree of growth reduction. An increase in oxygen concentration leads to an increase in enzymes counteracting oxidative stress for both species, and enhancement of heme utilization and iron-sulfur cluster assembly proteins for P. phosphoreum. Absence of oxygen appears to switch the metabolism towards fermentative pathways, where either ribose (P. phosphoreum), or glycogen (P. carnosum) appear to be the preferred substrates. Additionally, it promotes the use of alternative electron donors/acceptors, mainly formate and nitrate/nitrite. Stress response is manifested as enhanced expression of enzymes able to produce ammonia (e.g. carbonic anhydrase, hydroxylamine reductase) and regulate osmotic stress. Our results suggest that photobacteria do not sense the environmental levels of carbon dioxide but rather adapt to their own anaerobic metabolism. The regulation in presence of carbon dioxide is limited and strain-specific under anaerobic conditions. However, when oxygen at air-like concentration is present together with carbon dioxide the oxidative stress appears enhanced compared to air conditions (very low carbon dioxide), explained if both gases have a synergistic effect. This is further supported by the increase in oxygen concentration in presence of carbon dioxide. The atmosphere is able to fully inhibit P. carnosum, heavily reduce P. phosphoreum growth in vitro and trigger diversification of energy production with higher energetic cost, highlighting the importance of concomitant bacteria for their growth on raw meat under said atmosphere.

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Casini2022 - genome scale metabolic model (iMTD22IC) of Methanothermobacter thermautotrophicus Delta H

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