Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions

The Use of Yeast in Biosensing

Yeast has been used as a model for several diseases as it is the simplest unicellular eukaryote, safe and easy to culture and harbors most of the fundamental processes that are present in almost all higher eukaryotes, including humans. From understanding the pathogenesis of disease to drug discovery studies, yeast has served as an important biosensor. It is not only due to the conservation of genetics, amenable modification of its genome and easily accessible analytical methods, but also some characteristic features such as its ability to survive with defective mitochondria, making it a highly flexible microbe for designing whole-cell biosensing systems. The aim of this review is to report on how yeasts have been utilized as biosensors, reporting on responses to various stimuli.

Efficient Selection Scheme for Incorporating Noncanonical Amino Acids Into Proteins in Saccharomyces cerevisiae

With the advances in the field of expanded genetic code, the application of non-canonical amino acid (ncAA) is considered an effective strategy for protein engineering. However, cumbersome and complicated selection schemes limit the extensive application of this technology in Saccharomyces cerevisiae. To address this issue, a simplified selection scheme with confident results was developed and tested in this study. Based on a mutation library derived from Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS), a logic gate in synthetic biology was used to optimize screening procedures. We found that an "and" gate was more suitable than an "or" gate for isolating aminoacyl-tRNA synthetase from S. cerevisiae. The successful incorporation of O-methyltyrosine (OMeY) proved the utility and efficiency of this new selection scheme. After a round of positive selection, several new OMeY-tRNA synthetase (OMeYRS) mutants were screened, and their incorporation efficiency was improved. Furthermore, we characterized the insertion of several tyrosine analogs into Herceptine Fab and discovered that OMeYRS and its mutants were polyspecific. One of these mutants showed an optimal performance to incorporate different ncAAs into recombinant proteins in S. cerevisiae; this mutant was cloned and transfected into mammalian cells, and the results proved its functionality in HEK293 cells. This study could expand the application of ncAA in S. cerevisiae to construct efficient yeast cell factories for producing natural and synthetic products.

A microfluidic antibody bioarray for fast detection of human interleukins in low sample volumes

The antibody bioarray is a promising tool for the detection of proteins, which can be used as disease biomarkers. Therefore, we have developed a sandwich immunoassay-type bioarray using a microfluidic method to detect human interleukins that have diagnostic values. In the method development, we studied the effect of different factors that affect capture antibody immobilization, antibody–antigen interactions, and detection methods on the bioarray surface. The fluorescence signal obtained from different detection strategies was compared based on the signal fold-increase. This comparison showed that the use of covalent immobilization of capture antibodies, as opposed to their physical adsorption on the bioarray surface, increases the signal by 1.5 fold. Moreover, the use of protein G to achieve a better oriented immobilized capture antibody has resulted in a more than 3-fold signal enhancement.

Development of novel surface display platforms for anchoring heterologous proteins in Saccharomyces cerevisiae

Background

Cell surface display of recombinant proteins has become a powerful tool for biotechnology and biomedical applications. As a model eukaryotic microorganism, Saccharomyces cerevisiae is an ideal candidate for surface display of heterologous proteins. However, the frequently used commercial yeast surface display system, the a-agglutinin anchor system, often results in low display efficiency.

Results

We initially reconstructed the a-agglutinin system by replacing two anchor proteins with one anchor protein. By directly fusing the target protein to the N-terminus of Aga1p and inserting a flexible linker, the display efficiency almost doubled, and the activity of reporter protein α-galactosidase increased by 39%. We also developed new surface display systems. Six glycosylphosphatidylinositol (GPI) anchored cell wall proteins were selected to construct the display systems. Among them, Dan4p and Sed1p showed higher display efficiency than the a-agglutinin anchor system. Linkers were also inserted to eliminate the effects of GPI fusion on the activity of the target protein. We further used the newly developed Aga1p, Dan4p systems and Sed1p system to display exoglucanase and a relatively large protein β-glucosidase, and found that Aga1p and Dan4p were more suitable for immobilizing large proteins.

Conclusion

Our study developed novel efficient yeast surface display systems, that will be attractive tools for biotechnological and biomedical applications

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1133-x) contains supplementary material, which is available to authorized users.

Locating the binding domains of lysozyme with ionic liquids in aqueous solution via spectroscopic studies

The binding domains of lysozyme with ionic liquids (ILs, [C₄mim]BF₄, [C₄mim]Cl, [C₄mim]Br and [dmim]I) in aqueous solution was investigated by studying molecular interactions using spectroscopic techniques. Ultraviolet spectroscopy (UV) showed that the addition of ILs increased the absorption peak intensity of lysozyme at 210 nm by enhancing peptide bond valence electron transition. It is also found that a weak interaction between ILs and lysozyme chromophore groups was generated by analyzing the changes of absorption peak intensity near 280 nm. Fluorescence and Synchronous Fluorescence spectra results showed that four ILs had quenching effect on the fluorescent substances of lysozyme, and the quenching effect rose with increasing ILs concentration. Meanwhile, the interaction between lysozyme and ILs molecules is mainly based on Van der Waals force and two Tryptophan (Trp) residues (Trp62 or Trp108) at the active site of lysozyme molecules play a critical role in binding ILs to their own molecules.

Yeast arming systems: pros and cons of different protein anchors and other elements required for display

Yeast display is a powerful strategy that consists in exposing peptides or proteins of interest on the cell surface of this microorganism. Ever since initial experiments with this methodology were carried out, its scope has extended and many applications have been successfully developed in different science and technology fields. Several yeast display systems have been designed, which all involve introducting into yeast cells the gene fusions that contain the coding regions of a signal peptide, an anchor protein, to properly attach the target to the cell surface, and the protein of interest to be exposed, all of which are controlled by a strong promoter. In this work, we report the description of such elements for the alternative systems introduced by focusing particularly on anchor proteins. The comparisons made between them are included whenever possible, and the main advantages and inconveniences of each one are discussed. Despite the huge number of publications on yeast surface display and the revisions published to date, this topic has not yet been widely considered. Finally, given the growing interest in developing systems for non-Saccharomyces yeasts, the main strategies reported for some are also summarized.

Proteome-wide Identification of Novel Ceramide-binding Proteins by Yeast Surface cDNA Display and Deep Sequencing

Although the bioactive sphingolipid ceramide is an important cell signaling molecule, relatively few direct ceramide-interacting proteins are known. We used an approach combining yeast surface cDNA display and deep sequencing technology to identify novel proteins binding directly to ceramide. We identified 234 candidate ceramide-binding protein fragments and validated binding for 20. Most (17) bound selectively to ceramide, although a few (3) bound to other lipids as well. Several novel ceramide-binding domains were discovered, including the EF-hand calcium-binding motif, the heat shock chaperonin-binding motif STI1, the SCP2 sterol-binding domain, and the tetratricopeptide repeat region motif. Interestingly, four of the verified ceramide-binding proteins (HPCA, HPCAL1, NCS1, and VSNL1) and an additional three candidate ceramide-binding proteins (NCALD, HPCAL4, and KCNIP3) belong to the neuronal calcium sensor family of EF hand-containing proteins. We used mutagenesis to map the ceramide-binding site in HPCA and to create a mutant HPCA that does not bind to ceramide. We demonstrated selective binding to ceramide by mammalian cell-produced wild type but not mutant HPCA. Intriguingly, we also identified a fragment from prostaglandin D2synthase that binds preferentially to ceramide 1-phosphate. The wide variety of proteins and domains capable of binding to ceramide suggests that many of the signaling functions of ceramide may be regulated by direct binding to these proteins. Based on the deep sequencing data, we estimate that our yeast surface cDNA display library covers ∼60% of the human proteome and our selection/deep sequencing protocol can identify target-interacting protein fragments that are present at extremely low frequency in the starting library. Thus, the yeast surface cDNA display/deep sequencing approach is a rapid, comprehensive, and flexible method for the analysis of protein-ligand interactions, particularly for the study of non-protein ligands.