Publications of the institute

Journal Article (173)

1.
Journal Article
Muralidhara, P.; Weiste, C.; Collani, S.; Krischke, M.; Kreisz, P.; Draken, J.; Feil, R.; Mair, A.; Teige, M.; Müller, M. J. et al.; Schmid, M.; Becker, D.; Lunn, J. E.; Rolland, F.; Hanson, J.; Dröge-Laser, W.: Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling. Proceedings of the National Academy of Sciences of the United States of America 118 (37), e2106961118 (2021)
2.
Journal Article
Agrawal, S.; Karcher, D.; Ruf, S.; Erban, A.; Hertle, A. P.; Kopka, J.; Bock, R.: Riboswitch-mediated inducible expression of an astaxanthin biosynthetic operon in plastids. Plant Physiology (accepted)
3.
Journal Article
Olas, J. J.; Apelt, F.; Annunziata, M. G.; John, S.; Richard, S. I.; Gupta, S.; Kragler, F.; Balazadeh, S.; Mueller-Roeber, B.: Primary carbohydrate metabolism genes participate in heat stress memory at the shoot apical meristem of Arabidopsis thaliana. Molecular Plant 14, pp. 1508 - 1524 (2021)
4.
Journal Article
Orsi, E.; Claassens, N. J.; Nikel, P. I.; Lindner, S. N.: Growth-coupled selection of synthetic modules to accelerate cell factory development. Nature Communications 12 (1), 5295 (2021)
5.
Journal Article
Zhang, F.; Wu, J.; Sade, N.; Wu, S.; Egbaria, A.; Fernie, A. R.; Yan, J.; Qin, F.; Chen, W.; Brotman, Y. et al.; Dai, M.: Genomic basis underlying the metabolome-mediated drought adaptation of maize. Genome Biology 22 (1), 260 (2021)
6.
Journal Article
Aarabi, F.; Rakpenthai, A.; Barahimipour, R.; Gorka, M.; Alseekh, S.; Zhang, Y.; Salem, M.A.; Brückner, F.; Omranian, N.; Watanabe, M. et al.; Nikoloski, Z.; Giavalisco, P.; Tohge, T.; Graf, A.; Fernie, A. R.; Hoefgen, R.: Sulfur Deficiency Induced genes affect seed protein accumulation and composition under sulfate deprivation. Plant Physiology (2021)
7.
Journal Article
Liu, S.; Trejo-Arellano, M.S.; Qiu , Y.; Eklund, D.M.; Köhler, C.; Hennig, L.: H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha. Genome Biology 22 (1), 253 (2021)
8.
Journal Article
Xu, R.; Razaghi-Moghadam, Z.; Nikoloski, Z.: Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli. Bioinformatics (2021)
9.
Journal Article
Zhang, Y.; Scossa, Federico, F.; Fernie, A. R.: The genomes of Taxus species unveil novel candidates in the biosynthesis of taxoids. Molecular Plant (2021)
10.
Journal Article
Bellucci, E.; Aguilar, O. M.; Alseekh, S.; Bett, K.; Brezeanu, C.; Cook, D.; De la Rosa, L.; Delledonne, M.; Dostatny, D. F.; Ferreira, J. J. et al.; Geffroy, V.; Ghitarrini, S.; Kroc, M.; Kumar Agrawal, S.; Logozzo, G.; Marino, M.; Mary-Huard, T.; McClean, P.; Meglič, V.; Messer, T.; Muel, F.; Nanni, L.; Neumann, K.; Servalli, F.; Străjeru, S.; Varshney, R. K.; Vasconcelos, M. W.; Zaccardelli, M.; Zavarzin, A.; Bitocchi, E.; Frontoni, E.; Fernie, A. R.; Gioia, T.; Graner, A.; Guasch, L.; Prochnow, L.; Opperman, M.; Susek, K.; Tenaillon, M.; Papa, R.: The INCREASE project: Intelligent Collections of Food-Legume Genetic Resources for European Agrofood Systems. The Plant Journal (2021)
11.
Journal Article
Sato, H.; Santos-González, J.; Köhler, C.: Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy. eLife 10, e64593 (2021)
12.
Journal Article
Bouzon, M.; Döring, V.; Dubois, I.; Berger, A.; Stoffel, G.M.M.; Ramirez, L. C.; Meyer, S.N.; Fouré, M.; Roche, D.; Perret, A. et al.; Erb, T.J.; Bar-Even, A.; Lindner, S. N.: Change in cofactor specificity of oxidoreductases by adaptive evolution of an escherichia coli nadph-auxotrophic strain. mBio 12 (4), e00329-21 (2021)
13.
Journal Article
Peixoto, B.; Moraes, T. A.; Mengin, V.; Margalha, L.; Vicente, R.; Feil, R.; Höhne, M.; Sousa, A. G. G.; Lilue, J.; Stitt, M. et al.; Lunn, J. E.; Baena-González, E.: Impact of the SnRK1 protein kinase on sucrose homeostasis and the transcriptome during the diel cycle. Plant Physiology (2021)
14.
Journal Article
Zhu, F.; Fernie, A. R.: Plants upcycle gene functions to suit their roots. Trends in Plant Science (2021)
15.
Journal Article
Alseekh, S.; Aharoni, A.; Brotman, Y.; Contrepois, K.; D’Auria, J.; Ewald, J.; C. Ewald, J.; Fraser, P. D.; Giavalisco, P.; Hall, R. D. et al.; Heinemann, M.; Link, H.; Luo, J.; Neumann, S.; Nielsen, J.; de Souza, L. P.; Saito, K.; Sauer, U.; Schroeder, F. C.; Schuster, S.; Siuzdak, G.; Skirycz, A.; Sumner, L. W.; Snyder, M. P.; Tang, H.; Tohge, T.; Wang, Y.; Wen, W.; Wu, S.; Xu, G.; Zamboni, N.; Fernie, A. R.: Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature Methods 18 (7), pp. 747 - 756 (2021)
16.
Journal Article
Guadalupe Dominguez, P.; Conti, G.; Duffy, T.; Insani, M.; Alseekh, S.; Asurmendi, S.; Fernie, A. R.; Carrari, F.: Multi-omics analyses reveal the roles of the ASR1 transcription factor in tomato fruits. Journal of Experimental Botany (2021)
17.
Journal Article
Sedaghatmehr, M.; Thirumalaikumar, V. P.; Kamranfar, I.; Schulz, K.; Mueller-Roeber, B.; Sampathkumar, A.; Balazadeh, S.: Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery. Journal of Experimental Botany (2021)
18.
Journal Article
Stitt, M.; Borghi, G.L.; Arrivault, S.: Targeted Metabolite Profiling as a Top-Down Approach to Uncover Inter-Species Diversity and Identify Key Conserved Operational Features in the Calvin-Benson cycle. Journal of Experimental Botany 72 (17), pp. 5961 - 5986 (2021)
19.
Journal Article
Moreno, J.C.; Rojas, B.E.; Vicente, R.; Gorka, M.; Matz, T.; Kosmacz, M.; Peralta-Ariza, J.S.; Zhang, Y.; Alseekh, S.; Childs, D. et al.; Luzarowski, M.; Nikoloski, Z.; Zarivach, R.; Walther, D.; Hartman, M.D.; Figueroa, C.M.; Iglesias, A.A.; Fernie, A. R.; Skirycz, A.: Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. EMBO Journal, e106800 (2021)
20.
Journal Article
Altman, A.; Fan, L.; Foyer, C.; Cowling, W.; Mittler, R.; Qaim, M.; Weber, A.; Reynolds, M.; Varshney, R.; Fernie, A. R.: Past and Future Milestones of Plant Breeding. Trends in Plant Science 26 (6), pp. 530 - 538 (2021)
21.
Journal Article
Eng, R.C.; Schneider, R.; Matz, T.; Carter, R.; Ehrhardt, D. W.; Jönsson, H.; Nikoloski, Z.; Sampathkumar, A.: KATANIN and CLASP function at different spatial scales to mediate microtubule response to mechanical stress in Arabidopsis cotyledons. Current Biology 31 (15), pp. 3262 - 3274 (2021)
22.
Journal Article
Zupok, A.; Kozul, D.; Schöttler, M. A.; Niehörster, J.; Garbsch, F.; Liere, K.; Fischer, A.; Zoschke, R.; Malinova, I.; Bock, R. et al.; Greiner, S.: A photosynthesis operon in the chloroplast genome drives speciation in evening primroses. The Plant Cell 33 (8), pp. 2583 - 2601 (2021)
23.
Journal Article
Ancín, M.; Larraya, L.; Florez-Sarasa, I. D.; Bénard, C.; Fernández-San Millán, A.; Veramendi, J.; Gibon, Y.; Fernie, A. R.; Aranjuelo, I.; Farran, I.: Thioredoxin m overexpression in chloroplasts alters carbon and nitrogen partitioning in tobacco plants. Journal of Experimental Botany (2021)
24.
Journal Article
Ann DeTar, R.; Barahimipour, R.; Manavski, N.; Schwenkert, S.; Höhner, R.; Bölter, B.; Inaba, T.; Meurer, J.; Zoschke, R.; Kunz, H.-H.: Loss of inner-envelope K+/H+ exchangers impairs plastid rRNA maturation and gene expression. The Plant Cell 33 (7), pp. 2479 - 2505 (2021)
25.
Journal Article
Ashraf, M.; Mao, Q.; Hong, J.; Shi, L.; Ran, X.; Liaquat, F.; Uzair, M.; Liang, W.; Fernie, A. R.; Shi, J.: HSP70-16 and VDAC3 jointly inhibit seed germination under cold stress in Arabidopsis. Plant, Cell and Environment (2021)
26.
Journal Article
He, W.; Baysal, C.; Lobato Gómez, M.; Huang, X.; Alvarez, D.; Zhu, C.; Armario-Najera, V.; Blanco Perera, A.; Cerda Bennaser, P.; Saba-Mayoral, A. et al.; Sobrino-Mengual, G.; Vargheese, A.; Abranches, R.; Abreu, I. A.; Balamurugan, S.; Bock, R.; Buyel, J. F.; Cunha, N. B. d.; Daniell, H.; Faller, R.; Folgado, A.; Gowtham, I.; Häkkinen, S. T.; Shashi, K.; Ramalingam, S. K.; Lacorte, C.; Lomonossoff, G. P.; Luís, I. M.; K.-C. Ma, J.; McDonald, K. A.; Murad, A.; Nandi, S.; O’Keef, B.; Parthiban, S.; Paul, M. J.; Ponndorf, D.; Rech, E.; Rodrigues, J. C.M.; Ruf, S.; Schillberg, S.; Schwestka, J.; Shah, P. S.; Singh, R.; Stoger, E.; Twyman, R. M.; Varghese, I. P.; Vianna, G. R.; Webster, G.; Wilbers, R. H.P.; Christou, P.; Oksman-Caldentey, K.-M.; Capell, T.: Contributions of the international plant science community to the fight against infectious diseases in humans – part 2: affordable drugs in edible plants for endemic and re-emerging diseases. Plant Biotechnology Journal (2021)
27.
Journal Article
Lobato Gómez, M.; Huang, X.; Alvarez, D.; He, W.; Baysal, C.; Zhu, C.; Armario-Najera, V.; Blanco Perera, A.; Cerda Bennasser, P.; Saba-Mayoral, A. et al.; Sobrino-Mengual, G.; Vargheese, A.; Abranches, R.; Abreu, I. A.; Balamurugan, S.; Bock, R.; Buyel, J.F.; da Cunha; B, N.; Daniell, H.; Faller, R.; Folgado, A.; Gowtham, I.; Häkkinen, S.; Shashi, K.; Kumar Ramalingam, S.; Lacorte, C.; Lomonossoff, G. P.; Luís, I. M.; Ma, J. K.-C.; McDonald, K. A.; Murad, A.; Nandi, S.; O’Keef, B.; Oksman-Caldentey, K.-M.; Parthiban, S.; Paul, M.; Ponndorf, D.; Rech, E.; Rodrigues, J. C.M.; Ruf, S.; Schillberg, S.; Schwestka, J.; Shah, P. S.; Singh, R.; Stoger, E.; Twyman, R. M.; Varghese, I. P.; Vianna, G. R.; Webster, G.; Wilbers, R. H.P.; Capell, T.; Christou, P.: Contributions of the international plant science community to the fight against human infectious diseases – part 1: epidemic and pandemic diseases. Plant Biotechnology Journal (2021)
28.
Journal Article
Zimmermann, S. E.; Benstein, R. M.; Flores-Tornero, M.; Blau, S.; Anoman, A. D.; Rosa-Téllez, S.; Gerlich, S. C.; Salem, M.A.; Alseekh, S.; Kopriva, S. et al.; Wewer, V.; Flügge, U.-I.; Jacoby, R. P.; Fernie, A. R.; Giavalisco, P.; Ros, R.; Krueger, S.: The phosphorylated pathway of serine biosynthesis links plant growth with nitrogen metabolism. Plant Physiology 186 (3), pp. 1487 - 1506 (2021)
29.
Journal Article
de Souza, L. P.; Alseekh, S.; Scossa, F.; Fernie, A. R.: Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nature Methods 18, pp. 733 - 746 (2021)
30.
Journal Article
Wang, Z.; Butel, N.; Santos-González, J.; Simon, L.; Wärdig, C.; Köhler, C.: Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis. Genome Biology 22 (1), 141 (2021)
31.
Journal Article
Borghi, M.; Fernie, A. R.: From flowers to seeds: how the metabolism of flowers frames plant reproduction. The biochemist: the bulletin of the Biochemical Society 43 (3), pp. 14 - 18 (2021)
32.
Journal Article
Cortinovis, G.; Oppermann, M.; Neumann, K.; Graner, A.; Gioia, T.; Marsella, M.; Alseekh, S.; Fernie, A. R.; Papa, R.; Bellucci, E. et al.; Bitocchi, E.: Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean. Current Protocols in Plant Biology 1 (5), e133 (2021)
33.
Journal Article
Dobrica, M.-O.; van Eerde, A.; Tucureanu, C.; Onu, A.; Paruch, L.; Caras, I.; Vlase, E.; Steen, H.; Haugslien, S.; Alonzi, D. et al.; Zitzmann, N.; Bock, R.; Dubuisson, J.; Popescu, C.-I.; Stavaru, C.; Liu Clarke, J.; Branza-Nichita, N.: Hepatitis C virus E2 envelope glycoprotein produced in Nicotiana benthamiana triggers humoral response with virus-neutralizing activity in vaccinated mice. Plant Biotechnology Journal (2021)
34.
Journal Article
Ishihara, H.; Moraes, T. A.; Arrivault, S.; Stitt, M.: Assessing Protein Synthesis and Degradation Rates in Arabidopsis thaliana Using Amino Acid Analysis. Current Protocols 1 (5), e114 (2021)
35.
Journal Article
Viana, A. J. C.; Matiolli, C. C.; Newman, D. W.; Vieira, J. G. P.; Duarte, G. T.; Martins, M. C. M.; Gilbault, E.; Hotta, C. T.; Caldana, C.; Vincentz, M.: The sugar-responsive circadian clock regulator bZIP63 modulates plant growth. New Phytologist 231 (5), pp. 1875 - 1889 (2021)
36.
Journal Article
Yadav, V. K.; Santos-González, J.; Köhler, C.: INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis. Nucleic Acids Research 49 (8), pp. 4371 - 4385 (2021)
37.
Journal Article
Fernie, A. R.: Associating primary and specialized metabolism with salt induced osmotic stress tolerance in maize. New Phytologist 230 (6), pp. 2991 - 2093 (2021)
38.
Journal Article
Zhang, Y.; Giese, J.; Kerbler, S.M.-L.; Siemiatkowska, B.; de Souza, L. P.; Alpers, J.; Medeiros, D.B.; Hincha, D. K.; Daloso, D. M.; Stitt, M. et al.; Finkemeier, I.; Fernie, A. R.: Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. Molecular Plant 14 (7), pp. 1104 - 1118 (2021)
39.
Journal Article
Baptistella, J. L. C.; Llerena, J. P. P.; Domingues-Júnior, A. P.; Fernie, A. R.; Favarin, J. L.; Mazzafera, P.: Differential responses of three Urochloa species to low phosphorus availability. Annals of Applied Biology 179 (2), pp. 216 - 230 (2021)
40.
Journal Article
Wu, G.; Bock, R.: GUN control in retrograde signaling: How GENOMES UNCOUPLED proteins adjust nuclear gene expression to plastid biogenesis. The Plant Cell 33 (3), pp. 457 - 574 (2021)
41.
Journal Article
Scossa, F.; Fernie, A. R.: When a Crop Goes Back to the Wild: Feralization. Trends in Plant Science 26 (6), pp. 543 - 545 (2021)
42.
Journal Article
Malinova, I.; Zupok, A.; Massouh, A.; Schöttler, M. A.; Meyer, E. H.; Yaneva-Roder, L.; Szymanski, W. G.; Rößner, M.; Ruf, S.; Bock, R. et al.; Greiner, S.: Correction of Frameshift Mutations in the atpB Gene by Translational Recoding in Chloroplasts of Oenothera and Tobacco. The Plant Cell 33 (5), pp. 1682 - 1705 (2021)
43.
Journal Article
Fichtner, F.; Lunn, J. E.: The Role of Trehalose 6-Phosphate (Tre6P) in Plant Metabolism and Development. Annual Review of Plant Biology 72, pp. 737 - 760 (2021)
44.
Journal Article
Nowak, J.; Eng, R.C.; Matz, T.; Waack, M.; Persson, S.; Sampathkumar, A.; Nikoloski, Z.: A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells. Nature Communications 12 (1), 458 (2021)
45.
Journal Article
Schulz, P.; Piepenburg, K.; Lintermann, R.; Herde, M.; Schöttler, M. A.; Schmidt, L. K.; Ruf, S.; Kudla, J.; Romeis, T.; Bock, R.: Improving plant drought tolerance and growth under water limitation through combinatorial engineering of signaling networks. Plant Biotechnology Journal 19 (1), pp. 74 - 86 (2021)
46.
Journal Article
Hertle, A. P.; Haberl, B.; Bock, R.: Horizontal genome transfer by cell-to-cell travel of whole organelles. Science Advances 7 (1), eabd8215 (2021)
47.
Journal Article
Agudo-Canalejo, J.; Schultz, S. W.; Chino, H.; Migliano, S. M.; Saito, C.; Koyama-Honda, I.; Stenmark, H.; Brech, A.; May, A. I.; Mizushima, N. et al.; Knorr, R. L.: Wetting regulates autophagy of phase-separated compartments and the cytosol. Nature 591, pp. 142 - 146 (2021)
48.
Journal Article
Alseekh, S.; Kostova, D.; Bulut, M.; Fernie, A. R.: Genome-wide association studies: assessing trait characteristics in model and crop plants. Cellular and Molecular Life Sciences 78 (15), pp. 5743 - 5754 (2021)
49.
Journal Article
Ancín, M.; Larraya, L.; Florez-Sarasa, I. D.; Bénard, C.; Fernández-San Millán, A.; Veramendi, J.; Gibon, Y.; Fernie, A. R.; Aranjuelo, I.; Farran, I.: Overexpression of thioredoxin m in chloroplasts alters carbon and nitrogen partitioning in tobacco. Journal of Experimental Botany 72 (13), pp. 4949 - 4964 (2021)
50.
Journal Article
Aneklaphakij, C.; Saigo, T.; Watanabe, M.; Naake, T.; Fernie, A. R.; Bunsupa, S.; Satitpatipan, V.; Tohge, T.: Diversity of Chemical Structures and Biosynthesis of Polyphenols in Nut-Bearing Species. Frontiers in Plant Science 12, 642581 (2021)
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