Transposon-based genome editing of industrial microorganisms: advances, challenges, and prospects

As mobile genetic elements, transposons play a crucial role in the adaptive evolution and genome engineering of industrial microorganisms. Their applications range from high-throughput functional genomics, enabling systematic genotype-phenotype mapping via transposon sequencing, to the construction of random integration libraries for chassis development and directed evolution. Despite the emergence of precise editing tools such as CRISPR-Cas, transposon technology remains indispensable in non-model industrial strains owing to its operational simplicity and high efficiency. Recent discoveries of novel transposon systems, along with their functional enhancement, have further expanded their utility. Looking ahead, integrating transposon technology with strategies such as AI-assisted design and CRISPR-Cas-based systems will greatly advance our ability to decipher and engineer industrial microbial cell factories. This review summarizes the principles, challenges, and opportunities of transposon-associated technologies in industrial microorganisms, offering new insights into their roles in industrial biotechnology.