PMID:23224554

Citation	Al Mamun, AA , Lombardo, MJ , Shee, C , Lisewski, AM , Gonzalez, C , Lin, D , Nehring, RB , Saint-Ruf, C , Gibson, JL , Frisch, RL , Lichtarge, O , Hastings, PJ and Rosenberg, SM (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338:1344-8
Abstract	Mechanisms of DNA repair and mutagenesis are defined on the basis of relatively few proteins acting on DNA, yet the identities and functions of all proteins required are unknown. Here, we identify the network that underlies mutagenic repair of DNA breaks in stressed Escherichia coli and define functions for much of it. Using a comprehensive screen, we identified a network of ≥93 genes that function in mutation. Most operate upstream of activation of three required stress responses (RpoS, RpoE, and SOS, key network hubs), apparently sensing stress. The results reveal how a network integrates mutagenic repair into the biology of the cell, show specific pathways of environmental sensing, demonstrate the centrality of stress responses, and imply that these responses are attractive as potential drug targets for blocking the evolution of pathogens.
Links	PubMed Online version:10.1126/science.1226683
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Phenotype Annotations

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Phenotype of	Taxon Information	Genotype Information (if known)	Condition Information	OMP ID	OMP Term Name	ECO ID	ECO Term Name	Notes	Status
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: srlA777 Genotype of Experimental Strain : srlA777(del)::FRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ybjT Genotype of Experimental Strain : ybjT770(del)::FRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: treR Genotype of Experimental Strain : treR788(del)::FRTKanFRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: yjcC Genotype of Experimental Strain : yjcC755(del)::FRTKanFRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: yjcC Genotype of Experimental Strain : yjcC750::FRTKanFRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ytjB Genotype of Experimental Strain : ytjB(P)::Tn10dCam	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: arcA Genotype of Experimental Strain : arcA(P)::Tn10dCam	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ligA Genotype of Experimental Strain : ligA(P)::Tn10dCam	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: apaG Genotype of Experimental Strain : apaG762(del)::FRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: yqgE723 Genotype of Experimental Strain : yqgE723(del)::FRTKanFRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ihfA Genotype of Experimental Strain : ihfA786(del)FRTKanFRT	Reference Condition:					Decreased stress-induced mutagenesis (SIM) phenotype. Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
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