Pichia Pastoris Cultures Research Articles

Biomass estimation in Pichia pastoris cultures by combined single-wavelength fluorescence measurements.

In this work, the evolution of different biogenic fluorophores involved in the metabolism of Pichia pastoris was determined at four different single-wavelength pairs (excitation/emission) during batch culture in microwell plates and used for effective and reliable biomass estimation by means of chemometric tools. The chemometric tools for biomass estimation were multiple linear regression (MLR), partial least squares regression (PLSR), and principal component regression (PCR). Variable importance in the projection (VIP) scores were used to rate the importance of model input variables, indicating tryptophan as the most important variable for biomass estimation. A direct correlation between the single fluorescence signals of tryptophan and biomass was additionally set up. Results indicate a successful fitting of the MLR, PLSR, PCR, and direct tryptophan correlation models for the present case and confirm the relevance of biogenic fluorophores for bioprocess state variables monitoring. The root mean squared error of prediction (RMSEP) between the predicted and measured values for the validation batches was 0.017, 0.023, 0.025, and 0.049 g L(-1) dry cell weight for MLR, PLSR, PCR, and direct tryptophan correlation, respectively. The presented approach of indirectly measuring biomass based on combined single-wavelength fluorescence measurements can be used for the development of a low-cost alternative to 2D fluorescence spectroscopy. Biotechnol. Bioeng. 2016;113: 2394-2402. © 2016 Wiley Periodicals, Inc.

Biosynthesis and purification of histidine‐tagged human soluble catechol‐O‐methyltransferase

AbstractBACKGROUNDCatechol‐O‐methyltransferase (COMT, EC 2.1.1.6) has been implicated in several human diseases including Parkinson's disease and the most appropriated therapy depends on the efficacy of the COMT inhibitors applied. Therefore, more effective drugs for COMT inhibition are important, and the development of such inhibitors requires research with recombinant COMT.RESULTSThe time‐course production of biologically active hexa‐histidine‐tagged COMT in methanol‐induced Pichia pastoris cultures was evaluated and immobilized‐metal affinity chromatography was applied as the main capture step for the purification of the target enzyme that proved to be extremely efficient and selective. The best strategy allowed recovering soluble COMT at 300 mmol L−1 imidazol in a highly purified fraction with a purification fold of 81 and a bioactivity recovery of 57.35%. Using this strategy, a concentration of 3.68 mg L−1 of shake‐flask culture of highly purified recombinant COMT was obtained. Finally, the MALDI‐TOF/TOF analysis of the purified recombinant SCOMT demonstrated that it is correctly processed since no modifications in the primary sequence were observed.CONCLUSIONA new strategy was developed and implemented for the biosynthesis and purification of biologically active soluble COMT in a highly purified fraction with the ability to be inhibited by commercial Parkinson's disease inhibitors: 3,5‐dinitrocatechol and entacapone. © 2016 Society of Chemical Industry

Enhanced truncated-t-PA (CT-b) expression in high-cell-density fed-batch cultures of Pichia pastoris through optimization of a mixed feeding strategy by response surface methodology.

Recently, Pichia pastoris has been the focal point of interest as an expression system for production of many recombinant proteins. The study and optimization of feeding strategy are of major importance to achieve maximum volumetric productivity in fed-batch cultivations. Among different feeding strategies used in P. pastoris fed-batch cultures, those trying to maintain a constant specific growth rate have usually resulted in superior productivities. The objective of the present study was to investigate and optimize the co-feeding of glycerol and methanol to attain maximum expression of t-PA in P. pastoris fed-batch cultures with constant specific growth rate. The experiments were designed by response surface methodology, considering the specific feeding rates of methanol and glycerol as independent variables. In each experiment, glycerol and methanol were fed according to a predetermined equation to maintain a constant specific growth rate. It was found that with glycerol feeding for higher specific growth rates, the inhibitory properties of glycerol are more pronounced, while the best expression level was achieved when the ratio of µ set glycerol to that of methanol was around 1.67. In all specific growth rates tested, almost a similar ratio of the specific glycerol feeding rate to that of methanol led to the maximum protein production and activity. The statistical model predicted the optimal operating conditions for µ set glycerol and that of methanol to be 0.05 and 0.03 h(-1), respectively. Applying the optimum strategy, maximum of 52 g/L biomass, 300 mg/L t-PA and 340,000 IU/mL enzyme activity were obtained.

A mixed-mode resin with tryptamine ligand for human serum albumin separation

Mixed-mode chromatography (MMC) is a new technology that uses specially-designed ligands to improve the adsorption selectivity with multimodal protein–ligand interactions for protein separation. A new MMC resin TA-B-6FF with tryptamine as the functional ligand was prepared and used for human serum albumin (HSA) separation. Adsorption equilibria of plasma-derived HSA (pHSA) were investigated and compared with a commercial tryptophan-based resin (MX-Trp-650m), and the influence of pH and salt addition was studied. The results showed that weak acidic conditions (pH 5.0–7.0) were favorable for HSA adsorption. The maximum adsorption capacity of TA-B-6FF was 141.33mg/g at pH 5.0, which was two times higher than that of MX-Trp-650m. TA-B-6FF also showed better salt-tolerance than MX-Trp-650m. Moreover, TA-B-6FF was used to separate recombinant HSA (rHSA) from Pichia pastoris culture broth. The results indicated that rHSA could be directly captured by TA-B-6FF without dilution or pH adjustment. High purity (87.75%) of rHSA monomer could be obtained with a recovery of 98.53% through two-step elution process. Total content of rHSA monomer and degraded fragment was 99.75%, the removal of host cell proteins reached about 90%. The results demonstrate that new TA-B-6FF resin has a great potential for rHSA purification directly from the complex fermentation broth.

Statistical Medium Optimization for the Increased Production of Recombinant Phytase in the Fed-Batch Cultivation of Pichia pastoris

Abstract Using a 20-run central composite design, standard Basal Salt Media (BSM) was optimized for the production of recombinant phytase by Pichia pastoris in bioreactor-based fed-batch cultivations using glucose as the carbon source. The phytase activity in the supernatant of the cultures at the end of 48-hour runs was modeled as a function of the medium composition, and this model was successfully validated. Using Inductively Coupled Plasma spectroscopy (ICP), residual elements were quantified in the cultivation broth at the end of each run to confirm that differences in final cell density and enzyme activity were not due to nutrient depletion, but indeed associated with the variations in medium composition. The optimized media contains significantly lower concentration of the potassium and magnesium sources (28.7 g/l KH2PO4 and 4.8 g/l MgSO4·7H2O respectively), as well as a reduced concentration of trace salts, and based on experimental results, significantly outperforms standard media in terms of recombinant product yields under the same conditions.

Enrichment and identification of Δ(9)-Tetrahydrocannabinolic acid synthase from Pichia pastoris culture supernatants.

This data article refers to the report Δ9-Tetrahydrocannabinolic acid synthase (THCAS) production in Pichia pastoris enables chemical synthesis of cannabinoids (Lange et. al. 2015) [2]. THCAS was produced on a 2 L lab scale using recombinant P. pastoris KM71 KE1. Enrichment of THCAS as a technically pure enzyme was realized using dialysis and cationic exchange chromatography. nLC-ESI-MS/MS analysis identified THCAS in different fractions obtained by cationic exchange chromatography.

Translational arrest due to cytoplasmic redox stress delays adaptation to growth on methanol and heterologous protein expression in a typical fed-batch culture of Pichia pastoris.

ResultsWe have followed a typical fed-batch induction regime for heterologous protein production under the control of the AOX1 promoter using both microarray and metabolomic analysis. The genetic constructs involved 1 and 3 copies of the TRY1 gene, encoding human trypsinogen. In small-scale laboratory cultures, expression of the 3 copy-number construct induced the unfolded protein response (UPR) sufficiently that titres of extracellular trypsinogen were lower in the 3-copy construct than with the 1-copy construct. In the fed-batch-culture, a similar pattern was observed, with higher expression from the 1-copy construct, but in this case there was no significant induction of UPR with the 3-copy strain. Analysis of the microarray and metabolomic information indicates that the 3-copy strain was undergoing cytoplasmic redox stress at the point of induction with methanol. In this Crabtree-negative yeast, this redox stress appeared to delay the adaptation to growth on methanol and supressed heterologous protein production, probably due to a block in translation.ConclusionAlthough redox imbalance as a result of artificially imposed hypoxia has previously been described, this is the first time that it has been characterised as a result of a transient metabolic imbalance and shown to involve a stress response which can lead to translational arrest. Without detailed analysis of the underlying processes it could easily have been mis-interpreted as secretion stress, transmitted through the UPR.

Development and in silico analysis of a new nitrogen-limited feeding strategy for fed-batch cultures of Pichia pastoris based on a simple pH-control system

A novel fed-batch strategy based on a pH control system was devised in order to address some of the disadvantages associated with available control strategies for Pichia pastoris cultures. Changing settings of the controller, the tON/tOFF time ratio, adjusted the speed in which the ammonium hydroxide was added for pH control and the sole nitrogen source. Setting the tON/tOFF ratio to 0.5/0.5, 0.5/10 and 0.5/15 resulted in a decrease in the growth rate as the tOFF value increased. Therefore, the design allows running the culture at lower growth rates in a controlled way. Two high cell density cultures with tON/tOFF ratio of 0.5/10 and 0.5/20 were also fed ammonia with the same controller. Setting tON/tOFF at 0.5/10 and 0.5/20 led to an increase in final biomass and protein as the tOFF decreased. A metabolic model assessed the effect of nitrogen-limitation in high cell density cultures on the yeast metabolism. Model results show that fluxes of intracellular reactions such as glycolysis, the tricarboxylic cycle and the pentose-phosphate pathway are higher at tON/tOFF=0.5/10. Additionally, higher sensitivity of growth and protein production to oxygen at tON/tOFF=0.5/10 proves that oxygen limitation led to higher protein production in this case.

MCR-ALS on metabolic networks: Obtaining more meaningful pathways

With the aim of understanding the flux distributions across a metabolic network, i.e. within living cells, Principal Component Analysis (PCA) has been proposed to obtain a set of orthogonal components (pathways) capturing most of the variance in the flux data. The problems with this method are (i) that no additional information can be included in the model, and (ii) that orthogonality imposes a hard constraint, not always reasonably. To overcome these drawbacks, here we propose to use a more flexible approach such as Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) to obtain this set of biological pathways through the network. By using this method, different constraints can be included in the model, and the same source of variability can be present in different pathways, which is reasonable from a biological standpoint. This work follows a methodology developed for Pichia pastoris cultures grown on different carbon sources, lately presented in González-Martínez et al. (2014). In this paper a different grey modelling approach, which aims to incorporate a priori knowledge through constraints on the modelling algorithms, is applied to the same case of study. The results of both models are compared to show their strengths and weaknesses.

Temperature effect on recombinant protein production in continuous cultures of methylotrophic yeast Pichia pastoris: a comparative study of sorbitol and glycerol as a co-substrate

Temperature effect on recombinant protein production in continuous cultures of methylotrophic yeast Pichia pastoris: a comparative study of sorbitol and glycerol as a co-substrate

Purification of tag-free recombinant fumonisin esterase FumD from Pichia pastoris culture supernatant for use as calibration standard for enzyme quantification

Purification of tag-free recombinant fumonisin esterase FumD from Pichia pastoris culture supernatant for use as calibration standard for enzyme quantification

High level expression of Glomerella cingulata cutinase in dense cultures of Pichia pastoris grown under fed-batch conditions

A Pichia pastoris transformant carrying the cutinase cDNA of Glomerella cingulata was over-expressed in a 5L bioreactor (2.0L working volume) under fed-batch conditions. Bioreactor experiments rely on varying selected parameters in repeated rounds of optimisation: here these included duration of induction, pH and temperature. Highest cell densities (320gL−1 wet cell weight) with a cutinase production of 3800mgL−1 and an activity of 434UmL−1 were achieved 24h after induction with methanol in basal salt medium (at pH 5 and 28°C). Characterisation of the cutinase showed that it was stable between pH 6 and pH 11, had an optimum pH of 8.0 and retained activity for 30min at 50°C (optimum temperature 25°C).The preferred substrates of G. cingulata cutinase were the medium- to long-chain ρ-nitrophenyl esters of ρ-nitrophenylcaprylate (C8), ρ-nitrophenyllaurate (C12) and ρ-nitrophenylmyristate (C14), with the highest catalytic efficiency, kcat/Km of 7.7±0.7mM−1s−1 for ρ-nitrophenylcaprylate. Microscopic analyses showed that the G. cingulata cutinase was also capable of depolymerising the high molecular weight synthetic polyester, polyethylene terephthalate.

Recovery of Microquantities of Human Epidermal Growth Factor from Escherichia coli Homogenate and Pichia pastoris Culture Medium using Expanded Bed Adsorption

A rational design of recovery of microquantities of human Epidermal Growth Factor (hEGF) from different complex feedstocks using STREAMLINE Direct HST in expanded bed adsorption (EBA) was approached. The highest adsorption yields were achieved at pH 4.5, which was close to the isoelectric point of protein by utilizing mixed interaction that was offered by the adsorbent. Escherichia coli treated with osmotic shock and Pichia pastoris culture medium spiked with hEGF were applied as feedstocks to evaluate bed stability in the presence of cells. A recovery of 90% was achieved for both cells at pH 4.5. Effects of pH on the P. pastoris culture medium and E. coli homogenate were similar, indicating that both cells have negatively charged surfaces at pH 4.5. The cell transmission index (T) showed that there was no tendency for E. coli homogenate and yeast cells to bind to the matrix at pH 4.5. Because the electrostatic properties of cells and protein are pH dependent, the method presented for screening conditions for biomass and adsorbent is convenient for designing robust and reliable EBA purification processes. Lower ionic strength improved purification of hEGF from E. coli homogenate.

Metabolic flux understanding of Pichia pastoris grown on heterogenous culture media

Within the emergent field of Systems Biology, mathematical models obtained from physical–chemical laws (the so-called first principles-based models) of microbial systems are employed to discern the principles that govern cellular behaviour and achieve a predictive understanding of cellular functions. The reliance on this biochemical knowledge has the drawback that some of the assumptions (specific kinetics of the reaction system, unknown dynamics and values of the model parameters) may not be valid for all the metabolic possible states of the network. In this uncertainty context, the combined use of fundamental knowledge and data measured in the fermentation that describe the behaviour of the microorganism in the manufacturing process is paramount to overcome this problem. In this paper, a grey modelling approach is presented combining data-driven and first principles information at different scales, developed for Pichia pastoris cultures grown on different carbon sources. This approach will allow us to relate patterns of recombinant protein production to intracellular metabolic states and correlate intra and extracellular reactions in order to understand how the internal state of the cells determines the observed behaviour in P. pastoris cultivations.

Effects of temperature and glycerol and methanol‐feeding profiles on the production of recombinant galactose oxidase in Pichia pastoris

Optimization of protein production from methanol-induced Pichia pastoris cultures is necessary to ensure high productivity rates and high yields of recombinant proteins. We investigated the effects of temperature and different linear or exponential methanol-feeding rates on the production of recombinant Fusarium graminearum galactose oxidase (EC 1.1.3.9) in a P. pastoris Mut+ strain, under regulation of the AOX1 promoter. We found that low exponential methanol feeding led to 1.5-fold higher volumetric productivity compared to high exponential feeding rates. The duration of glycerol feeding did not affect the subsequent product yield, but longer glycerol feeding led to higher initial biomass concentration, which would reduce the oxygen demand and generate less heat during induction. A linear and a low exponential feeding profile led to productivities in the same range, but the latter was characterized by intense fluctuations in the titers of galactose oxidase and total protein. An exponential feeding profile that has been adapted to the apparent biomass concentration results in more stable cultures, but the concentration of recombinant protein is in the same range as when constant methanol feeding is employed. © 2014 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 30:728–735, 2014

Fast development of Pichia pastoris GS115 Mut+ cultures employing batch-to-batch control and hybrid semi-parametric modeling

In this paper, we implemented a model-based optimization platform for fast development of Pichia pastoris cultures employing batch-to-batch control and hybrid semi-parametric modeling. We illustrate the methodology with a P. pastoris GS115 strain expressing a single-chain antibody fragment (scFv) by determining the optimal time profiles of temperature, pH, glycerol feeding and methanol feeding that maximize the endpoint scFv titer. The first hybrid model was identified from data of six exploratory experiments carried out in a pilot 50-L reactor. This model was subsequently used to maximize the final scFv titer of the proceeding batch employing a dynamic optimization program. Thereupon, the optimized time profiles of control variables were implemented in the pilot reactor and the resulting new data set was used to re-identify the hybrid model and to re-optimize the next batch. The iterative batch-to-batch optimization was stopped after 4 complete optimized batches with the final scFv titer stabilizing at 49.5mg/L. In relation to the baseline batch (executed according to the Pichia fermentation guidelines by Invitrogen) a more than fourfold increase in scFv titer was achieved. The biomass concentration at induction and the methanol feeding rate profile were found to be the most critical control degrees of freedom to maximize scFv titer.

Enhancing pIFN-α Production and Process Stability in Fed-Batch Culture of Pichia pastoris by Controlling the Methanol Concentration and Monitoring the Responses of OUR/DO Levels

Effective expression of porcine interferon-α (pIFN-α) with recombinant Pichia pastoris was conducted in a bench-scale fermentor using an in situ methanol electrode-based feeding process with the control level of methanol concentration linearly increased to 10 g l⁻¹ for the first 20 h and maintained at 10 g l⁻¹ for the rest of expression phase. With this two-stage control process, the highest pIFN-α concentration reached a level of 1.81 g l⁻¹, which was 1.5-fold of that in the previous constant 10 g l⁻¹ induction experiments. There is an improvement of the pIFN-α productivity from more distribution of carbon flux to protein expression. The pIFN-α expression stability could be further enhanced by a simple on-line fault diagnosis method for methanol overfeeding based on oxygen uptake rate changing patterns. By implementing corrective action of feeding glycerol after fault detection, the production yield increased to twice the amount it would have been without the diagnosis.

Cell culture using centrifugal microfluidic platform with demonstration on Pichia pastoris

This paper discusses the vortical flow, mixing and cell culture of Pichia pastoris using a centrifugal microfluidic (CM) chamber. The resultant "spiral toroidal vortex" in the chamber is made up of a primary vortex induced from inertial acceleration/deceleration of the chamber superposed by a secondary toroidal vortex due to Coriolis acceleration acting on the primary vortex. A validated numerical fluid-flow model with minimized numerical diffusion effect has been developed to investigate the flow and consequently mixing of two-color liquids through cyclic constant acceleration-and-deceleration in the same rotation direction until homogeneous mixing of the two liquids in the CM chamber has been established. The specific mixing time is found to improve with increase in acceleration/deceleration and angular span of the chamber. An experimental CM platform with three cell-culture chambers of different angular spans has been built and Pichia pastoris cell culture has been successfully demonstrated. Cell growth can be monitored over time on the extracted samples by measuring the optical density at 600-nm wave-length. Comparing with conventional cell culture, Pichia pastoris cultured on CM platform exhibits a very short lag (cell preparation/budding) phase prior to the log phase (cell growth). While it takes 8 to 12 h for the conventional shake flask in the lag phase, it takes only 2 h for the CM platform irrespective of initial cell concentration (8.1 × 10(4) to 8.1 × 10(5)/ml), acceleration/deceleration (10 to 32/s(2)) and angular span of the culture chamber (π/12 to π/4), representing significant time reduction. This is largely attributed to better growth conditions due to enhanced mixing and appropriate shear-stress stimulation from the efficient spiral toroidal vortex.

Optimization of the pilot-scale production of an ice-binding protein by fed-batch culture of Pichia pastoris

Ice-binding proteins (IBPs) can bind to the ice crystal and inhibit its growth. Because this property of IBPs can increase the freeze-thaw survival of cells, IBPs have attracted the attention from industries for their potential use in biotechnological applications. However, their use was largely hampered by the lack of the large-scale recombinant production system. In this study, the codon-optimized IBP from Leucosporidium sp. (LeIBP) was constructed and subjected to high-level expression in methylotrophic Pichia pastoris system. In a laboratory-scale fermentation (7 L), the optimal induction temperature and pH were determined to be 25 °C and 6.0, respectively. Further, employing glycerol fed-batch phase prior to methanol induction phase enhanced the production of recombinant LelBP (rLeIBP) by ∼100 mg/l. The total amount of secreted proteins at these conditions (25 °C, pH 6.0, and glycerol fed-batch phase) was ∼443 mg/l, 60 % of which was rLeIBP, yielding ∼272 mg/l. In the pilot-scale fermentation (700 L) under the same conditions, the yield of rLeIBP was 300 mg/l. To our best knowledge, this result reports the highest production yield of the recombinant IBP. More importantly, the rLeIBP secreted into culture media was stable and active for 6 days of fermentation. The thermal hysteresis (TH) activity of rLeIBP was about 0.42 °C, which is almost the same to those reported previously. The availability of large quantities of rLeIBP may accelerate further application studies.

Dynamic modeling of methylotrophic Pichia pastoris culture with exhaust gas analysis: From cellular metabolism to process simulation

A systematic approach to establish a dynamic model of methylotrophic Pichia pastoris culture in bioreactor is presented on the basis of biomass compartmentalization and metabolic stoichiometry simplification. Besides direct state variables (i.e., biomass, glycerol, methanol, and ammonia), CER and OUR calculated from on-line exhaust gas analysis are included in the model. The model is directly and crossly validated with five experimental cultures involving glycerol growth and methanol feeding phases. Model parameters are identified with confidence intervals. Meanwhile, data consistency is straightforward checked between predicted CERs and measured CTRs. In addition, in the light of the model structure, the results of parameter sensitivity analysis verifies the relative “freedom” of biomass initial compartmentalization and the high output sensitivity when the substrate (glycerol or methanol) concentration is close to the affinity constant (KGly or KMeth). With the proposed model, a process control strategy can be accordingly developed, which is based on real-time monitoring and regulating of cellular metabolic state during culture.