A simple model-based control for Pichia pastoris allows a more efficient heterologous protein production bioprocess

Bioprocess in-line monitoring and control using Raman spectroscopy and Indirect Hard Modeling (IHM)

Process in-line monitoring and control are crucial to optimize the productivity of bioprocesses. A frequently applied Process Analytical Technology (PAT) tool for bioprocess in-line monitoring is Raman spectroscopy. However, evaluating bioprocess Raman spectra is complex and calibrating state-of-the-art statistical evaluation models is effortful. To overcome this challenge, we developed an Indirect Hard Modeling (IHM) prediction model in a previous study. The combination of Raman spectroscopy and the IHM prediction model enables non-invasive in-line monitoring of glucose and ethanol mass fractions during yeast fermentations with significantly less calibration effort than comparable approaches based on statistical models. In this study, we advance this IHM-based approach and successfully demonstrate that the combination of Raman spectroscopy and IHM is capable of not only bioprocess monitoring but also bioprocess control. For this purpose, we used this combination's in-line information as input of a simple on-off glucose controller to control the glucose mass fraction in Saccharomyces cerevisiae fermentations. When we performed two of these fermentations with different predefined glucose set points, we achieved similar process control quality as approaches using statistical models, despite considerably smaller calibration effort. Therefore, this study reaffirms that the combination of Raman spectroscopy and IHM is a powerful PAT tool for bioprocesses.

High-level production of recombinant HBcAg virus-like particles in a mathematically modelled P. pastoris GS115 Mut+ bioreactor process under controlled residual methanol concentration

Recombinant hepatitis B core antigen (HBcAg) molecules, produced in heterologous expression systems, self-assemble into highly homogenous and non-infectious virus-like particles (VLPs) that are under extensive research for biomedical applications. HBcAg production in the methylotrophic yeast P. pastoris has been well documented; however, productivity screening under various residual methanol levels has not been reported for bioreactor processes. HBcAg production under various excess methanol levels of 0.1, 1.0 and 2.0 g L⁻¹ was investigated in this research. Results indicate that, under these particular conditions, the total process and specific protein yields of 876–1308 mg L⁻¹ and 7.9–11.2 mg g_DCW⁻¹, respectively, were achieved after 67–75 h of cultivation. Produced HBcAg molecules were efficiently purified and the presence of highly immunogenic, correctly formed and homogenous HBcAg-VLPs with an estimated purity of 90% was confirmed by electron microscopy. The highest reported HBcAg yield of 1308 mg L⁻¹ and 11.2 mg g_DCW⁻¹ was achieved under limiting residual methanol concentration, which is about 2.5 times higher than the next highest reported result. A PI-algorithm-based residual methanol concentration feed rate controller was employed to maintain a set residual methanol concentration. Finally, mathematical process models to characterise the vegetative, dead and total cell biomass (X_v, X_d and X), substrate (Glycerol and Methanol) concentration, reactor volume (V), and product (HBcAg) dynamics during cultivation, were identified. A rare attempt to model the residual methanol concentration during induction is also presented.

Bioreactor-scale cell performance and protein production can be substantially increased by using a secretion signal that drives co-translational translocation in Pichia pastoris

Pichia pastoris (Komagataella spp.) has become one of the most important host organisms for production of heterologous proteins of biotechnological interest, many of them extracellular. The protein secretion pathway has been recognized as a limiting process in which many roadblocks have been pinpointed. Recently, we have identified a bottleneck at the ER translocation level. In earlier exploratory studies, this limitation could be largely overcome by using an improved chimeric secretion signal to drive proteins through the co-translational translocation pathway. Here, we have further tested at bioreactor scale the improved secretion signal consisting of the pre-Ost1 signal sequence, which drives proteins through co-translational translocation, followed by the pro region from the secretion signal of the Saccharomyces cerevisiae α-factor mating pheromone. For comparison, the commonly used full-length α-factor secretion signal, which drives proteins through post-translational translocation, was tested. These two secretion signals were fused to three different model proteins: the tetrameric red fluorescent protein E2-Crimson, which can be used to visualize roadblocks in the secretory pathway; the lipase 2 from Bacillus thermocatenulatus (BTL2); and the Rhizopus oryzae lipase (ROL). All strains were tested in batch cultivation to study the different growth parameters obtained. The strains carrying the improved secretion signal showed increased final production of the proteins of interest. Interestingly, they were able to grow at significantly higher maximum specific growth rates than their counterparts carrying the conventional secretion signal. These results were corroborated in a 5 L fed-batch cultivation, where the final product concentration and volumetric productivity were also shown to be improved.

Rhizopus oryzae Lipase, a Promising Industrial Enzyme: Biochemical Characteristics, Production and Biocatalytic Applications

Lipases are biocatalysts with a significant potential to enable a shift from current pollutant manufacturing processes to environmentally sustainable approaches. The main reason of this prospect is their catalytic versatility as they carry out several industrially relevant reactions as hydrolysis of fats in water/lipid interface and synthesis reactions in solvent-free or non-aqueous media such as transesterification, interesterification and esterification. Because of the outstanding traits of Rhizopus oryzae lipase (ROL), 1,3-specificity, high enantioselectivity and stability in organic media, its application in energy, food and pharmaceutical industrial sector has been widely studied. Significant advances have been made in the biochemical characterisation of ROL particularly in how its activity and stability are affected by the presence of its prosequence. In addition, native and heterologous production of ROL, the latter in cell factories like Escherichia coli, Saccharomyces cerevisiae and Komagataella phaffii (Pichia pastoris), have been thoroughly described. Therefore, in this review, we summarise the current knowledge about R. oryzae lipase (i) biochemical characteristics, (ii) production strategies and (iii) potential industrial applications.

Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review

The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.

Effect of dilution rate and methanol-glycerol mixed feeding on heterologous Rhizopus oryzae lipase production with Pichia pastoris Mut(+) phenotype in continuous culture

The induction using substrate mixtures is an operational strategy for improving the productivity of heterologous protein production with Pichia pastoris. Glycerol as a cosubstrate allows for growth at a higher specific growth rate, but also has been reported to be repressor of the expression from the AOX1 promoter. Thus, further insights about the effects of glycerol are required for designing the induction stage with mixed substrates. The production of Rhizopus oryzae lipase (ROL) was used as a model system to investigate the application of methanol-glycerol feeding mixtures in fast metabolizing methanol phenotype. Cultures were performed in a simple chemostat system and the response surface methodology was used for the evaluation of both dilution rate and methanol-glycerol feeding composition as experimental factors. Our results indicate that productivity and yield of ROL are strongly affected by dilution rate, with no interaction effect between the involved factors. Productivity showed the highest value around 0.04-0.06 h(-1) , while ROL yield decreased along the whole dilution rate range evaluated (0.03-0.1 h(-1) ). Compared to production level achieved with methanol-only feeding, the highest specific productivity was similar in mixed feeding (0.9 UA g-biomass(-1) h(-1) ), but volumetric productivity was 70% higher. Kinetic analysis showed that these results are explained by the effects of dilution rate on specific methanol uptake rate, instead of a repressor effect caused by glycerol feeding. It is concluded that despite the effect of dilution rate on ROL yield, mixed feeding strategy is a proper process option to be applied to P. pastoris Mut(+) phenotype for heterologous protein production.

Production of a sterol esterase from Ophiostoma piceae in batch and fed-batch bioprocesses using different Pichia pastoris phenotypes as cell factory

The potential biotechnological applications for the Ophiostoma piceae sterol esterase (OPE) are conditioned to the availability of high enzyme amounts at low prices. This enzyme is a versatile biocatalyst with different biotechnological applications. In this work a systematic study on its heterologous production in different Pichia pastoris strains and operational strategies is presented. The best results were obtained using an AOX1 defective yeast strain in a fed-batch bioprocess using methanol as inducer substrate at a set point of 2.5 g L(-1) and sorbitol as cosubstrate by means of a preprogramed exponential feeding rate at a μ = 0.02 h(-1) , reaching 30 U mL(-1) of enzyme and a volumetric productivity of 403.5 U L(-1) h(-1) . These values are twofold higher than those obtained with a Mut(+) phenotype using methanol a sole carbon source. OPE was the main protein secreted by the yeast, 55% for Mut(s) versus 25% for Mut(+.)

Optimization of five environmental factors to increase beta-propeller phytase production in Pichia pastoris and impact on the physiological response of the host

Recently, we engineered Pichia pastoris Mut(s) strains to produce several beta-propeller phytases, one from Bacillus subtilis and the others designed by a structure-guided consensus approach. Furthermore, we demonstrated the ability of P. pastoris to produce and secrete these phytases in an active form in shake-flask cultures. In the present work, we used a design of experiments strategy (Simplex optimization method) to optimize five environmental factors that define the culture conditions in the induction step to increase beta-propeller phytase production in P. pastoris bioreactor cultures. With the optimization process, up to 347,682 U (82,814 U/L or 6.4 g/L culture medium) of phytase at 68 h of induction was achieved. In addition, the impact of the optimization process on the physiological response of the host was evaluated. The results indicate that the increase in extracellular phytase production through the optimization process was correlated with an increase in metabolic activity of P. pastoris, shown by an increase in oxygen demand and methanol consumption, that increase the specific growth rate. The increase in extracellular phytase production also occurred with a decrease in extracellular protease activity. Moreover, the optimized culture conditions increased the recombinant protein secretion by up to 88%, along with the extracellular phytase production efficiency per cell.

A simple Pichia pastoris fermentation and downstream processing strategy for making recombinant pandemic Swine Origin Influenza a virus Hemagglutinin protein

The present Influenza vaccine manufacturing process has posed a clear impediment to initiation of rapid mass vaccination against spreading pandemic influenza. New vaccine strategies are therefore needed that can accelerate the vaccine production. Pichia offers several advantages for rapid and economical bulk production of recombinant proteins and, hence, can be attractive alternative for producing an effective influenza HA based subunit vaccine. The recombinant Pichia harboring the transgene was subjected to fed-batch fermentation at 10 L scale. A simple fermentation and downstream processing strategy is developed for high-yield secretory expression of the recombinant Hemagglutinin protein of pandemic Swine Origin Influenza A virus using Pichia pastoris via fed-batch fermentation. Expression and purification were optimized and the expressed recombinant Hemagglutinin protein was verified by sodium dodecyl sulfate polyacrylamide gel electrophoresis, Western blot and MALDI-TOF analysis. In this paper, we describe a fed-batch fermentation protocol for the secreted production of Swine Influenza A Hemagglutinin protein in the P. pastoris GS115 strain. We have shown that there is a clear relationship between product yield and specific growth rate. The fed-batch fermentation and downstream processing methods optimized in the present study have immense practical application for high-level production of the recombinant H1N1 HA protein in a cost effective way using P. pastoris.

Online analysis and process control in recombinant protein production (review)

Online analysis and control is essential for efficient and reproducible bioprocesses. A key factor in real-time control is the ability to measure critical variables rapidly. Online in situ measurements are the preferred option and minimize the potential loss of sterility. The challenge is to provide sensors with a good lifespan that withstand harsh bioprocess conditions, remain stable for the duration of a process without the need for recalibration, and offer a suitable working range. In recent decades, many new techniques that promise to extend the possibilities of analysis and control, not only by providing new parameters for analysis, but also through the improvement of accepted, well practiced, measurements have arisen.

Heterologous expression systems for lipases: a review

The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented. In this chapter, an overview of the most common microbial expression systems for the overproduction of microbial lipases is presented. Prokaryotic system as Escherichia coli and eukaryotic systems as Saccharomyces cerevisiae and Pichia pastoris are analyzed and compared in terms of productivity, operational, and downstream processing facilities. Finally, an overview of heterologous Candida rugosa and Rhizopus oryzae lipases, two of the most common lipases used in biocatalysis, is presented. In both cases, P. pastoris has been shown as the most promising host system.

Improvement of specific growth rate of Pichia pastoris for effective porcine interferon-α production with an on-line model-based glycerol feeding strategy

Effective expression of porcine interferon-α (pIFN-α) with recombinant Pichia pastoris was conducted in a bench-scale fermentor. The influence of the glycerol feeding strategy on the specific growth rate and protein production was investigated. The traditional DO-stat feeding strategy led to very low cell growth rate resulting in low dry cell weight (DCW) of about 90 g/L during the subsequent induction phase. The previously reported Artificial Neural Network Pattern Recognition (ANNPR) model-based glycerol feeding strategy improved the cell density to 120 g DCW/L, while the specific growth rate decreased from 0.15 to 0.18 to 0.03-0.08 h(-1) during the last 10 h of the glycerol feeding stage leading to a variation of the porcine interferon-α production, as the glycerol feeding scheme had a significant effect on the induction phase. This problem was resolved by an improved ANNPR model-based feeding strategy to maintain the specific growth rate above 0.11 h(-1). With this feeding strategy, the pIFN-α concentration reached a level of 1.43 g/L, more than 1.5-fold higher than that obtained with the previously adopted feeding strategy. Our results showed that increasing the specific growth rate favored the target protein production and the glycerol feeding methods directly influenced the induction stage. Consequently, higher cell density and specific growth rate as well as effective porcine interferon-α production have been achieved by our novel glycerol feeding strategy.

Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity

BACKGROUND

Constraint-based models enable structured cellular representations in which intracellular kinetics are circumvented. These models, combined with experimental data, are useful analytical tools to estimate the state exhibited (the phenotype) by the cells at given pseudo-steady conditions.

RESULTS

In this contribution, a simplified constraint-based stoichiometric model of the metabolism of the yeast Pichia pastoris, a workhorse for heterologous protein expression, is validated against several experimental available datasets. Firstly, maximum theoretical growth yields are calculated and compared to the experimental ones. Secondly, possibility theory is applied to quantify the consistency between model and measurements. Finally, the biomass growth rate is excluded from the datasets and its prediction used to exemplify the capability of the model to calculate non-measured fluxes.

CONCLUSIONS

This contribution shows how a small-sized network can be assessed following a rational, quantitative procedure even when measurements are scarce and imprecise. This approach is particularly useful in lacking data scenarios.

Production of a Rhizopus oryzae lipase from Pichia pastoris using alternative operational strategies

Different cultivation strategies have been compared for the production of Rhizopus oryzae lipase (ROL) from Pichia pastoris. Several drawbacks have been found using a methanol non-limited fed-batch. On the one hand, oxygen limitation appeared at early cell dry weights and, on the other hand, high cell death was observed. A temperature limited fed-batch has been proposed to solve both problems. However, in our case study a methanol non-limited fed-batch results in better productivities. Finally, a lower salt medium were used to overcome cell death problems and a temperature limited fed-batch was applied thereafter to solve oxygen transfer limitations. This combined strategy has resulted in lower productivities when compared to a methanol non-limited fed-batch. However the culture could be longer prolonged and a 1.3-fold purer final product was obtained mainly due to cell death reduction.