Nature and nurture: Enabling formate-dependent growth in Methanosarcina acetivorans
Data files
Jan 17, 2025 version files 36.20 KB
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README.md
1.46 KB
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Supplementary_formate_FJ-24-0948_20250114.xlsx
34.73 KB
Abstract
Methanogenic archaea are crucial in global carbon cycling as they produce around 1 Gt of the potent greenhouse gas methane annually. Major contributors belong to the order Methanosarcinales, represented by versatile methanogens that are capable of acetoclastic, methylotrophic, and CO2-reducing methanogenesis. The genetically tractable model methanogen Methanosarcina acetivorans by its nature shows versatility in substrate utilization and energy conservation pathways but cannot utilize formate. In this study, we expanded the primary metabolism of M. acetivorans to include formate-dependent methanogenesis. By introducing formate dehydrogenase, two metabolically engineered M. acetivorans strains acquired the capacity for formate-dependent methanogenesis. One catabolic pathway relies on formate-dependent methyl-reduction, and the other relies on formate-dependent CO2-reduction. Nurturing the M. acetivorans strain capable of CO2-reduction with adaptive laboratory evolution enabled growth and methanogenesis solely on formate, a metabolism only reported in methanogens without cytochromes. M. acetivorans also showed acetogenic potential where the formate-dependent CO2-reducing strain was able to divert ≈ 10% of carbon from the substrates provided to acetate instead of methane. Even though M. acetivorans lacks energy-converting hydrogenase and cannot use H2, we show that M. acetivorans has a yet-uncharacterized capacity to obtain reduced ferredoxins from oxidizing formate. Our work encourages a reevaluation of our understanding of formate utilization in Methanosarcinales. By enabling formate-dependent methanogenesis, we have expanded the substrate spectrum of a versatile model methanogen with cytochromes to include formate.
README: Nature and nurture: Enabling formate-dependent growth in Methanosarcina acetivorans
https://doi.org/10.5061/dryad.931zcrjvd
The dataset contains the raw data obtained to plot the growth curves (OD600 values) and the metabolite curves (Methane as measured using gas chromatography and methanol, formate, acetate, and pyruvate as measured using NMR). It also contains information on the media composition used in the experiments.
Description of the data and file structure
The Excel file contains 5 sheets- WWM73, JB-MF, JB-F2_HSF, JB-F2_HSMe, Media
Each Excel sheet contains the first column as time points and the rest of the columns in the format:
media-strain-metabolite-replicate number
For example in Sheet WWM73--- The heading of Column 2 is MF-WWM73-OD-1 where MF refers to the media in which strain WWM73 was grown. The data obtained is of optical density values of the first replicate.
Sheet WWM73 contains raw data for the Figure 4. Cells with 'n/a' represent data not available as NMR samples were not measured for the given time points.
Sheet JB-MF contains raw data for the Figure 6.
Sheets JB-F2_HSF and JB-F2_HSMe contain raw data for Figure 7. Cells with 'n/a' represent data not available as NMR samples were not measured for the given time points.
Sheet Media contains an explanation of the media abbreviation and composition.
The first column is time (hours)
Access information
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