TY - JOUR AB - The chromatophores of the cercozoan amoeba Paulinella are photosynthetic organelles that evolved from a cyanobacterial endosymbiont. Many nucleus-encoded chromatophore-targeted proteins carry unusual N-terminal targeting signals termed crTPs, which are bipartite. crTPpart1 likely mediates trafficking through the secretory pathway and is cleaved off during import, but crTPpart2 remains attached to its cargo protein and its function is unknown. To unravel the functional role of crTPpart2, here we elucidated the structures of crTPpart2 from two different chromatophore-targeted proteins by X-ray crystallography at ∼2.3 Å resolution. Interestingly, the crTPpart2 of both proteins adopts a structural fold. Both structures share a conserved structured core and a flexible N-terminal arm. The structured core resembles proteins of the γ-glutamyl cyclotransferase superfamily within which crTPpart2 structures form a protein (sub)-family. The proposed catalytic center typical for proteins with cyclotransferase activity is not conserved in crTPpart2. A Cys pair that is conserved in crTPpart2 of many chromatophore-targeted proteins has been captured as a disulfide bridge. Together, our data suggest that chromatophore-targeted proteins are imported in their folded state and that the fold adopted by crTPpart2 plays a functional role during import. The characterization of its structure and flexibility provides important steps towards elucidating this protein translocation mechanism. AU - Klimenko, V.* AU - Reiners, J.* AU - Applegate, V.* AU - Reimann, K.* AU - Popowicz, G.M. AU - Hoeppner, A.* AU - Papadopoulos, A.* AU - Smits, S.H.J.* AU - Nowack, E.C.M.* C1 - 75746 C2 - 58157 CY - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa SP - 9 TI - The Paulinella chromatophore transit peptide part2 adopts a structural fold similar to the γ-glutamyl-cyclotransferase fold. JO - Plant Physiol. VL - 199 IS - 2 PB - Oxford Univ Press Inc PY - 2025 SN - 0032-0889 ER - TY - JOUR AB - Cold stress during early development limits maize (Zea mays L.) production in temperate zones. Low temperatures restrict root growth and reprogram gene expression. Here, we provide a systematic transcriptomic landscape of maize primary roots, their tissues, and cell types in response to cold stress. The epidermis exhibited a unique transcriptomic cold response, and genes involved in root hair formation were dynamically regulated in this cell type by cold. Consequently, activation of genes involved in root hair tip growth contributed to root hair recovery under moderate cold conditions. The maize root hair defective mutants roothair defective 5 (rth5) and roothair defective 6 (rth6) displayed enhanced cold tolerance with respect to primary root elongation. Furthermore, dehydration response element-binding protein 2.1 (dreb2.1) was the only member of the dreb subfamily of AP2/EREB transcription factor genes upregulated in primary root tissues and cell types but exclusively downregulated in root hairs upon cold stress. Plants overexpressing dreb2.1 significantly suppressed root hair elongation after moderate cold stress. Finally, the expression of rth3 was regulated by dreb2.1 under cold conditions, while rth6 transcription was regulated by dreb2.1 irrespective of the temperature regime. We demonstrated that dreb2.1 negatively regulates root hair plasticity at low temperatures by coordinating the expression of root hair defective genes in maize. AU - Zhou, Y.* AU - Sommer, M.L.* AU - Meyer, A.* AU - Wang, D.* AU - Klaus, A.* AU - Stocker, T.* AU - Marcon, C.* AU - Schoof, H.* AU - Haberer, G. AU - Schön, C.C.* AU - Yu, P.* AU - Hochholdinger, F.* C1 - 71526 C2 - 56258 CY - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa SP - 2105-2120 TI - Cold mediates maize root hair developmental plasticity via epidermis-specific transcriptomic responses. JO - Plant Physiol. VL - 196 IS - 3 PB - Oxford Univ Press Inc PY - 2024 SN - 0032-0889 ER - TY - JOUR AB - Plant cell walls constitute physical barriers that restrict access of microbial pathogens to the contents of plant cells. The primary cell wall of multicellular plants predominantly consists of cellulose, hemicellulose, and pectin, and its composition can change upon stress. BETA-XYLOSIDASE4 (BXL4) belongs to a seven-member gene family in Arabidopsis (Arabidopsis thaliana), one of which encodes a protein (BXL1) involved in cell wall remodeling. We assayed the influence of BXL4 on plant immunity and investigated the subcellular localization and enzymatic activity of BXL4, making use of mutant and overexpression lines. BXL4 localized to the apoplast and was induced upon infection with the necrotrophic fungal pathogen Botrytis cinerea in a jasmonoyl isoleucine-dependent manner. The bxl4 mutants showed a reduced resistance to B. cinerea, while resistance was increased in conditional overexpression lines. Ectopic expression of BXL4 in Arabidopsis seed coat epidermal cells rescued a bxl1 mutant phenotype, suggesting that, like BXL1, BXL4 has both xylosidase and arabinosidase activity. We conclude that BXL4 is a xylosidase/arabinosidase that is secreted to the apoplast and its expression is upregulated under pathogen attack, contributing to immunity against B. cinerea, possibly by removal of arabinose and xylose side-chains of polysaccharides in the primary cell wall. AU - Guzha, A.* AU - McGee, R.* AU - Scholz, P.* AU - Hartken, D.* AU - Ludke, D.* AU - Bauer, K. AU - Wenig, M. AU - Zienkiewicz, K.* AU - Herrfurth, C.* AU - Feussner, I.* AU - Vlot, A.C. AU - Wiermer, M.* AU - Haughn, G.* AU - Ischebeck, T.* C1 - 64959 C2 - 52234 SP - 1794-1813 TI - Cell wall-localized BETA-XYLOSIDASE4 contributes to immunity of Arabidopsis against Botrytis cinerea. JO - Plant Physiol. VL - 189 IS - 3 PY - 2022 SN - 0032-0889 ER - TY - JOUR AB - Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that Cuscuta campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic Orobanche aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants. AU - Zangishei, Z.* AU - Annacondia, M.L.* AU - Gundlach, H. AU - Didriksen, A.* AU - Bruckmüller, J.* AU - Salari, H.* AU - Krause, K.* AU - Martinez, G.J.* C1 - 65760 C2 - 52903 SP - 1242-1259 TI - Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain. JO - Plant Physiol. VL - 190 IS - 2 PY - 2022 SN - 0032-0889 ER - TY - JOUR AB - Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. In addition to direct effects on transcriptional machinery, NO executes its signaling function via epigenetic mechanisms. We report that light intensity-dependent changes in NO correspond to changes in global histone acetylation (H3, H3K9 and H3K9/K14) in Arabidopsis (Arabidopsis thaliana) wild-type leaves, and that this relationship depends on S-nitrosoglutathione reductase (GSNOR) and histone deacetylase 6 (HDA6). The activity of HDA6 was sensitive to NO, demonstrating that NO participates in regulation of histone acetylation. ChIP-seq and RNA-seq analyses revealed that NO participates in the metabolic switch from growth and development to stress response. This coordinating function of NO might be particularly important in plant ability to adapt to a changing environment, and is therefore a promising foundation for mitigating the negative effects of climate change on plant productivity. AU - Ageeva-Kieferle, A. AU - Georgii, E. AU - Winkler, B. AU - Ghirardo, A. AU - Albert, A. AU - Hüther, P.* AU - Mengel, A. AU - Becker, C.* AU - Schnitzler, J.-P. AU - Durner, J. AU - Lindermayr, C. C1 - 62097 C2 - 50648 CY - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa SP - 336-360 TI - Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression. JO - Plant Physiol. VL - 187 IS - 1 PB - Oxford Univ Press Inc PY - 2021 SN - 0032-0889 ER - TY - JOUR AU - Veeragoni, S.R. AU - Lange, B. AU - Serrano, M.* AU - Nawrath, C.* AU - Bauer, S. AU - Schäffner, A. AU - Thordal-Christensen, H.* AU - Durner, J. AU - Gaupels, F. C1 - 57862 C2 - 48147 CY - 15501 Monona Drive, Rockville, Md 20855 Usa SP - 460-462 TI - Mutant muddle: Some arabidopsis eds5 mutant lines have a previously unnoticed second-site mutation in FAH1. JO - Plant Physiol. VL - 182 IS - 1 PB - Amer Soc Plant Biologists PY - 2020 SN - 0032-0889 ER - TY - JOUR AB - Shifts in the duration and intensity of ambient temperature impair plant development and reproduction, particularly male gametogenesis. Stress exposure causes meiotic defects or premature spore abortion in male reproductive organs, leading to male sterility. However, little is known about the mechanisms underlying stress and male sterility. To elucidate these mechanisms, we imposed a moderate transient heat stress on maize (Zea mays) plants at the tetrad stage of pollen development. After completion of pollen development at optimal conditions, stress responses were assessed in mature pollen. Transient heat stress resulted in reduced starch content, decreased enzymatic activity, and reduced pollen germination, resulting in sterility. A transcriptomic comparison pointed toward misregulation of starch, lipid, and energy biosynthesis-related genes. Metabolomic studies showed an increase of Suc and its monosaccharide components, as well as a reduction in pyruvate. Lipidomic analysis showed increased levels of unsaturated fatty acids and decreased levels of saturated fatty acids. In contrast, the majority of genes involved in developmental processes such as those required for auxin and unfolded protein responses, signaling, and cell wall biosynthesis remained unaltered. It is noteworthy that changes in the regulation of transcriptional and metabolic pathway genes, as well as heat stress proteins, remained altered even though pollen could recover during further development at optimal conditions. In conclusion, our findings demonstrate that a short moderate heat stress during the highly susceptible tetrad stage strongly affects basic metabolic pathways and thus generates germination-defective pollen, ultimately leading to severe yield losses in maize. AU - Begcy, K.* AU - Nosenko, T. AU - Zhou, L.Z.* AU - Fragner, L.* AU - Weckwerth, W.* AU - Dresselhaus, T.* C1 - 57115 C2 - 47524 CY - 15501 Monona Drive, Rockville, Md 20855 Usa SP - 683-700 TI - Male sterility in maize caused by transient heat stress during the tetrad stage of pollen development. JO - Plant Physiol. VL - 181 IS - 2 PB - Amer Soc Plant Biologists PY - 2019 SN - 0032-0889 ER - TY - JOUR AB - Symbioses between plants and mycorrhizal fungi are ubiquitous in ecosystems and strengthen the plants’ defense against aboveground herbivores. Here, we studied the underlying regulatory networks and biochemical mechanisms in leaves induced by ectomycorrhizae that modify herbivore interactions. Feeding damage and oviposition by the widespread poplar leaf beetle Chrysomela populi were reduced on the ectomycorrhizal hybrid poplar Populus × canescens. Integration of transcriptomics, metabolomics, and volatile emission patterns via mass difference networks demonstrated changes in nitrogen allocation in the leaves of mycorrhizal poplars, down-regulation of phenolic pathways, and up-regulation of defensive systems, including protease inhibitors, chitinases, and aldoxime biosynthesis. Ectomycorrhizae had a systemic influence on jasmonate-related signaling transcripts. Our results suggest that ectomycorrhizae prime wounding responses and shift resources from constitutive phenol-based to specialized protective compounds. Consequently, symbiosis with ectomycorrhizal fungi enabled poplars to respond to leaf beetle feeding with a more effective arsenal of defense mechanisms compared with nonmycorrhizal poplars, thus demonstrating the importance of belowground plant-microbe associations in mitigating aboveground biotic stress. AU - Kaling, M. AU - Schmidt, A.* AU - Moritz, F. AU - Rosenkranz, M. AU - Witting, M. AU - Kasper, K.* AU - Janz, D.* AU - Schmitt-Kopplin, P. AU - Schnitzler, J.-P. AU - Polle, A.* C1 - 52962 C2 - 44490 CY - Rockville SP - 2639-2656 TI - Mycorrhiza-triggered transcriptomic and metabolomic networks impinge on herbivore fitness. JO - Plant Physiol. VL - 176 IS - 4 PB - Amer Soc Plant Biologists PY - 2018 SN - 0032-0889 ER - TY - JOUR AB - Nitrogen dioxide (NO2) forms in plants under stress conditions, but little is known about its physiological functions. Here, we explored the physiological functions of NO2in plant cells using short-term fumigation of Arabidopsis (Arabidopsis thaliana) for 1 h with 10 µL L−1NO2.Although leaf symptoms were absent, the expression of genes related to pathogen resistance was induced. Fumigated plants developed basal disease resistance, or pattern-triggered immunity, against the necrotrophic fungus Botrytis cinerea and the hemibiotrophic bacterium Pseudomonas syringae. Functional salicylic acid and jasmonic acid (JA) signaling pathways were both required for the full expression of NO2-induced resistance against B. cinerea. An early peak of salicylic acid accumulation immediately after NO2exposure was followed by a transient accumulation of oxophytodienoic acid. The simultaneous NO2-induced expression of genes involved in jasmonate biosynthesis and jasmonate catabolism resulted in the complete suppression of JA and JA-isoleucine (JA-Ile) accumulation, which was accompanied by a rise in the levels of their catabolic intermediates 12-OH-JA, 12-OH-JA-Ile, and 12-COOH-JA-Ile. NO2-treated plants emitted the volatile monoterpene α-pinene and the sesquiterpene longifolene (syn. junipene), which could function in signaling or direct defense against pathogens. NO2-triggered B. cinerea resistance was dependent on enhanced early callose deposition and CYTOCHROME P450 79B2 (CYP79B2), CYP79B3, and PHYTOALEXIN DEFICIENT3 gene functions but independent of camalexin, CYP81F2, and 4-OH-indol-3-ylmethylgluco-sinolate derivatives. In sum, exogenous NO2triggers basal pathogen resistance, pointing to a possible role for endogenous NO2in defense signaling. Additionally, this study revealed the involvement of jasmonate catabolism and volatiles in pathogen immunity. AU - Mayer, D. AU - Mithöfer, A.* AU - Glawischnig, E.* AU - Georgii, E. AU - Ghirardo, A. AU - Kanawati, B. AU - Schmitt-Kopplin, P. AU - Schnitzler, J.-P. AU - Durner, J. AU - Gaupels, F. C1 - 54088 C2 - 45348 CY - 15501 Monona Drive, Rockville, Md 20855 Usa SP - 468-487 TI - Short-term exposure to nitrogen dioxide provides basal pathogen resistance. JO - Plant Physiol. VL - 178 IS - 1 PB - Amer Soc Plant Biologists PY - 2018 SN - 0032-0889 ER - TY - JOUR AB - It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges. AU - Friesner, J.* AU - Assmann, S.M.* AU - Bastow, R.* AU - Bailey-Serres, J.* AU - Beynon, J.* AU - Brendel, V.* AU - Buell, C.R.* AU - Bucksch, A.* AU - Busch, W.* AU - Demura, T.* AU - Dinneny, J.R.* AU - Doherty, C.J.* AU - Eveland, A.L.* AU - Falter-Braun, P. AU - Gehan, M.A.* AU - Gonzales, M.* AU - Grotewold, E.* AU - Gutiérrez, R.A.* AU - Krämer, U.* AU - Krouk, G.* AU - Ma, S.L.* AU - Markelz, R.J.C.* AU - Megraw, M.* AU - Meyers, B.C.* AU - Murray, J.A.H.* AU - Provart, N.J.* AU - Rhee, S.* AU - Smith, R.* AU - Spalding, E.P.* AU - Taylor, C.* AU - Teal, T.K.* AU - Torii, K.U.* AU - Town, C.* AU - Vaughn, M.* AU - Vierstra, R.* AU - Ware, D.* AU - Wilkins, O.* AU - Williams, C.* AU - Brady, S.M.* C1 - 52497 C2 - 44014 CY - Rockville SP - 1499-1509 TI - The next generation of training for arabidopsis researchers: Bioinformatics and quantitative biology. JO - Plant Physiol. VL - 175 IS - 4 PB - Amer Soc Plant Biologists PY - 2017 SN - 0032-0889 ER - TY - JOUR AB - Plants possessing dysfunctional plastids due to defects in pigment biosynthesis or translation are known to repress photosynthesis-associated nuclear genes (PhANGs) via retrograde signals from the disturbed organelles towards the nucleus. These signals are thought to be essential for proper biogenesis and function of the plastid. Mutants lacking plastid-encoded RNA polymerase-associated proteins (PAPs) display a genetic arrest in eoplast-chloroplast transition leading to an albino phenotype in the light. Retrograde signaling in these mutants, thus, could be expected to be similar as under conditions inducing plastid dysfunction. In order to answer this question we performed plastome- and genome-wide array analyses in the pap7-1 mutant of Arabidopsis. In parallel, we determined the potential overlap with light-regulated expression networks. To this end we performed a comparative expression profiling approach using light- and dark-grown wild-type plants as relative control for the expression profiles obtained from light-grown pap7-1 mutants. Our data indicate a specific impact of retrograde signals on metabolism related genes in pap7-1 mutants reflecting the starvation situation of the albino seedlings. In contrast light regulation of PhANGs and other nuclear gene groups appears to be fully functional in this mutant indicating that a block in chloroplast biogenesis per se does not repress expression of them as suggested by earlier studies. Only genes for light harvesting complex proteins displayed a significant repression indicating an exclusive retrograde impact on this gene family. Our results indicate that chloroplasts and arrested plastids each emit specific signals that control different target gene modules both in positive and negative manner. AU - Grübler, B.* AU - Merendino, L.* AU - Twardziok, S.O. AU - Mininno, M.* AU - Allorent, G.* AU - Chevalier, F.* AU - Liebers, M.* AU - Blanvillain, R.* AU - Mayer, K.F.X. AU - Lerbs-Mache, S.* AU - Ravanel, S.* AU - Pfannschmidt, T.* C1 - 51958 C2 - 43614 CY - Rockville SP - 1203-1219 TI - Light and plastid signals regulate different sets of genes in the albino mutant pap7-1. JO - Plant Physiol. VL - 175 IS - 2 PB - Amer Soc Plant Biologists PY - 2017 SN - 0032-0889 ER - TY - JOUR AB - Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by nitric oxide (NO); in plants, however, it is unknown whether NO affects histone acetylation. We found that treatment with the physiological NO donor S-nitrosoglutathione (GSNO) increased the abundance of several histone acetylation marks in Arabidopsis (Arabidopsis thaliana), which was strongly diminished in the presence of the NO scavenger 2-4-carboxyphenyl- 4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. This increase was likely triggered by NO-dependent inhibition of HDAC activity, since GSNO and S-nitroso-N-acetyl-DL-penicillamine significantly and reversibly reduced total HDAC activity in vitro (in nuclear extracts) and in vivo (in protoplasts). Next, genome-wide H3K9/14ac profiles in Arabidopsis seedlings were generated by chromatin immunoprecipitation sequencing, and changes induced by GSNO, GSNO/2-4-carboxyphenyl- 4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide or trichostatin A (an HDAC inhibitor) were quantified, thereby identifying genes that display putative NO-regulated histone acetylation. Functional classification of these genes revealed that many of them are involved in the plant defense response and the abiotic stress response. Furthermore, salicylic acid, which is the major plant defense hormone against biotrophic pathogens, inhibited HDAC activity and increased histone acetylation by inducing endogenous NO production. These data suggest that NO affects histone acetylation by targeting and inhibiting HDAC complexes, resulting in the hyperacetylation of specific genes. This mechanism might operate in the plant stress response by facilitating the stress-induced transcription of genes. AU - Mengel, A. AU - Ageeva-Kieferle, A. AU - Georgii, E. AU - Bernhardt, J.* AU - Wu, K.M.* AU - Durner, J. AU - Lindermayr, C. C1 - 50494 C2 - 42498 CY - Rockville SP - 1434-1452 TI - Nitric oxide modulates histone acetylation at stress genes by inhibition of histone deacetylases. JO - Plant Physiol. VL - 173 IS - 2 PB - Amer Soc Plant Biologists PY - 2017 SN - 0032-0889 ER - TY - JOUR AB - Systemic acquired resistance (SAR) is a plant defense response that provides long-lasting, broad-spectrum pathogen resistance to uninfected systemic leaves following an initial localized infection. In Arabidopsis thaliana, local infection with virulent or avirulent strains of Pseudomonas syringae pv. tomato (Pst) generates long-distance SAR signals that travel from locally infected to distant leaves through the phloem to establish SAR. In this study, a proteomics approach was used to identify proteins that accumulate in phloem exudates in response to the induction of SAR. To accomplish this, phloem exudates collected from mock-inoculated or SAR-induced leaves of wild-type Col-0 plants were subjected to label-free quantitative LC-MS/MS proteomics (liquid chromatography, tandem mass spectrometry). Comparing mock- and SAR-induced phloem exudate proteomes, 16 proteins were enriched in phloem exudates collected from SAR-induced plants, while 46 proteins were suppressed. SAR-related proteins TRXh3, ACBP6, and PR1 were enriched in phloem exudates of SAR-induced plants, demonstrating the strength of this approach and suggesting a role for these proteins in the phloem during SAR. To identify novel components of SAR, T-DNA mutants of differentially abundant phloem proteins were assayed for SAR competence. This analysis identified a number of new proteins (m-type thioredoxins, major latex protein-like protein, UVR8 photoreceptor) that contribute to the SAR response. The Arabidopsis SAR phloem proteome is a valuable resource for understanding SAR long-distance signaling and the dynamic nature of the phloem during plant-pathogen interactions. AU - Carella, P.* AU - Merl-Pham, J. AU - Wilson, D.C.* AU - Dey, S. AU - Hauck, S.M. AU - Vlot, A.C. AU - Cameron, R.K.* C1 - 48639 C2 - 41229 CY - Rockville SP - 1495-1510 TI - Comparative proteomics analysis of Arabidopsis phloem exudates collected during the induction of systemic acquired resistance. JO - Plant Physiol. VL - 171 IS - 2 PB - Amer Soc Plant Biologists PY - 2016 SN - 0032-0889 ER - TY - JOUR AB - Identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene multiple orthologous genes are predicted in the other genome and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied eleven organ-dependent and stress-induced gene expression patterns of 286 A. lyrata duplicated gene groups and compared them to the respective A. thaliana genes to predict putative expressologs and non-expressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four A. thaliana loss-of-function mutants we experimentally proved that predicted expressologs are indeed functional orthologs, while non-expressologs or non-functionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs. AU - Das, M. AU - Haberer, G. AU - Panda, A.* AU - Laha, S.D.* AU - Ghosh, T.C.* AU - Schäffner, A. C1 - 48825 C2 - 41453 CY - Rockville SP - 2343-2357 TI - Expression pattern similarities support the prediction of orthologs retaining common functions after gene duplication events. JO - Plant Physiol. VL - 171 IS - 4 PB - Amer Soc Plant Biologists PY - 2016 SN - 0032-0889 ER - TY - JOUR AB - Researchers have been examining the biological function(s) of isoprene in isoprene-emitting species for two decades. There is overwhelming evidence that leaf-internal isoprene increases the thermo-tolerance of plants and protects them against oxidative stress, thus mitigating a wide range of abiotic stresses. However, the mechanisms of abiotic stress mitigation by isoprene are still under debate. Here we assessed the impact of isoprene on the emission of NO and S-nitroso-proteome of isoprene-emitting (IE) and non-isoprene-emitting (NE) gray poplar (Populus × canescens (Aiton.) Sm.) after acute ozone fumigation. The short-term oxidative stress induced a rapid and strong emission of NO in NE compared to IE genotypes. Whereas IE and NE plants exhibited under non-stressful conditions only slight differences in their S-nitrosylation pattern, the in vivo S-nitroso-proteome of the NE genotype was more susceptible to ozone-induced changes compared to the IE plants. The results suggest that the nitrosative pressure (NO burst) is higher in NE plants, underlining the proposed molecular dialogue between isoprene and the free radical NO. Proteins belonging to the photosynthetic light and dark reactions, the TCA cycle, protein metabolism, and redox regulation exhibited an increased S-nitrosylation in NE samples compared to IE plants upon oxidative stress. Because the post-translational modification of proteins via S-nitrosylation often impacts enzymatic activities, the present data suggest that isoprene indirectly regulates the production of ROS via the control of the S-nitrosylation level of ROS-metabolizing enzymes, thus modulating the extent and velocity at which the ROS and NO signaling molecules are generated within a plant cell. AU - Vanzo, E. AU - Merl-Pham, J. AU - Velikova, V.B. AU - Ghirardo, A. AU - Lindermayr, C. AU - Hauck, S.M. AU - Bernhardt, J.* AU - Riedel, K.* AU - Durner, J. AU - Schnitzler, J.-P. C1 - 47842 C2 - 39511 CY - Rockville SP - 1945-1961 TI - Modulation of protein S-nitrosylation by isoprene emission in poplar. JO - Plant Physiol. VL - 170 IS - 4 PB - Amer Soc Plant Biologists PY - 2016 SN - 0032-0889 ER - TY - JOUR AU - Lindermayr, C. AU - Durner, J. C1 - 44077 C2 - 37630 CY - Rockville SP - 1209-1210 TI - Interplay of reactive oxygen species and nitric oxide: Nitric oxide coordinates reactive oxygen species homeostasis. JO - Plant Physiol. VL - 167 IS - 4 PB - Amer Soc Plant Biologists PY - 2015 SN - 0032-0889 ER - TY - JOUR AB - Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR.Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination. AU - Scheler, C. AU - Weitbrecht, K.* AU - Pearce, S.P.* AU - Hampstead, A.* AU - Büttner-Mainik, A.* AU - Lee, K.J.D.* AU - Voegele, A.* AU - Oracz, K.* AU - Dekkers, B.J.W.* AU - Wang, X.* AU - Wood, A.T.A.* AU - Bentsink, L.* AU - King, J.R.* AU - Knox, J.P.* AU - Holdsworth, M.J.* AU - Müller, K.B.* AU - Leubner-Metzger, G.* C1 - 43077 C2 - 36034 CY - Rockville SP - 200-215 TI - Promotion of testa rupture during garden cress germination involves seed compartment-specific expression and activity of pectin methylesterases. JO - Plant Physiol. VL - 167 IS - 1 PB - Amer Soc Plant Biologists PY - 2015 SN - 0032-0889 ER - TY - JOUR AB - Isoprene emissions from poplar plantations can influence atmospheric chemistry and regional climate. These emissions respond strongly to temperature, [CO2] and drought but the superimposed effect of these three climate change factors are, for the most part, unknown. Performing predicted climate change scenario simulations (periodic and chronic heat and drought spells (HDS) applied under elevated [CO2]), we analyzed volatile organic compound (VOC) emissions, photosynthetic performance, leaf growth and overall carbon (C) gain of poplar genotypes emitting (IE) and non-emitting (NE) isoprene. We aimed (i) to evaluate the proposed beneficial effect of isoprene emission on plant stress mitigation and recovery capacity and (ii) to estimate the cumulative net C gain under the projected future climate. During HDS, the chloroplastidic electron transport rate of NE plants became impaired, while IE plants maintained high values similar to unstressed controls. During recovery from HDS episodes, IE plants reached higher daily net CO2 assimilation rates compared to NE genotypes. Irrespective of the genotype, plants undergoing chronic HDS showed the lowest cumulative C gain. Under control conditions simulating ambient [CO2], the C gain was lower in the IE than NE plants. In summary, the data on the overall C gain and plant growth suggest that the beneficial function of isoprene emission in poplar might be of minor importance to mitigate predicted short-term climate extremes under elevated [CO2]. Moreover, we demonstrate that an analysis of the canopy-scale dynamics of isoprene emission and photosynthetic performance under multiple stresses is essential to understand the overall performance under proposed future conditions. AU - Vanzo, E. AU - Jud, W.* AU - Li, Z.* AU - Albert, A. AU - Domagalska, M.A.* AU - Ghirardo, A. AU - Niederbacher, B. AU - Frenzel, J.* AU - Beemster, G.T.* AU - Asard, H.* AU - Rennenberg, H.* AU - Sharkey, T.D.* AU - Hansel, A.* AU - Schnitzler, J.-P. C1 - 46330 C2 - 37588 SP - 560-575 TI - Facing the future - effects of short-term climate extremes on isoprene-emitting and non-emitting poplar. JO - Plant Physiol. VL - 169 IS - 1 PY - 2015 SN - 0032-0889 ER - TY - JOUR AB - Isoprene is a small lipophilic molecule with important functions in plant protection against abiotic stresses by improving membrane structure and scavenging reactive oxygen species. Here, we studied the lipid composition of thylakoid membranes and chloroplast ultrastructure in isoprene emitting (IE) and non-isoprene emitting (NE) poplars. We demonstrated that the total amount of mono- (MGDG), di-galactosyldiacylglycerols (DGDG), phospholipids (PL), and fatty acids is reduced in chloroplasts when isoprene biosynthesis is blocked. A significantly lower amount of unsaturated fatty acids, particularly linolenic acid (18:3) in NE chloroplasts was associated with the reduced fluidity of thylakoid membranes, which in turn negatively affects PSII photochemical efficiency (ΦPSII). The low ΦPSII in NE plants was negatively correlated with non-photochemical quenching (NPQ) and the energy-dependent (qE) component of NPQ. Transmission electron microscopy (TEM) revealed alterations in the chloroplast ultrastructure in NE compared with IE plants. NE chloroplasts were more rounded and contained less grana stacks and longer stroma thylakoids, more plastoglobules, and larger associative zones between chloroplasts and mitochondria. These results strongly support the idea that in isoprene-emitting species, the function of this molecule is closely associated with the structural organization and functioning of plastidic membranes. AU - Velikova, V.B. AU - Müller, C. AU - Ghirardo, A. AU - Rock, T. AU - Aichler, M. AU - Walch, A.K. AU - Schmitt-Kopplin, P. AU - Schnitzler, J.-P. C1 - 44876 C2 - 37033 CY - Rockville SP - 859-870 TI - Knocking down of isoprene emission modifies the lipid matrix of thylakoid membranes and influences the chloroplast ultrastructure in poplar. JO - Plant Physiol. VL - 168 IS - 3 PB - Amer Soc Plant Biologists PY - 2015 SN - 0032-0889 ER - TY - JOUR AB - Barley (Hordeum vulgare L.) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion base pair genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes (BACs) representing 14x haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96 % of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence (WGS) data from the individuals of two mapping populations with published BAC survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive WGS datasets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence. AU - Ariyadasa, R.* AU - Mascher, M.* AU - Nussbaumer, T. AU - Schulte, D.* AU - Frenkel, Z.* AU - Poursarebani, N.* AU - Zhou, R.* AU - Steuernagel, B.* AU - Gundlach, H. AU - Taudien, S.* AU - Felder, M.* AU - Platzer, M.* AU - Himmelbach, A.* AU - Schmutzer, T.* AU - Hedley, P.* AU - Muehlbauer, G.* AU - Scholz, U.* AU - Korol, A.* AU - Mayer, K.F.X. AU - Waugh, R.* AU - Langridge, P.* AU - Graner, A.* AU - Stein, N.* C1 - 28381 C2 - 33344 SP - 412-423 TI - A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. JO - Plant Physiol. VL - 164 IS - 1 PB - Amer. Soc. Plant Biologists PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - The transcription of the Arabidopsis thaliana GATA transcription factors GNC and GNL/CGA1 is controlled by several growth regulatory signals including light and the phytohormones auxin, cytokinin, and gibberellin. To date, GNC and GNL have been attributed functions in the control of germination, greening, flowering time, floral development, senescence, and floral organ abscission. GNC and GNL belong to the eleven-membered family of B-class GATA transcription factors that are characterized to date solely by their high sequence conservation within the GATA DNA-binding domain. The degree of functional conservation among the various B-class GATA family members is not understood. Here, we identify and examine B-class GATAs from Arabidopsis, tomato, Brachypodium, and barley. We find that B-class GATAs from these four species can be subdivided based on their short or long N-termini and the presence of the thirteen amino acid C-terminal LLM-domain with the conserved motif leucine-leucine-methionine (LLM). Through overexpression analyses and by complementation of a gnc gnl double mutant, we provide evidence that the length of the N-terminus may not allow distinguishing between the different B-class GATAs at the functional level. In turn, we find that the presence and absence of the LLM-domain in the overexpressors has differential effects on hypocotyl elongation, leaf shape, and petiole length as well as on gene expression. Thus, our analyses identify the LLM-domain as an evolutionarily conserved domain that determines B-class GATA factor identity and provides a further subclassification criterion for this transcription factor family. AU - Behringer, C.* AU - Bastakis, E.* AU - Ranftl, Q.* AU - Mayer, K.F.X. AU - Schwechheimer, C.* C1 - 31859 C2 - 34828 CY - Rockville SP - 293-305 TI - Functional diversification within the family of B-GATA transcription factors through the LLM-domain. JO - Plant Physiol. VL - 166 IS - 1 PB - Amer Soc Plant Biologists PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - Systemic acquired resistance (SAR) is an inducible immune response that depends on ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). Here, we show that Arabidopsis (Arabidopsis thaliana) EDS1 is required for both SAR signal generation in primary infected leaves and SAR signal perception in systemic uninfected tissues. In contrast to SAR signal generation, local resistance remains intact in eds1 mutant plants in response to Pseudomonas syringae delivering the effector protein AvrRpm1. We utilized the SAR-specific phenotype of the eds1 mutant to identify new SAR regulatory proteins in plants conditionally expressing AvrRpm1. Comparative proteomic analysis of apoplast-enriched extracts from AvrRpm1-expressing wild-type and eds1 mutant plants led to the identification of 12 APOPLASTIC, EDS1-DEPENDENT (AED) proteins. The genes encoding AED1, a predicted aspartyl protease, and another AED, LEGUME LECTIN-LIKE PROTEIN1 (LLP1), were induced locally and systemically during SAR signaling and locally by salicylic acid (SA) or its functional analog, benzo 1, 2, 3-thiadiazole-7-carbothioic acid S-methyl ester. Because conditional overaccumulation of AED1-hemagglutinin inhibited SA-induced resistance and SAR but not local resistance, the data suggest that AED1 is part of a homeostatic feedback mechanism regulating systemic immunity. In llp1 mutant plants, SAR was compromised, whereas the local resistance that is normally associated with EDS1 and SA as well as responses to exogenous SA appeared largely unaffected. Together, these data indicate that LLP1 promotes systemic rather than local immunity, possibly in parallel with SA. Our analysis reveals new positive and negative components of SAR and reinforces the notion that SAR represents a distinct phase of plant immunity beyond local resistance. AU - Breitenbach, H.H. AU - Wenig, M. AU - Wittek, F. AU - Jordá, L.* AU - Maldonado-Alconada, A.M.* AU - Sarioglu, H. AU - Colby, T.V.* AU - Knappe, C. AU - Bichlmeier, M. AU - Pabst, E. AU - Mackey, D.M.* AU - Parker, J.E.* AU - Vlot, A.C. C1 - 31686 C2 - 34653 CY - Rockville SP - 791-809 TI - Contrasting roles of the apoplastic aspartyl protease APOPLASTIC, ENHANCED DISEASE SUSCEPTIBILITY1-DEPENDENT1 and LEGUME LECTIN-LIKE PROTEIN1 in arabidopsis systemic acquired resistance. JO - Plant Physiol. VL - 165 IS - 2 PB - Amer Soc Plant Biologists PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - DEK1 of higher plants plays an essential role in position dependent signaling and consists of a large transmembrane domain (MEM) linked to a protease catalytic domain (CysPc) and a regulatory domain (C2L). Here we show that the postulated sensory Loop of the MEM domain plays an important role in the developmental regulation of DEK1 activity in the moss Physcomitrella patens. Compared with P. patens lacking DEK1 (∆dek1), the dek1∆loop mutant correctly positions the division plane in the bud apical cell. In contrast to an early developmental arrest of ∆dek1 buds, dek1∆loop develops aberrant gametophores lacking expanded phyllids resulting from mis-regulation of mitotic activity. In contrast to the highly conserved sequence of the catalytic CysPc domain, the Loop is highly variable in land plants. Functionally, the sequence from Marchantia polymorpha fully complements the dek1∆loop phenotype, whereas sequences from Zea mays and Arabidopsis thaliana give phenotypes with retarded growth and affected phyllid development. New bioinformatic analysis identifies MEM as a member of the Major Facilitator Superfamily, membrane transporters reacting to stimuli from the external environment. Transcriptome analysis comparing WT and ∆dek1 tissues identifies an effect of two groups of transcripts connected to dek1 mutant phenotypes, i.e. transcripts related to cell wall remodeling and regulation of the APB2 and APB3 transcription factors known to regulate bud initiation. Finally, new sequence data support the hypothesis that the advanced charophyte algae that evolved into ancestral land plants lost cytosolic calpains, retaining DEK1 as the sole calpain in the evolving land plant lineage. AU - Demko, V.* AU - Perroud, P.F.* AU - Johansen, W.* AU - Delwiche, C.F.* AU - Cooper, E.D.* AU - Remme, P.* AU - Ako, A.E.* AU - Kugler, K.G. AU - Mayer, K.F.X. AU - Quatrano, R.S.* AU - Olsen, O.A.* C1 - 32078 C2 - 34961 SP - 903-919 TI - Genetic analysis of DEK1 loop function in three-dimensional body patterning in physcomitrella patens. JO - Plant Physiol. VL - 166 IS - 2 PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - Leaf-to-leaf, systemic immune signaling known as systemic acquired resistance (SAR) is poorly understood in monocotyledonous plants. Here, we characterize systemic immunity in barley (Hordeum vulgare) triggered after primary leaf infection with either Pseudomonas syringae pathovar japonica (Psj) or Xanthomonas translucens pathovar cerealis (Xtc). Both pathogens induced resistance in systemic, uninfected leaves against a subsequent challenge infection with Xtc. In contrast to SAR in Arabidopsis thaliana, systemic immunity in barley was not associated with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 or the local or systemic accumulation of salicylic acid (SA). Instead, we documented a moderate local but not systemic induction of abscisic acid (ABA) after infection of leaves with Psj. In contrast to SA or its functional analog benzothiadiazole, local applications of the jasmonic acid methyl ester or ABA triggered systemic immunity to Xtc. RNA-seq analysis of local and systemic transcript accumulation revealed unique gene expression changes in response to both Psj and Xtc and a clear separation of local from systemic responses. The systemic response appeared relatively modest and quantitative RT-PCR associated systemic immunity with the local and systemic induction of two WRKY and two ETHYLENE RESPONSIVE FACTOR-like transcription factors. Systemic immunity against Xtc was further associated with transcriptional changes after a secondary/systemic Xtc challenge infection; these changes were dependent on the primary treatment. Taken together, bacteria-induced systemic immunity in barley may be mediated in part by WRKY and ERF-like transcription factors possibly facilitating transcriptional reprogramming to potentiate immunity. AU - Dey, S. AU - Wenig, M. AU - Langen, G.* AU - Sharma, S. AU - Kugler, K.G. AU - Knappe, C. AU - Hause, B.* AU - Bichlmeier, M. AU - Babaeizad, V.* AU - Imani, J.* AU - Janzik, I.* AU - Stempfl, T.* AU - Hueckelhoven, R.* AU - Kogel, K.H.* AU - Mayer, K.F.X. AU - Vlot, A.C. C1 - 32603 C2 - 35194 SP - 2133-2151 TI - Bacteria-triggered systemic immunity in barley appears to be associated with WRKY and ETHYLENE RESPONSIVE FACTORs but not with salicylic acid. JO - Plant Physiol. VL - 166 IS - 4 PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - The plastidic 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway is one of the most important pathways in plants and produces a large variety of essential isoprenoids. Its regulation, however, is still not well understood. Using stable isotope 13C-labeling technique, we analyzed the carbon (C) fluxes through the MEP-pathway and into the major plastidic isoprenoid products in isoprene-emitting (IE) and transgenic isoprene non-emitting (NE) grey poplar (Populus x canescens). We assessed the dependence on temperature, light intensity and atmospheric [CO2]. Isoprene biosynthesis was by far (99%) the main C-sink of MEP-pathway intermediates in mature poplar leaves, and its production required several-fold higher C-fluxes compared to NE leaves with almost zero isoprene emission. To compensate for the much lower demand for C, NE leaves drastically reduced the overall C-flux within the MEP-pathway. Feedback inhibition of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) activity by accumulated plastidic dimethylallyl diphosphate (DMADP) almost completely explained this reduction in C-flux. Our data demonstrate that short-term biochemical feedback regulation of DXS activity by plastidic DMADP is an important regulatory mechanism of the MEP-pathway. Despite being relieved from the large C demand of isoprene biosynthesis, NE plants redirected only approximately 0.5% of this 'saved' C towards essential non-volatile isoprenoids, i.e. β-carotene and lutein, most probably to compensate for the absence of isoprene and its antioxidant properties. AU - Ghirardo, A. AU - Wright, L.P.* AU - Bi, Z. AU - Rosenkranz, M. AU - Pulido, P.* AU - Rodríguez-Concepción, M.* AU - Niinemets, U.* AU - Brüggemann, N.* AU - Gershenzon, J.* AU - Schnitzler, J.-P. C1 - 30769 C2 - 33847 CY - Rockville SP - 37-51 TI - Metabolic flux analysis of plastidic isoprenoid biosynthesis in poplar leaves emitting and non-emitting isoprene. JO - Plant Physiol. VL - 165 IS - 1 PB - Amer Soc Plant Biologists PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - The 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway supplies precursors for plastidial isoprenoid biosynthesis including carotenoids, redox cofactor side chains, and biogenic volatile organic compounds. We examined the first enzyme of this pathway, 1-deoxy-D-xylulose-5-phosphate (DXP) synthase (DXS), using metabolic control analysis. Multiple Arabidopsis lines presenting a range of DXS activities were dynamically labeled with 13CO2 in an illuminated, climate-controlled, gas exchange cuvette. C was rapidly assimilated into MEP pathway intermediates, but not into the mevalonate pathway. A flux control coefficient (FCC) of 0.82 was calculated for DXS by correlating absolute flux to enzyme activity under photosynthetic steady state conditions, indicating that DXS is the major controlling enzyme of the MEP pathway. DXS manipulation also revealed a second pool of a downstream metabolite, 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcDP), metabolically isolated from the MEP pathway. DXS overexpression led to a 3-4 fold increase in MEcDP pool size but to a two-fold drop in maximal labeling. The existence of this pool was supported by residual MEcDP levels detected in dark-adapted transgenic plants. Both pools of MEcDP are closely modulated by DXS activity, as shown by the fact that the concentration control coefficient of DXS was twice as high for MEcDP (0.74) as for DXP (0.35) or dimethylallyl diphosphate (0.34). Despite the high FCC for DXS, its overexpression led to only modest increases in isoprenoid end products and photosynthetic rate. Diversion of flux via MEcDP may partly explain these findings and suggests new opportunities to engineer the MEP pathway. AU - Wright, L.P.* AU - Rohwer, J.M.* AU - Ghirardo, A. AU - Hammerbacher, A.* AU - Ortiz, M.* AU - Raguschke, B.* AU - Schnitzler, J.-P. AU - Gershenzon, J.* AU - Phillips, M.A.* C1 - 31843 C2 - 34800 CY - Rockville SP - 1488-1504 TI - 1-Deoxyxylulose 5-phosphate synthase controls flux through the 2-C-methylerythritol 4-phosphate pathway in Arabidopsis thaliana. JO - Plant Physiol. VL - 165 IS - 4 PB - Amer Soc Plant Biologists PY - 2014 SN - 0032-0889 ER - TY - JOUR AB - NEDD8 is an evolutionarily conserved 8 kD protein that is closely related to ubiquitin and that can be conjugated like ubiquitin to specific lysine residues of target proteins in eukaryotes. In contrast to ubiquitin, for which a broad range of substrate proteins is known, only a very limited number of NEDD8 target proteins have been identified to date. Best understood, and also evolutionarily conserved, is the NEDD8-modification (neddylation) of cullins, core subunits of the cullin-RING-type E3 ubiquitin ligases that promote the poly-ubiquitylation of degradation targets in eukaryotes. Here, we show that ML3 is a NEDD8- as well as ubiquitin-modified protein in Arabidopsis thaliana and examine the functional role of ML3 in the plant cell. Our analysis indicates that ML3 resides in the vacuole as well as in ER bodies. ER bodies are Brassicales-specific ER-derived organelles and, similarly to other ER body proteins, ML3 orthologues can only be identified in this order of flowering plants. ML3 gene expression is promoted by wounding as well as by the phytohormone jasmonic acid and repressed by ethylene, signals that are known to induce and repress ER body formation, respectively. Furthermore, ML3 protein abundance is dependent on NAI1, a master regulator of ER body formation in Arabidopsis thaliana. The regulation of ML3 expression and the localization of ML3 in ER bodies and the vacuole is in agreement with a demonstrated importance of ML3 in the defense to herbivore attack. Here, we extent the spectrum of ML3 biological functions by demonstrating a role in response to microbial pathogens. AU - Hakenjos, J.P.* AU - Bejai, S.* AU - Ranftl, Q.* AU - Behringer, C.* AU - Vlot, A.C. AU - Absmanner, B.* AU - Hammes, U.* AU - Heinzlmeir, S.* AU - Kuster, B.* AU - Schwechheimer, C.* C1 - 26833 C2 - 32409 SP - 135-149 TI - ML3 is a NEDD8- and ubiquitin-modified protein. JO - Plant Physiol. VL - 163 IS - 1 PB - Amer. Soc. Plant Biologists PY - 2013 SN - 0032-0889 ER - TY - JOUR AB - Analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and it has been used in intergeneric hybridization with ryegrasses to produce Festulolium cultivars. In this work we describe a new approach to analyze the large genome of meadow fescue, which involves reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts - individual chromosomes and groups of chromosomes. As the first step, we flow-sorted chromosome 4F and sequenced it by Illumina with ~50x coverage. This provided the first insight into the composition of the fescue genome, enabled the construction of virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice, Brachypodium, Sorghum and barley. Using GenomeZipper, we were able to confirm collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H (5HL). Several new tandem repeats were identified and physically mapped using FISH. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens a way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next generation sequencing of flow-sorted chromosomes enables an overview on chromosome structure and evolution at a resolution never achieved before. AU - Kopecky, D.* AU - Martis, M.M. AU - Cihalikova, J.* AU - Hribova, E.* AU - Vrana, J.* AU - Bartos, J.* AU - Kopecka, J.* AU - Cattonaro, F.* AU - Stoces, S.* AU - Novak, P.* AU - Neumann, P.* AU - Macas, J.* AU - Šimková, H.* AU - Studer, B.* AU - Asp, T.* AU - Baird, J.H.* AU - Navratil, P.* AU - Karafiatova, M.* AU - Kubaláková, M.* AU - Safar, J.* AU - Mayer, K.F.X. AU - Dolezel, J.* C1 - 27953 C2 - 32875 SP - 1323-1337 TI - Flow sorting and sequencing meadow fescue chromosome 4F. JO - Plant Physiol. VL - 163 IS - 3 PB - Amer. Soc. Plant Biologists PY - 2013 SN - 0032-0889 ER - TY - JOUR AB - Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources are yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne L.) genome on the basis of conserved synteny to barley (Hordeum vulgare L.) and the model grass genome Brachypodium (Brachypodium distachyon L.), as well as rice (Oryza sativa L.) and sorghum [Sorghum bicolor (L.) Moench]. A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macro-collinearity, and was then utilised to anchor a collection of perennial ryegrass genes in silico to their predicted genome position. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. AU - Pfeifer, M. AU - Martis, M.M. AU - Asp, T.* AU - Mayer, K.F.X. AU - Lübberstedt, T.* AU - Byrne, S.* AU - Frei, U.* AU - Studer, B.* C1 - 11341 C2 - 30619 SP - 571-582 TI - The Perennial Ryegrass GenomeZipper - targeted use of genome resources for comparative grass genomics. JO - Plant Physiol. VL - 161 IS - 2 PB - Amer. Soc. Plant Biologists PY - 2013 SN - 0032-0889 ER - TY - JOUR AB - The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One- and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time- and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome. AU - Fröhlich, A. AU - Gaupels, F. AU - Sarioglu, H. AU - Holzmeister, C. AU - Spannagl, M. AU - Durner, J. AU - Lindermayr, C. C1 - 8190 C2 - 30017 SP - 902-914 TI - Looking deep inside: Detection of low-abundance proteins in leaf extracts of arabidopsis and phloem exudates of pumpkin. JO - Plant Physiol. VL - 159 IS - 3 PB - Amer. Soc. Plant Biologists PY - 2012 SN - 0032-0889 ER - TY - JOUR AB - In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. AU - Gaupels, F. AU - Sarioglu, H. AU - Beckmann, M.* AU - Hause, B.* AU - Spannagl, M. AU - Draper, J.* AU - Lindermayr, C. AU - Durner, J. C1 - 11539 C2 - 30722 SP - 2285-2299 TI - Deciphering systemic wound responses of the pumpkin extrafascicular phloem by metabolomics and stable isotope-coded protein labeling. JO - Plant Physiol. VL - 160 IS - 4 PB - American Society of Plant Biologists PY - 2012 SN - 0032-0889 ER - TY - JOUR AB - Genes for mitochondrial and chloroplast proteins are distributed between the nuclear and organellar genomes. Organelle biogenesis and metabolism, therefore, require appropriate coordination of gene expression in the different compartments to ensure efficient synthesis of essential multiprotein complexes of mixed genetic origin. Whereas organelle-to-nucleus signaling influences nuclear gene expression at the transcriptional level, organellar gene expression (OGE) is thought to be primarily regulated posttranscriptionally. Here, we show that intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. Nearly 1,300 ATH1 microarray-based transcriptional profiles of nuclear and organellar genes for mitochondrial and chloroplast proteins in the model plant Arabidopsis (Arabidopsis thaliana) were analyzed. The activity of genes involved in organellar energy production (OEP) or OGE in each of the organelles and in the nucleus is highly coordinated. Intracompartmental networks that link the OEP and OGE gene sets serve to synchronize the expression of nucleus- and organelle-encoded proteins. At a higher regulatory level, coexpression of organellar and nuclear OEP/OGE genes typically modulates chloroplast functions but affects mitochondria only when chloroplast functions are perturbed. Under conditions that induce energy shortage, the intercompartmental coregulation of photosynthesis genes can even override intracompartmental networks. We conclude that dynamic intracompartmental and intercompartmental transcriptional networks for OEP and OGE genes adjust the activity of organelles in response to the cellular energy state and environmental stresses, and we identify candidate cis-elements involved in the transcriptional coregulation of nuclear genes. Regarding the transcriptional regulation of chloroplast genes, novel tentative target genes of σ factors are identified. AU - Leister, D.* AU - Wang, X. AU - Haberer, G. AU - Mayer, K.F.X. AU - Kleine, T.* C1 - 6668 C2 - 29077 CY - Rockville SP - 386-404 TI - Intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. JO - Plant Physiol. VL - 157 IS - 1 PB - Amer. Soc. Plant Biologists PY - 2011 SN - 0032-0889 ER - TY - JOUR AB - Mitochondria play an essential role in nitric oxide (NO) signal transduction in plants. Using the biotin-switch method in conjunction with nano-liquid chromatography and mass spectrometry, we identified 11 candidate proteins that were S-nitrosylated and/or glutathionylated in mitochondria of Arabidopsis (Arabidopsis thaliana) leaves. These included glycine decarboxylase complex (GDC), a key enzyme of the photorespiratory C(2) cycle in C3 plants. GDC activity was inhibited by S-nitrosoglutathione due to S-nitrosylation/S-glutathionylation of several cysteine residues. Gas-exchange measurements demonstrated that the bacterial elicitor harpin, a strong inducer of reactive oxygen species and NO, inhibits GDC activity. Furthermore, an inhibitor of GDC, aminoacetonitrile, was able to mimic mitochondrial depolarization, hydrogen peroxide production, and cell death in response to stress or harpin treatment of cultured Arabidopsis cells. These findings indicate that the mitochondrial photorespiratory system is involved in the regulation of NO signal transduction in Arabidopsis. AU - Palmieri, M.C. AU - Lindermayr, C. AU - Bauwe, H.* AU - Steinhauser, C. AU - Durner, J. C1 - 301 C2 - 27192 SP - 1514-1528 TI - Regulation of plant glycine decarboxylase by s-nitrosylation and glutathionylation. JO - Plant Physiol. VL - 152 IS - 3 PB - American Society of Plant Biologists PY - 2010 SN - 0032-0889 ER - TY - JOUR AB - Aquaporins are channel proteins that facilitate the transport of water across plant cell membranes. In this work, we used a combination of pharmacological and reverse genetic approaches to investigate the overall significance of aquaporins for tissue water conductivity in Arabidopsis (Arabidopsis thaliana). We addressed the function in roots and leaves of AtPIP1;2, one of the most abundantly expressed isoforms of the plasma membrane intrinsic protein family. At variance with the water transport phenotype previously described in AtPIP2;2 knockout mutants, disruption of AtPIP1;2 reduced by 20% to 30% the root hydrostatic hydraulic conductivity but did not modify osmotic root water transport. These results document qualitatively distinct functions of different PIP isoforms in root water uptake. The hydraulic conductivity of excised rosettes (K(ros)) was measured by a novel pressure chamber technique. Exposure of Arabidopsis plants to darkness increased K(ros) by up to 90%. Mercury and azide, two aquaporin inhibitors with distinct modes of action, were able to induce similar inhibition of K(ros) by approximately 13% and approximately 25% in rosettes from plants grown in the light or under prolonged (11-18 h) darkness, respectively. Prolonged darkness enhanced the transcript abundance of several PIP genes, including AtPIP1;2. Mutant analysis showed that, under prolonged darkness conditions, AtPIP1;2 can contribute to up to approximately 20% of K(ros) and to the osmotic water permeability of isolated mesophyll protoplasts. Therefore, AtPIP1;2 can account for a significant portion of aquaporin-mediated leaf water transport. The overall work shows that AtPIP1;2 represents a key component of whole-plant hydraulics. AU - Postaire, O.* AU - Tournaire-Roux, C.* AU - Grondin, A.* AU - Boursiac, Y.* AU - Morillon, R.* AU - Schäffner, A. AU - Maurel, C.* C1 - 1567 C2 - 27197 SP - 1418-1430 TI - A PIP1 aquaporin contributes to hydrostatic pressure-induced water transport in both the root and rosette of Arabidopsis. JO - Plant Physiol. VL - 152 IS - 3 PB - American Society of Plant Biologists PY - 2010 SN - 0032-0889 ER - TY - JOUR AB - Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind. AU - Mayer, K.F.X. AU - Taudien, S.* AU - Martis, M.M. AU - Šimková, H.* AU - Suchánková, P.* AU - Gundlach, H. AU - Wicker, T.* AU - Petzold, A.* AU - Felder, M.* AU - Steuernagel, B.* AU - Scholz, U.* AU - Graner, A.* AU - Platzer, M.* AU - Dolezel, J.* AU - Stein, N.* C1 - 2152 C2 - 26536 CY - ROCKVILLE SP - 496-505 TI - Gene content and virtual gene order of barley chromosome 1H. JO - Plant Physiol. VL - 151 IS - 2 PB - AMER SOC PLANT BIOLOGISTS PY - 2009 SN - 0032-0889 ER - TY - JOUR AB - Arabidopsis (Arabidopsis thaliana) NADPH oxidases have been reported to suppress the spread of pathogen-and salicylic acid-induced cell death. Here, we present dual roles of RBOHD (for respiratory burst oxidase homolog D) in an Arabidopsis-Alternaria pathosystem, suggesting either initiation or prevention of cell death dependent on the distance from pathogen attack. Our data demonstrate that a rbohD knockout mutant exhibits increased spread of cell death at the macroscopic level upon inoculation with the fungus Alternaria brassicicola. However, the cellular patterns of reactive oxygen species accumulation and cell death are fundamentally different in the AtrbohD mutant compared with the wild type. Functional RBOHD causes marked extracellular hydrogen peroxide accumulation as well as cell death in distinct, single cells of A. brassicicola-infected wild-type plants. This single cell response is missing in the AtrbohD mutant, where infection triggers spreading-type necrosis preceded by less distinct chloroplastic hydrogen peroxide accumulation in large clusters of cells. While the salicylic acid analog benzothiadiazole induces the action of RBOHD and the development of cell death in infected tissues, the ethylene inhibitor aminoethoxyvinylglycine inhibits cell death, indicating that both salicylic acid and ethylene positively regulate RBOHD and cell death. Moreover, A. brassicicola-infected AtrbohD plants hyperaccumulate ethylene and free salicylic acid compared with the wild type, suggesting negative feedback regulation of salicylic acid and ethylene by RBOHD. We propose that functional RBOHD triggers death in cells that are damaged by fungal infection but simultaneously inhibits death in neighboring cells through the suppression of free salicylic acid and ethylene levels. AU - Pogány, M. AU - von Rad, U. AU - Grün, S. AU - Dongó, A.* AU - Pintye, A.* AU - Simoneau, P.* AU - Bahnweg, G. AU - Kiss, L.* AU - Barna, B.* AU - Durner, J. C1 - 1100 C2 - 26356 CY - Rockville SP - 1459-1475 TI - Dual roles of reactive oxygen species and NADPH oxidase RBOHD in an Arabidopsis-Alternaria pathosystem. JO - Plant Physiol. VL - 151 IS - 3 PB - Amer Soc Plant Biologists PY - 2009 SN - 0032-0889 ER - TY - JOUR AU - Haberer, G. AU - Mader, M.T. AU - Kosarev, P. AU - Spannagl, M. AU - Yang, L. AU - Mayer, K.F.X. C1 - 5399 C2 - 24101 SP - 1589-1602 TI - Large-scale cis-element detection by analysis of correltaed expression and sequence conservation between arabidopsis and Brassica oleracea. JO - Plant Physiol. VL - 142 PY - 2006 SN - 0032-0889 ER - TY - JOUR AU - Haberer, G. AU - Gundlach, H. AU - Mayer, K.F.X. C1 - 3896 C2 - 23357 SP - 1612-1624 TI - Structure and architecture of the Maize genome. JO - Plant Physiol. VL - 139 PY - 2005 SN - 0032-0889 ER - TY - JOUR AU - Lindermayr, C. AU - Saalbach, G.* AU - Durner, J. C1 - 1364 C2 - 22591 SP - 921-930 TI - Proteomic identification of S-nitrosylated proteins in Arabidopsis. JO - Plant Physiol. VL - 137 PY - 2005 SN - 0032-0889 ER - TY - JOUR AU - Loeffler, C.* AU - Berger, S.* AU - Guy, A.* AU - Durand, T.* AU - Bringmann, G.* AU - Dreyer, M.* AU - von Rad, U. AU - Durner, J. AU - Mueller, M.J.* C1 - 4812 C2 - 22922 SP - 328-340 TI - B1-phytoprostanes trigger plant defense and detoxification responses. JO - Plant Physiol. VL - 137 PY - 2005 SN - 0032-0889 ER - TY - JOUR AU - Schoof, H. AU - Spannagl, M. AU - Yang, L. AU - Ernst, R. AU - Gundlach, H. AU - Haase, H. AU - Haberer, G. AU - Mayer, K.F.X. C1 - 3739 C2 - 23414 SP - 1301-1309 TI - Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses. JO - Plant Physiol. VL - 138 PY - 2005 SN - 0032-0889 ER - TY - JOUR AU - Vanderauwera, S.* AU - Zimmermann, P.* AU - Rombauts, S.* AU - Vandenabeele, S.* AU - Langebartels, C. AU - Gruissem, W.* AU - Inzé, D.* AU - van Breusegem, F.* C1 - 3608 C2 - 23034 SP - 806-821 TI - Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. JO - Plant Physiol. VL - 139 PY - 2005 SN - 0032-0889 ER - TY - JOUR AU - Wilkinson, M.* AU - Schoof, H. AU - Ernst, R. AU - Haase, D. C1 - 4721 C2 - 23355 SP - 5-17 TI - BioMOBY successfully integrates distributed heterogeneous bioinformatics Web services. The plaNet exemplar case. JO - Plant Physiol. VL - 138 PY - 2005 SN - 0032-0889 ER - TY - JOUR AU - Haberer, G. AU - Hindemitt, T. AU - Meyers, B.C.* AU - Mayer, K.F.X. C1 - 503 C2 - 22221 SP - 3009-3022 TI - Transcriptional similarities, dissimilarities and conservation of cis-elements in duplicated genes of Arabidopsis. JO - Plant Physiol. VL - 136 PY - 2004 SN - 0032-0889 ER - TY - JOUR AU - Lamotte, O.* AU - Gould, D.* AU - Lecourieux, D.* AU - Sequeira-Legrand, A.* AU - Lebrun-Garcia, A.* AU - Durner, J. AU - Pugin, A.* AU - Wendehenne, D.* C1 - 2458 C2 - 21805 SP - 516-529 TI - Analysis of nitric oxide signaling functions in tobacco cells challenged by the elicitor cryptogein. JO - Plant Physiol. VL - 135 PY - 2004 SN - 0032-0889 ER - TY - JOUR AB - We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation of S/MARs inside genes. In cases where S/MARs were predicted within genes, these intragenic S/MARs were preferentially located within the 5'-half, most prominently within introns 1 and 2. Using Arabidopsis whole-genome expression data generated by the massively parallel signature sequencing methodology, we found a negative correlation between S/MAR-containing genes and transcriptional abundance. Expressed sequence tag data correlated the same way with S/MAR-containing genes. Thus, intragenic S/MARs show a negative correlation with transcription level. For various genes it has been shown experimentally that S/MARs can function as transcriptional regulators and that they have an implication in stabilizing expression levels within transgenic plants. On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation. AU - Rudd, S. AU - Frisch, M.* AU - Grote, K.* AU - Meyers, B.C.* AU - Mayer, K.F.X. AU - Werner, T.* C1 - 28373 C2 - 33339 SP - 715-722 TI - Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. JO - Plant Physiol. VL - 135 IS - 2 PY - 2004 SN - 0032-0889 ER - TY - JOUR AU - Moeder, W. AU - Barry, C.S.* AU - Tauriainen, A.A.* AU - Betz, C. AU - Tuomainen, J.* AU - Utrianen, M.* AU - Grierson, D.* AU - Sandermann, H. AU - Langebartels, C. AU - Kangasjärvi, J.* C1 - 21984 C2 - 20512 SP - 1-9 TI - Ethylene synthesis regulated by biphasic induction of 1-aminocyclopropane-1-carboxylic acid synthase and 1-aminocyclopropane-1-carboxylic acid oxidase genes is regulated for hydrogen peroxide accumulation and cell death in ozone-exposed tomato. JO - Plant Physiol. VL - 130 PY - 2002 SN - 0032-0889 ER - TY - JOUR AU - Chiron, H.* AU - Drouet, A.* AU - Lieutier, F.* AU - Payer, H.-D. AU - Ernst, D. AU - Sandermann, H. C1 - 22182 C2 - 20886 SP - 865-872 TI - Gene induction of stilbene biosynthesis in scots pine in response to ozone treatment, wounding and fungal infection. JO - Plant Physiol. VL - 124 PY - 2000 SN - 0032-0889 ER - TY - JOUR AU - Navarre, D.A.* AU - Wendehenne, D.* AU - Durner, J. AU - Noad, R.* AU - Klessig, D.F.* C1 - 21806 C2 - 20008 SP - 573-582 TI - Nitric Oxide Modulates the Activity of Tobacco Aconitase. JO - Plant Physiol. VL - 122 PY - 2000 SN - 0032-0889 ER - TY - JOUR AB - Parsley (Petroselinum crispum L.) is known to respond to ultraviolet irradiation by the synthesis of flavone glycosides, whereas fungal or elicitor stress leads to the synthesis of furanocoumarin phytoalexins. We tested how these defensive pathways are affected by a single ozone treatment (200 nL L-1; 10 h). Assays were performed at the levels of transcripts, for enzyme activities, and for secondary products. The most rapid transcript accumulation was maximal at 3 h, whereas flavone glycosides and furanocoumarins were maximally induced at 12 and 24 h, respectively, after the start of ozone treatment. Ozone acted as a cross-inducer because the two distinct pathways were simultaneously induced. These results are consistent with the previously observed ozone induction of fungal and viral defense reactions in tobacco, spruce, and pine. AU - Eckey-Kaltenbach, H. AU - Ernst, D. AU - Heller, W. AU - Sandermann, H. C1 - 46493 C2 - 0 SP - 67-74 TI - Biochemical plant responses to ozone: IV. Cross-induction of defensive pathways in parsley (Petroselinum crispum L.) plants. JO - Plant Physiol. VL - 104 IS - 1 PY - 1994 SN - 0032-0889 ER - TY - JOUR AB - Suspension-cultured carrot cells (Daucus carota) and their protoplasts respond to a fungal elicitor prepared from the culture medium of Pythium aphanidermatum by accumulating 4-hydroxybenzoic acid (4-HBA). Protoplasts release the compound into the culture medium. Using 45CaCl2 as a tracer, we were able to demonstrate that the secretion of 4-HBA is preceded by a rapid increase in the Ca2+ influx and a concomitant K+ efflux. If the increased Ca2+ influx was prevented by ethyleneglycol-bis([beta]-aminoethylether)-N,N[prime]-tetraacetic acid, 4-HBA synthesis was inhibited by 70%. These results are discussed with regard to signal transduction from the plasma membrane to the nucleus of carrot protoplasts. AU - Bach, M. AU - Schnitzler, J.-P. AU - Seitz, H.-U. C1 - 20268 C2 - 13455 SP - 407-412 TI - Elicitor-induced Changes of Ca2+, Influx, K+ Efflux, and 4-hydroxybenzoic Acid Synthesis in Protoplasts of Daucus Carota L. JO - Plant Physiol. VL - 103 IS - 2 PY - 1993 SN - 0032-0889 ER - TY - JOUR AB - Suspension-cultured carrot cells (Daucus carota) and their protoplasts respond to a fungal elicitor prepared from the culture medium of Pythium aphanidermatum by accumulating 4-hydroxybenzoic acid (4-HBA). Protoplasts release the compound into the culture medium. Using 45CaCl2 as a tracer, we were able to demonstrate that the secretion of 4-HBA is preceded by a rapid increase in the Ca2+ influx and a concomitant K+ efflux. If the increased Ca2+ influx was prevented by ethyleneglycol-bis(β-aminoethyl ether)-N,N′-tetraacetic acid, 4-HBA synthesis was inhibited by 70%. These results are discussed with regard to signal transduction from the plasma membrane to the nucleus of carrot protoplasts. AU - Bach, M.* AU - Schnitzler, J.-P. AU - Seitz, H.U.* C1 - 40410 C2 - 0 SP - 407-412 TI - Elicitor-induced changes in Ca2+ influx, K+ efflux, and 4-hydroxybenzoic acid synthesis in protoplasts of Daucus carota L. JO - Plant Physiol. VL - 103 IS - 2 PY - 1993 SN - 0032-0889 ER - TY - JOUR AU - Bauer, S. AU - Galliano, H. AU - Pfeiffer, F. AU - Meßner, B. AU - Sandermann, H. AU - Ernst, D. C1 - 20743 C2 - 13963 SP - 1479-1480 TI - Plant Gene Register: Isolation and Characterization of a cDNA Clone Encoding a Novel Short- Chain Alcohol Dehydrogenase from Norway Spruce (Picea abies L. Karst). JO - Plant Physiol. VL - 103 PY - 1993 SN - 0032-0889 ER - TY - JOUR AU - Bauer, S. AU - Galliano, H. AU - Pfeiffer, F. AU - Meßner, B. AU - Sandermann, H. AU - Ernst, D.E.W. C1 - 40304 C2 - 40079 SP - 1479-1480 TI - Isolation and characterization of a cDNA clone encoding a novel short-chain alcohol dehydrogenase from Norway spruce (Picea abies L. Karst.). JO - Plant Physiol. VL - 103 IS - 4 PY - 1993 SN - 0032-0889 ER - TY - JOUR AB - Chlorotic and green needles from Norway spruce (Picea abies L.) trees were sampled in the Calcareous Bavarian Alps in winter. The needles were used for analysis of the mineral and pigment contents, the levels of antioxidants (ascorbate, glutathione), and the activities of protective enzymes (superoxide dismutase, catalase, ascorbate peroxidase, monodehydroascorbate radical reductase, dehydroascorbate reductase, glutathione reductase). In addition, the activities of two respiratory enzymes (glucose-6-phosphate dehydrogenase, NAD-malate dehydrogenase), which might provide the NADPH necessary for functioning of the antioxidative system, were determined. We found that chlorotic needles were severely manganese deficient (3 to 6 micrograms Mn per gram dry weight as compared with up to 190 micrograms Mn per gram dry weight in green needles) but had a similar dry weight to fresh weight ratio, had a similar protein content, and showed no evidence for enhanced lipid peroxidation as compared with green needles. In chlorotic needles, the level of total ascorbate and the activities of superoxide dismutase, monodehydroascorbate radical reductase, NAD-malate dehydrogenase, and glucose-6-phosphate dehydrogenase were significantly increased, whereas the levels of ascorbate peroxidase, dehydroascorbate reductase, glutathione reductase, and glutathione were not affected. The ratio of ascorbate to dehydroascorbate was similar in both green and chlorotic needles. These results suggest that in spruce needles monodehydroascorbate radical reductase is the key enzyme involved in maintaining ascorbate in its reduced state. The reductant necessary for this process may have been supplied at the expense of photosynthate. AU - Polle, A.* AU - Chakrabarti, K.* AU - Chakrabarti, S.* AU - Seifert, F.* AU - Schramel, P. AU - Rennenberg, H.* C1 - 40590 C2 - 38759 SP - 1084-1089 TI - Antioxidants and manganese deficiency in needles of Norway spruce (Picea abies L) trees. JO - Plant Physiol. VL - 99 IS - 3 PY - 1992 SN - 0032-0889 ER - TY - JOUR AU - Schraudner, M. AU - Ernst, D. AU - Langebartels, C. AU - Sandermann, H. C1 - 19638 C2 - 12757 SP - 1321-1328 TI - Biochemical Plant Response to Ozone. III. Activation of the Defense-Related Proteins ß-1,3- Glucanase and Chitinase in Tobacco Leavers. JO - Plant Physiol. VL - 99 PY - 1992 SN - 0032-0889 ER - TY - JOUR AU - Ernst, D. AU - Weyrauch, C. C1 - 19336 C2 - 12415 SP - 73-75 TI - D-myo-inositol 1,4,5-trisphosphate Levels in Rye Seedlings. JO - Plant Physiol. VL - 10 PY - 1991 SN - 0032-0889 ER - TY - JOUR AB - Polyamine metabolism was examined in tobacco (Nicotians tabacum L.) exposed to a single ozone treatment (5 or 7 hours) and then postcultivated in pollutant-free air. The levels of free and conjugated putrescine were rapidly increased in the ozone-tolerant cultiver Bel B and remained high for 3 days. This accumulation was preceded by a transient rise of L-arginine decarboxylase (ADC, EC 4.1.1.19) activity. The ozone-sensitive cultivar Bel W3 showed a rapid production of ethylene and high levels of 1-aminocyclopropane-1-carboxylic acid after 1 to 2 hours of exposure. Induction of putrescine levels and ADC activity was weak in this cultivar and was observed when necrotic lesions developed. Leaf injury occurred in both lines when the molar ratio of putrescine to 1-aminocyclopropane-1-carboxylic acid or ethylene fell short of a certain threshold value. Monocaffeoyl-putrescine, an effective scavenger for oxyradicals, was detected in the apoplastic fluid of the leaves of cv Bel B and increased upon exposure to ozone. This extracellular localization could allow scavenging of ozone-derived oxyradicals at the first site of their generation. Induction of either polyamine or ethylene pathways may represent a control mechanism for inhibition or promotion of lesion formation and thereby contribute to the disposition of plants for ozone tolerance. AU - Langebartels, C. AU - Kerner, K. AU - Leonardi, S. AU - Schraudner, M. AU - Trost, M. AU - Heller, W.E. AU - Sandermann, H.J. C1 - 40733 C2 - 11712 SP - 882-889 TI - Biochemical plant responses to ozone: I. Differential induction of polyamine and ethylene biosynthesis in tobacco. JO - Plant Physiol. VL - 95 IS - 3 PY - 1991 SN - 0032-0889 ER - TY - JOUR AB - Formation of the stilbenes pinosylvin and pinosylvin 3-methyl ether, as well as the activity of the biosynthetic enzyme stilbene synthase (pinosylvin-forming), were induced several hundred- to thousandfold in primary needles of 6-week-old pine (Pinus sylvestris L.) seedlings upon exposure to a single pulse of ozone of at least 0.15 microliters per liter. The seedlings required 4 hours of exposure as a minimum for the induction of stilbene biosynthesis when exposed to 0.2 microliters per liter ozone. Both stilbene synthase activity and stilbene accumulation increased with the duration of ozone treatment. The activity of phenylalanine ammonia-lyase and the activity of chalcone synthase, a key enzyme of the flavonoid pathway that uses the same substrates as stilbene synthase, were also stimulated about twofold by ozone. Stilbene biosynthesis appears to represent the first example of a dose-dependent biochemical response to ozone in a conifer species and may serve as a useful biomarker to study stress impacts on pine trees. AU - Rosemann, D. AU - Heller, W.E. AU - Sandermann, H.J. C1 - 40847 C2 - 38729 SP - 1280-1286 TI - Biochemical plant responses to ozone. II. Induction of stilbene biosynthesis in scots pine (Pinus sylvestris L.) seedlings. JO - Plant Physiol. VL - 97 IS - 4 PY - 1991 SN - 0032-0889 ER - TY - JOUR AU - Adams, W.W. AU - Winter, K. AU - Schreiber, U. AU - Schramel, P. C1 - 18306 C2 - 11504 SP - 1184-1190 TI - Photosynthesis and Chlorophyll Fluorescence Characteristics in Relationship to Changes in Pigment and Element Composition of Leaves of Plantanus occidentalis L. during Autumnal Leaf Senescence. JO - Plant Physiol. VL - 93 PY - 1990 SN - 0032-0889 ER - TY - JOUR AB - The loss of chlorophyll and total leaf nitrogen during autumnal senescence of leaves from the deciduous tree Plaianus occiderrtalis L. was accompanied by a marked decline in the photosynthetic capacity of O2 evolution on a leaf area basis. When expressed on a chlorophyll basis, however, the capacity for light-and CO2-saturaled O2 evolution did not decline, but rather increased as leaf chlorophyll content decreased. The photon yield of O2 evolution in white light (400-700 nanometers) declined markedly with decreases in leaf chlorophyll content below 150 milligrams of chlorophyll per square meter on both an incident and an absorbed basis, due largely to the absorption of light by nonphotosynthetic pigments which were not degraded as rapidly as the chlorophylls. Photon yields measured in, and corrected for the absorptance of, red light (630-700 nanometers) exhibited little change with the loss of chlorophyll. Furthermore, PSII photochemical efficiency, as determined from chlorophyll fluorescence, remained high, and the chlorophyll a/b ratio exhibited no decline except in leaves with extremely low chlorophyll contents. These data indicate that the efficiency for photochemical energy conversion of the remaining functional components was maintained at a high level during the natural course of autumnal senescence, and are consistent with previous studies which have characterized leaf senescence as being a controlled process. The loss of chlorophyll during senescence was also accompanied by a decline in fluorescence emanating from PSI, whereas there was little change in PSII fluorescence (measured at 77 Kelvin), presumably due to decreased reabsorption of PSII fluorescence by chlorophyll. Nitrogen was the only element examined to exhibit a decline with senescence on a dry weight basis. However, on a leaf area basis, all elements (C, Ca, K, Mg, N, P, S) declined in senescent leaves, although the contents of sulfur and calcium, which are not easily retranslocated, decreased to the smallest extent. AU - Adams, W.W.I.I.* AU - Winter, K.A.* AU - Schreiber, U.K.* AU - Schramel, P. C1 - 40856 C2 - 36391 SP - 1184-1190 TI - Photosynthesis and chlorophyll fluorescence characteristics in relationship to changes in pigment and element composition of leaves of Platanus occidentalis L. during autumnal leaf senescence. JO - Plant Physiol. VL - 92 IS - 4 PY - 1990 SN - 0032-0889 ER -