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 subcellu...
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| Format: | Article |
| Language: | en_US |
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Oxford University Press
2013
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| Online Access: | http://hdl.handle.net/1721.1/81341 https://orcid.org/0000-0002-6199-6855 https://orcid.org/0000-0002-7112-1454 |
| _version_ | 1826196383708741632 |
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| author | Mazumder, Aprotim Bathe, Mark Samson, Leona D. Pesudo Quiros, Laia McRee, Siobhan K. |
| author2 | Massachusetts Institute of Technology. Center for Environmental Health Sciences |
| author_facet | Massachusetts Institute of Technology. Center for Environmental Health Sciences Mazumder, Aprotim Bathe, Mark Samson, Leona D. Pesudo Quiros, Laia McRee, Siobhan K. |
| author_sort | Mazumder, Aprotim |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T10:26:00Z |
| format | Article |
| id | mit-1721.1/81341 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:26:00Z |
| publishDate | 2013 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/813412022-09-26T17:50:29Z Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae Mazumder, Aprotim Bathe, Mark Samson, Leona D. Pesudo Quiros, Laia McRee, Siobhan K. Massachusetts Institute of Technology. Center for Environmental Health Sciences Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Laboratory for Computational Cell Biology & Biophysics Koch Institute for Integrative Cancer Research at MIT Mazumder, Aprotim Bathe, Mark Samson, Leona D. Pesudo Quiros, Laia McRee, Siobhan K. 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. National Cancer Institute (U.S.) (R01-CA055042 (now NIEHS R01-ES022872)) Massachusetts Institute of Technology. Center for Environmental Health Sciences (Grant NIEHS P30-ES002109) National Cancer Institute (U.S.) (KI Center Grant U54-CA112967) National Cancer Institute (U.S.) (Cancer Center Support Grant P30-CA14051) National Institute of Environmental Health Sciences (R01-ES022872) MIT Faculty Start-up Fund Massachusetts Institute of Technology. Computational and Systems Biology Initiative (Merck & Co. Postdoctoral Fellowship) 2013-10-07T14:42:54Z 2013-10-07T14:42:54Z 2013-08 2013-07 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/81341 Mazumder, A., L. Q. Pesudo, S. McRee, M. Bathe, and L. D. Samson. “Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae.” Nucleic Acids Research (August 9, 2013). https://orcid.org/0000-0002-6199-6855 https://orcid.org/0000-0002-7112-1454 en_US http://dx.doi.org/10.1093/nar/gkt715 Nucleic Acids Research http://creativecommons.org/licenses/by-nc/3.0/ application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Mazumder, Aprotim Bathe, Mark Samson, Leona D. Pesudo Quiros, Laia McRee, Siobhan K. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae |
| title | Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae |
| title_full | Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae |
| title_fullStr | Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae |
| title_full_unstemmed | Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae |
| title_short | Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae |
| title_sort | genome wide single cell level screen for protein abundance and localization changes in response to dna damage in s cerevisiae |
| url | http://hdl.handle.net/1721.1/81341 https://orcid.org/0000-0002-6199-6855 https://orcid.org/0000-0002-7112-1454 |
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