Cathepsin B protease mediates high population density-induced mutagenesis to drive genome evolution and competitive growth

Density-dependent population regulation is widespread in the animal kingdom, but the underlying molecular mechanisms remain poorly understood. Here, we show that C. elegans animals respond to crowding stress by secreting CPR-4, a homologue of human cathepsin B cysteine protease, leading to chromosomal DNA damage in germ cells and high density-induced deficiencies that include increased embryonic lethality and larval arrest and decreased brood size. CPR-4 mediates these crowding responses through the insulin-like growth factor receptor DAF-2, multiple components in the insulin signaling pathway, and the SKN-1/Nrf transcription factor. Whole genome sequencing analyses of animals from 10 generations of continual growth in the crowded condition reveal that CPR-4-induced DNA damage produces an average of 2.8 more de novo genome mutations per animal per generation and a 87% increase in mutation rate compared with animals grown in the uncrowded condition. CPR-4-induced mutagenesis also facilitates evolution of the genomes through multi-generational crowding selection, leading to biased mutation distributions towards the intergenic regions over the gene bodies and crowd-dependent growth advantage. Therefore, CPR-4 acts as a crucial crowd-responding factor to induce genome mutagenesis, driving genome evolution and competitive growth of animals in response to crowding stress.