Complex transcriptional responses to macromolecular damaging agents: regulatory responses specific for SN2 alkylation and the MAG1 gene

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

An effective response to DNA damaging agents involves modulating numerous facets of cellular homeostasis in addition to DNA repair and cell-cycle checkpoint pathways. Fluorescence microscopy-based imaging offers the opportunity to simultaneously interrogate changes in both protein level and subcellular localization in response to DNA damaging agents at the single-cell level. We report here results from screening the yeast Green Fluorescent Protein (GFP)-fusion library to investigate global cellular protein reorganization on exposure to the alkylating agent methyl methanesulfonate (MMS). Broad groups of induced, repressed, nucleus- and cytoplasm-enriched proteins were identified. Gene Ontology and interactome analyses revealed the underlying cellular processes. Transcription factor (TF) analysis identified principal regulators of the response, and targets of all major stress-responsive TFs were enriched amongst the induced proteins. An unexpected partitioning of biological function according to the number of TFs targeting individual genes was revealed. Finally, differential modulation of ribosomal proteins depending on methyl methanesulfonate dose was shown to correlate with cell growth and with the translocation of the Sfp1 TF. We conclude that cellular responses can navigate different routes according to the extent of damage, relying on both expression and localization changes of specific proteins.

Network responses to DNA damaging agents

Global transcriptional profiling and large scale phenotypic studies have shown that eukaryotic cells mount a robust and complex response to damage. Further, systems biology approaches have employed powerful analytical methods to integrate global data sets with regulatory sequences, protein-DNA and protein-protein interactions, which have led to the identification of large networked responses to damage. A number of groups have shown that damage responsive networks embrace groups of highly connected genes and proteins and have illustrated that multiple interconnected cellular pathways respond to damage and moreover, dictate viability post damage. This review highlights some of the global studies that examine cellular responses to damage, and proposes that we should be moving from pathways to networks, in order to gain better insight into cellular defense mechanisms.