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Publikationen - Molekulare Signalverarbeitung

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Bücher und Buchkapitel

Möller, B.; Bürstenbinder, K. Semi-Automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level 199-203, (2019) ISBN: 978-1-5386-3640-4 DOI: 10.1109/ISBI.2019.8759145

The structure of the microtubule cytoskeleton provides valuable information related to morphogenesis of cells. The cytoskeleton organizes into diverse patterns that vary in cells of different types and tissues, but also within a single tissue. To assess differences in cytoskeleton organization methods are needed that quantify cytoskeleton patterns within a complete cell and which are suitable for large data sets. A major bottleneck in most approaches, however, is a lack of techniques for automatic extraction of cell contours. Here, we present a semi-automatic pipeline for cell segmentation and quantification of microtubule organization. Automatic methods are applied to extract major parts of the contours and a handy image editor is provided to manually add missing information efficiently. Experimental results prove that our approach yields high-quality contour data with minimal user intervention and serves a suitable basis for subsequent quantitative studies.

Chutia, R.; Abel, S.; Ziegler, J. Iron and Phosphate Deficiency Regulators Concertedly Control Coumarin Profiles in Arabidopsis thaliana Roots During Iron, Phosphate, and Combined Deficiencies Front Plant Sci 10, 113, (2019) DOI: 10.3389/fpls.2019.00113

Plants face varying nutrient conditions, to which they have to adapt to. Adaptive responses are nutrient-specific and strategies to ensure supply and homeostasis for one nutrient might be opposite to another one, as shown for phosphate (Pi) and iron (Fe) deficiency responses, where many genes are regulated in an opposing manner. This was also observed on the metabolite levels. Whereas root and exudate levels of catechol-type coumarins, phenylpropanoid-derived 2-benzopyranones, which facilitate Fe acquisition, are elevated after Fe deficiency, they are decreased after Pi deficiency. Exposing plants to combined Pi and Fe deficiency showed that the generation of coumarin profiles in Arabidopsis thaliana roots by Pi deficiency considerably depends on the availability of Fe. Similarly, the effect of Fe deficiency on coumarin profiles is different at low compared to high Pi availability. These findings suggest a fine-tuning of coumarin profiles, which depends on Fe and Pi availability. T-DNA insertion lines exhibiting aberrant expression of genes involved in the regulation of Pi starvation responses (PHO1, PHR1, bHLH32, PHL1, SPX1) and Fe starvation responses (BRUTUS, PYE, bHLH104, FIT) were used to analyze the regulation of the generation of coumarin profiles in Arabidopsis thaliana roots by Pi, Fe, and combined Pi and Fe deficiency. The analysis revealed a role of several Fe-deficiency response regulators in the regulation of Fe and of Pi deficiency-induced coumarin profiles as well as for Pi deficiency response regulators in the regulation of Pi and of Fe deficiency-induced coumarin profiles. Additionally, the regulation of Fe deficiency-induced coumarin profiles by Fe deficiency response regulators is influenced by Pi availability. Conversely, regulation of Pi deficiency-induced coumarin profiles by Pi deficiency response regulators is modified by Fe availability.
Bücher und Buchkapitel

Flores, R.; Gago-Zachert, S.; De la Peña, M.; Navarro, B. Chrysanthemum Chlorotic Mottle Viroid (Ed. A. Hadidi, et al.). 331-338, (2017) ISBN: eBook ISBN: 9780128017029; Hardcover ISBN: 9780128014981. DOI: 10.1016/B978-0-12-801498-1.00031-0

Bücher und Buchkapitel

Wasternack, C. Jasmonates: Synthesis, Metabolism, Signal Transduction and Action (2016) ISBN: ISBN 978-0-4700-1590-2 DOI: 10.1002/9780470015902.a0020138.pub2

Jasmonic acid and other fatty-acid-derived compounds called oxylipins are signals in stress responses and development of plants. The receptor complex, signal transduction components as well as repressors and activators in jasmonate-induced gene expression have been elucidated. Different regulatory levels and cross-talk with other hormones are responsible for the multiplicity of plant responses to environmental and developmental cues.
Bücher und Buchkapitel

Parniske, M.; Ried, M. Wahrnehmung und Interpretation symbiontischer Signale durch Pflanzen und ihre bakteriellen Partner (Deigele, C., ed.). 105-116, (2016) ISBN: 978-3-89937-214-4

Mutualistic symbioses between plant roots and microorganisms can reduce the demand for chemical fertilizers in agriculture. Most crops are able to establish arbuscular mycorrhiza (AM) symbiosis with fungi to take up phosphate more efficiently. A second symbiosis, nitrogen-fixing root nodule symbiosis, supersedes energy-intensive nitrogen fertilization: Legumes such as peas, clover and soybeans take up rhizobia – special bacteria that are capable of converting atmospheric nitrogen into ammonium – into their root cells. Plant root cells perceive rhizobia and AM fungi via very similar signaling molecules (N-acetylglucosamine tetra- or pentamers), even though the resultant developmental processes differ strongly. Interestingly, N-acetylglucosamine containing signals including fungal chitin- and bacterial peptidoglycan-fragments from their cell walls, also play a role in the recognition of pathogenic microorganisms.Despite the intrinsic sustainability potential of the nitrogen-fixing root nodule symbiosis, too much of a good thing, however, has led to global problems: The massive increase in global meat production is largely based on soybean. Large scale soybean monoculture destroyed ecosystems in South America. Large scale animal production results in excessive methane and nitrogen release into the environment, which causes climate change and death zones in marine ecosystems, respectively. This calls for a considerable reduction in meat consumption.
Bücher und Buchkapitel

Tissier, A.; Ziegler, J.; Vogt, T. Specialized Plant Metabolites: Diversity and Biosynthesis (Krauss, G.-J. & Nies, D. H., eds.). 14-37, (2015) ISBN: 978-3-527-31650-2 DOI: 10.1002/9783527686063.ch2

Plant secondary metabolites, also termed specialized plant metabolites, currently comprise more than 200 000 natural products that are all based on a few biosynthetic pathways and key primary metabolites. Some pathways like flavonoid and terpenoid biosynthesis are universally distributed in the plant kingdom, whereas others like alkaloid or cyanogenic glycoside biosynthesis are restricted to a limited set of taxa. Diversification is achieved by an array of mechanisms at the genetic and enzymatic level including gene duplications, substrate promiscuity of enzymes, cell‐specific regulatory systems, together with modularity and combinatorial aspects. Specialized metabolites reflect adaptations to a specific environment. The observed diversity illustrates the heterogeneity and multitude of ecological habitats and niches that plants have colonized so far and constitutes a reservoir of potential new metabolites that may provide adaptive advantage in the face of environmental changes. The code that connects the observed chemical diversity to this ecological diversity is largely unknown. One way to apprehend this diversity is to realize its tremendous plasticity and evolutionary potential. This chapter presents an overview of the most widespread and popular secondary metabolites, which provide a definite advantage to adapt to or to colonize a particular environment, making the boundary between the “primary” and the “secondary” old fashioned and blurry.

Wasternack, C.; Hause, B. Jasmonsäure – ein universelles Pflanzenhormon: Blütenduft, Abwehr, Entwicklung Biologie in unserer Zeit 44, 164 - 171, (2014) DOI: 10.1002/biuz.201410535

Jasmonsäure (JA) und ihre Metaboliten kommen in allen niederen und höheren Pflanzen vor. Sie sind universell wirksame, aus Lipiden gebildete Signalstoffe bei der Abwehr von biotischem und abiotischem Stress sowie in der pflanzlichen Entwicklung. Rezeptor und Komponenten von JA–Signalketten wurden identifiziert. In der Entwicklung von Blüten, Früchten, Samen, Trichomen oder in der Abwehr von Insekten und Pathogenen treten ähnliche JA-vermittelte Signalproteine auf, die eine Feinregulation der Prozesse erlauben und eine Verbindung (cross-talk) zu anderenPflanzenhormonen aufweisen.
Bücher und Buchkapitel

Wasternack, C. Jasmonates in plant growth and stress responses. (Tran, L.-S.; Pal, S.). Springer, 221-264, (2014) ISBN: 978-1-4939-0490-7 (hardcover) 978-1-4939-4814-7 (softcover) DOI: 10.1007/978-1-4939-0491-4_8

Abiotic and biotic stresses adversely affect plant growth and productivity. The phytohormones regulate key physiological events under normal and stressful conditions for plant development. Accumulative research efforts have discovered important roles of phytohormones and their interactions in regulation of plant adaptation to numerous stressors. Intensive molecular studies have elucidated various plant hormonal pathways; each of which consist of many signaling components that link a specific hormone perception to the regulation of downstream genes. Signal transduction pathways of auxin, abscisic acid, cytokinins, gibberellins and ethylene have been thoroughly investigated. More recently, emerging signaling pathways of brassinosteroids, jasmonates, salicylic acid and strigolactones offer an exciting gateway for understanding their multiple roles in plant physiological processes.At the molecular level, phytohormonal crosstalks can be antagonistic or synergistic or additive in actions. Additionally, the signal transduction component(s) of one hormonal pathway may interplay with the signaling component(s) of other hormonal pathway(s). Together these and other research findings have revolutionized the concept of phytohormonal studies in plants. Importantly, genetic engineering now enables plant biologists to manipulate the signaling pathways of plant hormones for development of crop varieties with improved yield and stress tolerance.This book, written by internationally recognized scholars from various countries, represents the state-of-the-art understanding of plant hormones’ biology, signal transduction and implications. Aimed at a wide range of readers, including researchers, students, teachers and many others who have interests in this flourishing research field, every section is concluded with biotechnological strategies to modulate hormone contents or signal transduction pathways and crosstalk that enable us to develop crops in a sustainable manner. Given the important physiological implications of plant hormones in stressful environments, our book is finalized with chapters on phytohormonal crosstalks under abiotic and biotic stresses. 

Ziegler, J.; Abel S. Analysis of amino acids by HPLC/electrospray negative ion tandem mass spectrometry using 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) derivatization Amino Acids 46, 2799-2808, (2014) DOI: 10.1007/s00726-014-1837-5

A new method for the determination of amino acids is presented. It combines established methods for the derivatization of primary and secondary amino groups with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) with the subsequent amino acid specific detection of the derivatives by LC–ESI–MS/MS using multiple reaction monitoring (MRM). The derivatization proceeds within 5 min, and the resulting amino acid derivatives can be rapidly purified from matrix by solid-phase extraction (SPE) on HR-X resin and separated by reversed-phase HPLC. The Fmoc derivatives yield several amino acid specific fragment ions which opened the possibility to select amino acid specific MRM transitions. The method was applied to all 20 proteinogenic amino acids, and the quantification was performedusing l-norvaline as standard. A limit of detection as low as 1 fmol/μl with a linear range of up to 125 pmol/μl could be obtained. Intraday and interday precisions were lower than10 % relative standard deviations for most of the amino acids. Quantification usingl-norvaline as internal standard gave very similar results compared to the quantificationusing deuterated amino acid as internal standards. Using this protocol, it was possible to record the amino acid profiles of only a single root from Arabidopsis thaliana seedlings and to compare it with the amino acid profiles of 20 dissected root meristems (200 μm).

Kopycki, J.; Wieduwild, E.; Kohlschmidt, J.; Brandt, W.; Stepanova, A.N.; Alonso, J.M.; Pedras, M.S.; Abel, S.; Grubb, C.D. Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition Biochem J 450, 37-46, (2013) DOI: 10.1042/BJ20121403

Plant genomes encode numerous small molecule glycosyltransferases which modulate the solubility, activity, immunogenicity and/or reactivity of hormones, xenobiotics and natural products. The products of these enzymes can accumulate to very high concentrations, yet somehow avoid inhibiting their own biosynthesis. Glucosyltransferase UGT74B1 (UDP-glycosyltransferase 74B1) catalyses the penultimate step in the core biosynthetic pathway of glucosinolates, a group of natural products with important functions in plant defence against pests and pathogens. We found that mutation of the highly conserved Ser284 to leucine [wei9-1 (weak ethylene insensitive)] caused only very mild morphological and metabolic phenotypes, in dramatic contrast with knockout mutants, indicating that steady state glucosinolate levels are actively regulated even in unchallenged plants. Analysis of the effects of the mutation via a structural modelling approach indicated that the affected serine interacts directly with UDP-glucose, but also predicted alterations in acceptor substrate affinity and the kcat value, sparking an interest in the kinetic behaviour of the wild-type enzyme. Initial velocity and inhibition studies revealed that UGT74B1 is not inhibited by its glycoside product. Together with the effects of the missense mutation, these findings are most consistent with a partial rapid equilibrium ordered mechanism. This model explains the lack of product inhibition observed both in vitro and in vivo, illustrating a general mechanism whereby enzymes can continue to function even at very high product/precursor ratios.
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