title: Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks.
abstract: 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.
authors.affiliation: Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer, NY 12144-3456, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Rooney
authors.forename: Ajish D
authors.initials: AD
authors.lastname: George
authors.forename: Ashish
authors.initials: A
authors.lastname: Patil
authors.forename: Ulrike
authors.initials: U
authors.lastname: Begley
authors.forename: Erin
authors.initials: E
authors.lastname: Bessette
authors.forename: Maria R
authors.initials: MR
authors.lastname: Zappala
authors.forename: Xin
authors.initials: X
authors.lastname: Huang
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Conklin
authors.forename: Richard P
authors.initials: RP
authors.lastname: Cunningham
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Begley
mesh_terms: 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
chemical_list: D029968:Escherichia coli Proteins; D009153:Mutagens; D008741:Methyl Methanesulfonate