TY - JOUR A1 - Lucia Gomez-Porras, Judith A1 - Mauricio Riano-Pachon, Diego A1 - Benito, Begona A1 - Haro, Rosario A1 - Sklodowski, Kamil A1 - Rodriguez-Navarro, Alonso A1 - Dreyer, Ingo T1 - Phylogenetic analysis of K+ transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants JF - Frontiers in plant science N2 - As heritage from early evolution, potassium (K+) is absolutely necessary for all living cells. It plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. Land plants even enlarged this spectrum of K+ utilization after having gone ashore, despite the fact that K+ is far less available in their new oligotrophic habitats than in sea water. Inevitably, plant cells had to improve and to develop unique transport systems for K+ accumulation and distribution. In the past two decades a manifold of K+ transporters from flowering plants has been identified at the molecular level. The recently published genome of the fern ally Selaginella moellendorffii now helps in providing a better understanding on the molecular changes involved in the colonization of land and the development of the vasculature and the seeds. In this article we present an inventory of K+ transporters of this lycophyte and pigeonhole them together with their relatives from the moss Physcomitrella patens, the monocotyledon Oryza sativa, and two dicotyledonous species, the herbaceous plant Arabidopsis thaliana, and the tree Populus trichocarpa. Interestingly, the transition of green plants from an aqueous to a dry environment coincides with a dramatic reduction in the diversity of voltage-gated potassium channels followed by a diversification on the basis of one surviving K+ channel class. The first appearance of K+ release (K-out) channels in S. moellendorffii that were shown in Arabidopsis to be involved in xylem loading and guard cell closure coincides with the specialization of vascular plants and may indicate an important adaptive step. KW - potassium KW - transport KW - channel KW - voltage-dependent KW - voltage-independent KW - high-affinity KW - Selaginella Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00167 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Fernandez-Nino, Miguel A1 - Giraldo, Daniel A1 - Lucia Gomez-Porras, Judith A1 - Dreyer, Ingo A1 - Gonzalez Barrios, Andres Fernando A1 - Arevalo-Ferro, Catalina T1 - A synthetic multi-cellular network of coupled self-sustained oscillators JF - PLoS one N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0180155 SN - 1932-6203 VL - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Voelker, Camilla A1 - Gomez-Porras, Judith Lucia A1 - Becker, Dirk A1 - Hamamoto, Shin A1 - Uozumi, Nobuyuki A1 - Gambale, Franco A1 - Müller-Röber, Bernd A1 - Czempinski, Katrin A1 - Dreyer, Ingo T1 - Roles of tandem-pore K plus channels in plants : a puzzle still to be solved N2 - The group of voltage-independent K+ channels in Arabidopsis thaliana consists of six members, five tandem-pore channels (TPK1-TPK5) and a single K-ir-like channel (KCO3). All TPK/KCO channels are located at the vacuolar membrane except for TPK4, which was shown to be a plasma membrane channel in pollen. The vacuolar channels interact with 14-3-3 proteins (also called General Regulating Factors, GRFs), indicating regulation at the level of protein-protein interactions. Here we review current knowledge about these ion channels and their genes, and highlight open questions that need to be urgently addressed in future studies to fully appreciate the physiological functions of these ion channels. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=1435-8603 U6 - https://doi.org/10.1111/j.1438-8677.2010.00353.x SN - 1435-8603 ER - TY - JOUR A1 - Naso, Alessia A1 - Dreyer, Ingo A1 - Pedemonte, Laura A1 - Testa, Ilaria A1 - Gomez-Porras, Judith Lucia A1 - Usai, Cesare A1 - Müller-Röber, Bernd A1 - Diaspro, Alberto A1 - Gambale, Franco A1 - Picco, Cristiana T1 - The role of the C-terminus for functional heteromerization of the plant channel KDC1 N2 - 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. Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/00063495 U6 - https://doi.org/10.1016/j.bpj.2009.02.055 SN - 0006-3495 ER - TY - THES A1 - Gómez-Porras, Judith Lucia T1 - In silico identification of genes regulated by abscisic acid in Arabidopsis thaliana (L.) Heynh. T1 - In silico Identifikation von Abszisinsaeure-regulierten Genen in Arabidopsis thaliana (L.) Heynh. N2 - Abscisic acid (ABA) is a major plant hormone that plays an important role during plant growth and development. During vegetative growth ABA mediates (in part) responses to various environmental stresses such as cold, drought and high salinity. The response triggered by ABA includes changes in the transcript level of genes involved in stress tolerance. The aim of this project was the In silico identification of genes putatively regulated by ABA in A. thaliana. In silico predictions were combined with experimental data in order to evaluate the reliability of computational predictions. Taking advantage of the genome sequence of A. thaliana publicly available since 2000, 1 kb upstream sequences were screened for combinations of cis-elements known to be involved in the regulation of ABA-responsive genes. It was found that around 10 to 20 percent of the genes of A. thaliana might be regulated by ABA. Further analyses of the predictions revealed that certain combinations of cis-elements that confer ABA-responsiveness were significantly over-represented compared with results in random sequences and with random expectations. In addition, it was observed that other combinations that confer ABA-responsiveness in monocotyledonous species might not be functional in A. thaliana. It is proposed that ABA-responsive genes in A. thaliana show pairs of ABRE (abscisic acid responsive element) with MYB binding sites, DRE (dehydration responsive element) or with itself. The analysis of the distances between pairs of cis-elements suggested that pairs of ABREs are bound by homodimers of ABRE binding proteins. In contrast, pairs between MYB binding sites and ABRE, or DRE and ABRE showed a distance between cis-elements that suggested that the binding proteins interact through protein complexes and not directly. The comparison of computational predictions with experimental data confirmed that the regulatory mechanisms leading to the induction or repression of genes by ABA is very incompletely understood. It became evident that besides the cis-elements proposed in this study to be present in ABA-responsive genes, other known and unknown cis-elements might play an important role in the transcriptional regulation of ABA-responsive genes. For example, auxin-related cis elements, or the cis-elements recognized by the NAM-family of transcription factors (Non-Apical meristem). This work documents the use of computational and experimental approaches to analyse possible interactions between cis-elements involved in the regulation of ABA-responsive genes. The computational predictions allowed the distinction between putatively relevant combinations of cis-elements from irrelevant combinations of cis-elements in ABA-responsive genes. The comparison with experimental data allowed to identify certain cis-elements that have not been previously associated to the ABA-mediated transcriptional regulation, but that might be present in ABA-responsive genes (e.g. auxin responsive elements). Moreover, the efforts to unravel the gene regulatory network associated with the ABA-signalling pathway revealed that NAM-transcription factors and their corresponding binding sequences are important components of this network. N2 - Pflanzen reagieren auf aeußere Stresseinwirkung (z.B. Trockenheit oder Hitze) u.a. mit der Bildung bestimmter Hormone. Diese Hormone wiederum bewirken eine Vielzahl komplexer Reaktionen (z.B. im Stoffwechsel und in der Genexpression), die zum Ziel haben, die Pflanzen widerstandsfaehiger gegen die Stresssituation zu machen. Ein wichtiges Stresshormon ist die Abzisinsaeure (ABA, fuer engl. „abscisic acid“). Experimentell koennen Pflanzen durch die Gabe von ABA zu Reaktionen gezwungen werden, die normalerweise nur unter Stressbedingungen beobachtet werden. Hierzu zaehlen vor allem eine Reduktion der Spaltoeffnungen in den Blaettern, um den Wasserverlust infolge von Transpiration zu minimieren, und eine massive Umprogrammierung der Genexpression. In der vorliegenden Arbeit wurde der Einfluss von ABA auf die Genexpression in der Modellpflanze Arabidopsis thaliana untersucht. Hierzu wurden bioinformatorische und experimentelle Ansaetze verknuepft. Die bioinformatorischen Ansaetze bedienten sich der bekannten Sequenz des Genoms von A. thaliana. Mit Hilfe verschiedener geeigneter Computerprogramme wurden im Genom Gene identifiziert, deren Expression potentiell durch ABA reguliert wird. Die so erhaltenen Vorhersagen der verschiedenen Programme wurden miteinander und mit eigenen als auch mit publizierten experimentellen Daten verglichen, um die Qualitaet der Vorhersagen zu beurteilen. Die wichtigste Schlussfolgerung aus den Ergebnissen dieser Arbeit ist, dass gegenwaertig bioinformatorische Ansaetze allein nicht ausreichen, um biologische Prozesse zufriedenstellend zu analysieren. In der vorliegenden Arbeit ermoeglichte erst eine Kombination aus bioinformatorischen und experimentellen Ansaetzen die Generierung neuer, abgesicherter Hypothesen zur ABA-induzierten Umprogrammierung der Genexpression. KW - Bioinformatik KW - Abszisinsäure KW - Promotoren KW - bioinformatics KW - regulation KW - ABA KW - Arabidopsis Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-7401 ER -