In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli

An unusual glycerol-3-phosphate dehydrogenase in Sulfolobus acidocaldarius elucidates the diversity of glycerol metabolism across Archaea

Glycerol is highly abundant in natural ecosystems and serves as both an important carbon source for microorganisms as well as a promising feedstock for industrial applications. However, the pathways involved in glycerol degradation in Archaea remain unclear. Here, we show that the thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius can grow with glycerol as its sole carbon source and characterize the mechanisms involved in glycerol utilization. We show that after uptake involving facilitated diffusion, glycerol is phosphorylated to glycerol-3-phosphate by glycerol kinase (GK), followed by oxidation to dihydroxyacetone phosphate catalyzed by an unusual glycerol-3-phosphate dehydrogenase (G3PDH) with a previously undescribed type of membrane anchoring via a CoxG-like protein. Furthermore, we show that while S. acidocaldarius has two paralogous GK/G3PDH copies (saci_1117-1119, saci_2031-2033) with similar biochemical activity, only saci_2031-2033 is highly upregulated and essential on glycerol, suggesting that distinct enzyme pairs may be regulated by different environmental conditions. Finally, we explore the diversity of glycerol metabolism enzymes across the Archaea domain, revealing a high versatility of G3PDHs with respect to interacting proteins, electron transfer mechanisms, and modes of membrane anchoring. Our findings help to elucidate the mechanisms involved in glycerol utilization in Archaea, highlighting unique evolutionary strategies that likely enabled adaptation to different lifestyles.

Acetol biosynthesis enables NADPH balance during nitrogen limitation in engineered Escherichia coli

BACKGROUND

Nutrient limitation strategies are commonly applied in bioprocess development to engineered microorganisms to further maximize the production of the target molecule towards theoretical limits. Biomass formation is often limited under the limitation of key nutrients, and understanding how fluxes in central carbon metabolism are re-routed during the transition from nutrient excess to nutrient-limited condition is vital to target and tailor metabolic engineering strategies. Here, we report the physiology and intracellular flux distribution of an engineered acetol-producing Escherichia coli on glycerol under nitrogen-limited, non-growing production conditions.

RESULTS

Acetol production in the engineered E. coli strain is triggered upon nitrogen depletion. During nitrogen limitation, glycerol uptake decreased, and biomass formation rates ceased. We applied 13C-flux analysis with 2-13C glycerol during exponential growth and nitrogen starvation to elucidate flux re-routing in the central carbon metabolism. The results indicate a metabolically active non-growing state with significant flux re-routing towards acetol biosynthesis and reduced flux through the central carbon metabolism. The acetol biosynthesis pathway is favorable for maintaining the NADPH/NADP+ balance.

CONCLUSION

The results reported in this study illustrate how the production of a value-added chemical from a waste stream can be connected to the metabolism of the whole-cell biocatalyst, making product formation mandatory for the cell to maintain its NADPH/NADP+ balance. This has implications for process design and further metabolic engineering of the whole-cell biocatalyst.

Exploring the substrate scope of glycerol dehydrogenase GldA from E. coli BW25113 towards cis-dihydrocatechol derivatives

Glycerol dehydrogenase (GldA) from Escherichia coli BW25113, naturally catalyzes the oxidation of glycerol to dihydroxyacetone. It is known that GldA exhibits promiscuity towards short-chain C₂-C₄ alcohols. However, there are no reports regarding the substrate scope of GldA towards larger substrates. Herein we demonstrate that GldA can accept bulkier C₆-C₈ alcohols than previously anticipated. Overexpression of the gldA gene in the knockout background, E. coli BW25113 ΔgldA, was strikingly effective converting 2 mM of the compounds: cis-dihydrocatetechol, cis-(1 S,2 R)- 3-methylcyclohexa-3,5-diene-1,2-diol and cis-(1 S,2 R)- 3-ethylcyclohexa-3,5-diene-1,2-diol, into 2.04 ± 0.21 mM of catechol, 0.62 ± 0.11 mM 3-methylcatechol, and 0.16 ± 0.02 mM 3-ethylcatechol, respectively. In-silico studies on the active site of GldA enlightened the decrease in product formation as the steric substrate demand increased. These results are of high interests for E. coli-based cell factories expressing Rieske non-heme iron dioxygenases, producing cis-dihydrocatechols, since such sough-after valuable products can be immediately degraded by GldA, substantially hampering the expected performance of the recombinant platform.

Infant Vitamin D Supplements, Fecal Microbiota and Their Metabolites at 3 Months of Age in the CHILD Study Cohort

Infant vitamin D liquid formulations often contain non-medicinal excipients such as glycerin (ie. glycerol) and 1,2-propanediol (1,2-PD). We examined whether infant vitamin D supplementation is associated with fecal glycerol and 1,2-PD concentrations at 3 months of age and characterized associations between these two molecules, and gut microbiota and their metabolites. Fecal metabolites and microbiota were quantified using Nuclear Magnetic Resonance Spectroscopy and 16S rRNA sequencing, respectively, in 575 infants from the CHILD Study at 3 months of age. Vitamin D supplement use was determined using questionnaires. Vitamin D supplementation was associated with greater odds of high 1,2-PD (adjusted OR 1.65 95% CI: 1.06, 2.53) and with decreased odds of high fecal glycerol (adjusted OR: 0.62 95% CI: 0.42, 0.90) after adjustment for breastfeeding and other covariates. Our findings were confirmed in linear regression models; vitamin D supplementation was positively associated with fecal 1,2-PD and inversely associated with glycerol (aβ: 0.37, 95% CI 0.03, 0.71 & aβ: -0.23 95% CI -0.44, -0.03, respectively). Fecal 1,2-PD and glycerol concentrations were negatively correlated with each other. Positive correlations between fecal 1,2-PD, Bifidobacteriaceae, Lactobacillaceae, Enterobacteriaceae and acetate levels were observed. Our research demonstrates that infant vitamin D supplement administration may differentially and independently influence infant gut microbiota metabolites.