Advancing yeast metabolism for a sustainable single carbon bioeconomy

Abstract

Single carbon (C1) molecules are considered as valuable substrates for biotechnology, as they serve as intermediates of carbon dioxide recycling, and enable bio-based production of a plethora of substances of our daily use without relying on agricultural plant production. Yeasts are valuable chassis organisms for biotech production, and they are able to use C1 substrates either natively or as synthetic engineered strains. This minireview highlights native yeast pathways for methanol and formate assimilation, their engineering, and the realization of heterologous C1 pathways including CO2, in different yeast species. Key features determining the choice among C1 substrates are discussed, including their chemical nature and specifics of their assimilation, their availability, purity, and concentration as raw materials, as well as features of the products to be made from them.

Keywords: bioeconomy; carbon dioxide; formate; methanol; sustainability.

Figure 1.

Schematic overview of a circular single carbon bioeconomy. CO₂ emissions from various industries can be harvested and reduced to methanol and formate, and serve as carbon and energy sources for the conversion to value-added products by C1-assimilating yeast strains.

Figure 2.

Metabolic pathways for C1 assimilation in yeasts. (a) Xylulose monophosphate (XuMP) cycle for methanol assimilation in methylotrophic yeasts. (b) Recombinant Calvin–Benson–Bassham (CBB) cycle, realized on the blueprint of the XuMP cycle in K. phaffii; native enzymes in pink, cytosolic enzymes targeted to peroxisome in cyan (PTS = peroxisomal targeting sequence), heterologous enzymes in green; AOX1 and DAS1/2 knockout (K.O.) (Δaox1, Δdas1/2). (c) Native reductive glycine pathway, identified in K. phaffii; GCV = glycine cleavage system. Enzyme abbreviations: Aox, alcohol oxidase; Cha1, catabolic l-serine (l-threonine) deaminase; Dak2, dihydroxyacetone kinase 2; Das, dihydroxyacetone synthase; Fld, formaldehyde dehydrogenase; Fdh1, formate dehydrogenase; Fba1-2, fructose 1,6-bisphosphate aldolase; Fbp1, fructose 1,6-bisphosphatase 1; Rki1-2, ribose 5-phosphate ketol-isomerase; RuBisCO, ribulose 1,5-bisphosphate carboxylase/oxygenase; Shb17, sedoheptulose 1,7-bisphosphatase; Fgh, S-formylglutathione hydrolase; Shm, S-adenosylmethionine hydrolase; Tkl1, transketolase 1; Tpi1, triose-phosphate isomerase 1; Lpd, dihydrolipoamide dehydrogenase; Mis, C1 tetrahydrofolate synthase; Pgk1, phosphoglycerate kinase 1; PRK, phosphoribulokinase; Tdh3, glyceraldehyde 3-phosphate dehydrogenase 3. Metabolite abbreviations: DHA, dihydroxyacetone; DHAP, dihydroxyacetone phosphate; E4P, erythrose 4-phosphate; Fald, formaldehyde; F6P, fructose 6-phosphate; FBP, fructose bisphosphate; GAP, glyceraldehyde 3-phosphate; GSH, glutathione; Gly, glycine; MeOH, methanol; R5P, ribose 5-phosphate; Ru5P, ribulose 5-phosphate; S1,7BP, sedoheptulose 1,7-bisphosphate; S7P, sedoheptulose 7-phosphate; Ser, serine; THF, tetrahydrofolate; Xu5P, xylulose 5-phosphate.

Figure 3.

Advantages and disadvantages of different C1 carbon sources, in perspective with traditional substrates for industrial biotechnology.