@article{TabatabaeiAlseekhShahidetal.2022,
  author    = {Tabatabaei, Iman and Alseekh, Saleh and Shahid, Mohammad and Leniak, Ewa and Wagner, Mateusz and Mahmoudi, Henda and Thushar, Sumitha and Fernie, Alisdair R. and Murphy, Kevin M. and Schm{\"o}ckel, Sandra M. and Tester, Mark and M{\"u}ller-R{\"o}ber, Bernd and Skirycz, Aleksandra and Balazadeh, Salma},
  title     = {The diversity of quinoa morphological traits and seed metabolic composition},
  series = {Scientific data},
  volume    = {9},
  journal   = {Scientific data},
  number    = {1},
  publisher = {Nature Research},
  address   = {Berlin},
  issn      = {2052-4463},
  doi       = {10.1038/s41597-022-01399-y},
  pages     = {7},
  year      = {2022},
  abstract  = {Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.},
  language  = {en}
}
@article{CzarnockaVanDerKelenWillemsetal.2017,
  author    = {Czarnocka, Weronika and Van Der Kelen, Katrien and Willems, Patrick and Szechynska-Hebda, Magdalena and Shahnejat-Bushehri, Sara and Balazadeh, Salma and Rusaczonek, Anna and M{\"u}ller-R{\"o}ber, Bernd and Van Breusegem, Frank and Karpinski, Stanislaw},
  title     = {The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator},
  series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  volume    = {40},
  journal   = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0140-7791},
  doi       = {10.1111/pce.12994},
  pages     = {2644 -- 2662},
  year      = {2017},
  abstract  = {Since its discovery over two decades ago as an important cell death regulator in Arabidopsis thaliana, the role of LESION SIMULATING DISEASE 1 (LSD1) has been studied intensively within both biotic and abiotic stress responses as well as with respect to plant fitness regulation. However, its molecular mode of action remains enigmatic. Here, we demonstrate that nucleo-cytoplasmic LSD1 interacts with a broad range of other proteins that are engaged in various molecular pathways such as ubiquitination, methylation, cell cycle control, gametogenesis, embryo development and cell wall formation. The interaction of LSD1 with these partners is dependent on redox status, as oxidative stress significantly changes the quantity and types of LSD1-formed complexes. Furthermore, we show that LSD1 regulates the number and size of leaf mesophyll cells and affects plant vegetative growth. Importantly, we also reveal that in addition to its function as a scaffold protein, LSD1 acts as a transcriptional regulator. Taken together, our results demonstrate that LSD1 plays a dual role within the cell by acting as a condition-dependent scaffold protein and as a transcription regulator.},
  language  = {en}
}
@article{BrotmanLandauPninietal.2012,
  author    = {Brotman, Yariv and Landau, Udi and Pnini, Smadar and Lisec, Jan and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Zilberstein, Aviah and Willmitzer, Lothar and Chet, Ilan and Viterbo, Ada},
  title     = {The LysM Receptor-Like Kinase LysM RLK1 is required to activate defense and abiotic-stress responses induced by overexpression of fungal chitinases in arabidopsis plants},
  series = {Molecular plant},
  volume    = {5},
  journal   = {Molecular plant},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1674-2052},
  doi       = {10.1093/mp/sss021},
  pages     = {1113 -- 1124},
  year      = {2012},
  abstract  = {Application of crab shell chitin or pentamer chitin oligosaccharide to Arabidopsis seedlings increased tolerance to salinity in wild-type but not in knockout mutants of the LysM Receptor-Like Kinase1 (CERK1/LysM RLK1) gene, known to play a critical role in signaling defense responses induced by exogenous chitin. Arabidopsis plants overexpressing the endochitinase chit36 and hexoaminidase excy1 genes from the fungus Trichoderma asperelleoides T203 showed increased tolerance to salinity, heavy-metal stresses, and Botrytis cinerea infection. Resistant lines, overexpressing fungal chitinases at different levels, were outcrossed to lysm rlk1 mutants. Independent homozygous hybrids lost resistance to biotic and abiotic stresses, despite enhanced chitinase activity. Expression analysis of 270 stress-related genes, including those induced by reactive oxygen species (ROS) and chitin, revealed constant up-regulation (at least twofold) of 10 genes in the chitinase-overexpressing line and an additional 76 salt-induced genes whose expression was not elevated in the lysm rlk1 knockout mutant or the hybrids harboring the mutation. These findings elucidate that chitin-induced signaling mediated by LysM RLK1 receptor is not limited to biotic stress response but also encompasses abiotic-stress signaling and can be conveyed by ectopic expression of chitinases in plants.},
  language  = {en}
}
@article{WinckRianoPachonSommeretal.2012,
  author    = {Winck, Flavia V. and Riano-Pachon, Diego M. and Sommer, Frederik and Rupprecht, Jens and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {The nuclear proteome of the green alga Chlamydomonas reinhardtii},
  series = {Proteomics},
  volume    = {12},
  journal   = {Proteomics},
  number    = {1},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  issn      = {1615-9853},
  doi       = {10.1002/pmic.201000782},
  pages     = {95 -- 100},
  year      = {2012},
  abstract  = {Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1\% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms.},
  language  = {en}
}
@article{SedaghatmehrMuellerRoeberBalazadeh2016,
  author    = {Sedaghatmehr, Mastoureh and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma},
  title     = {The plastid metalloprotease FtsH6 and small heat shock protein HSP21 jointly regulate thermomemory in Arabidopsis},
  series = {Nature Communications},
  volume    = {7},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/ncomms12439},
  pages     = {14},
  year      = {2016},
  abstract  = {Acquired tolerance to heat stress is an increased resistance to elevated temperature following a prior exposure to heat. The maintenance of acquired thermotolerance in the absence of intervening stress is called 'thermomemory' but the mechanistic basis for this memory is not well defined. Here we show that Arabidopsis HSP21, a plastidial small heat shock protein that rapidly accumulates after heat stress and remains abundant during the thermomemory phase, is a crucial component of thermomemory. Sustained memory requires that HSP21 levels remain high. Through pharmacological interrogation and transcriptome profiling, we show that the plastid-localized metalloprotease FtsH6 regulates HSP21 abundance. Lack of a functional FtsH6 protein promotes HSP21 accumulation during the later stages of thermomemory and increases thermomemory capacity. Our results thus reveal the presence of a plastidial FtsH6-HSP21 control module for thermomemory in plants.},
  language  = {en}
}
@article{NasoDreyerPedemonteetal.2009,
  author    = {Naso, Alessia and Dreyer, Ingo and Pedemonte, Laura and Testa, Ilaria and Gomez-Porras, Judith Lucia and Usai, Cesare and M{\"u}ller-R{\"o}ber, Bernd and Diaspro, Alberto and Gambale, Franco and Picco, Cristiana},
  title     = {The role of the C-terminus for functional heteromerization of the plant channel KDC1},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2009.02.055},
  year      = {2009},
  abstract  = {Voltage-gated potassium channels are formed by the assembly of four identical (homotetramer) or different (heterotetramer) subunits. Tetramerization of plant potassium channels involves the C-terminus of the protein. We investigated the role of the C-terminus of KDC1, a Shaker-like inward-rectifying K+ channel that does not form functional homomeric channels, but participates in the formation of heteromeric complexes with other potassium alpha- subunits when expressed in Xenopus oocytes. The interaction of KDC1 with KAT1 was investigated using the yeast two- hybrid system, fluorescence and electrophysiological studies. We found that the KDC1-EGFP fusion protein is not targeted to the plasma membrane of Xenopus oocytes unless it is coexpressed with KAT1. Deletion mutants revealed that the KDC1 C- terminus is involved in heteromerization. Two domains of the C-terminus, the region downstream the putative cyclic nucleotide binding domain and the distal part of the C-terminus called K-HA domain, contributed to a different extent to channel assembly. Whereas the first interacting region of the C-terminus was necessary for channel heteromerization, the removal of the distal KHA domain decreased but did not abolish the formation of heteromeric complexes. Similar results were obtained when coexpressing KDC1 with the KAT1-homolog KDC2 from carrots, thus indicating the physiological significance of the KAT1/KDC1 characterization. Electrophysiological experiments showed furthermore that the heteromerization capacity of KDC1 was negatively influenced by the presence of the enhanced green fluorescence protein fusion.},
  language  = {en}
}
@article{BanksNishiyamaHasebeetal.2011,
  author    = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.},
  title     = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants},
  series = {Science},
  volume    = {332},
  journal   = {Science},
  number    = {6032},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.1203810},
  pages     = {960 -- 963},
  year      = {2011},
  abstract  = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.},
  language  = {en}
}
@article{GliwickaBalazadehCaldanaetal.2009,
  author    = {Gliwicka, Marta and Balazadeh, Salma and Caldana, Camila and M{\"u}ller-R{\"o}ber, Bernd and Gaj, Malgorzata D.},
  title     = {The use of multi-qPCR platform and tan1 mutant in identification of TF genes involved in somatic embryogenesis in Arabidopsis},
  issn      = {0001-5296},
  year      = {2009},
  language  = {en}
}
@article{GarapatiFeilLunnetal.2015,
  author    = {Garapati, Prashanth and Feil, Regina and Lunn, John Edward and Van Dijck, Patrick and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {169},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {1},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.15.00917},
  pages     = {379 -- 390},
  year      = {2015},
  abstract  = {Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1.},
  language  = {en}
}
@article{WittZanorMuellerRoeber2004,
  author    = {Witt, Isabell and Zanor, Maria Ines and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Transcription factor function search : how do individual factors regulate agronomical important processes in plants? (Subproject A)},
  isbn      = {3-00-011587-0},
  year      = {2004},
  language  = {en}
}