Characterisation of acetogen formatotrophic potential using<i>E. limosum</i>

Wood, Jamin C.; Gonzalez-Garcia, R. Axayacatl; Daygon, Venea Dara; Talbo, Gert; Plan, Manuel R.; Marcellin, Esteban; Virdis, Bernardino

doi:10.1101/2022.11.02.514939

Cited by 2 publications

(9 citation statements)

References 55 publications

(86 reference statements)

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“…14,21 For the formate intracellular concentration, the equivalent was between 10 times higher, or 50 times lower, than the extracellular concentration. 23…”

Section: Methodsmentioning

confidence: 99%

“…Whereas in formatotrophic growth, where the total ATP, NAD, NADP, and CoA pool sizes were low, causing stress conditions, here they are all of the same order of magnitude for MeOH/CO 2 /0.4D and 3MeOH/Formate/CO 2 /0.4D (Figure 2, Figure 3). 23 For example, whilst adding formate to MeOH/CO 2 /0.4D almost doubled the acetyl-CoA pool (0.577±0.245 µmol/gDCW compared to 0.300±0.133 µmol/gDCW), adding MeOH/CO 2 to formate/0.4D increased it more than 40-fold.…”

Section: Formate Triggers a Beneficial Intracellular State During Met...mentioning

confidence: 96%

“…14,21 For the formate intracellular concentration, the equivalent was between 10 times higher, or 50 times lower, than the extracellular concentration. 23 Minimum metabolites concentrations were set to be 0.1 µM, and 1 nM for dissolved gases unless directly measured and evaluated from Henry's law (H 2 , CO 2 and CO). CO 2 total concentration, c, was calculated from partial pressure, p, as,…”

Section: Thermodynamic and Kinetic Metabolic Flux Analysismentioning

confidence: 99%

“…Hence, both formate and methanol together may be important for future synthetic C3 production. 23 Methanol also helps overcome some of the limitations of formate metabolism. Whereas in formatotrophic growth, where the total ATP, NAD, NADP, and CoA pool sizes were low, causing stress conditions, here they are all of the same order of magnitude for MeOH/CO 2 /0.4D and 3MeOH/Formate/CO 2 /0.4D (Figure 2, Figure 3).…”

Section: Formate Triggers a Beneficial Intracellular State During Met...mentioning

confidence: 99%

“…N = stirrer speed; BR = biological replicates; pH = pH setpoint, BC = biomass concentration. Formate/0.4D is provided for comparison from23 .…”

mentioning

confidence: 99%

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Molecular understanding ofEubacterium limosumchemostat methanol metabolism

Wood

Gonzalez-Garcia

Daygon

et al. 2022

Preprint

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Methanol is a promising renewable energy carrier that can be used as a favourable substrate for biotechnology, due to its high energy efficiency conversion and ease of integration within existing infrastructure. Some acetogenic bacteria have the native ability to utilise methanol, along with other C1substrates such as CO2and formate, to produce valuable chemicals. Continuous cultures favour economically viable bioprocesses, however, the performance of acetogens has not been investigated at the molecular level when grown on methanol. Here we present steady-state chemostat quantification of the metabolism ofEubacterium limosum, finding maximum methanol uptake rates up to 640±22 mmol/gDCW/d, with significant fluxes to butyrate. To better understand metabolism of acetogens under methanol growth conditions, we sampled chemostats for proteomics and metabolomics. Changes in protein expression and intracellular metabolomics highlighted key aspects of methanol metabolism, and highlighted bottleneck conditions preventing formation of the more valuable product, butanol. Interestingly, a small amount of formate in methylotrophic metabolism triggered a cellular state known in other acetogens to correlate with solventogenesis. Unfortunately, this was prevented by post-translation effects including an oxidised NAD pool. There remains uncertainty around ferredoxin balance at the methylene-tetrahydrofolate reductase (MTHFR) and at the Rnf level.

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“…14,21 For the formate intracellular concentration, the equivalent was between 10 times higher, or 50 times lower, than the extracellular concentration. 23…”

Section: Methodsmentioning

confidence: 99%

Section: Formate Triggers a Beneficial Intracellular State During Met...mentioning

confidence: 96%

Section: Thermodynamic and Kinetic Metabolic Flux Analysismentioning

confidence: 99%

Section: Formate Triggers a Beneficial Intracellular State During Met...mentioning

confidence: 99%

“…N = stirrer speed; BR = biological replicates; pH = pH setpoint, BC = biomass concentration. Formate/0.4D is provided for comparison from23 .…”

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confidence: 99%

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Molecular understanding ofEubacterium limosumchemostat methanol metabolism

Wood

Gonzalez-Garcia

Daygon

et al. 2022

Preprint

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Genomic potential and physiological characteristics of C1 metabolism in novel acetogenic bacteria

Yu,

Park,

Lee

et al. 2023

Front. Microbiol.

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Acetogenic bacteria can utilize C1 compounds, such as carbon monoxide (CO), formate, and methanol, via the Wood-Ljungdahl pathway (WLP) to produce biofuels and biochemicals. Two novel acetogenic bacteria of the family Eubacteriaceae ES2 and ES3 were isolated from Eulsukdo, a delta island in South Korea. We conducted whole genome sequencing of the ES strains and comparative genome analysis on the core clusters of WLP with Acetobacterium woodii DSM1030T and Eubacterium limosum ATCC8486T. The methyl-branch cluster included a formate transporter and duplicates or triplicates copies of the fhs gene, which encodes formyl-tetrahydrofolate synthetase. The formate dehydrogenase cluster did not include the hydrogenase gene, which might be replaced by a functional complex with a separate electron bifurcating hydrogenase (HytABCDE). Additionally, duplicated copies of the acsB gene, encoding acetyl-CoA synthase, are located within or close to the carbonyl-branch cluster. The serum bottle culture showed that ES strains can utilize a diverse range of C1 compounds, including CO, formate, and methanol, as well as CO2. Notably, ES2 exhibited remarkable resistance to high concentrations of C1 substrates, such as 100% CO (200 kPa), 700 mM formate, and 500 mM methanol. Moreover, ES2 demonstrated remarkable growth rates under 50% CO (0.45 h−1) and 200 mM formate (0.34 h−1). These growth rates are comparable to or surpassing those previously reported in other acetogenic bacteria. Our study introduces novel acetogenic ES strains and describes their genetic and physiological characteristics, which can be utilized in C1-based biomanufacturing.

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Characterisation of acetogen formatotrophic potential usingE. limosum

Cited by 2 publications

References 55 publications

Molecular understanding ofEubacterium limosumchemostat methanol metabolism

Molecular understanding ofEubacterium limosumchemostat methanol metabolism

Genomic potential and physiological characteristics of C1 metabolism in novel acetogenic bacteria

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