Conversion of CO2 into organic acids by engineered autotrophic yeast

The increase of CO₂ emissions due to human activity is one of the preeminent reasons for the present climate crisis. In addition, considering the increasing demand for renewable resources, the upcycling of CO₂ as a feedstock gains an extensive importance to establish CO₂-neutral or CO₂-negative industrial processes independent of agricultural resources. Here we assess whether synthetic autotrophic Komagataella phaffii (Pichia pastoris) can be used as a platform for value-added chemicals using CO₂ as a feedstock by integrating the heterologous genes for lactic and itaconic acid synthesis. ¹³C labeling experiments proved that the resulting strains are able to produce organic acids via the assimilation of CO₂ as a sole carbon source. Further engineering attempts to prevent the lactic acid consumption increased the titers to 600 mg L⁻¹, while balancing the expression of key genes and modifying screening conditions led to 2 g L⁻¹ itaconic acid. Bioreactor cultivations suggest that a fine-tuning on CO₂ uptake and oxygen demand of the cells is essential to reach a higher productivity. We believe that through further metabolic and process engineering, the resulting engineered strain can become a promising host for the production of value-added bulk chemicals by microbial assimilation of CO₂, to support sustainability of industrial bioprocesses.

Between 2011 and 2020 the annual average CO₂ emission due to human activity exceeded 38 gigatons, of which around 22 gigatons are removed again from the atmosphere to terrestrial and ocean CO₂ sinks. This imbalance, mostly due to combustion of fossil fuels, causes the steady increase in CO₂ levels in the atmosphere which is one of the primary reasons for the climate crisis our planet is facing today (1).Biologically produced fuels and commodity chemicals bear the potential to counteract this deleterious development, but the most common feedstocks used for bioproduction, such as glucose, sucrose and starch rely on agricultural production and are bearing the risk to threaten food security. Using autotrophic microorganisms as production platforms exploits the potential of CO₂ itself as an alternative carbon source. In nature, autotrophic microorganisms play a major role in CO₂ fixation by fixing 200 gigatons of CO₂ every year (2). However, the rates of most natural microbial CO₂ fixing pathways are low: the photosynthetic efficiency in cyanobacteria is limited to 1 to 2% which makes industrial processes using photoautotrophs economically less feasible (3). Chemoautotrophs may overcome this barrier as their energy harvesting processes are more efficient than light harvesting of photoautotrophs.One well-known autotroph that is being developed for biological production of materials is Cupriavidus necator (formerly known as Ralstonia eutropha). By harvesting energy with a controlled Knallgas reaction these bacteria assimilate CO₂ via the Calvin-Benson-Bessham (CBB) cycle. Besides naturally produced polyhydroxyalkanoates (PHA), metabolic pathway engineering enabled the production of several other chemicals (4–7).Several chemolithotrophic bacteria were demonstrated as production hosts for various chemicals such as ethanol, 2,3-butanediol, butanol, isopropanol, acetone, or isobutyric acid via natural carbon assimilation pathways (8–11). In addition to natural CO₂ fixing microorganisms, implementation of heterologous CO₂ fixing pathways to heterotrophic microorganisms like Myceliophthora thermophila provided a mixotrophic strain that is able to produce malic acid with a higher yield compared to the parent strain in which only the reductive tricarboxylic acid (TCA) cycle is used for the production (12).Natural chemoautotrophs have a large potential to convert CO₂ to chemicals. However, they are often recalcitrant to genetic editing, have complex nutrient demands, or may require complex process technological solutions like the transfer of gaseous substrates and energy sources. To circumvent some of these limitations well established prokaryotic and eukaryotic production hosts have been engineered to assimilate CO₂. The bacterial workhorse Escherichia coli and the yeast Komagataella phaffii (Pichia pastoris) were provided with the CBB cycle, enabling them to assimilate CO₂ by using formate or methanol, respectively, as energy sources. Both engineered microorganisms can grow sustainably with CO₂ as carbon source (13, 14). Conceptually formate and methanol are regarded as sustainable feedstocks for biotechnology when they are derived from CO₂ by hydrogenation or electrochemical reduction (15).To make an impact on the global CO₂ household such autotrophic processes need to convert CO₂ into bulk products. Besides ethanol, short chain organic acids are the second largest group of chemicals manufactured by industrial biotechnology. The market of biologically produced organic acids is expected to reach more than $36 billion by 2026 (16). The annual bioproduction of some of the key organic acids (citric, acetic, lactic, succinic acid) is more than 12 million metric tons (17–20). Recently, itaconic acid has also gained attention as a promising chemical building block with an estimated market increase to 170 kilotons per year and $260 million in 2025 (21). Lactic and itaconic acid are feedstocks for polymer production so that they, and other biobased commodity chemicals compete for the annual polymer production of more than 300 million tons, a volume that denotes a significant impact on the global CO₂ balance.Here, we set out to evaluate if the autotrophic K. phaffii strain can be used as a platform for organic acid production. Synthetic autotrophy was introduced to K. phaffii by converting the native peroxisomal methanol assimilation pathway, the xylulose monophosphate (XuMP) cycle, into the CBB cycle (13). To achieve that, the formaldehyde assimilating enzyme dihydroxyacetone synthase (DAS) was replaced by a bacterial ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and phosphoribulose kinase (PRK) from spinach was added to supply ribulose bisphosphate from XuMP precursors. Four yeast glycolytic enzymes were targeted to peroxisomes to close the CBB cycle to glyceraldehyde 3-phosphate (G3P), both as an intermediate and the product of the assimilation cycle (Fig. 1 A and B). In the present work, using modular synthetic biology tools, we implemented the genes for lactic and itaconic acid synthesis plus accessory genes into the K. phaffii genome and demonstrate that the autotrophic K. phaffii strain is capable of producing organic acids solely from CO₂ as carbon source.Open in a separate windowFig. 1.Expression of cadA and ldhL enables organic acid production in synthetic autotrophic K. phaffii. (A–D) Schematic pathways. (A) In wild-type K. phaffii methanol is oxidized to formaldehyde (black arrow) and assimilated in the XuMP cycle (orange arrows) or dissimilated to CO₂, respectively (purple arrow). (B) synthetic autotrophy in K. phaffii: the native assimilatory branch of methanol utilization was interrupted by deleting DAS1 and DAS2 (dashed gray line). AOX1 was knocked out to reduce the rate of formaldehyde formation which could be toxic to the cells. RuBisCO and PRK were integrated to complete a functional CBB cycle (green arrows). Additionally, two bacterial chaperones, groEL and groES, were overexpressed to assist the folding of RuBisCO. TDH3, PGK1, TKL1, TPI1 carrying each a peroxisomal targeting signal were overexpressed to assure the localization of the entire CBB cycle in peroxisomes. More details about the engineering strategy can be found in ref. (13). (C) Itaconic acid (red) and (D) lactic acid production (blue), (E) growth profiles, and (F) organic acid production profiles of the producing strains and the control. Time axis corresponds to the production phase under autotrophic conditions. At least three biological replicates were used in the screening to monitor the producing strains. Shades represent the SDs (±). 3PG: 3-phosphoglycerate, AcCoA: acetyl-coenzyme A, AOX1 and AOX2: alcohol oxidase 1 and 2, cadA: cis-aconitate decarboxylase, CBB cycle: Calvin-Benson-Bassham cycle, CISA_c: cytosolic cis-aconitate, CISA_m: mitochondrial cis-aconitate, DAS1 and DAS2: dihydroxyacetone synthase 1 and 2, DHA: dihydroxyacetone, FAL: formaldehyde, G3P: glyceraldehyde 3-phosphate, ITA: itaconic acid, LA: lactic acid, ldhL: L-lactate dehydrogenase, MeOH: methanol, mttA: mitochondrial tricarboxylic acid transporter, NAD⁺/NADH: nicotinamide adenine dinucleotide, PRK: phosphoribulokinase, PYR: pyruvate, RuBP: ribulose 1,5-bisphosphate, RuBisCO: ribulose 1,5-bisphosphate carboxylase/oxygenase, Xu5P: xylulose 5-phosphate, XuMP cycle: xylulose monophosphate cycle.