TY - JOUR A1 - Christian, Jan-Ole A1 - Braginets, Rostyslav A1 - Schulze, Waltraud X. A1 - Walther, Dirk T1 - Characterization and prediction of protein phosphorylation hotspots in Arabidopsis thaliana JF - Frontiers in plant science N2 - The regulation of protein function by modulating the surface charge status via sequence-locally enriched phosphorylation sites (P-sites) in so called phosphorylation "hotspots" has gained increased attention in recent years. We set out to identify P-hotspots in the model plant Arabidopsis thaliana. We analyzed the spacing of experimentally detected P-sites within peptide-covered regions along Arabidopsis protein sequences as available from the PhosPhAt database. Confirming earlier reports (Schweiger and Lanial, 2010), we found that, indeed, P-sites tend to cluster and that distributions between serine and threonine P-sites to their respected closest next P-site differ significantly from those for tyrosine P-sites. The ability to predict P-hotspots by applying available computational P-site prediction programs that focus on identifying single P-sites was observed to be severely compromised by the inevitable interference of nearby P-sites. We devised a new approach, named HotSPotter, for the prediction of phosphorylation hotspots. HotSPotter is based primarily on local amino acid compositional preferences rather than sequence position-specific motifs and uses support vector machines as the underlying classification engine. HotSPotter correctly identified experimentally determined phosphorylation hotspots in A. thaliana with high accuracy. Applied to the Arabidopsis proteome, HotSPotter-predicted 13,677 candidate P-hotspots in 9,599 proteins corresponding to 7,847 unique genes. Hotspot containing proteins are involved predominantly in signaling processes confirming the surmised modulating role of hotspots in signaling and interaction events. Our study provides new bioinformatics means to identify phosphorylation hotspots and lays the basis for further investigating novel candidate P-hotspots. All phosphorylation hotspot annotations and predictions have been made available as part of the PhosPhAt database at http://phosphat.mpimp-golm.mpg.de. KW - protein phosphorylation KW - hotspots KW - Arabidopsis thaliana KW - support vector machines KW - regulation Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00207 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Gonzalez, Wendy A1 - Riedelsberger, Janin A1 - Morales-Navarro, Samuel E. A1 - Caballero, Julio A1 - Alzate-Morales, Jans H. A1 - Gonzalez-Nilo, Fernando D. A1 - Dreyer, Ingo T1 - The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids JF - The biochemical journal N2 - The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2-2.5 pH units) is perceived by voltage-gated inward potassium channels (K-in) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal K-in channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal K-in channel KAT1, mutations in the unique histidine exposed to the solvent (His(267)) do not affect the pH dependency. We demonstrate in the present study that His(267) of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe(266) shifts its pK(a) to undetectable values through a cation-pi interaction. Instead, we show that Glu(240) placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu(240), several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel. KW - Arabidopsis thaliana KW - channel protein structure KW - channel protein-proton interaction KW - KAT1 KW - pH regulation KW - potassium chanel Y1 - 2012 U6 - https://doi.org/10.1042/BJ20111498 SN - 0264-6021 VL - 442 IS - 7 SP - 57 EP - 63 PB - Portland Press CY - London ER - TY - JOUR A1 - Meyer, Rhonda C. A1 - Witucka-Wall, Hanna A1 - Becher, Martina A1 - Blacha, Anna Maria A1 - Boudichevskaia, Anastassia A1 - Dörmann, Peter A1 - Fiehn, Oliver A1 - Friedel, Svetlana A1 - von Korff, Maria A1 - Lisec, Jan A1 - Melzer, Michael A1 - Repsilber, Dirk A1 - Schmidt, Renate A1 - Scholz, Matthias A1 - Selbig, Joachim A1 - Willmitzer, Lothar A1 - Altmann, Thomas T1 - Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids JF - The plant journal N2 - Heterosis-associated cellular and molecular processes were analyzed in seeds and seedlings of Arabidopsis thaliana accessions Col-0 and C24 and their heterotic hybrids. Microscopic examination revealed no advantages in terms of hybrid mature embryo organ sizes or cell numbers. Increased cotyledon sizes were detectable 4 days after sowing. Growth heterosis results from elevated cell sizes and numbers, and is well established at 10 days after sowing. The relative growth rates of hybrid seedlings were most enhanced between 3 and 4 days after sowing. Global metabolite profiling and targeted fatty acid analysis revealed maternal inheritance patterns for a large proportion of metabolites in the very early stages. During developmental progression, the distribution shifts to dominant, intermediate and heterotic patterns, with most changes occurring between 4 and 6 days after sowing. The highest incidence of heterotic patterns coincides with establishment of size differences at 4 days after sowing. In contrast, overall transcript patterns at 4, 6 and 10 days after sowing are characterized by intermediate to dominant patterns, with parental transcript levels showing the largest differences. Overall, the results suggest that, during early developmental stages, intermediate gene expression and higher metabolic activity in the hybrids compared to the parents lead to better resource efficiency, and therefore enhanced performance in the hybrids. KW - heterosis KW - seedlings KW - metabolite profiling KW - transcript profiling KW - morphological analysis KW - Arabidopsis thaliana KW - biomass Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-313X.2012.05021.x SN - 0960-7412 VL - 71 IS - 4 SP - 669 EP - 683 PB - Wiley-Blackwell CY - Hoboken ER -