Species-specific metabolic networks shape evolutionary routes to functional rescue

Abstract

Metabolic networks are highly interconnected. Still, it remains unclear whether organism-and environment-specific factors shape their capacity to evolve in response to metabolic stress or whether it follows general principles. Here, we studied metabolic evolvability in Bacillus subtilis using auxotrophic mutants lacking central biosynthetic enzymes. Across two genetic backgrounds with contrasting biofilm-forming capacities and under direct or gradual selection through nutrient gradients, B. subtilis bypassed 9 of 17 essential functions. Rescue was more frequent in the biofilm-proficient background and under gradual selection, which was also associated with more mutations in coding regions, particularly nonsynonymous. Adaptation proceeded through loss-of-function mutations that relieved regulatory or enzymatic constraints and redirected metabolic flux. Comparison with Escherichia coli revealed substantial differences in bypassability and genetic routes that persisted under matched conditions, although two cross-species solutions converged at the pathway level. Our data show species-specific metabolic networks shape available rescue routes, while ecological context influences their evolutionary accessibility during adaptation.