Dynamic Lysine Acetylation Disrupts Isocitrate Lyase Function and Enables Metabolic Optimisation

Proteomic studies have suggested that Escherichia coli isocitrate lyase (ICL) undergoes multiple acetylation events, partially inhibiting its activity. However, the molecular basis of this regulation and the contribution of individual lysine residues had not been defined. This study demonstrates that acetylation of ICL in E. coli is acetyl-phosphate-dependent and reversible by the CobB deacetylase, establishing a key post-translational regulatory mechanism within the glyoxylate shunt. Site-specific acetylation at K13 and K308 inhibits ICL activity by destabilising the tetrameric assembly and rendering the protein more prone to degradation, whereas lysine-to-arginine substitutions at these positions alleviate this inhibition, enhancing carbon flux distribution, metabolic flexibility and biomass yield without the burden of plasmid-based overexpression. Leveraging this regulatory insight, a KR mutant bearing lysine-to-arginine substitutions at residues 13 and 308, engineered directly into the chromosomal aceA gene, maintained wild-type growth rates while reducing acetate overflow and improving metabolic balance during glucose depletion and acetate assimilation, leading to a 61% increase in lycopene production. These findings highlight regulatory-based metabolic engineering as a powerful strategy to optimise bioproduction and pave the way for extending this approach to other central metabolic enzymes to develop robust microbial cell factories for the sustainable synthesis of biofuels, biochemicals and high-value compounds.