@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} } @phdthesis{Dreyer2005, author = {Dreyer, Ingo}, title = {Biophysikalische und molekulare Grundlagen der Regulation des Kaliumtransports in Pflanzen}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7708}, school = {Universit{\"a}t Potsdam}, year = {2005}, abstract = {Kaliumionen (K+) sind die am h{\"a}ufigsten vorkommenden anorganischen Kationen in Pflanzen. Gemessen am Trockengewicht kann ihr Anteil bis zu 10\% ausmachen. Kaliumionen {\"u}bernehmen wichtige Funktionen in verschiedenen Prozessen in der Pflanze. So sind sie z.B. essentiell f{\"u}r das Wachstum und f{\"u}r den Stoffwechsel. Viele wichtige Enzyme arbeiten optimal bei einer K+ Konzentration im Bereich von 100 mM. Aus diesem Grund halten Pflanzenzellen in ihren Kompartimenten, die am Stoffwechsel beteiligt sind, eine kontrollierte Kaliumkonzentration von etwa 100 mM aufrecht. Die Aufnahme von Kaliumionen aus dem Erdreich und deren Transport innerhalb der Pflanze und innerhalb einer Pflanzenzelle wird durch verschiedene Kaliumtransportproteine erm{\"o}glicht. Die Aufrechterhaltung einer stabilen K+ Konzentration ist jedoch nur m{\"o}glich, wenn die Aktivit{\"a}t dieser Transportproteine einer strikten Kontrolle unterliegt. Die Prozesse, die die Transportproteine regulieren, sind bis heute nur ansatzweise verstanden. Detailliertere Kenntnisse auf diesem Gebiet sind aber von zentraler Bedeutung f{\"u}r das Verst{\"a}ndnis der Integration der Transportproteine in das komplexe System des pflanzlichen Organismus. In dieser Habilitationsschrift werden eigene Publikationen zusammenfassend dargestellt, in denen die Untersuchungen verschiedener Regulationsmechanismen pflanzlicher Kaliumkan{\"a}le beschrieben werden. Diese Untersuchungen umfassen ein Spektrum aus verschiedenen proteinbiochemischen, biophysikalischen und pflanzenphysiologischen Analysen. Um die Regulationsmechanismen grundlegend zu verstehen, werden zum einen ihre strukturellen und molekularen Besonderheiten untersucht. Zum anderen werden die biophysikalischen und reaktionskinetischen Zusammenh{\"a}nge der Regulationsmechanismen analysiert. Die gewonnenen Erkenntnisse erlauben eine neue, detailliertere Interpretation der physiologischen Rolle der Kaliumtransportproteine in der Pflanze.}, subject = {Kaliumion}, language = {de} } @article{DreyerBlatt2009, author = {Dreyer, Ingo and Blatt, Michael R.}, title = {What makes a gate? : the ins and outs of Kv-like K+ channels in plants}, issn = {1360-1385}, doi = {10.1016/j.tplants.2009.04.001}, year = {2009}, abstract = {Gating of K+ and other ion channels is 'hard-wired' within the channel protein. So it remains a puzzle how closely related channels in plants can show an unusually diverse range of biophysical properties. Gating of these channels lies at the heart of K+ mineral nutrition, signalling, abiotic and biotic stress responses in plants. Thus, our knowledge of the molecular mechanics underpinning K+ channel gating will be important for rational engineering of related traits in agricultural crops. Several key studies have added significantly to our understanding of channel gating in plants and have challenged current thinking about analogous processes found in animal K+ channels. Such studies highlight how much of K+ channel gating remains to be explored in plants.}, language = {en} } @article{DreyerGajdanowicz2009, author = {Dreyer, Ingo and Gajdanowicz, Pawel}, title = {Regulation of the gating mode of the Arabidopsis K+ channel AKT2 is important for adaptation to abiotic stress}, issn = {1095-6433}, doi = {10.1016/j.cbpa.2009.04.426}, year = {2009}, language = {en} } @article{DreyerPoreeSchneideretal.2004, author = {Dreyer, Ingo and Poree, Fabien and Schneider, A. and Mittelstadt, J. and Bertl, Adam and Sentenac, H. and Thibaud, Jean-Baptiste and M{\"u}ller-R{\"o}ber, Bernd}, title = {Assembly of plant Shaker-like K-out channels requires two distinct sites of the channel alpha-subunit}, issn = {0006-3495}, year = {2004}, abstract = {SKOR and GORK are outward-rectifying plant potassium channels from Arabidopsis thaliana. They belong to the Shaker superfamily of voltage-dependent K+ channels. Channels of this class are composed of four alpha-subunits and subunit assembly is a prerequisite for channel function. In this study the assembly mechanism of SKOR was investigated using the yeast two-hybrid system and functional assays in Xenopus oocytes and in yeast. We demonstrate that SKOR and GORK physically interact and assemble into heteromeric K-out channels. Deletion mutants and chimeric proteins generated from SKOR and the K-in channel alpha-subunit KAT1 revealed that the cytoplasmic C-terminus of SKOR determines channel assembly. Two domains thatchannel a-subunit KAT1 revealed that the cytoplasmic C-terminus of SKOR determines channel assembly. Two domains that are crucial for channel assembly were identified: i), a proximal interacting region comprising a putative cyclic nucleotide-binding domain together with 33 amino acids just upstream of this domain, and ii), a distal interacting region showing some resemblance to the K-T domain of KAT1. Both regions contributed differently to channel assembly. Whereas the proximal interacting region was found to be active on its own, the distal interacting region required an intact proximal interacting region to be active. K-out alpha-subunits did not assemble with K-in alpha-subunits because of the absence of interaction between their assembly sites}, language = {en} } @article{FernandezNinoGiraldoLuciaGomezPorrasetal.2017, author = {Fernandez-Nino, Miguel and Giraldo, Daniel and Lucia Gomez-Porras, Judith and Dreyer, Ingo and Gonzalez Barrios, Andres Fernando and Arevalo-Ferro, Catalina}, title = {A synthetic multi-cellular network of coupled self-sustained oscillators}, series = {PLoS one}, volume = {12}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0180155}, pages = {11}, year = {2017}, abstract = {Engineering artificial networks from modular components is a major challenge in synthetic biology. In the past years, single units, such as switches and oscillators, were successfully constructed and implemented. The effective integration of these parts into functional artificial self-regulated networks is currently on the verge of breakthrough. Here, we describe the design of a modular higher-order synthetic genetic network assembled from two independent self-sustained synthetic units: repressilators coupled via a modified quorum-sensing circuit. The isolated communication circuit and the network of coupled oscillators were analysed in mathematical modelling and experimental approaches. We monitored clustering of cells in groups of various sizes. Within each cluster of cells, cells oscillate synchronously, whereas the theoretical modelling predicts complete synchronization of the whole cellular population to be obtained approximately after 30 days. Our data suggest that self-regulated synchronization in biological systems can occur through an intermediate, long term clustering phase. The proposed artificial multicellular network provides a system framework for exploring how a given network generates a specific behaviour.}, language = {en} } @article{GajdanowiczGarciaMataGonzalezetal.2009, author = {Gajdanowicz, Pawel and Garcia-Mata, Carlos and Gonzalez, Wendy and Morales-Navarro, Samuel El{\"i}as and Sharma, Tripti and Gonzalez-Nilo, Fernando Danilo and Gutowicz, Jan and M{\"u}ller-R{\"o}ber, Bernd and Blatt, Michael R. and Dreyer, Ingo}, title = {Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2008.02749.x}, year = {2009}, abstract = {The family of voltage-gated potassium channels in plants presumably evolved from a common ancestor and includes both inward-rectifying (K-in) channels that allow plant cells to accumulate K+ and outward-rectifying (K-out) channels that mediate K+ efflux. Despite their close structural similarities, the activity of Kin channels is largely independent of K+ and depends only on the transmembrane voltage, whereas that of K-out channels responds to the membrane voltage and the prevailing extracellular K+ concentration. Gating of potassium channels is achieved by structural rearrangements within the last transmembrane domain (S6). Here we investigated the functional equivalence of the S6 helices of the Kin channel KAT1 and the K-out channel SKOR by domain-swapping and site-directed mutagenesis. Channel mutants and chimeras were analyzed after expression in Xenopus oocytes. We identified two discrete regions that influence gating differently in both channels, demonstrating a lack of functional complementarity between KAT1 and SKOR. Our findings are supported by molecular models of KAT1 and SKOR in the open and closed states. The role of the S6 segment in gating evolved differently during specialization of the two channel subclasses, posing an obstacle for the transfer of the K+-sensor from K-out to K-in channels.}, language = {en} } @article{GajdanowiczMichardSandmannetal.2011, author = {Gajdanowicz, Pawel and Michard, Erwan and Sandmann, Michael and Rocha, Marcio and Correa, Luiz Gustavo Guedes and Ramirez-Aguilar, Santiago J. and Gomez-Porras, Judith L. and Gonzalez, Wendy and Thibaud, Jean-Baptiste and van Dongen, Joost T. and Dreyer, Ingo}, title = {Potassium (K plus ) gradients serve as a mobile energy source in plant vascular tissues}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {2}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1009777108}, pages = {864 -- 869}, year = {2011}, abstract = {The essential mineral nutrient potassium (K(+)) is the most important inorganic cation for plants and is recognized as a limiting factor for crop yield and quality. Nonetheless, it is only partially understood how K(+) contributes to plant productivity. K(+) is used as a major active solute to maintain turgor and to drive irreversible and reversible changes in cell volume. K(+) also plays an important role in numerous metabolic processes, for example, by serving as an essential cofactor of enzymes. Here, we provide evidence for an additional, previously unrecognized role of K(+) in plant growth. By combining diverse experimental approaches with computational cell simulation, we show that K(+) circulating in the phloem serves as a decentralized energy storage that can be used to overcome local energy limitations. Posttranslational modification of the phloem-expressed Arabidopsis K(+) channel AKT2 taps this "potassium battery," which then efficiently assists the plasma membrane H(+)-ATPase in energizing the transmembrane phloem (re) loading processes.}, language = {en} } @article{GarciaMataWangGajdanowiczetal.2010, author = {Garcia-Mata, Carlos and Wang, Jianwen and Gajdanowicz, Pawel and Gonzalez, Wendy and Hills, Adrian and Donald, Naomi and Riedelsberger, Janin and Amtmann, Anna and Dreyer, Ingo and Blatt, Michael R.}, title = {A minimal cysteine motif required to activate the SKOR K+ channel of Arabidopsis by the reactive oxygen species H2O2}, issn = {0021-9258}, doi = {10.1074/jbc.M110.141176}, year = {2010}, abstract = {Reactive oxygen species (ROS) are essential for development and stress signaling in plants. They contribute to plant defense against pathogens, regulate stomatal transpiration, and influence nutrient uptake and partitioning. Although both Ca2+ and K+ channels of plants are known to be affected, virtually nothing is known of the targets for ROS at a molecular level. Here we report that a single cysteine (Cys) residue within the Kv-like SKOR K+ channel of Arabidopsis thaliana is essential for channel sensitivity to the ROS H2O2. We show that H2O2 rapidly enhanced current amplitude and activation kinetics of heterologously expressed SKOR, and the effects were reversed by the reducing agent dithiothreitol (DTT). Both H2O2 and DTT were active at the outer face of the membrane and current enhancement was strongly dependent on membrane depolarization, consistent with a H2O2-sensitive site on the SKOR protein that is exposed to the outside when the channel is in the open conformation. Cys substitutions identified a single residue, Cys(168) located within the S3 alpha-helix of the voltage sensor complex, to be essential for sensitivity to H2O2. The same Cys residue was a primary determinant for current block by covalent Cys S-methioylation with aqueous methanethiosulfonates. These, and additional data identify Cys168 as a critical target for H2O2, and implicate ROS-mediated control of the K+ channel in regulating mineral nutrient partitioning within the plant.}, language = {en} } @inproceedings{GonzalezRiedelsbergerMoralesNavarroetal.2012, author = {Gonzalez, W. and Riedelsberger, J. and Morales-Navarro, S. E. and Caballero, Julio and Alzate-Morales, Jans H. and Gonzalez-Nilo, F. D. and Dreyer, Ingo}, title = {The pH sensor of the plant K plus uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids}, series = {The FEBS journal}, volume = {279}, booktitle = {The FEBS journal}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1742-464X}, pages = {455 -- 455}, year = {2012}, language = {en} }