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Die Arbeitsgruppe Proteomanalytik verbindet modernste Proteom-Wissenschaft mit der Pflanzenforschung. Es ist unser Forschungsgebiet, die dynamische Umstrukturierung des Proteoms, d. h. die Proteinabundanz, sub-zelluläre Lokalisierung, posttranslationale Modifikation und Proteininteraktion in diversen biologischen Szenarien quantitativ zu erfassen. Zu diesem Zweck bedient sich die Arbeitsgruppe der ultra-performance Flüssigkeitschromatographie gekoppelt mit der hochauflösenden Massenspektrometrie.

Abb.1 und 2. Moderne Massenspektrometrie zur Peptid- und Proteinmessung.
Abb.1 und 2. Moderne Massenspektrometrie zur Peptid- und Proteinmessung.

Kürzlich haben wir eine pflanzenspezifische Deep-Proteomics Strategie etabliert und optimiert. Diese macht es möglich zwischen 6,000 und 9,000 Proteine aus einer Pflanzengewebeprobe zu quantifizieren. Sie werden zusammen mit Metabolomics und gerichteter Proteomanalyse angewandt um eine Rolle des Pflanzenhormones Auxin/IAA in der Arabidopsis thaliana Immunantwort näher zu beleuchten. Des Weiteren werden verschieden Gewebe im Lauf des Pflanzenentwicklungszyklus gemessen. Es wurden zum jetzigen Zeitpunkt Proteinexpressionsdaten von fast 16,000 open reading frames (60% des proteinkodierenden Arabidopsis Genoms) gesammelt. Diese werden verwendet um proteomweite, globale und lokale korrelierte Proteinabundanz zu erforschen.

Abb. 3. Breite massenspektrometrische Abdeckung des Arabidopsis thaliana Proteoms.
Abb. 3. Breite massenspektrometrische Abdeckung des Arabidopsis thaliana Proteoms.

Gerichtete Proteomanalytik ist seit langem ein Pendant zu der Discovery-Proteomics in unserer Arbeitsgruppe. Diese wurde vor allem durch akkurate Messung der Peptidfragmentionenmassen mittels des QExactive Plus Massenspektrometers vorangetrieben. Die akkuraten Messungen ermöglichen die Peptididentifizierung und Kartierung der exakten Position posttranslationaler Modifikationen (PTM) mit geringer Fehlerwahrscheinlichkeit. PTM sind für die Proteinfunktion gleichbedeutend wie die Translation der Polypeptidkette selbst. Es werden eine Vielzahl Studien zur quantitativen Messung und Lokalisierung verschiedener PTM durchgeführt, mit einem wachsenden Interesse an Histomodifizerungen und Epigenetik.

Somit erforscht die Arbeitsgruppe die zentralen Fragenstellungen des IPB aus der Perspektive der Veränderungen der zellulären Proteine als Ganzes.




  • Orbitrap Velos Pro (Thermo Scientific)
  • QExactive Plus (Thermo Scientific)



  • EASY-nLC II (Thermo Scientific)
  • EASY-nLC 1000 (Thermo Scientific)
  • Ultimate 3000 (Thermo Scientific)



  • Mascot v.2.5
  • Mascot Distiller
  • Proteome Discoverer v.1.4
  • Progenesis QIP
  • Scaffold 4/ Scaffold PTM 2 Image Quant TL
  • Skyline
  • MaxQuant
  • Perseus
  • MapMan

Das Team

Dr. Wolfgang Hoehenwarter

Abukhalaf, Mohammad Doktorand
Herr, Tobias Wissenschaftliche Hilfskraft
Proksch, Carsten Technischer Mitarbeiter
Thieme, Domenika Technische Mitarbeiterin

Publikationen nach Tag: Proteomics

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Chen, Y.; Hoehenwarter, W. Rapid and reproducible phosphopeptide enrichment by tandem metal oxide affinity chromatography: application to boron deficiency induced phosphoproteomics Plant J 98, 370-384, (2019) DOI: 10.1111/tpj.14215

Mass spectrometry has been instrumental in enabling the study of molecular signaling on a cellular scale by way of site‐specific quantification of protein post‐translational modifications, in particular phosphorylation. Here we describe an updated tandem metal oxide affinity chromatography (MOAC) combined phosphoprotein/phosphopeptide enrichment strategy, a scalable phosphoproteomics approach that allows rapid identification of thousands of phosphopeptides in plant materials. We implemented modifications to several steps of the original tandem MOAC procedure to increase the amount of quantified phosphopeptides and hence site‐specific phosphorylation of proteins in a sample beginning with the less amounts of tissue and a substantially smaller amount of extracted protein. We applied this technology to generate time‐resolved maps of boron signaling in Arabidopsis roots. We show that the successive enrichment of phosphoproteins in a first and phosphopeptide extraction in a second step using our optimized procedure strongly enriched the root phosphoproteome. Our results reveal that boron deficiency affects over 20% of the measured root phosphoproteome and that many phosphorylation sites with known biological function, and an even larger number of previously undescribed sites, are modified during the time course of boron deficiency. We identify transcription factors as key regulators of hormone signaling pathways that modulate gene expression in boron deprived plants. Furthermore, our phosphorylation kinetics data demonstrate that mitogen‐activated protein kinase (MAPK) cascades mediate polarized transport of boron in Arabidopsis roots. Taken together, we establish and validate a robust approach for proteome‐wide phosphorylation analysis in plant biology research.

Soboleva, A.; Mavropulo-Stolyarenko, G.; Karonova, T.; Thieme, D.; Hoehenwarter, W.; Ihling, C.; Stefanov, V.; Grishina, T.; Frolov, A. Multiple Glycation Sites in Blood Plasma Proteins as an Integrated Biomarker of Type 2 Diabetes Mellitus Int J Mol Sci 20, 2329, (2019) DOI: 10.3390/ijms20092329

Type 2 diabetes mellitus (T2DM) is one of the most widely spread metabolic diseases. Because of its asymptomatic onset and slow development, early diagnosis and adequate glycaemic control are the prerequisites for successful T2DM therapy. In this context, individual amino acid residues might be sensitive indicators of alterations in blood glycation levels. Moreover, due to a large variation in the half-life times of plasma proteins, a generalized biomarker, based on multiple glycation sites, might provide comprehensive control of the glycemic status across any desired time span. Therefore, here, we address the patterns of glycation sites in highly-abundant blood plasma proteins of T2DM patients and corresponding age- and gender-matched controls by comprehensive liquid chromatography-mass spectrometry (LC-MS). The analysis revealed 42 lysyl residues, significantly upregulated under hyperglycemic conditions. Thereby, for 32 glycation sites, biomarker behavior was demonstrated here for the first time. The differentially glycated lysines represented nine plasma proteins with half-lives from 2 to 21 days, giving access to an integrated biomarker based on multiple protein-specific Amadori peptides. The validation of this biomarker relied on linear discriminant analysis (LDA) with random sub-sampling of the training set and leave-one-out cross-validation (LOOCV), which resulted in an accuracy, specificity, and sensitivity of 92%, 100%, and 85%, respectively.

Hedtke, T.; Schräder, C. U.; Heinz, A.; Hoehenwarter, W.; Brinckmann, J.; Groth, T.; Schmelzer, C. E. H. A comprehensive map of human elastin cross‐linking during elastogenesis FEBS J 286, 3594-3610, (2019) DOI: 10.1111/febs.14929

Elastin is an essential structural protein in the extracellular matrix of vertebrates. It is the core component of elastic fibers, which enable connective tissues such as those of the skin, lungs or blood vessels to stretch and recoil. This function is provided by elastin's exceptional properties, which mainly derive from a unique covalent cross‐linking between hydrophilic lysine‐rich motifs of units of the monomeric precursor tropoelastin. To date, elastin's cross‐linking is poorly investigated. Here, we purified elastin from human tissue and cleaved it into soluble peptides using proteases with different specificities. We then analyzed elastin's molecular structure by identifying unmodified residues, post‐translational modifications and cross‐linked peptides by high‐resolution mass spectrometry and amino acid analysis. The data revealed the presence of multiple isoforms in parallel and a complex and heterogeneous molecular interconnection. We discovered that the same lysine residues in different monomers were simultaneously involved in various cross‐link types or remained unmodified. Furthermore, both types of cross‐linking domains, Lys‐Pro and Lys‐Ala domains, participate not only in bifunctional inter‐ but also in intra‐domain cross‐links. We elucidated the sequences of several desmosine‐containing peptides and the contribution of distinct domains such as 6, 14 and 25. In contrast to earlier assumptions proposing that desmosine cross‐links are formed solely between two domains, we elucidated the structure of a peptide that proves a desmosine formation with participation of three Lys‐Ala domains. In summary, these results provide new and detailed insights into the cross‐linking process, which takes place within and between human tropoelastin units in a stochastic manner.

Mora Huertas, A. C.; Schmelzer, C. E. H.; Luise, C.; Sippl, W.; Pietzsch, M.; Hoehenwarter, W.; Heinz, A. Degradation of tropoelastin and skin elastin by neprilysin Biochimie 146, 73-78, (2018) DOI: 10.1016/j.biochi.2017.11.018

Neprilysin is also known as skin fibroblast-derived elastase, and its up-regulation during aging is associated with impairments of the elastic fiber network, loss of skin elasticity and wrinkle formation. However, information on its elastase activity is still limited. The aim of this study was to investigate the degradation of fibrillar skin elastin by neprilysin and the influence of the donor's age on the degradation process using mass spectrometry and bioinformatics approaches. The results showed that cleavage by neprilysin is dependent on previous damage of elastin. While neprilysin does not cleave young and intact skin elastin well, it degrades elastin fibers from older donors, which may further promote aging processes. With regards to the cleavage behavior of neprilysin, a strong preference for Gly at P1 was found, while Gly, Ala and Val were well accepted at P1′ upon cleavage of tropoelastin and skin elastin. The results of the study indicate that the progressive release of bioactive elastin peptides by neprilysin upon skin aging may enhance local tissue damage and accelerate extracellular matrix aging processes.

Kowarschik, K.; Hoehenwarter, W.; Marillonnet, S.; Trujillo, M. UbiGate: a synthetic biology toolbox to analyse ubiquitination. New Phytol. 217, 1749-1763, (2018) DOI: 10.1111/nph.14900

   Ubiquitination is mediated by an enzymatic cascade that results in the modification of substrate proteins, redefining their fate. This post-translational modification is involved in most cellular processes, yet its analysis faces manifold obstacles due to its complex and ubiquitous nature. Reconstitution of the ubiquitination cascade in bacterial systems circumvents several of these problems and was shown to faithfully recapitulate the process.    Here, we present UbiGate − a synthetic biology toolbox, together with an inducible bacterial expression system – to enable the straightforward reconstitution of the ubiquitination cascades of different organisms in Escherichia coli by ‘Golden Gate’ cloning.    This inclusive toolbox uses a hierarchical modular cloning system to assemble complex DNA molecules encoding the multiple genetic elements of the ubiquitination cascade in a predefined order, to generate polycistronic operons for expression.    We demonstrate the efficiency of UbiGate in generating a variety of expression elements to reconstitute autoubiquitination by different E3 ligases and the modification of their substrates, as well as its usefulness for dissecting the process in a time- and cost-effective manner.
Publikationen in Druck

Teh, O.-K.; Lee, C.-W.; Ditengou, F. A.; Klecker, T.; Furlan, G.; Zietz, M.; Hause, G.; Eschen-Lippold, L.; Hoehenwarter, W.; Lee, J.; Ott, T.; Trujillo, M. Phosphorylation of the exocyst subunit Exo70B2 contributes to the regulation of its function BioRxiv (2018) DOI: 10.1101/266171

The exocyst is a conserved hetero-octameric complex mediating early tethering during exocytosis. Its Exo70 subunit plays a critical role as a spatiotemporal regulator by mediating numerous protein and lipid interactions. However, a molecular understanding of the exocyst function remains challenging. We show that Exo70B2 locates to dynamic foci at the plasma membrane and transits through a BFA-sensitive compartment, reflecting its canonical function in secretion. However, treatment with the salicylic acid (SA) defence hormone analogue Benzothiadiazole (BTH), or the immunogenic peptide flg22, induced Exo70B2 transport into the vacuole. We uncovered two ATG8-interacting motifs (AIMs) located in the C-terminal domain (C-domain) of Exo70B2 that mediate its recruitment into the vacuole. Moreover, we also show that Exo70B2 is phosphorylated near the AIMs and mimicking phosphorylation enhanced ATG8 interaction. Finally, Exo70B2 phosphonull lines were hypersensitive to BTH and more resistant to avirulent bacteria which induce SA production. Our results suggests a molecular mechanism in which phosphorylation of Exo70B2 by MPK3 functions in a feed-back system linking cellular signalling to the secretory pathway.

Schräder, C. U.; Heinz, A.; Majovsky, P.; Karaman Mayack, B.; Brinckmann, J.; Sippl, W.; Schmelzer, C. E. H. Elastin is heterogeneously cross-linked J Biol Chem 293, 15107-15119, (2018) DOI: 10.1074/jbc.RA118.004322

Elastin is an essential vertebrate protein responsible for the elasticity of force-bearing tissues such as those of the lungs, blood vessels, and skin. One of the key features required for the exceptional properties of this durable biopolymer is the extensive covalent cross-linking between domains of its monomer molecule tropoelastin. To date, elastin’s exact molecular assembly and mechanical properties are poorly understood. Here, using bovine elastin, we investigated the different types of cross-links in mature elastin to gain insight into its structure. We purified and proteolytically cleaved elastin from a single tissue sample into soluble cross-linked and non-cross-linked peptides that we studied by high-resolution MS. This analysis enabled the elucidation of cross-links and other elastin modifications. We found that the lysine residues within the tropoelastin sequence were simultaneously unmodified and involved in various types of cross-links with different other domains. The Lys-Pro domains were almost exclusively linked via lysinonorleucine, whereas Lys-Ala domains were found to be cross-linked via lysinonorleucine, allysine aldol, and desmosine. Unexpectedly, we identified a high number of intramolecular cross-links between lysine residues in close proximity. In summary, we show on the molecular level that elastin formation involves random cross-linking of tropoelastin monomers resulting in an unordered network, an unexpected finding compared with previous assumptions of an overall beaded structure.

Mamontova, T.; Lukasheva, E.; Mavropolo-Stolyarenko, G.; Proksch, C.; Bilova, T.; Kim, A.; Babakov, V.; Grishina, T.; Hoehenwarter, W.; Medvedev, S.; Smolikova, G.; Frolov, A. Proteome Map of Pea (Pisum sativum L.) Embryos Containing Different Amounts of Residual Chlorophylls Int J Mol Sci 19, 4066, (2018) DOI: 10.3390/ijms19124066

Due to low culturing costs and high seed protein contents, legumes represent the main global source of food protein. Pea (Pisum sativum L.) is one of the major legume crops, impacting both animal feed and human nutrition. Therefore, the quality of pea seeds needs to be ensured in the context of sustainable crop production and nutritional efficiency. Apparently, changes in seed protein patterns might directly affect both of these aspects. Thus, here, we address the pea seed proteome in detail and provide, to the best of our knowledge, the most comprehensive annotation of the functions and intracellular localization of pea seed proteins. To address possible intercultivar differences, we compared seed proteomes of yellow- and green-seeded pea cultivars in a comprehensive case study. The analysis revealed totally 1938 and 1989 nonredundant proteins, respectively. Only 35 and 44 proteins, respectively, could be additionally identified after protamine sulfate precipitation (PSP), potentially indicating the high efficiency of our experimental workflow. Totally 981 protein groups were assigned to 34 functional classes, which were to a large extent differentially represented in yellow and green seeds. Closer analysis of these differences by processing of the data in KEGG and String databases revealed their possible relation to a higher metabolic status and reduced longevity of green seeds.

Frolov, A.; Didio, A.; Ihling, C.; Chantzeva, V.; Grishina, T.; Hoehenwarter, W.; Sinz, A.; Smolikova, G.; Bilova, T.; Medvedev, S. The effect of simulated microgravity on the Brassica napus seedling proteome. Funct Plant Biol 45, 440-452, (2018) DOI: 10.1071/FP16378

The magnitude and the direction of the gravitational field represent an important environmental factor affecting plant development. In this context, the absence or frequent alterations of the gravity field (i.e. microgravity conditions) might compromise extraterrestrial agriculture and hence space inhabitation by humans. To overcome the deleterious effects of microgravity, a complete understanding of the underlying changes on the macromolecular level is necessary. However, although microgravity-related changes in gene expression are well characterised on the transcriptome level, proteomic data are limited. Moreover, information about the microgravity-induced changes in the seedling proteome during seed germination and the first steps of seedling development is completely missing. One of the valuable tools to assess gravity-related issues is 3D clinorotation (i.e. rotation in two axes). Therefore, here we address the effects of microgravity, simulated by a two-axial clinostat, on the proteome of 24- and 48-h-old seedlings of oilseed rape (Brassica napus L.). The liquid chromatography-MS-based proteomic analysis and database search revealed 95 up- and 38 downregulated proteins in the tryptic digests obtained from the seedlings subjected to simulated microgravity, with 42 and 52 annotations detected as being unique for 24- and 48-h treatment times, respectively. The polypeptides involved in protein metabolism, transport and signalling were annotated as the functional groups most strongly affected by 3-D clinorotation. 

Frolov, A.; Mamontova, T.; Ihling, C.; Lukasheva, E.; Bankin, M.; Chantseva, V.; Vikhnina, M.; Soboleva, A.; Shumilina, J.; Mavropolo-Stolyarenko, G.; Grishina, T.; Osmolovskaya, N.; Zhukov, V.; Hoehenwarter, W.; Sinz, A.; Tikhononovich, I.; Wessjohann, L.; Bilova, T.; Smolikova, G.; Medvedev, S. Mining seed proteome: from protein dynamics to modification profiles Biol Commun 63, 43-58, (2018) DOI: 10.21638/spbu03.2018.106

In the modern world, crop plants represent a major source of daily consumed foods. Among them, cereals and legumes — i.e. the crops accumulating oils, carbohydrates and proteins in their seeds — dominate in European agriculture, tremendously impacting global protein consumption and biodiesel production. Therefore, the seeds of crop plants attract the special attention of biologists, biochemists, nutritional physiologists and food chemists. Seed development and germination, as well as age- and stress-related changes in their viability and nutritional properties, can be addressed by a variety of physiological and biochemical methods. In this context, the methods of functional genomics can be applied to address characteristic changes in seed metabolism, which can give access to stress-resistant genotypes. Among these methods, proteomics is one of the most effective tools, allowing mining metabolism changes on the protein level. Here we discuss the main methodological approaches of seed proteomics in the context of physiological changes related to environmental stress and ageing. We provide a comprehensive comparison of gel- and chromatographybased approaches with a special emphasis on advantages and disadvantages of both strategies in characterization of the seed proteome.

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