Modified uvsY by N-terminal hexahistidine tag addition enhances efficiency of recombinase polymerase amplification to detect SARS-CoV-2 DNA

Terminator: A Software Package for Fast and Local Optimization of His-Tag Placement for Protein Affinity Purification

Although the use of affinity tags can greatly improve purification of expressed enzymes, the placement of affinity tags can significantly impact the expression, solubility, and function of recombinant proteins. To facilitate the optimal design of 6xHis-tagged constructs for protein purification, we developed Terminator, a Python-based software package, which takes a UniProt ID or existing protein sequence as input, identifies related sequences, maps sequence conservation retrieved from ConSurf onto protein 3D structures retrieved from the PDB and SWISS-MODEL, and analyzes proximity to cavities and functional sites to recommend the N- or C-terminus for placement of 6xHis fusion tags <15 residues in length. The package also outputs a document with available purification and activity literature for the target and closely related proteins organized by year. Comparative analysis of Terminator predictions against published experimental tag behavior for 6xHis fusion tags <15 residues in length demonstrates an 86-100% accuracy in predicting the relative risk of ill effects between termini and a 92-93% accuracy in predicting the absolute risk of modifying individual termini. This reliability of Terminator's analysis suggests that proximity to surface cavities, not burial of wild-type termini, is the most reliable predictor of ill effects arising from short 6xHis fusion tags. This tool aims to expedite construct design and enhance the successful production of well-behaved proteins for studies in enzymology and biocatalysis with minimal need for computational resources, programming knowledge, or familiarity with protein-tag interference mechanisms.

Rapid detection assays for Bacillus anthracis, Yersinia pestis, and Brucella spp. via triplex-recombinase polymerase amplification

BACKGROUND

Bacillus anthracis (B. anthracis), Yersinia pestis (Y. pestis), and Brucella spp. are zoonotic bacteria that cause anthrax, plague, and brucellosis, respectively. Outbreaks typically occur in remote regions with poor transportation and limited laboratory testing. Therefore, a simple, sensitive, multiplex nucleic acid detection method is essential for effective disease management and control.

METHODS

Primers and probes for the three pathogens were designed to reduce interference from related strains. Three recombinase polymerase amplification (RPA) reactions were conducted at 39 °C for 10 min to produce species-specific fluorescence signals for the three pathogens. These were integrated, and conditions were optimized for rapid, sensitive triplex-RPA assays without cross-reactivity. A triplex-RPA reaction with lateral flow dipsticks (LFDs) was developed and applied to blood samples, newly isolated strains, and simulated samples.

RESULTS

Highly sensitive and specific primers and probes were developed, achieving a maximum sensitivity of 1 copy/µL in single-reaction RPA. The optimized triplex RPA detection technique, combined with fluorescence, effectively identified B. anthracis, Y. pestis, and Brucella spp. within 20 min, whereas LFDs achieved detection in 10 min. The assay also performed comparably to conventional polymerase chain reaction techniques when tested on blood samples, newly isolated strains, and simulated samples.

CONCLUSIONS

This study offers reliable methods for detecting B. anthracis, Y. pestis, and Brucella spp. in rural hospitals and public health initiatives.

Achieving unprecedented stability in lyophilized recombinase polymerase amplification with thermostable pyruvate kinase from Thermotoga maritima

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. Considering the onsite use of RPA reagents, lyophilized RPA reagents with long storage stability are highly desired. In this study, as one of the approaches to solve this problem, we attempted to use a thermostable pyruvate kinase (PK). PK gene was isolated from a thermophilic bacterium Thermotoga maritima (Tma-PK). Tma-PK was expressed in Escherichia coli and purified from the cells. Tma-PK exhibited higher thermostability than human PK. The purified Tma-PK preparation was applied to RPA as an ATP-regenerating enzyme. Liquid RPA reagent with Tma-PK exhibited the same performance as that with human PK. Lyophilized RPA reagent with Tma-PK exhibited higher performance than that with human PK. Combined with our previous results of RPA reagents of thermostable Pol from a thermophilic bacterium, Aeribacillus pallidus, the results in this study suggest that thermostable enzymes are preferable to mesophilic ones as a component in lyophilized RPA reagents.

Increase in the solubility of uvsY using a site saturation mutagenesis library for application in a lyophilized reagent for recombinase polymerase amplification

BACKGROUND

Recombinase uvsY from bacteriophage T4, along with uvsX, is a key enzyme for recombinase polymerase amplification (RPA), which is used to amplify a target DNA sequence at a constant temperature. uvsY, though essential, poses solubility challenges, complicating the lyophilization of RPA reagents. This study aimed to enhance uvsY solubility.

METHODS

Our hypothesis centered on the C-terminal region of uvsY influencing solubility. To test this, we generated a site-saturation mutagenesis library for amino acid residues Lys91-Glu134 of the N-terminal (His)6-tagged uvsY.

RESULTS

Screening 480 clones identified A116H as the variant with superior solubility. Lyophilized RPA reagents featuring the uvsY variant A116H demonstrated enhanced performance compared to those with wild-type uvsY.

CONCLUSIONS

The uvsY variant A116H emerges as an appealing choice for RPA applications, offering improved solubility and heightened lyophilization feasibility.

Soluble expression and purification of recombinant bovine ferritin H-chain

Ferritin is a potential medicine delivery vehicle and vaccine platform, and its efficient expression is a prerequisite for widespread application. This study introduces a soluble expression strategy for recombinant bovine ferritin heavy chain (rFTH) in a prokaryotic system and an improved protein purification method. The amplified rFTH gene was ligated into the prokaryotic expression vector pET30a. The recombinant vectors with the N-terminal His-tag(N-His) or C-terminal His-tag(C-His) were translated and expressed separately. The results showed that the solubility of rFTH with C-His was significantly higher than that with N-His. The expression of rFTH with C-His was attempted at 37 °C and 16 °C, respectively. The results showed that the proportion of soluble protein expressed at 37 °C was more than 90%, higher than that expressed at 16 °C. Then rFTH with C-His was purified successfully using anion exchange chromatography, modified PEG precipitation, and dialysis. The rFTH protein was characterized using SDS-PAGE, Native-PAGE, Western blot, transmission electron microscopy, and dynamic light scattering. The results demonstrated that the purified rFTH protein self-assembled into ferritin nanoparticles with a regular shape and uniform size. This study sheds new light on the soluble expression of ferritin and provides a foundation for the construction of bovine ferritin nanoparticle production platforms.

Application of recombinant human pyruvate kinase in recombinase polymerase amplification

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41°C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. In this study, we attempted to use pyruvate kinase instead of creatine kinase (CK) that has been consistently used as an ATP-regenerating enzyme in RPA. Human pyruvate kinase M1 (PKM) was expressed in Escherichia coli and purified from the cells. RPA with PKM was performed at 41°C with the in vitro synthesized urease subunit β (ureB) DNA from Ureaplasma parvum serovar 3 as a standard DNA. The optimal concentrations of PKM and phosphoenolpyruvate were 20 ng/μL and 10 mM, respectively. The RPA reaction with PKM was more sensitive than that with CK. PKM exhibited higher thermostability than CK, suggesting that the RPA reagents with PKM are preferable to those with CK for onsite use.

Recombinase polymerase amplification using novel thermostable strand-displacing DNA polymerases from Aeribacillus pallidus and Geobacillus zalihae

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), and strand-displacing DNA polymerase (Pol). Component instability and the need to store commercial kits in a deep freezer until use are some limitations of RPA. In a previous study, Bacillus stearothermophilus Pol (Bst-Pol) was used as a thermostable strand-displacing DNA polymerase in RPA. Here, we attempted to optimize the lyophilization conditions for RPA with newly isolated thermostable DNA polymerases for storage at room temperature. We isolated novel two thermostable strand-displacing DNA polymerases, one from a thermophilic bacterium Aeribacillus pallidus (H1) and the other from Geobacillus zalihae (C1), and evaluated their performances in RPA reaction. Urease subunit β (UreB) DNA from Ureaplasma parvum serovar 3 was used as a model target for evaluation. The RPA reaction with H1-Pol or C1-Pol was performed at 41 °C with the in vitro synthesized standard UreB DNA. The minimal initial copy numbers of standard DNA from which the amplified products were observed were 600, 600, and 6000 copies for RPA with H1-Pol, C1-Pol, and Bst-Pol, respectively. Optimization was carried out using RPA components, showing that the lyophilized RPA reagents containing H1-Pol exhibited the same performance as the corresponding liquid RPA reagents. In addition, lyophilized RPA reagents with H1-Pol showed almost the same activity after two weeks of storage at room temperature as the freshly prepared liquid RPA reagents. These results suggest that lyophilized RPA reagents with H1-Pol are preferable to liquid RPA reagents for onsite use.