Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198-207 Andersen JS, Wilkinson CJ, Myoru T, Mortensen P, Nigg EA, Mann M (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426:570-574

Atwal GS, Huber JL, Huber SC (1998) Phosphorylated nitrate reductase and 14-3-3 proteins. Site of interaction, effects of ions, and evidence for an amp-binding site on 14-3-3 proteins. Plant Physiol 118:1041-1048 Barker L et al (2000) SUT2, a putative sucrose sensor in sieve elements. Plant Cell 12:1153-1164

Bauerle PA, Huttner WB (1985) Tyrosine sulfation of yolk proteins 1, 2, and 3 in Droso-

phila melanogaster. J Biol Chem 260:6434-6439 Beausoleil SA et al (2004) Large-scale characterization of HeLa cell nuclear phosphopro-

teins. Proc Natl Acad Sci USA 101:12130-12135 Blagoev B, Kratchmarova I, Ong S-E, Nielsen M, Foster L, Mann M (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 21:315-318 Blagoev B, Ong S-E, Kratchmarova I, Mann M (2004) Temporal ordering of signaling networks by quantitative proteomics. Nat Biotechnol 22:1139-1145 Butterbrodt T, Thurow C, Gatz C (2006) Chromatin immunoprecipitation analysis of the tobacco PR-1a- and the truncated CaMV 35S promoter reveals differences in salicylic acid-dependent TGA factor binding and histone acetylation. Plant Mol Biol 61:665-674

de Hoog C, Mann M (2004) Proteomics. Annu Rev Genomics Hum Genet 5:267-293 Dephoure N, Howson RW, Blethrow JD, Shokat KM, O'Shea EK (2005) Combining chemical genetics and proteomics to identify protein kinase substrates. Proc Natl Acad Sci USA 102:17940-17945

Dunkley TPJ, Griffin JL, Dupree P, Lilley KS (2004) Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 3:1128-1134 Ehsan H, Ray WK, Phinney BS, Wang X, Huber SC, Clouse SD (2005) Interaction of Arabidopsis BRASSINOSTEROID-INSENSITIVE 1 receptor kinase with a homolog of mammalian TGF-ß receptor interacting protein. Plant J 43:251-261 Elia AEH, Cantley LC, Yaffe MB (2003) Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science 299:1228-1231 Eng J, McCormack AL, Yates JRI (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976-989

Engelsberger WR, Erban A, Kopka J, Schulze WX (2006) Metabolic labeling of plant cell cultures with K15NO3 as a tool for quantitative analysis of proteins and metabolites. Plant Methods 2:1-11

Espejo A, Cote J, Bednarek A, Richard S, Bedford MT (2002) A protein-domain microar-

ray identifies novel protein-protein interactions. Biochem J 367:697-702 Eubel H, Heinemeyer J, Sunderhaus S, Braun HP (2004) Respiratory chain supercomplexes in plant mitochondria. Plant Physiol Biochem 42:937-942 Eubel H, Braun HP, Millar AH (2005) Blue-native PAGE in plants: a tool in analysis of protein-protein interactions. Plant Methods 1:1-13 Fuglsang AT et al (1999) Binding of 14-3-3 protein to the plasma membrane H(+)-ATPase AHA2 involves the three C-terminal residues Tyr(946)-Thr-Val and requires phosphorylation of Thr(947). J Biol Chem 274:36774-36780 Galski H, De Groot N, Ilan J, Hochberg AA (1983) Phosphorylation of tyrosine in cultured human placenta. Biochim Biophys Acta 761:284-290 Gavin AC et al (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147 Gavin AC et al (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631-636

Glinski M, Weckwerth W (2005) Differential multisite phosphorylation of the trehalose-6-phosphate synthase gene family in Arabidopsis thaliana: a mass spectrometry-based process for multiparallel peptide library phosphorylation analysis. Mol Cell Pro-teomics 4:1614-1625

Glinski M, Romeis T, Witte CP, Wienkoop S, Weckwerth W (2003) Stable isotope labeling of phosphopeptides for multiparallel kinase target analysis and identification of phosphorylation sites. Rapid Commun Mass Spectrom 17:1579-1584 Grefen C, Harter K (2004) Plant two-component systems: principles, functions, complexity and cross talk. Planta 219:733-742 Gruhler A, Schulze WX, Matthiesen R, Mann M, Jensen ON (2005) Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol Cell Proteomics 4:1697-1702 Hanai H, Nakayama D, Yang H, Matsubayashi Y, Hirota Y, Sakagami Y (2000) Existence of a plant tyrosylprotein sulfotransferase: novel plant enzyme catalyzing tyrosine O-sulfation of preprophytosulfokine variants in vitro. FEBS Lett 470:97-101 Heinemeyer J, Eubel H, Wehmhoner D, Jansch L, Braun HP (2004) Proteomic approach to characterize the supramolecular organization of photosystems in higher plants. Phytochemistry 65:1683-1692

Ho Y et al (2002) Systematic identification of protein complexes in Saccharomyces cere-

visiae by mass spectrometry. Nature 415:180-183 Houseman BT, Huh JH, Kron SJ, Mrksich M (2002) Peptide chips for the quantitative evaluation of protein kinase activity. Nat Biotechnol 20:270-274 Huber SC, Huber JL (1996) Role and regulation of sucrose-phosphate synthase in higher plants. Annu Rev Plant Physiol Plant Mol Biol 47:431-444 Ishihama Y et al (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4:1265-1272 Jones AM, Bennett MH, Mansfield JW, Grant M (2006) Analysis of the defence phos-phoproteome of Arabidopsis thaliana using differential mass tagging. Proteomics 6:4155-4165

Kay BK, Kasanov J, Yamabhai M (2001) Screening phage-displayed combinatorial peptide libraries. Methods 24:240-246 Manning F, Cantley LC (2002) Hitting the target: emerging technologies in the search for kinase substrates. Sci STKE 162:1-4 Nelson CJ, Hegeman AD, Harms AC, Sussman MR (2006) A quantitative analysis of Arabidopsis plasma membrane using trypsin-catalyzed 18O labeling. Mol Cell Proteomics 5:1382-1395

Niittyla T, Frommer WB, Schulze WX (2007) Dynamics of phosphorylation in starved

Arabidopsis seedlings upon sucrose resupply. Mol Cell Proteomics 6:1711-1726 Nühse TS, Stensballe A, Jensen ON, Peck J (2003) Large-scale analysis of in vivo phos-phorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics 2:1234-1243 Olayioye M, Neve RM, Lane HA, Hynes NE (2000) The ErbB signaling network: receptor heterodimerization in development and cancer. EMBO J 19:3159-3169 Olsen JV, Mann M (2004) Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci USA 101:1341713422

Olsen JV et al (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127:635-648 Pawson T, Gish GD (1992) SH2 and SH3 domains: from structure to function. Cell 71:359362

Pawson T, Scott JD (1997) Signaling through scaffold, anchoring, and adaptor proteins. Science 278:2075-2080

Peck SC (2006) Analysis of protein phosphorylation: methods and strategies for studying kinases and substrates. Plant J 45:512-522 Peltier JB et al (2006) The oligomeric stromal proteome of Arabidopsis thaliana chloro-

plasts. Mol Cell Proteomics 5:114-133 Pevzner PA, Mulyukov Z, Dancik V, Tang CL (2001) Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res 11:290-299

Reinders J, Sickmann A (2005) State-of-the-art in phosphoproteomics. Proteomics 5:4052-4061

Reinders A, Schulze W, Thaminy S, Stagljar I, Frommer WB, Ward JM (2002) Intra- and intermolecular interactions in sucrose transporters at the plasma membrane detected by the split-ubiquitin system and functional assays. Structure 10:763-772 Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030-1032

Rohila JS, Chen M, Cerny R, Fromm ME (2004) Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J 38:172-181 Rohila JS et al (2006) Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J 46:1-13 Russinova E et al (2004) Heterodimerization and endocytosis of Arabidopsis brassinos-

teroid receptors BRI1 and AtSERK3 (BAK1). Plant Cell 16:3216-3229 Schulze W, Mann M (2004) A novel proteomic screen for peptide-protein interactions.

J Biol Chem 279:10756-10764 Schulze W, Deng L, Mann M (2005) The phosphotyrosine interactome of the ErbB-

receptor kinase family. Mol Syst Biol. doi:10.1038/msb4100012:E1-E13 Shah K, Liu Y, Deirmengian C, Shokat KM (1997) Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc Natl Acad Sci USA 94:3565-3570 Tai HH, Tai GC, Beardmore T (2005) Dynamic histone acetylation of late embryonic genes during seed germination. Plant Mol Biol 59:909-925 Toroser D, Athwal GS, Huber SC (1998) Site-specific regulatory interaction between spinach leaf sucrose-phosphate synthase and 14-3-3 proteins. FEBS Lett 435:110-114 Tsuji H, Saika H, Tsutsumi N, Hirai A, Nakazono M (2006) Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice. Plant Cell Physiol 47:995-1003 von Mering C et al (2002) Comparative assessment of large-scale data sets of proteinprotein interactions. Nature 417:339-403 Wang X et al (2005) Identification and functional analysis of in vivo phosphorylation sites of the Arabidopsis brassinosteroid-insensitive 1 receptor kinase. Plant Cell 17:16851703

Washburn MP, Wolters D, Yates JRI (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242-247 Xu CR et al (2005) Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis. Proc Natl Acad Sci USA 102:14469-14474

Plant Cell Monogr (10)

L. Bogre and G. Beemster: Plant Growth Signaling

DOI 10.1007/7089_2007_152/Published online: 26 January 2008

© Springer-Verlag Berlin Heidelberg 2008

0 0

Post a comment