Research for the Environment

Department of Proteomics

Department of Proteomics , Helmholtz-Zentrum für Umweltforschung - UFZ

Head of the Department:
Prof. Dr. Martin von Bergen
Christine Becher

phone +49 341 235-1264
fax +49 341 235-1787

Permoserstraße 15
04318 Leipzig, Germany

Proteins are the active player in human cells and in those of all kinds of organisms. Altogether they form what is called the proteome of a cell. The cells produce a specific proteome according to the environmental and developmental circumstances and to the needs of the specific cell line by transcribing the genetic information, stored as DNA, into proteins. Proteins are involved in all physiological processes and therefore are a good aim for reaching a better comprehension of biological processes and diseases. Furthermore, disease affected cells display a different protein pattern than healthy ones and so this protein pattern can be used for diagnostics.

In the Department of Proteomics at the UFZ we will focus on the role of proteins in the origin of environmentally caused diseases like allergy and other pathological changes of the immune system and on unravelling the enzymatic mechanisms of microbial degradation of pollutants. The samples from model systems or patients get analysed in terms of the abundance and modification of the proteome. These investigations will improve the molecular understanding of the cause and course of disease.

This defines the aim of the department of proteomics to obtain an improved understanding of the molecular mechanisms of environmentally caused diseases and biological processes in the environment.


  • Ahrens, V.M., Kostelnik, K.B., Rennert, R., Böhme, D., Kalkhof, S., Kosel, D., Weber, L., von Bergen, M., Beck-Sickinger, A.G., (2015):
    A cleavable cytolysin–neuropeptide Y bioconjugate enables specific drug delivery and demonstrates intracellular mode of action
    J. Control. Release 209 , 170 - 178
    full text (url)
  • Bargiela, R., Herbst, F.-A., Martínez-Martínez, M., Seifert, J., Rojo, D., Cappello, S., Genovese, M., Crisafi, F., Denaro, R., Chernikova, T.N., Barbas, C., von Bergen, M., Yakimov, M.M., Ferrer, M., Golyshin, P.N., (2015):
    Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation
    Proteomics 15 (20), 3508 - 3520
    full text (url)
  • Bastida, F., García, C., von Bergen, M., Moreno, J.L., Richnow, H.H., Jehmlich, N., (2015):
    Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study
    Appl. Soil Ecol. 93 , 65 - 67
    full text (url)
  • Beyer, A., Baumann, S., Scherz, G., Stahl, J., von Bergen, M., Friese, A., Roesler, U., Kietzmann, M., Honscha, W., (2015):
    Effects of ceftiofur treatment on the susceptibility of commensal porcine E.coli – comparison between treated and untreated animals housed in the same stable
    BMC Vet. Res. 11 , art. 265
    full text (url)
  • Feltens, R., Roeder, S., Otto, W., Borte, M., Lehmann, I., von Bergen, M., Wissenbach, D.K., (2015):
    Evaluation of population and individual variances of urinary phthalate metabolites in terms of epidemiological studies
    Journal of Chromatography & Separation Techniques 6 (6), art. 1000290
    full text (url)
  • Goris, T., Schiffmann, C.L., Gadkari, J., Schubert, T., Seifert, J., Jehmlich, N., von Bergen, M., Diekert, G., (2015):
    Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates
    Sci. Rep. 5 , art. 13794
    full text (url)
  • Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow, H.H., Jehmlich, N., von Bergen, M., Chen, Y., Murrell, J.C., (2015):
    Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph
    Environ. Microbiol. 17 (10), 4007 - 4018
    full text (url)
  • Halwachs, S., Mahnke, H., Ballent, M., Baumann, S., von Bergen, M., Viviani, P., Lanusse, C., Honscha, W., Lifschitz, A., (2015):
    ABCG2-mediated transport of anthelmintic drugs in the mammary gland of dairy cows
    J. Vet. Pharmacol. Ther. 38 (S1), 43 - 44
    full text (url)
  • Herberth, G., Offenberg, K., Rolle-Kampczyk, U., Bauer, M., Otto, W., Röder, S., Grützmann, K., Sack, E., Simon, J.-C., Borte, M., von Bergen, M., Lehmann, I., (2015):
    Endogenous metabolites and inflammasome activity in early childhood and links to respiratory diseases
    J. Allergy Clin. Immunol. 136 (2), 495 - 497
    full text (url)
  • Hoeke, H., Roeder, S., Bertsche, T., Lehmann, I., Borte, M., von Bergen, M., Wissenbach, D.K., (2015):
    Monitoring of drug intake during pregnancy by questionnaires and LC-MS/MS drug urine screening: evaluation of both monitoring methods
    Drug Test. Anal. 7 (8), 695 - 702
    full text (url)
  • Hofmann, T., Fischer, A.W., Meiler, J., Kalkhof, S., (2015):
    Protein structure prediction guided by crosslinking restraints – A systematic evaluation of the impact of the crosslinking spacer length
    Methods 89 , 79 - 90
    full text (url)
  • Hofmann, T., Samsonov, S.A., Pichert, A., Lemmnitzer, K., Schiller, J., Huster, D., Pisabarro, M.T., von Bergen, M., Kalkhof, S., (2015):
    Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry
    Methods 89 , 45 - 53
    full text (url)
  • Hoth, N., Gniese, C., Rakoczy, J., Weber, A., Kümmel, S., Reichel, S., Freese, C., Hache, M., Kassahun, A., Schulz, A., Fischer, H., Mühling, M., Starke, R., Kahnt, R., Vogt, C., Richnow, H.-H., Krüger, M., Schippers, A., Schlömann, M., (2015):
    CO2BioPerm — influence of bio-geochemical CO2-transformation processes on the long-term permeability
    In: Liebscher, A., Münch, U., (eds.)
    Geological Storage of CO2 – Long Term Security Aspects. GEOTECHNOLOGIEN Science Report No. 22
    Advanced Technologies in Earth Sciences
    Springer, Berlin, Heidelberg, p. 73 - 96
    full text (url)
  • Jouy, F., Müller, S.A., Wagner, J., Otto, W., von Bergen, M., Tomm, J.M., (2015):
    Integration of conventional quantitative and phospho-proteomics reveals new elements in activated Jurkat T-cell receptor pathway maintenance
    Proteomics 15 (1), 25 - 33
    full text (url)
  • Kalkhof, S., Dautel, F., Loguercio, S., Baumann, S., Trump, S., Jungnickel, H., Otto, W., Rudzok, S., Potratz, S., Luch, A., Lehmann, I., Beyer, A., von Bergen, M., (2015):
    Pathway and time-resolved benzo[a]pyrene toxicity on Hepa1c1c7 cells at toxic and subtoxic exposure
    J. Proteome Res. 14 (1), 164 - 182
    full text (url)
  • Kirsten, H., Al-Hasani, H., Holdt, L., Gross, A., Beutner, F., Krohn, K., Ahnert, P., Burkhardt, R., Reiche, K., Hackermüller, J., Löffler, M., Teupser, D., Thiery, J., Scholz, M., (2015):
    Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci
    Hum. Mol. Genet. 24 (16), 4746 - 4763
    full text (url)
  • Kostelnik, K.B., Els-Heindl, S., Klöting, N., Baumann, S., von Bergen, M., Beck-Sickinger, A.G., (2015):
    High metabolic in vivo stability and bioavailability of a palmitoylated ghrelin receptor ligand assessed by mass spectrometry
    Bioorg. Med. Chem. 23 (14), 3925 - 3932
    full text (url)
  • Kümmel, S., Herbst, F.-A., Bahr, A., Duarte, M., Pieper, D.H., Jehmlich, N., Seifert, J., von Bergen, M., Bombach, P., Richnow, H.H., Vogt, C., (2015):
    Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers
    FEMS Microbiol. Ecol. 91 (3), fiv006
    full text (url)
  • Kurteva-Yaneva, N., Zahn, M., Weichler, M.-T., Starke, R., Harms, H., Müller, R.H., Sträter, N., Rohwerder, T., (2015):
    Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase
    J. Biol. Chem. 290 , 9727 - 9737
    full text (url)
  • Linton, S.M., Cameron, M.S., Gray, M.C., Donald, J.A., Saborowski, R., von Bergen, M., Tomm, J.M., Allardyce, B.J., (2015):
    A glycosyl hydrolase family 16 gene is responsible for the endogenous production of β-1,3-glucanases within decapod crustaceans
    Gene 569 (2), 203 - 217
    full text (url)
  • Lünsmann, V., Kappelmeyer, U., Benndorf, R., Martínez-Lavanchy, P.M., Taubert, A., Adrian, L., Duarte, M., Pieper, D.H., von Bergen, M., Müller, J.A., Heipieper, H.J., Jehmlich, N., (2015):
    In-situ Protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model
    Environ. Microbiol.
  • Martínez-Lavanchy, P.M., Chen, Z., Lünsmann, V., Marin-Cevada, V., Vilchez-Vargas, R., Pieper, D.H., Reiche, N., Kappelmeyer, U., Imparato, V., Junca, H., Nijenhuis, I., Müller, J.A., Kuschk, P., Heipieper, H.J., (2015):
    Microbial toluene removal in hypoxic model constructed wetlands occurs predominantly via the ring monooxygenation pathway
    Appl. Environ. Microb. 81 (18), 6241 - 6252
    full text (url)
  • Müller, S.A., Pernitzsch, S.R., Haange, S.-B., Uetz, P., von Bergen, M., Sharma, C.M., Kalkhof, S., (2015):
    Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori
    J. Proteomics 126 , 34 - 45
    full text (url)
  • Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P.F., (2015):
    Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
    RNA 21 (5), 801 - 812
    full text (url)
  • Pagani, M., Rockstroh, M., Schuster, M., Rossetti, G., Moro, M., Crosti, M., Tomm, J.M., (2015):
    Reference proteome of highly purified human Th1 cells reveals strong effects on metabolism and protein ubiquitination upon differentiation
    Proteomics 15 (21), 3644 - 3647
    full text (url)
  • Palatinszky, M., Herbold, C., Jehmlich, N., Pogoda, M., Han, P., von Bergen, M., Lagkouvardos, I., Karst, S.M., Galushko, A., Koch, H., Berry, D., Daims, H., Wagner, M., (2015):
    Cyanate as an energy source for nitrifiers
    Nature 524 , 105 - 108
    full text (url)
  • Pöritz, M., Schiffmann, C.L., Hause, G., Heinemann, U., Seifert, J., Jehmlich, N., von Bergen, M., Nijenhuis, I., Lechner, U., (2015):
    Dehalococcoides mccartyi strain DCMB5 respires a broad spectrum of chlorinated aromatic compounds
    Appl. Environ. Microb. 81 (2), 587 - 596
    full text (url)
  • Remane, D., Grunwald, S., Hoeke, H., Mueller, A., Roeder, S., von Bergen, M., Wissenbach, D.K., (2015):
    Validation of a multi-analyte HPLC-DAD method for determination of uric acid, creatinine, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid and 2-methylhippuric acid in human urine
    J. Chromatogr. B 998–999 , 40 - 44
    full text (url)
  • Sachsenberg, T., Herbst, F.-A., Taubert, M., Kermer, R., Jehmlich, N., von Bergen, M., Seifert, J., Kohlbacher, O., (2015):
    MetaProSIP: Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics
    J. Proteome Res. 14 (2), 619 - 627
    full text (url)
  • Schaubeck, M., Clavel, T., Lagkouvardos, M., Calasan, J., Haange, S.-B., Jehmlich, N., von Bergen, M., Basic, M., Bleich, A., Haller, D., (2015):
    Transmissive Crohn's disease-like ileitis is caused by functional dysbiosis in the intestinal microbiota independent of inflammation-driven Paneth cell failure
    J. Crohns Colitis 9 (Suppl. 1), S1
    full text (url)
  • Scherz, G., Beyer, A., Stahl, J., Roesler, U., Friese, A., von Bergen, M., Kietzmann, M., Honscha, W., (2015):
    Occurrence of cephalosporin resistant and ESBL-producing commensal Escherichia coli in the microbiota from swine treated with ceftiofur
    J. Vet. Pharmacol. Ther. 38 (S1), 92 - 93
    full text (url)
  • Seyhan, D., Jehmlich, N., von Bergen, M., Fersch, J., Rother, M., (2015):
    Selenocysteine-independent suppression of UGA codons in the archaeon Methanococcus maripaludis
    Biochim. Biophys. Acta-Gen. Subj. 1850 , 2385 - 2392
    full text (url)
  • Tautenhahn, H.-M., Brückner, S., Baumann, S., Winkler, S., Otto, W., von Bergen, M., Bartels, M., Christ, B., (2015):
    Attenuation of postoperative acute liver failure by mesenchymal stem cell treatment due to metabolic implications
    Ann. Surg.
    full text (url)
  • Tobalina, L., Bargiela, R., Pey, J., Herbst, F.-A., Lores, I., Rojo, D., Barbas, C., Peláez, A.I., Sánchez, J., von Bergen, M., Seifert, J., Ferrer, M., Planes, F.J., (2015):
    Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
    Bioinformatics 31 (11), 1771 - 1779
    full text (url)
  • von Bergen, M., (2015):
    Substrate shift induces phylogenetic and functional changes in the gut mucosal microbiota adapted to a high fat diet
    Mol. Syst. Biol.
  • Winkler, S., Kalkhof, S., Hempel, M., Brückner, S., von Bergen, M., Christ, B., (2015):
    Validierung des Modells der durch eine Methionin-Cholin-freie Diät induzierten Nicht-alkoholischer Steatohepatitis (NASH) durch Proteomanalysen
    Zeitschrift für Gastroenterologie 53 , KG090
    full text (url)
  • Zanker, D., Otto, W., Chen, W., von Bergen, M., Tomm, J., (2015):
    Compartment resolved reference proteome map from highly purified naïve, activated, effector, and memory CD8+ murine immune cells
    Proteomics 15 (11), 1808 - 1812
    full text (url)