A5081126095- PARP inhibition in cancer therapy
- Biosimilars and Bioanalytical Methods
- Photosynthetic Processes and Mechanisms
- Advanced Proteomics Techniques and Applications
- Health Systems, Economic Evaluations, Quality of Life
- Photoreceptor and optogenetics research
- Glycosylation and Glycoproteins Research
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Algal biology and biofuel production
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Metabolomics and Mass Spectrometry Studies
- Protein Structure and Dynamics
- Hemoglobin structure and function
- Carbohydrate Chemistry and Synthesis
- Light effects on plants
- Enzyme Structure and Function
- Spectroscopy and Quantum Chemical Studies
- Mitochondrial Function and Pathology
- Business Process Modeling and Analysis
- Semantic Web and Ontologies
- Plant Stress Responses and Tolerance
- Antioxidant Activity and Oxidative Stress
Heidelberg University
2020-2025
University of Münster
2008-2017
Institute of Plant Biology and Biotechnology
2014
City College of New York
2008
Centre National de la Recherche Scientifique
2002-2007
University of Freiburg
2002-2007
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2002-2007
CEA Paris-Saclay
2002-2005
Max Planck Institute of Biophysics
2005
Photo‐generated reactive oxygen species in herbicide‐treated photosystem II were investigated by spin‐trapping. While the production of OH and O 2 − was herbicide‐independent, 1 with a phenolic twice that urea herbicide. This correlates reported influence these herbicides on redox properties semiquinone Q A fits hypothesis is produced charge recombination reactions are stimulated herbicide binding modulated nature When bound, at level P + Pheo thermodynamically favoured forming chlorophyll...
Cyclic photosynthetic electron flow (CEF) is crucial to photosynthesis because it participates in the control of chloroplast energy and redox metabolism, particularly induced under adverse environmental conditions. Here we report that down-regulation localized Ca 2+ sensor (CAS) protein by an RNAi approach Chlamydomonas reinhardtii results strong inhibition CEF anoxia. Importantly, this rescued increase extracellular concentration, inferring -dependent. Furthermore, identified a protein,...
Chlamydomonas reinhardtii is a green unicellular eukaryotic model organism for studying relevant biological and biotechnological questions. The availability of genomic resources the growing interest in C. as an emerging cell factory industrial production biopharmaceuticals require in-depth analysis protein N-glycosylation this organism. Accordingly, we used comprehensive approach including genomic, glycomic, glycoproteomic techniques to unravel pathway reinhardtii. Using...
Abstract Summary: pymzML is an extension to Python that offers (i) easy access mass spectrometry (MS) data allows the rapid development of tools, (ii) a very fast parser for mzML data, standard format in MS and (iii) set functions compare or handle spectra. Availability implementation: requires Python2.6.5+ fully compatible with Python3. The module freely available on http://pymzml.github.com pypi, published under LGPL license no additional modules be installed. Contact: christian@fufezan.net
Abstract In plants and algae, the serine/threonine kinase STN7/STT7, orthologous protein kinases in Chlamydomonas reinhardtii Arabidopsis (Arabidopsis thaliana), respectively, is an important regulator acclimation to changing light environments. this work, we assessed STT7-dependent phosphorylation under high C. reinhardtii, known fully induce expression of LIGHT-HARVESTING COMPLEX STRESS-RELATED PROTEIN3 (LHCSR3) a nonphotochemical quenching mechanism, relationship anoxia where activity...
In the new release of pymzML (v2.0), we have optimized speed this established tool for mass spectrometry data analysis to adapt increasing amounts in spectrometry. Thus, integrated faster libraries numerical calculations, improved retrieving algorithms and source code. Importantly, rapidly growing file sizes, developed a generalizable compression scheme very fast random access applied concept mzML files retrieve spectral data.pymzML performs at par with C programs when it comes processing...
Chemical modifications of transfer RNA (tRNA) molecules are evolutionarily well conserved and critical for translation tRNA structure. Little is known how these nucleoside respond to physiological stress. Using mass spectrometry complementary methods, we defined modification levels in six yeast species response elevated temperatures. We show that 2-thiolation uridine at position 34 (s 2 U ) impaired temperatures exceeding 30°C the commonly used Saccharomyces cerevisiae laboratory strains...
Multiplexed quantitative proteomics enabled complex workflows to study the mechanisms by which small molecule drugs interact with proteome such as thermal profiling (TPP) or multiplexed dynamics (mPDP). TPP measures changes in protein stability response drug treatment and thus informs on direct targets downstream regulation events, while mPDP approach enables discovery of regulated synthesis degradation events caused molecules other perturbations. The isobaric mass tags available for have...
Pseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation position 38/39 tRNAs. However, molecular mechanisms by which it recognizes its RNA targets achieves site specificity remain elusive. Here, we determine single-particle cryo-EM structures PUS3 apo form bound to three tRNAs, showing how symmetric homodimer tRNAs positions target uridine next active site. Structure-guided...
We report the characterization of effects A249S mutation located within binding pocket primary quinone electron acceptor, Q(A), in D2 subunit photosystem II Thermosynechococcus elongatus. This shifts redox potential Q(A) by approximately -60 mV. mutant provides an opportunity to test hypothesis, proposed earlier from herbicide-induced effects, that photoinhibition (light-induced damage photosynthetic apparatus) is modulated Q(A). Thus influence on was investigated vivo and vitro. Compared...
To investigate the functional importance of Proton Gradient Regulation5-Like1 (PGRL1) for photosynthetic performances in moss Physcomitrella patens, we generated a pgrl1 knockout mutant. Functional analysis revealed diminished nonphotochemical quenching (NPQ) as well decreased capacity cyclic electron flow (CEF) pgrl1. Under anoxia, where CEF is induced, quantitative proteomics evidenced severe down-regulation photosystems but up-regulation chloroplast NADH dehydrogenase complex,...
The scaffold protein Vac14 acts in a complex with the lipid kinase PIKfyve and its counteracting phosphatase FIG4, regulating interconversion of phosphatidylinositol-3-phosphate to phosphatidylinositol-3,5-bisphosphate. Dysfunctional mutants, deficiency one components, or inhibition enzymatic activity results formation large vacuoles cells. How these are generated which processes involved only poorly understood. Here we show that ectopic overexpression wild-type as well PIKfyve-binding...
Abstract Calcium (Ca 2+ ) and redox signalling play important roles in acclimation processes from archaea to eukaryotic organisms. Herein we characterized a unique protein Chlamydomonas reinhardtii that has the competence integrate Ca - redox-related signalling. This protein, designated as calredoxin (CRX), combines four -binding EF-hands thioredoxin (TRX) domain. A crystal structure of CRX, at 1.6 Å resolution, revealed an unusual calmodulin-fold EF-hands, which is functionally linked via...
The biosynthesis of multiple secondary metabolites in the phytopathogenic ascomycete Fusarium fujikuroi is strongly affected by nitrogen availability. Here, we present first genome-wide transcriptome and proteome analysis that compared wild type deletion mutants two major regulators AreA AreB. We show AreB acts not simply as an antagonist counteracting expression target genes suggested based on yeast model. Both GATA transcription factors affect a large diverse set common well specific...
Abstract While many aspects of archaeal cell biology remain relatively unexplored, systems approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount MS data generated often remains incompletely analyzed due to a lack sophisticated bioinformatic tools and field-specific biological expertise interpretation. Here we present initiation Archaeal Proteome Project (ArcPP), community-based effort comprehensively analyze...
Post-transcriptional chemical modifications of (t)RNA molecules are crucial in fundamental biological processes, such as translation. Despite their importance and accumulating evidence linking them to various human diseases, technical challenges have limited detection accurate quantification. Here, we present a sensitive capillary nanoflow liquid chromatography mass spectrometry (nLC-MS) pipeline for quantitative high-resolution analysis ribonucleoside from complex samples. We evaluated two...
A gene coding for water-soluble chlorophyll-binding protein (WSCP) from Brassica oleracea var. Botrys has been used to express the protein, extended by a hexahistidyl tag, in Escherichia coli. The refolded vitro study its pigment binding behavior. Recombinant WSCP was found bind two chlorophylls (Chls) per tetrameric complex but no carotenoids accordance with previous observations native [Satoh, H., Nakayama, K., Okada, M. (1998) J. Biol. Chem. 273, 30568−30575]. binds Chl a, b,...
Plants are able to deal with variable environmental conditions; when exposed strong illumination, they safely dissipate excess energy as heat and increase their capacity for scavenging reacting oxygen species. Both these protection mechanisms involve activation of the xanthophyll cycle, in which carotenoid violaxanthin is converted zeaxanthin by de-epoxidase, using ascorbate source reducing power. In this work, following determination three-dimensional structure de-epoxidase catalytic...
Iron is a crucial cofactor in numerous redox-active proteins operating bioenergetic pathways including respiration and photosynthesis. Cellular iron management essential to sustain sufficient energy production minimize oxidative stress. To produce for cell growth, the green alga Chlamydomonas reinhardtii possesses metabolic flexibility use light and/or carbon sources such as acetate. investigate interplay between iron-deficiency response growth requirements under distinct trophic conditions,...
Proteomics data integration has become a broad field with variety of programs offering innovative algorithms to analyze increasing amounts data. Unfortunately, this software diversity leads many problems as soon the is analyzed using more than one algorithm for same task. Although it was shown that combination multiple peptide identification yields robust results, only recently unified approaches are emerging; however, workflows that, example, aim optimize search parameters or employ...
The secondary quinone acceptor, QB, has been studied in photosystem II (PSII) isolated from Thermosynechococcus (T.) elongatus. Thermoluminescence indicated that QB was present this preparation. An EPR signal observed at low temperature g = 1.9 attributed to Fe2+QB- on the basis of characteristic period-of-two variations its intensity depending number laser flashes given 20 °C. When samples showing were illuminated 77 K, an 1.66 appeared with amplitude proportional signal. This is QA-Fe2+QB-...
Abstract Nonbonding interactions are essential for protein stability and maintenance of secondary structure. Their strength, however, is not always experimentally accessible. One example the collagen, which in part due to Buergi‐Duntiz or n → π* between peptide backbone atoms [DeRider et al ., J Am Chem Soc 2002;124:2497–2505]. Here, overall frequency proteins has been investigated. The analysis a nonredundant set structures showed that 45.1% all residues have conformation favoring...