Synthetic protein interactions reveal a functional map of the cell

eLife

Volumn 5, Issue APRIL2016, 2016, Pages

  Berry, Lisa K ^a   Ólafsson, Guðjón ^a   Ledesma Fernández, Elena ^a,b   Thorpe, Peter H ^a  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTIC CELL; FUNGAL CELL CULTURE; HOMEOSTASIS; INTRACELLULAR SPACE; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; QUANTITATIVE STUDY; SACCHAROMYCES CEREVISIAE; METABOLISM; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT;

PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN;

PROTEIN BINDING; PROTEIN INTERACTION MAPS; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84964555874     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.13053     Document Type: Article

References (41)

1. Akiyoshi B, Sarangapani KK, Powers AF, Nelson CR, Reichow SL, Arellano-Santoyo H, Gonen T, Ranish JA, Asbury CL, Biggins S. 2010. Tension directly stabilizes reconstituted kinetochore-microtubule attachments. Nature 468: 576-579. doi: 10.1038/nature09594
2. Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Michael Cherry J. 2012. YeastMine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database 2012: bar062. doi: 10.1093/database/bar062
3. Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL. 2010. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nature Methods 7: 1017-1024. doi: 10.1038/nmeth.1534
4. Biggins S. 2013. The composition, functions, and regulation of the budding yeast kinetochore. Genetics 194: 817-846. doi: 10.1534/genetics.112.145276
5. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 2-2: 115-132. doi: 10.1002/(SICI)1097-0061(19980130)14: 2<115:: AID-YEA204>3.0.CO;2-2
6. Breker M, Gymrek M, Schuldiner M. 2013. A novel single-cell screening platform reveals proteome plasticity during yeast stress responses. The Journal of Cell Biology 200: 839-850. doi: 10.1083/jcb.201301120
7. Chong YT, Koh JL, Friesen H, Duffy SK, Duffy K, Cox MJ, Moses A, Moffat J, Boone C, Andrews BJ. 2015. Yeast proteome dynamics from single cell imaging and automated analysis. Cell 161: 1413-1424. doi: 10.1016/j.cell.2015.04.051
8. Ciferri C, Pasqualato S, Screpanti E, Varetti G, Santaguida S, Dos Reis G, Maiolica A, Polka J, De Luca JG, De Wulf P, Salek M, Rappsilber J, Moores CA, Salmon ED, Musacchio A. 2008. Implications for kinetochore-microtubule attachment from the structure of an engineered Ndc80 complex. Cell 133: 427-439. doi: 10.1016/j.cell.2008.03.020
9. Collins SR, Schuldiner M, Krogan NJ, Weissman JS. 2006. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 7: R63. doi: 10.1186/gb-2006-7-7-r63
10. Das J, Yu H. 2012. HINT: High-quality protein interactomes and their applications in understanding human disease. BMC Systems Biology 6: 92. doi: 10.1186/1752-0509-6-92
11. Devit M, Cullen PJ, Branson M, Sprague GF, Fields S. 2005. Forcing interactions as a genetic screen to identify proteins that exert a defined activity. Genome Research 15: 560-565. doi: 10.1101/gr.3259905
12. Dittmar JC, Reid RJ, Rothstein R. 2010. ScreenMill: a freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. BMC Bioinformatics 11: 353. doi: 10.1186/1471-2105-11-353
13. Dittmar JC, Pierce S, Rothstein R, Reid RJ. 2013. Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens. Proceedings of the National Academy of Sciences of the United States of America 110: 7389-7394. doi: 10.1073/pnas.1219582110
14. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. 2009. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: 48. doi: 10.1186/1471-2105-10-48
15. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 95: 14863-14868. doi: 10.1073/pnas.95.25.14863
16. Grallert A, Chan KY, Alonso-Nuñez ML, Madrid M, Biswas A, Alvarez-Tabarés I, Connolly Y, Tanaka K, Robertson A, Ortiz JM, Smith DL, Hagan IM. 2013. Removal of centrosomal PP1 by NIMA kinase unlocks the MPF feedback loop to promote mitotic commitment in S. pombe. Current Biology: CB 23: 213-222. doi: 10.1016/j.cub.2012.12.039
17. Haruki H, Nishikawa J, Laemmli UK. 2008. The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Molecular Cell 31: 925-932. doi: 10.1016/j.molcel.2008.07.020
18. Hepp MI, Alarcon V, Dutta A, Workman JL, Gutiérrez JL. 2014. Nucleosome remodeling by the SWI/SNF complex is enhanced by yeast high mobility group box (HMGB) proteins. Biochimica Et Biophysica Acta 1839: 764-772. doi: 10.1016/j.bbagrm.2014.06.014
19. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O’Shea EK. 2003. Global analysis of protein localization in budding yeast. Nature 425: 686-691. doi: 10.1038/nature02026
20. Hung MC, Link W. 2011. Protein localization in disease and therapy. Journal of Cell Science 124: 3381-3392. doi: 10.1242/jcs.089110
21. Joglekar AP, Bouck DC, Molk JN, Bloom KS, Salmon ED. 2006. Molecular architecture of a kinetochore-microtubule attachment site. Nature Cell Biology 8: 581-585. doi: 10.1038/ncb1414
22. Lambert JP, Mitchell L, Rudner A, Baetz K, Figeys D. 2009. A novel proteomics approach for the discovery of chromatin-associated protein networks. Molecular & Cellular Proteomics: MCP 8: 870-882. doi: 10.1074/mcp.M800447-MCP200
23. Ledesma-Fernández E, Thorpe PH. 2015. Fluorescent foci quantitation for high-throughput analysis. Journal of Biological Methods 2: 22. doi: 10.14440/jbm.2015.62
24. Lubbock AL, Katz E, Harrison DJ, Overton IM. 2013. TMA Navigator: Network inference, patient stratification and survival analysis with tissue microarray data. Nucleic Acids Research 41: W562-568. doi: 10.1093/nar/gkt529
25. Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ. 2008. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 322: 597-602. doi: 10.1126/science.1162790
26. Ólafsson G, Thorpe PH. 2015. Synthetic physical interactions map kinetochore regulators and regions sensitive to constitutive Cdc14 localization. Proceedings of the National Academy of Sciences of the United States of America 112: 10413-10418. doi: 10.1073/pnas.1506101112
27. Ramey VH, Wong A, Fang J, Howes S, Barnes G, Nogales E. 2011. Subunit organization in the Dam1 kinetochore complex and its ring around microtubules. Molecular Biology of the Cell 22: 4335-4342. doi: 10.1091/mbc.E11-07-0659
28. Reid RJ, González-Barrera S, Sunjevaric I, Alvaro D, Ciccone S, Wagner M, Rothstein R. 2011. Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I-induced DNA damage. Genome Research 21: 477-486. doi: 10.1101/gr.109033.110
29. Robinson MS, Sahlender DA, Foster SD. 2010. Rapid inactivation of proteins by rapamycin-induced rerouting to mitochondria. Developmental Cell 18: 324-331. doi: 10.1016/j.devcel.2009.12.015
30. Rothbauer U, Zolghadr K, Tillib S, Nowak D, Schermelleh L, Gahl A, Backmann N, Conrath K, Muyldermans S, Cardoso MC, Leonhardt H. 2006. Targeting and tracing antigens in live cells with fluorescent nanobodies. Nature Methods 3: 887-889. doi: 10.1038/nmeth953
31. Rothbauer U, Zolghadr K, Muyldermans S, Schepers A, Cardoso MC, Leonhardt H. 2008. A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins. Molecular & Cellular Proteomics: MCP 7: 282-289. doi: 10.1074/mcp.M700342-MCP200
32. Saldanha AJ. 2004. Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248. doi: 10.1093/bioinformatics/bth349
33. Scott JD, Pawson T. 2009. Cell signaling in space and time: where proteins come together and when they’re apart. Science 326: 1220-1224. doi: 10.1126/science.1175668
34. Shang C, Hazbun TR, Cheeseman IM, Aranda J, Fields S, Drubin DG, Barnes G. 2003. Kinetochore protein interactions and their regulation by the Aurora kinase Ipl1p. Molecular Biology of the Cell 14: 3342-3355. doi: 10.1091/mbc.E02-11-0765
35. Sherman F. 2002. Getting started with yeast. Methods in Enzymology 350: 3-41.
36. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. 2006. BioGRID: a general repository for interaction datasets. Nucleic Acids Research 34: D535-539. doi: 10.1093/nar/gkj109
37. Stirling PC, Bloom MS, Solanki-Patil T, Smith S, Sipahimalani P, Li Z, Kofoed M, Ben-Aroya S, Myung K, Hieter P. 2011. The complete spectrum of yeast chromosome instability genes identifies candidate CIN cancer genes and functional roles for ASTRA complex components. PLoS Genetics 7: e1002057. doi: 10.1371/journal.pgen.1002057
38. Thomas BJ, Rothstein R. 1989. The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene. Genetics 123: 725-738.
39. Tkach JM, Yimit A, Lee AY, Riffle M, Costanzo M, Jaschob D, Hendry JA, Ou J, Moffat J, Boone C, Davis TN, Nislow C, Brown GW. 2012. Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nature Cell Biology 14: 966-976. doi: 10.1038/ncb2549
40. Wei RR, Al-Bassam J, Harrison SC. 2007. The Ndc80/HEC1 complex is a contact point for kinetochore-microtubule attachment. Nature Structural & Molecular Biology 14: 54-59. doi: 10.1038/nsmb1186
41. Zou H, Rothstein R. 1997. Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 90: 87-96. doi: 10.1016/S0092-8674(00)80316-5