Knockout of a highly GC‐rich gene in Burkholderia pyrrocinia by recombineering with freeze‐thawing transformation

Genetic transformation is a valuable and essential method that provides powerful insights into the gene function of microorganisms and contributes to the construction of engineered bacteria. Here, we developed a novel genetic transformation system to easily knock out a highly GC‐rich gene (74.71% GC) from Burkholderia pyrrocinia JK‐SH007, a biocontrol strain of poplar canker disease. This system revealed a reliable selectable marker (trimethoprim resistance gene, Tmp) and a simplified, efficient transformation method (6,363.64 CFU/μg, pHKT2) that was developed via freeze‐thawing. The knockout recombineering of B. pyrrocinia JK‐SH007 was achieved through a suicide plasmid with a three‐fragment mutagenesis construct. The three‐fragment cassette for mutagenesis was generated by overlap extension and touchdown PCRs and composed of Tmp flanked by GC‐rich upstream and downstream fragments from B. pyrrocinia JK‐SH007. The mutant strain (ΔBpEG), which was verified by PCR, lost 93.3% of its ability to degrade carboxymethyl cellulose over 40 days. Overall, this system may contribute to future research on B. pyrrocinia traits.