Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii

Abstract

Hexanoic acid and its derivatives have been recently recognized as value-added materials and can be synthesized by several microbes. Of them, Megasphaera elsdenii has been considered as an interesting hexanoic acid producer because of its capability to utilize a variety of carbons sources. However, the cellular metabolism and physiology of M. elsdenii still remain uncharacterized. Therefore, in order to better understand hexanoic acid synthetic metabolism in M. elsdenii, we newly reconstructed its genome-scale metabolic model, iME375, which accounts for 375 genes, 521 reactions, and 443 metabolites. A constraint-based analysis was then employed to evaluate cell growth under various conditions. Subsequently, a flux ratio analysis was conducted to understand the mechanism of bifurcated hexanoic acid synthetic pathways, including the typical fatty acid synthetic pathway via acetyl-CoA and the TCA cycle in a counterclockwise direction through succinate. The resultant metabolic states showed that the highest hexanoic acid production could be achieved when the balanced fractional contribution via acetyl-CoA and succinate in reductive TCA cycle was formed in various cell growth rates. The highest hexanoic acid production was maintained in the most perturbed flux ratio, as phosphoenolpyruvate carboxykinase (pck) enables the bifurcated pathway to form consistent fluxes. Finally, organic acid consuming simulations suggested that succinate can increase both biomass formation and hexanoic acid production.

Hydrogen as a Co-electron Donor for Chain Elongation With Complex Communities

“…ASVs of these two genera had established presence before lactate addition, hence their growth could have relied on the presence of yeast extract, interspecies metabolite transfer or H 2 consumption. Their closest related species ( Caproicibacter fermentans and M. elsdenii ) are best known for their abilities to produce caproate from sugars or lactate ( M. elsdenii ) ( Rosenberg et al, 2014 ; Flaiz et al, 2019 ; Lee et al, 2020 ), but neither for hydrogenotrophy nor ethanol consumption. Interestingly, in one of the first reports on M. elsdenii ( Elsden and Lewis, 1953 ), the species was shown to consume H 2 together with pyruvate while realizing CE metabolism when SCC were available.…”

Butyryl/Caproyl-CoA:Acetate CoA-transferase: cloning, expression and characterization of the key enzyme involved in medium-chain fatty acid biosynthesis

“…This may be attributed to the distant genetic relationship between M. elsdenii and the other five bacteria. Although M. elsdenii produces caproic acid via acetyl-CoA and succinate [ 23 ], the functions of the CoATs may differ between strain CPB6 and M. elsdenii . The 3D structures of CoATs among C. tyrobutyricum BEY8, Lachnospiraceae bacterium, and A. hadrus shared almost the same conformation of α-helices and β-strands except for some slight variation in the loops ( Figure 4 D–F).…”

Butyryl/Caproyl-CoA:Acetate CoA-Transferase: Cloning, Expression and Characterization of the Key Enzyme Involved in Medium-Chain Fatty Acid Biosynthesis

“…This may be attributed to the distant genetic relationship between M. elsdenii and the other five bacteria. Although M. elsdenii produces caproic acid via acetyl-CoA and succinate (34), the functions of the CoATs may differ between strain CPB6 and M. elsdenii . The 3D structures of CoATs among C. tyrobutyricum BEY8, Lachnospiraceae bacterium, and A. hadrus shared almost the same conformation of α-helices and β-strands except for some slight variation in the loops (Fig.…”

“…This may be attributed to the distant genetic relationship between M. elsdenii and the other five bacteria. Although M. elsdenii produces caproic acid via acetyl-CoA and succinate (34), the functions of the CoATs may differ between strain CPB6 and M.…”