\ PortEco: portal for E. coli research

We are still making minor changes. Feel free to use the browser, but be sure to check back later too

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.



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)
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)
rpoHP3 promoter use defective
E upstream confirmed; % decreases σE activity relative to WT)
UV sensitive
(SOS response deficient candidate)
Spontaneous SOS-deficient Not
Find more information about ruvB via PortEco


  1. 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
  2. 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
  3. 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
  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. 5.0 5.1 expected to be similar to ruvC


Back to top

Coming soon...

Download data files

Back to top

Excel versions of supplemental tables: