Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks.
The identification of cellular responses to damage can promote mechanistic insight into stress signalling. We have screened a library of 3968 Escherichia coli gene-deletion mutants to identify 99 gene products that modulate the toxicity of the alkylating agent methyl methanesulfonate (MMS). We have developed an ontology mapping approach to identify functional categories over-represented with MMS-toxicity modulating proteins and demonstrate that, in addition to DNA re-synthesis (replication, recombination, and repair), proteins involved in mRNA processing and translation influence viability after MMS damage. We have also mapped our MMS-toxicity modulating proteins onto an E. coli protein interactome and identified a sub-network consisting of 32 proteins functioning in DNA repair, mRNA processing, and translation. Clustering coefficient analysis identified seven highly connected MMS-toxicity modulating proteins associated with translation and mRNA processing, with the high connectivity suggestive of a coordinated response. Corresponding results from reporter assays support the idea that the SOS response is influenced by activities associated with the mRNA-translation interface.
Rooney
John P
JP
Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer, NY 12144-3456, USA.
George
Ajish D
AD
Patil
Ashish
A
Begley
Ulrike
U
Bessette
Erin
E
Zappala
Maria R
MR
Huang
Xin
X
Conklin
Douglas S
DS
Cunningham
Richard P
RP
Begley
Thomas J
TJ
D000478:Alkylation; D004249:DNA Damage; D004260:DNA Repair; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D016680:Genome, Bacterial; D008741:Methyl Methanesulfonate / Q000494:pharmacology*; D009153:Mutagens / Q000494:pharmacology; D009154:Mutation; D010641:Phenotype; D014176:Protein Biosynthesis; D049490:Systems Biology; D014158:Transcription, Genetic
D029968:Escherichia coli Proteins; D009153:Mutagens; D008741:Methyl Methanesulfonate