Comparative Genomic Analysis Reveals Key Changes in the Genome of Acremonium chrysogenum That Occurred During Classical Strain Improvement for Production of Antibiotic Cephalosporin C

From the 1950s to the present, the main tool for obtaining fungal industrial producers of secondary metabolites remains the so-called classical strain improvement (CSI) methods associated with multi-round random mutagenesis and screening for the level of target products. As a result of the application of such techniques, the yield of target secondary metabolites in high-yielding (HY) strains was increased hundreds of times compared to the wild-type (WT) parental strains. However, the events that occur at the molecular level during CSI programs are still unknown. In this paper, an attempt was made to identify characteristic changes at the genome level that occurred during CSI of the <i>Acremonium chrysogenum</i> WT strain (ATCC 11550) and led to the creation of the <i>A. chrysogenum</i> HY strain (RNCM F-4081D), which produces 200-300 times more cephalosporin C, the starting substance for obtaining cephalosporin antibiotics of the 1st-5th generations. We identified 3730 mutational changes, 56 of which led to significant disturbances in protein synthesis and concern: (i) enzymes of primary and secondary metabolism; (ii) transporters, including MDR; (iii) regulators, including cell cycle and chromatin remodeling; (iv) other processes. There was also a focus on mutations occurring in the biosynthetic gene clusters (BGCs) of the HY strain; polyketide synthases were found to be hot spots for mutagenesis. The obtained data open up the possibility not only for understanding the molecular basis for the increase in cephalosporin C production in <i>A. chrysogenum</i> HY, but also show the universal events that occur when improving mold strains for the production of secondary metabolites by classical methods.