Development of Recombinant Antibody by Yeast Surface Display Technology

Recombinant antibodies have emerged as powerful tools in various fields, including therapeutics, diagnostics, and research applications. The selection of high-affinity antibodies with desired specificity is a crucial step in the development of recombinant antibody-based products. In recent years, yeast surface display technology has gained significant attention as a robust and versatile platform for antibody selection. This graphical review provides an overview of the yeast surface display technology and its applications in recombinant antibody selection. We discuss the key components involved in the construction of yeast surface display libraries, including the antibody gene libraries, yeast host strains, and display vectors. Furthermore, we highlight the strategies employed for affinity maturation and optimization of recombinant antibodies using yeast surface display. Finally, we discuss the advantages and limitations of this technology compared to other antibody selection methods. Overall, yeast surface display technology offers a powerful and efficient approach for the selection of recombinant antibodies, enabling the rapid generation of high-affinity antibodies for various applications.

Raman spectroscopy of yeast cells cultured on a deuterated substrate

Raman spectroscopy of cells cultured in a deuterated substrate is a promising approach to the characterization of mass transfer and enzymatic reactions in living cells. Here, we studied the potential of this approach using the example of yeast cells cultured under aerobic and anaerobic conditions. In our experiments, unadapted to D2O Saccharomyces cerevisiae were cultured in a medium with different concentrations of deuterium oxide and deuterated glucose. It has been shown that the addition of even 10% heavy water leads to a general decrease in the amount of lipids in cells. In the Raman spectra of cells cultured at high concentrations of D2O, additional peaks are found, which are associated with the deuteration of entire chemical groups. We observed a similar effect in the ethanol synthesized by yeast fermentation, the deuteration of which also depends on the concentration of D2O. The results on the characterization of cell deuteration turned out to be in qualitative agreement with the known estimate that aerobic metabolism is 15 times more active than ethanol fermentation. The results of our work determine new limitations and prospects for further application and development of the Raman method of spectroscopy of deuterium tags.

Biofabricated yeast: super-soldier for detoxification of heavy metals

The advances in nanotechnology have shown enormous impacts in environmental technology as a potent weapon for degradation of toxic organic pollutants and detoxification of heavy metals. It is either by in-situ or ex-situ adaptive strategies. Mycoremediation of environmental pollutants has been a success story of the past decade, by employing the wide arsenal of biological capabilities of fungi. Recently, the proficiency and uniqueness of yeast cell surface alterations have encouraged the generation of engineered yeast cells as dye degraders, heavy metal reduction and its recovery, and also as detoxifiers of various hazardous xenobiotic compounds. As a step forward, recent trends in research are towards developing biologically engineered living materials as potent, biocompatible and reusable hybrid nanomaterials. They include chitosan-yeast nanofibers, nanomats, nanopaper, biosilica hybrids, and TiO₂-yeast nanocomposites. The nano-hybrid materials contribute significantly as supportive stabilizer, and entrappers, which enhances the biofabricated yeast cells' functionality. This field serves as an eco-friendly cutting-edge cocktail research area. In this review, we highlight recent research on biofabricated yeast cells and yeast-based biofabricated molecules, as potent heavy metals, toxic chemical detoxifiers, and their probable mechanistic properties with future application perspectives.

Scanning electrochemical microscopy based irreversible destruction of living cells

In this research, scanning electrochemical microscopy combined with electrochemical impedance spectroscopy has been applied to irreversible electroporation of active yeast cells by causing cell death. This finding is important for the development of irreversible electroporation technique, which could be suitable for the curing of cancerous tissues, because during this research cell death has been achieved using relatively low ultramicro-electrode (UME) voltage, precisely of 2.0 V vs Ag/AgCl,Cl^-sat. It was determined that the irreversibly electroporated area of immobilized yeast cells was located directly below the UME and was of approximately 20 times larger width than the diameter of the UME, leaving undamaged cells out of this area. The ability of SECM to move the UME with high accuracy in x, y, and z directions and the ability to use electrodes of various diameters as well as the fact that the diameter of the electroporated area depends on the diameter of the UME and on the distance between the UME and the surface, what offers the possibility to establish targeted electroporation systems for selective treatment of tissues.

Scanning electrochemical microscope as a tool for the electroporation of living yeast cells

In this study, a scanning electrochemical microscope (SECM) was for the first time adapted to perform the electroporation process of living yeast cells. We have demonstrated that relatively low voltage pulses of 1-2 V vs. Ag/AglCl,Cl^-_sat applied to gold-based ultramicroelectrode (Au-UME) are performing reversible electroporation of yeast cells immobilized on fluorine-doped tin oxide (FTO)/glass surface. SECM and electrochemical impedance spectroscopy (EIS) were used for the determination of quantitative electrochemical characteristics before and after the electroporation. The electrochemical impedance spectroscopy (EIS) illustrated significant electrochemical changes of electroporated yeast cells, while SECM feedback mode surface vertical scan current-distance curves showed that the diameter of the area affected by the electrical pulse is about 25 times larger than the diameter of the Au-UME used for the electroporation process. The results presented in this research open up a possibility to develop a targeted electroporation system which will affect only the selected area of tissue or some other cell-covered surface. Such model is promising for the selective treatment of selected cells in tissues and/or other sensitive biological systems while selecting the location and size of electroporated areas.

Removal of phosphorus from wastewater by Diutina rugosa BL3: Efficiency and pathway

A novel phosphorus removal yeast BL3 was isolated from an alternating anaerobic/aerobic biofilter and identified as Diutina rugosa by 26S rDNA gene sequence analysis. Yeast BL3 could effectively remove phosphorus from synthetic wastewater containing 2-20 mg/L phosphorus under optimal environmental conditions. The highest phosphorus removal efficiency was above 70% under the conditions of DO 6.86 mg/L, C/P ratios of 60, N/P ratios of 3.3, pH 6.0-9.0, and at 25.0-35.0 °C. The phosphorus distribution in the aqueous solution and different components of yeast BL3 analysis indicated that around 55%-70% and 20%-40% of removed phosphorus were transferred into extracellular polymeric substances (EPS) and yeast cells, respectively. The plausible phosphorus transfer pathway was proposed based on the phosphorus distribution and species analysis, suggesting the important role of EPS as a phosphorus reservoir. These results indicate that yeast BL3 can efficiently remove phosphorus under aerobic conditions without alternating anaerobic/aerobic cycling, and thus has significant potential for practical application in wastewater phosphorus removal.

Impacts of Magnetic Immobilization on the Growth and Metabolic Status of Recombinant Pichia pastoris

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.

Synchronisation of glycolytic activity in yeast cells

Glycolysis is the central metabolic pathway of almost every cell and organism. Under appropriate conditions, glycolytic oscillations may occur in individual cells as well as in entire cell populations or tissues. In many biological systems, glycolytic oscillations drive coherent oscillations of other metabolites, for instance in cardiomyocytes near anorexia, or in pancreas where they lead to a pulsatile release of insulin. Oscillations at the population or tissue level require the cells to synchronize their metabolism. We review the progress achieved in studying a model organism for glycolytic oscillations, namely yeast. Oscillations may occur on the level of individual cells as well as on the level of the cell population. In yeast, the cell-to-cell interaction is realized by diffusion-mediated intercellular communication via a messenger molecule. The present mini-review focuses on the synchronisation of glycolytic oscillations in yeast. Synchronisation is a quorum-sensing phenomenon because the collective oscillatory behaviour of a yeast cell population ceases when the cell density falls below a threshold. We review the question, under which conditions individual cells in a sparse population continue or cease to oscillate. Furthermore, we provide an overview of the pathway leading to the onset of synchronized oscillations. We also address the effects of spatial inhomogeneities (e.g., the formation of spatial clusters) on the collective dynamics, and also review the emergence of travelling waves of glycolytic activity. Finally, we briefly review the approaches used in numerical modelling of synchronized cell populations.

Impacts of Magnetic Immobilization on the Recombinant Proteins Structure Produced in Pichia pastoris System

Pichia pastoris expression system was introduced with post-translation process similar to higher eukaryotes. Preliminary studies were performed toward process intensification and magnetic immobilization of this system. In this experiment, effects of magnetic immobilization on the structure of recombinant protein were evaluated. P. pastoris cell which express human serum albumin (HSA) was used as a model. The cells were immobilized with various concentrations of APTES coated magnetite nanoparticles. HSA production was done over 5 days induction and structure of the product was analyzed by UV-vis, fluorescence, and ATR-FTIR spectroscopy. Second derivative deconvolution method was used to analyze the secondary structure of HSA. P. pastoris cell that were immobilized with 0.5 and 1 mg/mL of nanoparticles were produced HSA with intact structure. But immobilization with 2 mg/mL of nanoparticles resulted in some modifications in the secondary structures (i.e., α-helixes and β-turns) of produced HSA. Based on these data, immobilization of P. pastoris cells with 0.5 or 1 mg/mL of nanoparticles is completely efficient for cell harvesting and has any effect on the structure of recombinant product. These findings revealed that decoration of microbial cells with high concentrations of nanoparticles has some impacts on the structure of secretory proteins.

A systematic study of the antimicrobial mechanisms of cold atmospheric-pressure plasma for water disinfection

Waterborne diseases caused by pathogenic microorganisms pose a severe threat to human health. Cold atmospheric-pressure plasma (CAP) has recently gained much interest as a promising fast, effective, economical and eco-friendly method for water disinfection. However, the antimicrobial mechanism of CAP in aqueous environments is still not clearly understood. Herein, we investigate the role of several short-lived reactive oxygen species (ROS) and cellular responses in the CAP inactivation of yeast cells in water. The results show that singlet oxygen (¹O₂), hydroxyl radical (OH) and superoxide anion (O₂^-) are generated in this plasma-water system, and O₂^- served as the precursor of OH. The 5-min plasma treatment resulted in the effective inactivation (more than 2-log reduction) of yeast cells in water. The ROS scavengers significantly increased the survival ratio in the following order: water < D-Man (scavenging OH) < SOD (scavenging O₂^-) < L-His (scavenging ¹O₂), indicating that ¹O₂ contributes the most to the yeast inactivation. In addition, the acidic pH had a synergetic antimicrobial effect with ROS against the yeast cells. During the CAP inactivation process, yeast cells underwent apoptosis in the first 3 min due to the accumulation of intracellular ROS, mitochondrial dysfunction and intracellular acidification, later followed by necrosis under longer exposure times, attributed to the destruction of the cell membrane. Additionally, L-His could switch the cell fate from necrosis to apoptosis through mitigating plasma-induced oxidative stress, indicating that the level of oxidative stress is a critical factor for cell death fate determination. These findings provide comprehensive insights into the antimicrobial mechanism of CAP, which can promote the development of CAP as an alternative water disinfection strategy.

The Kärger vs bi-exponential model: Theoretical insights and experimental validations

We revise three common models accounting for water exchange in pulsed-gradient spin-echo measurements: a bi-exponential model with time-dependent water fractions, the Kärger model, and a modified Kärger model designed for restricted diffusion, e.g. inside cells. The three models are compared and applied to experimental data from yeast cell suspensions. The Kärger model and the modified Kärger model yield very close results and accurately fit the data. The bi-exponential model, although less rigorous, has a natural physical interpretation and suggests a new experimental modality to estimate the water exchange time.

Investigation the cytotoxicity and photo-induced toxicity of carbon dot on yeast cell

Carbon dots (CDs) as a new fluorescent material with excellent water solubility, chemical inertness, and easy surface modification are a good candidate for bioimaging and biosensing due to their low toxicity and good biocompatibility. Although carbon is not an intrinsically toxic substance, carbon nanomaterials such as CDs may cause risks to human health and the potentially hazardous effects of CDs on various living systems must be completely determined. So far, cytotoxicity studies of CDs have focused on human cells and are mainly conducted on limited cell lines. In the present study, toxicity assessment of CDs was evaluated on yeast cells Pichia pastoris as a unicellular eukaryotic model. Results revealed dose-dependent toxicity of CDs on yeast cells and less relative cell growth in 25 mg/ml of CDs as compared to the control group. CDs binding curve confirmed the interaction between CDs and surface of yeast cells. SEM images showed that the CDs caused cell shrinkage and hole formation on the surface of yeast cells and also induced slightly cell deformation. It was demonstrated that CDs could generate the ROS dose-dependently. Finally, results showed the growth inhibition and ROS generation effects of CDs were enhanced at light exposure, as an important environmental factor. These findings could have important implications for applications of CDs.

Employing proteomic analysis to compare Paracoccidioides lutzii yeast and mycelium cell wall proteins

Paracoccidioidomycosis is an important systemic mycosis caused by thermodimorphic fungi of the Paracoccidioides genus. During the infective process, the cell wall acts at the interface between the fungus and the host. In this way, the cell wall has a key role in growth, environment sensing and interaction, as well as morphogenesis of the fungus. Since the cell wall is absent in mammals, it may present molecules that are described as target sites for new antifungal drugs. Despite its importance, up to now few studies have been conducted employing proteomics in for the identification of cell wall proteins in Paracoccidioides spp. Here, a detailed proteomic approach, including cell wall-fractionation coupled to NanoUPLC-MS^E, was used to study and compare the cell wall fractions from Paracoccidioides lutzii mycelia and yeast cells. The analyzed samples consisted of cell wall proteins extracted by hot SDS followed by extraction by mild alkali. In summary, 512 proteins constituting different cell wall fractions were identified, including 7 predicted GPI-dependent cell wall proteins that are potentially involved in cell wall metabolism. Adhesins previously described in Paracoccidioides spp. such as enolase, glyceraldehyde-3-phosphate dehydrogenase were identified. Comparing the proteins in mycelium and yeast cells, we detected some that are common to both fungal phases, such as Ecm33, and some specific proteins, as glucanase Crf1. All of those proteins were described in the metabolism of cell wall. Our study provides an important elucidation of cell wall composition of fractions in Paracoccidioides, opening a way to understand the fungus cell wall architecture.

Chemical treatment and chitosan coating of yeast cells to improve the encapsulation and controlled release of bovine serum albumin

We investigate the encapsulation of bovine serum albumin (BSA) in chemical-treated and chitosan-coated yeast cells, Saccharomyces cerevisiae (S. cerevisiae), for the controlled release of BSA. The chemical treatment can sufficiently enlarge the small-sized cell-wall cavities and/or break the integrity for the entrance of BSA to the interior of yeast cells, and the additional chitosan coating can well prevent the rapid release of encapsulated BSA from the yeast-derived microcapsules. The sodium hydroxide pretreated S. cerevisiae gives a maximum encapsulation yield of (10.1 ± 0.2)% for BSA. An additional coating of S. cerevisiae with chitosan can reduce the initial burst release of BSA and extend the release period from 24 h in the chitosan-free case to 48 h in phosphate buffer at pH 7.4. The prepared microcapsules can well keep the shapes and sizes of yeast cells and thus show uniform sizes of 3.85 ± 0.81 μm. The encapsulated BSA well retains its pristine ultraviolet spectroscopic and chromatographic behaviors. The present microencapsulation protocol has the advantages of convenient and mild operation, high encapsulation efficiency, and organic solvent-free nature, which is of reference value for establishing high-performance controllable biomacromolecule-delivery systems.

Different characteristics between menadione and menadione sodium bisulfite as redox mediator in yeast cell suspension

Menadione promoted the production of active oxygen species (AOS) in both yeast cell suspension and the crude enzymes from the cells, but menadione sodium bisulfite (MSB) had little effect on the production of AOS in the cell suspension. MSB kept the stable increase in the electron transfer from intact yeast cells to anode compared to menadione, but the electron transfer promoted by MSB was inhibited in permeabilized yeast cell suspension. Menadione promoted oxidation of NAD(P)H much faster than MSB in permeabilized yeast cell suspension, suggesting the oxidative stress due to consumption of NAD(P)H. The proliferation of yeast cells was inhibited by menadione under aerobic conditions rather than anaerobic conditions, and the inhibitory effect was reduced by superoxide dismutase and catalase. The effect of MSB on the proliferation was much smaller than that of menadione. The above facts suggest that harmless MSB promotes the electron transfer from plasma membrane of yeast cells to anode. On the other hand, harmful menadione might promote the electron transfer from cytosol and plasma membrane to anode and dissolved oxygen.

Effects of Selenium on Morphological Changes in Candida utilis ATCC 9950 Yeast Cells

This paper presents the results of microscopic examinations of the yeast cells cultured in yeast extract-peptone-dextrose (YPD) media supplemented with sodium selenite(IV). The analysis of the morphological changes in yeast cells aimed to determine whether the selected selenium doses and culturing time may affect this element accumulation in yeast cell structures in a form of inorganic or organic compounds, as a result of detoxification processes. The range of characteristic morphological changes in yeasts cultivated in experimental media with sodium selenite(IV) was observed, including cell shrinkage and cytoplasm thickening of the changes within vacuole structure. The processes of vacuole disintegration were observed in aging yeast cells in culturing medium, which may indicate the presence of so-called ghost cells lacking intracellular organelles The changes occurring in the morphology of yeasts cultured in media supplemented with sodium selenite were typical for stationary phase of yeast growth. From detailed microscopic observations, larger surface area of the cell (6.03 μm(2)) and yeast vacuole (2.17 μm(2)) were noticed after 24-h culturing in the medium with selenium of 20 mg Se(4+)/L. The coefficient of shape of the yeast cells cultured in media enriched with sodium selenite as well as in the control YPD medium ranged from 1.02 to 1.22. Elongation of cultivation time (up to 48 and 72 h) in the media supplemented with sodium selenite caused a reduction in the surface area of the yeast cell and vacuole due to detoxification processes.

Synthesis of polypyrrole within the cell wall of yeast by redox-cycling of [Fe(CN)6](3-)/[Fe(CN)6](4-)

Yeast cells are often used as a model system in various experiments. Moreover, due to their high metabolic activity, yeast cells have a potential to be applied as elements in the design of biofuel cells and biosensors. However a wider application of yeast cells in electrochemical systems is limited due to high electric resistance of their cell wall. In order to reduce this problem we have polymerized conducting polymer polypyrrole (Ppy) directly in the cell wall and/or within periplasmic membrane. In this research the formation of Ppy was induced by [Fe(CN)6](3-)ions, which were generated from K4[Fe(CN)6], which was initially added to polymerization solution. The redox process was catalyzed by oxido-reductases, which are present in the plasma membrane of yeast cells. The formation of Ppy was confirmed by spectrophotometry and atomic force microscopy. It was confirmed that the conducting polymer polypyrrole was formed within periplasmic space and/or within the cell wall of yeast cells, which were incubated in solution containing pyrrole, glucose and [Fe(CN)6](4-). After 24h drying at room temperature we have observed that Ppy-modified yeast cell walls retained their initial spherical form. In contrast to Ppy-modified cells, the walls of unmodified yeast have wrinkled after 24h drying. The viability of yeast cells in the presence of different pyrrole concentrations has been evaluated.

Yeast as a model system to screen purine derivatives against human CDK1 and CDK2 kinases

Cyclin-dependent kinases (Cdk) play crucial roles in cell cycle progression. Aberrant activation of Cdk1 has been observed in a number of primary tumors and Cdk2 is deregulated in various malignancies. The therapeutic value of targeting Cdk1 and Cdk2 has been explored in a number of experimental systems. In the present study, taking advantage of the fact that deletion of the yeast CDC28 gene is functionally complemented by human CDK1 or CDK2, we set up an in vivo screen system to evaluate the inhibitory potency of purine derivatives against these two human Cdks. We constructed three isogenic strains highly sensitive to small molecules and harboring genes CDK1, CDK2 or CDC28, under the control of the CDC28 promoter. In a proof of principle assay, we determined the inhibitory effect of 82 purine derivatives on the growth rate of these strains. Thirty-three of them were revealed to be able to inhibit the Cdk1- or Cdk2-harboring strains but not the Cdc28-harboring strain, suggesting a specific inhibitory effect on human Cdks. Our data demonstrate that the yeast-based assay is an efficient system to identify potential specific inhibitors that should be preferentially selected for further investigation in cultured human cell lines.

Cellular fractionation--yeast cells

In proteomics research, one essential step among enrichment techniques is subcellular fractionation. This is of special importance for analyzing intracellular organelles and multiprotein complexes. Subcellular fractionation is a flexible and adjustable approach to reducing sample complexity and is most efficiently combined with high-resolution 2-D gel/mass spectrometry analysis as well as with gel-independent techniques.

Method for measuring mRNA decay rate in Saccharomyces cerevisiae

Eukaryotic mRNA degradation is an essential aspect of gene regulation. Properly turning off transcript generation ensures that protein synthesis does not occur indefinitely. By ensuring that all mRNAs are destroyed, cells can adapt quickly to changing physiological and environmental conditions. Eukaryotic cytoplasmic mRNA degradation is predominately initiated by removal of the poly(A) tail at the 3' end (deadenylation). Following deadenylation, either the mRNA is degraded in a 3'-5' manner or the cap is removed and the mRNA is degraded 5'-3' (reviewed in Coller and Parker, 2004). Determining mRNA decay rates, as indicated by mRNA half-life, is vital to understand how mRNA stability is modulated under various physiological conditions.