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Browse and analyze data from Al Mamun et al. (Science 2012) Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks 338:1344-1348

This dataset of 93 genes was constructed by screening E. coli for mutants deficient in mutagenic repair of DNA breaks under stress, followed by secondary screens for genes that participate in activation of stress responses. This study identifies a network of genes involved in stress-induced mutagenesis (the SIM Network). This data browser allows you to examine the classification of SIM network genes and explore the data from different assays on individual network genes. You can also download excel versions of the supplemental tables from the paper.

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lexA

Classification Regulators
Gene-product description Transcriptional repressor of the SOS DNA-damage response genes
References PMID:1103845[1]
SIM defect strength Moderate
Previously known Not found [2][3]

Mutagenesis Assays

Papillation assay defect
(fold-decrease in number of papillae compared with WT)
3.8 ± 0.5
Quantitative Lac assay defect
(mean fold decrease in mutation rate compared with WT)
3.3 ± 0.4 [4]
Chromosomal Tet assay defect
(mean fold decrease in TetR mutant frequency compared with WT)
5.2 ± 0.54 [5]
Chromosomal Nal assay defect
(mean fold decrease in NalR mutant frequency compared with WT)
20 ± 5

Screens for genes upstream of stress responses

σS upstream
(% decreases σS activity relative to WT)
Not
Suppressed by mutation in arcB
Suppressed by mutation in arcA
Suppressed by mutation in rssB
Epistatic with rpoS mutation
SDS-EDTA sensitive
E upstream candidate)
Not
rpoHP3 promoter use defective
E upstream confirmed; % decreases σE activity relative to WT)
UV sensitive
(SOS response deficient candidate)
Sensitive
Spontaneous SOS-deficient Yes
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References

  1. Radman, M (1975) SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci. 5A 355-67 PubMed
  2. Cairns, J & Foster, PL (1991) Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128 695-701 PubMed
  3. McKenzie, GJ et al. (2000) The SOS response regulates adaptive mutation. Proc. Natl. Acad. Sci. U.S.A. 97 6646-51 PubMed
  4. He, AS et al. (2006) Roles of E. coli double-strand-break-repair proteins in stress-induced mutation. DNA Repair (Amst.) 5 258-73 PubMed
  5. Shee, C et al. (2011) Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 108 13659-64 PubMed

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Excel versions of supplemental tables: