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Proteome Analytics

The spatio-temporal remodeling of the proteome, the cellular complement of all proteoforms, is a primary phenotype determinant. As such we are interested in quantifying protein expression dynamics, i.e. the changing abundance, subcellular localization, post translational modification and interaction of proteins in various biological scenarios. It is our goal to gain an understanding of the intricate mechanisms of plant proteome biology.

Fig.1 and 2. Cutting edge mass spectrometry is used to measure peptides and proteins.
Fig.1 and 2. Cutting edge mass spectrometry is used to measure peptides and proteins.

Recently our research group has streamlined and optimized the discovery proteomics approach and adapted it to plants. This technology now allows us to routinely quantify from 6,000 to 9,000 proteins (protein groups) per tissue sample with at least one unique peptide and a peptide and protein FDR threshold of 1%.

A primary research interest of the group is the effects of phytohormones in biotic and abiotic stress adaption. We are applying the deep proteomics strategy in combination with metabolomics and targeted proteomics measurements to shed more light on the interplay of the canonical defense phytohormones salicylic acid, jasmonate and ethylene but also on the role of auxin in the hormone signal signature in reshaping the proteome to resist pathogen attack.

Deep proteomics measurements of various tissues throughout plant development led to date to the accumulation of mass spectrometric evidence of nearly 16,000 protein coding genes which is about 60% of Arabidopsis thaliana open reading frames. This extensive coverage of the Arabidopsis genome is being used to investigate proteome wide correlation of protein abundance in different tissues as well as correlated local protein expression of genes in smaller and larger neighborhoods.

Fig. 3. Deep coverage of the Arabidopsis thaliana proteome
Fig. 3. Deep coverage of the Arabidopsis thaliana proteome

Targeted proteomics approaches are also well established in the group as a complement to discovery proteomics. These were particularly advanced by accurate measurement of fragment ion masses with the QExactive Plus mass spectrometer. This allows interpretation of MS/MS spectra and assignment of PTMs to peptide primary structure with low error probability. Reversible, multi-site PTM has as much an impact on protein function as translation of the nascent polypeptide itself. Numerous directed and undirected proteomics studies that quantify site-specific protein PTM are being performed with a growing interest in histone modification and epigenetics.

Equipment and Instrumentation


Mass Spectrometry

  • 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

The Team

Dr. Wolfgang Hoehenwarter

Staff Member
Abukhalaf, Mohammad Master Student
Herr, Tobias Research Assistant
Proksch, Carsten Technician
Thieme, Domenika Technician

Publications by Tag: Proteomics

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Displaying results 1 to 10 of 42.


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.

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.


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. 

Schönberg, A., Rödiger, A., Mehwald, W., Galonska, J., Christ, G., Helm, S., Thieme, D., Majovsky, P., Hoehenwarter, W. & Baginsky, S. Identification of STN7/STN8 kinase targets reveals connections between electron transport, metabolism and gene expression.  Plant J 90, 1176–1186 , (2017) DOI: 10.1111/tpj.13536

The thylakoid-associated kinases STN7 and STN8 are involved in short- and long-term acclimation of photosynthetic electron transport to changing light conditions. Here we report the identification of STN7/STN8 in vivo targets that connect photosynthetic electron transport with metabolism and gene expression. Comparative phosphoproteomics with the stn7 and stn8 single and double mutants identified two proteases, one RNA-binding protein, a ribosomal protein, the large subunit of Rubisco and a ferredoxin-NADP reductase as targets for the thylakoid-associated kinases. Phosphorylation of three of the above proteins can be partially complemented by STN8 in the stn7 single mutant, albeit at lower efficiency, while phosphorylation of the remaining three proteins strictly depends on STN7. The properties of the STN7-dependent phosphorylation site are similar to those of phosphorylated light-harvesting complex proteins entailing glycine or another small hydrophobic amino acid in the −1 position. Our analysis uncovers the STN7/STN8 kinases as mediators between photosynthetic electron transport, its immediate downstream sinks and long-term adaptation processes affecting metabolite accumulation and gene expression.

Balcke, G. U., Bennewitz, S., Bergau, N., Athmer, B., Henning, A., Majovsky, P., Jiménez-Gómez, J. M., Hoehenwarter, W. & Tissier, A. Multi-Omics of tomato glandular trichomes reveals distinct features of central carbon metabolism supporting high productivity of specialized metabolites Plant Cell 29, 960-983, (2017) DOI: 10.1105/tpc.17.00060

Glandular trichomes are metabolic cell factories with the capacity to produce large quantities of secondary metabolites. Little is known about the connection between central carbon metabolism and metabolic productivity for secondary metabolites in glandular trichomes. To address this gap in our knowledge, we performed comparative metabolomics, transcriptomics, proteomics and 13C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession. Specific features of glandular trichomes that drive the formation of secondary metabolites could be identified. Tomato type VI trichomes are photosynthetic but acquire their carbon essentially from leaf sucrose. The energy and reducing power from photosynthesis are used to support the biosynthesis of secondary metabolites, while the comparatively reduced Calvin-Benson-Bassham cycle activity may be involved in recycling metabolic CO2. Glandular trichomes cope with oxidative stress by producing high levels of polyunsaturated fatty acids, oxylipins, and glutathione. Finally, distinct mechanisms are present in glandular trichomes to increase the supply of precursors for the isoprenoid pathways. Particularly, the citrate-malate shuttle supplies cytosolic acetyl CoA and plastidic glycolysis and malic enzyme support the formation of plastidic pyruvate. A model is proposed on how glandular trichomes achieve high metabolic productivity. 

Al Shweiki, M. H. D. R., Mönchgesang, S., Majovsky, P., Thieme, D., Trutschel, D. & Hoehenwarter, W. Assessment of Label-Free quantification in discovery proteomics and impact of technological factors and natural variability of protein abundance. J Proteome Res. 16 , 1410–1424, (2017) DOI: 10.1021/acs.jproteome.6b00645

We evaluated the state of label-free discovery proteomics focusing especially on technological contributions and contributions of naturally occurring differences in protein abundance to the intersample variability in protein abundance estimates in this highly peptide-centric technology. First, the performance of popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant, and Progenesis QIP, was benchmarked using their default parameters and some modified settings. Beyond this, the intersample variability in protein abundance estimates was decomposed into variability introduced by the entire technology itself and variable protein amounts inherent to individual plants of the Arabidopsis thaliana Col-0 accession. The technical component was considerably higher than the biological intersample variability, suggesting an effect on the degree and validity of reported biological changes in protein abundance. Surprisingly, the biological variability, protein abundance estimates, and protein fold changes were recorded differently by the software used to quantify the proteins, warranting caution in the comparison of discovery proteomics results. As expected, ∼99% of the proteome was invariant in the isogenic plants in the absence of environmental factors; however, few proteins showed substantial quantitative variability. This naturally occurring variation between individual organisms can have an impact on the causality of reported protein fold changes.


Strehmel, N., Hoehenwarter, W., Mönchgesang, S., Majovsky, P., Krüger, S., Scheel, D. & Lee, J. Stress-reated mitogen-activated protein kinases stimulate the accumulation of small molecules and proteins in Arabidopsis thaliana root exudates. Front Plant Sci 8 , 1292, (2017) DOI: 10.3389/fpls.2017.01292

A delicate balance in cellular signaling is required for plants to respond to microorganisms or to changes in their environment. Mitogen-activated protein kinase (MAPK) cascades are one of the signaling modules that mediate transduction of extracellular microbial signals into appropriate cellular responses. Here, we employ a transgenic system that simulates activation of two pathogen/stress-responsive MAPKs to study release of metabolites and proteins into root exudates. The premise is based on our previous proteomics study that suggests upregulation of secretory processes in this transgenic system. An advantage of this experimental set-up is the direct focus on MAPK-regulated processes without the confounding complications of other signaling pathways activated by exposure to microbes or microbial molecules. Using non-targeted metabolomics and proteomics studies, we show that MAPK activation can indeed drive the appearance of dipeptides, defense-related metabolites and proteins in root apoplastic fluid. However, the relative levels of other compounds in the exudates were decreased. This points to a bidirectional control of metabolite and protein release into the apoplast. The putative roles for some of the identified apoplastic metabolites and proteins are discussed with respect to possible antimicrobial/defense or allelopathic properties. Overall, our findings demonstrate that sustained activation of MAPKs alters the composition of apoplastic root metabolites and proteins, presumably to influence the plant-microbe interactions in the rhizosphere. The reported metabolomics and proteomics data are available via Metabolights (Identifier: MTBLS441) and ProteomeXchange (Identifier: PXD006328), respectively.

Hempel, F., Stenzel, I., Heilmann, M., Krishnamoorthy, P., Menzel, W., Golbik, R., Helm, S., Dobritzsch, D., Baginsky, S., Lee, J., Hoehenwarter, W. & Heilmann, I. MAPKs influence pollen tube growth by controlling the formation of Phosphatidylinositol 4,5-Bisphosphate in an apical plasma membrane domain.  Plant Cell 29, 3030-3050, (2017) DOI: 10.1105/tpc.17.00543

An apical plasma membrane domain enriched in the regulatory phospholipid phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] is critical for polar tip growth of pollen tubes. How the biosynthesis of PtdIns(4,5)P2 by phosphatidylinositol 4-phosphate 5-kinases (PI4P 5-kinases) is controlled by upstream signaling is currently unknown. The pollen-expressed PI4P 5-kinase PIP5K6 is required for clathrin-mediated endocytosis and polar tip growth in pollen tubes. Here, we identify PIP5K6 as a target of the pollen-expressed mitogen-activated protein kinase MPK6 and characterize the regulatory effects. Based on an untargeted mass spectrometry approach, phosphorylation of purified recombinant PIP5K6 by pollen tube extracts could be attributed to MPK6. Recombinant MPK6 phosphorylated residues T590 and T597 in the variable insert of the catalytic domain of PIP5K6, and this modification inhibited PIP5K6 activity in vitro. PIP5K6 interacted with MPK6 in yeast two-hybrid tests, immuno-pull-down assays, and by bimolecular fluorescence complementation at the apical plasma membrane of pollen tubes. In vivo, MPK6 expression resulted in reduced plasma membrane association of a fluorescent PtdIns(4,5)P2 reporter and decreased endocytosis without impairing membrane association of PIP5K6. Effects of PIP5K6 expression on pollen tube growth and cell morphology were attenuated by coexpression of MPK6 in a phosphosite-dependent manner. Our data indicate that MPK6 controls PtdIns(4,5)P2 production and membrane trafficking in pollen tubes, possibly contributing to directional growth.

Huck, N. V., Leissing, F., Majovsky, P., Buntru, M., Aretz, C., Flecken, M., Müller, J. P. J., Vogel, S., Schillberg, S., Hoehenwarter, W., Conrath, U. & Beckers, G. J. M. Combined 15N-labeling and tandemMOAC quantifies phosphorylation of MAP kinase substrates downstream of MKK7 in Arabidopsis. Front Plant Sci 8, 2050, (2017) DOI: 10.3389/fpls.2017.02050

Reversible protein phosphorylation is a widespread posttranslational modification that plays a key role in eukaryotic signal transduction. Due to the dynamics of protein abundance, low stoichiometry and transient nature of protein phosphorylation, the detection and accurate quantification of substrate phosphorylation by protein kinases remains a challenge in phosphoproteome research. Here, we combine tandem metal-oxide affinity chromatography (tandemMOAC) with stable isotope 15N metabolic labeling for the measurement and accurate quantification of low abundant, transiently phosphorylated peptides by mass spectrometry. Since tandemMOAC is not biased toward the enrichment of acidophilic, basophilic, or proline-directed kinase substrates, the method is applicable to identify targets of all these three types of protein kinases. The MKK7-MPK3/6 module, for example, is involved in the regulation of plant development and plant basal and systemic immune responses, but little is known about downstream cascade components. Using our here described phosphoproteomics approach we identified several MPK substrates downstream of the MKK7-MPK3/6 phosphorylation cascade in Arabidopsis. The identification and validation of dynamin-related protein 2 as a novel phosphorylation substrate of the MKK7-MPK3/6 module establishes a novel link between MPK signaling and clathrin-mediated vesicle trafficking.

Furlan, G., Nakagami, H., Eschen-Lippold, L., Jiang, X., Majovsky, P., Kowarschik, K., Hoehenwarter, W., Lee, J. & Trujillo, M. Changes in PUB22 ubiquitination modes triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 dampen the immune response Plant Cell 29, 726-745, (2017) DOI: 10.1105/tpc.16.00654

Crosstalk between post-translational modifications such as ubiquitination and phosphorylation play key roles in controlling the duration and intensity of signalling events to ensure cellular homeostasis. However, the molecular mechanisms underlying the regulation of negative feedback loops remain poorly understood. Here we uncover a pathway in Arabidopsis thaliana by which a negative feedback loop involving the E3 ubiquitin ligase PUB22 that dampens the immune response is triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 (MPK3), best known for its function in the activation of signalling. PUB22's stability is controlled by MPK3-mediated phosphorylation of residues localized in and adjacent to the E2 docking domain. We show that phosphorylation is critical for stabilization by inhibiting PUB22 oligomerization and thus autoubiquitination. The activity switch allows PUB22 to dampen the immune response. This regulatory mechanism also suggests that autoubiquitination, which is inherent to most single unit E3s in vitro, can function as a self-regulatory mechanism in vivo. 

This page was last modified on 23.07.2018.

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