Effect of nitric oxide on gene transcription – S-nitrosylation of nuclear proteins

Nitric oxide (NO) plays an important role in many different physiological processes in plants. It mainly acts by post-translationally modifying proteins. Modification of cysteine residues termed as S-nitrosylation is believed to be the most important mechanism for transduction of bioactivity of NO. The first proteins found to be nitrosylated were mainly of cytoplasmic origin or isolated from mitochondria and peroxisomes. Interestingly, it was shown that redox-sensitive transcription factors are also nitrosylated and that NO influences the redox-dependent nuclear transport of some proteins. This implies that NO plays a role in regulating transcription and/or general nuclear metabolism which is a fascinating new aspect of NO signaling in plants. In this review, we will discuss the impact of S-nitrosylation on nuclear plant proteins with a focus on transcriptional regulation, describe the function of this modification and draw also comparisons to the animal system in which S-nitrosylation of nuclear proteins is a well characterized concept

Deciphering the S-Nitrosylome of Arabipdosis thaliana during the defense response

Comunicaciones a congreso

Proteomic identification of s-nitrosylated proteins in arabidopsis thaliana in response to pathogen infection

Comunicaciones a congreso

Elimination Distance to Bounded Degree on Planar Graphs

We study the graph parameter elimination distance to bounded degree, which was introduced by Bulian and Dawar in their study of the parameterized complexity of the graph isomorphism problem. We prove that the problem is fixed-parameter tractable on planar graphs, that is, there exists an algorithm that given a planar graph G and integers d and k decides in time f(k,d)? n^c for a computable function f and constant c whether the elimination distance of G to the class of degree d graphs is at most k

Antioxidant Systems are Regulated by Nitric Oxide-Mediated Post-translational Modifications (NO-PTMs)

Nitric oxide (NO) is a biological messenger that orchestrates a plethora of plant functions, mainly through post-translational modifications (PTMs) such as S-nitrosylation or tyrosine nitration. In plants, hundreds of proteins have been identified as potential targets of these NO-PTMs under physiological and stress conditions indicating the relevance of NO in plant-signaling mechanisms. Among these NO protein targets, there are different antioxidant enzymes involved in the control of reactive oxygen species (ROS), such as H2O2, which is also a signal molecule. This highlights the close relationship between ROS/NO signaling pathways. The major plant antioxidant enzymes, including catalase, superoxide dismutases (SODs) peroxiredoxins (Prx) and all the enzymatic components of the ascorbate-glutathione (Asa-GSH) cycle, have been shown to be modulated to different degrees by NO-PTMs. This mini-review will update the recent knowledge concerning the interaction of NO with these antioxidant enzymes, with a special focus on the components of the Asa-GSH cycle and their physiological relevance.JB-M would like to thank the Ministry of Science and Innovation for funding the Ph.D. fellowship (F.P.U.). This study was supported by an ERDF grant co-financed by the Ministry of Economy and Competitiveness (project BIO2012-33904), Junta de Andalucía (P10-AGR-6038 and groups BIO286 and BIO192) and RECUPERA2020 in Spain.Peer reviewedPeer Reviewe

Total synthesis and absolute configuration assignment of MRSA active garcinol and isogarcinol

A short total synthesis of (±)-garcinol and (±)-isogarcinol, two endo-type B PPAPs with reported activity against methiciline resistant Staphylococcus aureus (MRSA), is presented. The separation of framework-constructing from framework-decorating steps and the application of two highly regio- and stereoselective Pd-catalysed allylations, that is, the Pd-catalysed decarboxylative Tsuji-Trost allylation and the diastereoselective Pd-catalysed allyl-allyl cross-coupling, are key elements that allowed the total synthesis to be accomplished within 13 steps starting from acetylacetone. After separation of the enantiomers the absolute configurations of the four natural products (i.e., (-)-garcinol, (+)-guttiferone E (i.e., ent-garcinol), (-)-isogarcinol, and (+)-isoxanthochymol (i.e., ent-isogarcinol)) were assigned based on ECD spectroscopy.Fil: Socolsky, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Instituto de Quimica del Noroeste; Argentina. Universidad Nacional de Tucumán; ArgentinaFil: Plietker, Bernd . Universität Stuttgart. Institut für Organische Chemie; Alemani

Elimination distance to bounded degree on planar graphs

We study the graph parameter elimination distance to bounded degree, which was introduced by Bulian and Dawar in their study of the parameterized complexity of the graph isomorphism problem. We prove that the problem is fixed-parameter tractable on planar graphs, that is, there exists an algorithm that given a planar graph $G$ and integers $d$ and $k$ decides in time $f(k,d)\cdot n^c$ for a computable function~$f$ and constant $c$ whether the elimination distance of $G$ to the class of degree $d$ graphs is at most $k$

Double Coverage with Machine-Learned Advice

We study the fundamental online k-server problem in a learning-augmented setting. While in the traditional online model, an algorithm has no information about the request sequence, we assume that there is given some advice (e.g. machine-learned predictions) on an algorithm's decision. There is, however, no guarantee on the quality of the prediction and it might be far from being correct. Our main result is a learning-augmented variation of the well-known Double Coverage algorithm for k-server on the line (Chrobak et al., SIDMA 1991) in which we integrate predictions as well as our trust into their quality. We give an error-dependent competitive ratio, which is a function of a user-defined confidence parameter, and which interpolates smoothly between an optimal consistency, the performance in case that all predictions are correct, and the best-possible robustness regardless of the prediction quality. When given good predictions, we improve upon known lower bounds for online algorithms without advice. We further show that our algorithm achieves for any k an almost optimal consistency-robustness tradeoff, within a class of deterministic algorithms respecting local and memoryless properties. Our algorithm outperforms a previously proposed (more general) learning-augmented algorithm. It is remarkable that the previous algorithm crucially exploits memory, whereas our algorithm is memoryless. Finally, we demonstrate in experiments the practicability and the superior performance of our algorithm on real-world data.Comment: Accepted at ITCS 202

Speed-Oblivious Online Scheduling: Knowing (Precise) Speeds is not Necessary

We consider online scheduling on unrelated (heterogeneous) machines in a speed-oblivious setting, where an algorithm is unaware of the exact job-dependent processing speeds. We show strong impossibility results for clairvoyant and non-clairvoyant algorithms and overcome them in models inspired by practical settings: (i) we provide competitive learning-augmented algorithms, assuming that (possibly erroneous) predictions on the speeds are given, and (ii) we provide competitive algorithms for the speed-ordered model, where a single global order of machines according to their unknown job-dependent speeds is known. We prove strong theoretical guarantees and evaluate our findings on a representative heterogeneous multi-core processor. These seem to be the first empirical results for scheduling algorithms with predictions that are evaluated in a non-synthetic hardware environment.Comment: To appear at ICML 202

Molekulare, physiologische und biochemische Charakterisierung der Genfamilie für 4-Cumarat:Coenzym A Ligase aus Sojabohne (Glycine max L.)

Die 4-Cumarat:Coenzym A Ligase (4CL) ist ein Enzym des allgemeinen Phenylpropanstoffwechsels, das aktivierte Hydroxyzimtsäure-Ester zur Synthese spezifischer Phenylpropanoide bereitstellt. In vielen Pflanzen kommen strukturell und funktionell sehr ähnliche 4CL-Isoformen vor, weshalb diesem Enzym dort nur eine beschränkte regulatorische Funktion bei der Verteilung der unterschiedlich substituierten Zimtsäurederivate für nachfolgende Synthesen zugesprochen wird. Durch Isolierung der cDNA der von Knobloch und Hahlbrock (1975) partiell gereinigten Ligase 1 und der Vervollständigung der kodierenden Sequenz der Gm4CL4 konnte mit großer Wahrscheinlichkeit die Genfamilie der Sojabohne-4CLs komplettiert werden. Mit der cDNA der Gm4CL1 war außerdem erstmals eine 4CL-Sequenz verfügbar, die für eine Sinapinsäure-umsetzende 4CL kodiert. Zusammen mit den bereits beschriebenen 4CL-Isoenzymen 2 und 3 (Uhlmann und Ebel, 1993; Möllers, 1997) existieren in Sojabohne somit mindestens vier 4CL-Isoformen. Die unterschiedlichen Substratspezifitäten der rekombinanten Proteine, die Fähigkeit, die gesamte Gruppe der pflanzlichen Hxdroxyzimtsäuren zu aktivieren und die differentielle Synthese der Gm4CL-Isoformen nach Elicitor-Behandlung von Sojabohnezellkulturen bzw. Infektion von Sojabohnekeimlingen weisen auf eine bedeutende regulatorische Funktion der 4CL hinsichtlich der Bereitstellung unterschiedlich substituierter Zimtsäurederivate zur Synthese spezifische Phenylpropanoide in Sojabohne hin. Dabei scheinen Gm4CL1 und Gm4CL2 vor allem an der Synthese von Phenylpropanoiden beteiligt zu sein, die für Wachstum und Entwicklung der Pflanzen benötigt werden, während Gm4CL3 und Gm4CL4 aktivierte Zimtsäuren bereitstellen, die aufgrund von Umweltveränderungen benötigt werden. Die 4CL wird mit Acyl-CoA Ligasen, Peptidsynthetasen und Luciferase zur Familie der AMP-bindenden Proteine zusammengefaßt. Diesen Enzymen ist nicht nur der Mechanismus der AMP-Aktivierung gemeinsam, sondern sie besitzen auch Ähnlichkeiten in ihren Proteinstrukturen. Durch Bildung von Hybridenzymen zwischen Gm4CL1 und Gm4CL3 konnte der zentrale Sequenzbereich der 4CL als Substratspezifität-determinierende Region ermittelt werden. Mit Hilfe der Informationen, die von der Kristallstruktur der Phenylalaninaktivierenden Untereinheit der Gramicidin-S-Synthetase gewonnen wurden, konnten vier mögliche Substratbindemotive der 4CL identifiziert werden. Innerhalb eines dieser Motive unterscheidet sich die Gm4CL1 von allen anderen bisher klonierten 4CLs durch den Verlust eines Aminosäurerestes, wodurch die Gm4CL1 in der Lage ist, hochsubstituierte Zimsäurederivate zu aktivieren. Wird der entsprechende Aminosäurerest der Gm4CL2 (Gm4CL2dV345) und Gm4CL3 (Gm4CL3dV367) entfernt, können beide Deletionsmutanten Sinapinsäure umsetzen. Außerdem ist Gm4CL3dV367 in der Lage, 3,4-Dimethoxyzimtsäure zu aktivieren und zeigt eine deutlich erhöhte Affinität gegenüber Ferulasäure. Durch das Entfernen einer einzigen Aminosäure können somit hochsubstituierte Zimtsäurederivate umgesetzt werden. Die Möglichkeit, die Substratspezifität dieses zentralen Enzymes des Phenylpropanstoffwechsels zu modifizieren, eröffnet die Herstellung transgener Pflanzen mit gewünschtem Phenylpropanoid-Profil