Several affinity tags commonly used in chromatographic purification

Synthesis of magnetic nanoparticles functionalized with histidine and nickel to immobilize His-tagged enzymes using β-galactosidase as a model

The aim of this study was to synthesize iron magnetic nanoparticles functionalized with histidine and nickel (Fe₃O₄-His-Ni) to be used as support materials for oriented immobilization of His-tagged recombinant enzymes of high molecular weight, using β-galactosidase as a model. The texture, morphology, magnetism, thermal stability, pH and temperature reaction conditions, and the kinetic parameters of the biocatalyst obtained were assessed. In addition, the operational stability of the biocatalyst in the lactose hydrolysis of cheese whey and skim milk by batch processes was also assessed. The load of 600 U_enzyme/g_support showed the highest recovered activity value (~50%). After the immobilization process, the recombinant β-galactosidase (HisGal) showed increased substrate affinity and greater thermal stability (~50×) compared to the free enzyme. The immobilized β-galactosidase was employed in batch processes for lactose hydrolysis of skim milk and cheese whey, resulting in hydrolysis rates higher than 50% after 15 cycles of reuse. The support used was obtained in the present study without modifying chemical agents. The support easily recovered from the reaction medium due to its magnetic characteristics. The iron nanoparticles functionalized with histidine and nickel were efficient in the oriented immobilization of the recombinant β-galactosidase, showing its potential application in other high-molecular-weight enzymes.

Efficient Molecular Biological Manipulations with Improved Strategies Based on Novel Escherichia coli Vectors

In this study, some novel plasmids have been constructed for flexible and zero-background molecular cloning, more efficient expression, and purification of proteins with improved strategies. The plasmids pANY4-pL18-ccdB and pANY4-pR18/pL18-ccdB have different promoters in the complementary DNA strands. Therefore, recombinant plasmids for either isopropyl-β-d-thiogalactoside-induced or temperature-induced protein expression could be simultaneously constructed in a single molecular cloning process for parallel comparison. Intriguingly, the mutated pL18 and pR18/pL18 promoters performed similar to or even better than the T7 promoter when used for promoting the expression of the GFP or pfLamA enzyme. Moreover, the plasmid pANY8 containing the His-elastin-like polypeptide (ELP)-intein multifunctional tag was constructed, and special purification protocol was designed to obtain purified proteins without the requirement of time-consuming dialysis steps to remove imidazole and high concentration of salt ions. Additionally, the urea-based denaturation and refolding processes can be conveniently integrated into the ELP-mediated precipitation protocol for purification of insoluble inclusion bodies, omitting the time-consuming dialysis steps.

Metal-Free Polymer-Based Affinity Medium for Selective Purification of His6-Tagged Proteins

We report a metal free synthetic hydrogel copolymer with affinity and selectivity for His6-tagged peptides and proteins. Small libraries of copolymers incorporating charged and hydrophobic functional groups were screened by an iterative process for His6 peptide affinity. The monomer selection was guided by interactions found in the crystal structure of an anti-His tag antibody-His6 peptide antigen complex. Synthetic copolymers incorporating a phenylalanine-derived monomer were found to exhibit strong affinity for both His6-containing peptides and proteins. The proximity of both aromatic and negatively charged functional groups were important factors for the His6 affinity of hydrogel copolymers. His6 affinity was not compromised by the presence of enzyme cleavage sequences. The His6-copolymer interactions are pH sensitive: the copolymer selectively captured His6 peptides at pH 7.8 while the interactions were substantially weakened at pH 8.6. This provided mild conditions for releasing His6-tagged proteins from the copolymer. Finally, a synthetic copolymer coated chromatographic medium was prepared and applied to the purification of a His6-tagged protein from an E. coli expression system. The results establish that a synthetic copolymer-based affinity medium can function as an effective alternative to immobilized metal ion columns for the purification of His6-tagged proteins.

Theoretical basis for stabilizing messenger RNA through secondary structure design

RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery, and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. These computational tests were carried out on both model mRNAs and COVID-19 mRNA vaccine candidates. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity, and their folding is robust to temperature, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1, and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.

Recombinant expression of HIV-1 protease using soluble fusion tags in Escherichia coli: A vital tool for functional characterization of HIV-1 protease

HIV-1 protease expression in the laboratory is demanding because of its high cytotoxicity, making it difficult to express in bacterial expression systems such as Escherichia coli. To overcome these challenges, HIV-1 protease fusion with solubility enhancing tags helps to mitigate its cytotoxic effect and drive its expression as a soluble protein. Therefore, this review focuses on the expression of bioactive HIV-1 protease using solubility-enhancing fusion tags in Escherichia coli and summarises the characteristic features of the different common fusion tags that have been used in the expression of HIV-1 protease. This review will assist researchers with their choice of protein fusion tag for HIV-1 protease expression.

Selective ene-reductase immobilization to magnetic nanoparticles through a novel affinity tag

BACKGROUND

Magnetic nanoparticles (MNPs) are becoming more important as carriers, because of their large specific surface area and easy separability. They are increasingly used in enzyme technology, diagnostics, and drug delivery.

MAJOR RESULTS

For the directed and almost irreversible immobilization of proteins on MNPs, we have developed a new selective (His-Arg)₄ peptide-tag, that binds fusion proteins directly from an E. coli cell lysate to non-functionalized, low-cost MNPs. Using the immobilization of an ene-reductase as an example, we could demonstrate that the fusion with this tag increases thermostability without reducing overall activity (ER w/o tag: t_1/2  = 3.7 h, (HR)₄ -ER: t_1/2  = 9.9 h). Immobilization by adsorption in Tris buffer resulted in very high enzyme loads with approx. 380 mg g^-1 and 67% residual activity. The immobilization on the MNPs allowed a fast concentration, buffer exchange, and reuse. While about 50% of the activity was lost after the first reuse, we were able to show that the activity did not decrease further and was stable for another nine cycles.

CONCLUSION

According to our studies, our tag highly works for any kind of immobilization on MNPs and holds the potential for enzyme immobilizations as well as for drug delivery and sensors.

Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry

Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.

Enhancing the promiscuity of a member of the Caspase protease family by rational design

The N-terminal cleavage of fusion tags to restore the native N-terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in-silico to yield enhanced promiscuity toward different N-terminal amino acids. Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease. These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations. The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results. Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids. We believe that the created mutants constitute an important step toward generalized procedures to restore original N-termini of recombinant fusion proteins.

The Activities of the Gelsolin Homology Domains of Flightless-I in Actin Dynamics

Flightless-I is a unique member of the gelsolin superfamily alloying six gelsolin homology domains and leucine-rich repeats. Flightless-I is an established regulator of the actin cytoskeleton, however, its biochemical activities in actin dynamics are still largely elusive. To better understand the biological functioning of Flightless-I we studied the actin activities of Drosophila Flightless-I by in vitro bulk fluorescence spectroscopy and single filament fluorescence microscopy, as well as in vivo genetic approaches. Flightless-I was found to interact with actin and affects actin dynamics in a calcium-independent fashion in vitro. Our work identifies the first three gelsolin homology domains (1–3) of Flightless-I as the main actin-binding site; neither the other three gelsolin homology domains (4–6) nor the leucine-rich repeats bind actin. Flightless-I inhibits polymerization by high-affinity (∼nM) filament barbed end capping, moderately facilitates nucleation by low-affinity (∼μM) monomer binding, and does not sever actin filaments. Our work reveals that in the presence of profilin Flightless-I is only able to cap actin filament barbed ends but fails to promote actin assembly. In line with the in vitro data, while gelsolin homology domains 4–6 have no effect on in vivo actin polymerization, overexpression of gelsolin homology domains 1–3 prevents the formation of various types of actin cables in the developing Drosophila egg chambers. We also show that the gelsolin homology domains 4–6 of Flightless-I interact with the C-terminus of Drosophila Disheveled-associated activator of morphogenesis formin and negatively regulates its actin assembly activity.

An ssDNA aptamer specific for detection and purification of hexahistidine-tagged proteins

Aptamers are small-sized RNA or ssDNA ligands with a unique structure, which have high specificity and affinity to their cognate targets. Thus, in addition to the extensive values in various bio-medical fields, aptamers can also be alternatively used as affinity ligands in the bioprocess, such as for protein purification. In the present study, a hexahistidine specific aptamer named AptHis-C, was developed through the SELEX methodology, which has high affinity to hexahistidine, and its dissociation constant was as low as 20.8 nM. The structural prediction revealed that AptHis-C contains two connected stem-loop conformations. AptHis-C can only specifically recognize recombinant proteins with the hexahistidine-tag in simple or complex situations, and not to those with other tags. When immobilized on magnetic beads, AptHis-C can be used as a tool for hexahistidine-tagged recombinant protein purification. Its effectiveness is as good as traditional Ni-based beads. Besides, due to the intrinsic characteristics of nucleic acids, such as high thermal/chemical stability, immobilized aptamer-magnetic beads can be reused many times without an obvious decrease of purification effectiveness. This aptamer may represent a novel method for the detection and purification of hexahistidine-tagged recombinant proteins.

Characterization of an anti-FLAG antibody binding protein in V. cholerae

FLAG-tags are commonly used for protein abundance measurements and for identification of protein-protein interactions in living cells. We have observed that the cholera pathogen Vibrio cholerae encodes a FLAG-antibody-reactive protein and identified this protein as an outer membrane porin, Porin4, which contains a sequence very similar to the 3xFLAG epitope tag. We have demonstrated the binding affinity of the conserved peptide sequence (called Porin 4 tag) in Porin4 against monoclonal anti-FLAG M2 antibody. In addition, we created a porin4 deletion mutant, which can be used for background-less FLAG antibody detection experiments.

A Biological and Immunological Characterization of Schistosoma Japonicum Heat Shock Proteins 40 and 90α

We characterized Schistosoma japonicum HSP40 (Sjp40) and HSP90α (Sjp90α) in this study. Western blot analysis revealed both are present in soluble egg antigens and egg secretory proteins, implicating them in triggering the host immune response after secretion from eggs into host tissues. These observations were confirmed by immunolocalization showing both HSPs are located in the Reynolds’ layer within mature eggs, suggesting they are secreted by miracidia and accumulate between the envelope and the eggshell. Both HSPs are present in the musculature and parenchyma of adult males and in the vitelline cells of females; only Sjp90α is present on the tegument of adults. Sjp40 was able to enhance the expression of macrophages, dendritic cells, and eosinophilic cells in mouse liver non-parenchymal cells, whereas rSjp90α only stimulated the expression of dendritic cells. T helper 1 (Th1), Th2, and Th17 responses were increased upon rSjp40 stimulation in vitro, but rSjp90 only stimulated an increased Th17 response. Sjp40 has an important role in reducing the expression of fibrogenic gene markers in hepatic stellate cells in vitro. Overall, these findings provide new information on HSPs in S. japonicum, improving our understanding of the pathological roles they play in their interaction with host immune cells.

Novel short peptide tag from a bacterial toxin for versatile applications

The specific recognition between a monoclonal antibody (mAb) and its epitope can be used in a tag system that has proved valuable in a wide range of biological applications. Herein, we describe a novel tag called RA-tag that is composed of a seven amino acid sequence (DIDLSRI) and recognized by a highly specific mAb, 47RA, against the bacterial toxin Vibrio vulnificus RtxA1/MARTX_Vv. By using recombinant proteins with the RA-tag at the N-terminal, C-terminal, or an internal site, we demonstrated that the tag system could be an excellent biological system for both protein purification and protein detection in enzyme-linked immunosorbent, Western blot, flow cytometry, and immunofluorescence staining analyses in Escherichia coli, mammalian cell lines, yeast, and plant. In addition, our RA-tag/47RA mAb combination showed high sensitivity and reliable affinity (K_D = 5.90 × 10^-8 M) when compared with conventional tags. Overall, our results suggest that the RA-tag system could facilitate the development of a broadly applicable tag system for biological research.

BioID Combined with Mass Spectrometry to Study Herpesvirus Protein-Protein Interaction Networks

Herpes viruses are important human pathogens that cause a wide range of diseases from skin lesions to malignancies. Protein interactions drive many cellular events and mediate a number of biochemical pathways leading to different physiological outcomes. Protein interactions between viral proteins and host proteins play significant roles in viral entry, replication and suppression of host-immune responses. Therefore, the study of virus-host interactions promises significant advancement in designing therapeutics to control infection and disease. Various approaches are employed in the field to study and identify protein interactions that combine affinity purification along with different detection methods. Advancements in protein purification and high-throughput detection methods have resulted in an unprecedented level of discovery. Here we detail the use of proximity dependent biotinylation (BioID) as a means of affinity purification coupled with the use of LC-MS/MS for the detection and identification of protein-protein interaction networks.

Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development

Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.

MS-based strategies for identification of protein SUMOylation modification

Protein SUMOylation modification conjugated with small ubiquitin-like modifiers (SUMOs) is one kind of PTMs, which exerts comprehensive roles in cellular functions, including gene expression regulation, DNA repair, intracellular transport, stress responses, and tumorigenesis. With the development of the peptide enrichment approaches and MS technology, more than 6000 SUMOylated proteins and about 40 000 SUMO acceptor sites have been identified. In this review, we summarize several popular approaches that have been developed for the identification of SUMOylated proteins in human cells, and further compare their technical advantages and disadvantages. And we also introduce identification approaches of target proteins which are co-modified by both SUMOylation and ubiquitylation. We highlight the emerging trends in the SUMOylation field as well. Especially, the advent of the clustered regularly interspaced short palindromic repeats/ Cas9 technique will facilitate the development of MS for SUMOylation identification.

Gluthathione S-transferase-resuscitation-promoting factor B recombinant protein of <em>Mycobacterium tuberculosis</em> induces the production of interferon-γ and interleukin-12 in mice splenocytes

BACKGROUND As the only TB vaccine available, Bacillus Calmette-Guérin shows variable efficacy in adults and does not provide protection against the resuscitation of latent TB infections. Resuscitation-promoting factor B (RpfB) is a protein produced by Mycobacterium tuberculosis during the resuscitation phase and is promising as a novel TB vaccine. This study was aimed to analyze the immunogenicity of the gluthathione S-transferase (GST)-RpfB recombinant protein on mice splenocytes in vitro.  METHODS After induction with isopropyl β-D-1-thiogalactopyranoside, the protein was extracted by sonication followed by solubilization in 8 M urea buffer. Protein was then re-natured and purified with a GST chromatography column. The isolated protein was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot using anti-GST antibodies, and its concentration was determined using the Bradford method. Each group of splenocytes was treated with 25 μg/ ml of the recombinant protein (GST-RpfB), GST, and phytohemagglutinin. Antigen induction was repeated twice at 24 and 72 hours. The supernatant was collected at 96 hours and interferon gamma (IFNγ), interleukin (IL-12, IL-4, and IL-10) levels were measured with enzyme-linked immunosorbent assays.  RESULTS GST-RpfB recombinant proteins were expressed in the form of inclusion bodies with a molecular weight of approximately 66 kDa. Based on the independent t-test, GST-RpfB stimulated IFNγ and IL-12 production but not IL-4 and IL-10.  CONCLUSIONS The GST-RpfB protein has been immunogenically proven and is a potential candidate as a novel subunit TB vaccine.

Emerging biomaterials for downstream manufacturing of therapeutic proteins

Downstream processing is considered one of the most challenging phases of industrial manufacturing of therapeutic proteins, accounting for a large portion of the total production costs. The growing demand for therapeutic proteins in the biopharmaceutical market in addition to a significant rise in upstream titers have placed an increasing burden on the downstream purification process, which is often limited by high cost and insufficient capacities. To achieve efficient production and reduced costs, a variety of biomaterials have been exploited to improve the current techniques and also to develop superior alternatives. In this work, we discuss the significance of utilizing traditional biomaterials in downstream processing and review the recent progress in the development of new biomaterials for use in protein separation and purification. Several representative methods will be highlighted and discussed in detail, including affinity chromatography, non-affinity chromatography, membrane separations, magnetic separations, and precipitation/phase separations. STATEMENT OF SIGNIFICANCE: Nowadays, downstream processing of therapeutic proteins is facing great challenges created by the rapid increase of the market size and upstream titers, starving for significant improvements or innovations in current downstream unit operations. Biomaterials have been widely used in downstream manufacturing of proteins and efforts have been continuously devoted to developing more advanced biomaterials for the implementation of more efficient and economical purification methods. This review covers recent advances in the development and application of biomaterials specifically exploited for various chromatographic and non-chromatographic techniques, highlighting several promising alternative strategies.

Enhancing the detection of Toxoplasma gondii via an anti-SAG1 scFv-alkaline phosphatase immunoconjugate

The purpose of this study was to implement a fluorometric method for enhancing the detection sensitivity of Toxoplasma gondii in biological fluids. To address this challenge, we designed and produced a recombinant immunoconjugate tool based on a single-chain antibody fragment anti-T. gondii SAG1 antigen (scFvSG15) genetically fused to the bacterial alkaline phosphatase (AP) using 4-methyl-umbelliferyl-phosphate as fluorogenic substrate. The anti-SAG1 scFv-AP conjugate was fully bifunctional and was used successfully in different assays including immunoblot, fluorometric ELISA and direct immunofluorescence. The fluorometric immunoassay afforded an extremely low detection limit (1 tachyzoite/well), which was in agreement with the real-time PCR control test. The immunofluorescence imaging has provided captivating visual evidence of T. gondii detection. These results strongly suggest that the recombinant anti-SAG1-AP conjugate generated here might serve as useful and highly sensitive immunoassay probe to direct detect T. gondii in a one-step procedure, opening up new perspectives for diagnosis of toxoplasmosis.

Enhancing chimeric hydrophobin II-vascular endothelial growth factor A165 expression in Pichia pastoris and its efficient purification using hydrophobin counterpart

We report cloning and expressing of recombinant human VEGF-A₁₆₅, fused at the N-terminal with Hydrophobin II (HFBII) from Trichoderma reseei, in yeast Pichia pastoris. We validated the construct using SDS-PAGE and ELISA against VEGF-A₁₆₅ and efficiently performed protein purification and enrichment based on HFBII counterpart and using an aqueous two-phase system (ATPS) with nonionic surfactant X-114. We studied the effects of various culture medium additives and interaction effects of positive factors to increase the recombinant HFBII-VEGF-A₁₆₅ production. Supplementing the Pichia pastoris cell culture medium with Mg²⁺, Polysorbate 20 (PS 20), and 4-phenylbutyrate (PBA) improved the expression of the chimeric protein. Orthogonal experiments showed that the optimal condition to achieve maximal HFBII-VEGF-A₁₆₅ production was with the addition of PBA, PS 20, and MgSO₄. Under this condition, the production of the target protein was 4.5 times more than that in the medium without the additives. Overall, our approach to produce chimeric HFBII-VEGF-A₁₆₅ and selectively capture it in ATPS is promising for large-scale protein production without laborious downstream processing.

Nanoparticle-supported temperature responsive polymer brushes for affinity separation of histidine-tagged recombinant proteins

We developed a modular approach for the preparation of nanoparticle-supported polymer brushes carrying repeating iminodiacetate units for affinity separation of histidine-tagged recombinant proteins. The nanoparticle-supported polymer brushes were prepared via the combination of surface-initiated atom transfer radical polymerization with Cu(I)-catalyzed azide-alkyne cycloaddition reaction. The nanocomposite materials were characterized to determine the particle size, morphology, organic content, densities of polymer chains and the affinity ligand. Protein binding assay illustrated that the iminodiacetate-rich polymer brushes enable to selectively bind histidine-tagged recombinant proteins in the presence of abundant interfering proteins. More importantly, the protein binding capacity can be tuned by adjusting the environmental temperature. STATEMENT OF SIGNIFICANCE: The nanoparticle core-polymer brush structure enables selective binding of histidine-tagged recombinant proteins via multiple metal-coordination interactions. The soft and flexible structure of the polymer brushes was found beneficial for lowering the steric hindrance in protein binding. Taking advantage of the conformational changes of the polymer brushes at different temperatures, it is possible to modulate the protein binding on the nanocomposite by adjusting the environmental temperature. In general, the iminodiacetate-rich core-brush nano adsorbents are attractive for purifying histidine-tagged recombinant proteins practically. The synthetic approach reported here may be expanded to develop other advanced functional materials for applications in various biomedical fields ranging from biosensors to drug delivery.

Improving an Escherichia coli-based biocatalyst for terpenol glycosylation by variation of the expression system

Glycosides are becoming increasingly more relevant for various industries as low-cost whole-cell-biocatalysts are now available for the manufacture of glycosides. However, there is still a need to optimize the biocatalysts. The aim of this work was to increase the titre of terpenyl glucosides in biotransformation assays with E. coli expressing VvGT14ao, a glycosyltransferase gene from grape (Vitis vinifera). Seven expression plasmids differing in the resistance gene, origin of replication, promoter sequence, and fusion protein tag were generated and transformed into four different E. coli expression strains, resulting in 18 strains that were tested for glycosylation efficiency with terpenols and a phenol. E. coli BL21(DE3)/pET-SUMO_VvGT14ao yielded the highest titres. The product concentration was improved 8.6-fold compared with E. coli BL21(DE3)pLysS/pET29a_VvGT14ao. The selection of a small solubility-enhancing protein tag and exploitation of the T7 polymerase-induction system allowed the formation of increased levels of functional recombinant protein, thereby improving the performance of the whole-cell biocatalyst.

Pick a Tag and Explore the Functions of Your Pet Protein

Protein tags have been essential for advancing our knowledge of the function of proteins, their localization, and the mapping of their interaction partners. Expressing epitope-tagged proteins has become a standard practice in every life science laboratory and, thus, continues to enable new studies. In recent years, several new tagging moieties have entered the limelight, many of them bringing new functionalities, such as targeted protein degradation, accurate quantification, and proximity labeling. Other novel tags aim at tackling research questions in challenging niches. In this review, we elaborate on recently introduced tags and the opportunities they provide for future research endeavors. In addition, we highlight how the genome-engineering revolution may boost the field of protein tags.

Spy&Go purification of SpyTag-proteins using pseudo-SpyCatcher to access an oligomerization toolbox

Peptide tags are a key resource, introducing minimal change while enabling a consistent process to purify diverse proteins. However, peptide tags often provide minimal benefit post-purification. We previously designed SpyTag, forming an irreversible bond with its protein partner SpyCatcher. SpyTag provides an easy route to anchor, bridge or multimerize proteins. Here we establish Spy&Go, enabling protein purification using SpyTag. Through rational engineering we generated SpyDock, which captures SpyTag-fusions and allows efficient elution. Spy&Go enabled sensitive purification of SpyTag-fusions from Escherichia coli, giving superior purity than His-tag/nickel-nitrilotriacetic acid. Spy&Go allowed purification of mammalian-expressed, N-terminal, C-terminal or internal SpyTag. As an oligomerization toolbox, we established a panel of SpyCatcher-linked coiled coils, so SpyTag-fusions can be dimerized, trimerized, tetramerized, pentamerized, hexamerized or heptamerized. Assembling oligomers for Death Receptor 5 stimulation, we probed multivalency effects on cancer cell death. Spy&Go, combined with simple oligomerization, should have broad application for exploring multivalency in signaling.

Development of a Phage Display Panning Strategy Utilizing Crude Antigens: Isolation of MERS-CoV Nucleoprotein human antibodies

Antibody phage display has been pivotal in the quest to generate human monoclonal antibodies for biomedical and research applications. Target antigen preparation is a main bottleneck associated with the panning process. This includes production complexity, downstream purification, quality and yield. In many instances, purified antigens are preferred for panning but this may not be possible for certain difficult target antigens. Here, we describe an improved procedure of affinity selection against crude or non-purified antigen by saturation of non-binders with blocking agents to promote positive binder enrichment termed as Yin-Yang panning. A naïve human scFv library with kappa light chain repertoire with a library size of 109 was developed. The improved Yin-Yang biopanning process was able to enrich monoclonal antibodies specific to the MERS-CoV nucleoprotein. Three unique monoclonal antibodies were isolated in the process. The Yin-Yang biopanning method highlights the possibility of utilizing crude antigens for the isolation of monoclonal antibodies by phage display.

Purification of proteins with native terminal sequences using a Ni(II)-cleavable C-terminal hexahistidine affinity tag

The role of the termini of protein sequences is often perturbed by remnant amino acids after the specific protease cleavage of the affinity tags and/or by the amino acids encoded by the plasmid at/around the restriction enzyme sites used to insert the genes. Here we describe a method for affinity purification of a metallonuclease with its precisely determined native termini. First, the gene encoding the target protein is inserted into a newly designed cloning site, which contains two self-eliminating BsmBI restriction enzyme sites. As a consequence, the engineered DNA code of Ni(II)-sensitive Ser-X-His-X motif is fused to the 3'-end of the inserted gene followed by the gene of an affinity tag for protein purification purpose. The C-terminal segment starting from Ser mentioned above is cleaved off from purified protein by a Ni(II)-induced protease-like action. The success of the purification and cleavage was confirmed by gel electrophoresis and mass spectrometry, while structural integrity of the purified protein was checked by circular dichroism spectroscopy. Our new protein expression DNA construct is an advantageous tool for protein purification, when the complete removal of affinity or other tags, without any remaining amino acid residue is essential. The described procedure can easily be generalized and combined with various affinity tags at the C-terminus for chromatographic applications.

An efficient and quantitative assay for epitope-tagged therapeutic protein development with a capillary western system

Aim: To develop and validate a reliable, robust and efficient assay to detect and quantify biologic compounds in vitro and in vivo during early stage of a biotherapeutic agent discovery. Methodology & results: An enrichment-free immunoassay method was developed to quantify a polyhistidine N- and FLAG C-terminally-tagged recombinant protein of ∼55 kDa. The target proteins were purified by a nickel-based matrix via tag affinity, followed by probing with biotinylated antitag antibody and subsequently detected by streptavidin-horseradish peroxidase conjugate using an automated capillary-based western system. Conclusion: A simple, highly sensitive and efficient immunoassay protocol was established to assess the in vitro stability and pharmacokinetic properties of propitious recombinant proteins in vivo in mouse to support early stage development of a biotherapeutic lead.

Self-Immobilizing Biocatalysts Maximize Space–Time Yields in Flow Reactors

Maximizing space–time yields (STY) of biocatalytic flow processes is essential for the establishment of a circular biobased economy. We present a comparative study in which different biocatalytic flow reactor concepts were tested with the same enzyme, the (R)-selective alcohol dehydrogenase from Lactobacillus brevis (LbADH), that was used for stereoselective reduction of 5-nitrononane-2,8-dione. The LbADH contained a genetically encoded streptavidin (STV)-binding peptide to enable self-immobilization on STV-coated surfaces. The purified enzyme was immobilized by physisorption or chemisorption as monolayers on the flow channel walls, on magnetic microbeads in a packed-bed format, or as self-assembled all-enzyme hydrogels. Moreover, a multilayer biofilm with cytosolic-expressed LbADH served as a whole-cell biocatalyst. To enable cross-platform comparison, STY values were determined for the various reactor modules. While mono- and multilayer coatings of the reactor surface led to STY < 10, higher productivity was achieved with packed-bed reactors (STY ≈ 100) and the densely packed hydrogels (STY > 450). The latter modules could be operated for prolonged times (>6 days). Given that our approach should be transferable to other enzymes, we anticipate that compartmentalized microfluidic reaction modules equipped with self-immobilizing biocatalysts would be of great utility for numerous biocatalytic and even chemo-enzymatic cascade reactions under continuous flow conditions.

In-plate recapturing of a dual-tagged recombinant Fasciola antigen (FhLAP) by a monoclonal antibody (US9) prevents non-specific binding in ELISA

Recombinant proteins expressed in E. coli are frequently purified by immobilized metal affinity chromatography (IMAC). By means of this technique, tagged proteins containing a polyhistidine sequence can be obtained up to 95% pure in a single step, but some host proteins also bind with great affinity to metal ions and contaminate the sample. A way to overcome this problem is to include a second tag that is recognized by a preexistent monoclonal antibody (mAb) in the gene encoding the target protein, allowing further purification. With this strategy, the recombinant protein can be directly used as target in capture ELISA using plates sensitized with the corresponding mAb. As a proof of concept, in this study we engineered a Trichinella-derived tag (MTFSVPIS, recognized by mAb US9) into a His-tagged recombinant Fasciola antigen (rFhLAP) to make a new chimeric recombinant protein (rUS9-FhLAP), and tested its specificity in capture and indirect ELISAs with sera from sheep and cattle. FhLAP was selected since it was previously reported to be immunogenic in ruminants and is expressed in soluble form in E. coli, which anticipates a higher contamination by host proteins than proteins expressed in inclusion bodies. Our results showed that a large number of sera from non-infected ruminants (mainly cattle) reacted in indirect ELISA with rUS9-FhLAP after single-step purification by IMAC, but that this reactivity disappeared testing the same antigen in capture ELISA with mAb US9. These results demonstrate that the 6XHis and US9 tags can be combined when double purification of recombinant proteins is required.

A Brief Reminder of Systems of Production and Chromatography-Based Recovery of Recombinant Protein Biopharmaceuticals

Recombinant proteins are produced for various applications in laboratory and industrial settings. Among them, therapeutic applications have evolved into a mature field in recent years, affecting the face of contemporary medical treatment. This, in turn, has stimulated an ever-greater need for innovative technologies for the description, expression, and purification of recombinant protein biopharmaceuticals. Therefore, many biopharmaceuticals are synthesized in heterologous systems to obtain satisfactory yields that cannot be provided by natural sources. As more than 35 years has passed since the first recombinant biopharmaceutical (human insulin) successfully completed clinical trials in humans, we provide a brief review of the available prokaryotic and eukaryotic expression systems, listing the advantages and disadvantages of their use. Some examples of therapeutic proteins expressed in heterologous hosts are also provided. Moreover, technologies for the universal extraction of protein molecules are mentioned here, as is the methodology of their purification.

Non-chromatographic purification of Teriparatide with a pH-responsive CspB tag

Cell surface protein B (CspB) from Corynebacterium glutamicum is used as a pH-responsive peptide tag to enable a simple solid-liquid separation method for isolating a CspB fusion protein. Here we demonstrate the first application of a CspB tag for the purification of Teriparatide, which is a biologic drug that is prescribed for osteoporosis. The Teriparatide was constructed as CspB50TEV-Teriparatide, comprising 50 amino acid residues of CspB, the cleavage site of TEV protease, and Teriparatide. CspB50TEV-Teriparatide was expressed in a culture supernatant by C. glutamicum secretion system at 3.0 g/L (equivalent to approximately 1.2 g/L Teriparatide). The CspB50TEV-Teriparatide was precipitated by reducing the pH of the culture supernatant, and the precipitate was then dissolved in a neutral buffer. A TEV protease treatment was applied to cleave the Teriparatide from the CspB50TEV-Teriparatide. Then, the remaining digested CspB50TEV, undigested CspB50TEV-Teriparatide, and TEV protease were precipitated in an acidic pH, whereas the soluble Teriparatide remained in the supernatant. The process had a yield of 96.5% and resulted in Teriparatide with a purity of 98.0% and productivity of 1.1 g/L of C. glutamicum culture. Thus, tag-free Teriparatide was successfully purified from the CspB fusion protein using only pH changes, centrifugation, and protease digestion without the need for chromatography. This versatile purification protocol is expected to be applicable to various proteins from laboratory to industrial scales.

Role of Ca2+ in Mediating Plant Responses to Extracellular ATP and ADP

Among the most recently discovered chemical regulators of plant growth and development are extracellular nucleotides, especially extracellular ATP (eATP) and extracellular ADP (eADP). Plant cells release ATP into their extracellular matrix under a variety of different circumstances, and this eATP can then function as an agonist that binds to a specific receptor and induces signaling changes, the earliest of which is an increase in the concentration of cytosolic calcium ([Ca2+]cyt). This initial change is then amplified into downstream-signaling changes that include increased levels of reactive oxygen species and nitric oxide, which ultimately lead to major changes in the growth rate, defense responses, and leaf stomatal apertures of plants. This review presents and discusses the evidence that links receptor activation to increased [Ca2+]cyt and, ultimately, to growth and diverse adaptive changes in plant development. It also discusses the evidence that increased [Ca2+]cyt also enhances the activity of apyrase (nucleoside triphosphate diphosphohydrolase) enzymes that function in multiple subcellular locales to hydrolyze ATP and ADP, and thus limit or terminate the effects of these potent regulators.

A Novel Method of Affinity Tag Cleavage in the Purification of a Recombinant Thermostable Lipase from Aneurinibacillus thermoaerophilus Strain HZ

The development of an efficient and economical purification method is required to obtain a pure and mature recombinant protein in a simple process with high efficiency. Hence, a new technique was invented to cleave the tags from the N-terminal region of recombinant fusion HZ lipase in the absence of protease treatment. The recombinant pET32b/rHZ lipase was overexpressed into E. coli BL21 (DE3). Affinity chromatography was performed as the first step of purification. The stability of the protein was then tested in different temperatures. The fused Trx-His-S-tags to the rHZ lipase was cleaved by treatment of the fusion protein at 20 °C in 100 mM Tris-HCl buffer, pH 8.0. The precipitated tag was removed, and the mature recombinant enzyme was further characterized to specify its properties. A purification yield of 78.9% with 1.3-fold and 21.8 mg total purified mature protein was obtained from 50 mL starting a bacterial culture. N-terminal sequencing of purified recombinant HZ lipase confirmed the elimination of the 17.4 kDa tag from one amino acid before the native start codon (Methionine) of the protein. The mature rHZ lipase was highly active at 65 °C and a pH of 7.0, with a half-life of 2 h 15 min at 55 °C and 45 min at 60 °C. The rHZ lipase showed a preference for the hydrolysis of natural oil with a long carbon chain (C18) and medium-size acyl chain p-nitrophenyl esters (C10). The enzyme remained stable in the presence of nonpolar organic solvents, and its activity was increased by polar organic solvents. This study thus demonstrates a simple and convenient purification method which resulted in the high yield of mature enzyme along with unique and detailed biochemical characterization of rHZ lipase, making the enzyme favorable in various industrial applications.

Pull-down Assay on Streptavidin Beads and Surface Plasmon Resonance Chips for SWATH-MS-based Interactomics

BACKGROUND/AIM

Pul-down assay is a popular in vitro method for identification of physical interactors of selected proteins. Here, for the first time, we compared three conventional variants of pull-down assay with the streptavidin-modified surface plasmon resonance (SPR) chips for the detection of PDZ and LIM domain protein 2 (PDLIM2) interaction partners.

MATERIALS AND METHODS

PDLIM2 protein-protein interactions were analysed by three variants of pull-down assay on streptavidin beads using LC-MS/MS in "Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH)" mode and compared with LC-SWATH-MS/MS data from SPR chips.

RESULTS

The results showed that (i) the use of SPR chip led to comparable data compared to on-column streptavidin beads, (ii) gravity flow and microflow in wash and elution steps provided better results than centrifugation, and (iii) type and concentration of detergent did not significantly affect the interactome data of cancer-associated PDLIM2.

CONCLUSION

Our study supports further application of SPR-based affinity purification with SWATH mass spectrometry for reproducible and controlled characterization of cancer-associated interactomes.

Nonantioxidant Tetramethoxystilbene Abrogates α-Synuclein-Induced Yeast Cell Death but Not That Triggered by the Bax or βA4 Peptide

The overexpression of α-synuclein (α-syn) and its aggregation is the hallmark of Parkinson's disease. The α-syn aggregation results in the formation of Lewy bodies that causes neuronal cell death. Therefore, the small molecules that can protect neuronal cells from α-syn toxicity or inhibit the aggregation of α-syn could emerge as anti-Parkinson agents. Herein, a library of methoxy-stilbenes was screened for their ability to restore the cell growth from α-syn toxicity, using a yeast strain that stably expresses two copies of a chromosomally integrated human α-syn gene. Tetramethoxy-stilbene 4s, a nonantioxidant, was the most capable of restoring cell growth. It also rescues the more toxic cells that bear three copies of wild-type or A53T-mutant α-syn, from cell growth block. Its EC₅₀ values for growth restoration of the 2-copy wild-type and the 3-copy mutant α-syn strains are 0.95 and 0.35 μM, respectively. Stilbene 4s mitigates mitochondrial membrane potential loss, negates ROS production, and prevents nuclear DNA-fragmentation, all hallmarks of apoptosis. However, 4s does not rescue cells from the death-inducing effects of Bax and βA4, which suggest that 4s specifically inhibits α-syn-mediated toxicity in the yeast. Our results signify that simultaneous use of multiple yeast-cell-based screens can facilitate revelation of compounds that may have the potential for further investigation as anti-Parkinson's agents.

Heterologous Biosynthesis of the Fungal Sesquiterpene Trichodermol in Saccharomyces cerevisiae

Trichodermol, a fungal sesquiterpene derived from the farnesyl diphosphate pathway, is the biosynthetic precursor for trichodermin, a member of the trichothecene class of fungal toxins produced mainly by the genera of Trichoderma and Fusarium. Trichodermin is a promising candidate for the development of fungicides and antitumor agents due to its significant antifungal and cytotoxic effects. It can also serve as a scaffold to generate new congeners for structure-activity relationship (SAR) study. We reconstructed the biosynthetic pathway of trichodermol in Saccharomyces cerevisiae BY4741, and investigated the effect of produced trichodermol on the host by de novo RNA sequencing (RNA-Seq) and quantitative Real-time PCR analyses. Co-expression of pESC::FgTRI5 using plasmid pLLeu-tHMGR-UPC2.1 led to trichodiene production of 683 μg L^-1, while integration of only the codon-optimized FgTRI5 into the chromosome of yeast improved the production to 6,535 μg L^-1. Subsequent expression of the codon-optimized cytochrome P450 monooxygenase encoding genes, TaTRI4 and TaTRI11, resulted in trichodermol, with an estimated titer of 252 μg L^-1 at shake flask level. RNA-Seq and qPCR analyses revealed that the produced trichodermol downregulated the expression of the genes involved in ergosterol biosynthesis, but significantly upregulated the expression of PDR5 related to membrane transport pathway in S. cerevisiae. Collectively, we achieved the first heterologous biosynthesis of trichodermol by reconstructing its biosynthetic pathway in yeast, and the reconstructed pathway will serve as a platform to generate trichodermin analogs as potential candidates for agrochemicals and anticancer agents through further optimizations.

Purification of Antibacterial CHAPK Protein Using a Self-Cleaving Fusion Tag and Its Activity Against Methicillin-Resistant Staphylococcus aureus

Therapeutic LysK-CHAP is a potent anti-staphylococcal protein that could be utilized as an antibiotic substitute. Intein-mediated protein purification is a reasonable and cost-effective method that is most recently used for recombinant therapeutic protein production. Intein (INT) is the internal parts of the protein that can be separated from the immature protein during protein splicing process. This sequence requires no specific enzyme or cofactor for separation. INT sequence and their characteristic of self-cleavage by thiol induction, temperature, and pH changes are used for protein purification. The current study presents the expression of CHAP_K262 domain of LysK gene that is fused with INT/chitin-binding sequence while evaluating its purification procedure and antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). The coding gene sequence of LysK-CHAP (CHAP_K262) in pET22-b was amplified with polymerase chain reaction (PCR); the digested product was then cloned into the pTXB1 vector. Electrophoresis confirmed the cloning accuracy of the gene. The pTXB1-CHAP_K262 plasmid was transformed to the Escherichia coli ER₂₅₆₆ (E. coli ER₂₅₆₆) expression strain and analyzed for expression of the recombinant protein by SDS-PAGE and Western blotting methods. Finally, CHAP_K262 was purified by chitin affinity column using INT tag technology and confirmed by SDS-PAGE. Lytic activity of the purified protein was investigated by disk diffusion method. Cloning of CHAP_K262 into the pTXB1 vector, which comprised INT/chitin-binding sequence, was successfully achieved. The SDS-PAGE data also revealed successful expression of the CHAP_K262-INT fusion protein and Western blotting method validated the accuracy of the protein. Moreover, purification of CHAP_K262 protein was induced by dithiothreitol (DTT) and confirmed by SDS-PAGE. Finally, inhibition zone in MRAS culture medium confirmed antibacterial activity of the protein. Application of intein-mediated antibacterial protein is an appropriate and streamlined method for one-step purification of CHAP_K262 as a therapeutic and antibacterial protein. Self-cleaving tags like intein are cost-effective and could be used as a proper purification method for industrial purposes.

Enhanced stability of a chimeric hepatitis B core antigen virus-like-particle (HBcAg-VLP) by a C-terminal linker-hexahistidine-peptide

BACKGROUND

Virus-like-particles (VLPs) are attractive nanoparticulate scaffolds for broad applications in material/biological sciences and medicine. Prior their functionalization, specific adaptations have to be carried out. These adjustments frequently lead to disordered particles, but the particle integrity is an essential factor for the VLP suitability. Therefore, major requirements for particle stabilization exist. The objective of this study was to evaluate novel stabilizing elements for functionalized chimeric hepatitis B virus core antigen virus-like particles (HBcAg-VLP), with beneficial characteristics for vaccine development, imaging or delivery.

RESULTS

The effects of a carboxy-terminal polyhistidine-peptide and an intradimer disulfide-bridge on the stability of preclinically approved chimeric HBcAg-VLPs were assessed. We purified recombinant chimeric HBcAg-VLPs bearing different modified C-termini and compared their physical and chemical particle stability by quantitative protein-biochemical and biophysical techniques. We observed lower chemical resistance of T = 3- compared to T = 4-VLP (triangulation number) capsids and profound impairment of accessibility of hexahistidine-peptides in assembled VLPs. Histidines attached to the C-terminus were associated with superior mechanical and/or chemical particle stability depending on the number of histidine moieties. A molecular modeling approach based on cryo-electron microscopy and biolayer interferometry revealed the underlying structural mechanism for the strengthening of the integrity of VLPs. Interactions triggering capsid stabilization occur on a highly conserved residue on the basis of HBcAg-monomers as well as on hexahistidine-peptides of adjacent monomers. This new stabilization mechanism appears to mimic an evolutionary conserved stabilization concept for hepadnavirus core proteins.

CONCLUSIONS

These findings establish the genetically simply transferable C-terminal polyhistidine-peptide as a general stabilizing element for chimeric HBcAg-VLPs to increase their suitability.

High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives

The ease of genetic manipulation, low cost, rapid growth and number of previous studies have made Escherichia coli one of the most widely used microorganism species for producing recombinant proteins. In this post-genomic era, challenges remain to rapidly express and purify large numbers of proteins for academic and commercial purposes in a high-throughput manner. In this review, we describe several state-of-the-art approaches that are suitable for the cloning, expression and purification, conducted in parallel, of numerous molecules, and we discuss recent progress related to soluble protein expression, mRNA folding, fusion tags, post-translational modification and production of membrane proteins. Moreover, we address the ongoing efforts to overcome various challenges faced in protein expression in E. coli, which could lead to an improvement of the current system from trial and error to a predictable and rational design.