HGPRGDel: GPR-Aware Learning and Ranking for Growth-Coupled Gene Deletion Design

Abstract

Designing microbial strains for growth-coupled production, in which cellular growth is linked to the synthesis of a target compound through genetic interventions, is a fundamental goal in metabolic engineering. Constraint-based methods can identify growth-coupled deletion strategies, but design for each target typically requires a separate search across a large number of possible gene-deletion combinations. This motivates a reusable approach that learns from previously evaluated strain designs to prioritize candidate interventions before downstream constraint-based evaluation. We present a reproducible protocol for growth-coupled gene deletion design that learns and ranks gene-deletion priorities for each target metabolite. Using computationally curated deletion strategies as learning resources, the protocol generates continuous deletion-priority rankings, constructs candidate strategies at adjustable search-space budgets, and evaluates these candidates through constraint-based metabolic analysis. Its learning component, HGPRGDel, explicitly represents gene-protein-reaction (GPR) logic, capturing how multiple genes can jointly support a reaction or alternative genes can maintain its activity, while integrating molecular and reaction-level information. Across e_coli_core, iMM904, and iML1515, the protocol achieves the highest macro-F1 and AUC among the evaluated learning configurations. HGPRGDel's rankings recovered an average of 90% of the reference deletion genes from MetNetComp by examining fewer genes than the evaluated baseline methods. By separating learned intervention prioritization from downstream constraint-based assessment, the protocol provides a reproducible framework for reusing strain-design knowledge while controlling the size of the candidate space and retaining mechanistic evaluation of growth-coupled production.