Project Z2

Quantitative methods for the analysis of the spatial and temporal dynamic changes of the proteome during host-pathogen interaction

Based on the progress achieved in the area of mass spectrometry, proteomics, the large-scale study of proteins, has evolved into a powerful approach that enables quantification of several thousand proteins from a microorganism on a global scale. Proteomics is therefore one of the keystones of systems biology approaches which describe host-pathogen interactions. Project Z2 provides a sophisticated proteome analysis platform to specific A (Aspergillus) and C (Candida) projects of the CRC/TR FungiNet. The portfolio of proteome techniques includes 2D-gel electrophoresis and LC-MS/MS-based shotgun proteomic methods for identifying and quantifying the proteome of an organism on the level of peptides (“bottom-up” approach). Furthermore, we have established a serological proteome analysis method for the characterization of fungal protein antigens. In this funding period, our aim is to broaden the portfolio of proteomic methods. These include metabolic labeling, the investigation of different post-translational modifications (phosphorylation, acetylation, ubiquitination, protein thiol oxidation), absolute quantification of proteins based on quantifier peptides and subcellular fractionation (for example vesicles) to improve the dynamic range of proteome analyses. With MALDI MS Imaging (MSI) we are now able to analyze the spatial distribution of low molecular weight compounds like secondary metabolites, toxins and proteins in the interaction of the fungal pathogen and the host.

Methods for the proteomic analysis of host-fungal pathogen interactions.
Methods for the proteomic analysis of host-fungal pathogen interactions.
Principal Investigators
Publications
Author Year Title Journal Links
Rafiq M, Rivieccio F, Zimmermann AK, Visser C, Bruch A, Krüger T, González Rojas K, Kniemeyer O, Blango MG, Brakhage AA 2022 PLB-985 neutrophil-like cells as a model to study Aspergillus fumigatus pathogenesis. mSphere e0094021 PubMed
Brandt P, Gerwien F, Wagner L, Krüger T, Ramirez-Zavala B, Mirhakkak MH, Schäuble S, Kniemeyer O, Panagiotou G, Brakhage AA, Morschhäuser J, Vylkova S 2022 Candida albicans SR-Like Protein Kinases Regulate Different Cellular Processes: Sky1 Is Involved in Control of Ion Homeostasis, While Sky2 Is Important for Dipeptide Utilization. Frontiers Cellular Infection Microbiology doi:0.3389/fcimb.2022.850531 Front. Cell. Infect. Microbiol.
Niemiec MJ, Kapitan M, Himmel M, Döll K, Krüger T, Köllner TG, Auge I, Kage F, Alteri CJ, Mobley HLT, Monsen T, Linde S, Nietzsche S, Kniemeyer O, Brakhage AA, Jacobsen ID 2022 Augmented Enterocyte Damage During Candida albicans and Proteus mirabilis Coinfection. Front Cell Infect Microbiol. 12:866416 PubMed
Raguž L, Peng C, Rutaganira FUN, Krüger T, Stanisic A, Jautzus T, Kries H, Kniemeyer O, Brakhage AA, King N, Beemelmanns C 2022 Total Synthesis and Functional Evaluation of IORs, Sulfonolipid-based Inhibitors of Cell Differentiation in Salpingoeca rosetta Angew. Chem. Int. Ed. e202209105 Angew. Chem. Int. Ed.
Acosta España JD, Hassan MA, Hea-Reung P,  Schwartze VU, Schäuble S,  Krüger T,  Kniemeyer O, Brakhage AA, Voigt K 2022 Novel hydrophobic binding surface proteins are instrumental for phagocytosis of Lichtheimia corymbifera by macrophages. Medical Mycology 60 (1) :myac072P343 Medical Mycology
de Assis LJ, Silva LP, Bayram O, Dowling P, Kniemeyer O, Krüger T, Brakhage AA, Chen Y, Dong L, Tan K, Wong KH, Ries LNA, Goldman GH 2021 Carbon catabolite repression in filamentous fungi is regulated by phosphorylation of the transcription factor CreA. mBio 12: e03146-20 PubMed
Strømland Ø, Kallio JP, Pschibul A, Skoge RH, Harðardóttir HM, Sverkeli LJ, Heinekamp T, Kniemeyer O, Migaud M, Makarov MV, Gossmann TI, Brakhage AA, Ziegler M 2021 Discovery of fungal surface NADases predominantly present in pathogenic species. Nat Commun 12: 1631 PubMed
Lauruschkat CD, Page L, White PL, Etter S, Davies HE, Duckers J, Ebel F, Schnack E, Backx M, Dragan M, Schlegel N, Kniemeyer O, Brakhage AA, Einsele H, Loeffler J, Wurster S 2021 Development of a simple and robust whole blood assay with dual co-stimulation to quantify the release of T-cellular signature cytokines in response to Aspergillus fumigatus antigens. J Fungi 7: 462 MDPI
Page L, Wallstabe J, Lother J, Bauser M, Kniemeyer O, Strobel L, Voltersen V, Teutschbein J, Hortschansky P, Morton CO, Brakhage AA, Topp M, Einsele H, Wurster S, Loeffler J 2021 CcpA- and Shm2-pulsed myeloid dendritic cells induce T-cell activation and enhance the neutrophilic oxidative burst response to Aspergillus fumigatus. Front Immunol 12: 659752 PubMed
Mogavero S, Sauer FM, Brunke S, Allert S, Schulz D, Wisgott S, Jablonowski N, Elshafee O, Krüger T, Kniemeyer O, Brakhage AA, Naglik JR, Dolk E, Hube B 2021 Candidalysin delivery to the invasion pocket is critical for host epithelial damage induced by Candida albicans. Cell microbiol 23: e13378 PubMed
Wich M, Greim S, Ferreira-Gomes M, Krüger T, Kniemeyer O, Brakhage AA, Jacobsen ID, Hube B, Jungnickel B 2021 Functionality of the human antibody response to Candida albicans. Virulence 12: 3137-48 PubMed
López-Berges MS, Scheven MT, Hortschansky P, Misslinger M, Baldin C, Gsaller F, Werner ER, Krüger T, Kniemeyer O, Weber J, Brakhage AA, Haas H 2021 The bZIP Transcription Factor HapX Is Post-Translationally Regulated to Control Iron Homeostasis in Aspergillus fumigatus. Int J Mol Sci. 22(14): 7739 PubMed
Radosa S, Sprague JL, Lau SH, Tóth R, Linde J, Krüger T, Sprenger M, Kasper L, Westermann M, Kniemeyer O, Hube B, Brakhage AA, Gácser A, Hillmann F 2021 The fungivorous amoeba Protostelium aurantium targets redox homeostasis and cell wall integrity during intracellular killing of Candida parapsilosis. Cell Microbiol. 23(11): e13389 PubMed
Shopova IA, Belyaev I, Dasari P, Jahreis S, Stroe MC, Cseresnyés Z, Zimmermann AK, Medyukhina A, Svensson CM, Krüger T, Szeifert V, Nietzsche S, Conrad T, Blango MG, Kniemeyer O, Lilienfeld-Toal Mv, Zipfel PF, Ligeti E, Figge MT, Brakhage AA 2020 Human neutrophils produce antifungal extracellular vesicles against Aspergillus fumigatus. mBio 11: e00596-20 PubMed
Halder LD, Jo EAH, Hasan MZ, Ferreira-Gomes M, Krüger T, Westermann M, Palme DI, Rambach G, Beyersdorf N, Speth C, Jacobsen ID, Kniemeyer O, Jungnickel B, Zipfel PF, Skerka C 2020 Immune modulation by complement receptor 3 dependent human monocyte TGF-β1-transporting vesicles. Nat Commun 11: 2331 PubMed
Blango MG, Pschibul A, Rivieccio F, Krüger T, Muhammad R, Jia L, Zheng T, Goldmann M, Voltersen V, Li Jun, Panagiotou G, Kniemeyer O, Brakhage AA 2020 Dynamic surface proteomes of allergenic fungal conidia. J Proteome Res 19: 2092-104 PubMed
Hassan MIA, Kruse J, Krüger T, Dahse HM, Cseresnyés Z, Blango MG, Slevogt H, Hörhold F, Ast V, König R, Figge MT, Kniemeyer O, Brakhage AA, Voigt K 2020 Functional surface proteomic profiling reveals the host heat-shock protein A8 as a mediator of Lichtheimia corymbifera recognition by murine alveolar macrophages. Environ Microbiol 22: 3722-40 PubMed
Ruben S, Garbe E, Mogavero S, Albrecht-Eckardt D, Hellwig D, Häder A, Krüger T, Gerth K, Jacobsen ID, Elshafee O, Brunke S, Hünniger K, Kniemeyer O, Brakhage AA, Morschhäuser J, Hube B, Vylkova S, Kurzai O, Martin R 2020 Ahr1 and Tup1 contribute to the transcriptional control of virulence-associated genes in Candida albicans. mBio 11: e00206-20 PubMed
Jia LJ, Krüger T, Blango MG, von Eggeling F, Kniemeyer O, Brakhage AA 2020 Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection. mSphere 5: e00535-20 PubMed
Satish S, Jimenez-Ortigosa C, Zhao Y, Lee MH, Dolgov E, Krüger T, Park S, Denning DW, Kniemeyer O, Brakhage AA, Perlin DS 2019 Stress-induced changes in the lipid microenvironment of β-(1,3)-D-glucan synthase cause clinically important echinocandin resistance in Aspergillus fumigatus. mBio 10: e00779-19 PubMed
Bacher P, Hohnstein T, Beerbaum E, Röcker M, Kaufmann S, Brandt C, Röhmel J, Stervbo U, Nienen M, Babel N, Milleck J, Assenmacher M, Cornely OA, Heine G, Worm M, Creutz P, Tabeling C, Ruwwe-Glösenkamp C, Sander LE, Brunke S, Hube B, Blango M, Kniemeyer O, Brakhage AA, Schwarz C, Scheffold A 2019 Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. Cell 176: 1340-55 PubMed
Shekhova E, Ivanova L, Krüger T, Stroe MC, Macheleidt J, Kniemeyer O, Brakhage AA 2019 Redox proteomic analysis reveals oxidative modifications of proteins by increased levels of intracellular reactive oxygen species during hypoxia adaptation of Aspergillus fumigatus. Proteomics 19: 1800339 PubMed
Hoffmann F, Umbreit C, Krüger T, Pelzel D, Ernst G, Kniemeyer O, Guntinas-Lichius O, Berndt A, von Eggeling F 2019 Identification of proteomic markers in head and neck cancer using MALDI-MS imaging, LC-MS/MS, and immunohistochemistry. Proteomics Clin Appl 13: e1700173 PubMed
Schmidt H, Vlaic S, Krüger T, Schmidt F, Balkenhol J, Dandekar T, Guthke R, Kniemeyer O, Heinekamp T, Brakhage AA 2018 Proteomics of Aspergillus fumigatus conidia-containing phagolysosomes identifies processes governing immune evasion. Mol Cell Proteomics 17: 1084-96 PubMed
Richardson JP, Mogavero S, Moyes DL, Blagojevic M, Krüger T, Verma AH, Coleman BM, De La Cruz Diaz J, Schulz D, Ponde NO, Carrano G, Kniemeyer O, Wilson D, Bader O, Enoiu SI, Ho J, Kichik N, Gaffen SL, Hube B, Naglik J 2018 Processing of Candida albicans Ece1p is critical for Candidalysin maturation and fungal virulence. mBio 9: e02178-17 PubMed
Kurucz V, Krüger T, Antal K, Dietl AM, Haas H, Pócsi I, Kniemeyer O, Emri T 2018 Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion. BMC Genomics 19: 357 PubMed
Conrad T, Kniemeyer O, Henkel SG, Krüger T, Mattern DJ, Valiante V, Guthke R, Jacobsen ID, Brakhage AA, Vlaic S, Linde J 2018 Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol 12: 88 PubMed
Voltersen V, Blango MG, Herrmann S, Schmidt F, Heinekamp T, Strassburger M, Krüger T, Bacher P, Lother J, Weiss E, Hünniger K, Liu H, Hortschansky P, Scheffold A, Löffler J, Krappmann S, Nietzsche S, Kurzai O, Einsele H, Kniemeyer O, Filler SG, Reichard U, Brakhage AA 2018 Proteome analysis reveals the conidial surface protein CcpA essential for virulence of the pathogenic fungus Aspergillus fumigatus. mBio 9: e01557-18 PubMed
Pohlers S, Martin R, Krüger T, Hellwig D, Hänel F, Kniemeyer O, Saluz HP, Van Dijck P, Ernst JF, Brakhage A, Mühlschlegel FA, Kurzai O 2017 Lipid signaling via Pkh1/2 regulates fungal CO2 sensing through the kinase Sch9. mBio 8: e02211-16 PubMed
Teutschbein J, Simon S, Lother J, Springer J, Hortschansky P, Morton CO, Löffler J, Einsele H, Conneally E, Rogers TR, Guthke R, Brakhage AA, Kniemeyer O 2016 Proteomic profiling of serological responses to Aspergillus fumigatus antigens in patients with invasive aspergillosis. J Proteome Res 15: 1580-91 PubMed
Moyes DL, Wilson D, Richardson JP, Mogavero S, Tang SX, Wernecke J, Höfs S, Gratacap RL, Robbins J, Runglall M, Murciano C, Blagojevic M, Thavaraj S, Förster TM, Hebecker B, Kasper L, Vizcay G, Iancu SI, Kichik N, Häder A, Kurzai O, Luo T, Krüger T, Kniemeyer O, Cota E, Bader O, Wheeler RT, Gutsmann T, Hube B, Naglik JR 2016 Candidalysin is a fungal peptide toxin critical for mucosal infection. Nature 532: 64-8 PubMed
Bacher P, Heinrich F, Stervbo U, Nienen M, Vahldieck M, Iwert C, Vogt K, Kollet J, Babel N, Sawitzki B, Schwarz C, Bereswill S, Heimesaat MM, Heine G, Gadermaier G, Asam C, Assenmacher M, Kniemeyer O, Brakhage AA, Ferreira F, Wallner M, Worm M, Scheffold A 2016 Regulatory T cell specificity directs tolerance versus allergy against aeroantigens in humans. Cell 167: 1067-78.e16 PubMed
Luo T, Krüger T, Knüpfer U, Kasper L, Wielsch N, Hube B, Kortgen A, Bauer M, Giamarellos-Bourboulis EJ, Dimopoulos G, Brakhage AA, Kniemeyer O 2016 Immunoproteomic analysis of antibody responses to extracellular proteins of Candida albicans revealing the importance of glycosylation for antigen recognition. J Proteome Res 15: 2394-406 PubMed
Kniemeyer O, Ebel F, Krüger T, Bacher P, Scheffold A, Luo T, Strassburger M, Brakhage AA 2016 Immunoproteomics of Aspergillus for the development of biomarkers and immunotherapies. Proteomics Clin Appl 10: 910-21 PubMed
Baldin C, Valiante V, Krüger T, Schafferer L, Haas H, Kniemeyer O, Brakhage AA 2015 Comparative proteomics of a tor inducible Aspergillus fumigatus mutant reveals involvement of the tor kinase in iron regulation. Proteomics 15: 2230-43 PubMed
Altwasser R, Baldin C, Weber J, Guthke R, Kniemeyer O, Brakhage AA, Linde J, Valiante V 2015 Network modeling reveals cross talk of MAP kinases during adaptation to caspofungin stress in Aspergillus fumigatus. PLoS One 10: e0136932 PubMed
Krüger T, Luo T, Schmidt H, Shopova I, Kniemeyer O 2015 Challenges and strategies for proteome analysis of the interaction of human pathogenic fungi with host immune cells. Proteomes 3: 467-95 PubMed
Heinekamp T, Schmidt H, Lapp K, Pähtz V, Shopova I, Köster-Eiserfunke N, Krüger T, Kniemeyer O, Brakhage AA 2015 Interference of Aspergillus fumigatus with the immune response. Semin Immunopathol 37: 141-52 PubMed
Hillmann F, Linde J, Beckmann N, Cyrulies M, Strassburger M, Heinekamp T, Haas H, Guthke R, Kniemeyer O, Brakhage AA 2014 The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93: 539-53 PubMed
Lapp K, Vödisch M, Kroll K, Strassburger M, Kniemeyer O, Heinekamp T, Brakhage AA 2014 Characterisation of the Aspergillus fumigatus detoxification systems for reactive nitrogen intermediates and impact on virulence. Front Microbiol 5: 469 PubMed