Conditional Epistatic Interaction Maps Reveal Global
Functional Rewiring of Genome Integrity Pathways
in Escherichia coli
Kumar. et al. (2015)
- Like eukaryotes, bacteria have evolved sophisticated mechanisms to sense and repair DNA damage. While the genetic components of the bacterial DNA damage response (DDR) have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here we address this knowledge gap by performing systematic, unbiased, quantitative synthetic genetic screens to uncover widespread changes in the genetic interaction (GI) network for the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. GIs identified from untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as novel nucleases involved in nucleotide excision repair and DNA replication or recombination. Furthermore, screens conducted under DNA damaging conditions reveal extensive reorganization of the GI network, and the distinct GI patterns observed suggest many new DDR roles for both annotated and uncharacterized genes. We found that the functional links within modules (complexes and pathways) were stable in both conditions, as opposed to GIs between modules, which appear to be reorganized in response to perturbation. As well, functionally linked genes, showed a genomic integrity response that appears conserved across proteobacteria. This unique resource expands our understanding of the DDR, as well as functional relationships between bacterial genes at a systems level.
From this website, you can access and download annotations, interactions and supplementary data
for all E. coli DNA repair genes analyzed in this study.
© 2015 Babu Lab, University of Regina |
Website designed and created by: Sadhna Phanse
E-mail questions or comments to: sadhna.phanse@utoronto.ca
E-mail questions or comments to: sadhna.phanse@utoronto.ca