Scientific Publications

Proteomics, Systems Biology and Bioinformatics

Zulawski M, Braginets R, Schulze WX (2013) PhosPhAt goes kinases – Searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. Nucleic Acids Research, 41: D1176-1184

Christian JO, Braginets R, Schulze WX, Walther D (2012) Characterization and prediction of protein phosphorylation hotspots in Arabidopsis thaliana. Frontiers in Plant Science, 3: 207

Zauber H, Mosler S, von Heßberg A, Schulze WX (2012) Dynamics of salivary proteins and metabolites during extreme endurance sports – A case study. Proteomics, 12 (13): 2221-2235

Engelsberger WR, Schulze WX (2012) Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen starved Arabidopsis seedlings. Plant Journal, 69 (6): 978-995

Joshi HJ, Hirsch-Hoffmann M, Bärenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AME, Briggs SP, Castleden I, Tanz SK, Millar H, Heazlewood JL (2011) MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiology, 155 (1): 259-270

Keinath NF, Kierszniowska S, Lorek J, Bourdais G, Kessler SA, Asano H, Grossniklaus U, Schulze WX, Robatzek S, Panstruga R (2010) PAMP-induced changes in plasma membrane compartmentalization reveal novel components of plant immunity. Journal of Biological Chemistry, 285 (50): 39140-39149

Riano-Pachon DM, Kleesen S, Neigenfind J, Durek P, Weber E, Engelsberger WR, Walther D, Selbig J, Schulze WX, Kersten B (2010) Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 11: 411

Durek P, Schmidt R, Heazlewood JL, Jones A, MacLean D, Nagel A, Kersten B, Schulze WX (2010) PhosPhAt: The Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Research 38: D828-834

Piques MC, Schulze WX, Höhne M, Gibon Y, Rohwer J, Stitt M (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Molecular Systems Biology 5 (314): E1-E17

Pertl H, Schulze WX, Obermeyer G (2009) The pollen organelle membrane proteome reveals highly spatial-temporal dynamics during germination and tube growth. Journal of Proteome Research 8 (11): 5142-5152

Kierszniowska S, Seiwert B, Schulze WX (2009) Definition of Arabidopsis sterol-rich membrane microdomains by differential treatment with methyl-ß-cyclodextrin and quantitative proteomics. Molecular and Cellular Proteomics 8 (4): 612-623

Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX (2008) PhosPhAt: A Database of phosphorylation sites in Arabidopsis thaliana and a plant specific phosphorylation site predictor. Nucleic Acids Research 36: D1015-D1021

Niittylä T, Fuglsang AT, Palmgren MG, Frommer WB, Schulze WX (2007) Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Molecular and Cellular Proteomics 6 (10): 1711-1726

Hummel J, Niemann M, Wienkoop S, Schulze W, Steinhauser D, Selbig J, Walther D, Weckwerth W (2007) ProMEX: a maß spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics 8: 216-223

Proteomics Method Development

Zauber H, Schulze WX (2012) Proteomics wants cRacker: Automated standardized data analysis of LC/MS derived proteomic data. Journal of Proteome Research, 11 (11): 5548-5555

Arsova B, Zauber H, Schulze WX (2012) Precision, proteome coverage and dynamic range of Arabidopsis proteome profiling using 15N metabolic labelling and label-free approaches. Molecular and Cellular Proteomics 11 (9): 619-628

Kierszniowska S, Walther D, Schulze WX (2009) Ratio-dependent significance thresholds in reciprocal 15N-labeling experiments as a robust tool in detection candidate proteins responding to biological treatment. Proteomics 9 (7): 1916-1924

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 (14): 1-11

Gruhler A, Schulze WX, Matthisen R, Mann M, Jensen ON (2005) Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Molecular and Cellular Proteomics 4: 1697-1702

Schulze WX (2005) Protein analysis in dissolved organic carbon: What proteins from organic debris, soil leachates and surface waters can tell us - a perspective. Biogeosciences 2: 75-86

Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2005) A proteomic fingerprint of dissolved organic carbon and soil particles. Oecologia 143 (3): 335-343

Schulze WX, Deng L, Mann M (2005) Phosphotyrosine interactome of the ErbB-receptor kinase family. Molecular Systems Biology 1 (5): E1-E13

Schulze WX, Mann M (2004) A novel proteomic screen for peptide-protein interactions. Journal of Biological Chemisty 279 (11): 10756-10764

Nutrient Transport and Sensing

Schulze WX, Schneider T, Starck S, Martinoia E, Trentmann O (2012) Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters. Plant Journal, 69 (3): 529-541

Krügel U, He HX, Gier K, Reins J, Chincinska I, Grimm B, Schulze WX, Kühn C (2012) The potato sucrose transporter StSUT1 interacts with a DRM-associated protein disulfide isomerase. Molecular Plant, 5 (1): 43-62

Lanquar V, Loque D, Hörmann F, Yuan L, Bohner A, Engelsberger WR, Lalonde S, Schulze WX, von Wiren N, Frommer WB (2009) Feedback inhibition of ammonium uptake by a phospho-dependent allosteric mechanism. The Plant Cell 21 (11): 3610-3622

Schulze WX, Reinders A, Ward JM, Lalonde S, Frommer WB (2003) Interactions between co-expressed Arabidopsis sucrose transporters in the split-ubiquitin system. BMC Biochemistry 4: 3

Reinders A, Schulze W*, Kühn C*, Barker L, Ward J, Frommer WB (2002) Protein-protein interactions between sucrose transporters of different affinities co-localized in the same enucleate sieve element. The Plant Cell 14 (7): 1567-1577
*equal contribution

Schulze W*, Reinders A*, 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 (6): 763-772
*equal contribution

Barker L, Kühn C, Weise A, Schulz A, Gebhardt C, Hirner B, Hellmann H, Schulze W, Ward JM, Frommer WB (2000) SUT2, a Putative Sucrose Sensor in Sieve Elements. The Plant Cell 12 (7): 1153-1164

Schulze W, Weise A, Frommer WB, Ward JM (2000) Function of the cytosolic N-terminus of sucrose transporter AtSUT2 in substrate affinity. FEBS Letters 485: 189-194

Carbon Metabolism in Arabidopsis

Pyl ET, Piques M, Ivakov A, Schulze W, Ishihara H, Stitt M, Sulpice R. (2012) Metabolism and growth in Arabidopsis depend on the daytime temperature but are temperature-compensated against cool nights. Plant Cell, 24 (6): 2443-2469

Hädrich N, Hendriks JHM, Kötting O, Arrivault S, Feil R, Zeeman, SC, Gibon Y, Schulze WX, Stitt M, Lunn JE (2012) Mutagenesis of the regulatory cysteine-81 in the APS1 subunit of ADP-glucose pyrophosphorylase alters diurnal starch turnover in Arabidopsis thaliana leaves. Plant Journal, 70 (2): 231-242

Schulze W, Schulze ED, Stadler J, Heilmeier H, Stitt M, Mooney HA (1994) Growth and reproduction of Arabidopsis thaliana in relation to storage of starch and nitrate in the wild-type and in starch deficient and nitrate-uptake-deficient mutants. Plant, Cell and Environment 17: 795-809

Schulze W, Stitt M, Schulze ED, Neuhaus HE, Fichtner K (1991) A quantification of the significance of assimilatory starch for growth of Arabidopsis thaliana L. Heynh. Plant Physiology 95 (3): 890-895

Schulze W (1991) Assimilationsstärke fördert das Wachstum von Arabidopsis thaliana. Junge Wissenschaft 22 (6): 36-42

Carnivorous Plants

Schulze WX*, Sanggaard KW*, Kreuzer I, Knudsen AD, Bemm F, Thogersen IB, Bräutigam A, Thomsen LR, Schliesky S, Dyrlund TF, Escalante-Pérez M, Becker D, Schulz J, Karring H, Weber A, Hojrup P, Hedrich R, Enghild JJ (2012) The protein composition of the digestive fluid from the Venus flytrap sheds light on prey digestion mechanisms. Molecular and Cellular Proteomics, accepted
*equal contribution

Schulze W, Schulze ED, Schulze I, Oren R (2001) Quantification of insect nitrogen utilization by the venus fly trap Dionaea muscipula catching prey with highly variable isotope signatures. Journal of Experimental Botany 52 (358): 1041-1049

Schulze W, Frommer WB, Ward JM (1999) Transporters for ammonium, amino acids and peptides are expressed in pitchers of the carnivorous plant Nepenthes. The Plant Journal 17 (6): 637-646

Schulze W, Schulze ED, Pate JS, Gillison AN (1997) The nitrogen supply from soils and insects during growth of the pitcher plants Nepenthes mirabilis, Cephalotus follicularis and Darlingtonia californica. Oecologia 112: 464-471

Schulze ED, Gebauer G, Schulze W, Pate JS (1991) The utilization of nitrogen from insect capture by different growth fors of Drosera from southwest Australia. Oecologia 87: 240-246

Schulze W (1991) Das Experiment: Versuche mit insektenfangenden Pflanzen. Biologie in Unserer Zeit 21 (6): 307-312

Schulze W, Schulze ED (1990) Insect capture and growth of the insectivorous Drosera rotundifolia L. Oecologia 82: 427-429

Plant Ecology

Birkhofer K, Schöning I, Alt F, Herold N, Klamer B, Maraun M, Marhan S, Oelman Y, Wubet T, Yukorn A, Begerow D, Berner D, Buscot F, Daniel R, Diekötter T, Ehnes RB, Erdmann G, Fischer C, Foesel B, Groh J, Gutknecht J, Kandeler E, Lang C, Lohaus G, Meyer A, Nack H, Näther A, Overmann J, Polle A, Pollierer MM, Scheu S, Schloter M, Schulze ED, Schulze W, Weinert J, Weisser W, Wolters V, Schrumpf M (2012) General relationships between abiotic soil properties and soil biota across spatial scales and different land-use types. PLoS ONE, 7(8): e43292

Wirth C, Schulze ED, Schulze W, von Stünzner-Karbe D, Ziegler W, Miljukova IM, Sogatchev A, Varlagin AB, Panvyorov M, Grigoriev S, Kusnetzova W, Siry M, Hardes G, Zimmermann R, Vygodskaya NN (1999) Above-ground biomass and structure of pristine Siberian Scots pine forests as controlled by competition and fire. Oecologia 121: 66-80

Schulze ED, Lloyd, J, Kelliher FM, Wirth C, Rebmann C, Lühker B, Mund M, Milykova I, Schulze W, Ziegler, Varlagin A, Valentini R, Dore S, Grigoriev S, Kolle O, Vygodskaya NN (1999) Productivity of forests in the Eurosiberian boreal region and their potential to act as a carbon sink - A synthesis. Global Change Biology 5: 703-722

Schulze ED, Farquhar GD, Miller JM, Schulze W, Walker BH, Williams RJ (1999) Interpretation of increased foliar d15N in woody species along a rainfall gradient in northern Australia. Australian Journal of Plant Physiology 26: 296-298

Schulze ED, Williams R, Farquhar GD, Schulze W, Langridge J, Miller J, Walker B (1998) Carbon and nitrogen isotope discrimination and nitrogen nutrition of trees along a rainfall gradient in northern Australia. Australian Journal of Plant Physiology 25: 413-425

Schulze ED, Ellis R, Schulze W, Trimborn P, Ziegler H (1996) Diversity of metabolic types and d13C carbon isotope ratios in the grass flora of Namibia in relation to growth form, precipitation and habitat conditions. Oecologia 106: 352-369

Schulze ED, Schulze W, Kelliher FM, Vygodskaya NN, Ziegler W, Kobak I, Koch H, Arneth A, Kusnetsova WA, Sogatchev A, Issajev A, Bauer G, Hollinger DY (1995) Aboveground biomass and nitrogen nutrition in a crhonosequence of pristine Dahurian Larix stands in eastern Siberia. Canadian Journal of Forest Research 25: 943-960

Reviews and Book Chapters

Arsova B, Schulze WX (2012) Current status of the plant phosphorylation site database PhosPhAt and its use as a resource for molecular plant physiology. Frontiers in Plant Science, 3: 132

Arsova B, Kierszniowska S, Schulze WX (2012) The use of heavy nitrogen in quantitative proteomics-experiments in plants. Trends in Plant Science, 17 (2): 102-112

Schulze WX (2010) Proteomic approaches to understand protein phosphorylation in pathway modulation. Current Opinion in Plant Biology 13: 1-8

Schulze WX, Usadel B (2010) Quantitation in Mass-Spectrometry-Based Proteomics. Annual Review of Plant Biology. 61: 491-516

Kersten, B, Agrawal, GK, Durek P, Neigenfind J, Schulze W, Walther D, Rakwal R (2009) Plant phosphoproteomics: An update. Proteomics 9: 964-988

Schulze W (2008) Mass spectrometry based proteomics as a tool for the analysis of protein-protein interactions in signaling processes. In: Bögre L, Beemster TGS (eds.) Plant Cell Monographs: Plant Growth Signalling. Springer Verlag, Berlin.

Frommer WB, Schulze WX, Lalonde S (2003) Hexokinase, Jack-of-all-trades. Science 300: 261-263

Schulze W, and Schulze ED (1994) The significance of assimilatory starch for growth in Arabidopsis thaliana wild-type and starchless mutants. In: Schulze ED and Caldwell MM (eds.) Ecological Studies Volume 100: Ecophysiology of Photosynthesis. Springer Verlag, Berlin

Collaborative Work

Mastrobuoni G, Irgang S, Pietzke M, Wenzel M, Assmus HE, Schulze WX, Kempa S (2012) Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii. BMC Genomics, 13 (1): 215

Gaude N, Schulze WX, Franken P, Krajinski F (2012) Cell type-specific protein and transcription profiles implicate periarbuscular membrane synthesis as an important carbon sink in the mycorrhizal symbiosis. Plant Signaling and Behavior, 7 (4): 461-464

Ramirez-Aguilar SJ, Keuthe M, Rocha M, Fedyaev VV, Kramp K, Gupta KJ, Rasmusson AG, Schulze WX, van Dongen JT (2011) The composition of plant mitochondrial supercomplexes changes with the oxygen availability. Journal of Biological Chemistry, 286 (50): 43045-43053

Pertl H, Rittmann S, Schulze WX, Obermeyer G (2011) Identification of lily pollen 14-3-3 isoforms and their sub-cellular and time dependent expression profile. Biological Chemistry, 392: 249–262

Apel W, Schulze WX, Bock R (2010) Identification of protein stability determinants in chloroplasts . Plant Journal 63: 636-650

Rogalski M, Schöttler MA, Thiele W, Schulze WX, Bock R (2008) Rpl33, a nonessential plastid-encoded ribosomal protein in tobacco, is required under cold stress conditions. The Plant Cell 20 (8): 2221-2237

Erba EB, Matthisen R, Bunkenborg J, Schulze WX, Di Stefano P, Cabodi S, Tarone G, Defilippi P, Jensen ON (2007) Quantitation of multisite EGF receptor phosphorylation using maß spectrometry and a novel normalization approach. Journal of Proteome Research 6 (7): 2768-2785