biostudies-literatureUnknown11(40)Menuhin-Gruman IEvolutionary instability is a persistent challenge in synthetic biology, often leading to the loss of heterologous gene expression over time. Here, we present STABLES, a gene fusion strategy that links a gene of interest (GOI) to an essential endogenous gene (EG), with a "leaky" stop codon in between. This ensures both selective pressure against deleterious mutations and the high expression of the GOI. By leveraging a machine learning framework, we predict optimal GOI-EG pairs on the basis of bioinformatic and biophysical features, identify linkers likely to minimize protein misfolding, and optimize DNA sequences for stability and expression. Experimental validation in <i>Saccharomyces cerevisiae</i> demonstrated substantial improvements in stability and productivity for fluorescent proteiScience advanceseadx0796https://www.ebi.ac.uk/biostudies/studies/S-EPMC12487889biostudies-literatureAI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.PMC12487889Menuhin-Gruman INaki DBergman SArbel-Groissman MTuller TfalseAI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.Evolutionary instability is a persistent challenge in synthetic biology, often leading to the loss of heterologous gene expression over time. Here, we present STABLES, a gene fusion strategy that links a gene of interest (GOI) to an essential endogenous gene (EG), with a "leaky" stop codon in between. This ensures both selective pressure against deleterious mutations and the high expression of the GOI. By leveraging a machine learning framework, we predict optimal GOI-EG pairs on the basis of bioinformatic and biophysical features, identify linkers likely to minimize protein misfolding, and optimize DNA sequences for stability and expression. Experimental validation in <i>Saccharomyces cerevisiae</i> demonstrated substantial improvements in stability and productivity for fluorescent protei2025-01-01T00:00:00Z2025 Oct2026-06-04T01:32:51.043Z2026-05-03T03:14:10.596ZS-EPMC124878894103260010.1126/sciadv.adx0796