Genomic signatures highlight stress-response evasion and translational tuning as key drivers of Escherichia coli adaptation to fluorinated tryptophans

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, involved in DNA mismatch repair, allowed replication errors to accumulate, generating transient hypermutator states that accelerated evolutionary exploration but were not required for successful adaptation. Reconstruction experiments confirmed that loss of stringent response control and altered TrpRS function together increased fitness during fluorotryptophan incorporation. Together, these results suggest that adaptation does not appear to primarily rely on establishing a fundamentally new fluorine-based biochemistry, but rather on adjustment of stress-response regulation and translational control. More broadly, this work establishes a general framework for understanding, and ultimately engineering, microbial adaptation to non-natural metabolites through targeted modification of regulatory and translational control nodes rather than metabolic redesign.

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