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Publications - Stress and Develop Biology

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Landgraf, R.; Smolka, U.; Altmann, S.; Eschen-Lippold, L.; Senning, M.; Sonnewald, S.; Weigel, B., Frolova, N.; Strehmel, N.; Hause, G.; Scheel, D.; Böttcher, C.; Rosahl, S. The ABC transporter ABCG1 is required for suberin formation in potato tuber periderm Plant Cell 26, 3403-3415, (2014) DOI: 10.1105/tpc.114.124776

The lipid biopolymer suberin plays a major role as a barrier both at plant-environment interfaces and in internal tissues, restricting water and nutrient transport. In potato (Solanum tuberosum), tuber integrity is dependent on suberized periderm. Using microarray analyses, we identified ABCG1 , encoding an ABC transporter, as a gene responsive to the pathogen-associated molecular pattern Pep-13. Further analyses revealed that ABCG1 is expressed in roots and tuber periderm, as well as in wounded leaves. Transgenic ABCG1-RNAi potato plants with downregulated expression of ABCG1 display major alterations in both root and tuber morphology, whereas the aerial part of the ABCG1-RNAi plants appear normal. The tuber periderm and root exodermis show reduced suberin staining and disorganized cell layers. Metabolite analyses revealed reduction of esterified suberin components and hyperaccumulation of putative suberin precursors in the tuber periderm of RNA interference plants, suggesting that ABCG1 is required for the export of suberin components.

Sheikh, A.H.; Raghuram, B.; Eschen-Lippold, L.; Scheel, D.; Lee, J.; Sinha, A.K. Agroinfiltration by cytokinin-producing Agrobacterium strain GV3101 primes defense responses in Nicotiana tabacum. Mol Plant Microbe Interact 27, 1175-1185, (2014) DOI: 10.1094/MPMI-04-14-0114-R

Transient infiltrations in tobacco are commonly used in plant studies but the host response to different disarmed Agrobacterium strains is not fully understood. The present study shows that the pre-treatment with disarmed Agrobacterium tumefaciens strain GV3101 primes the defense response to subsequent infection by Pseudomonas syringae in Nicotiana tabacum. The presence of a trans-zeatin synthase (tzs) gene in strain GV3101 may be partly responsible for the priming response as the tzs deficient Agrobacterium strain LBA4404 only weakly imparts such responses. Besides inducing the expression of defense-related genes like PR-1 and NHL10, GV3101 pre-treatment increased the expression of tobacco mitogen-activated protein kinase pathway genes like MEK2, WIPK and SIPK . Furthermore, the GV3101 strain showed a stronger effect than the LBA4404 strain in activating phosphorylation of the tobacco MAP kinases, WIPK and SIPK, which presumably primes the plant immune machinery. Lower doses of exogenously applied cytokinins increased the activation of MAPKs while higher doses decreased the activation, suggesting a balanced level of cytokinins is required to generate defense response in planta. The current study serves as a cautionary warning for plant researchers over the choice of Agrobacterium strains and their possible consequences on subsequent pathogen-related studies.

Seybold, H.; Trempel, F.; Ranf, S.; Scheel, D.; Romeis, T.; Lee, J. Ca2+ signalling in plant immune response: from pattern recognition receptors to Ca2+ decoding mechanisms. New Phytol 204, 782–790, (2014) DOI: 10.1111/nph.13031

Ca2+ is a ubiquitous second messenger for cellular signalling in various stresses and developmental processes. Here, we summarize current developments in the roles of Ca2+ during plant immunity responses. We discuss the early perception events preceding and necessary for triggering cellular Ca2+ fluxes, the potential Ca2+-permeable channels, the decoding of Ca2+ signals predominantly via Ca2+-dependent phosphorylation events and transcriptional reprogramming. To highlight the complexity of the cellular signal network, we briefly touch on the interplay between Ca2+-dependent signalling and selected major signalling mechanisms – with special emphasis on reactive oxygen species at local and systemic levels.

Strehmel, N.; Böttcher, C.; Schmidt, S.; Scheel, D. Profiling of secondary metabolites in root exudates of Arabidopsis thaliana Phytochemistry 108, 35–46, (2014) DOI: 10.1016/j.phytochem.2014.10.003

To explore the chemical composition of root exudates of the model plant Arabidopsis thaliana a workflow for nontargeted metabolite profiling of the semipolar fraction of root exudates was developed. It comprises hydroponic plant cultivation and sampling of root exudates under sterile conditions, sample preparation by solid-phase extraction and analysis by reversed-phase UPLC/ESI-QTOFMS. Following the established workflow, root exudates of six-week-old plants were profiled and a set of reproducibly occurring molecular features was compiled. To structurally elucidate the corresponding metabolites, accurate mass tandem mass spectrometry and on-line hydrogen/deuterium exchange were applied. Currently, a total of 103 compounds were detected and annotated by elemental composition of which more than 90 were structurally characterized or classified. Among them, 42 compounds were rigorously identified using an authenticated standard. The compounds identified so far include nucleosides, deoxynucleosides, aromatic amino acids, anabolites and catabolites of glucosinolates, dipeptides, indolics, salicylic and jasmonic acid catabolites, coumarins, mono-, di- and trilignols, hydroxycinnamic acid derivatives and oxylipins and exemplify the high chemical diversity of plant root exudates

Siersleben, S.; Penselin, D.; Wenzel, C.; Albert, S.; Knogge, W. PFP1, a gene encoding an Epc-N domain-containing protein, is essential forpathogenicity of the barley pathogen Rhynchosporium commune. Eukaryot. Cell 13, 1026-1035, (2014) DOI: 10.1128/EC.00043-14

Scald caused by Rhynchosporium commune is an important foliar disease of barley. Insertion mutagenesis of R. commune generated a non-pathogenic fungal mutant, which carries the inserted plasmid in the upstream region of a gene named PFP1. The characteristic feature of the gene product is an Epc-N domain. This motif is also found in homologous proteins shown to be components of histone acetyltransferase (HAT) complexes of fungi and animals. Therefore, PFP1 is suggested to be the subunit of a HAT complex in R. commune with an essential role in the epigenetic control of fungal pathogenicity. Targeted PFP1 disruption also yielded non-pathogenic mutants, which showed wild-type like growth ex planta except for the occurrence of hyphal swellings. Complementation of the deletion mutants with the wild-type gene reestablished pathogenicity and suppressed the hyphal swellings. However, despite wild-type level PFP1 expression the complementation mutants did not reach wild-type level virulence. This indicates that the function of the protein complex and, thus, fungal virulence is influenced by a position-affected long-range control of PFP1 expression. 

Böttcher, C.; Chapman, A.; Fellermeier, F.; Choudhary, M.; Scheel, D.; Glawischnig, E. The Biosynthetic Pathway of Indole-3-Carbaldehyde and Indole-3-Carboxylic Acid Derivatives in Arabidopsis1 Plant Physiol. 165, 841–853, (2014) DOI: 10.1104/pp.114.235630

Indolic secondary metabolites play an important role in pathogen defense in cruciferous plants. In Arabidopsis (Arabidopsis thaliana), in addition to the characteristic phytoalexin camalexin, derivatives of indole-3-carbaldehyde (ICHO) and indole-3-carboxylic acid (ICOOH) are synthesized from tryptophan via the intermediates indole-3-acetaldoxime and indole-3-acetonitrile. Based on feeding experiments combined with nontargeted metabolite profiling, their composition in nontreated and silver nitrate (AgNO3)-treated leaf tissue was comprehensively analyzed. As major derivatives, glucose conjugates of 5-hydroxyindole-3-carbaldehyde, ICOOH, and 6-hydroxyindole-3-carboxylic acid were identified. Quantification of ICHO and ICOOH derivative pools after glucosidase treatment revealed that, in response to AgNO3 treatment, their total accumulation level was similar to that of camalexin. ARABIDOPSIS ALDEHYDE OXIDASE1 (AAO1), initially discussed to be involved in the biosynthesis of indole-3-acetic acid, and Cytochrome P450 (CYP) 71B6 were found to be transcriptionally coexpressed with camalexin biosynthetic genes. CYP71B6 was expressed in Saccharomyces cerevisiae and shown to efficiently convert indole-3-acetonitrile into ICHO and ICOOH, thereby releasing cyanide. To evaluate the role of both enzymes in the biosynthesis of ICHO and ICOOH derivatives, knockout and overexpression lines for CYP71B6 and AAO1 were established and analyzed for indolic metabolites. The observed metabolic phenotypes suggest that AAO1 functions in the oxidation of ICHO to ICOOH in both nontreated and AgNO3-treated leaves,whereas CYP71B6 is relevant for ICOOH derivative biosynthesis specifically after induction. In summary, a model for the biosynthesis of ICHO and ICOOH derivatives is presented.

Thum, A.; Mönchgesang, S.; Westphal, L.; Lübken, T.; Rosahl, S.; Neumann, S.; Posch, S. Supervised Penalized Canonical Correlation Analysis arXiv (2014)

The canonical correlation analysis (CCA) is commonly used to analyze data sets with paired data, e.g. measurements of gene expression and metabolomic intensities of the same experiments. This allows to find interesting relationships between the data sets, e.g. they can be assigned to biological processes. However, it can be difficult to interpret the processes and often the relationships observed are not related to the experimental design but to some unknown parameters.Here we present an extension of the penalized CCA, the supervised penalized approach (spCCA), where the experimental design is used as a third data set and the correlation of the biological data sets with the design data set is maximized to find interpretable and meaningful canonical variables. The spCCA was successfully tested on a data set of Arabidopsis thaliana with gene expression and metabolite intensity measurements and resulted in eight significant canonical variables and their interpretation. We provide an R-package under the GPL license.

Kumar, A.; Gopalswamy, M.; Wishart, C.; Henze, M.; Eschen-Lippold, L.; Donnelly, D.; Balbach, J. N-Terminal Phosphorylation of Parathyroid Hormone (PTH) Abolishes Its Receptor Activity ACS Chem Biol 9, 2465–2470, (2014) DOI: 10.1021/cb5004515

The parathyroid hormone (PTH) is an 84-residue peptide, which regulates the blood Ca2+ level via GPCR binding and subsequent activation of intracellular signaling cascades. PTH is posttranslationally phosphorylated in the parathyroid glands; however, the functional significance of this processes is not well characterized. In the present study, mass spectrometric analysis revealed three sites of phosphorylation, and NMR spectroscopy assigned Ser1, Ser3, and Ser17 as modified sites. These sites are located at the N-terminus of the hormone, which is important for receptor recognition and activation. NMR shows further that the three phosphate groups remotely disturb the α-helical propensity up to Ala36. An intracellular cAMP accumulation assay elucidated the biological significance of this phosphorylation because it ablated the PTH-mediated signaling. Our studies thus shed light on functional implications of phosphorylation at native PTH as an additional level of regulation 

Heymann, T.; Westphal, L.; Wessjohann, L.; Glomb, M. A. Growing and Processing Conditions Lead to Changes in the Carotenoid Profile of Spinach J. Agric. Food Chem. 62, 4960–4967, (2014) DOI: 10.1021/jf501136g

This study aimed to evaluate the influence of different light regimens during spinach cultivation on the isomeric composition of β-carotene. Irradiation with a halogen lamp, which has a wavelength spectrum close to that of daylight, was used to mimic field-grown conditions. The additional use of optical filters was established as a model system for greenhouse cultivation. Field-grown model systems led to a preferential increase of 9-cis-β-carotene, whereas 13-cis-β-carotene was just formed at the beginning of irradiation. Additionally 9,13-di-cis-β-carotene decreased significantly in the presence of energy-rich light. Isomerization of β-carotene was strongly suppressed during irradiation in greenhouse-grown model systems and led to significant differences. These results were verified in biological samples. Authentic field-grown spinach (Spinacia oleracea L.) showed among changes of other isomers a significantly higher level of 9-cis-isomers (7.52 ± 0.14%) and a significantly lower level of 9,13-di-cis-isomers (0.25 ± 0.03%) compared to authentic greenhouse-grown spinach (6.49 ± 0.11 and 0.76 ± 0.05%). Almost all analyzed commercial spinach samples (fresh and frozen) were identified as common field-grown cultivation. Further investigations resulted in a clear differentiation of frozen commercial samples from fresh spinach, caused by significantly higher levels of 13-cis- and 15-cis-β-carotene as a result of industrial blanching processes.

Schober, D.; Wilson, M.; Jacob, D.; Moing, A.; Mayer, G.; Eisenacher, M.; Salek, R. M.; Neumann; S. Ontology usage in Omics Standards Initiatives: Pros and Cons of enriching XML data formats with controlled vocabulary terms IMISE-REPORT 1/2014, G 1-6 (36-42), (2014)

We here review a method of XML data enrichment with controlled vocabularies (CV) in light of end-user compliance. We outline the reasons that made major standard initiatives in proteomics and metabolomics use this data enrichment scheme on omics data in favor of more formal approaches, e.g. description logics (DL) knowledge bases. We show that in comparison to other knowledge representation formalisms, the list of prerequisite skills on the user-side and the learning threshold is significantly lower, making the approach feasible for bioinformaticians with average skill levels, i.e. basic XML knowledge. Additionally our approach allows to source out the ‘business logics’ from the terminology into external rules. This enables the successive and encapsulated addition of semantics in a flexible way.
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