Metabolic engineering of Pichia pastoris for malic acid production from methanol

Rewiring the methanol assimilation pathway in the methylotrophic yeast Pichia pastoris for high-level production of erythritol

Methanol, which is non-food competing, abundant, inexpensive, and potentially renewable, serves as an ideal alternative feedstock for biomanufacturing. Although engineered methylotrophic yeasts have successfully achieved gram-scale production of C2 (acetyl-CoA), C3 (pyruvate), and C6 (fructose-6-phosphate) building blocks from methanol, the production of C4-based (i.e. erythrose-4-phosphate) chemicals remains unexplored. This study demonstrates high-level methanol-to-erythritol production by rewiring the methanol assimilation pathway of Pichia pastoris, achieved through trimming and strengthening the carbon rearrangement network (CRN). Notably, we introduced a bacterial ribulose monophosphate (RuMP) pathway in addition to the native xylulose monophosphate (XuMP) pathway of P. pastoris, creating a hybrid network that significantly improved erythritol production and reduced pentitol byproduct formation. Combining these strategies generated a high-producing recombinant strain, achieving titers up to 31.5 g/L in fermentor culture. This study validates the feasibility of engineering P. pastoris for the efficient conversion of methanol to valuable erythrose-4-phosphate (E4P)-based chemicals. The CRN rewiring strategies employed here offer a valuable reference for engineering methylotrophic cell factories for the production of a wide range of chemicals from methanol.

Technological advancement spurs Komagataella phaffii as a next-generation platform for sustainable biomanufacturing

Biomanufacturing stands as a cornerstone of sustainable industrial development, necessitating a shift toward non-food carbon feedstocks to alleviate agricultural resource competition and advance a circular bioeconomy. Methanol, a renewable one‑carbon substrate, has emerged as a pivotal candidate due to its abundance, cost-effectiveness, and high reduction potential, further bolstered by breakthroughs in CO₂ hydrogenation-based synthesis. Capitalizing on this momentum, the methylotrophic yeast Komagataella phaffii has undergone transformative technological upgrades, evolving from a conventional protein expression workhorse into an intelligent bioproduction chassis. This paradigm shift is fundamentally driven by converging innovations across CRISPR-empowered advancement in genome editing and AI-powered metabolic pathway design in K. phaffii. The integration of CRISPR systems with droplet microfluidics high-throughput screening has redefined strain engineering efficiency, achieving much higher editing precision than traditional homologous recombination while compressing the "design-build-test-learn" cycle. Concurrently, machine learning-enhanced genome-scale metabolic models facilitate dynamic flux balancing, enabling simultaneous improvements in product titers, carbon yields, and volumetric productivity. Finally, technological advancement promotes the application of K. phaffii, including directing more efficiently metabolic flux toward nutrient products, and strengthening efficient synthesis of excreted proteins. As DNA synthesis automation and robotic experimentation platforms mature, next-generation breakthroughs in genome modification, cofactor engineering, and AI-guided autonomous evolution will further cement K. phaffii as a next-generation platform for decarbonizing global manufacturing paradigms. This technological trajectory positions methanol-based biomanufacturing as a cornerstone of the low-carbon circular economy.

Engineering glycolytic pathway for improved Lacto-N-neotetraose production in pichia pastoris

Lacto-N-neotetraose (LNnT) is a primary solid component of human milk oligosaccharides (HMOs) with various promising health effects for infants. LNnT production by GRAS (generally recognized as safe) microorganisms has attracted considerable attention. However, few studies have emphasized Pichia Pastoris as a cell factory for LNnT's production. Here, we have reported the first-ever synthesis of LNnT employing P. pastoris as the host. Initially, LNnT biosynthetic pathway genes β-1,3-N-acetylglucosaminyltransferase (lgtA) and β-1,4-galactostltransferase (lgtB) along with lactose permease (lac12) and galactose epimerase (gal10) were integrated into the genome of P. pastoris, but only 0.139 g/L LNnT was obtained. Second, the titer of LNnT was improved to 0.162 g/L via up-regulating genes to strengthen the supply of precursors, UDP-GlcNAc (Uridine diphosphate N-acetylglucosamine) and UDP-Gal (Uridine diphosphate galactose), for LNnT biosynthesis. Third, by knocking out critical mediator pfk (6-phosphofructokinase) genes in glycolysis, the major glucose metabolic flux was rewired to the LNnT biosynthesis pathway. As a result, the strain accumulated 0.867 g/L LNnT in YPG medium supplemented with glucose and lactose. Finally, LNnT production was increased to 1.24 g/L in a 3 L bioreactor. The work aimed to explore the potential of P. pastoris as a for LNnT production.

Enhanced methanol-xylose co-utilization strategy in Komagataella phaffii

Bio-manufacturing based on non-food carbon sources is conducive to alleviating the global food crisis and greenhouse effect. However, the mechanism of the utilization of methanol and xylose in Komagataella phaffii based on endogenous metabolic pathways has not been fully explored. In this study, transcriptomics revealed a positive correlation between methanol metabolic efficiency and the transcription level of genes related to xylose metabolism and phosphate metabolism. By providing sufficient phosphate to the strain, the methanol utilization rate of the Komagataella phaffii GA01 strain was improved, and the final biomass reached 7.5 g DCW/L. Metabolomics further confirmed that methanol could effectively activate xylose metabolism of the strain, and the consumption rates of methanol and xylose of the Komagataella phaffii GA01 strain could reach 3.87 g/L/d and 1.83 g/L/d, which were 34 % and 357.5 % higher than that of the wild-type strain, respectively. This study further promotes the application of methanol and xylose in microbial fermentation.

Metabolic engineering of Komagataella phaffii for enhanced 3-hydroxypropionic acid (3-HP) production from methanol

BACKGROUND

Bioconversion of methanol derived from CO2 reduction into value-added chemicals provides a unique approach for mitigating global warming and reducing fossil fuels dependence. Production of 3-hydroxypropionic acid (3-HP), a key building block for the development of biobased products such as acrylates and 1,3-propanediol, has been successfully achieved using methanol as the sole carbon and energy source in the methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris). However, challenges remain in meeting commercially relevant concentrations, yields and productivities of 3-HP, prompting further strain optimization. In the present study, we have combined metabolic engineering strategies aiming at increasing metabolic precursors supply and redirecting carbon flux towards 3-HP production.

RESULTS

A combinatorial metabolic engineering strategy targeting precursors supply and 3-HP export was applied to the original 3-HP producing K. phaffii strain harboring the synthetic β-alanine pathway and a mutated NADP-dependent formate dehydrogenase from Pseudomonas sp. 101 (PseFDH(V9)). To do so, several genes encoding enzymes catalyzing reactions immediately upstream of the β-alanine pathway were overexpressed to enhance precursors availability. However, only the overexpression of the pyruvate carboxylase PYC2 gene significantly increased the 3-HP yield on biomass (YP/X) in small-scale cultivations. Co-overexpression of PYC2 and the lactate permeases ESBP6 and JEN1 genes led to a 55% improvement in 3-HP titer and product yield in methanol deep-well plate cultures compared to the reference strain, mostly due to Esbp6 activity, proving its effectiveness as a 3-HP transporter. Deletion of the native formate dehydrogenase gene FDH1 did not increase methanol flux entering the assimilatory pathway. Instead, knockout strains showed severe growth defects due to toxic intermediates accumulation. Co-expression of the PseFDH(V9) encoding gene in these strains failed to compensate for the loss of the native FDH. The strain combining PYC2, ESBP6, and JEN1 overexpression was further tested in fed-batch cultures at pH 5, achieving a 3-HP concentration of 27.0 g l- 1, with a product yield of 0.19 g g- 1, and a volumetric productivity of 0.56 g l- 1 h- 1 for the methanol feeding phase of the cultivations. These results represent a 42% increase in final concentration and over 20% improvement in volumetric productivity compared to the original 3-HP-producing strain. Furthermore, bioreactor-scale cultivations at pH 3.5 revealed increased robustness of the strains overexpressing monocarboxylate transporters.

CONCLUSIONS

Our results point out the potential of lactate transporters to efficiently drive 3-HP export in K. phaffii, leading to higher titers, yields, and productivities, even at lower pH conditions.

Advancing yeast metabolism for a sustainable single carbon bioeconomy

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.

Non-conventional yeasts: promising cell factories for organic acid bioproduction

Microbial production of organic acids has been hindered by the poor acid tolerance of microorganisms and the high costs of waste salt reprocessing. The robustness of non-conventional microorganisms in an acidic environment makes it possible to produce organic acids at low pH and greatly simplifies downstream processing. In this review we discuss the environmental adaptability features of non-conventional yeasts, as well as the latest developments in genomic engineering strategies that have facilitated metabolic engineering of these strains. We also use selected examples of three-carbon (C3), C4, and C6 organic acids to illustrate the ongoing efforts and challenges of using non-conventional yeasts for organic acid production. This review provides theoretical guidance for the construction of highly robust organic acid producers.

Enhancing D-lactic acid production by optimizing the expression of D-LDH gene in methylotrophic yeast Komagataella phaffii

BACKGROUND

Currently, efficient technologies producing useful chemicals from alternative carbon resources, such as methanol, to replace petroleum are in demand. The methanol-utilizing yeast, Komagataella phaffii, is a promising microorganism to produce chemicals from methanol using environment-friendly microbial processes. In this study, to achieve efficient D-lactic acid production from methanol, we investigated a combination of D-lactate dehydrogenase (D-LDH) genes and promoters in K. phaffii. The yeast strain was constructed by integrating a gene cassette containing the identified gene and promoter into the rDNA locus of K. phaffii, followed by post-transformational gene amplification. Subsequently, D-lactic acid production from methanol was evaluated.

RESULTS

Among the five D-LDH genes and eight promoters tested, the combination of LlDLDH derived from Leuconostoc lactis and CAT1 and FLD1 promoters was suitable for expression in K. phaffii. GS115_CFL/Z3/04, the best-engineered strain constructed via integration of LlDLDH linked to CAT1 and FLD1 promoters into the rDNA locus and post-transformational gene amplification, produced 5.18 g/L D-lactic acid from methanol. To the best of our knowledge, the amount of D-lactic acid from methanol produced by this engineered yeast is the highest reported value to date when utilizing methanol as the sole carbon source.

CONCLUSIONS

This study demonstrated the effectiveness of combining different enzyme genes and promoters using multiple promoters with different induction and repression conditions, integrating the genes into the rDNA locus, and further amplifying the genes after transformation in K. phaffii. Using our established method, other K. phaffii strains can be engineered to produce various useful chemicals in the future.

Evolutionary engineering of Saccharomyces cerevisiae: Crafting a synthetic methylotroph via self-reprogramming

Methanol, as a non-edible feedstock, offers a promising sustainable alternative to sugar-based substrates in biochemical production. Despite progress in engineering methanol assimilation in nonmethylotrophs, the full transformation into methanol-dependent synthetic methylotrophs remains a formidable challenge. Here, moving beyond the conventional rational design principle, we engineered a synthetic methylotrophic Saccharomyces cerevisiae through genome rearrangement and adaptive laboratory evolution. This evolutionarily advanced strain unexpectedly shed the heterologous methanol assimilation pathway and demonstrated the robust growth on sole methanol. We discovered that the evolved strain likely realized methanol assimilation through a previously unidentified Adh2-Sfa1-rGly (ASrG) pathway, facilitating the concurrent assimilation of formate and CO2. Furthermore, the incorporation of electron transfer material C3N4 quantum dots obviously enhanced methanol-dependent growth, emphasizing the role of energy availability in the ASrG pathway. This breakthrough introduces a previously unidentified C1 utilization pathway and highlights the exceptional adaptability and self-evolving capacity of the S. cerevisiae metabolic network.

Formate from THF-C1 metabolism induces the AOX1 promoter in formate dehydrogenase-deficient Komagataella phaffii

In Komagataella phaffii (Pichia pastoris), formate is a recognized alternative inducer to methanol for expression systems based on the AOX1 promoter (pAOX1). By disrupting the formate dehydrogenase encoding FDH1 gene, we converted such a system into a self-induced one, as adding any inducer in the culture medium is no longer requested for pAOX1 induction. In cells, formate is generated from serine through the THF-C1 metabolism, and it cannot be converted into carbon dioxide in a FdhKO strain. Under non-repressive culture conditions, such as on sorbitol, the intracellular formate generated from the THF-C1 metabolism is sufficient to induce pAOX1 and initiate protein synthesis. This was evidenced for two model proteins, namely intracellular eGFP and secreted CalB lipase from C. antarctica. Similar protein productivities were obtained for a FdhKO strain on sorbitol and a non-disrupted strain on sorbitol-methanol. Considering a K. Phaffii FdhKO strain as a workhorse for recombinant protein synthesis paves the way for the further development of methanol-free processes in K. phaffii.

Dynamically Regulating Homologous Recombination Enables Precise Genome Editing in Ogataea polymorpha

Methylotrophic yeast Ogataea polymorpha has become a promising cell factory due to its efficient utilization of methanol to produce high value-added chemicals. However, the low homologous recombination (HR) efficiency in O. polymorpha greatly hinders extensive metabolic engineering for industrial applications. Overexpression of HR-related genes successfully improved HR efficiency, which however brought cellular stress and reduced chemical production due to constitutive expression of the HR-related gene. Here, we engineered an HR repair pathway using the dynamically regulated gene ScRAD51 under the control of the l-rhamnose-induced promoter PLRA3 based on the previously constructed CRISPR-Cas9 system in O. polymorpha. Under the optimal inducible conditions, the appropriate expression level of ScRAD51 achieved up to 60% of HR rates without any detectable influence on cell growth in methanol, which was 10-fold higher than that of the wild-type strain. While adopting as the chassis strain for bioproductions, the dynamically regulated recombination system had 50% higher titers of fatty alcohols than that static regulation system. Therefore, this study provided a feasible platform in O. polymorpha for convenient genetic manipulation without perturbing cellular fitness.

Candida boidinii isolates from olive curation water: a promising platform for methanol-based biomanufacturing

Methanol is a promising feedstock for biomanufacturing, but the efficiency of methanol-based bioprocesses is limited by the low rate of methanol utilization pathways and methanol toxicity. Yeast diversity is an attractive biological resource to develop efficient bioprocesses since any effort with strain improvement is more deserving if applied to innate robust strains with relevant catabolic and biosynthetic potential. The present study is in line with such rational and describes the isolation and molecular identification of seven isolates of the methylotrophic species Candida boidinii from waters derived from the traditional curation of olives, in different years, and from contaminated superficial soil near fuel stations. The yeast microbiota from those habitats was also characterized. The four C. boidinii isolates obtained from the curation of olives' water exhibited significantly higher maximum specific growth rates (range 0.15-0.19 h-1), compared with the three isolates obtained from the fuel contaminated soils (range 0.05-0.06 h-1) when grown on methanol as the sole C-source (1% (v/v), in shake flasks, at 30°C). The isolates exhibit significant robustness towards methanol toxicity that increases as the cultivation temperature decreases from 30°C to 25°C. The better methanol-based growth performance exhibited by C. boidinii isolates from olives´ soaking waters could not be essentially attributed to higher methanol tolerance. These methanol-efficient catabolizing isolates are proposed as a promising platform to develop methanol-based bioprocesses.

Hansenula polymorpha methanol metabolism genes enhance recombinant protein production in Komagataella phaffi

Recombinant protein production in Komagataella phaffi (K. phaffi), a widely utilized host organism, can be optimized by enhancing the metabolic flux in the central carbon metabolism pathways. The methanol utilization pathway (MUT) during methanol-based growth plays a crucial role in providing precursors and energy for cell growth and development. This study investigated the impact of boosting the methanol dissimilation pathway, a branch of MUT that plays a vital role in detoxifying formaldehyde and providing energy in the form of NADH, in K. phaffi. This was achieved by integrating two orthologous genes from Hansenula polymorpha into the K. phaffi genome: formaldehyde dehydrogenase (HpFLD) and formate dehydrogenase (HpFMDH). The HpFLD and HpFMDH genes were isolated from the Hansenula polymorpha genome and inserted under the regulation of the pAOX1 promoter in the genome of recombinant K. phaffi that already contained a single copy of model protein genes (eGFP or EGII). The expression levels of these model proteins were assessed through protein activity assays and gene expression analysis. The findings revealed that while both orthologous genes positively influenced model protein production, HpFMDH exhibited a more pronounced upregulation in expression compared to HpFLD. Co-expression of both orthologous genes demonstrated synergistic effects, resulting in approximately a twofold increase in the levels of the model proteins detected. This study provides valuable insights into enhancing the production capacity of recombinant proteins in K. phaffi.

Engineering Yeast Peroxisomes for α-Bisabolene Production from Sole Methanol with the Aid of Proteomic Analysis

Microbial metabolic engineering provides a feasible approach to sustainably produce advanced biofuels and biochemicals from renewable feedstocks. Methanol is an ideal feedstock since it can be massively produced from CO2 through green energy, such as solar energy. However, engineering microbes to transform methanol and overproduce chemicals is challenging. Notably, the microbial production of isoprenoids from methanol is still rarely reported. Here, we extensively engineered Pichia pastoris (syn. Komagataella phaffii) for the overproduction of sesquiterpene α-bisabolene from sole methanol by optimizing the mevalonate pathway and peroxisomal compartmentalization. Furthermore, through label-free quantification (LFQ) proteomic analysis of the engineered strains, we identified the key bottlenecks in the peroxisomal targeting pathway, and overexpressing the limiting enzyme EfmvaE significantly improved α-bisabolene production to 212 mg/L with the peroxisomal pathway. The engineered strain LH122 with the optimized peroxisomal pathway produced 1.1 g/L α-bisabolene under fed-batch fermentation in shake flasks, achieving a 69% increase over that of the cytosolic pathway. This study provides a viable approach for overproducing isoprenoid from sole methanol in engineered yeast cell factories and shows that proteomic analysis can help optimize the organelle compartmentalized pathways to enhance chemical production.

Efficient production of itaconic acid from the single-carbon substrate methanol with engineered Komagataella phaffii

BACKGROUND

Amidst the escalating carbon dioxide levels resulting from fossil fuel consumption, there is a pressing need for sustainable, bio-based alternatives to underpin future global economies. Single-carbon feedstocks, derived from CO2, represent promising substrates for biotechnological applications. Especially, methanol is gaining prominence for bio-production of commodity chemicals.

RESULTS

In this study, we show the potential of Komagataella phaffii as a production platform for itaconic acid using methanol as the carbon source. Successful integration of heterologous genes from Aspergillus terreus (cadA, mttA and mfsA) alongside fine-tuning of the mfsA gene expression, led to promising initial itaconic acid titers of 28 g·L-1 after 5 days of fed-batch cultivation. Through the combined efforts of process optimization and strain engineering strategies, we further boosted the itaconic acid production reaching titers of 55 g·L-1 after less than 5 days of methanol feed, while increasing the product yield on methanol from 0.06 g·g-1 to 0.24 g·g-1.

CONCLUSION

Our results highlight the potential of K. phaffii as a methanol-based platform organism for sustainable biochemical production.

A synthetic methylotrophic Escherichia coli as a chassis for bioproduction from methanol

Methanol synthesized from captured greenhouse gases is an emerging renewable feedstock with great potential for bioproduction. Recent research has raised the prospect of methanol bioconversion to value-added products using synthetic methylotrophic Escherichia coli, as its metabolism can be rewired to enable growth solely on the reduced one-carbon compound. Here we describe the generation of an E. coli strain that grows on methanol at a doubling time of 4.3 h-comparable to many natural methylotrophs. To establish bioproduction from methanol using this synthetic chassis, we demonstrate biosynthesis from four metabolic nodes from which numerous bioproducts can be derived: lactic acid from pyruvate, polyhydroxybutyrate from acetyl coenzyme A, itaconic acid from the tricarboxylic acid cycle and p-aminobenzoic acid from the chorismate pathway. In a step towards carbon-negative chemicals and valorizing greenhouse gases, our work brings synthetic methylotrophy in E. coli within reach of industrial applications.

An Eclectic Review on Dicarboxylic Acid Production Through Yeast Cell Factories and Its Industrial Prominence

Dicarboxylic acid (DCA) is a multifaceted chemical intermediate, recoursed to produce many industrially important products such as adhesives, plasticizers, lubricants, polymers, etc. To bypass the shortcomings of the chemical methods of synthesis of DCA and to reduce fossil fuel footprints, bio-based synthesis is gaining attention. In pursuit of an eco-friendly sustainable alternative method of DCA production, microbial cell factories, and renewable organic resources are gaining popularity. Among the plethora of microbial communities, yeast is being favored industrially compared to bacterial fermentation due to its hyperosmotic and low pH tolerance and flexibility for gene manipulations. By application of rapidly evolving genetic manipulation techniques, the bio-based DCA production could be made more precise and economical. To bridge the gap between supply and demand of DCA, many strategies are employed to improve the fermentation. This review briefly outlines the advancements in DCA production using yeast cell factories with the exemplification of strain improvement strategies.

CRISPR/Cas9-based toolkit for rapid marker recycling and combinatorial libraries in Komagataella phaffii

Komagataella phaffii, a nonconventional yeast, is increasingly attractive to researchers owing to its posttranslational modification ability, strict methanol regulatory mechanism, and lack of Crabtree effect. Although CRISPR-based gene editing systems have been established in K. phaffii, there are still some inadequacies compared to the model organism Saccharomyces cerevisiae. In this study, a redesigned gRNA plasmid carrying red and green fluorescent proteins facilitated plasmid construction and marker recycling, respectively, making marker recycling more convenient and reliable. Subsequently, based on the knockdown of Ku70 and DNA ligase IV, we experimented with integrating multiple DNA fragments at a single locus. A 26.5-kb-long DNA fragment divided into 11 expression cassettes for lycopene synthesis could be successfully integrated into a single locus at one time with a success rate of 57%. A 27-kb-long DNA fragment could also be precisely knocked out with a 50% positive rate in K. phaffii by introducing two DSBs simultaneously. Finally, to explore the feasibility of rapidly balancing the expression intensity of multiple genes in a metabolic pathway, a yeast combinatorial library was successfully constructed in K. phaffii using lycopene as an indicator, and an optimal combination of the metabolic pathway was identified by screening, with a yield titer of up to 182.73 mg/L in shake flask fermentation. KEY POINTS: • Rapid marker recycling based on the visualization of a green fluorescent protein • One-step multifragment integration and large fragment knockout in the genome • A random assembly of multiple DNA elements to create yeast libraries in K. phaffii.

Unveiling malic acid biorefinery: Comprehensive insights into feedstocks, microbial strains, and metabolic pathways

The over-reliance on fossil fuels and resultant environmental issues necessitate sustainable alternatives. Microbial fermentation of biomass for malic acid production offers a viable, eco-friendly solution, enhancing resource efficiency and minimizing ecological damage. This review covers three core aspects of malic acid biorefining: feedstocks, microbial strains, and metabolic pathways. It emphasizes the significance of utilizing biomass sugars, including the co-fermentation of different sugar types to improve feedstock efficiency. The review discusses microbial strains for malic acid fermentation, addressing challenges related to by-products from biomass breakdown and strategies for overcoming them. It delves into the crucial pathways and enzymes for malic acid production, outlining methods to optimize its metabolism, focusing on enzyme regulation, energy balance, and yield enhancement. These insights contribute to advancing the field of consolidated bioprocessing in malic acid biorefining.

Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha

BACKGROUND

One carbon (C1) molecules such as methanol have the potential to become sustainable feedstocks for biotechnological processes, as they can be derived from CO2 and green hydrogen, without the need for arable land. Therefore, we investigated the suitability of the methylotrophic yeast Ogataea polymorpha as a potential production organism for platform chemicals derived from methanol. We selected acetone, malate, and isoprene as industrially relevant products to demonstrate the production of compounds with 3, 4, or 5 carbon atoms, respectively.

RESULTS

We successfully engineered O. polymorpha for the production of all three molecules and demonstrated their production using methanol as carbon source. We showed that the metabolism of O. polymorpha is well suited to produce malate as a product and demonstrated that the introduction of an efficient malate transporter is essential for malate production from methanol. Through optimization of the cultivation conditions in shake flasks, which included pH regulation and constant substrate feeding, we were able to achieve a maximum titer of 13 g/L malate with a production rate of 3.3 g/L/d using methanol as carbon source. We further demonstrated the production of acetone and isoprene as additional heterologous products in O. polymorpha, with maximum titers of 13.6 mg/L and 4.4 mg/L, respectively.

CONCLUSION

These findings highlight how O. polymorpha has the potential to be applied as a versatile cell factory and contribute to the limited knowledge on how methylotrophic yeasts can be used for the production of low molecular weight biochemicals from methanol. Thus, this study can serve as a point of reference for future metabolic engineering in O. polymorpha and process optimization efforts to boost the production of platform chemicals from renewable C1 carbon sources.

Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems

Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.

Advances in the dynamic control of metabolic pathways in Saccharomyces cerevisiae

The metabolic engineering of Saccharomyces cerevisiae has great potential for enhancing the production of high-value chemicals and recombinant proteins. Recent studies have demonstrated the effectiveness of dynamic regulation as a strategy for optimizing metabolic flux and improving production efficiency. In this review, we provide an overview of recent advancements in the dynamic regulation of S. cerevisiae metabolism. Here, we focused on the successful utilization of transcription factor (TF)-based biosensors within the dynamic regulatory network of S. cerevisiae. These biosensors are responsive to a wide range of endogenous and exogenous signals, including chemical inducers, light, temperature, cell density, intracellular metabolites, and stress. Additionally, we explored the potential of omics tools for the discovery of novel responsive promoters and their roles in fine-tuning metabolic networks. We also provide an outlook on the development trends in this field.

Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid

BACKGROUND

Methanol is increasingly gaining attraction as renewable carbon source to produce specialty and commodity chemicals, as it can be generated from renewable sources such as carbon dioxide (CO2). In this context, native methylotrophs such as the yeast Komagataella phaffii (syn Pichia pastoris) are potentially attractive cell factories to produce a wide range of products from this highly reduced substrate. However, studies addressing the potential of this yeast to produce bulk chemicals from methanol are still scarce. 3-Hydroxypropionic acid (3-HP) is a platform chemical which can be converted into acrylic acid and other commodity chemicals and biopolymers. 3-HP can be naturally produced by several bacteria through different metabolic pathways.

RESULTS

In this study, production of 3-HP via the synthetic β-alanine pathway has been established in K. phaffii for the first time by expressing three heterologous genes, namely panD from Tribolium castaneum, yhxA from Bacillus cereus, and ydfG from Escherichia coli K-12. The expression of these key enzymes allowed a production of 1.0 g l-1 of 3-HP in small-scale cultivations using methanol as substrate. The addition of a second copy of the panD gene and selection of a weak promoter to drive expression of the ydfG gene in the PpCβ21 strain resulted in an additional increase in the final 3-HP titer (1.2 g l-1). The 3-HP-producing strains were further tested in fed-batch cultures. The best strain (PpCβ21) achieved a final 3-HP concentration of 21.4 g l-1 after 39 h of methanol feeding, a product yield of 0.15 g g-1, and a volumetric productivity of 0.48 g l-1 h-1. Further engineering of this strain aiming at increasing NADPH availability led to a 16% increase in the methanol consumption rate and 10% higher specific productivity compared to the reference strain PpCβ21.

CONCLUSIONS

Our results show the potential of K. phaffii as platform cell factory to produce organic acids such as 3-HP from renewable one-carbon feedstocks, achieving the highest volumetric productivities reported so far for a 3-HP production process through the β-alanine pathway.

The potential of CO2-based production cycles in biotechnology to fight the climate crisis

Rising CO2 emissions have pushed scientists to develop new technologies for a more sustainable bio-based economy. Microbial conversion of CO2 and CO2-derived carbon substrates into valuable compounds can contribute to carbon neutrality and sustainability. Here, we discuss the potential of C1 carbon sources as raw materials to produce energy, materials, and food and feed using microbial cell factories. We provide an overview of potential microbes, natural and synthetic C1 utilization pathways, and compare their metabolic driving forces. Finally, we sketch a future in which C1 substrates replace traditional feedstocks and we evaluate the costs associated with such an endeavor.

Design and Construction of Artificial Biological Systems for One-Carbon Utilization

The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.

Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories

Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.

Economical production of Pichia pastoris single cell protein from methanol at industrial pilot scale

BACKGROUND

Methanol, synthesized from CO2, is a potentially sustainable one-carbon (C1) resource for biomanufacturing. The use of methanol as a feedstock to produce single cell protein (SCP) has been investigated for decades as an alternative to alleviate the high global demand for animal-derived proteins. The methylotrophic yeast Pichia pastoris is an ideal host for methanol-based SCP synthesis due to its natural methanol assimilation ability. However, improving methanol utilization, tolerance to higher temperature, and the protein content of P. pastoris are also current challenges, which are of great significance to the economical industrial application using methanol as a feedstock for SCP production.

RESULTS

In the present work, adaptive laboratory evolution (ALE) has been employed to overcome the low methanol utilization efficiency and intolerance to a higher temperature of 33 °C in P. pastoris, associated with reduced carbon loss due to the lessened detoxification of intracellular formaldehyde through the dissimilation pathway and cell wall rearrangement to temperature stress resistance following long-term evolution as revealed by transcriptomic and phenotypic analysis. By strengthening nitrogen metabolism and impairing cell wall synthesis, metabolic engineering further increased protein content. Finally, the engineered strain via multi-strategy produced high levels of SCP from methanol in a pilot-scale fed-batch culture at 33 °C with a biomass of 63.37 g DCW/L, methanol conversion rate of 0.43 g DCW/g, and protein content of 0.506 g/g DCW. SCP obtained from P. pastoris contains a higher percentage of protein compared to conventional foods like soy, fish, meat, whole milk, and is a source of essential amino acids, including methionine, lysine, and branched-chain amino acids (BCAAs: valine, isoleucine, leucine).

CONCLUSIONS

This study clarified the unique mechanism of P. pastoris for efficient methanol utilization, higher temperature resistance, and high protein synthesis, providing a P. pastoris cell factory for SCP production with environmental, economic, and nutritional benefits.

A novel CRISPR/Cas9 system with high genomic editing efficiency and recyclable auxotrophic selective marker for multiple-step metabolic rewriting in Pichia pastoris

The methylotrophic budding yeast Pichia pastoris has been utilized to the production of a variety of heterologous recombinant proteins owing to the strong inducible alcohol oxidase promoter (pAOX1). However, it is difficult to use P. pastoris as the chassis cell factory for high-valuable metabolite biosynthesis due to the low homologous recombination (HR) efficiency and the limitation of handy selective markers, especially in the condition of multistep biosynthetic pathways. Hence, we developed a novel CRISPR/Cas9 system with highly editing efficiencies and recyclable auxotrophic selective marker (HiEE-ReSM) to facilitate cell factory in P. pastoris. Firstly, we improved the HR rates of P. pastoris through knocking out the non-homologous-end-joining gene (Δku70) and overexpressing HR-related proteins (RAD52 and RAD59), resulting in higher positive rate compared to the basal strain, achieved 97%. Then, we used the uracil biosynthetic genes PpURA3 as the reverse screening marker, which can improve the recycling efficiency of marker. Meanwhile, the HR rate is still 100% in uracil auxotrophic yeast. Specially, we improved the growth rate of uracil auxotrophic yeast strains by overexpressing the uracil transporter (scFUR4) to increase the uptake of exogenous uracil from medium. Meanwhile, we explored the optimal concentration of uracil (90 mg/L) for strain growth. In the end, the HiEE-ReSM system has been applied for the inositol production (250 mg/L) derived from methanol in P. pastoris. The systems will contribute to P. pastoris as an attractive cell factory for the complex compound biosynthesis through multistep metabolic pathway engineering and will be a useful tool to improve one carbon (C1) bio-utilization.

Methanol-based biomanufacturing of fuels and chemicals using native and synthetic methylotrophs

Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction, abundance, and low price. Native methylotrophic yeasts and bacteria have been investigated for the production of fuels and chemicals. Alternatively, synthetic methylotrophic strains are also being developed by reconstructing methanol utilization pathways in model microorganisms, such as Escherichia coli. Owing to the complex metabolic pathways, limited availability of genetic tools, and methanol/formaldehyde toxicity, the high-level production of target products for industrial applications are still under development to satisfy commercial feasibility. This article reviews the production of biofuels and chemicals by native and synthetic methylotrophic microorganisms. It also highlights the advantages and limitations of both types of methylotrophs and provides an overview of ways to improve their efficiency for the production of fuels and chemicals from methanol.

Bioconversion of C1 feedstocks for chemical production using Pichia pastoris

Bioconversion of C1 feedstocks for chemical production offers a promising solution to global challenges such as the energy and food crises and climate change. The methylotroph Pichia pastoris is an attractive host system for the production of both recombinant proteins and chemicals from methanol. Recent studies have also demonstrated its potential for utilizing CO2 through metabolic engineering or coupling with electrocatalysis. This review focuses on the bioconversion of C1 feedstocks for chemical production using P. pastoris. Herein the challenges and feasible strategies for chemical production in P. pastoris are discussed. The potential of P. pastoris to utilize other C1 feedstocks - including CO2 and formate - is highlighted, and new insights from the perspectives of synthetic biology and material science are proposed.

Engineering the methylotrophic yeast Ogataea polymorpha for lactate production from methanol

Introduction: Lactate has gained increasing attention as a platform chemical, particularly for the production of the bioplastic poly-lactic acid (PLA). While current microbial lactate production processes primarily rely on the use of sugars as carbon sources, it is possible to envision a future where lactate can be produced from sustainable, non-food substrates. Methanol could be such a potential substrate, as it can be produced by (electro)chemical hydrogenation from CO₂. Methods: In this study, the use of the methylotrophic yeast Ogataea polymorpha as a host organism for lactate production from methanol was explored. To enable lactate production in Ogataea polymorpha, four different lactate dehydrogenases were expressed under the control of the methanol-inducible MOX promoter. The L-lactate dehydrogenase of Lactobacillus helveticus performed well in the yeast, and the lactate production of this engineered strain could additionally be improved by conducting methanol fed-batch experiments in shake flasks. Further, the impact of different nitrogen sources and the resulting pH levels on production was examined more closely. In order to increase methanol assimilation of the lactate-producing strain, an adaptive laboratory evolution experiment was performed. Results and Discussion: The growth rate of the lactate-producing strain on methanol was increased by 55%, while at the same time lactate production was preserved. The highest lactate titer of 3.8 g/L in this study was obtained by cultivating this evolved strain in a methanol fed-batch experiment in shake flasks with urea as nitrogen source. This study provides a proof of principle that Ogataea polymorpha is a suitable host organism for the production of lactate using methanol as carbon source. In addition, it offers guidance for the engineering of methylotrophic organisms that produce platform chemicals from CO₂-derived substrates. With reduced land use, this technology will promote the development of a sustainable industrial biotechnology in the future.

The cofactor challenge in synthetic methylotrophy: bioengineering and industrial applications

Methanol is a promising feedstock for industrial bioproduction: it can be produced renewably and has high solubility and limited microbial toxicity. One of the key challenges for its bio-industrial application is the first enzymatic oxidation step to formaldehyde. This reaction is catalysed by methanol dehydrogenases (MDH) that can use NAD⁺, O₂ or pyrroloquinoline quinone (PQQ) as an electron acceptor. While NAD-dependent MDH are simple to express and have the highest energetic efficiency, they exhibit mediocre kinetics and poor thermodynamics at ambient temperatures. O₂-dependent methanol oxidases require high oxygen concentrations, do not conserve energy and thus produce excessive heat as well as toxic H₂O₂. PQQ-dependent MDH provide a good compromise between energy efficiency and good kinetics that support fast growth rates without any drawbacks for process engineering. Therefore, we argue that this enzyme class represents a promising solution for industry and outline engineering strategies for the implementation of these complex systems in heterologous hosts.

Engineering Komagataella phaffii to biosynthesize cordycepin from methanol which drives global metabolic alterations at the transcription level

Cordycepin has the potential to be an alternative to the disputed herbicide glyphosate. However, current laborious and time-consuming production strategies at low yields based on Cordyceps militaris lead to extremely high cost and restrict its application in the field of agriculture. In this study, Komagataella phaffii (syn. Pichia pastoris) was engineered to biosynthesize cordycepin from methanol, which could be converted from CO2. Combined with fermentation optimization, cordycepin content in broth reached as high as 2.68 ± 0.04 g/L within 168 h, around 15.95 mg/(L·h) in productivity. Additionally, a deaminated product of cordycepin was identified at neutral or weakly alkaline starting pH during fermentation. Transcriptome analysis found the yeast producing cordycepin was experiencing severe inhibition in methanol assimilation and peroxisome biogenesis, responsible for delayed growth and decreased carbon flux to pentose phosphate pathway (PPP) which led to lack of precursor supply. Amino acid interconversion and disruption in RNA metabolism were also due to accumulation of cordycepin. The study provided a unique platform for the manufacture of cordycepin based on the emerging non-conventional yeast and gave practical strategies for further optimization of the microbial cell factory.

Focus and Insights into the Synthetic Biology-Mediated Chassis of Economically Important Fungi for the Production of High-Value Metabolites

Substantial progress has been achieved and knowledge gaps addressed in synthetic biology-mediated engineering of biological organisms to produce high-value metabolites. Bio-based products from fungi are extensively explored in the present era, attributed to their emerging importance in the industrial sector, healthcare, and food applications. The edible group of fungi and multiple fungal strains defines attractive biological resources for high-value metabolites comprising food additives, pigments, dyes, industrial chemicals, and antibiotics, including other compounds. In this direction, synthetic biology-mediated genetic chassis of fungal strains to enhance/add value to novel chemical entities of biological origin is opening new avenues in fungal biotechnology. While substantial success has been achieved in the genetic manipulation of economically viable fungi (including Saccharomyces cerevisiae) in the production of metabolites of socio-economic relevance, knowledge gaps/obstacles in fungal biology and engineering need to be remedied for complete exploitation of valuable fungal strains. Herein, the thematic article discusses the novel attributes of bio-based products from fungi and the creation of high-value engineered fungal strains to promote yield, bio-functionality, and value-addition of the metabolites of socio-economic value. Efforts have been made to discuss the existing limitations in fungal chassis and how the advances in synthetic biology provide a plausible solution.

Improving Methanol Utilization by Reducing Alcohol Oxidase Activity and Adding Co-Substrate of Sodium Citrate in Pichia pastoris

Methanol, which produced in large quantities from low-quality coal and the hydrogenation of CO2, is a potentially renewable one-carbon (C1) feedstock for biomanufacturing. The methylotrophic yeast Pichia pastoris is an ideal host for methanol biotransformation given its natural capacity as a methanol assimilation system. However, the utilization efficiency of methanol for biochemical production is limited by the toxicity of formaldehyde. Therefore, reducing the toxicity of formaldehyde to cells remains a challenge to the engineering design of a methanol metabolism. Based on genome-scale metabolic models (GSMM) calculations, we speculated that reducing alcohol oxidase (AOX) activity would re-construct the carbon metabolic flow and promote balance between the assimilation and dissimilation of formaldehyde metabolism processes, thereby increasing the biomass formation of P. pastoris. According to experimental verification, we proved that the accumulation of intracellular formaldehyde can be decreased by reducing AOX activity. The reduced formaldehyde formation upregulated methanol dissimilation and assimilation and the central carbon metabolism, which provided more energy for the cells to grow, ultimately leading to an increased conversion of methanol to biomass, as evidenced by phenotypic and transcriptome analysis. Significantly, the methanol conversion rate of AOX-attenuated strain PC110-AOX1-464 reached 0.364 g DCW/g, representing a 14% increase compared to the control strain PC110. In addition, we also proved that adding a co-substrate of sodium citrate could further improve the conversion of methanol to biomass in the AOX-attenuated strain. It was found that the methanol conversion rate of the PC110-AOX1-464 strain with the addition of 6 g/L sodium citrate reached 0.442 g DCW/g, representing 20% and 39% increases compared to AOX-attenuated strain PC110-AOX1-464 and control strain PC110 without sodium citrate addition, respectively. The study described here provides insight into the molecular mechanism of efficient methanol utilization by regulating AOX. Reducing AOX activity and adding sodium citrate as a co-substrate are potential engineering strategies to regulate the production of chemicals from methanol in P. pastoris.

Overproduction of Patchoulol in Metabolically Engineered Komagataella phaffii

Patchoulol, a plant-derived sesquiterpene compound, is widely used in perfumes, cosmetics, and pharmaceuticals. Microbial production provides a promising alternative approach for the efficient and sustainable production of patchoulol. However, there are no systematic engineering studies on Komagataella phaffii aimed at achieving high-yield patchoulol production. Herein, by fusion overexpression of FPP synthase and patchoulol synthase (ERG20LPTS), increasing the precursor supply, adjusting the copy number of ERG20LPTS and PTS, and combined with adding auxiliary carbon source and methanol concentration optimization, we constructed a high-yield patchoulol-producing strain P6H53, which produced 149.64 mg/L patchoulol in shake-flask fermentation with methanol as the substrate. In fed-batch fermentation, strain P6H53 achieved the highest production (2.47 g/L, 21.48 mg/g DCW, and 283.25 mg/L/d) to date in a 5 L fermenter. This study will lay a good foundation for the development of K. phaffii as a promising chassis microbial cell for the synthesis of patchoulol and other sesquiterpenes with methanol as the carbon source.

Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production

Carbon dioxide (CO2 ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H2 -dependent CO2 gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO2 as sole carbon feedstock and H2 as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO2 into C1 products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO2 abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.

Metabolic engineering of the acid-tolerant yeast Pichia kudriavzevii for efficient L-malic acid production at low pH

Currently, the biological production of L-malic acid (L-MA) is mainly based on the fermentation of filamentous fungi at near-neutral pH, but this process requires large amounts of neutralizing agents, resulting in the generation of waste salts when free acid is obtained in the downstream process, and the environmental hazards associated with the waste salts limit the practical application of this process. To produce L-MA in a more environmentally friendly way, we metabolically engineered the acid-tolerant yeast Pichia kudriavzevii and achieved efficient production of L-MA through low pH fermentation. First, an initial L-MA-producing strain that relies on the reductive tricarboxylic acid (rTCA) pathway was constructed. Subsequently, the L-MA titer and yield were further increased by fine-tuning the flux between the pyruvate and oxaloacetate nodes. In addition, we found that the insufficient supply of NADH for cytoplasmic malate dehydrogenase (MDH) hindered the L-MA production at low pH, which was resolved by overexpressing the soluble pyridine nucleotide transhydrogenase SthA from E. coli. Transcriptomic and metabolomic data showed that overexpression of EcSthA contributed to the activation of the pentose phosphate pathway and provided additional reducing power for MDH by converting NADPH to NADH. Furthermore, overexpression of EcSthA was found to help reduce the accumulation of the by-product pyruvate but had no effect on the accumulation of succinate. In microaerobic batch fermentation in a 5-L fermenter, the best strain, MA009-10-URA3 produced 199.4 g/L L-MA with a yield of 0.94 g/g glucose (1.27 mol/mol), with a productivity of 1.86 g/L/h. The final pH of the fermentation broth was approximately 3.10, meaning that the amount of neutralizer used was reduced by more than 50% compared to the common fermentation processes using filamentous fungi. To our knowledge, this is the first report of the efficient bioproduction of L-MA at low pH and represents the highest yield of L-MA in yeasts reported to date.

Improving the productivity of malic acid by alleviating oxidative stress during Aspergillus niger fermentation

BACKGROUND

As an attractive platform chemical, malic acid has been commonly used in the food, feed and pharmaceutical field. Microbial fermentation of biobased sources to produce malic acid has attracted great attention because it is sustainable and environment-friendly. However, most studies mainly focus on improving yield and ignore shortening fermentation time. A long fermentation period means high cost, and hinders the industrial applications of microbial fermentation. Stresses, especially oxidative stress generated during fermentation, inhibit microbial growth and production, and prolong fermentation period. Previous studies have shown that polypeptides could effectively relieve stresses, but the underlying mechanisms were poorly understood.

RESULTS

In this study, polypeptides (especially elastin peptide) addition improves the productivity of malic acid in A. niger, resulting in shortening of fermentation time from 120 to 108 h. Transcriptome and biochemical analyses demonstrated that both antioxidant enzyme-mediated oxidative stress defense system, such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), and nonenzymatic antioxidant system, such as glutathione, were enhanced in the presence of elastin peptide, suggesting elastin peptide relieving oxidative stresses is involved in many pathways. In order to further investigate the relationship between oxidative stress defense and malic acid productivity, we overexpressed three enzymes (Sod1, CAT, Tps1) related to oxidation resistance in A. niger, respectively, and these resulting strains display varying degree of improvement in malic acid productivity. Especially, the strain overexpressing the Sod1 gene achieved a malate titer of 91.85 ± 2.58 g/L in 96 h, corresponding to a productivity of 0.96 g/L/h, which performs better than elastin peptide addition.

CONCLUSIONS

Our investigation provides an excellent reference for alleviating the stress of the fungal fermentation process and improving fermentation efficiency.

Current advances of Pichia pastoris as cell factories for production of recombinant proteins

Pichia pastoris (syn. Komagataella spp.) has attracted extensive attention as an efficient platform for recombinant protein (RP) production. For obtaining a higher protein titer, many researchers have put lots of effort into different areas and made some progress. Here, we summarized the most recent advances of the last 5 years to get a better understanding of its future direction of development. The appearance of innovative genetic tools and methodologies like the CRISPR/Cas9 gene-editing system eases the manipulation of gene expression systems and greatly improves the efficiency of exploring gene functions. The integration of novel pathways in microorganisms has raised more ideas of metabolic engineering for enhancing RP production. In addition, some new opportunities for the manufacture of proteins have been created by the application of novel mathematical models coupled with high-throughput screening to have a better overview of bottlenecks in the biosynthetic process.

Developing methylotrophic microbial platforms for a methanol-based bioindustry

Methanol, a relatively cheap and renewable single-carbon feedstock, has gained considerable attention as a substrate for the bio-production of commodity chemicals. Conventionally produced from syngas, along with emerging possibilities of generation from methane and CO2, this C1 substrate can serve as a pool for sequestering greenhouse gases while supporting a sustainable bio-economy. Methylotrophic organisms, with the inherent ability to use methanol as the sole carbon and energy source, are competent candidates as platform organisms. Accordingly, methanol bioconversion pathways have been an attractive target for biotechnological and bioengineering interventions in developing microbial cell factories. This review summarizes the recent advances in methanol-based production of various bulk and value-added chemicals exploiting the native and synthetic methylotrophic organisms. Finally, the current challenges and prospects of streamlining these methylotrophic platforms are discussed.

Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins

The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2.

Synthetic methylotrophic yeasts for the sustainable fuel and chemical production

Global energy-related emissions, in particular carbon dioxide, are rapidly increasing. Without immediate and strong reductions across all sectors, limiting global warming to 1.5 °C and thus mitigating climate change is beyond reach. In addition to the expansion of renewable energies and the increase in energy efficiency, the so-called Carbon Capture and Utilization technologies represent an innovative approach for closing the carbon cycle and establishing a circular economy. One option is to combine CO₂ capture with microbial C₁ fermentation. C₁-molecules, such as methanol or formate are considered as attractive alternative feedstock for biotechnological processes due to their sustainable production using only CO₂, water and renewable energy. Native methylotrophic microorganisms can utilize these feedstock for the production of value-added compounds. Currently, constraints exist regarding the understanding of methylotrophic metabolism and the available genetic engineering tools are limited. For this reason, the development of synthetic methylotrophic cell factories based on the integration of natural or artificial methanol assimilation pathways in biotechnologically relevant microorganisms is receiving special attention. Yeasts like Saccharomyces cerevisiae and Yarrowia lipolytica are capable of producing important products from sugar-based feedstock and the switch to produce these in the future from methanol is important in order to realize a CO₂-based economy that is independent from land use. Here, we review historical biotechnological applications, the metabolism and the characteristics of methylotrophic yeasts. Various studies demonstrated the production of a broad set of promising products from fine chemicals to bulk chemicals by applying methylotrophic yeasts. Regarding synthetic methylotrophy, the deep understanding of the methylotrophic metabolism serves as the basis for microbial strain engineering and paves the way towards a CO₂-based circular bioeconomy. We highlight design aspects of synthetic methylotrophy and discuss the resulting chances and challenges using non-conventional yeasts as host organisms. We conclude that the road towards synthetic methylotrophic yeasts can only be achieved through a combination of methods (e.g., metabolic engineering and adaptive laboratory evolution). Furthermore, we presume that the installation of metabolic regeneration cycles such as supporting carbon re-entry towards the pentose phosphate pathway from C₁-metabolism is a pivotal target for synthetic methylotrophy.

Fusing an exonuclease with Cas9 enhances homologous recombination in Pichia pastoris

BACKGROUND

The methylotrophic yeast Pichia pastoris is considered as an ideal host for the production of recombinant proteins and chemicals. However, low homologous recombination (HR) efficiency hinders its precise and extensive genetic manipulation. To enhance the homology-directed repair over non-homologous end joining (NHEJ), we expressed five exonucleases that were fused with the Cas9 for enhancing end resection of double strand breaks (DSBs) of DNA cuts.

RESULTS

The endogenous exonuclease Mre11 and Exo1 showed the highest positive rates in seamless deletion of FAA1, and fusing the MRE11 to the C-terminal of CAS9 had the highest positive rate and relatively high number of clones. We observed that expression of CAS9-MRE11 significantly improved positive rates when simultaneously seamless deletion of double genes (from 76.7 to 86.7%) and three genes (from 10.8 to 16.7%) when overexpressing RAD52. Furthermore, MRE11 overexpression significantly improved the genomic integration of multi-fragments with higher positive rate and clone number.

CONCLUSIONS

Fusion expression of the endogenous exonuclease Mre11 with Cas9 enhances homologous recombination efficiency in P. pastoris. The strategy described here should facilitate the metabolic engineering of P. pastoris toward high-level production of value-added compounds.

Comparative proteomics analysis of Pichia pastoris cultivating in glucose and methanol

The methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii) has been extensively engineered for protein production, and is attracting attention as a chassis cell for methanol biotransformation toward production of small molecules. However, the relatively unclear methanol metabolism hampers the metabolic rewiring to improve the biosynthetic efficiency. We here performed a label-free quantitative proteomic analysis of Pichia pastoris when cultivated in minimal media containing methanol and glucose, respectively. There were 243, 158 up-regulated proteins and 244, 304 down-regulated proteins in log and stationary phase, respectively, when cultivated in methanol medium compared with that of glucose medium. Peroxisome enrichment further improved the characterization of more differentially expressed proteins (481 proteins in log phase and 524 proteins in stationary phase). We demonstrated the transaldolase isoenzyme (Tal2, Protein ID: C4R244) was highly up-regulated in methanol medium cultivation, which plays an important role in methanol utilization. Our work provides important information for understanding methanol metabolism in methyltrophic yeast and will help to engineer methanol biotransformation in P. pastoris.

Efficient fatty acid synthesis from methanol in methylotrophic yeast

Methanol is an attractive C1 feedstock with high abundance and low cost in bio-manufacturing. However, the metabolic construction of cell factories to utilize methanol for chemicals production remains a challenge due to the toxic intermediates and complicated metabolic pathways. The group of Zhou rescued methylotrophic yeast from cell death and achieved high-level production of free fatty acids from methanol through a combination of adaptive laboratory evolution, rational metabolic engineering and multi-omics analysis.

Methanol biotransformation toward high-level production of fatty acid derivatives by engineering the industrial yeast Pichia pastoris

Methanol-based biorefinery is a promising strategy to achieve carbon neutrality goals by linking CO₂ capture and solar energy storage. As a typical methylotroph, Pichia pastoris shows great potential in methanol biotransformation. However, challenges still remain in engineering methanol metabolism for chemical overproduction. Here, we present the global rewiring of the central metabolism for efficient production of free fatty acids (FFAs; 23.4 g/L) from methanol, with an enhanced supply of precursors and cofactors, as well as decreased accumulation of formaldehyde. Finally, metabolic transforming of the fatty acid cell factory enabled overproduction of fatty alcohols (2.0 g/L) from methanol. This study demonstrated that global metabolic rewiring released the great potential of P. pastoris for methanol biotransformation toward chemical overproduction.

Toward Methanol-Based Biomanufacturing: Emerging Strategies for Engineering Synthetic Methylotrophy in Saccharomyces cerevisiae

The global expansion of biomanufacturing is currently limited by the availability of sugar-based microbial feedstocks, which require farmland for cultivation and therefore cannot support large increases in production without impacting the human food supply. One-carbon feedstocks, such as methanol, present an enticing alternative to sugar because they can be produced independently of arable farmland from organic waste, atmospheric carbon dioxide, and hydrocarbons such as biomethane, natural gas, and coal. The development of efficient industrial microorganisms that can convert one-carbon feedstocks into valuable products is an ongoing challenge. This review discusses progress in the field of synthetic methylotrophy with a focus on how it pertains to the important industrial yeast, Saccharomyces cerevisiae. Recent insights generated from engineering synthetic methylotrophic xylulose- and ribulose-monophosphate cycles, reductive glycine pathways, and adaptive laboratory evolution studies are critically assessed to generate novel strategies for the future engineering of methylotrophy in S. cerevisiae.

Rescuing yeast from cell death enables overproduction of fatty acids from sole methanol

Methanol is an ideal feedstock for biomanufacturing that can be beneficial for global carbon neutrality; however, the toxicity of methanol limits the efficiency of methanol metabolism toward biochemical production. We here show that engineering production of free fatty acids from sole methanol results in cell death with decreased cellular levels of phospholipids in the methylotrophic yeast Ogataea polymorpha, and cell growth is restored by adaptive laboratory evolution. Whole-genome sequencing of the adapted strains reveals that inactivation of LPL1 (encoding a putative lipase) and IZH3 (encoding a membrane protein related to zinc metabolism) preserve cell survival by restoring phospholipid metabolism. Engineering the pentose phosphate pathway and gluconeogenesis enables high-level production of free fatty acid (15.9 g l^-1) from sole methanol. Preventing methanol-associated toxicity underscores the link between lipid metabolism and methanol tolerance, which should contribute to enhancing methanol-based biomanufacturing.