Enhancing the Heterologous Expression of a Thermophilic Endoglucanase and Its Cost-Effective Production in Pichia pastoris Using Multiple Strategies.

Although Pichia pastoris was successfully used for heterologous gene expression for more than twenty years, many factors influencing protein expression remain unclear. Here, we optimized the expression of a thermophilic endoglucanase from Thermothielavioides terrestris (TtCel45A) for cost-effective production in Pichia pastoris. To achieve this, we established a multifactorial regulation strategy that involved selecting a genome-editing system, utilizing neutral loci, incorporating multiple copies of the heterologous expression cassette, and optimizing high-density fermentation for the co-production of single-cell protein (SCP). Notably, even though all neutral sites were used, there was still a slight difference in the enzymatic activity of heterologously expressed TtCel45A. Interestingly, the optimal gene copy number for the chromosomal expression of TtCel45A was found to be three, indicating limitations in translational capacity, post-translational processing, and secretion, ultimately impacting protein yields in P. pastoris. We suggest that multiple parameters might influence a kinetic competition between protein elongation and mRNA degradation. During high-density fermentation, the highest protein concentration and endoglucanase activity of TtCel45A with three copies reached 15.8 g/L and 9640 IU/mL, respectively. At the same time, the remaining SCP of P. pastoris exhibited a crude protein and amino acid content of up to 59.32% and 46.98%, respectively. These findings suggested that SCP from P. pastoris holds great promise as a sustainable and cost-effective alternative for meeting the global protein demand, while also enabling the production of thermophilic TtCel45A in a single industrial process.

Assessment of chemical constitution and aroma properties of kiwi wines obtained from pure and mixed fermentation with Wickerhamomyces anomalus and Saccharomyces cerevisiae.

BACKGROUND: To improve the aroma of kiwi wine through the utilization of Wickerhamomyces anomalus, kiwi juice was fermented using a selected W. anomalus strain in pure culture and mixed fermentations with Saccharomyces cerevisiae, which was inoculated simultaneously and sequentially. The physicochemical indices, volatile compounds and aroma properties of the kiwi wines were assessed. RESULTS: The study suggested that the ethanol, color indices and organic acids of the wines were closely related to the method of inoculation. Compared with the pure S. cerevisiae fermentation, the mixed fermentations produced more varieties and concentrations of volatiles. The sequential fermentations increased the concentrations of esters and terpenes, improving the flower and sweet fruit notes of the wines. The simultaneous inoculation enhanced the contents of esters and aldehydes, intensifying the flower, sweet and sour fruit of the wines. Partial least-squares regression analysis showed that esters and terpenes contributed greatly to the flower and sweet fruit aroma, whereas aldehydes were the major contributors to the sour note. CONCLUSION: Based on our results, the mixed fermentations not only enriched the types and concentrations of volatiles, but also had better sensory properties. © 2021 Society of Chemical Industry.

Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice.

Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

Heterologous expression of nattokinase from B. subtilis natto using Pichia pastoris GS115 and assessment of its thrombolytic activity.

BACKGROUND: Nattokinase is a fibrinolytic enzyme that has huge market value as a nutritional supplement for health promotion. In order to increase nattokinase yields, fermentation conditions, strains, cultivation media, and feeding strategies have been optimized. Nattokinase has been expressed using several heterologous expression systems. Pichia pastoris heterologous expression system was the alternative. RESULTS: This report aimed to express high levels of nattokinase from B. subtilis natto (NK-Bs) using a Pichia pastoris heterologous expression system and assess its fibrinolytic activity in vivo. Multicopy expression strains bearing 1-7 copies of the aprN gene were constructed. The expression level of the target protein reached a maximum at five copies of the target gene. However, multicopy expression strains were not stable in shake-flask or high-density fermentation, causing significant differences in the yield of the target protein among batches. Therefore, P. pastoris bearing a single copy of aprN was used in shake-flask and high-density fermentation. Target protein yield was 320 mg/L in shake-flask fermentation and approximately 9.5 g/L in high-density fermentation. The recombinant nattokinase showed high thermo- and pH-stability. The present study also demonstrated that recombinant NK-Bs had obvious thrombolytic activity. CONCLUSIONS: This study suggests that the P. pastoris expression system is an ideal platform for the large-scale, low-cost preparation of nattokinase.

Assessment of Cytotoxicity of α-Synuclein in Budding Yeast Using a Spot Growth Assay and Fluorescent Microscopy.

The budding yeast Saccharomyces cerevisiae is a model organism amenable both to genetic analysis and cell biology. Due to these advantages, yeast has provided platforms to examine the properties of pathogenic proteins involved in human diseases. The methods used to examine the cytotoxicity and intracellular localization of α-Synuclein, a human neuronal protein implicated in Parkinson's disease, using yeast have been described herein. These methods are readily accessible to researchers or graduate students unfamiliar with experiments using yeast and applicable to larger scale analyses, such as high-throughput genetic and chemical screenings.

Assessment of quorum sensing effects of tyrosol on fermentative performance by chief ethnic fermentative yeasts from northeast India.

AIM: Tyrosol, a quorum sensing molecule in yeasts, was reported to reduce lag phase and induces hyphae formation during cell proliferation. However, evidence of any enhancing effect of tyrosol in cellular proliferation within fermentative environment is unclear. In this investigation, selected yeast cells were assessed for their ability to synthesize tyrosol followed by examining the role of the molecule during fermentation. METHODS AND RESULTS: Tyrosols were characterized in four fermentative yeasts viz., Saccharomyces cerevisiae, Wickerhamomyces anomalus, Candida glabrata and Candida tropicalis isolated from traditional fermentative cakes of northeast India. All the isolates synthesized tyrosol while C. tropicalis exhibited filamentous growth in response to tyrosols retrieved from other isolates. Purified tyrosols showed protective behaviour in C. tropicalis and S. cerevisiae under ethanol mediated oxidative stress. During fermentation, tyrosol significantly enhanced growth of W. anomalus in starch medium while C. tropicalis exhibited growth enhancement in starch and glucose sources. The chief fermentative yeast S. cerevisiae showed notable enhancement in fermentative capacity in starch medium under the influence of tyrosol con-commitment of ethanol production. CONCLUSION: The study concludes that tyrosol exerts unusual effect in cellular growth and fermentative ability of both Saccharomyces and non-Saccharomyces yeasts. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of expression of tyrosol by non-conventional yeasts, where the molecule was found to exert enhancing effect during fermentation, thereby augmenting the process of metabolite production during traditional fermentation.

A Pilot Safety Assessment for Recombinant Epinephelus lanceolatus Piscidin Yeast Powder as a Drug Food Additive after Subacute and Subchronic Administration to SD Rats.

Recombinant Epinephelus lanceolatus piscidin (RELP) was previously shown to improve growth performance and immune response when used as a feed additive for Gallus gallus domesticus. However, the long-term toxicity of RELP has not be thoroughly investigated. In the present study, we evaluated the subacute and subchronic oral toxicities of RELP in SD rats by hematological, biochemical, and histopathological analyses. To determine subacute and subchronic toxicities, male and female rats were fed with RELP 1000 mg/kg bodyweight/day for 28 and 90 days, respectively. Bodyweight and food intake were unchanged by RELP treatment over the course of the studies. After exposure, samples of blood, heart, lung, liver, and kidney were collected and analyzed. Results demonstrated that RELP exposure did not cause any observable hematological, biochemical, or histological abnormalities in SD rats. Thus, RELP may be a safe feed additive for use in agriculture and aquaculture.

Design of a MAPK signalling cascade balances energetic cost versus accuracy of information transmission.

Cellular processes are inherently noisy, and the selection for accurate responses in presence of noise has likely shaped signalling networks. Here, we investigate the trade-off between accuracy of information transmission and its energetic cost for a mitogen-activated protein kinase (MAPK) signalling cascade. Our analysis of the pheromone response pathway of budding yeast suggests that dose-dependent induction of the negative transcriptional feedbacks in this network maximizes the information per unit energetic cost, rather than the information transmission capacity itself. We further demonstrate that futile cycling of MAPK phosphorylation and dephosphorylation has a measurable effect on growth fitness, with energy dissipation within the signalling cascade thus likely being subject to evolutionary selection. Considering optimization of accuracy versus the energetic cost of information processing, a concept well established in physics and engineering, may thus offer a general framework to understand the regulatory design of cellular signalling systems.

Assessment of chemical composition and sensorial properties of ciders fermented with different non-Saccharomyces yeasts in pure and mixed fermentations.

This work presents the attempt to enhance the flavor complexity of cider fermented by different non-Saccharomyces species. Pichia kluyveri and Hanseniaspora vineae pure cultures were used as reference ciders. Mixed cultures between all 4 species gave 5 fermentations, where Hanseniaspora uvarum or Torulaspora quercuum were included for apple juice fermentation. Chemical composition and sensorial properties of all ciders were studied. The results indicated that the growth of P. kluyveri and H. vineae were interreacted and also affected by H. uvarum and T. quercuum. H. vineae was more capable of consuming sugar than P. kluyveri. Ciders from the single culture fermentation with P. kluyveri (Pk), as well as from mixed fermentation with P. kluyveri and H. uvarum (Pk-Hu), had high residual sugar, sugar/acid ratio, and glucose-fructose consumption ratio. Large shifts in the consumption and production of organic acids and polyphenols among all ciders were observed. The calculation of the relative odor activity value (rOAV) showed that 17 volatile compounds had an rOAV >1 in at least one sample, and acetate esters and ethyl esters were the groups with the highest number of volatile compounds of importance to the cider aroma. Among these 17 compounds, 3-methylbutyl acetate, 2-methylbutyl acetate, ethyl hexanoate, ethyl octanoate, and ß-damascenone exhibited high rOAVs in some ciders and might contribute fruity, floral, and sweet features to the cider aroma. Besides, the tropical fruity aroma from 3-methylbutyl acetate was only perceived in Pk and Pk-Hu. The partial least squares regression (PLSR) analysis revealed that acetate esters contributed positively to the roasted and cooked odor of all ciders. This is the first study evaluating simultaneous fermentation of two non-Saccharomyces yeasts to produce cider, which provides new insights into cider production.

Bioremediation of palm oil mill effluent (POME) using indigenous Meyerozyma guilliermondii.

Despite being a key Malaysian economic contributor, the oil palm industry generates a large quantity of environmental pollutant known as palm oil mill effluent (POME). Therefore, the need to remediate POME has drawn a mounting interest among environmental scientists. This study has pioneered the application of Meyerozyma guilliermondii with accession number (MH 374161) that was isolated indigenously in accessing its potential to degrade POME. This strain was able to treat POME in shake flask experiments under aerobic condition by utilising POME as a sole source of carbon. However, it has also been shown that the addition of suitable carbon and nitrogen sources has significantly improved the degradation potential of M. guilliermondii. The remediation of POME using this strain resulted in a substantial reduction of chemical oxygen demand (COD) of 72%, total nitrogen of 49.2% removal, ammonical nitrogen of 45.1% removal, total organic carbon of 46.6% removal, phosphate of 60.6% removal, and 92.4% removal of oil and grease after 7 days of treatment period. The strain also exhibited an extracellular lipase activity which promotes better wastewater treatment. Additionally, Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) analyses have specifically shown that M. guilliermondii strain can degrade hydrocarbons, fatty acids, and phenolic compounds present in the POME. Ultimately, this study has demonstrated that M. guilliermondii which was isolated indigenously exhibits an excellent degrading ability. Therefore, this strain is suitable to be employed in the remediation of POME, contributing to a safe discharge of the effluent into the environment.

Enhancing Electricity Generation Using a Laccase-Based Microbial Fuel Cell with Yeast Galactomyces reessii on the Cathode.

The fungi associated with termites secrete enzymes such as laccase (multi-copper oxidase) that can degrade extracellular wood matrix. Laccase uses molecular oxygen as an electron acceptor to catalyze the degradation of organic compounds. Owing to its ability to transfer electrons from the cathodic electrode to molecular oxygen, laccase has the potential to be a biocatalyst on the surface of the cathodic electrode of a microbial fuel cell (MFC). In this study, a two-chamber MFC using the laccase-producing fungus Galactomyces reessii was investigated. The fungus cultured on coconut coir was placed in the cathode chamber, while an anaerobic microbial community was maintained in the anode chamber fed by industrial rubber wastewater and supplemented by sulfate and a pH buffer. The laccase-based biocathode MFC (lbMFC) produced the maximum open circuit voltage of 250 mV, output voltage of 145 mV (with a 1,000 Ω resistor), power density of 59 mW/m2, and current density of 278 mA/m2, and a 70% increase in half-cell potential. This study demonstrated the capability of laccase-producing yeast Galactomyces reessii as a biocatalyst on the cathode of the two-chamber lbMFC.

Comparative assessment of fermentative capacity of different xylose-consuming yeasts.

BACKGROUND: Understanding the effects of oxygen levels on yeast xylose metabolism would benefit ethanol production. In this work, xylose fermentative capacity of Scheffersomyces stipitis, Spathaspora passalidarum, Spathaspora arborariae and Candida tenuis was systematically compared under aerobic, oxygen-limited and anaerobic conditions. RESULTS: Fermentative performances of the four yeasts were greatly influenced by oxygen availability. S. stipitis and S. passalidarum showed the highest ethanol yields (above 0.44 g g-1) under oxygen limitation. However, S. passalidarum produced 1.5 times more ethanol than S. stipitis under anaerobiosis. While C. tenuis showed the lowest xylose consumption rate and incapacity to produce ethanol, S. arborariae showed an intermediate fermentative performance among the yeasts. NAD(P)H xylose reductase (XR) activity in crude cell extracts correlated with xylose consumption rates and ethanol production. CONCLUSIONS: Overall, the present work demonstrates that the availability of oxygen influences the production of ethanol by yeasts and indicates that the NADH-dependent XR activity is a limiting step on the xylose metabolism. S. stipitis and S. passalidarum have the greatest potential for ethanol production from xylose. Both yeasts showed similar ethanol yields near theoretical under oxygen-limited condition. Besides that, S. passalidarum showed the best xylose consumption and ethanol production under anaerobiosis.

Can Sophorolipids prevent biofilm formation on silicone catheter tubes?

Given the impact of biofilms in health care environment and the increasing antibiotic resistance and/or tolerance, new strategies for preventing that occurrence in medical devices are obligatory. Thus, biomaterials surface functionalization with active compounds can be a valuable approach. In the present study the ability of the biosurfactants sophorolipids to prevent biofilms formation on silicone rubber aimed for medical catheters was investigated. Sophorolipids produced by Starmerella bombicola, identified by HPLC-MS/MS were used to cover silicone and surface characterization was evaluated through contact angle measurements and FTIR-ATR. Results revealed that sophorolipids presence on silicone surface decreased the hydrophobicity of the material and biofilm formation of Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922. Antibiofilm activity was evaluated through different methods and was more pronounced against S. aureus. Furthermore, biocompatibility of silicone specimens with HaCaT cells was also obtained. From this study it was possible to conclude that sophorolipids seem to be a favourable approach for coating silicone catheters. Such compounds may represent a novel source of antibiofilm agents for technological development passing through strategies of permanent functionalization of surfaces.

Assessment of Schwanniomyces occidentalis as a host for protein production using the wide-range Xplor2 expression platform.

The wide-range transformation/expression platform, Xplor2, was employed for the assessment of Schwanniomyces occidentalis as a potential producer of the recombinant proteins human IFNα2a (IFNα2a) and S. occidentalis fructofuranosidase (SFfase), and its efficiency was compared to that of Arxula adeninivorans. ADE2 and URA3 genes from both yeast species were isolated, characterized and used as selection markers in combination with the IFNα2a and SFfase expression modules, which used the strong constitutive A. adeninivorans-derived TEF1 promoter. Yeast rDNA integrative expression cassettes and yeast integrative expression cassettes equipped with a selection marker and expression modules were transformed into auxotrophic S. occidentalis and A. adeninivorans strains and a quantitative comparison of the expression efficiency was made. Whilst IFNα2a was mainly accumulated extracellularly (>95 %) in A. adeninivorans, extracellular SFfase (>90 %) was detected in both yeast species. The DNA composition of the selection marker modules and expression modules, especially their open reading frame codon usage, affects auxotrophy recovery as well as protein expression. Auxotrophy recovery was only achieved with selection marker modules of the homologous gene donor yeast. The concentration of recombinant IFNα2a was fivefold higher in A. adeninivorans (1 mg L(-1)), whereas S. occidentalis accumulated 1.5- to 2-fold more SFfase (0.5 Units ml(-1)). These results demonstrate the extension of the use of the wide-range expression platform Xplor2 to another yeast species of biotechnological interest.

The improvement of riboflavin production in Ashbya gossypii via disparity mutagenesis and DNA microarray analysis.

We generated a high riboflavin-producing mutant strain of Ashbya gossypii by disparity mutagenesis using mutation of DNA polymerase δ in the lagging strand, resulting in loss of DNA repair function by the polymerase. Among 1,353 colonies generated in the first screen, 26 mutants produced more than 3 g/L of riboflavin. By the second screen and single-colony isolation, nine strains that produced more than 5.2 g/L of riboflavin were selected as high riboflavin-producing strains. These mutants were resistant to oxalic acid and hydrogen peroxide as antimetabolites. One strain (W122032) produced 13.7 g/L of riboflavin in a 3-L fermentor using an optimized medium. This represents a ninefold improvement on the production of the wild-type strain. Proteomic analysis revealed that ADE1, RIB1, and RIB5 proteins were expressed at twofold higher levels in this strain than in the wild type. DNA microarray analysis showed that purine and riboflavin biosynthetic pathways were upregulated, while pathways related to carbon source assimilation, energy generation, and glycolysis were downregulated. Genes in the riboflavin biosynthetic pathway were significantly overexpressed during both riboflavin production and stationary phases, for example, RIB1 and RIB3 were expressed at greater than sixfold higher levels in this strain compared to the wild type. These results indicate that the improved riboflavin production in this strain is related to a shift in carbon flux from ß-oxidation to the riboflavin biosynthetic pathway.

Characterization of vinasses from five certified brands of origin (CBO) and use as economic nutrient for the xylitol production by Debaryomyces hansenii.

Vinasses coming from the five CBOs of Galicia, north-western Spain, were characterized, and successfully employed as economic nutritional supplements for xylitol production by Debaryomyces hansenii. All fermentations can be modelled showing kinetic patterns fairly described by the mathematical models. No negative effect of the phenolic compounds in the liquid phase on the initial volumetric rate of product formation (r(P)(0)) was observed. Multiple linear regression analysis was used to describe the effect of metals and initial xylose acting on P(max) and Y(P/S). Zn was the most influential variable. Besides, partial least-squares regression models show a clear separation, based on the first two principal components, between the whole vinasses and the liquid fractions, which provided the higher P(max), with the exception of CBO 4, where P(max)=40.4 g/L, was achieved using the solid and liquid fraction.

Production of interleukin-6 in Arxula adeninivorans, Hansenula polymorpha and Saccharomyces cerevisiae by applying the wide-range yeast vector (CoMed) system to simultaneous comparative assessment.

A wide-range yeast vector (CoMed) system has been applied to the comparative assessment of three different yeast platforms for the production of human interleukin-6. A vector equipped with an rRNA gene targeting sequence and an Arxula adeninivorans-derived LEU2 gene was used for simultaneous transformation of auxotrophic A. adeninivorans, Hansenula polymorpha and Saccharomyces cerevisiae strains. IL6 was expressed under control of the strong constitutive A. adeninivorans-derived TEF1 promoter, which is functional in all yeast species analyzed so far. Secreted IL-6 was found to be correctly processed from an MFalpha1-IL6 precursor in A. adeninivorans only, whereas N-terminally truncated proteins were observed in H. polymorpha and S. cerevisiae.

Assessment of Hansenula polymorpha and Arxula adeninivorans-derived rDNA-targeting elements for the design of Arxula adeninivorans expression vectors.

Different targeting sequences derived from the Arxula adeninivorans and Hansenula polymorpha rDNA clusters were tested in A. adeninivorans integration/expression vectors. For element identification, the rDNA unit of A. adeninivorans (accession number ) was first isolated and characterized in addition to the known H. polymorpha unit. The rDNA is a cluster of some forty 7653-bp units without the 5S rDNA gene. The selected elements were integrated into a set of A. adeninivorans expression/integration vectors harbouring a TEF1 promoter - amyA ORF - PHO5 terminator sequence as reporter gene. No differences in mitotic stability, copy number and transformation frequency were observed. All transformants harboured a single copy integrated into the rDNA by a homologous recombination. In contrast, the choice of the rDNA targeting sequence was found to be of impact on productivity. Use of ETS-18S-5.8S fragments from both organisms resulted in a more than 50% increase in comparison to the use of other elements, independent of the orientation within the vector.

Flow cytometric assessment of cell structural and functional changes induced by acetic acid in the yeasts Zygosaccharomyces bailii and Saccharomyces cerevisiae.

Flow cytometry (FCM) was used with different viability dyes to assess changes in cell structure and function induced by acetic acid (AA) in populations of Zygosaccharomyces bailii (AA resistant) and Saccharomyces cerevisiae (AA sensitive). Kinetic changes in esterase activity, intracellular dye processing, and membrane integrity were monitored, and to detect those changes we used three assays involving fluorescein diacetate hydrolysis, FUN-1 processing, and propidium iodide exclusion, respectively. In S. cerevisiae, the decrease in the ability to process FUN-1 preceded the decrease in esterase activity, and there was loss of cell membrane integrity after incubation with AA. In Z. bailii, with higher AA concentrations, there was a similar decrease in the ability to process FUN-1, which also preceded the loss of cell membrane integrity. Changes in esterase activity in this yeast induced by AA treatment could not be monitored because the changes occurred independently of the presence of the acid. For control samples (untreated cells killed with 10% v/v of AA), the percentages of nonaltered cells as estimated by FCM and percentages of viable cells as estimated by colony forming unit (CFU) counts were identical. However, for cell samples treated for short periods with 3% (v/v) or less of AA, none of the dyes produced FCM results comparable to those produced by CFU counts.

[Effect of yeast growth limitation on the respiratory chain, the economic coefficient and the critical oxygen concentration for respiration]. / Vliianie limitirovaniia rosta drozhzhei na dykhatel'nuiu tsep', ékonomicheskii koéffitsient i kriticheskuiu dlia dykhaniia kontsentratsiiu kisloroda.

The effect of the yeast growth limitation by oxygen on the economical coefficient (EC), the operation of the cyanide resistant electron transport pathway (CrETP), and the critical for respiration oxygen concentration concentration ([O2]cr) was studied. The operation of CrETP was found to differ among various yeasts growing on glucose: it could function during both the exponential phase and limitation of growth (Torulopsis candida), or only in the conditions of growth limitation (Candida tropicalis, C. mycoderma, C. lipolytica), sometimes for a very long period (Endomyces geotrichum); in certain cases (C. utilis), it cannot be detected at all. If the main respiratory chain is inhibited by cyanide (i. e. if only CrETP operates), the value of [O2]cr sharply increases; such an increase can be also found in the absence of cyanide but in the conditions of active operation of CrETP. Apparently, the value of [O2]cr is higher for cyanide resistant oxydase of the studied organisms than for cytochrome oxydase. A decrease in EC observed upon the limitation of yeast growth by oxygen (Lozinov et al., 1974) correlates with the appearance or intensification of CrETP. Therefore, the decrease of EC can be attributed to the operation of non-phosphorylating CrETP which occurs in all the studied yeasts (with an exception of C. utilis) when their growth is limited by oxygen.