Single Protein Production Research Articles

Structural duality enables a single protein to act as a toxin–antidote pair for meiotic drive

In sexual reproduction, selfish genetic elements known as killer meiotic drivers (KMDs) bias inheritance by eliminating gametes that do not carry them. The selective killing behavior of most KMDs can be explained by a toxin-antidote model, where a toxin harms all gametes while an antidote provides resistance to the toxin in carriers. This study investigates whether and how the KMD element tdk1 in the fission yeast Schizosaccharomyces pombe deploys this strategy. Intriguingly, tdk1 relies on a single protein product, Tdk1, for both killing and resistance. We show that Tdk1 exists in a nontoxic tetrameric form during vegetative growth and meiosis but transforms into a distinct toxic form in spores. This toxic form acquires the ability to interact with the histone reader Bdf1 and assembles into supramolecular foci that disrupt mitosis in noncarriers after spore germination. In contrast, Tdk1 synthesized during germination of carrier spores is nontoxic and acts as an antidote, dismantling the preformed toxic Tdk1 assemblies. Replacement of the N-terminal region of Tdk1 with a tetramer-forming peptide reveals its dual roles in imposing an autoinhibited tetrameric conformation and facilitating the assembly of supramolecular foci when autoinhibition is released. Moreover, we successfully reconstituted a functional KMD element by combining a construct that exclusively expresses Tdk1 during meiosis ("toxin-only") with another construct that expresses Tdk1 specifically during germination ("antidote-only"). This work uncovers a remarkable example of a single protein employing structural duality to form a toxin-antidote pair, expanding our understanding of the mechanisms underlying toxin-antidote systems.

Producing recombinant proteins in Vibrio natriegens

The diversity of chemical and structural attributes of proteins makes it inherently difficult to produce a wide range of proteins in a single recombinant protein production system. The nature of the target proteins themselves, along with cost, ease of use, and speed, are typically cited as major factors to consider in production. Despite a wide variety of alternative expression systems, most recombinant proteins for research and therapeutics are produced in a limited number of systems: Escherichia coli, yeast, insect cells, and the mammalian cell lines HEK293 and CHO. Recent interest in Vibrio natriegens as a new bacterial recombinant protein expression host is due in part to its short doubling time of ≤ 10 min but also stems from the promise of compatibility with techniques and genetic systems developed for E. coli. We successfully incorporated V. natriegens as an additional bacterial expression system for recombinant protein production and report improvements to published protocols as well as new protocols that expand the versatility of the system. While not all proteins benefit from production in V. natriegens, we successfully produced several proteins that were difficult or impossible to produce in E. coli. We also show that in some cases, the increased yield is due to higher levels of properly folded protein. Additionally, we were able to adapt our enhanced isotope incorporation methods for use with V. natriegens. Taken together, these observations and improvements allowed production of proteins for structural biology, biochemistry, assay development, and structure-based drug design in V. natriegens that were impossible and/or unaffordable to produce in E. coli.

Protein-Specific Signal Peptides for Mammalian Vector Engineering.

Expression of recombinant proteins in mammalian cell factories relies on synthetic assemblies of genetic parts to optimally control flux through the product biosynthetic pathway. In comparison to other genetic part-types, there is a relative paucity of characterized signal peptide components, particularly for mammalian cell contexts. In this study, we describe a toolkit of signal peptide elements, created using bioinformatics-led and synthetic design approaches, that can be utilized to enhance production of biopharmaceutical proteins in Chinese hamster ovary cell factories. We demonstrate, for the first time in a mammalian cell context, that machine learning can be used to predict how discrete signal peptide elements will perform when utilized to drive endoplasmic reticulum (ER) translocation of specific single chain protein products. For more complex molecular formats, such as multichain monoclonal antibodies, we describe how a combination of in silico and targeted design rule-based in vitro testing can be employed to rapidly identify product-specific signal peptide solutions from minimal screening spaces. The utility of this technology is validated by deriving vector designs that increase product titers ≥1.8×, compared to standard industry systems, for a range of products, including a difficult-to-express monoclonal antibody. The availability of a vastly expanded toolbox of characterized signal peptide parts, combined with streamlined in silico/in vitro testing processes, will permit efficient expression vector re-design to maximize titers of both simple and complex protein products.

A New Role of Acute Phase Proteins: Local Production Is an Ancient, General Stress-Response System of Mammalian Cells.

The prevailing general view of acute-phase proteins (APPs) is that they are produced by the liver in response to the stress of the body as part of a systemic acute-phase response. We demonstrated a coordinated, local production of these proteins upon cell stress by the stressed cells. The local, stress-induced APP production has been demonstrated in different tissues (kidney, breast cancer) and with different stressors (hypoxia, fibrosis and electromagnetic heat). Thus, this local acute-phase response (APR) seems to be a universal mechanism. APP production is an ancient defense mechanism observed in nematodes and fruit flies as well. Local APP production at the tissue level is also supported by sporadic literature data for single proteins; however, the complex, coordinated, local appearance of this stress response has been first demonstrated only recently. Although a number of literature data are available for the local production of single acute-phase proteins, their interpretation as a local, coordinated stress response is new. A better understanding of the role of APPs in cellular stress response may also be of diagnostic/prognostic and therapeutic significance.

PEGylation and antioxidant effects of a human glutathione peroxidase 1 mutant.

Human glutathione peroxidase1 (hGPx1) is a good antioxidant and potential drug, but the limited availability and poor stability of hGPx1 have affected its development and application. To solve this problem, we prepared a hGPx1 mutant (GPx1M) with high activity in an Escherichia coli BL21(DE3)cys auxotrophic strain using a single protein production (SPP) system. In this study, the GPx1M was conjugated with methoxypolyethylene glycol-succinimidyl succinate (SS-mPEG, Mw = 5 kDa) chains to enhance its stability. SS-mPEG-GPx1M and GPx1M exhibited similar enzymatic activity and stability toward pH and temperature change, and in a few cases, SS-mPEG-GPx1M was discovered to widen the range of pH stability and increase the temperature stability. Lys 38 was confirmed as PEGylated site by liquid-mass spectrometry. H9c2 cardiomyoblast cells and Sprague-Dawley (SD) rats were used to evaluate the effects of GPx1M and SS-mPEG-GPx1M on preventing or alleviating adriamycin (ADR)-mediated cardiotoxicity, respectively. The results indicated that GPx1M and SS-mPEG-GPx1M had good antioxidant effects in vitro and in vivo, and the effect of SS-mPEG-GPx1M is more prominent than GPx1M in vivo. Thus, PEGylation might be a promising method for the application of GPx1M as an important antioxidant and potential drug.

Improvement of stability and in vivo antioxidant effect of human glutathione peroxidase mutant by PEGylation

Human glutathione peroxidase (GPx), as an important kind of antioxidant enzyme, is often used for the removal of reactive oxygen species. Unfortunately, the application has been hindered by its limited source and poor stability. To solve these problems, human glutathione peroxidase mutant (GPxM) with high activity and yield was obtained using Escherichia coli BL21(DE3) cys auxotrophic strain and the single-protein production system in our previous work. However, the antioxidant effect of this novel recombinant protein drug in animals has not been demonstrated, and its immunogenicity and short biological half-life as a biological macromolecule may have seriously hindered its clinical application. Therefore, it is important to find an effective strategy to address the above issues. In this work, PEGylated GPxM was prepared by conjugating the corresponding mutant with monomethoxy polyethylene glycol succinimidyl succinate (SS-mPEG). We researched the structure, stability, pharmacokinetic properties, antioxidant effect in vivo and protective mechanism against adriamycin (ADR)-mediated cardiotoxicity of modified products, and compared with the above properties of GPxM. The results revealed that GPxM had an excellent antioxidant effect in vivo, and PEGylation can enhance the stability, half-life and antioxidant effect of GPxM while reducing immunogenicity. In addition, the above improvement of PEGylated GPx1M was stronger than that of monoPEGylated GPx4M. Hence, PEGylation might be an effective method to broaden the applications of GPxM as the important antioxidant drug, especially the PEGylated GPx1M with high antioxidant effect.

Production of Recombinant PRMT Proteins using the Baculovirus Expression Vector System

Protein arginine methyltransferases (PRMTs) methylate arginine residues on a wide variety of proteins that play roles in numerous cellular processes. PRMTs can either mono- or dimethylate arginine guanidino groups symmetrically or asymmetrically. The enzymology of these proteins is a complex and intensely investigated area that requires milligram quantities of high-quality recombinant protein. The baculovirus expression vector system (BEVS) employing Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Spodoptera frugiperda 9 (Sf9) insect cells has been used for expression screening and production of many PRMTs, including PRMT 1, 2, and 4 through 9. To simultaneously screen for the expression of multiple constructs of these proteins, including domains and truncated fragments as well as the full-length proteins, we have applied scalable methods utilizing adjustable and programmable multichannel pipettes, combined with 24- and 96-well plates and blocks. Overall, these method adjustments enabled a large-scale generation of bacmid DNA, recombinant viruses, and protein expression screening. Using culture vessels with a high-fill volume of Sf9 cell suspension helped to overcome space limitations in the production pipeline for single batch large-scale protein production. Here, we describe detailed protocols for the efficient and cost-effective expression of functional PRMTs for biochemical, biophysical, and structural studies.

Production of Recombinant PRMT Proteins using the Baculovirus Expression Vector System.

Protein arginine methyltransferases (PRMTs) methylate arginine residues on a wide variety of proteins that play roles in numerous cellular processes. PRMTs can either mono- or dimethylate arginine guanidino groups symmetrically or asymmetrically. The enzymology of these proteins is a complex and intensely investigated area that requires milligram quantities of high-quality recombinant protein. The baculovirus expression vector system (BEVS) employing Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Spodoptera frugiperda 9 (Sf9) insect cells has been used for expression screening and production of many PRMTs, including PRMT 1, 2, and 4 through 9. To simultaneously screen for the expression of multiple constructs of these proteins, including domains and truncated fragments as well as the full-length proteins, we have applied scalable methods utilizing adjustable and programmable multichannel pipettes, combined with 24- and 96-well plates and blocks. Overall, these method adjustments enabled a large-scale generation of bacmid DNA, recombinant viruses, and protein expression screening. Using culture vessels with a high-fill volume of Sf9 cell suspension helped to overcome space limitations in the production pipeline for single batch large-scale protein production. Here, we describe detailed protocols for the efficient and cost-effective expression of functional PRMTs for biochemical, biophysical, and structural studies.

English

English

The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis.

Structural and biophysical characterization of molecular mechanisms of disease‐causing pathogens, such as Mycobacterium tuberculosis, often requires recombinant expression of large amounts highly pure protein. For the production of mycobacterial proteins, overexpression in the fast‐growing and non‐pathogenic species Mycobacterium smegmatis has several benefits over the standard Escherichia coli expression strains. However, unlike for E. coli, the range of expression vectors currently available is limited. Here we describe the development of the pMy vector series, a set of expression plasmids for recombinant production of single proteins and protein complexes in M. smegmatis. By incorporating an alternative selection marker, we show that these plasmids can also be used for co‐expression studies. All vectors in the pMy vector series are available in the Addgene repository (www.addgene.com).

Screening of 2A peptides for polycistronic gene expression in yeast.

A complexity of pathway expression in yeast compared to prokaryotes is the need for separate promoters and terminators for each gene expressed. Single transcript expression and separated protein production is possible via the use of 2A viral peptides, but detailed characterization to assess their suitability and applications is needed. The present work aimed to characterize multiple 2A peptide sequences to determine suitability for metabolic engineering applications in Saccharomyces cerevisiae. We screened 22 peptides placed between fluorescent protein sequences. Cleaving efficiency was calculated by western blot intensity of bands corresponding to the cleaved and uncleaved forms of the reporter. Three out of the 22 sequences showed high cleavage efficiency: 2A peptide from Equine rhinitis B virus (91%), Porcine teschovirus-1 (85%) and Operophtera brumata cypovirus-18 (83%). Furthermore, expression of the released protein was comparable to its monocistronic expression. As a proof-of-concept, the triterpene friedelin was successfully produced in the same yeast strain by expressing its synthase with the truncated form of HMG1 linked by the 2A peptide of ERBV-1, with production titers comparable to monocistronic expression (via separate promoters). These results suggest that these peptides could be suitable for expression and translation of multiple proteins in metabolic engineering applications in S. cerevisiae.

A novel 76-mer peptide mimic with the synergism of superoxide dismutase and glutathione peroxidase.

The balance of oxidation and reduction in the body requires the synergistic effect of various antioxidant enzymes. Therefore, the construction of enzyme mimics with multiple antioxidant activities is important and beneficial for further research on the synergistic effects of antioxidant enzymes and their mechanism of action. To explore the synergistic effect of superoxide dismutase (SOD) and glutathione peroxidase (GPx), a 76-mer selenium-containing peptide (Se-76P) mimic containing the active SOD and GPx centers was designed. Moreover, a cell-penetrating peptide was introduced into Se-76P by structure modeling, and then, Se-76P was expressed by a single-protein production combined with the cysteine auxotrophic double-expression system of Escherichia coli. The results suggest that Se-76P exhibits SOD and GPx activities, following the GPx activity of 109U/mg protein and the SOD activity of 1218U/mg protein. The labeled Se-76P with FITC fluorescence was verified to enter the L02 cells successfully; it improved the antioxidant activity in cells and promoted the consumption of glucose and synthesis of glycogen. The injection of Se-76P subcutaneously decreased the levels of blood glucose and malondialdehyde of lipid peroxidation produced in mice, indicating that Se-76P had antioxidative properties and a certain regulatory role of glucose metabolism. The data analysis provides further clarification that Se-76P can regulate insulin signal transduction to play an insulin-like role, which not only has a greater significance for further elucidating the catalytic mechanism of the enzyme and their synergistic effects on each other but also has enormous medicinal potential.

Reconstructing protein and gene phylogenies using reconciliation and soft-clustering.

The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on alternative protein isoforms. These methods often lead to inaccurate gene tree reconstructions that require to be corrected before phylogenetic analyses. Here, we propose a new approach for the reconstruction of gene trees and protein trees accounting for alternative protein isoforms. We extend the concept of reconciliation to protein trees, and we define a new reconciliation problem called MinDRGT that consists in finding a gene tree that minimizes a double reconciliation cost with a given protein tree and a given species tree. We define a second problem called MinDRPGT that consists in finding a protein supertree and a gene tree minimizing a double reconciliation cost, given a species tree and a set of protein subtrees. We propose a shift from the traditional view of protein ortholog groups as hard-clusters to soft-clusters and we study the MinDRPGT problem under this assumption. We provide algorithmic exact and heuristic solutions for versions of the problems, and we present the results of applications on protein and gene trees from the Ensembl database. The implementations of the methods are available at https://github.com/UdeS-CoBIUS/Protein2GeneTree and https://github.com/UdeS-CoBIUS/SuperProteinTree .

Expression and characterization of recombinant bifunctional enzymes with glutathione peroxidase and superoxide dismutase activities

To balance the production and decomposition of reactive oxygen species, living organisms have generated antioxidant enzymes and non-enzymatic antioxidant defense systems. Glutathione peroxidase (GPx) and superoxide dismutase (SOD) are two important antioxidant enzymes. Apart from their catalytic functions, they protect each other, resulting in more efficient removal of reactive oxygen species, protection of cells against injury, and maintenance of the normal metabolism of reactive oxygen species. SOD catalyzes the dismutation of the superoxide anion (O2•−) to oxygen (O2) and hydrogen peroxide (H2O2). H2O2 is then detoxified to water by GPx. In this study, human GPx1Ser and the Alvinella pompejana SOD (ApSOD) gene were used to design and generate several recombinant proteins with both GPx and SOD activities by combining traditional fusion protein technology, a cysteine auxotrophic expression system, and a single protein production (SPP) system. Among the fusion proteins, Se-hGPx1Ser-L-ApSOD exhibited the highest SOD and GPx activities. Additional research was conducted to better understand the properties of Se-hGPx1Ser-L-ApSOD. The synergism of Se-hGPx1Ser-L-ApSOD was evaluated by using an in vitro model. This research may facilitate future studies on the cooperation and catalytic mechanisms of GPx and SOD. We believe that the bifunctional enzyme has potential applications as a potent antioxidant.

Detection of recombinant human lactoferrin and lysozyme produced in a bitransgenic cow

Lactoferrin and lysozyme are 2 glycoproteins with great antimicrobial activity, being part of the nonspecific defensive system of human milk, though their use in commercial products is difficult because human milk is a limited source. Therefore, many investigations have been carried out to produce those proteins in biological systems, such as bacteria, yeasts, or plants. Mammals seem to be more suitable as expression systems for human proteins, however, especially for those that are glycosylated. In the present study, we developed a bicistronic commercial vector containing a goat β-casein promoter and an internal ribosome entry site fragment between the human lactoferrin and human lysozyme genes to allow the introduction of both genes into bovine adult fibroblasts in a single transfection. Embryos were obtained by somatic cell nuclear transfer, and, after 6 transferences to recipients, 3 pregnancies and 1 viable bitransgenic calf were obtained. The presence of the vector was confirmed by fluorescent in situ hybridization of skin cells. At 13 mo of life and after artificial induction of lactation, both recombinant proteins were found in the colostrum and milk of the bitransgenic calf. Human lactoferrin concentration in the colostrum was 0.0098 mg/mL and that in milk was 0.011 mg/mL; human lysozyme concentration in the colostrum was 0.0022 mg/mL and that in milk was 0.0024 mg/mL. The molar concentration of both human proteins revealed no differences in protein production of the internal ribosome entry site upstream and downstream protein. The enzymatic activity of lysozyme in the transgenic milk was comparable to that of human milk, being 6 and 10 times higher than that of bovine lysozyme present in milk. This work represents an important step to obtain multiple proteins or enhance single protein production by using animal pharming and fewer regulatory and antibiotic-resistant foreign sequences, allowing the design of humanized milk with added biological value for newborn nutrition and development. Transgenic animals can offer a unique opportunity to the dairy industry, providing starting materials suitable to develop specific products with high added value.

Cold-Shock Expression System in E. coli for Protein NMR Studies.

The cold-shock system using the pCold vector is one of the most effective Escherichia coli heterologous protein expression systems. It allows the improvement of the expression level of the protein of interest in a soluble fraction. In this chapter, we describe practical procedures for the overexpression of heterologous protein of interest by using the pCold vector or the single-protein production system. The latter is one of the most advanced pCold technologies for isotope labeling of the target protein and its NMR studies.

Suppression of the toxicity of Bac7 (1-35), a bovine peptide antibiotic, and its production in E. coli.

Bac7 (1–35) is an Arg- and Pro-rich peptide antibiotic, produced in bovine cells to protect them from microbial infection. It has been demonstrated to inhibit the protein synthesis in E. coli, leading to cell death. Because of its toxicity, no cost effective methods have been developed for Bac7 production in Escherichia coli for its potential clinical use. Here, we found a method to suppress Bac7 (1–35) toxicity in E. coli to establish its high expression system, in which Bac7 (1–35) was fused to the C-terminal end of protein S, a major spore-coat protein from Myxococcus xanthus, using a linker containing a Factor Xa cleavage site. The resulting His6-PrS2-Bac7 (1–35) (PrS2 is consisted of two N-terminal half domains of protein S connected in tandem) was well expressed using the Single-Protein Production (SPP) system at low temperature and subsequently purified in a single step by using a Ni column. The combination of protein S fusion and its expression in the SPP system at low temperature appeared to suppress Bac7 (1–35) toxicity. Both the purified His6-PrS2-Bac7 (1–35) and His6-PrS2-Bac7 (1–35) treated by Factor Xa were proven to be a potent inhibitor for cell-free protein synthesis.

박테리아의 toxin-antitoxin system과 생명공학기술 응용

Toxin-antitoxin (TA) systems are ubiquitous genetic modules that are evolutionally conserved in bacteria and archaea. TA systems composed of an intracellular toxin and its antidote (antitoxin) are currently classified into five types. Commonly, activation of toxins under stress conditions inhibits diverse cellular processes and consequently induces cell death or reversible growth inhibition. These effects of toxins play various physiological roles in such as regulation of gene expression, growth control (stress response), programmed cell arrest, persister cells, programmed cell death, phage protection, stabilization of mobile genetic elements or postsegregational killing of plasmid-free cells. Accordingly, bacterial TA systems are commonly considered as stress-responsive genetic modules. However, molecule screening for activation of toxin in TA system is available as development of antimicrobial agents. In addition, cytotoxic effect induced by toxin is used as effective cloning method with antitoxic effect of antitoxin; consequently cells containing cloning vector inserted a target gene can survive and false-positive transformants are removed. Also, TA system is applicable to efficient single protein production in biotechnology industry because toxins that are site-specific ribonuclease inhibit protein synthesis except for target protein. Furthermore, some TA systems that induce apoptosis in eukaryotic cells such as cancer cells or virus-infected cells would have a wide range of applications in eukaryotes, and it will lead to new ways of treating human disease. In this review, we summarize the current knowledge on bacterial TA systems and their applications.

T cell development is regulated by the coordinated function of two Lck promoters (IRM7P.701)

Abstract Lck is a T cell lineage-specific tyrosine kinase that is critical for T cell development and activation. Expression of an identical Lck protein can be mediated by two promoters, the proximal and distal lck promoters, but the function of these promoters during T cell development has not been directly assessed. We generated mutant mice by inactivating either one of the two lck promoters. Lck-PROX mice, in which only the proximal promoter is functional, had normal levels of Lck protein and thymic development through the CD4-CD8- double negative (DN) stage of T cell development, but reduced levels of Lck later in development and a dramatic reduction of mature single positive thymic T cells. In contrast, Lck-DIST mice, in which only the distal promoter was functional, were deficient in Lck and severely defective in early T cell development, with a block at the DN3 stage equivalent to the defect seen in complete Lck knockouts. Interestingly, the small number of peripheral T cells that developed in Lck-DIST mice expressed Lck protein and proliferated normally in response to TCR/CD3 cross-linking, while those of Lck-PROX mice were deficient in Lck and defective in response to TCR stimulation. These results define the coordinated requirements for proximal and distal lck promoters during T cell development and represent a unique direct demonstration of the requirement for alternative promoters in allowing developmental stage-specific regulation of a single protein product.

Characterization of recombinant human gastrointestinal glutathione peroxidase mutant produced in Escherichia coli

Gastrointestinal glutathione peroxidase (GI-GPx, GPx2) is a selenium-dependent enzyme and regarded as the first line of defense against oxidative stress caused by ingested pro-oxidants or gut microbes. As the essential part of the catalytic site of GPx2, selenocysteine (Sec) is encoded by an in-frame UGA stop codon, which makes the expression of human GPx2 (hGPx2) using traditional recombinant DNA technology difficult. In order to produce bioactive recombinant hGPx2, the gene of hGPx2 was designed with the conversion of the codons for four cysteine (Cys) residues to the codons for serine (Ser) residues and the codon for Sec-40 was changed to the codon for Cys. This recombinant seleno-hGPx2 mutant was obtained using a single protein production system in a cysteine (Cys) auxotrophic strain, in which Sec was introduced into the protein via tRNACys misleading. The activity of this mutant was in the same order of magnitude as that of hGPx4, but about one order of magnitude lower than that of hGPx1 and hGPx3. Further study showed that the mutant exhibited pH and temperature optima of 7.4 and 25°C, respectively. The results obtained from the kinetic analysis demonstrated that it followed a typical ping-pong mechanism similar to native GPx. As there was no report on the activity of purified GPx2, this research was valuable in recognizing native GPx2. In addition, a three-dimensional structure of seleno-hGPx2 mutant was constructed, which could facilitate further analysis of the role and the catalytic mechanism of native GPx2.