Protein Mass Spectrometry: Publications (all group members)
2021
Pruitt RN, Locci F, Wanke F, Zhang L, Saile SC, Joe A, Karelina D, Hua C, Fröhlich K, Wan WL, Hu M, Rao S, Stolze SC, Harzen A, Gust AA, Harter K, Joosten MHAJ, Thomma BPHJ, Zhou JM, Dangl JL, Weigel D, Nakagami H, Oecking C, Kasmi FE, Parker JE, Nürnberger T, “The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity”, Nature, 2021 Sep 8. doi: 10.1038/s41586-021-03829-0. Online ahead of print.
Marques DN, Stolze SC, Harzen A, Nogueira ML, Batagin-Piotto KD, Piotto FA, Mason C, Azevedo RA, Nakagami H, “Comparative phosphoproteomic analysis of tomato genotypes with contrasting cadmium tolerance”, Plant Cell Reports, 2021 Aug 19. doi: 10.1007/s00299-021-02774-6. Online ahead of print.
Besse L, Besse A, Stolze SC, Sobh A, Zaal EA, van der Ham AJ, Ruiz M, Phuyal S, Büchler L, Sathianathan M, Florea BI, Borén J, Ståhlman M, Huber J, Bolomsky A, Ludwig H, Hannich JT, Loguinov A, Everts B, Berkers CR, Pilon M, Farhan H, Vulpe CD, Overkleeft HS, Driessen C, “Treatment with HIV-protease inhibitor nelfinavir identifies membrane lipid composition and fluidity as a therapeutic target in advanced multiple myeloma”, Cancer Research, 81(17):4581-4593 (2021)
Iwakawa H, Melkonian K, Schlüter T, Jeon HW, Nishihama R, Motose H, Nakagami H#, “Agrobacterium-mediated transient transformation of Marchantia liverworts”, Plant Cell & Physiology, 2021 Aug 12:pcab126. doi: 10.1093/pcp/pcab126. Online ahead of print. (#corresponding author)
Matsumoto A, Schlüter T, Melkonian K, Takeda A, Nakagami H, Mine A, “A versatile Tn7 transposon-based bioluminescence tagging tool for quantitative and spatial detection of bacteria in plants”, Plant Communications, Online ahead of print. https://doi.org/10.1016/j.xplc.2021.100227
Kimura T, Haga K, Nomura Y, Higaki T, Nakagami H, Sakai T, “Phosphorylation of NONPHOTOTROPIC HYPOCOTYL3 affects photosensory adaptation during the phototropic response”, Plant Physiology, https://doi.org/10.1093/plphys/kiab281 Online ahead of print.
Sun X, Lapin D, Feehan JM, Stolze SC, Kramer K, Dongus JA, Rzemieniewski J, Blanvillain-Baufumé S, Harzen A, Bautor J, Derbyshire P, Menke FLH, Finkemeier I, Nakagami H, Jones JDG, Parker JE, “Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity”, Nature Communications, 12(1):3335 (2021)
Ma KW, Niu Y, Jia Y, Ordon J, Copeland C, Emonet A, Geldner N, Guan R, Stolze SC, Nakagami H, Garrido-Oter R, Schulze-Lefert P. “Coordination of microbe-host homeostasis by crosstalk with plant innate immunity”, Nature Plants, 7(6):814-825 (2021)
Sanagi M, Aoyama S, Kubo A, Lu Y, Sato Y, Ito S, Abe M, Mitsuda N, Ohme-Takagi M, Kiba T, Nakagami H, Rolland F, Yamaguchi J, Imaizumi T, Sato T, “Low nitrogen conditions accelerate flowering by modulating the phosphorylation state of FLOWERING BHLH 4 in Arabidopsis”, Proceedings of the National Academy of Sciences of the United States of America, 118(19):e2022942118 (2021)
2020
Nobori T, Wang Y, Wu J, Stolze SC, Tsuda Y, Finkemeier I, Nakagami H, Tsuda K, “Multidimensional gene regulatory landscape of a bacterial pathogen in plants”, Nature Plants, https://doi.org/10.1038/s41477-020-0690-7 (2020)
Stolze SC, Nakagami H#, Targeted quantification of phosphopeptides by parallel reaction monitoring (PRM), Methods in Molecular Biology, 2139:213-224 (2020) (#corresponding author)
Nakano RT#, Ishihama N, Wang Y, Takagi J, Uemura T, Schulze-Lefert P, Nakagami H#, “Apoplastic fluid preparation from Arabidopsis thaliana leaves upon interaction with a non-adapted powdery mildew pathogen”, Methods in Molecular Biology, 2139:79-88 (2020) (#joint corresponding authors)
Li X, Sanagi M, Lu Y, Nomura Y, Stolze SC, Yasuda S, Saijo Y, Schulze WX, Feil R, Stitt M, Lunn JE, Nakagami H#, Sato T#, Yamaguchi J, “Protein phosphorylation dynamics under identification of a cell death-related receptor-like kinase in Arabidopsis”, Frontiers in Plant Science, Apr 3;11:377 (2020) (#joint corresponding authors)
Sang Q, Pajoro A, Sun H, Song B, Yang X, Stolze SC, Andrés F, Schneeberger K, Nakagami H, Coupland G, “Mutagenesis of a quintuple mutant impaired in environmental responses reveals roles for CHROMATIN REMODELING 4 in Arabidopsis floral transition”, The Plant Cell, 32(5):1479-1500 (2020)
Kimura S, Hunter K, Vaahtera L, Tran HC, Citterico M, Vaattovaara A, Rokka A, Stolze SC, Harzen A, Meißner L, Tabea Wilkens MMT, Hamann T, Toyota M, Nakagami H, Wrzaczek M, “CRK2 and C-terminal phosphorylation of NADPH oxidase RBOHD regulate ROS production in Arabidopsis”, The Plant Cell, 32(4):1063-1080 (2020)
2019
Kato S, Okamura E, Matsunaga TM, Nakayama M, Kawanishi Y, Ichinose T, Iwane AH, Sakamoto T, Imoto Y, Ohnuma M, Nomura Y, Nakagami H, Kuroiwa H, Kuroiwa T, Matsunaga S, “Cyanidioschyzon merolae aurora kinase phosphorylates evolutionarily conserved sites on its target to regulate mitochondrial division”, Communications Biology, 2:477 (2019)
Koide E, Suetsugu N, Iwano M, Gotoh E, Nomura Y, Stolze SC, Nakagami H, Kohchi T, Nishihama R, “Regulation of photosynthetic carbohydrate metabolism by a Raf-like kinase in the liverwort Marchantia polymorpha”, Plant Cell & Physiology, 61(3):631-643 (2019)
Matsui H, Iwakawa H, Hyon GS, Yotsui I, Katou S, Monte I, Nishihama R, Franzen R, Solano R, Nakagami H#, “Isolation of natural fungal pathogens from Marchantia polymorpha reveals antagonism between salicylic acid and jasmonate during liverwort-fungus interactions”, Plant Cell & Physiology, 61(2):442 (2019) (#corresponding author)
Yang C, Sofroni K, Wijnker E, Hamamura Y, Carstens L, Harashima H, Stolze SC, Vezon D, Chelysheva L, Orban-Nemeth Z, Pochon G, Nakagami H, Schlögelhofer P, Grelon M, Schnittger A, “The Arabidopsis Cdk1/Cdk2 homolog CDKA;1 controls chromosome axis assembly during plant meiosis”, The EMBO Journal, 39(3):e101625 (2019)
Ishikawa S, Barrero JM, Takahashi F, Nakagami H, Peck SC, Gubler F, Shinozaki K, Umezawa T, “Comparative phosphoproteomic analysis reveals a decay of ABA signaling in barley embryos during after-ripening”, Plant Cell & Physiology, 60(12):2758-2768 (2019)
Sano N, Takebayashi Y, To A, Mhiri C, Rajjou L, Nakagami H#, Kanekatsu M#, “Shotgun proteomic analysis highlights roles of long-lived mRNAs and de novo transcribed mRNAs upon imbibition in rice embryos”, Plant Cell & Physiology, 60(11):2584-2596 (2019) (#joint corresponding authors)
Carella P, Gogleva A, Hoey DJ, Bridgen AJ, Stolze SC, Nakagami H, Schornack S, “Conserved biochemical defenses underpin host responses to oomycete infection in an early-divergent land plant lineage”, Current Biology, 29(14):2282-2294.e5 (2019)
Hu Z, Ghosh A, Stolze SC, Horváth M, Bai B, Schaefer S, Zündorf S, Liu S, Harzen A, Hajheidari M, Sarnowski TJ, Nakagami H, Koncz Z, Koncz C, “Gene modification by fast-track recombineering for cellular localization and isolation of components of plant protein complexes”, The Plant Journal, Oct;100(2):411-429 (2019)
Zhao L, Phuong LT, Luan MT, Fitrianti AN, Matsui H, Nakagami H, Noutoshi Y, Yamamoto M, Ichinose Y, Shiraishi T, Toyoda K, “A class III peroxidase PRX34 is a component of disease resistance in Arabidopsis”, Journal of General Plant Pathology, 85, 405–412 (2019)
Yang C, Hamamura Y, Sofroni K, Böwer F, Stolze SC, Nakagami H, Schnittger A, “SWITCH 1/DYAD is a WINGS APART-LIKE antagonist that maintains sister chromatid cohesion in meiosis”, Nature Communications, 10(1):1755 (2019)
Shinkawa H, Kajikawa M, Nomura Y, Ogura M, Sawaragi Y, Yamano T, Nakagami H, Sugiyama N, Ishihama Y, Kanesaki Y, Yoshikawa H, Fukuzawa H, “Algal protein kinase, triacylglycerol accumulation regulator 1, modulates cell viability and gametogenesis in carbon/nitrogen-imbalanced conditions”, Plant Cell & Physiology, 60(4):916-930 (2019)
Uemura T, Nakano RT, Takagi J, Wang Y, Kramer K, Finkemeier I, Nakagami H, Tsuda K, Ueda T, Schulze-Lefert P, Nakano A, “A Golgi-released subpopulation of the trans-Golgi network mediates protein secretion in Arabidopsis”, Plant Physiology, 179(2):519-532 (2019)
Meng Q, Gupta R, Min CW, Kim J, Kramer K, Wang Y, Park SR, Finkemeier I, Kim ST, “A proteomic insight into the MSP1 and flg22 induced signaling in Oryza sativa leaves”, Journal of Proteomics, 196:120-130 (2019)
2018
Fichman Y, Koncz Z, Reznik N, Miller G, Szabados L, Kramer K, Nakagami H, Fromm H, Koncz C, Zilberstein A, “SELENOPROTEIN O is a chloroplast protein involved in ROS scavenging and its absence increases dehydration tolerance in Arabidopsis thaliana”, Plant Science, 270:278-291 (2018)
Myouga F, Takahashi K, Tanaka R, Nagata N, Kiss AZ, Funk C, Nomura Y, Nakagami H, Jansson S, Shinozaki K, “Stable accumulation of photosystem II requires ONE-HELIX PROTEIN1 (OHP1) of the light harvesting-like family”, Plant Physiology, 176(3):2277-2291 (2018)
Yokoo S, Inoue S, Suzuki N, Amakawa N, Matsui H, Nakagami H, Takahashi A, Arai R, Katou S, “Comparative analysis of plant isochorismate synthases reveals structural mechanisms underlying their distinct biochemical properties”, Bioscience Reports, 8(2) (2018)
Oide M, Okajima K, Nakagami H, Kato T, Sekiguchi Y, Oroguchi T, Hikima T, Yamamoto M, Nakasako M, “Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis”, The Journal of Biological Chemistry, 293(3):963-972 (2018)
Soethoudt M, Stolze SC, Westphal MV, van Stralen L, Martella A, van Rooden EJ, Guba W, Varga ZV, Deng H, van Kasteren SI, Grether U, IJzerman AP, Pacher P, Carreira EM, Overkleeft HS, Ioan-Facsinay A, Heitman LH, van der Stelt M, “Selective photoaffinity probe that enables assessment of cannabinoid CB2 receptor expression and ligand engagement in human cells”, Journal of the American Chemical Society, 140(19):6067-6075 (2018)
Besse A, Stolze SC, Rasche L, Weinhold N, Morgan GJ, Kraus M, Bader J, Overkleeft HS, Besse L, Driessen C, “Carfilzomib resistance due to ABCB1/MDR1 overexpression is overcome by nelfinavir and lopinavir in multiple myeloma”, Leukemia, 32(2):391-401 (2018)
Birkenbihl RP, Kracher B, Ross A, Kramer K, Finkemeier I, Somssich IE, “Principles and characteristics of the Arabidopsis WRKY regulatory network during early MAMP-triggered immunity”, The Plant Journal, 96(3):487-502 (2018)
Wozny D, Kramer K, Finkemeier I, Acosta IF, Koornneef M, “Genes for seed longevity in barley identified by genomic analysis on near isogenic lines”, Plant, Cell & Environment, 41(8):1895-1911 (2018)
Gupta R, Min CW, Kramer K, Agrawal GK, Rakwal R, Park KH, Wang Y, Finkemeier I, Kim ST, “A multi-omics analysis of Glycine max leaves reveals alteration in flavonoid and isoflavonoid metabolism upon ethylene and abscisic acid treatment”, Proteomics, 18(7):e1700366 (2018)
2017
Matsui H, Nomura Y, Egusa M, Hamada T, Hyon GS, Kaminaka H, Watanabe Y, Ueda T, Trujillo M, Shirasu K, Nakagami H#, “The GYF domain protein PSIG1 dampens the induction of cell death during plant-pathogen interactions”, PLoS Genetics, 13(10):e1007037 (2017) (#corresponding author)
Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J, “Insights into land plant evolution garnered from the Marchantia polymorpha genome”, Cell, 171(2):287-304.e15 (2017)
Furlan G, Nakagami H, Eschen-Lippold L, Jiang X, Majovsky P, Kowarschik K, Hoehenwarter W, Lee J, Trujillo M, “Changes in PUB22 ubiquitination modes triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 dampen the immune response”, The Plant Cell, 29(4):726-745 (2017)
Née G, Kramer K, Nakabayashi K, Yuan B, Xiang Y, Miatton E, Finkemeier I, Soppe WJJ, “DELAY OF GERMINATION1 requires PP2C phosphatases of the ABA signalling pathway to control seed dormancy”, Nature Communications, 8(1):72 (2017)
Besse A, Besse L, Stolze SC, Rasche L, Weinhold N, Morgan GJ, Kraus M, Bader J, Overkleeft HS, Driessen C, “Expression of MDR1 mediates Carfilzomib resistance in MM and PCL patients and may be overcome by HIV protease inhibitors Nelfinavir and Lopinavir”, Clinical Lymphoma, Myeloma & Leukemia, 17(1):e32 (2017)
2016
Yamada K, Saijo Y, Nakagami H, Takano Y, “Regulation of sugar transporter activity for antibacterial defense in Arabidopsis”, Science, 354(6318):1427-1430 (2016)
Yamada K, Yamaguchi K, Shirakawa T, Nakagami H, Mine A, Ishikawa K, Fujiwara M, Narusaka M, Narusaka Y, Ichimura K, Kobayashi Y, Matsui H, Nomura Y, Nomoto M, Tada Y, Fukao Y, Fukamizo T, Tsuda K, Shirasu K, Shibuya N, Kawasaki T, “The Arabidopsis CERK1-associated kinase PBL27 connects chitin perception to MAPK activation”, The EMBO Journal, 35(22):2468-2483 (2016)
Harashima H, Dissmeyer N, Hammann P, Nomura Y, Kramer K, Nakagami H, Schnittger A, “Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1”, BMC Plant Biology, 16(1):209 (2016)
Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE, “Circadian profiling of the Arabidopsis proteome using 2D-DIGE”, Frontiers in Plant Science, 7:1007 (2016)
Cifuentes M, Jolivet S, Cromer L, Harashima H, Bulankova P, Renne C, Crismani W, Nomura Y, Nakagami H, Sugimoto K, Schnittger A, Riha K, Mercier R, “TDM1 regulation determines the number of meiotic divisions”, PLoS Genetics, 12(2):e1005856 (2016)
Bowman JL, Araki T, Arteaga-Vazquez MA, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin SS, Nagasaki H, Nakagami H, Nakajima K, Nakamura Y, Ohashi-Ito K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato KT, Zachgo S, Kohchi T, “The naming of names: Guidelines for gene nomenclature in Marchantia”, Plant Cell & Physiology, 57(2):257-61 (2016)
Schulz M, Filary B, Kühn S, Colby T, Harzen A, Schmidt J, Sicker D, Hennig L, Hofmann D, Disko U, Anders N, “Benzoxazolinone detoxification by N-Glucosylation: The multi-compartment-network of Zea mays L”, Plant Signaling & Behavior, 11(1):e1119962 (2016)
Lazzaretti D, Veith K, Kramer K, Basquin C, Urlaub H, Irion U, Bono F, “The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease”, Nature Structural & Molecular Biology, 23(8):705-13 (2016)
Rösler SM, Kramer K, Finkemeier I, Humpf HU, Tudzynski B, “The SAGA complex in the rice pathogen Fusarium fujikuroi: structure and functional characterization”, Molecular Microbiology, 102(6):951-974 (2016)
Ruhe J, Agler MT, Placzek A, Kramer K, Finkemeier I, Kemen EM, “Obligate biotroph pathogens of the genus Albugo are better adapted to active host defense compared to niche competitors”, Frontiers in Plant Science, 7:820 (2016)
Xiang Y, Song B, Née G, Kramer K, Finkemeier I, Soppe WJ, “Sequence polymorphisms at the REDUCED DORMANCY5 pseudophosphatase underlie natural variation in Arabidopsis dormancy”, Plant Physiology, 171(4):2659-70 (2016)
Sindlinger J, Bierlmeier J, Geiger LC, Kramer K, Finkemeier I, Schwarzer D, “Probing the structure-activity relationship of endogenous histone deacetylase complexes with immobilized peptide-inhibitors”, Journal of Peptide Science, 22(5):352-9 (2016)Stolze SC, Liu N, Wijdeven RH, Tuin AW, van den Nieuwendijk AM, Florea BI, van der Stelt M, van der Marel GA, Neefjes JJ, Overkleeft HS, “Photo-crosslinking of clinically relevant kinases using H89-derived photo-affinity probes”, Molecular Biosystems, 12(6):1809-17 (2016)
1996 - 2015
Egusa M, Matsui H, Urakami T, Okuda S, Ifuku S, Nakagami H, Kaminaka H, “Chitin nanofiber elucidates the elicitor activity of polymeric chitin in plants”, Frontiers in Plant Science, 6:1098 (2015)
Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE, “Quantitative circadian phosphoproteomic analysis of Arabidopsis reveals extensive clock control of key components in physiological, metabolic and signaling pathways”, Molecular & Cellular Proteomics, 14(8):2243-60 (2015)
Mogami J, Fujita Y, Yoshida T, Tsukiori Y, Nakagami H, Nomura Y, Fujiwara T, Nishida S, Yanagisawa S, Ishida T, Takahashi F, Morimoto K, Kidokoro S, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K, “Two distinct families of protein kinases are required for plant growth under high external Mg2+ concentrations in Arabidopsis”, Plant Physiology, 167(3):1039-57 (2015)
González-Rodríguez VE, Liñeiro E, Colby T, Harzen A, Garrido C, Cantoral JM, Schmidt J, Fernández-Acero FJ, “Proteomic profiling of Botrytis cinerea conidial germination”, Archives of Microbiology, 197(2):117-33 (2015)
Zaman U, Richter FM, Hofele R, Kramer K, Sachsenberg T, Kohlbacher O, Lenz C, Urlaub H, “Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions”, Molecular & Cellular Proteomics, 14(12):3196-210 (2015)
Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H, “Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry”, Methods, 89:138-48 (2015)
Qamar S, Kramer K, Urlaub H, “Studying RNA-protein interactions of pre-mRNA complexes by mass spectrometry”, Methods in Enzymology, 558:417-63 (2015)
Nakaminami K, Matsui A, Nakagami H, Minami A, Nomura Y, Tanaka M, Morosawa T, Ishida J, Takahashi S, Uemura M, Shirasu K, Seki M, “Analysis of differential expression patterns of mRNA and protein during cold-acclimation and de-acclimation in Arabidopsis”, Molecular & Cellular Proteomics, 13(12):3602-11 (2014)
Matsui H, Fujiwara M, Hamada S, Shimamoto K, Nomura Y, Nakagami H, Takahashi A, Hirochika H, “Plasma membrane localization is essential for Oryza sativa Pto-interacting protein 1a-mediated negative regulation of immune signaling in rice”, Plant Physiology, 166(1):327-36 (2014)
Kondo Y, Ito T, Nakagami H, Hirakawa Y, Saito M, Tamaki T, Shirasu K, Fukuda H, “Plant GSK3 proteins regulate xylem cell differentiation downstream of TDIF-TDR signalling”, Nature Communications, 5:3504 (2014)
Nakagami H#, “StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics”, Methods in Molecular Biology, 1072:595-607 (2014) (#corresponding author)
Chandrasekar B, Colby T, Emran Khan Emon A, Jiang J, Hong TN, Villamor JG, Harzen A, Overkleeft HS, van der Hoorn RA, “Broad-range glycosidase activity profiling”, Molecular & Cellular Proteomics, 13(10):2787-800 (2014)
Murmann T, Carrillo-García C, Veit N, Courts C, Glassmann A, Janzen V, Madea B, Reinartz M, Harzen A, Nowak M, Perner S, Winter J, Probstmeier R, “Staurosporine and extracellular matrix proteins mediate the conversion of small cell lung carcinoma cells into a neuron-like phenotype”, PLoS One, 9(2):e86910 (2014)
Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, Urlaub H, “Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins”, Nature Methods, 11(10):1064-70 (2014)
Loedige I, Stotz M, Qamar S, Kramer K, Hennig J, Schubert T, Löffler P, Längst G, Merkl R, Urlaub H, Meister G, “The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation”, Genes & Development, 28(7):749-64 (2014)
Fujita S, Pytela J, Hotta T, Kato T, Hamada T, Akamatsu R, Ishida Y, Kutsuna N, Hasezawa S, Nomura Y, Nakagami H, Hashimoto T, “An atypical tubulin kinase mediates stress-induced microtubule depolymerization in Arabidopsis”, Current Biology, 23(20):1969-78 (2013)
Delaunois B, Colby T, Belloy N, Conreux A, Harzen A, Baillieul F, Clément C, Schmidt J, Jeandet P, Cordelier S, “Large-scale proteomic analysis of the grapevine leaf apoplastic fluid reveals mainly stress-related proteins and cell wall modifying enzymes”, BMC Plant Biology, 13:24 (2013)
El-Akhal MR, Colby T, Cantoral JM, Harzen A, Schmidt J, Fernández-Acero FJ, “Proteomic analysis of conidia germination in Colletotrichum acutatum”, Archives of Microbiology, 195(4):227-46 (2013)
Stolze SC, Meltzer M, Ehrmann M, Kaiser M, “Ahp cyclodepsipeptides: the impact of the Ahp residue on the "canonical inhibition" of S1 serine proteases”, ChemBioChem, 14(11):1301-8 (2013)
Stolze SC, Kaiser M, “Case studies of the synthesis of bioactive cyclodepsipeptide natural products”, Molecules, 18(2):1337-67 (2013)
Nakagami H#, Sugiyama N, Ishihama Y#, Shirasu K#, “Shotguns in the front line: phosphoproteomics in plants”, Plant Cell & Physiology, 53(1):118-24 (2012) (#joint corresponding authors)
March TJ, Richter D, Colby T, Harzen A, Schmidt J, Pillen K, “Identification of proteins associated with malting quality in a subset of wild barley introgression lines”, Proteomics, 12(18):2843-51 (2012)
Wahler D, Colby T, Kowalski NA, Harzen A, Wotzka SY, Hillebrand A, Fischer R, Helsper J, Schmidt J, Schulze Gronover C, Prüfer D, “Proteomic analysis of latex from the rubber-producing plant Taraxacum brevicorniculatum”, Proteomics, 12(6):901-5 (2012)
Schmidt C, Kramer K, Urlaub H, “Investigation of protein-RNA interactions by mass spectrometry--Techniques and applications”, Journal of Proteomics, 75(12):3478-94 (2012)
Schmitzová J, Rasche N, Dybkov O, Kramer K, Fabrizio P, Urlaub H, Lührmann R, Pena V, “Crystal structure of Cwc2 reveals a novel architecture of a multipartite RNA-binding protein”, The EMBO Journal, 31(9):2222-34 (2012)
Stolze SC, Deu E, Kaschani F, Li N, Florea BI, Richau KH, Colby T, van der Hoorn RA, Overkleeft HS, Bogyo M, Kaiser M, “The antimalarial natural product symplostatin 4 is a nanomolar inhibitor of the food vacuole falcipains”, Chemistry & Biology, 19(12):1546-55 (2012)
Stolze SC, Kaiser M, “Challenges in the syntheses of peptidic natural products”, Synthesis, 44:1755-77 (2012)
Stolze SC, Meltzer M, Ehrmann M, Kaiser M, “Development of a solid-phase approach to the natural product class of Ahp-containing cyclodepsipeptides”, European Journal of Organic Chemistry, 8:1615-25 (2012)
Joshi HJ, Hirsch-Hoffmann M, Baerenfaller 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 AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL, “MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data”, Plant Physiology, 155(1):259-70 (2011)
Colby T, Röhrig H, Harzen A, Schmidt J, “Modified metal-oxide affinity enrichment combined with 2D-PAGE and analysis of phosphoproteomes”, Methods in Molecular Biology, 779:273-86 (2011)
Müller M, Heym RG, Mayer A, Kramer K, Schmid M, Cramer P, Urlaub H, Jansen RP, Niessing D, “A cytoplasmic complex mediates specific mRNA recognition and localization in yeast”, PLoS Biology, 9(4):e1000611 (2011)
Kramer K, Hummel P, Hsiao H, Luo X, Wahl M, Urlaub H, “Mass spectrometric analysis of proteins cross-linked to 4-thio-uracil- and 5-bromo-uracil-substituted RNA”, International Journal of Mass Spectrometry, 304(2-3):184-94 (2011)
Kosetsu K, Matsunaga S, Nakagami H, Colcombet J, Sasabe M, Soyano T, Takahashi Y, Hirt H, Machida Y, “The MAP kinase MPK4 is required for cytokinesis in Arabidopsis thaliana”, The Plant Cell, 22(11):3778-90 (2010)
Nakagami H#, Sugiyama N#, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K, “Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants”, Plant Physiology, 153(3):1161-74 (2010) (#joint first authors)
Fernández-Acero FJ, Colby T, Harzen A, Carbú M, Wieneke U, Cantoral JM, Schmidt J, “2-DE proteomic approach to the Botrytis cinerea secretome induced with different carbon sources and plant-based elicitors”, Proteomics, 10(12):2270-80 (2010)
Consonni C, Bednarek P, Humphry M, Francocci F, Ferrari S, Harzen A, Ver Loren van Themaat E, Panstruga R, “Tryptophan-derived metabolites are required for antifungal defense in the Arabidopsis mlo2 mutant”, Plant Physiology, 152(3):1544-61 (2010)
Stolze SC, Meltzer M, Ehrmann M, Kaiser M, “Solid phase total synthesis of the 3-amino-6-hydroxy-2-piperidone (Ahp) cyclodepsipeptide and protease inhibitor Symplocamide A”, Chemical Communications, 46(46):8857-9 (2010)
Fernández-Acero FJ, Colby T, Harzen A, Cantoral JM, Schmidt J, “Proteomic analysis of the phytopathogenic fungus Botrytis cinerea during cellulose degradation”, Proteomics, 9(10):2892-902 (2009) Noir S, Colby T, Harzen A, Schmidt J, Panstruga R, “A proteomic analysis of powdery mildew (Blumeria graminis f.sp. hordei) conidiospores”, Molecular Plant Pathology, 10(2):223-36 (2009)
Sugiyama N#, Nakagami H#, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y, “Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis”, Molecular Systems Biology, 4:193 (2008) (#joint first authors)
Röhrig H, Colby T, Schmidt J, Harzen A, Facchinelli F, Bartels D, “Analysis of desiccation-induced candidate phosphoproteins from Craterostigma plantagineum isolated with a modified metal oxide affinity chromatography procedure”, Proteomics, 8(17):3548-60 (2008)
Shabab M, Shindo T, Gu C, Kaschani F, Pansuriya T, Chintha R, Harzen A, Colby T, Kamoun S, van der Hoorn RA, “Fungal effector protein AVR2 targets diversifying defense-related cys proteases of tomato”, The Plant Cell, 20(4):1169-83 (2008)
Djamei A#, Pitzschke A#, Nakagami H#, Rajh I, Hirt H, “Trojan horse strategy in Agrobacterium transformation: abusing MAPK defense signaling”, Science, 318(5849):453-6 (2007) (#joint first authors)
Nakagami H, Soukupová H, Schikora A, Žárský V, Hirt H, “A mitogen-activated protein kinase kinase kinase mediates reactive oxygen species homeostasis in Arabidopsis”, The Journal of Biological Chemistry, 281(50):38697-704 (2006)
Veronese P, Nakagami H, Bluhm B, Abuqamar S, Chen X, Salmeron J, Dietrich RA, Hirt H, Mengiste T, “The membrane-anchored BOTRYTIS-INDUCED KINASE1 plays distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens”, The Plant Cell, 18(1):257-73 (2006)
Nakagami H, Pitzschke A, Hirt H, “Emerging MAP Kinase Pathways in Plant Stress Signalling”, Trends in Plant Science, 10(7):339-46 (2005)
Jonak C, Nakagami H, Hirt H, “Heavy metal stress. Activation of distinct mitogen-activated protein kinase pathways by copper and cadmium”, Plant Physiology, 136(2):3276-83 (2004)
Nakagami H, Kiegerl S, Hirt H, “OMTK1, a novel MAPKKK, channels oxidative stress signaling through direct MAPK interaction”, The Journal of Biological Chemistry, 279(26):26959-66 (2004)
Nakagami H, Kawamura K, Sugisaka K, Sekine M, Shinmyo A, “Phosphorylation of retinoblastoma-related protein by the cyclin D/cyclin-dependent kinase complex is activated at the G1/S-phase transition in tobacco”, The Plant Cell, 14(8):1847-57 (2002)
Sorrell DA, Menges M, Healy JM, Deveaux Y, Amano C, Su Y, Nakagami H, Shinmyo A, Doonan JH, Sekine M, Murray JA, “Cell cycle regulation of cyclin-dependent kinases in tobacco Bright Yellow-2(BY-2) cells”, Plant Physiology, 126(3):1214-1223 (2001)
Sekine M, Ito M, Uemukai K, Maeda Y, Nakagami H, Shinmyo A, “Isolation and characterization of the E2F-like gene in plants”, FEBS Letter, 460(1):117-122 (1999)
Nakagami H#, Sekine M#, Murakami H, Shinmyo A, “Tobacco retinoblastoma-related protein phosphorylated by a distinct cyclin dependent kinase complex with Cdc2/cyclin D in vitro”, The Plant Journal, 18(3):243-252 (1999) (#joint first authors)
Hirata K, Nakagami H, Takashina J, Mahmud T, Kobayashi M, In Y, Ishida T, Miyamoto K, “Novel violet pigment, Nostocine A, an extracellular metabolite from cyanobacterium Nostoc spongiaeforme”, Heterocycles, 43(7):1513-1519 (1996)
Hirata K, Takashina J, Nakagami H, Ueyama S, Murakami K, Kanamori T, Miyamoto K, “Growth inhibition of various organisms by a violet pigment, Nostocine A, produced by Nostoc spongiaeforme”, Bioscience, Biotechnology, and Biochemistry, 60(11):1905-6 (1996)