biostudies-literatureHaas DNational Science Foundatione0163022https://www.ebi.ac.uk/biostudies/studies/S-EPMC9426524biostudies-literatureUnknown13(4)Analysis of the genes retained in the minimized <i>Mycoplasma</i> JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that severmBioMetabolite Damage and Damage Control in a Minimal Genome.PMC9426524MCB-1840320MCB-1611846MCB-1611952MCB-1818344MCB-1611711MCB-1840301Kurilyak IGlass JILerma-Ortiz CFolz JHenry CSBruner SDWise KSBrown GHuang LHanson ADHaas DSun LBeaudoin GAWde Crecy-Lagard VLuthey-Schulten ZWilson MAFiehn OBreuer MYakunin AFLin JThamm AMSun JfalseMetabolite Damage and Damage Control in a Minimal Genome.Analysis of the genes retained in the minimized <i>Mycoplasma</i> JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that sever2022-01-01T00:00:00Z2022 Aug2025-05-29T16:11:40.099Z2025-04-04T09:32:32.5ZS-EPMC94265243586278610.1128/mbio.01630-22