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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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- All SIM network genes
- SIM network genes upstream of rpoE
- SIM network genes upstream of rpoS
- UV-sensitive SIM network genes upstream of the SOS response
- Essential SIM network genes and promoter mutations
ruvB
| Classification | DNA replication and repair |
|---|---|
| Gene-product description | Branch migration of Holliday junctions |
| References | PMID:1608954[1] |
| SIM defect strength | Strong |
| Previously known | Not found [2][3] |
Mutagenesis Assays | |
| Papillation assay defect (fold-decrease in number of papillae compared with WT) |
Not tested |
| Quantitative Lac assay defect (mean fold decrease in mutation rate compared with WT) |
16 ± 5 [4] |
| Chromosomal Tet assay defect (mean fold decrease in TetR mutant frequency compared with WT) |
Not tested [5] |
| Chromosomal Nal assay defect (mean fold decrease in NalR mutant frequency compared with WT) |
Not tested [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 (σE upstream candidate) |
Not |
| rpoHP3 promoter use defective (σE upstream confirmed; % decreases σE activity relative to WT) |
|
| UV sensitive (SOS response deficient candidate) |
Sensitive |
| Spontaneous SOS-deficient | Not |
| Find more information about ruvB via PortEco | |
References
- ↑ Parsons, CA et al. (1992) Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions. Proc. Natl. Acad. Sci. U.S.A. 89 5452-6 PubMed
- ↑ Harris, RS et al. (1996) Opposing roles of the holliday junction processing systems of Escherichia coli in recombination-dependent adaptive mutation. Genetics 142 681-91 PubMed
- ↑ Foster, PL et al. (1996) Two enzymes, both of which process recombination intermediates, have opposite effects on adaptive mutation in Escherichia coli. Genetics 142 25-37 PubMed
- ↑ 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
- ↑ 5.0 5.1 expected to be similar to ruvC
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Download data files
Back to topExcel versions of supplemental tables:
- Table S03. Stress-induced mutation rates of previously unpublished SIM network mutants in quantitative assay.xlsx
- Table S08. sigmaS activity of catalase-defective mutants.xlsx
- Table S02. Genes of the stress-induced-mutagenesis network.xlsx
- Table S09. Upregulating sigmaS via arcB, arcA or rssB mutations partially restores SIM-proficiency to electron transfer mutants.xlsx
- Table S04. Escherichia coli strains and plasmid used.xlsx
- Table S10. RpoS acts in the same pathway (is epistatic with) electron transfer mutations in DSB-dependent SIM.xlsx
- Table S01. Summary of stress-induced-mutagenesis network genetic analyses.xlsx
- Table S05. Validation of SIM network mutants by Tet and Nal mutation assays.xlsx
- Table S11. sigmaE activity of SDS-EDTA-sensitive mutants.xlsx
- Table S06. Correlations of the magnitudes of SIM-deficiency in four stress-induced mutation assays.xlsx