Efficient One-Step Fusion PCR Based on Dual-Asymmetric Primers and Two-Step Annealing

Genetic Engineering of Acidithiobacillus ferridurans Using CRISPR Systems To Mitigate Toxic Release in Biomining

Biomining processes utilize microorganisms, such as Acidithiobacillus, to extract valuable metals by producing sulfuric acid and ferric ions that dissolve sulfidic minerals. However, excessive production of these compounds can result in metal structure corrosion and groundwater contamination. Synthetic biology offers a promising solution to improve Acidithiobacillus strains for sustainable, eco-friendly, and cost-effective biomining, but genetic engineering of these slow-growing microorganisms is challenging with current inefficient and time-consuming methods. To address this, we established a CRISPR-dCas9 system for gene knockdown in A. ferridurans JAGS, successfully downregulating the transcriptional levels of two genes involved in sulfur oxidation. More importantly, we constructed an all-in-one CRISPR-Cas9 system for fast and efficient genome editing in A. ferridurans JAGS, achieving seamless gene deletion (HdrB3), promoter substitution (Prus to Ptac), and exogenous gene insertion (GFP). Additionally, we created a HdrB-Rus double-edited strain and performed biomining experiments to extract Ni from pyrrhotite tailings. The engineered strain demonstrated a similar Ni recovery rate to wild-type A. ferridurans JAGS but with significantly lower production of iron ions and sulfuric acid in leachate. These high-efficient CRISPR systems provide a powerful tool for studying gene functions and creating useful recombinants for synthetic biology-assisted biomining applications in the future.

Hapten-labeled fusion-polymerase chain reaction of multiple marker genes for the application of immunochromatographic test

A variety of methods have been reported using polymerase chain reaction (PCR)-based nucleic acid testing (NAT) because of its potential to be used in highly sensitive inspection systems. Among these NATs, fusion-PCR (also called as overlap-extension-PCR) has been focused on this study and adopted to generate the fused amplicon composed of plural marker gene fragments for detection. Generally, conventional agarose gel electrophoresis followed by gel staining is employed to check the PCR results. However, these are time-consuming processes that use specific equipment. To overcome these disadvantages, the immunochromatographic test (ICT) for the detection of PCR amplicons with hapten-labels that were generated by PCR using hapten-labeled primers was also adopted in this study. Based on these concepts, we constructed the systems of hapten-labeled fusion-PCR (HL-FuPCR) followed by ICT (HL-FuPCR-ICT) for the two and three marker genes derived from pathogenic microbe. As a result, we successfully developed a two marker genes system for the pathogenic influenza A virus and a three marker genes system for the penicillin-resistant Streptococcus pneumoniae. These detection systems of HL-FuPCR-ICT are characterized by simple handling and rapid detection within few minutes, and also showed the results as clear lines. Thus, the HL-FuPCR-ICT system introduced in this study has potential for use as a user-friendly inspection tool with the advantages especially in the detection of specific strains or groups expressing the characteristic phenotype(s) such as antibiotic resistance and/or high pathogenicity even in the same species.

Construction expression and immunogenicity of a novel trivalent outer membrane protein (OmpU-A-II) from three bacterial pathogens in Japanese eels (Anguilla japonica)

Vibrio vulnificus, Edwardsiella anguillarum and Aeromonas hydrophila are three common bacterial pathogens in cultivated eels. To protect farming eels from infection by these pathogens, a trivalent outer membrane protein (OMP) containing partial sequences of OmpU from V. vulnificus, OmpA from E. anguillarum and OmpII from A. hydrophila was expressed and purified; then, the OMP was used as a vaccine to immunize Japanese eels (Anguilla japonica). Whole-blood cell proliferation, antibody titres and complement and lysozyme activities were detected at different days post-immunization (dpi), and the relative per cent survival (RPS) was determined after eels were infected with V. vulnificus, E. anguillarum or A. hydrophila at 28 dpi. The results showed that the OMP significantly stimulates the antibody titres. At 14 days after the challenge (i.e. at 28 dpi), the RPS of OMP against V. vulnificus, E. anguillarum and A. hydrophila was 20%, 70% and 11.1%, respectively. The construction, expression and immunogenicity of a trivalent Omp were reported for the first time, and this study will provide a valuable reference for the development of fish multiplex vaccines.