Publications of Joachim Kopka

Journal Article (202)

1.
Journal Article
Cheong, B.E.; Beine-Golovchuk, O.; Gorka, M.; Ho, W.W.H.; Martinez-Seidel, F.; Firmino, A.; Skirycz, A.; Roessner, U.; Kopka, J.: Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation. Scientific Reports 11 (1), 2410 (2021)
2.
Journal Article
Franzisky, B. L.; Geilfus, C.-M.; Romo-Perez, M. L.; Fehrle, I.; Erban, A.; Kopka, J.; Zorb, C.: Acclimatisation of guard cell metabolism to long-term salinity. Plant, Cell and Environment 44 (3), pp. 870 - 884 (2021)
3.
Journal Article
Luzarowski, M.; Vicente, R.; Kiselev, A.; Wagner, M.; Schlossarek, D.; Erban, A.; de Souza, L. P.; Childs, D.; Wojciechowska, I.; Luzarowska, U. et al.; Gorka, M.; Sokolowska, E.; Kosmacz, M.; Moreno, J.C.; Brzezinska, A.; Vegesna, B.; Kopka, J.; Fernie, A. R.; Willmitzer, L.; Ewald, J. C.; Skirycz, A.: Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Communications Biology 4 (1), 181 (2021)
4.
Journal Article
Martinez-Seidel, F.; Beine-Golovchuk, O.; Hsieh, Y.-C.; El Eshraky, K.; Gorka, M.; Cheong, B.-E.; Jimenez‐posada, E.V.; Walther, D.; Skirycz, A.; Roessner, U. et al.; Kopka, J.; Firmino, A.: Spatially enriched paralog rearrangements argue functionally diverse ribosomes arise during cold acclimation in arabidopsis. International Journal of Molecular Sciences 22 (11), 6160 (2021)
5.
Journal Article
Martinez-Seidel, F.; Suwanchaikasem, P.; Nie, S.; Leeming, M.G.; Firmino, A.; Williamson, N.A.; Kopka, J.; Roessner, U.; Boughton, B.A.: Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems. Frontiers in Plant Science 12, 656683 (2021)
6.
Journal Article
Melo, T.O.; Franciscon, L.; Brown, G.; Kopka, J.; Cunha, L.; Martinez-Seidel, F.; Madureira, L.A.D.S.; Hansel, F.A.: Univariate statistical analysis of gas chromatography – mass spectrometry fingerprints analyses. Chemical Data Collections 33, 100719 (2021)
7.
Journal Article
Pries, C.; Razaghi-Moghadam, Z.; Kopka, J.; Nikoloski, Z.: Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism. Scientific Reports 11 (1), 4787 (2021)
8.
Journal Article
Samo, N.; Ebert, A.; Kopka, J.; Mozgová, I.: Plant chromatin, metabolism and development – an intricate crosstalk. Current Opinion in Plant Biology 61, 102002 (2021)
9.
Journal Article
Schaarschmidt, S.; Lawas, L.M.F.; Kopka, J.; Jagadish, S. V. K.; Zuther, E.: Physiological and molecular attributes contribute to high night temperature tolerance in cereals. Plant, Cell and Environment (2021)
10.
Journal Article
Schumacher, C.; Krannich, C. T.; Maletzki, L.; Koehl, K. I.; Kopka, J.; Sprenger, H.; Hincha, D. K.; Seddig, S.; Peters, R.; Hamera, S. et al.; Zuther, E.; Haas, M.; Horn, R.: Unravelling Differences in Candidate Genes for Drought Tolerance in Potato (Solanum tuberosum L.) by Use of New Functional Microsatellite Markers. Genes 12 (4), 494 (2021)
11.
Journal Article
Schumacher, C.; Thümecke, S.; Schilling, F.; Koehl, K. I.; Kopka, J.; Sprenger, H.; Hincha, D. K.; Walther, D.; Seddig, S.; Peters, R. et al.; Zuther, E.; Haas, M.; Horn, R.: Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato (Solanum tuberosum L.). International Journal of Molecular Sciences 22 (11), 6123 (2021)
12.
Journal Article
Takahashi, D.; Johnson, K.; Hao, P.; Tuong, T.; Erban, A.; Sampathkumar, A.; Bacic, A.; Livingston III, D. P.; Kopka, J.; Kuroha, T. et al.; Yokoyama, R.; Nishitani, K.; Zuther, E.; Hincha, D. K.: Cell wall modification by the xyloglucan endotransglucosylase/hydrolase XTH19 influences freezing tolerance after cold and sub-zero acclimation. Plant, Cell and Environment 44 (3), pp. 915 - 930 (2021)
13.
Journal Article
Tedesco, S.; Erban, A.; Gupta, S.; Kopka, J.; Fevereiro, P.; Kragler, F.; Pina, A.: The Impact of Metabolic Scion–Rootstock Interactions in Different Grapevine Tissues and Phloem Exudates. Metabolites 11 (6), 349 (2021)
14.
Journal Article
Cotton, C. A. R.; Bernhardsgrütter, I.; He, H.; Burgener, S.; Schulz, L.; Paczia, N.; Dronsella, B.; Erban, A.; Toman, S.; Dempfle, M. et al.; de Maria, A.; Kopka, J.; Lindner, S. N.; Erb, T. J.; Bar-Even, A.: Underground isoleucine biosynthesis pathways in E. coli. eLife 9, e54207 (2020)
15.
Journal Article
Firmino, A.; Gorka, M.; Graf, A.; Skirycz, A.; Martinez-Seidel, F.; Zander, K.; Kopka, J.; Beine-Golovchuk, O.: Separation and paired proteome profiling of plant chloroplast and cytoplasmic ribosomes. Plants 9 (7), 892 (2020)
16.
Journal Article
Haas, M.; Sprenger, H.; Zuther, E.; Peters, R.; Seddig, S.; Walther, D.; Kopka, J.; Hincha, D. K.; Koehl, K. I.: Can Metabolite- and Transcript-Based Selection for Drought Tolerance in Solanum tuberosum Replace Selection on Yield in Arid Environments? Frontiers in Plant Science 11, 1071 (2020)
17.
Journal Article
Kalampokis, I.F.; Erban, A.; Amillis, S.; Diallinas, G.; Kopka, J.; Aliferis, K.A.: Untargeted metabolomics as a hypothesis-generation tool in plant protection product discovery: Highlighting the potential of trehalose and glycerol metabolism of fungal conidiospores as novel targets. Metabolomics 16 (7), 79 (2020)
18.
Journal Article
Martinez-Seidel, F.; Beine-Golovchuk, O.; Hsieh, Y.-C.; Kopka, J.: Systematic review of plant ribosome heterogeneity and specialization. Frontiers in Plant Science 11, 948 (2020)
19.
Journal Article
Moing, A.; Allwood, J. W.; Aharoni, A.; Baker, J.; Beale, M. H.; Ben-Dor, S.; Biais, B.; Brigante, F.; Burger, Y.; Deborde, C. et al.; Erban, A.; Faigenboim, A.; Gur, A.; Goodacre, R.; Hansen, T. H.; Jacob, D.; Katzir, N.; Kopka, J.; Lewinsohn, E.; Maucourt, M.; Meir, S.; Miller, S.; Mumm, R.; Oren, E.; Paris, H. S.; Rogachev, I.; Rolin, D.; Saar, U.; Schjoerring, J. K.; Tadmor, Y.; Tzuri, G.; de Vos, R. C.H.; Ward, J. L.; Yeselson, E.; Hall, R. D.; Schaffer, A. A.: Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity. Metabolites 10 (3), 121 (2020)
20.
Journal Article
Schaarschmidt, S.; Lawas, L.M.F.; Glaubitz, U.; Li, X.; Erban, A.; Kopka, J.; Krishna Jagadish, S.V.; Hincha, D. K.; Zuther, E.: Season affects yield and metabolic profiles of rice (Oryza sativa) under high night temperature stress in the field. International Journal of Molecular Sciences 21 (9), 3187 (2020)
21.
Journal Article
Treves, H.; Siemiatkowska, B.; Luzarowska, U.; Murik, O.; Fernandez-Pozo, N.; Moraes, T. A.; Erban, A.; Armbruster, U.; Brotman, Y.; Kopka, J. et al.; Rensing, S. A.; Szymanski, J.; Stitt, M.: Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga. Nature Plants 6, pp. 1031 - 1043 (2020)
22.
Journal Article
Whitcomb, S. J.; Rakpenthai, A.; Brückner, F.; Fischer, A.; Parmar, S.; Erban, A.; Kopka, J.; Hawkesford, M.J.; Hoefgen, R.: Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. Frontiers in Plant Science 11, 1118 (2020)
23.
Journal Article
Lawas, L.M.F.; Erban, A.; Kopka, J.; Jagadish, S. V. K.; Zuther, E.; Hincha, D. K.: Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field. GigaScience 8 (8), giz102 (2019)
24.
Journal Article
Lawas, L.M.F.; Li, X.; Erban, A.; Kopka, J.; Jagadish, S. V. K.; Zuther, E.; Hincha, D. K.: Metabolic responses of rice cultivars with different tolerance to combined drought and heat stress under field conditions. GigaScience 8 (5), giz050 (2019)
25.
Journal Article
Armarego-Marriott, T.; Kowalewska, L.; Burgos, A.; Fischer, A.; Thiele, W.; Erban, A.; Strand, D.; Kahlau, S.; Hertle, A. P.; Kopka, J. et al.; Walther, D.; Reich, Z.; Schöttler, M. A.; Bock, R.: Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves. Plant Physiology 180 (1), pp. 654 - 681 (2019)
26.
Journal Article
Awada, R.; Campa, C.; Gibault, E.; Dechamp, E.; Georget, F.; Lepelley, M.; Abdallah, C.; Erban, A.; Martinez-Seidel, F.; Kopka, J. et al.; Legendre, L.; Leran, S.; Conejero, G.; Verdeil, J.-L.; Crouzillat, D.; Breton, D.; Bertrand, B.; Etienne, H.: Unravelling the Metabolic and Hormonal Machinery During Key Steps of Somatic Embryogenesis: A Case Study in Coffee. International Journal of Molecular Sciences 20 (19), 4665 (2019)
27.
Journal Article
Calabrese, S.; Cusant, L.; Sarazin, A.; Niehl, A.; Erban, A.; Brulé, D.; Recorbet, G.; Wipf, D.; Roux, C.; Kopka, J. et al.; Boller, T.; Courty, P.-E.: Imbalanced regulation of fungal nutrient transports according to phosphate availability in a symbiocosm formed by poplar, sorghum and Rhizophagus irregularis. Frontiers in Plant Science 10, 1617 (2019)
28.
Journal Article
Erban, A.; Fehrle, I.; Martinez-Seidel, F.; Brigante, F.; Más, A. L.; Baroni, V.; Wunderlin, D.; Kopka, J.: Discovery of food identity markers by metabolomics and machine learning technology. Scientific Reports 9 (1), 9697 (2019)
29.
Journal Article
Heyneke, E.; Watanabe, M.; Erban, A.; Duan, G.; Buchner, P.; Walther, D.; Kopka, J.; Hawkesford, M. J.; Hoefgen, R.: Effect of Senescence Phenotypes and Nitrate Availability on Wheat Leaf Metabolome during Grain Filling. Agronomy 9 (6), 305 (2019)
30.
Journal Article
Li, L.; Krznar, P.; Erban, A.; Agazzi, A.; Martin-Levilain, J.; Supale, S.; Kopka, J.; Zamboni, N.; Maechler, P.: Metabolomics identifies a biomarker revealing in vivo loss of functional β-cell mass before diabetes onset. Diabetes 68 (12), pp. 2272 - 2286 (2019)
31.
Journal Article
Madhavan, S.; Paranidharan, V.; Erban, A.; Al-Sadi, A.M.; Kopka, J.; Velazhahan, R.: The metabolic response of suspension-cultured cells from blast-resistant and -susceptible rice (Oryza sativa L.) genotypes to a Pyricularia oryzae elicitor. Indian Phytopathology 72 (2), pp. 195 - 202 (2019)
32.
Journal Article
Nieva, A.S.; Vilas, J.M.; Gárriz, A.; Maiale, S.J.; Menéndez, A.B.; Erban, A.; Kopka, J.; Ruiz, O.A.: The fungal endophyte Fusarium solani provokes differential effects on the fitness of two Lotus species. Plant Physiology and Biochemistry 144, pp. 100 - 109 (2019)
33.
Journal Article
Richter, J. A.; Behr, J. H.; Erban, A.; Kopka, J.; Zoerb, C.: Ion-dependent metabolic responses of Vicia faba L. to salt stress. Plant, Cell and Environment 42 (1-SI), pp. 295 - 309 (2019)
34.
Journal Article
Schwachtje, J.; Whitcomb, S. J.; Firmino, A.; Zuther, E.; Hincha, D. K.; Kopka, J.: Induced, Imprinted, and Primed Responses to Changing Environments: Does Metabolism Store and Process Information? Frontiers in Plant Science 10, 106 (2019)
35.
Journal Article
Takahashi, D.; Gorka, M.; Erban, A.; Graf, A.; Kopka, J.; Zuther, E.; Hincha, D. K.: Both cold and sub-zero acclimation induce cell wall modification and changes in the extracellular proteome in Arabidopsis thaliana. Scientific Reports 9 (1), 2289 (2019)
36.
Journal Article
Ulaszewska, M. M.; Weinert, C. H.; Trimigno, A.; Portmann, R.; Andres Lacueva, C.; Badertscher, R.; Brennan, L.; Brunius, C.; Bub, A.; Capozzi, F. et al.; Rosso, M. C.; Cordero, C. E.; Daniel, H.; Durand, S.; Egert, B.; Ferrario, P. G.; Feskens, E. J. M.; Franceschi, P.; Garcia-Aloy, M.; Giacomoni, F.; Giesbertz, P.; Gonzalez-Dominguez, R.; Hanhineva, K.; Hemeryck, L. Y.; Kopka, J.; Kulling, S. E.; Llorach, R.; Manach, C.; Mattivi, F.; Migne, C.; Munger, L. H.; Ott, B.; Picone, G.; Pimentel, G.; Pujos-Guillot, E.; Riccadonna, S.; Rist, M. J.; Rombouts, C.; Rubert, J.; Skurk, T.; Harsha, P. S. C. S.; Van Meulebroek, L.; Vanhaecke, L.; Vazquez-Fresno, R.; Wishart, D.; Vergeres, G.: Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies. Molecular Nutriton & Food Research 63 (1-SI), 1800384 (2019)
37.
Journal Article
Wenke, K.; Kopka, J.; Schwachtje, J.; van Dongen, J. T.; Piechulla, B.: Volatiles of rhizobacteria Serratia and Stenotrophomonas alter growth and metabolite composition of Arabidopsis thaliana. Plant Biology 21 (SI suppl.), pp. 109 - 119 (2019)
38.
Journal Article
Zuther, E.; Schaarschmidt, S.; Fischer, A.; Erban, A.; Pagter, M.; Mubeen, U.; Giavalisco, P.; Kopka, J.; Sprenger, H.; Hincha, D. K.: Molecular signatures associated with increased freezing tolerance due to low temperature memory in Arabidopsis. Plant, Cell and Environment 42 (3- SI), pp. 854 - 873 (2019)
39.
Journal Article
Atanasov, K. E.; Liu, C.; Erban, A.; Kopka, J.; Parker, J. E.; Alcázar, R.: NLR Mutations Suppressing Immune Hybrid Incompatibility and Their Effects on Disease Resistance. Plant Physiology 177 (3), pp. 1152 - 1169 (2018)
40.
Journal Article
Beine-Golovchuk, O.; Firmino, A.; Dabrowska, A.; Schmidt, S.; Erban, A.; Walther, D.; Zuther, E.; Hincha, D. K.; Kopka, J.: Plant Temperature Acclimation and Growth Rely on Cytosolic Ribosome Biogenesis Factor Homologs. Plant Physiology 176 (3), pp. 2251 - 2276 (2018)
41.
Journal Article
Geuss, D.; Lortzing, T.; Schwachtje, J.; Kopka, J.; Steppuhn, A.: Oviposition by Spodoptera exigua on Solanum dulcamara Alters the Plant’s Response to Herbivory and Impairs Larval Performance. International Journal of Molecular Sciences 19 (12), 4008 (2018)
42.
Journal Article
Rai, S.; Lucius, S.; Kern, R.; Bauwe, H.; Kaplan, A.; Kopka, J.; Hagemann, M.: The Synechocystis sp PCC 6803 Genome Encodes Up to Four 2-Phosphoglycolate Phosphatases. Frontiers in Plant Science 9, 1718 (2018)
43.
Journal Article
Ruebsam, H.; Kirsch, F.; Reimann, V.; Erban, A.; Kopka, J.; Hagemann, M.; Hess, W. R.; Klaehn, S.: The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp PCC 6803. Environmental Microbiology Reports 20 (8-SI), pp. 2757 - 2768 (2018)
44.
Journal Article
Schwachtje, J.; Fischer, A.; Erban, A.; Kopka, J.: Primed primary metabolism in systemic leaves: a functional systems analysis. Scientific Reports 8, 216 (2018)
45.
Journal Article
Sprenger, H.; Erban, A.; Seddig, S.; Rudack, K.; Thalhammer, A.; Le, M. Q.; Walther, D.; Zuther, E.; Koehl, K. I.; Kopka, J. et al.; Hincha, D. K.: Metabolite and transcript markers for the prediction of potato drought tolerance. Plant Biotechnology Journal 16 (4), pp. 939 - 950 (2018)
46.
Journal Article
Dethloff, F.; Orf, I.; Kopka, J.: Rapid in situ 13C tracing of sucrose utilization in Arabidopsis sink and source leaves. Plant Methods 13 (1), 87 (2017)
47.
Journal Article
Pagter, M.; Alpers, J.; Erban, A.; Kopka, J.; Zuther, E.; Hincha, D. K.: Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana. BMC Genomics 18 (1), 731 (2017)
48.
Journal Article
Andersen, U. B.; Kjaer, K. H.; Erban, A.; Alpers, J.; Hincha, D. K.; Kopka, J.; Zuther, E.; Pagter, M.: Impact of seasonal warming on overwintering and spring phenology of blackcurrant. Environmental and Experimental Botany 140, pp. 96 - 109 (2017)
49.
Journal Article
Glaubitz, U.; Li, X.; Schaedel, S.; Erban, A.; Sulpice, R.; Kopka, J.; Hincha, D. K.; Zuther, E.: Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles. Plant, Cell and Environment 40 (1), pp. 121 - 137 (2017)
50.
Journal Article
Heyneke, E.; Watanabe, M.; Erban, A.; Duan, G. Y.; Buchner, P.; Walther, D.; Kopka, J.; Hawkesford, M. J.; Hoefgen, R.: Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply. Frontiers in Plant Science 8, 2048 (2017)
51.
Journal Article
Kopka, J.; Schmidt, S.; Dethloff, F.; Pade, N.; Berendt, S.; Schottkowski, M.; Martin, N.; Dühring, U.; Kuchmina, E.; Enke, H. et al.; Kramer, D.; Wilde, A.; Hagemann, M.; Friedrich, A.: Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002. Biotechnology for Biofuels 10 (1), 56 (2017)
52.
Journal Article
Rahmoune, B.; Morsli, A.; Khelifi-Slaoui, M.; Khelifi, L.; Strueh, A.; Erban, A.; Kopka, J.; Prell, J.; van Dongen, J. T.: Isolation and characterization of three new PGPR and their effects on the growth of Arabidopsis and Datura plants. Journal of Plant Interaction 12 (1), pp. 1 - 6 (2017)
53.
Journal Article
Rotsch, A.H.; Kopka, J.; Feussner, I.; Ischebeck, T.: Central metabolite and sterol profiling divides tobacco male gametophyte development and pollen tube growth into eight metabolic phases. The Plant Journal 92 (1), pp. 129 - 146 (2017)
54.
Journal Article
Treves, H.; Murik, O.; Kedem, I.; Eisenstadt, D.; Meir, S.; Rogachev, I.; Szymanski, J.; Keren, N.; Orf, I.; Tiburcio, A. F. et al.; Alcazar, R.; Aharoni, A.; Kopka, J.; Kaplan, A.: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga. Current Biology 27 (16), pp. 2559 - 2567 (2017)
55.
Journal Article
Zarza, X.; Atanasov, K. E.; Marco, F.; Arbona, V.; Carrasco, P.; Kopka, J.; Fotopoulos, V.; Munnik, T.; Gomez-Cadenas, A.; Tiburcio, A. F. et al.; Alcazar, R.: Polyamine oxidase 5 loss-of-function mutations in Arabidopsis thaliana trigger metabolic and transcriptional reprogramming and promote salt stress tolerance. Plant, Cell and Environment 40 (4), pp. 527 - 542 (2017)
56.
Journal Article
Staroske, N.; Conrad, U.; Kumlehn, J.; Hensel, G.; Radchuk, R.; Erban, A.; Kopka, J.; Weschke, W.; Weber, H.: Increasing abscisic acid levels by immunomodulation in barley grains induces precocious maturation without changing grain composition. Journal of Experimental Botany 67 (9), pp. 2675 - 2687 (2016)
57.
Journal Article
Coleto, I.; Trenas, A. T.; Erban, A.; Kopka, J.; Pineda, M.; Alamillo, J. M.: Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris. Plant, Cell and Environment 39 (8), pp. 1767 - 1779 (2016)
58.
Journal Article
Fuentes, P.; Zhou, F.; Erban, A.; Karcher, D.; Kopka, J.; Bock, R.: A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop. eLife 5, e13664 (2016)
59.
Journal Article
Gal, A.; Wirth, R.; Kopka, J.; Fratzl, P.; Faivre, D.; Scheffel, A.: Macromolecular recognition directs calcium ions to coccolith mineralization sites. Science 353 (6299), pp. 590 - 593 (2016)
60.
Journal Article
Hilker, M.; Schwachtje, J.; Baier, M.; Balazadeh, S.; Bäurle, I.; Geiselhardt, S.; Hincha, D. K.; Kunze, R.; Mueller-Roeber, B.; Rillig, M. C. et al.; Rolff, J.; Romeis, T.; Schmülling, T.; Steppuhn, A.; van Dongen, J.; Whitcomb, S. J.; Wurst, S.; Zuther, E.; Kopka, J.: Priming and memory of stress responses in organisms lacking a nervous system. Biological Reviews 91 (4), pp. 1118 - 1133 (2016)
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