@article{LissoAltmannMuessig2006, author = {Lisso, Janina and Altmann, Thomas and M{\"u}ssig, Carsten}, title = {The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {580}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {22}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2006.07.079}, pages = {4851 -- 4856}, year = {2006}, abstract = {The human NF-X1 protein and homologous proteins in eukaryotes represent a class of transcription factors which are characterised. by NF-X1 type zinc finger motifs. The Arabidopsis genome encodes two NF-X1 homologs, which we termed AtNFXL1 and AtNFXL2. Growth and survival was impaired in atnfxl1 knock-out mutants and AtNFXL1-antisense plants under salt stress in comparison to wild-type plants. In contrast, 35S: :AtNFXL1 plants showed higher survival rates. The AtNFXL2 protein potentially plays an antagonistic role. The Arabidopsis NF-X1 type zinc finger proteins likely are part of regulatory mechanisms, which protect major processes such as photosynthesis.}, language = {en} } @article{SchwarteTiedemann2011, author = {Schwarte, Sandra and Tiedemann, Ralph}, title = {A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana}, series = {Molecular biology and evolution}, volume = {28}, journal = {Molecular biology and evolution}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msr008}, pages = {1861 -- 1876}, year = {2011}, abstract = {Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.}, language = {en} } @article{FettkeNunesNesiFernieetal.2011, author = {Fettke, J{\"o}rg and Nunes-Nesi, Adriano and Fernie, Alisdair R. and Steup, Martin}, title = {Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana}, series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, volume = {168}, journal = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, number = {12}, publisher = {Elsevier}, address = {Jena}, issn = {0176-1617}, doi = {10.1016/j.jplph.2010.09.008}, pages = {1415 -- 1425}, year = {2011}, abstract = {Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites as DPE2. Thus, the two glucosyl transferases interconnect the cytosolic pools of glucose and glucose 1-phosphate. Due to the complex monosaccharide pattern, other heteroglycan-interacting proteins (Hips) are expected to exist. Identification of those proteins was approached by using two types of affinity chromatography. Heteroglycans from leaves of Arabidopsis thaliana (Col-0) covalently bound to Sepharose served as ligands that were reacted with a complex mixture of buffer-soluble proteins from Arabidopsis leaves. Binding proteins were eluted by sodium chloride. For identification, SDS-PAGE, tryptic digestion and MALDI-TOF analyses were applied. A strongly interacting polypeptide (approximately 40 kDa; designated as HIP1.3) was observed as product of locus At1g09340. Arabidopsis mutants deficient in HIP1.3 were reduced in growth and contained heteroglycans displaying an altered monosaccharide pattern. Wild type plants express HIP1.3 most strongly in leaves. As revealed by immuno fluorescence, HIP1.3 is located in the cytosol of mesophyll cells but mostly associated with the cytosolic surface of the chloroplast envelope membranes. In an HIP1.3-deficient mutant the immunosignal was undetectable. Metabolic profiles from leaves of this mutant and wild type plants as well were determined by GC-MS. As compared to the wild type control, more than ten metabolites, such as ascorbic acid, fructose, fructose bisphosphate, glucose, glycine, were elevated in darkness but decreased in the light. Although the biochemical function of HIP1.3 has not yet been elucidated, it is likely to possess an important function in the central carbon metabolism of higher plants.}, language = {en} } @article{ParlitzKunzeMuellerRoeberetal.2011, author = {Parlitz, Steffi and Kunze, Reinhard and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {Regulation of photosynthesis and transcription factor expression by leaf shading and re-illumination in Arabidopsis thaliana leaves}, series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, volume = {168}, journal = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, number = {12}, publisher = {Elsevier}, address = {Jena}, issn = {0176-1617}, doi = {10.1016/j.jplph.2011.02.001}, pages = {1311 -- 1319}, year = {2011}, abstract = {Leaf senescence of annual plants is a genetically programmed developmental phase. The onset of leaf senescence is however not exclusively determined by tissue age but is modulated by various environmental factors. Shading of individual attached leaves evokes dark-induced senescence. The initiation and progression of dark-induced senescence depend on the plant and the age of the affected leaf, however. In several plant species dark-induced senescence is fully reversible upon re-illumination and the leaves can regreen, but the regreening ability depends on the duration of dark incubation. We studied the ability of Arabidopsis thaliana leaves to regreen after dark-incubation with the aim to identify transcription factors (TFs) that are involved in the regulation of early dark-induced senescence and regreening. Two days shading of individual attached leaves triggers the transition into a pre-senescence state from which the leaves can largely recover. Longer periods of darkness result in irreversible senescence. Large scale qRT-PCR analysis of 1872 TF genes revealed that 649 of them are regulated in leaves during normal development, upon shading or re-illumination. Leaf shading triggered upregulation of 150 TF genes, some of which are involved in controlling senescence. Of those, 39 TF genes were upregulated after two days in the dark and regained pre-shading expression level after two days of re-illumination. Furthermore, a larger number of 422 TF genes were down regulated upon shading. In TF gene clusters with different expression patterns certain TF families are over-represented.}, language = {en} } @article{MeyerWituckaWallBecheretal.2012, author = {Meyer, Rhonda C. and Witucka-Wall, Hanna and Becher, Martina and Blacha, Anna Maria and Boudichevskaia, Anastassia and D{\"o}rmann, Peter and Fiehn, Oliver and Friedel, Svetlana and von Korff, Maria and Lisec, Jan and Melzer, Michael and Repsilber, Dirk and Schmidt, Renate and Scholz, Matthias and Selbig, Joachim and Willmitzer, Lothar and Altmann, Thomas}, title = {Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids}, series = {The plant journal}, volume = {71}, journal = {The plant journal}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2012.05021.x}, pages = {669 -- 683}, year = {2012}, abstract = {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.}, language = {en} } @article{GonzalezRiedelsbergerMoralesNavarroetal.2012, author = {Gonzalez, Wendy and Riedelsberger, Janin and Morales-Navarro, Samuel E. and Caballero, Julio and Alzate-Morales, Jans H. and Gonzalez-Nilo, Fernando D. and Dreyer, Ingo}, title = {The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids}, series = {The biochemical journal}, volume = {442}, journal = {The biochemical journal}, number = {7}, publisher = {Portland Press}, address = {London}, issn = {0264-6021}, doi = {10.1042/BJ20111498}, pages = {57 -- 63}, year = {2012}, abstract = {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.}, 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{BeninaObataMehterovetal.2013, author = {Benina, Maria and Obata, Toshihiro and Mehterov, Nikolay and Ivanov, Ivan and Petrov, Veselin and Toneva, Valentina and Fernie, Alisdair R. and Gechev, Tsanko S.}, title = {Comparative metabolic profiling of Haberlea rhodopensis, Thellungiella halophyla, and Arabidopsis thaliana exposed to low temperature}, series = {Frontiers in plant science}, volume = {4}, journal = {Frontiers in plant science}, number = {1}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2013.00499}, pages = {11}, year = {2013}, abstract = {Haberlea rhodopensis is a resurrection species with extreme resistance to drought stress and desiccation but also with ability to withstand low temperatures and freezing stress. In order to identify biochemical strategies which contribute to Haberlea's remarkable stress tolerance, the metabolic reconfiguration of H. rhodopensis during low temperature (4 degrees C) and subsequent return to optimal temperatures (21 degrees C) was investigated and compared with that of the stress tolerant Thellungiella halophyla and the stress sensitive Arabidopsis thaliana. Metabolic analysis by GC-MS revealed intrinsic differences in the metabolite levels of the three species even at 21 degrees C. H. rhodopensis had significantly more raffinose, melibiose, trehalose, rhamnose, myo-inositol, sorbitol, galactinol, erythronate, threonate, 2-oxoglutarate, citrate, and glycerol than the other two species. A. thaliana had the highest levels of putrescine and fumarate, while T halophila had much higher levels of several amino acids, including alanine, asparagine, beta-alanine, histidine, isoleucine, phenylalanine, serine, threonine, and valine. In addition, the three species responded differently to the low temperature treatment and the subsequent recovery, especially with regard to the sugar metabolism. Chilling induced accumulation of maltose in H. rhodopensis and raffinose in A. thaliana but the raffinose levels in low temperature exposed Arabidopsis were still much lower than these in unstressed Haberlea. While all species accumulated sucrose during chilling, that accumulation was transient in H. rhodopensis and A. thaliana but sustained in T halophila after the return to optimal temperature. Thus, Haberlea's metabolome appeared primed for chilling stress but the low temperature acclimation induced additional stress-protective mechanisms. A diverse array of sugars, organic acids, and polyols constitute Haberlea's main metabolic defence mechanisms against chilling, while accumulation of amino acids and amino acid derivatives contribute to the low temperature acclimation in Arabidopsis and Thellungiella. Collectively, these results show inherent differences in the metabolomes under the ambient temperature and the strategies to respond to low temperature in the three species.}, language = {en} } @misc{SharmaDreyerRiedelsberger2013, author = {Sharma, Tripti and Dreyer, Ingo and Riedelsberger, Janin}, title = {The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana}, series = {Frontiers in plant science}, volume = {4}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2013.00224}, pages = {16}, year = {2013}, abstract = {Potassium (K+) is inevitable for plant growth and development. It plays a crucial role in the regulation of enzyme activities, in adjusting the electrical membrane potential and the cellular turgor, in regulating cellular homeostasis and in the stabilization of protein synthesis. Uptake of K+ from the soil and its transport to growing organs is essential for a healthy plant development. Uptake and allocation of K+ are performed by K+ channels and transporters belonging to different protein families. In this review we summarize the knowledge on the versatile physiological roles of plant K+ channels and their behavior under stress conditions in the model plant Arabidopsis thaliana.}, language = {en} } @article{NguyenSchippersGoniRamosetal.2013, author = {Nguyen, Hung M. and Schippers, Jos H. M. and Goni-Ramos, Oscar and Christoph, Mathias P. and Dortay, Hakan and van der Hoorn, Renier A. L. and M{\"u}ller-R{\"o}ber, Bernd}, title = {An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana}, series = {The plant journal}, volume = {74}, journal = {The plant journal}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12097}, pages = {25 -- 36}, year = {2013}, abstract = {In both animal and plant kingdoms, body size is a fundamental but still poorly understood attribute of biological systems. Here we report that the Arabidopsis NAC transcription factor Regulator of Proteasomal Gene Expression' (RPX) controls leaf size by positively modulating proteasome activity. We further show that the cis-element recognized by RPX is evolutionarily conserved between higher plant species. Upon over-expression of RPX, plants exhibit reduced growth, which may be reversed by a low concentration of the pharmacological proteasome inhibitor MG132. These data suggest that the rate of protein turnover during growth is a critical parameter for determining final organ size.}, language = {en} } @article{MatallanaRamirezRaufFarageBarhometal.2013, author = {Matallana-Ramirez, Lilian P. and Rauf, Mamoona and Farage-Barhom, Sarit and Dortay, Hakan and Xue, Gang-Ping and Droege-Laser, Wolfgang and Lers, Amnon and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis}, series = {Molecular plant}, volume = {6}, journal = {Molecular plant}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-2052}, doi = {10.1093/mp/sst012}, pages = {1438 -- 1452}, year = {2013}, abstract = {The NAC transcription factor ORE1 is a key regulator of senescence in Arabidopsis thaliana. Here, we demonstrate that senescence-induced and cell death-associated BIFUNCTIONAL NUCLEASE1 (BFN1) is a direct downstream target of ORE1, revealing a previously unknown regulatory cascade.Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoterreporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence.}, language = {en} } @article{LukoszekMuellerRoeberIgnatova2013, author = {Lukoszek, Radoslaw and M{\"u}ller-R{\"o}ber, Bernd and Ignatova, Zoya}, title = {Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {587}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {22}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2013.09.033}, pages = {3692 -- 3695}, year = {2013}, abstract = {Up to 15\% of the genes in different genomes overlap. This architecture, although beneficial for the genome size, represents an obstacle for simultaneous transcription of both genes. Here we analyze the interference between RNA-polymerase II (Pol II) and RNA-polymerase III (Pol III) when transcribing their target genes encoded on opposing strands within the same DNA fragment in Arabidopsis thaliana. The expression of a Pol II-dependent protein-coding gene negatively correlated with the transcription of a Pol III-dependent, tRNA-coding gene set. We suggest that the architecture of the overlapping genes introduces an additional layer of control of gene expression. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.}, language = {en} } @article{MahlowHejaziKuhnertetal.2014, author = {Mahlow, Sebastian and Hejazi, Mahdi and Kuhnert, Franziska and Garz, Andreas and Brust, Henrike and Baumann, Otto and Fettke, J{\"o}rg}, title = {Phosphorylation of transitory starch by -glucan, water dikinase during starch turnover affects the surface properties and morphology of starch granules}, series = {New phytologist : international journal of plant science}, volume = {203}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.12801}, pages = {495 -- 507}, year = {2014}, abstract = {Glucan, water dikinase (GWD) is a key enzyme of starch metabolism but the physico-chemical properties of starches isolated from GWD-deficient plants and their implications for starch metabolism have so far not been described. Transgenic Arabidopsis thaliana plants with reduced or no GWD activity were used to investigate the properties of starch granules. In addition, using various in vitro assays, the action of recombinant GWD, -amylase, isoamylase and starch synthase 1 on the surface of native starch granules was analysed. The internal structure of granules isolated from GWD mutant plants is unaffected, as thermal stability, allomorph, chain length distribution and density of starch granules were similar to wild-type. However, short glucan chain residues located at the granule surface dominate in starches of transgenic plants and impede GWD activity. A similarly reduced rate of phosphorylation by GWD was also observed in potato tuber starch fractions that differ in the proportion of accessible glucan chain residues at the granule surface. A model is proposed to explain the characteristic morphology of starch granules observed in GWD transgenic plants. The model postulates that the occupancy rate of single glucan chains at the granule surface limits accessibility to starch-related enzymes.}, language = {en} } @article{OmidbakhshfardWinckArvidssonetal.2014, author = {Omidbakhshfard, Mohammad Amin and Winck, Flavia Vischi and Arvidsson, Samuel Janne and Riano-Pachon, Diego M. and M{\"u}ller-R{\"o}ber, Bernd}, title = {A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana}, series = {Journal of integrative plant biology}, volume = {56}, journal = {Journal of integrative plant biology}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1672-9072}, doi = {10.1111/jipb.12151}, pages = {527 -- 538}, year = {2014}, abstract = {The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.}, language = {en} } @article{SchwarteWegnerHavensteinetal.2015, author = {Schwarte, Sandra and Wegner, Fanny and Havenstein, Katja and Groth, Detlef and Steup, Martin and Tiedemann, Ralph}, title = {Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana}, series = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, volume = {87}, journal = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, number = {4-5}, publisher = {Springer}, address = {Dordrecht}, issn = {0167-4412}, doi = {10.1007/s11103-015-0293-2}, pages = {489 -- 519}, year = {2015}, abstract = {Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.}, language = {en} } @article{ApeltBreuerNikoloskietal.2015, author = {Apelt, Federico and Breuer, David and Nikoloski, Zoran and Stitt, Mark and Kragler, Friedrich}, title = {Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth}, series = {The plant journal}, volume = {82}, journal = {The plant journal}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12833}, pages = {693 -- 706}, year = {2015}, abstract = {Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge.}, language = {en} } @article{UdDinRaufGhafooretal.2016, author = {Ud-Din, Aziz and Rauf, Mamoona and Ghafoor, S. and Khattak, M. N. K. and Hameed, M. W. and Shah, H. and Jan, S. and Muhammad, K. and Rehman, A. and Inamullah,}, title = {Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana}, series = {Genetics and molecular research}, volume = {15}, journal = {Genetics and molecular research}, publisher = {FUNPEC}, address = {Ribeirao Preto}, issn = {1676-5680}, doi = {10.4238/gmr.15027439}, pages = {11}, year = {2016}, abstract = {Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative realtime polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.}, language = {en} } @article{CzesnickLenhard2016, author = {Czesnick, Hj{\"o}rdis and Lenhard, Michael}, title = {Antagonistic control of flowering time by functionally specialized poly(A) polymerases in Arabidopsis thaliana}, series = {The plant journal}, volume = {88}, journal = {The plant journal}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.13280}, pages = {570 -- 583}, year = {2016}, abstract = {Polyadenylation is a critical 3-end processing step during maturation of pre-mRNAs, and the length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerase (PAPS) isoforms fulfilling specialized functions, as reflected by their different mutant phenotypes. While PAPS1 affects several processes, such as the immune response, organ growth and male gametophyte development, the roles of PAPS2 and PAPS4 are largely unknown. Here we demonstrate that PAPS2 and PAPS4 promote flowering in a partially redundant manner. The enzymes act antagonistically to PAPS1, which delays the transition to flowering. The opposite flowering-time phenotypes in paps1 and paps2 paps4 mutants are at least partly due to decreased or increased FLC activity, respectively. In contrast to paps2 paps4 mutants, plants with increased PAPS4 activity flower earlier than the wild-type, concomitant with reduced FLC expression. Double mutant analyses suggest that PAPS2 and PAPS4 act independently of the autonomous pathway components FCA, FY and CstF64. The direct polyadenylation targets of the three PAPS isoforms that mediate their effects on flowering time do not include FLC sense mRNA and remain to be identified. Thus, our results uncover a role for canonical PAPS isoforms in flowering-time control, raising the possibility that modulating the balance of the isoform activities could be used to fine tune the transition to flowering. Significance Statement The length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. Arabidopsis has three isoforms of nuclear poly(A) polymerase (PAPS): PAPS1 plays a major role in organ growth and plant defence. Here we show that PAPS2 and PAPS4 redundantly promote flowering and act antagonistically to PAPS1, which delays flowering. We suggest that modulating the activity of these isoforms fine-tunes the transition to flowering.}, language = {en} } @article{SmirnovaFernieSpahnetal.2017, author = {Smirnova, Julia and Fernie, Alisdair R. and Spahn, Christian M. T. and Steup, Martin}, title = {Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants}, series = {Analytical biochemistry : methods in the biological sciences}, volume = {532}, journal = {Analytical biochemistry : methods in the biological sciences}, publisher = {Elsevier}, address = {San Diego}, issn = {0003-2697}, doi = {10.1016/j.ab.2017.05.026}, pages = {72 -- 82}, year = {2017}, abstract = {Maltose frequently occurs as intermediate of the central carbon metabolism of prokaryotic and eukaryotic cells. Various mutants possess elevated maltose levels. Maltose exists as two anomers, (alpha- and beta-form) which are rapidly interconverted without requiring enzyme-mediated catalysis. As maltose is often abundant together with other oligoglucans, selective quantification is essential. In this communication, we present a photometric maltose assay using 4-alpha-glucanotransferase (AtDPE2) from Arabidopsis thaliana. Under in vitro conditions, AtDPE2 utilizes maltose as glucosyl donor and glycogen as acceptor releasing the other hexosyl unit as free glucose which is photometrically quantified following enzymatic phosphorylation and oxidation. Under the conditions used, DPE2 does not noticeably react with other di- or oligosaccharides. Selectivity compares favorably with that of maltase frequently used in maltose assays. Reducing end interconversion of the two maltose anomers is in rapid equilibrium and, therefore, the novel assay measures total maltose contents. Furthermore, an AtDPE2-based continuous photometric assay is presented which allows to quantify beta-amylase activity and was found to be superior to a conventional test. Finally, the AtDPE2-based maltose assay was used to quantify leaf maltose contents of both Arabidopsis wild type and AtDPE2-deficient plants throughout the light-dark cycle. These data are presented together with assimilatory starch levels. (C) 2017 Published by Elsevier Inc.}, language = {en} } @article{SakurabaBuelbuelPiaoetal.2017, author = {Sakuraba, Yasuhito and B{\"u}lb{\"u}l, Selin and Piao, Weilan and Choi, Giltsu and Paek, Nam-Chon}, title = {Arabidopsis EARLY FLOWERING3 increases salt tolerance by suppressing salt stress response pathways}, series = {The plant journal}, volume = {92}, journal = {The plant journal}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.13747}, pages = {1106 -- 1120}, year = {2017}, language = {en} }