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In 2020 and 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, caused a global pandemic. Vaccines are expected to reduce the pressure of prevention and control, and have become the most effective strategy to solve the pandemic crisis. SARS-CoV-2 infects the host by binding to the cellular receptor angiotensin converting enzyme 2 (ACE2) via the receptor-binding domain (RBD) of the surface spike (S) glycoprotein. In this study, a candidate vaccine based on a RBD recombinant subunit was prepared by means of a novel glycoengineered yeast Pichia pastoris expression system with characteristics of glycosylation modification similar to those of mammalian cells. The candidate vaccine effectively stimulated mice to produce high-titer anti-RBD specific antibody. Furthermore, the specific antibody titer and virus-neutralizing antibody (NAb) titer induced by the vaccine were increased significantly by the combination of the double adjuvants Al(OH)3 and CpG. Our results showed that the virus-NAb lasted for more than 6 months in mice. To summarize, we have obtained a SARS-CoV-2 vaccine based on the RBD of the S glycoprotein expressed in glycoengineered Pichia pastoris, which stimulates neutralizing and protective antibody responses. A technical route for fucose-free complex-type N-glycosylation modified recombinant subunit vaccine preparation has been established.

Retaining β-mannanases are glycoside hydrolases (GHs) that can potentially be applied for synthesis of glycosides by catalysis of transglycosylation reactions. A novel active-site double mutant (R171 K/E205D) of the catalytic module (CM) of the family GH5 Trichoderma reesei β-mannanase (TrMan5A) was expressed in Pichia pastoris and purified. TrMan5A, CM and CM-variants R171 K and R171 K/E205D had pH optima between pH 4.0-5.3 and showed >80% remaining activity after incubation at 40 °C for 48 h. The enzymes were screened for transglycosylation capacity toward oligomeric and polymeric donor substrates and alcohol acceptors using mass-spectrometry. Hydrolysis and transglycosylation products were analysed by a novel HPLC procedure using an NH2 column. R171 K/E205D was superior in reactions with mannotetraose and the acceptor allyl alcohol, it had twice as high propensity for transglycosylation as wild-type TrMan5A. Wild-type TrMan5A produced the highest amounts of allyl β-mannosides (with 1-3 mannosyls) from locust bean galactomannan. Applying enzyme synergy, adding the GH27 guar α-galactosidase to the reaction (to cleave off galactomannan side-groups), gave a 2.1-fold increase of allyl mannosides and simultaneously a significant production of allyl galactopyranoside, increasing overall yield of allyl glycosides 4.4-fold, from 2.2% to 9.8%. The enzymatic synthesis of reactive allyl glycosides opens up for production of novel biomaterials and glycopolymers.

Objective: Oral infections and dental caries are considered serious health problems. Therefore, searching for new agents with antimicrobial properties seems to be crucial. This study aimed to evaluate the antimicrobial activity of the recombinant Thrombocidin-1 [TC-1] peptide on some oral pathogens. Also, the cytotoxicity of this peptide on human gingival fibroblast cells was investigated. Methods & Materials: In this study, Pichia pastoris was used for the expression of recombinant TC-1. The microbroth dilution method was used to determine the minimum inhibitory concentration [MIC] and minimum bacterial concentration [MBC]. It tested against four main oral pathogens; Streptococcus mutans, Streptococcus salivarius, Streptococcus oralis, and Enterococcus faecalis. Moreover, the cytotoxicity analysis was done on gingival fibroblast cells by the MTT method. The data were analyzed using a two-way analysis of variance [ANOVA] and Tukey’s HSD tests. Results: The most bactericidal effect of TC-1 was against S. salivarius, the highest bacteriostatic effect was against S. salivarius, and S. oralis had the lowest MIC value of 1.512 μg/ml. The Thrombocidin- 1 peptide showed lower antibacterial properties against E. faecalis compared with CHX, unlike the stronger antimicrobial effect on examined streptococci. According to cytotoxicity examination, no concentration of TC-1 presented over 50% growth inhibition [IC50] of the fibroblasts cells. Conclusion: Based on antimicrobial tests and cytotoxicity results, the Thrombocidin-1 peptide may be useful as a safe antibacterial agent against some oral pathogens in dental materials.

As a common phenomenon existing in almost all genomes, codon usage bias has been studied for a long time. Codon optimization is a frequently used strategy to accelerate protein synthesis rate. Besides regulating protein translation speed, codon usage bias has also be reported to affect co-translation folding and transcription. P. pastoris is a well-developed expression system, whose efficiency is tightly correlated with commercial value. However, few studies focus on the role of codon usage bias in affecting protein expression in P. pastoris. Besides, many genes in P. pastoris genome show significant negative correlation between codon usage bias and protein structural disorder tendency. It’s not known whether this feature is important for their expression. In order to answer these questions, we picked 4 P. pastoris gene candidates with strong negative correlation between codon usage bias and protein structural disorder. We then performed full-length codon optimization which completely eliminated the correlation. Protein and RNA assays were then used to compare protein and mRNA levels before and after codon optimization. As a result, codon optimization failed to elevate their protein expression levels, and even resulted in a decrease. As represented by the trypsin sensitivity assays, codon optimization also altered the protein structure of 0616 and 0788. Besides protein, codon optimization also affected mRNA levels. Shown by in vitro and in vivo RNA degradation assays, the mRNA stability of 0616, 0788 and 0135 were also altered by codon optimization. For each gene, the detailed effect may be related with its specific sequence and protein structure. Our results suggest that codon usage bias is an important factor to regulate gene expression level, as well as mRNA and protein stabilities in P. pastoris. “Extreme” codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored. Compromised strategies should be tried if expression is not successful. Besides, codon optimization may affect protein structural conformation more severely in structural disordered proteins.

A metal-resistant engineered Pichia pastoris was developed here to fulfil the metal bioleaching in aqueous conditions. Parent and recombinant yeasts were grown in YPD medium containing different concentrations of ion metals. XRD, electron microscopy and particle size analyser were used for the characterisation and the nanoparticle analyses. The nanoparticle production kinetics were studied by ICP-OES. The cytotoxicity of nanoparticles was assayed against human cell lines. Media colours changed to a range from purplish-brown to grey during early fermentation stages. The maximum biosorption capacities were recorded 81.23 and 493.35 mg/g for gold and palladium in batch conditions, respectively. Various physical investigations proved monodispersed spherical nanoparticles around 100 nm in size. Pure palladium nanoparticles and PdCl2 represented the least cytotoxic potency towards T47D and EPG85.257 cells. The results demonstrated that the genetically modified yeast is a cost-effective, high-throughput, robust, and facile system for metal biosorption.

Compared with the traditional suspension fermentation, immobilised biofilm fermentation has advantages of strong resistance, high yield and continuous fermentation and is conducive to improving the industrial fermentation methods. The formation of a biofilm on correct supports is critical to immobilised fermentation. In this study, Pichia pastoris was used to understand and control the modification of surface properties of supports and cells. Following deletion of gene PAS_chr2-1_0773, in P. pastoris △0773, the cell-surface negative charge density decreased and hydrophobicity improved, which was conducive to adhesion. Therefore, according to the changing trend of cell surface properties, cotton fibre was used with succinic anhydride (SA) to modify the carrier for changing the surface properties for efficient conduction of immobilised fermentation. In the fermentation process, the adhesion between the modified cotton fibre and yeast was better than that between an unmodified cotton fibre and yeast, and the additive amount increased by ∼25 %. The enzyme activity of the △0773-cotton-SA fermentation system reached 302.7 U/mL, which was 39.6 % higher than that of the original fermentation system. Therefore, this study provides a guide for significant improvement of immobilised fermentation of fungi.

Background: Pichia pastoris is one of the most popular eukaryotic hosts for producing heterologous proteins, while increasing the secretion of target proteins is still a top priority for their application in industrial fields. Recently, the research effort to enhance protein production has focused on up-regulating the unfolded protein response (UPR). Objective: We evaluated the effects of activated UPR via Hac1p co-expression with the promoter AOX1 (PAOX1) or GAP (PGAP) on the expression of recombinant chitosanase (rCBS) in P. pastoris. Method: The DNA sequence encoding the chitosanase was chemically synthesized and cloned into pPICZαA, and the resulting pPICZαA/rCBS was transformed into P. pastoris for expressing rCBS. The P. pastorisHAC1i cDNA was chemically synthesized and cloned into pPIC3.5K to give pPIC3.5K/Hac1p. The HAC1i cDNA was cloned into PGAPZB and then inserted with the HIS4 gene from pAO815 to construct the vector PGAPZB/Hac1p/HIS4. For co-expression of Hac1p, the two plasmids pPIC3.5K/Hac1p and PGAPZB/Hac1p/HIS4 were transformed into P. pastoris harboring the CBS gene. The rCBS was assessed based on chitosanase activity and analyzed by SDSPAGE. The enhanced Kar2p was detected with western blotting to evaluate UPR. Results: Hac1p co-expression with PAOX1 enhanced rCBS secretion by 41% at 28°C. Although the level of UPR resulting from Hac1p co-expression with PAOX1 was equivalent to that with PGAP in terms of the quantity of Kar2p (a hallmark of the UPR), substitution of PGAP for PAOX1 further increased rCBS production by 21%. The methanol-utilizing phenotype of P. pastoris did not affect rCBS secretion with or without co-expression of Hac1p. Finally, Hac1p co-expression with PAOX1 or PGAP promoted rCBS secretion from 22 to 30°C and raised the optimum induction temperature. Conclusion: The study indicated that Hac1p co-expression with PAOX1 or PGAP is an effective strategy to trigger UPR of P. pastoris and a feasible means for improving the production of rCBS therein.

Recombinant Pichia pastoris biomass surface-expressing the viral binding protein PmRab7 (YSD-PmRab7) was prepared by fed-batch, aerobic fermentation with methanol induction for 48 h. By cell based ELISA assay, immunofluorescence and flow cytometry, 45% of the YSD-PmRab7 cells were positive for PmRab7. Freeze dried YSD-PmRab7 cells were added to formulated shrimp feed pellets at 0.25 g and 0.5 g per g feed and fed to 2 shrimp groups for 7 days prior to challenge with white spot syndrome virus (WSSV). Controls consisted of 1 shrimp group fed normal pellets and one fed pellets containing P. pastoris carrying an empty gene cassette. At 10 days post challenge, survival in the two control groups was 6.7 ± 6.6%, while it was 26.7 ± 6.6% in the 0.25 g YSD-PmRab7 group and significantly higher (p 0.05) in the 0.5 g YSD-PmRab7 group at 46.7 ± 10.1%. Nested PCR assays and histopathological analysis revealed significantly lower WSSV replication levels in the 0.5 g YSD-PmRab7 group. The results indicated potential for development of YSD-PmRab7 cells as an oral prophylactic against WSSV in shrimp.

When producing recombinant proteins with Pichia pastoris, cultivation parameters, such as induction temperature, dissolved oxygen level and residual methanol concentration play a crucial role in product biosynthesis and subsequent purification, therefore to maximize protein yields, the optimization of these parameters is imperative. Two different Pichia pastoris cultivation strategies for HBsAg VLP production in a 5 L stirred-tank bioreactor and the influence of different cultivation parameters on product yield were investigated. Residual methanol concentrations were controlled at low (>0.01 g/L), medium (1.5-2.0 g/L) and high (5.0-6.0 g/L) levels using a PI-based feed rate control algorithm based on the online methanol sensor signal. Product was purified using a novel and rapid purification method including steps of ammonium sulfate precipitation, size-exclusion chromatography and hydrophobic interaction chromatography. Employing an in-situ methanol sensor probe, the PI-based methanol feed rate control algorithm provided residual methanol concentration control with an average deviation of ±0.4 g/L from set-point value. Employing a cultivation protocol with an increased methanol concentration controlled at 6.0 g/L and a reduced DO level below 10 %, resulting in a final dry cell biomass concentration of 140 g/L and purified HBsAg VLPs yield of 186 mg/L. Developed purification method proved advantageous to other described methods, as it did not include time consuming extraction and centrifugation steps.

The xyloglucanase gene (RmXEG12A) from Rhizomucor miehei CAU432 was successfully expressed in Pichia pastoris. The highest xyloglucanase activity of 25,700 U mL−1 was secreted using high cell density fermentation. RmXEG12A was optimally active at pH 7.0 and 65 °C, respectively. The xyloglucanase exhibited the highest specific activity towards xyloglucan (7915.5 U mg−1). RmXEG12A was subjected to hydrolyze tamarind powder to produce xyloglucan oligosaccharides with the degree of polymerization (DP) 7–9. The hydrolysis ratio of xyloglucan in tamarind powder was 89.8%. Moreover, xyloglucan oligosaccharides (2.0%, w/w) improved the water holding capacity (WHC) of yoghurt by 1.1-fold and promoted the growth of Lactobacillus bulgaricus and Streptococcus thermophiles by 2.3 and 1.6-fold, respectively. Therefore, a suitable xyloglucanase for tamarind powder hydrolysis was expressed in P. pastoris at high level and xyloglucan oligosaccharides improved the quality of yoghurt.

Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris.

For Pichia pastoris fermentation process with multi-operating conditions, it is difficult to predict the cell concentration under the new operating conditions by the soft sensor model established under the specific operating conditions. Inspired by the idea of transfer learning, a method based on an improved balanced distribution adaptive regularization extreme learning machine (IBDA-RELM) was proposed to solve the problem. The domain adaptation (DA) method in transfer learning is developed to reduce distribution distance by transforming data. However, the joint distribution adaptation (JDA) and the balanced distribution adaptation (BDA) in DA cannot be directly applied to regression problems. The fuzzy sets (FSs) method was proposed to solve this issue. Finally, a soft sensor model of Pichia pastoris cell concentration was realized by inputting the converted data to the RELM model. Simulation verification was carried out with three operating conditions at the scene of fermentation. The transfer effects of three DA methods, including transfer component analysis (TCA), improved joint distribution adaptation (IJDA) as well as IBDA, were compared. The predicted results show that IBDA-RELM had a better performance in the soft sensor of Pichia pastoris cell concentration under multi-operating conditions.

Tannin acyl hydrolases or tannases (E.C.3.1.1.20) are enzymes that hydrolyze the ester bond of tannins to produce gallic acid and glucose. We engineered the Aspergillus niger GH1 tannase sequence and Pichia pastoris strains to produce and secrete the enzyme as a single-chain protein. The recombinant tannase was N-glycosylated, had a molecular mass after N-deglycosylation of 65.4 kDa, and showed activity over broad pH and temperature ranges, with optimum pH and temperature of 5.0 and 20 °C. Furthermore, the single-chain tannase had an 11-fold increased specific activity in comparison to the double-chain A. niger GH1 tannase, which was also produced in P. pastoris. Structural analysis suggested that the high specific activity may be due to the presence of a flexible loop in the lid domain, which can control and drive the substrate to the active site. In contrast, the low specific activity of the double-chain tannase may be due to the presence of a disordered and flexible loop that could hinder the substrate's access to the binding site. Based on its biochemical properties, high specific activity, and the possibility of its production in P. pastoris, the tannase described could be used in food and beverage processing at low and medium temperatures.

Pichia pastoris has been widely exploited for the heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value chemicals and pharmaceuticals. Effective synthetic biology tools for genetic engineering are essential for industrial and biotechnological research in this yeast. Here, we describe a novel and efficient genome editing method mediated by the CRISPR-Cpf1 system, which could facilitate the deletion of large DNA fragments and integration of multiplexed gene fragments. The CRISPR-Cpf1 system exhibited a precise and high editing efficiency for single-gene disruption (99 ± 0.8%), duplex genome editing (65 ± 2.5% to 80 ± 3%), and triplex genome editing (30 ± 2.5%). In addition, the deletion of large DNA fragments of 20kb and one-step integration of multiple genes were first achieved using the developed CRISPR-Cpf1 system. Taken together, this study provides an efficient and simple gene editing tool for P. pastoris. The novel multiloci gene integration method mediated by CRISPR-Cpf1 may accelerate the ability to engineer this methylotrophic yeast for metabolic engineering and genome evolution in both biotechnological and biomedical applications.

Downstream processing is an expensive step for industrial production of recombinant proteins. Cell immobilization is known as one of the ideal solutions in regard to process intensification. In recent years, magnetic immobilization was introduced as a new technique for cell immobilization. This technique was successfully employed to harvest many bacterial and eukaryotic cells. But there are no data about the influence of magnetic immobilization on the eukaryotic inducted recombinant cells. In this study, impacts of magnetic immobilization on the growth and metabolic status of induced recombinant Pichia pastoris as a valuable eukaryotic model cells were investigated. Results based on colony-forming unit, OD600, and trypan blue assay indicated that magnetic immobilization had no adverse effect on the growth and viability of P. pastoris cells. Also, about 20-40% increase in metabolic activity was recorded in immobilized cells that were decorated with 0.5-2 mg/mL nanoparticles. Total protein and carbohydrate of the cells were also measured as main indicatives for cell function and no significant changes were observed in the immobilized cells. Current data show magnetic immobilization as a biocompatible technique for application in eukaryotic expression systems. Results can be considered for further developments in P. pastoris-based expression systems.

Background Glucoamylase is an important industrial enzyme in the saccharification of starch into glucose. However, its poor thermostability and low catalytic efficiency limit its industrial saccharification applications. Therefore, improving these properties of glucoamylase is of great significance for saccharification in the starch industry. Results In this study, a novel glucoamylase-encoding gene TlGa15B from the thermophilic fungus Talaromyces leycettanus JCM12802 was cloned and expressed in Pichia pastoris. The optimal temperature and pH of recombinant TlGa15B were 65 ℃ and 4.5, respectively. TlGa15B exhibited excellent thermostability at 60 ℃. To further improve thermostability without losing catalytic efficiency, TlGa15B-GA1 and TlGa15B-GA2 were designed by introducing disulfide bonds and optimizing residual charge–charge interactions in a region distant from the catalytic center. Compared with TlGa15B, mutants showed improved optimal temperature, melting temperature, specific activity, and catalytic efficiency. The mechanism underlying these improvements was elucidated through molecular dynamics simulation and dynamics cross-correlation matrices analysis. Besides, the performance of TlGa15B-GA2 was the same as that of the commercial glucoamylase during saccharification. Conclusions We provide an effective strategy to simultaneously improve both thermostability and catalytic efficiency of glucoamylase. The excellent thermostability and high catalytic efficiency of TlGa15B-GA2 make it a good candidate for industrial saccharification applications.

In this study, we report the identification and characterization of an acetyl xylan esterase, designated as AoAXEC, which was previously annotated as a hypothetical protein encoded by AO090023000158 in the Aspergillus oryzae genomic database. Based on its amino acid sequence, a low sequence identity to known acetyl xylan esterases was observed in the sequence of characterized acetyl xylan esterase. The gene fused with α-factor signal sequence of Saccharomyces cerevisiae instead of the native signal sequence was cloned into a vector, pPICZαC, and expressed successfully in Pichia pastoris as an active extracellular protein. The purified recombinant protein had pH and temperature optima of 7.0 and 50 °C, respectively, and was stable up to 50 °C. The optimal substrate for hydrolysis by the purified recombinant AoAXEC, among a panel of α-naphthyl esters (C2–C16), was α-naphthyl propionate (C3), with an activity of 0.35 ± 0.006 units/mg protein. No significant difference of the Km value was observed between C3 (2.3 ± 0.7 mM) and C2 (1.9 ± 0.4 mM). In contrast, kcat value for C3 (18 ± 3.9 s−1) was higher compared to C2 (4.5 ± 0.7 s−1). The purified recombinant enzyme displayed a low activity toward acyl chain substrates containing eight or more carbon atoms. Recombinant AoAXEC catalyzed the release of acetic acid from wheat arabinoxylan. However, no activity was detected on methyl esters of ferulic, p-coumaric, caffeic, or sinapic acids. Additionally, the liberation of phenolic acids, such as ferulic acid, from wheat arabinoxylan was not exhibited by the recombinant protein.

The contamination of foods and feeds with mycotoxins has been an issue of global significance. For mycotoxin detoxification, enzymatic biodegradation using laccase has received much attention. In this study, a laccase gene lac2 from the fungus Pleurotus pulmonarius was expressed in the Pichia pastoris X33 yeast strain to produce recombinant proteins. Enzymatic properties of recombinant Lac2 and its ability to degrade zearalenone (ZEN) and Aflatoxin B1 (AFB1) in the presence of four mediators (ABTS, TEMPO, AS and SA) were investigated. Result showed that the optimum pH and temperature of recombinant Lac2 were 3.5 and 55 °C, respectively. Lac2 was not sensitive to heat and stable under both acidic and alkaline conditions. Lac2-ABTS and Lac2-AS were efficient systems for ZEN degradation over a wide range of pH (4–8) and temperature (40–60 °C). Lac2-AS was the most efficient system for AFB1 degradation, reaching 99.82% of degradation at pH 7 and 37 °C after 1 h of incubation. Finally, the Lac2-mediator oxidation products were structurally characterized. This study lays a solid foundation for the application of Lac2 laccase combined with AS for degrading mycotoxin in food and feed.

Abstract The development of enzymatic processes for the environmentally friendly production of 2,5-furandicarboxylic acid (FDCA), a renewable precursor for bioplastics, from 5-hydroxymethylfurfural (HMF) has gained increasing attention over the last years. Aryl-alcohol oxidases (AAOs) catalyze the oxidation of HMF to 5-formyl-2-furancarboxylic acid (FFCA) through 2,5-diformylfuran (DFF) and have thus been applied in enzymatic reaction cascades for the production of FDCA. AAOs are flavoproteins that oxidize a broad range of benzylic and aliphatic allylic primary alcohols to the corresponding aldehydes, and in some cases further to acids, while reducing molecular oxygen to hydrogen peroxide. These promising biocatalysts can also be used for the synthesis of flavors, fragrances, and chemical building blocks, but their industrial applicability suffers from low production yield in natural and heterologous hosts. Here we report on heterologous expression of a new aryl-alcohol oxidase, MaAAO, from Moesziomyces antarcticus at high yields in the methylotrophic yeast Pichia pastoris (recently reclassified as Komagataella phaffii). Fed-batch fermentation of recombinant P. pastoris yielded around 750 mg of active enzyme per liter of culture. Purified MaAAO was highly stable at pH 2–9 and exhibited high thermal stability with almost 95% residual activity after 48 h at 57.5 °C. MaAAO accepts a broad range of benzylic primary alcohols, aliphatic allylic alcohols, and furan derivatives like HMF as substrates and some oxidation products thereof like piperonal or perillaldehyde serve as building blocks for pharmaceuticals or show health-promoting effects. Besides this, MaAAO oxidized 5-hydroxymethyl-2-furancarboxylic acid (HMFCA) to FFCA, which has not been shown for any other AAO so far. Combining MaAAO with an unspecific peroxygenase oxidizing HMFCA to FFCA in one pot resulted in complete conversion of HMF to FDCA within 144 h. MaAAO is thus a promising biocatalyst for the production of precursors for bioplastics and bioactive compounds. Key points • MaAAO from M. antarcticus was expressed in P. pastoris at 750 mg/l. • MaAAO oxidized 5-hydroxymethyl-2-furancarboxylic acid (HMFCA). • Complete conversion of HMF to 2,5-furandicarboxylic acid by combining MaAAO and UPO.

Pectinases are widely used in a variety of industrial processes. However, their application is limited by low catalytic processivity, reduced stability, high cost, and poor re-use compatibility. These drawbacks may be overcome by enzyme immobilization with ferromagnetic nanoparticles, which are easily recovered by a magnetic field. In this work, an endopolygalacturonase from Chondrostereum purpureum (EndoPGCp) expressed in Pichia pastoris was immobilized on glutaraldehyde-activated chitosan ferromagnetic nanoparticles (EndoPGCp-MNP) and used to supplement a commercial enzyme cocktail. No significant differences in biochemical and kinetic properties were observed between EndoPGCp-MNP and EndoPGCp, although the EndoPGCp-MNP showed slightly increased thermostability. Cocktail supplementation with EndoPGCp-MNP increased reducing sugar release from orange wastes by 1.8-fold and showed a synergistic effect as compared to the free enzyme. Furthermore, EndoPGCp-MNP retained 65% of the initial activity after 7 cycles of re-use. These properties suggest that EndoPGCp-MNP may find applications in the processing of pectin-rich agroindustrial residues.

Glucose oxidase (GOD) has many practical applications, but its poor thermostability limits its broader use. In this research, three primary mutants of wild-type GOD were designed using rational mutagenesis, and the GODm mutant was constructed by combinatorial design. The expression, purification, and enzymatic properties of the mutants were studied. The specific enzyme activity of GODm was 2.10-fold higher than that of wild type, and the (kcat/Km) value was increased by 1.45-fold. After treatment at 55 ℃ for 3 h, GODm retained 37.5% of its enzymatic activity, and the half-life (t1/2) of GODm at 55 ℃ and 65 ℃ was 2.28-fold and 3.36-fold higher than that of wild type, respectively. By analyzing the three-dimensional structure of wild type and the GODm mutant, it was found that T30V formed a new hydrogen bond with FAD and strengthened the hydrophobic interaction, D315K optimized the surface electrostatic interaction, and A162T improved the efficiency of the electron pathway. Thus, a novel mutant with improved thermostability and catalytic efficiency was obtained in this research.

Proteases are one of the most innovative products used to improve the efficiency of feed additives. Due to their hydrolytic properties, they enhance the absorption of amino acids, which can reduce the protein content and the cost of feeds. The subtilisin-like proteinase of Bacillus pumilus 3–19 is a promising candidate for industrial use as a feed additive. However, in order to obtain a high yield of the enzyme, it is necessary to develop a highly efficient expression system. The aim of the study was to obtain stable expression of the optimized B. pumilus 3–19 protease gene in the Pichia pastoris expression system and evaluate the correlation of enzyme activity with the choice of vector type and signal peptides. The efficient secretion of subtilisin-like protease into the culture fluid of the recombinant yeast strains was confirmed. The study showed that the incubation time affects the synthesis of protease in P. pastoris, and the maximum activity of the enzyme was observed at 72 h of growth of the yeast culture. Yeast strains with constructs based on the low-copy vector pPINK-LC showed higher protease activity (U/mL) in the hydrolysis of azocasein (2.63 ± 0.16 for killer signal peptide (SP), 2.49 ± 0.08 for α-mating factor presequence, 2.19 ± 0.11 for lysozyme SP) than strains with constructs based on the pPINK-HC vector (1.86 ± 0.09 for killer SP, 2.21 ± 0.07 for α-mating factor presequence, 1.31 ± 0.11 for lysozyme SP), regardless of which signal peptide was used. The ability of the recombinant protease to hydrolyze a specific substrate confirms that the enzyme is a member of the subtilisin family. The maximum protease activity was obtained for yeast strains with pPINK-LC-killer-aprBp (5.75 ± 0.08 U/mL) and pPINK-LC-α-mat.factor-aprBp (4.33 ± 0.07 U/mL) constructs. This study demonstrated that the subtilisin-like protease from recombinant P. pastoris strains exhibits proteolytic activity, which depends on the incubation time and the choice of signal peptide and vector. The production of bacillary protease by the heterologous yeast-based expression system makes this system promising for the development of new feed additives for animal husbandry.

β-Alanine (3-aminopropionic acid) is the only naturally occurring β-amino acid and an important precursor for the synthesis of a variety of nitrogen-containing chemicals. Fermentative production of β-alanine from renewable feedstocks such as glucose has attracted significant interest in recent years. Methanol has become an emerging and promising renewable feedstock for biomanufacturing as an alternative to glucose. In this work, we demonstrated the feasibility of β-alanine production from methanol using Pichia pastoris (Komagataella phaffii) as a methylotrophic cell factory. L-Aspartate-α-decarboxylases (ADCs) from different sources were screened and expressed in P. pastoris, followed by the optimization of aspartate decarboxylation by increasing the ADC copy number and C4 precursor supply via the overexpression of aspartate dehydrogenase. The production potential of the best strain was further evaluated in a 1-L fermenter, and a β-alanine titer of 5.6 g/L was obtained. To our best knowledge, this is the highest metabolite production titer ever reached in P. pastoris using methanol as the substrate. Graphic abstract

Diosgenin has been widely used as a precursor in the pharmaceutical industry. The conventional diosgenin production method, direct acid hydrolysis, can cause severe environmental pollution and has low production efficiency. In this study, the β-glucosidase FBG1 was successfully over-expressed in Pichia pastoris. The engineered yeast was grown in 5- and 50-L bioreactors to a high-cell-density, and the resulting recombinant FBG1 without purification was directly used for trillin biocatalysis. A novel enzymatic biocatalysis method was established through efficient biocatalysis of trillin by recombinant FBG1 and a practical diosgenin purification process. Diosgenin production reached ∼1.7 mg/mL under optimized biocatalysis conditions with a corresponding ∼94 % trillin conversion. The production process was further scaled up from 2 mL to 20, 200, and 2000 mL working volumes, producing equivalent efficiency. This recombinant enzyme biocatalysis process resulted in ∼680 mg diosgenin when 1 g trillin was processed, together with ∼90 % environmental impact elimination and ∼36 % cost reduction. Enzymatic biocatalysis can convert trillin into a high-value-added pharmaceutical precursor of diosgenin with high eco-efficiency, cost-effectiveness, and sustainability is presented here for the first time and is a promising method for future applications in industrial processes.

BACKGROUND: The yeast Pichia pastoris is a popular host organism for production of a range of biological products, several of which are intracellular. The disruption of yeast cells by homogenisation also releases large quantities of lipids, which can foul the downstream membranes and chromatography matrices used for purification. This work examines lipid removal from yeast cells following homogenisation by enzymatic degradation and its impact on the performance of the subsequent centrifugation and filtration. RESULTS: Lipase treatment of cell homogenate at 37°C for 2 hours, followed by clarification using a scale-down mimic of disc stack centrifugation, resulted in a 6.5-fold improvement in solids removal when compared to untreated feed material. The lipase treated and untreated materials that had undergone initial centrifugation were then tested for filtration performance by passing the material through a 0.45 μm polyethylene sulfone membrane under constant flux. A 50% increase in throughput was observed in comparison to the untreated material. CONCLUSION: This proof-of-concept data suggests enzymatic digestion of lipids, analogous to the widely performed DNA reduction using nucleases, could be a valuable process improvement strategy.

Traditional production of industrial and therapeutic proteins by eukaryotic cells typically requires large-scale fermentation capacity. As a result, these systems are not easily portable or reusable for on-demand protein production applications. In this study, we employ Bioproduced Proteins On Demand (Bio-POD), a F127-bisurethane methacrylate hydrogel-based technique that immobilizes engineered Pichia pastoris for preservable, on-demand production and secretion of medium- and high-molecular weight proteins (in this case, SEAP, α-amylase, and anti-HER2). The gel samples containing encapsulated-yeast demonstrated sustained protein production and exhibited productivity immediately after lyophilization and rehydration. The hydrogel platform described here is the first hydrogel immobilization using a P. pastoris system to produce recombinant proteins of this breadth. These results highlight the potential of this formulation to establish a cost-effective bioprocessing strategy for on-demand protein production.

VP28 is an envelope protein of White Spot Syndrome Virus (WSSV), which has been shown in previous studies to induce a high immune response in shrimp. VP28 has been produced in some host systems such as Escherichia coli, Bacillus subtilis, and Pichia pastoris as free protein. Here we showed a new strategy of anchoring VP28 on the Saccharomyces cerevisiae yeast surface and using the yeast cell extract combined with probiotic as an oral vaccine for shrimp farming. We have successfully constructed a recombinant yeast cell capable of expressing VP28 on the cell surface. The feeding diet combined with VP28 anchored yeast cell extract provided significant assurance to Litopenaeus vannamei, challenged by WSSV, resulting in a relative percent survival (RPS) of 87.10 ± 2.15%. Interestingly, the utilization of VP28 anchored yeast cell extract could enhance the efficiency of probiotic strains like Lactobacillus and Bacillus on shrimp farming. The results in both laboratory scales and field trials using extract of VP28 displaying Saccharomyces showed a growth-promoting effect in shrimp, assessed through average shrimp weight. Taken together, our results in this study demonstrated a new successful strategy of using yeast cell surface as a tool to produce VP28-based oral vaccine for shrimp aquaculture. • A new strategy of using VP28 antigen as anchored protein on S. cerevisiae yeast cell surface (S. cerevisiae::VP28) • The utilization of VP28 antigen and yeast as S. cerevisiae::VP28 extract enhanced potential protection of Litopenaeus vannamei against White Spot Syndrome Virus (RPS 87.10%) • The use of S. cerevisiae::VP28 extract increased efficiency of probiotic on shrimp growth-promoting effect either lab-scale or field trial.

β-1,3-oligoglucoside is widely used as a functional food additive and a physiologically active compound. To efficiently produce β-1,3-oligoglucosides through curdlan hydrolysis, the endo-β-1,3-glucanase gene from Trichoderma harzianum was expressed in Pichia pastoris KM71 for the first time in order to construct a high-yield endo-β-1,3-glucanase strain. Optimal conditions for cell culture and endo-β-1,3-glucanase induction were subsequently determined in shake flask experiments. Recombinant endo-β-1,3-glucanase activity was then evaluated in a 7 L bioreactor, reaching a maximum of 198.57 U/mL after of 118 h fermentation. The recombinant endo-β-1,3-glucanase optimally functioned at pH 5.5 and 50 °C in addition to being stable over a pH range of 4.0–6.0 and a temperature range of 30 °C – 50 °C. In addition, the expressed glucanase could efficiently hydrolyze scleroglucan and schizophyllan to produce branched oligoglucosides exhibiting different degrees of polymerization (DP 3–10) and structures. The high enzyme activity and specificity towards polysaccharides with β-1,3-linked glucose residues as primary chains renders recombinant endo-β-1,3-glucanase an ideal candidate enzyme for the industrial production of oligoglucosides.

The development of a quick, single-step cloning system for generation of multiexon gene expression constructs is presented. The system allows efficient and cost-effective assembly of multiple exons of interest genes into different expression plasmids in both Escherichia coli and Pichia pastoris. The high cloning efficiency and low cost of the system make it ideal for a novel workflow for the assembly of intron-bearing genes for expression in two different expression hosts.

Cholesterol oxidases (CHOXs) are flavin‐adenine dinucleotide‐dependent oxidoreductases with a range of biotechnological applications. There remains an urgent need to identify novel CHOX family members to meet the demands of enzyme markets worldwide. Here, we report the cloning, heterologous expression, and structural modeling of the cholesterol oxidase of Acinetobacter sp. strain RAMD. The cholesterol oxidase gene was cloned and expressed in pGEM®‐T and pET‐28a(+) vectors, respectively, using a gene‐specific primer based on the putative cholesterol oxidase ORF of Acinetobacter baumannii strain AB030 (GenBank [gb] locus tag: IX87_05230). The obtained nucleotide sequence (1671 bp, gb: MK575469.2), translated to a protein designated choxAB (556 amino acids), was overexpressed as inclusion bodies (IBs) (MW ˜ 62 kDa) in 1 mm IPTG‐induced Escherichia coli BL21 (DE3) Rosetta cells. The optimized expression conditions (1 mm IPTG with 2% [v/v] glycerol and at room temperature) yielded soluble active choxAB of 0.45 U·mL−1, with 56.25‐fold enhancement. The recombinant choxAB was purified to homogeneity using Ni2+‐affinity agarose column with specific activity (0.054 U·mg−1), yield (8.1%), and fold purification (11.69). Capillary isoelectric‐focusing indicated pI of 8.77 for choxAB. LC‐MS/MS confirmed the IBs (62 kDa), with 82.6% of the covered sequence being exclusive to A. baumannii cholesterol oxidase (UniProtKB: A0A0E1FG24). The 3D structure of choxAB was predicted using the LOMETS webtool with the cholesterol oxidase template of Streptomyces sp. SA‐COO (PDB: 2GEW). The predicted secondary structure included 18 α‐helices and 12 β‐strands, a predicted catalytic triad (E220, H380, and N514), and a conserved FAD‐binding sequence (GSGFGGSVSACRLTEKG). Future studies should consider fusion to solubilization tags and switching to the expression host Pichia pastoris to reduce IB formation., The cholesterol oxidase (choxAB) encoding ORF (1671 bp & 556 a.a) of Acinetobacter sp. strain RAMD was cloned (pGEM®‐T vector) and overexpressed (pET‐28a(+) vector) in E. coli BL21(DE3) Rosetta cells as inclusion bodies for the first time. Optimized production for recombinant soluble choxAB yields active choxAB (0.45 U·mL−1). The purified recombinant choxAB (62 kDa) showed 0.054 U·mg−1 and 11.69‐fold purification.

Low-expression levels remain a challenge in the quest to use the small laccase (rSLAC) as a viable catalyst. In this study, a recombinant Pichia pastoris strain (rSLAC-GAP-AOX) producing rSLAC under both AOX and GAP promoters (located in two different plasmids) was generated and cultivated in the presence of methanol and mixed feed (methanol:glycerol). Induction with methanol resulted in a maximum laccase activity of 1200 U/L for rSLAC-GAP-AOX which was approximately 2.4-fold higher than rSLAC-AOX and 5.1-fold higher than rSLAC-GAP. The addition of methanol:glycerol in a stoichiometric ratio of 9:1 consistently improved biomass and led to a 1.5-fold increase in rSLAC production as compared to induction with methanol alone. The rSLAC removed 95% of 5 mg/L ciprofloxacin (CIP) and 99% of 100 mg/L tetracycline (TC) in the presence of a mediator. Removal of TC resulted in complete elimination of antibacterial activity while up to 48% reduction in antibacterial activity was observed when CIP was removed. Overall, the present study highlights the effectiveness of a double promoter system in enhancing SLAC production.

It is widely known that an adequate intake of proteins with essential amino acids stimulates the production of essential nonprotein substances for the body, such as serotonin, thyroid hormones, and glutathione. Biotechnology applications can focus on food and its benefits for human health, either by improving the nutritional value of existing foods or developing new alternatives that can help resolve the effects of poor nutrition. The yeast Pichia pastoris has been designated as a GRAS (generally recognized as safe) microorganism and is currently used to produce a large number of recombinant proteins. In this study, a 100% synthetic protein was expressed intracellularly as a protein with high nutritional quality that contains a 75% ratio of essential amino acids using the expression system of the yeast P. pastoris. This approach might offer future possibilities for using the modified yeast as a single-cell protein source in the livestock industry and the food supplement market to reduce total protein intake.

Background The antimicrobial peptide LL37 is produced by white blood cells (mainly neutrophils) and various epithelial cells, and has the outstanding advantages of participating in immune regulation, causing chemotaxis of immune cells and promoting wound healing. However, the central domain of LL37 needs to be improved in terms of antimicrobial activity. Results In this study, the amino acid substitution method was used to improve the antimicrobial activity of the LL37 active center, and a dimeric design with a better selection index was selected. A flexible linker was selected and combined with the 6 × His-SUMO tag and LG was successfully expressed using Pichia pastoris as a host. Recombinant LG displayed strong antimicrobial activity by destroying the cell membrane of bacteria but had low hemolytic activity. In addition, compared with monomeric peptide FR, rLG had improved ability to tolerate salt ions. Conclusion This research provides new ideas for the production of modified AMPs in microbial systems and their application in industrial production.

A study was carried out to investigate the characterization of a novel Aspergillus sulphureus JCM01963 xylanase (AS-xyn10A) with a carbohydrate binding module (CBM) and its application in degrading alkali pretreated corncob, rapeseed meal and corn stover alone and in combination with a commercial cellulase. In this study, the 3D structure of AS-xyn10A, which contained a CBM at C-terminal. AS-xyn10A and its CBM-truncated variant (AS-xyn10A-dC) was codon-optimized and over-expressed in Komagaella phaffii X-33 (syn. Pichia pastoris) and characterized with optimal condition at 70 °C and pH 5.0, respectively. AS-xyn10A displayed high activity to xylan extracted from corn stover, corncob, and rapeseed meal. The concentration of hydrolyzed xylo-oligosaccharides (XOSs) reached 1592.26 μg/mL, 1149.92 μg/mL, and 621.86 μg/mL, respectively. Xylobiose was the main product (~70%) in the hydrolysis mixture. AS-xyn10A significantly synergized with cellulase to improve the hydrolysis efficiency of corn stover, corncob, and rapeseed meal to glucose. The degree of synergy (DS) was 1.32, 1.31, and 1.30, respectively. Simultaneously, XOSs hydrolyzed with AS-xyn10A and cellulase was improved by 46.48%, 66.13% and 141.45%, respectively. In addition, CBM variant decreased the yields of xylo-oligosaccharide and glucose in rapeseed meal degradation. This study provided a novel GH10 endo-xylanase, which has potential applications in hydrolysis of biomass.

β-Galactosidases are key enzymes in the food industry. Apart from the hydrolysis of the saccharide bond of lactose, they also catalyze transgalactosylation reactions, producing galactooligosaccharides (GOS) with prebiotic activity. Here we report the heterologous production in Pichia pastoris of a novel β-galactosidase from the fungus Thermothielavioides terrestris. The enzyme (TtbGal1) was purified and characterized, showing optimal activity at 60 °C and pH 4. TtbGal1 is thermostable, retaining almost full activity for 24 h at 50 °C. It was applied to the production of GOS from defined lactose solutions and acid whey, a liquid waste from the Greek yoghurt industry, reaching yields of 19.4 % and 14.8 %, respectively. HILIC-ESI-QTOF-MS analysis revealed the production of GOS with up to 4 saccharide monomers. The results demonstrate efficient GOS production catalyzed by TtbGal1, valorizing acid whey, a waste with a heavy polluting load from the dairy industry.

The production of curdlan oligosaccharides, a multifunctional and valuable carbohydrate, by hydrolyzing polysaccharides is of great interest. The endo-β-1,3-glucanase derived from Trichoderma harzianum was expressed in Pichia pastoris with three commonly used promoters (AOX1, GAP and FLD1). The purified recombinant endo-β-1,3-glucanase expressed by Pichia pastoris with GAP promoter displayed high specific activity at pH 5.5 and 50 °C. Thereafter, a co-culture system of Pichia pastoris GS115 (GAP promoter) and Agrobacterium sp. was constructed in which Agrobacterium sp.-metabolized curdlan can be directly hydrolyzed by Pichia pastoris-secreted endo-β-1,3-glucanase to produce functional curdlan oligosaccharides. The co-culture conditions were optimized and the process was carried out in a 7-L bioreactor. The maximum yield of curdlan oligosaccharides reached 18.77 g/L with 3–10 degrees of polymerization. This study presents a novel and easy curdlan oligosaccharide production strategy that can replace traditional sophisticated production procedures and could potentially be implemented for production of other oligosaccharides.

Background The methylotrophic yeast Pichia pastoris is an appealing production host for a variety of recombinant proteins, including biologics. In this sense, various genetic- and non-genetic-based techniques have been implemented to improve the production efficiency of this expression platform. Loss of supression (Los1) encodes a non-essential nuclear tRNA exporter in Saccharomyces cerevisiae, which its deletion extends replicative lifespan. Herein, a los1-deficient strain of P. pastoris was generated and characterized. Methods A gene disruption cassette was prepared and transformed into an anti-CD22-expressing strain of P. pastoris. A δ los1 mutant was isolated and confirmed. The drug sensitivity of the mutant was also assessed. The growth pattern and the level of anti-CD22 single-chain variable fragment (scFv) expression were compared between the parent and mutant strains. Resuults The los1 homologue was found to be a non-essential gene in P. pastoris. Furthermore, the susceptibility of los1 deletion strain to protein synthesis inhibitors was altered. This strain showed an approximately 1.85-fold increase in the extracellular level of anti-CD22 scFv (p < 0.05). The maximum concentrations of total proteins secreted by δ los1 and parent strains were 125 mg/L and 68 mg/L, respectively. Conclusion The presented data suggest that the targeted disruption of los1 homologue in P. pastoris can result in a higher expression level of our target protein. Findings of this study may improve the current strategies used in optimizing the productivity of recombinant P. pastoris strains.

The cholinesterase-based spectrophotometric assay, also called enzyme inhibition method, is a good choice for rapid detection of organophosphate pesticides (OPs) and carbamate pesticides (CPs). Obviously, the cholinesterase is the core reagent in enzyme inhibition method. In our previous work, a recombinant acetylcholinesterase 2 from Bombyx mori (rBmAChE2) was expressed in yeast successfully and exhibited great sensitivity. However, the yield of rBmAChE2 is not desirable. In this study, a codon optimization strategy was employed to enhance the yield of rBmAChE2 in Pichia pastoris GS115. Results showed that by replacing 6 key rare codons and increasing the percentage of bases G and C up to 46.85%, codon adaptation index (CAI) of Bombyx mori acetylcholinesterase 2 (bmace2) gene was improved from 0.70 to 0.81. After being transformed into Pichia pastoris GS115 via electroporation, the expression transformant can produce 139.7 U/mL secretory codon-optimized rBmAChE2 (opt-rBmAChE2) in the culture supernatant, 3.62 times higher than that of strain bearing the wild-type bmace2 gene. Meanwhile, opt-rBmAChE2 displayed on the yeast surface was up to 2280.02 U/g, 2.8 times higher than wild-type displayed rBmAChE2. In addition, either secretory or surface-displayed opt-rBmAChE2 maintained the similar sensitivities to the wild-type rBmAChE2 for tested inhibitors. Furthermore, the detection limits of the opt-rBmAChE2-based enzyme inhibition method for 10 kinds of OPs or CPs (0.01-2.69 mg/kg) were lower than most of the indexes present in current standard method (GB/T 5009.199-2003) or the maximum residue limits (GB 2763-2019) in China. The results might contribute to the utilization of rBmAChE2 for pesticide residue screening detection in practice.

The response surface methodology was used for the optimization of different submerged fermentation conditions for the production of recombinant laccase Lcc1 in Pichia pastoris KM71H. The initial screening of production parameters was performed using a Plackett–Burman design, and the variables with significant effects on laccase production were identified as follows: medium initial pH, methanol additive amount and liquid volume. These variables were selected for further optimization studies using a Box-Behnken design. The results indicated that the optimum fermentation conditions were as follows: medium optimal initial pH value of 7.01, methanol additive amount of 0.63% (v/v) per 24 h and liquid volume of 19.50% (v/v). These conditions provided the highest laccase enzyme activity of 12,491 U/L, resulting in a 3-fold increase in the production of recombinant laccase. Using industrial basic salt as culture medium, the maximum enzyme activity of Lcc1 was 22,594 U/L after high-density fermentation, which was 1.8-fold increase by shake flask optimization. Furthermore, partially purified laccase was used for the degradation of the octyl phenol and 4-tert-octylphenol, which displayed excellent degradation capacity. After 24 h, the degradation rate of 200 mg/L of 4-tert-octylphenol at 40 °C, pH 4.5 using 50 mM tartaric acid buffer with 1500 U/L purified laccase enzyme in L/A (laccase/ABTS) system was 97.2%. For octyl phenol, the degradation rate was 93.1%. All of the results suggested that the laccase Lcc1 significantly reduced or eliminated the toxicity of octyl phenol and 4-tert-octylphenol, which may be suitable for typical phenolic pollutants in the environment.

Microbial production of α-farnesene from renewable raw materials is a feasible alternative to traditional petroleum craft. Recently, the research on improving α-farnesene production in Pichia pastoris mainly focused on cytoplasmic engineering, while comprehensive engineering of multiple subcellular compartments is rarely reported. Here, we first sought to confirm that the isopentenol utilization pathway (IUP) could act as a two-step shortcut for IPP synthesis in P. pastoris peroxisomes. In addition, we proposed dual regulation of cytoplasm and peroxisomes to boost α-farnesene synthesis in P. pastoris X33, thus the resultant strain produced 2.18 ± 0.04 g/L, which was 1.3 times and 2.1 times than that of the strain only with peroxisomal or cytoplasmic engineering, respectively. The α-farnesene production achieved 2.56 ± 0.04 g/L in shake flasks after carbon source cofeeding, which was the highest reported production in worldwide literatures to the best of my knowledge. Therefore, we propose these strategies as efficient approaches to enhancing α-farnesene production in P. pastoris, which might bring new ideas for the biosynthesis of high-value compounds.

Summary The use of the methylotrophic yeast Pichia pastoris (Komagataella phaffi) to produce heterologous proteins has been largely reported. However, investigations addressing the potential of this yeast to produce bulk chemicals are still scarce. In this study, we have studied the use of P. pastoris as a cell factory to produce the commodity chemical 3‐hydroxypropionic acid (3‐HP) from glycerol. 3‐HP is a chemical platform which can be converted into acrylic acid and to other alternatives to petroleum‐based products. To this end, the mcr gene from Chloroflexus aurantiacus was introduced into P. pastoris. This single modification allowed the production of 3‐HP from glycerol through the malonyl‐CoA pathway. Further enzyme and metabolic engineering modifications aimed at increasing cofactor and metabolic precursors availability allowed a 14‐fold increase in the production of 3‐HP compared to the initial strain. The best strain (PpHP6) was tested in a fed‐batch culture, achieving a final concentration of 3‐HP of 24.75 g l−1, a product yield of 0.13 g g−1 and a volumetric productivity of 0.54 g l−1 h−1, which, to our knowledge, is the highest volumetric productivity reported in yeast. These results benchmark P. pastoris as a promising platform to produce bulk chemicals for the revalorization of crude glycerol and, in particular, to produce 3‐HP., Production of 3‐HP through the Malonyl‐CoA pathway was achieved in Pichia pastoris. Expressing the two subunits of the Malonyl‐CoA reductase separately led to a substantial increase in 3‐HP production. Further metabolic engineering to increase precursors availability increased the 3‐HP titre, achieving a final product concentration of 24.75 g l−1 in fed‐batch cultures, and the highest 3‐HP volumetric productivity value reported for yeast to date (0.54 g l−1 h−1).

Fungal peroxygenases (UPOs) have emerged as oxyfunctionalization catalysts of tremendous interest in recent years. However, their widespread use in the field of biocatalysis is still hampered by their challenging heterologous production, substantially limiting the panel of accessible enzymes for investigation and enzyme engineering. Building upon previous work on UPO production in yeast, we have developed a combined promoter and signal peptide shuffling system for episomal high throughput UPO production in the industrially relevant, methylotrophic yeast Pichia pastoris. Eleven endogenous and orthologous promoters were shuffled with a diverse set of 17 signal peptides. Three previously described UPOs were selected as first test set, leading to the identification of beneficial promoter/signal peptide combinations for protein production. We applied the system then successfully to produce two novel UPOs: MfeUPO from Myceliophthora fergusii and MhiUPO from Myceliophthora hinnulea. To demonstrate the feasibility of the developed system to other enzyme classes, it was applied for the industrially relevant lipase CalB and the laccase Mrl2. In total, approximately 3200 transformants of eight diverse enzymes were screened and the best promoter/signal peptide combinations studied at various cofeeding, derepression, and induction conditions. High volumetric production titers were achieved by subsequent creation of stable integration lines and harnessing orthologous promoters from Hansenula polymorpha. In most cases promising yields were also achieved without the addition of methanol under derepressed conditions. To foster the use of the episomal high throughput promoter/signal peptide Pichia pastoris system, we made all plasmids available through Addgene.

The CH2 domain is a critical element of the human Immunoglobulin G (IgG) constant region. Although the CH2 domain is the least stable domain in IgG, it is also a promising scaffold candidate for developing novel therapeutic approaches. Recently, we succeeded in preparing glycosylated and non-glycosylated CH2 domain in the host organism Pichia pastoris. Herein, we verified that glycosylation of the CH2 domain decreased both, its tendency to aggregate and its immunogenicity in mice, suggesting that aggregation and immunogenicity are related. In addition, we have produced in P. pastoris a stabilized version of the CH2 domain with and without glycan, and their propensity to aggregate evaluated. We found that stabilization alone significantly decreased the aggregation of the CH2 domain. Moreover, the combination of glycosylation and stabilization completely suppressed its aggregation behavior. Since protein aggregation is related to immunogenicity, the combination of glycosylation and stabilization to eliminate the aggregation behavior of a protein could be a fruitful strategy to generate promising immunoglobulin scaffolds.

Purpose: Ocriplasmin (Jetrea TM) is a FDA approved recombinant enzyme utilized to treat a human medical condition called vitreomacular adhesion (VMA). The safety and effectiveness of ocriplasmin for VMA treatment has been confirmed in clinical studies. This is a recombinant C-terminal fragment of human plasmin produced using yeast Pichia pastoris. Since ocriplasmin does not contain any O- or N-glycosylation or some other post-translational modifications, bacterial expression systems such as Escherichia coli could be considered as an economical host for recombinant expression. In the present study, we aimed to evaluate the efficiency of E. coli expression system for high-level expression of recombinant ocriplasmin. Methods: The gene coding for ocriplasmin was cloned and expressed in E. coli BL21. The bacterial cells were cultured on large scale and the expressed recombinant protein was purified using Ni-NTA chromatography. Refolding of denatured ocriplasmin to active enzyme was carried out by the stepwise removal of denaturant. The identity of recombinant ocriplasmin was confirmed using western blotting and ELISA assays. The presence of the active ocriplasmin was monitored by the hydrolytic activity assay against the chromogenic substrate S-2403. Results: The final yield of E. coli BL21-produced ocriplasmin was approximately 1 mg/ml which is greater than that produced by P. pastoris. Using western blotting and ELISA assay, the identity of recombinant ocriplasmin was confirmed. The hydrolysis of chromogenic substrate S-2403 verified the functional activity of E. coli produced ocriplasmin. Conclusion: The results of this study indicated that E. coli could be used for high level expression of ocriplasmin. Although the recombinant protein was expressed as inclusion body, the stepwise refolding leads to the biologically active proteins that can potentially be used for therapeutic purposes.

The sapN gene, encoding the extracellular subtilisin SAPN, a serine alkaline protease from Melghiribacillus thermohalophilus Nari2AT, was isolated, sequenced, and heterologously expressed in Escherichia coli BL21(DE3)pLysS using pUT57 and pTrc99A vectors and in E. coli BL21-AI™ using the Gateway™ pDEST™ 17 vector. Conversely, three cassettes encoding pre-pro-subtilisin (rSAPN/SP-Pro-M), pro-subtilisin (rSAPN/Pro-M), and the mature-subtilisin (rSAPN/M) were hyperexpressed in Pichia pastoris SMD1168 and X33 using the pPICZαC vector. rSAPNs were purified, characterized, and compared to wild-type SAPN. The deduced amino acid sequences exhibited high similarity with subtilisins from Bacillus strains. The highest sequence identity (96 %) was observed with the Bacillus licheniformis MP1 protease, with a 10-residue difference. Compared to SAPN and untagged rSAPNs, (His)6-tagged enzymes showed the highest activity and stability at alkaline pH and high temperature, the highest hydrolysis degree on crab and shrimp by-products, and the best catalytic efficiency. It was found that His6-rSAPN/SP-Pro-Ms expressed in P. pastoris strains was more active than those produced in E. coli. To initiate structure-function relationships, a 3D-model of the Pro-SAPN was built based on the available structures of common subtilisins. These data constitute a pivotal first step toward the creation of new efficient rSAPNs with enhanced catalytic properties and high potential for biotechnological and industrial uses.

Background Biomass valorization has been suggested as a sustainable alternative to petroleum-based energy and commodities. In this context, the copper radical oxidases (CROs) from Auxiliary Activity Family 5/Subfamily 2 (AA5_2) are attractive biocatalysts for the selective oxidation of primary alcohols to aldehydes. Originally defined by the archetypal galactose 6-oxidase from Fusarium graminearum, fungal AA5_2 members have recently been shown to comprise a wide range of specificities for aromatic, aliphatic and furan-based alcohols. This suggests a broader substrate scope of native CROs for applications. However, only 10% of the annotated AA5_2 members have been characterized to date. Results Here, we define two homologues from the filamentous fungi Fusarium graminearum and F. oxysporum as predominant aryl alcohol oxidases (AAOs) through recombinant production in Pichia pastoris, detailed kinetic characterization, and enzyme product analysis. Despite possessing generally similar active-site architectures to the archetypal FgrGalOx, FgrAAO and FoxAAO have weak activity on carbohydrates, but instead efficiently oxidize specific aryl alcohols. Notably, both FgrAAO and FoxAAO oxidize hydroxymethyl furfural (HMF) directly to 5-formyl-2-furoic acid (FFCA), and desymmetrize the bioproduct glycerol to the uncommon L-isomer of glyceraldehyde. Conclusions This work expands understanding of the catalytic diversity of CRO from AA5_2 to include unique representatives from Fusarium species that depart from the well-known galactose 6-oxidase activity of this family. Detailed enzymological analysis highlights the potential biotechnological applications of these orthologs in the production of renewable plastic polymer precursors and other chemicals.

A gene construct encoding the mature region of Talaromyces minioluteus dextranase (EC 3.2.1.11) fused to the Saccharomyces cerevisiae SUC2 signal sequence was expressed in Pichia pastoris under the constitutive glyceraldehyde 3–phosphate dehydrogenase promoter (pGAP). The increase of the transgene dosage from one to two and four copies enhanced proportionally the extracellular yield of the recombinant enzyme (r-TmDEX) without inhibiting cell growth. The volumetric productivity of the four-copy clone in fed batch fermentation (51 h) using molasses as carbon source was 1706 U/L/h. The secreted N-glycosylated r-TmDEX was optimally active at pH 4.5–5.5 and temperature 50–60 °C. The addition of sucrose (600 g/L) as a stabilizer retained intact the r-TmDEX activity after 1-h incubation at 50–60 °C and pH 5.5. Bacterial dextran in deteriorated sugarcane juice was completely removed by applying a crude preparation of secreted r-TmDEX. The high yield of r-TmDEX in methanol-free cultures and the low cost of the fed batch fermentation make the P. pastoris pGAP-based expression system appropriate for the large scale production of dextranase and its use for dextran removal at sugar mills.

Streptokinase is a well-established cost-effective therapeutic molecule for thrombo-embolic complications. In the current study, a tag-free variant of streptokinase with a native N-terminus (N-rSK) was developed using the Pichia expression system. A three-copy clone was screened that secreted 1062 mg/L of N-rSK in the complex medium at shake flask level. The biologically active (67,552.61 IU/mg) N-rSK recovered by anion exchange chromatography was predicted to contain 15.43% α-helices, 26.43% β-sheets. The fermentation run in a complex medium yielded a poor quality product due to excessive N-rSK degradation. Therefore, modified basal salt medium was also employed during fermentation operations to reduce the proteolytic processing of the recombinant product. The concomitant feeding of 1 g/L/h soya flour hydrolysate with methanol during the protein synthesis phase reduced the proteolysis and yielded 2.29 g/L of N-rSK. The fermentation medium was also supplemented with urea during growth and induction phases. The combined feeding approach of nitrogen-rich soya flour hydrolysate and urea during bioreactor operations showed significant improvement in protein stability and resulted in a 4-fold increase in N-rSK concentration to a level of 4.03 g/L over shake flask. Under optimized conditions, the volumetric productivity and specific product yield were 52.33 mg/L/h and 33.24 mg/g DCW, respectively.

Abstract Folding and processing of proteins in the endoplasmic reticulum (ER) are major impediments in the production and secretion of proteins from Pichia pastoris (Komagataella sp.). Overexpression of recombinant genes can overwhelm the innate secretory machinery of the P. pastoris cell, and incorrectly folded proteins may accumulate inside the ER. To restore proper protein folding, the cell naturally triggers an unfolded protein response (UPR) pathway, which upregulates the expression of genes coding for chaperones and other folding-assisting proteins (e.g., Kar2p, Pdi1, Ero1p) via the transcription activator Hac1p. Unfolded/misfolded proteins that cannot be repaired are degraded via the ER-associated degradation (ERAD) pathway, which decreases productivity. Co-expression of selected UPR genes, along with the recombinant gene of interest, is a common approach to enhance the production of properly folded, secreted proteins. Such an approach, however, is not always successful and sometimes, protein productivity decreases because of an unbalanced UPR. This review summarizes successful chaperone co-expression strategies in P. pastoris that are specifically related to overproduction of foreign proteins and the UPR. In addition, it illustrates possible negative effects on the cell’s physiology and productivity resulting from genetic engineering of the UPR pathway. We have focused on Pichia’s potential for commercial production of valuable proteins and we aim to optimize molecular designs so that production strains can be tailored to suit a specific heterologous product. Key points • Chaperones co-expressed with recombinant genes affect productivity in P. pastoris. • Enhanced UPR may impair strain physiology and promote protein degradation. • Gene copy number of the target gene and the chaperone determine the secretion rate.

Mycobacterial acid-resistant protease (MarP) is a membrane-associated serine protease involved in the survival of Mycobacterium tuberculosis in macrophages; here we produced MarP in the yeast Pichia pastoris and study its involvement in macrophage immune modulation. Pichia pastoris vectors, harboring a full-length or a partial sequence of MarP, were constructed. GS115 clones were selected, and homologous recombination at the AOX1 locus was assessed by PCR. Protein was purified by nickel affinity chromatography, and its effect on the cytokine profile was tested in human monocytes. Only the partial MarP protein (121–397 a.a.) lacking the transmembrane domain was successfully expressed as an N-glycosylated proteolytically active protease. In vitro stimulation of THP-1 cells with MarP promoted the release of TNF-α and IL-10. Mycobacterial MarP was successfully expressed in P. pastoris, and it is capable of cytokine release in vitro.