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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Main Points of the Paper

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Materials and Methods Used

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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: pepP Genotype of Experimental Strain : pepP759(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.
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: yfjL Genotype of Experimental Strain : yfjL(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: lrp Genotype of Experimental Strain : Irp787(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: mall Genotype of Experimental Strain : mall768(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: acrA Genotype of Experimental Strain : acrA748(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: trxB Genotype of Experimental Strain : trxB786(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: fre Genotype of Experimental Strain : fre784(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: cspC Genotype of Experimental Strain : cspC747(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: barA Genotype of Experimental Strain : barA784(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: ifhA786 Genotype of Experimental Strain : ihfA786(del)FRTKanFRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). A strong mutation, SIM was reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ubiA+ Genotype of Experimental Strain : ubiA::Tn10dCam	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ubiE778 Genotype of Experimental Strain : ubiE778(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: hfq722 Genotype of Experimental Strain : hfq722(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: nuoJ762 Genotype of Experimental Strain : nuoJ762(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: nuoC768 Genotype of Experimental Strain : nuoC768(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: nuoL760 Genotype of Experimental Strain : nuoL760(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: ubiH758 Genotype of Experimental Strain : ubiH758(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: dsbA723 Genotype of Experimental Strain : dsbA723(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: nuoH764 Genotype of Experimental Strain : nuoH764(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: yifE782 Genotype of Experimental Strain : yifE782(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: rppH754 Genotype of Experimental Strain : rppH754(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: rpoE2072 Genotype of Experimental Strain : rpoE2072::Tn10dCam	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: prc Genotype of Experimental Strain : prc755(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: lon725 Genotype of Experimental Strain : lon725(del)::FRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: nagC725 Genotype of Experimental Strain : nagC725(del)::FRTKanFRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: nuoG+ Genotype of Experimental Strain : nuoG::Tn10dCam	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: SMR4562 NCBI Taxon ID: 83333	Genotype of Reference Strain: rbsK781 Genotype of Experimental Strain : rbsK781(del)::FRTKanFRT	Reference Condition:					A Stress Induced Mutagenesis phenotype (SIM). The mutation caused a significant decrease in SIM, with mutant frequency being reduced by over 90 percent of wild type levels. See table S3 for full experimental data.
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References

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