@article{RocchettiSharmaWulfetangeetal.2012, author = {Rocchetti, Alessandra and Sharma, Tripti and Wulfetange, Camilla and Scholz-Starke, Joachim and Grippa, Alexandra and Carpaneto, Armando and Dreyer, Ingo and Vitale, Alessandro and Czempinski, Katrin and Pedrazzini, Emanuela}, title = {The putative K+ channel subunit AtKCO3 forms stable dimers in arabidopsis}, series = {Frontiers in plant science}, volume = {3}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2012.00251}, pages = {13}, year = {2012}, abstract = {The permeation pore of K+ channels is formed by four copies of the pore domain. AtKCO3 is the only putative voltage-independent K+ channel subunit of Arabidopsis thaliana with a single pore domain. KCO3-like proteins recently emerged in evolution and, to date, have been found only in the genus Arabidopsis (A. thaliana and A. lyrata). We show that the absence of KCO3 does not cause marked changes in growth under various conditions. Only under osmotic stress we observed reduced root growth of the kco3-1 null-allele line. This phenotype was complemented by expressing a KCO3 mutant with an inactive pore, indicating that the function of KCO3 under osmotic stress does not depend on its direct ability to transport ions. Constitutively overexpressed AtKCO3 or AtKCO3::G FP are efficiently sorted to the tonoplast indicating that the protein is approved by the endoplasmic reticulum quality control. However, vacuoles isolated from transgenic plants do not have significant alterations in current density. Consistently, both AtKCO3 and AtKCO3::GFP are detected as homodimers upon velocity gradient centrifugation, an assembly state that would not allow for activity. We conclude that if AtKCO3 ever functions as a K+ channel, active tetramers are held by particularly weak interactions, are formed only in unknown specific conditions and may require partner proteins.}, language = {en} } @article{LuciaGomezPorrasMauricioRianoPachonBenitoetal.2012, author = {Lucia Gomez-Porras, Judith and Mauricio Riano-Pachon, Diego and Benito, Begona and Haro, Rosario and Sklodowski, Kamil and Rodriguez-Navarro, Alonso and Dreyer, Ingo}, title = {Phylogenetic analysis of K+ transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants}, series = {Frontiers in plant science}, volume = {3}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2012.00167}, pages = {13}, year = {2012}, abstract = {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.}, language = {en} } @article{ChristianBraginetsSchulzeetal.2012, author = {Christian, Jan-Ole and Braginets, Rostyslav and Schulze, Waltraud X. and Walther, Dirk}, title = {Characterization and prediction of protein phosphorylation hotspots in Arabidopsis thaliana}, series = {Frontiers in plant science}, volume = {3}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2012.00207}, pages = {14}, year = {2012}, abstract = {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.}, language = {en} } @article{BalazadehJaspertArifetal.2012, author = {Balazadeh, Salma and Jaspert, Nils and Arif, Muhammad and M{\"u}ller-R{\"o}ber, Bernd and Maurino, Veronica G.}, title = {Expression of ROS-responsive genes and transcription factors after metabolic formation of H2O2 in chloroplasts}, series = {Frontiers in plant science}, volume = {3}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2012.00234}, pages = {30}, year = {2012}, abstract = {Glycolate oxidase (GO) catalyses the oxidation of glycolate to glyoxylate, thereby consuming O-2 and producing H2O2. In this work, Arabidopsis thaliana plants expressing GO in the chloroplasts (GO plants) were used to assess the expressional behavior of reactive oxygen species (ROS)-responsive genes and transcription factors (TFs) after metabolic induction of H2O2 formation in chloroplasts. In this organelle, GO uses the glycolate derived from the oxygenase activity of RubisCO. Here, to identify genes responding to an abrupt production of H2O2 in chloroplasts we used quantitative real-time PCR (qRT-PCR) to test the expression of 187 ROS-responsive genes and 1880 TFs after transferring GO and wild-type (WT) plants grown at high CO2 levels to ambient CO2 concentration. Our data revealed coordinated expression changes of genes of specific functional networks 0.5 h after metabolic induction of H2O2 production in GO plants, including the induction of indole glucosinolate and camalexin biosynthesis genes. Comparative analysis using available microarray data suggests that signals for the induction of these genes through H2O2 may originate in the chloroplast. The TF profiling indicated an up-regulation in GO plants of a group of genes involved in the regulation of proanthocyanidin and anthocyanin biosynthesis. Moreover, the upregulation of expression of IF and IF interacting proteins affecting development (e.g., cell division, stem branching, flowering time, flower development) would impact growth and reproductive capacity, resulting in altered development under conditions that promote the formation of H2O2.}, language = {en} } @article{SpijkermanWackerWeithoffetal.2012, author = {Spijkerman, Elly and Wacker, Alexander and Weithoff, Guntram and Leya, Thomas}, title = {Elemental and fatty acid composition of snow algae in Arctic habitats}, series = {Frontiers in microbiology}, volume = {3}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2012.00380}, pages = {15}, year = {2012}, abstract = {Red, orange or green snow is the macroscopic phenomenon comprising different eukaryotic algae. Little is known about the ecology and nutrient regimes in these algal communities. Therefore, eight snow algal communities from five intensively tinted snow fields in western Spitsbergen were analysed for nutrient concentrations and fatty acid (FA) composition. To evaluate the importance of a shift from green to red forms on the FA-variability of the field samples, four snow algal strains were grown under nitrogen replete and moderate light (+N+ML) or N-limited and high light (-N+HL) conditions. All eight field algal communities were dominated by red and orange cysts. Dissolved nutrient concentration of the snow revealed a broad range of NH4+ (<0.005-1.2 mg NI-1) and only low PO43- (< 18 mu g P I-1) levels. The external nutrient concentration did not reflect cellular nutrient ratios as C:N and C:P ratios of the communities were highest at locations containing relatively high concentrations of NH4- and PO43-. Molar N:P ratios ranged from 11 to 21 and did not suggest clear limitation of a single nutrient. On a per carbon basis, we found a 6-fold difference in total FA content between the eight snow algal communities, ranging from 50 to 300 mg FA g C-1. In multivariate analyses total FA content opposed the cellular N:C quota and a large part of the FA variability among field locations originated from the abundant FAs C181n-9, C18 2n-6, and C183n-3. Both field samples and snow algal strains grown under -N+HL conditions had high concentrations of C181n-9. FAs possibly accumulated due to the cessation of growth. Differences in color and nutritional composition between patches of snow algal communities within one snow field were not directly related to nutrient conditions. We propose that the highly patchy distribution of snow algae within and between snow fields may also result from differences in topographical and geological parameters such as slope, melting water rivulets, and rock formation.}, language = {en} } @misc{KaplanHarelKaplanLevyetal.2012, author = {Kaplan, Aaron and Harel, Moshe and Kaplan-Levy, Ruth N. and Hadas, Ora and Sukenik, Assaf and Dittmann-Th{\"u}nemann, Elke}, title = {The languages spoken in the water body (or the biological role of cyanobacterial toxins)}, series = {Frontiers in microbiology}, volume = {3}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2012.00138}, pages = {11}, year = {2012}, abstract = {Although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. In this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. We examine the experimental evidence supporting some of the dogmas in the field and raise several open questions to be dealt with in future research. We do not discuss the health and environmental implications of toxin presence in the water body.}, language = {en} } @article{BickelTangGrossart2012, author = {Bickel, Samantha L. and Tang, Kam W. and Grossart, Hans-Peter}, title = {Ciliate epibionts associated with crustacean zooplankton in German lakes - distribution, motility, and bacterivory}, series = {Frontiers in microbiology}, volume = {3}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2012.00243}, pages = {11}, year = {2012}, abstract = {Ciliate epibionts associated with crustacean zooplankton are widespread in aquatic systems, but their ecological roles are little known. We studied the occurrence of ciliate epibionts on crustacean zooplankton in nine German lakes with different limnological features during the summer of 2011. We also measured the detachment and re-attachment rates of the ciliates, changes in their motility, and the feeding rates of attached vs. detached ciliate epibionts. Epibionts were found in all lakes sampled except an acidic lake with large humic inputs. Epibiont prevalence was as high as 80.96\% on the cladoceran Daphnia cucullata, 67.17\% on the cladoceran Diaphanosoma brachyurum, and 46.67\% on the calanoid copepod Eudiaptomus gracilis. Both cladoceran groups typically had less than 10 epibionts per individual, while the epibiont load on E. gracilis ranged from 1 to >30 epibionts per individual. After the death of the zooplankton host, the peritrich ciliate epibiont Epistylis sp. detached in an exponential fashion with a half-life of 5 min, and 98\% detached within 30 min, leaving behind the stalks used for attachment. Immediately after detachment, the ciliates were immotile, but 62\% became motile within 60 min. When a new host was present, only 27\% reattached after 120 min. The average measured ingestion rate and clearance rate of Epistylis were 11,745 bacteria ciliate(-1) h(-1) and 24.33 mu l ciliate(-1) h(-1), respectively. Despite their high feeding rates, relatively low epibiont abundances were observed in the field, which suggests either diversion of energy to stalk formation, high metabolic loss by the epibionts, or high mortality among the epibiont populations.}, language = {en} } @article{LauterbachRistowGemeinholzer2012, author = {Lauterbach, Daniel and Ristow, Michael and Gemeinholzer, Birgit}, title = {Population genetics and fitness in fragmented populations of the dioecious and endangered Silene otites (Caryophyllaceae)}, series = {Plant systematics and evolution}, volume = {298}, journal = {Plant systematics and evolution}, number = {1}, publisher = {Springer}, address = {Wien}, issn = {0378-2697}, doi = {10.1007/s00606-011-0533-0}, pages = {155 -- 164}, year = {2012}, abstract = {Population fragmentation is often correlated with loss of genetic diversity and reduced fitness. Obligate out-crossing (dioecy) is expected to enhance genetic diversity, reduce genetic differentiation, and avoid inbreeding depression through frequent gene flow. However, in highly fragmented populations dioecy has only diminishing effects upon genetic structure as pollination limitations (e.g. flight distance of pollinators) most often restrict inter-population gene flow in insect pollinated species. In fragmented dry grasslands in northeastern Germany, we analysed genetic structure, fitness, and habitat quality of the endangered dioecious Silene otites (Caryophyllaceae). Using AFLP markers, a high level of differentiation among ten populations was found (F (st) = 0.36), while the intra-population genetic diversities (H (E) = 0.165-0.240) were similar as compared to hermaphroditic species. There was neither a correlation between geographic and genetic distance nor between genetic diversity and population size, which indicates reduced gene flow among populations and random genetic drift. Plant size was positively correlated with genetic diversity. Seed set and number of juveniles were positively related to population size. Higher total coverage resulted in reduced plant fitness, and the number of juveniles was negatively correlated to cryptogam cover. Additionally, we found a sex ratio bias towards more male plants in larger populations. Overall, our results indicate that on a regional geographic scale dioecy does not necessarily prevent genetic erosion in the case of habitat fragmentation, especially in the absence of long distance seed and pollen dispersal capacity.}, language = {en} } @article{AraujoNunesNesiNikoloskietal.2012, author = {Araujo, Wagner L. and Nunes-Nesi, Adriano and Nikoloski, Zoran and Sweetlove, Lee J. and Fernie, Alisdair R.}, title = {Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {35}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/j.1365-3040.2011.02332.x}, pages = {1 -- 21}, year = {2012}, abstract = {The tricarboxylic acid (TCA) cycle is a crucial component of respiratory metabolism in both photosynthetic and heterotrophic plant organs. All of the major genes of the tomato TCA cycle have been cloned recently, allowing the generation of a suite of transgenic plants in which the majority of the enzymes in the pathway are progressively decreased. Investigations of these plants have provided an almost complete view of the distribution of control in this important pathway. Our studies suggest that citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA ligase, succinate dehydrogenase, fumarase and malate dehydrogenase have control coefficients flux for respiration of -0.4, 0.964, -0.123, 0.0008, 0.289, 0.601 and 1.76, respectively; while 2-oxoglutarate dehydrogenase is estimated to have a control coefficient of 0.786 in potato tubers. These results thus indicate that the control of this pathway is distributed among malate dehydrogenase, aconitase, fumarase, succinate dehydrogenase and 2-oxoglutarate dehydrogenase. The unusual distribution of control estimated here is consistent with specific non-cyclic flux mode and cytosolic bypasses that operate in illuminated leaves. These observations are discussed in the context of known regulatory properties of the enzymes and some illustrative examples of how the pathway responds to environmental change are given.}, language = {en} } @article{StojanovicMarkovicKleinpeteretal.2012, author = {Stojanovic, Milovan and Markovic, Rade and Kleinpeter, Erich and Baranac-Stojanovic, Marija}, title = {Synthesis of thiazolidine-fused heterocycles via exo-mode cyclizations of vinylogous N-acyliminium ions}, series = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, volume = {10}, journal = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, number = {3}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1477-0520}, doi = {10.1039/c1ob06451g}, pages = {575 -- 589}, year = {2012}, abstract = {Syntheses of thiazolidine-fused heterocycles via exo-mode cyclizations of vinylogous N-acyliminium ions incorporating heteroatom-based nucleophiles have been examined and discussed. The formation of (5,6)-membered systems was feasible with all nucleophiles tried (O, S and N), while the closing of the five-membered ring was restricted to O- and S-nucleophiles. The closure of a four-membered ring failed. Instead, the bicyclic (5,6)-membered acetal derivative and the tricyclic system with an eight-membered central ring were obtained from the substrates containing O and S nucleophilic moieties, respectively. The reaction outcome and stereochemistry are rationalized using quantum chemical calculations at B3LYP/6-31G(d) level. The exclusive cis-stereoselectivity in the formation of (5,6)- and (5,5)-membered systems results from thermodynamic control, whereas the formation of the eight-membered ring was kinetically controlled.}, language = {en} }