LoQAtE - Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Breker, Michal ^a   Gymrek, Melissa ^b   Moldavski, Ofer ^a   Schuldiner, Maya ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN CONTAINING TCP1; DITHIOTHREITOL; HYDROGEN PEROXIDE; MESSENGER RNA; NITROGEN; PROTEASOME; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN; GREEN FLUORESCENT PROTEIN;

ARTICLE; GENE MUTATION; HUMAN COMPUTER INTERACTION; INTERNET; LOCALIZAITON AND QUANTITATION ATLAS OF THE YEAST PROTEOME DATABASE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN LOCALIZATION; SACCHAROMYCES CEREVISIAE; GENE REGULATORY NETWORK; GENETICS; METABOLISM; ACCESS TO INFORMATION; BIOINFORMATICS; DATA PROCESSING; FUNGAL GENETICS; FUNGUS GROWTH; MICROSCOPY; MOLECULAR DYNAMICS; ONLINE SYSTEM; PROTEIN FUNCTION; TRANSCRIPTION REGULATION;

DATABASES, PROTEIN; GENE REGULATORY NETWORKS; INTERNET; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 84891762584     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt933     Document Type: Article

References (32)

1. Frenkel-Morgenstern, M., Cohen, A.A., Geva-Zatorsky, N., Eden, E., Prilusky, J., Issaeva, L, Sigal, A., Cohen-Saidon, C, Liron, Y., Cohen, L. et al. (2010) Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Nucleic Acids Res., 38, D508-D512.
2. Aragon, T., van Anken, E., Pincus, D., Serafimova, I.M., Korennykh, A.V., Rubio, CA. and Walter, P. (2009) Messenger RNA targeting to endoplasmic reticulum stress signalling sites. Nature, 457, 736-740.
3. Beyer, A., Hollunder, J., Nasheuer, H.P. and Wilhelm, T. (2004) Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Proteomics, 3, 1083-1092.
4. Breker, M., Gymrek, M. and Schuldiner, M. (2013) A novel single-cell screening platform reveals proteome plasticity during yeast stress responses. J. Cell Biol., 200, 839-850.
5. Eden, E., Geva-Zatorsky, N., Issaeva, I., Cohen, A., Dekel, E., Danon, T., Cohen, L., Mayo, A. and Alon, U. (2011) Proteome half-life dynamics in living human cells. Science, 331, 764-768.
6. Erjavec, N., Larsson, L., Grantham, J. and Nystrom, T. (2007) Accelerated aging and failure to segregate damaged proteins in Sir2 mutants can be suppressed by overproducing the protein aggregation-remodeling factor Hsp104p. Genes Dev., 21, 2410-2421.
7. Hedbacker, K., Townley, R. and Carlson, M. (2004) Cyclic AMP-dependent protein kinase regulates the subcellular localization of Snf1-Sip1 protein kinase. Mol. Cell. Biol., 24, 1836-1843.
8. Lee, M.V., Topper, S.E., Hubler, S.L., Hose, J., Wenger, CD., Coon, J.J. and Gasch, A.P. (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol. Syst. Biol., 7, 514.
9. Sigal, A., Milo, R., Cohen, A., Geva-Zatorsky, N., Klein, Y., Alaluf, I., Swerdlin, N., Perzov, N., Danon, T., Liron, Y. et al. (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat. Methods, 3, 525-531.
10. Tkach, J.M., Yimit, A., Lee, AY., Riffle, M., Costanzo, M., Jaschob, D., Hendry, J.A., Ou, J., Moffat, J., Boone, C. et al. (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat. Cell Biol., 14, 966-976.
11. Newman, J.R., Ghaemmaghami, S., Ihmels, J., Breslow, D.K., Noble, M., DeRisi, J.L. and Weissman, J.S. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441, 840-846.
12. Stathopoulos-Gerontides, A., Guo, J.J. and Cyert, M.S. (1999) Yeast calcineurin regulates nuclear localization of the Crz1p transcription factor through dephosphorylation. Genes Dev., 13, 798-803.
13. Toulmay, A. and Prinz, WA. Direct imaging reveals stable, micrometer-scale lipid domains that segregate proteins in live cells. J. Cell Biol, 202, 35-44.
14. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G, Botstein, D. and Brown, P.O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
15. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, CD., Bennett, HA., Coffey, E., Dai, H., He, Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
16. Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T.I., True, H.L., Lander, E.S. and Young, R.A. (2001) Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell, 12, 323-337.
17. Roh, T.Y. and Zhao, K. (2008) High-resolution, genome-wide mapping of chromatin modifications by GMAT. Methods Mol. Biol., 387, 95-108.
18. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S. and O'Shea, E.K. (2003) Global analysis of protein localization in budding yeast. Nature, 425, 686-691.
19. Nadler-Holly, M., Breker, M., Gruber, R., Azia, A., Gymrek, M., Eisenstein, M., Willison, K.R., Schuldiner, M. and Horovitz, A. Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins revealed by high-throughput microscopy analysis. Proc. Natl Acad. Sci. USA, 109, 18833-18838.
20. Picotti, P., Clement-Ziza, M., Lam, H., Campbell, D.S., Schmidt, A., Deutsch, E.W., Rost, H., Sun, Z., Rinner, O., Reiter, L. et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature, 494, 266-270.
21. de Godoy, L.M., Olsen, J.V., Cox, J., Nielsen, M.L., Hubner, N.C., Frohlich, F., Walther, T.C. and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature, 455, 1251-1254.
22. Teixeira, M.C., Monteiro, P., Jain, P., Tenreiro, S., Fernandes, A.R., Mira, N.P., Alenquer, M., Freitas, A.T., Oliveira, A.L. and Sa-Correia, I. (2006) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res., 34, D446-D451.
23. Monteiro, P.T., Mendes, N.D., Teixeira, M.C., d'Orey, S., Tenreiro, S., Mira, N.P., Pais, H., Francisco, A.P., Carvalho, A.M., Lourenco, A.B. et al. (2008) YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res., 36, D132-D136.
24. Abdulrehman, D., Monteiro, P.T., Teixeira, M.C., Mira, N.P., Lourenco, A.B., dos Santos, S.C., Cabrito, T.R., Francisco, A.P., Madeira, S.C., Aires, R.S. et al. (2010) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res., 39, D136-D140.
25. Natter, K., Leitner, P., Faschinger, A., Wolinski, H., McCraith, S., Fields, S. and Kohlwein, S.D. (2005) The spatial organization of lipid synthesis in the yeast Saccharomyces cerevisiae derived from large scale green fluorescent protein tagging and high resolution microscopy. Mol. Cell. Proteomics, 4, 662-672.
26. Habeler, G., Natter, K., Thallinger, G.G., Crawford, M.E., Kohlwein, S.D. and Trajanoski, Z. (2002) YPL.db: the yeast protein localization database. Nucleic Acids Res., 30, 80-83.
27. Kals, M., Natter, K., Thallinger, G.G., Trajanoski, Z. and Kohlwein, S.D. (2005) YPL.db2: the yeast protein localization database, version 2.0. Yeast, 22, 213-218.
28. Wiwatwattana, N. and Kumar, A. (2005) Organelle DB: a crossspecies database of protein localization and function. Nucleic Acids Res., 33, D598-604.
29. Wiwatwattana, N., Landau, C.M., Cope, G.J., Harp, G.A. and Kumar, A. (2007) Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Res., 35, D810-D814.
30. Frenkel-Morgenstern, M., Cohen, A.A., Geva-Zatorsky, N., Eden, E., Prilusky, J., Issaeva, I., Sigal, A., Cohen-Saidon, C., Liron, Y., Cohen, L. et al. (2010) Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Nucleic Acids Res., 38, D508-D512.
31. Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S. et al. (2010) Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol., 28, 1248-1250.
32. Desiere, F., Deutsch, E.W., Nesvizhskii, A.I., Mallick, P., King, N.L., Eng, J.K., Aderem, A., Boyle, R., Brunner, E., Donohoe, S. et al. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol., 6, R9.