Publications

2019

Tuco, E., Witt, M., Abert, C., Bock-Bierbaum, T., Su, M.-Y., Trapannone, R., Sztacho, M., Danieli, A., Shi, X., Zaffagnini, G., Gamper, A., Schuschnig, M., Fracchiolla, D., Bernklau, D., Romanov, J., Hartl, M., Hurley, J.H., Daumke, O., and Martens, S. (2019). FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates. Molecular Cell. in press

Gómez-Díaz, C., Ikeda, F. (2019). Roles of ubiquitin in autophagy and cell death. Semin Cell Dev Biol. (in press)

2018

Acosta-Alvear D*, Karagöz GE*, Fröhlich F, Li H, Walther TC, Walter P. (2018) The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1. Elife. 7. * equal contribution.

Ebner, P., Poetsch, I., Deszcz, L., Hoffmann, T., Zuber, J., and Ikeda, F. (2018). The iap family member bruce regulates autophagosome-lysosome fusion. Nat Commun. 9:599.

Fennell, L.M., Rahighi, S., and Ikeda, F. (2018). Linear ubiquitin chain-binding domains. FEBS J. 285:2746-61.

Ikeda, F. (2018). The anti-apoptotic ubiquitin conjugating enzyme birc6/bruce regulates autophagosome-lysosome fusion. Autophagy. 14:1283-84.

Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luehrmann R, Stark H (2018). Structure and Conformational Dynamics of the Human Spliceosomal Bact Complex. Cell 172, 1–11

Hellerschmied, D., Roessler, M., Lehner, A., Gazda, L., Stejskal, K., Imre, R., Mechtler, K., Dammermann, A., Clausen, T. (2018) UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins. Nat Commun. 9:484

Zaffagnini, G., Savova, A., Danieli, A., Romanov, J., Tremel, S., Ebner, M., Peterbauer, T., Sztacho, M., Trapannone, R., Tarafder, A.K., Sachse, C., and Martens, S. (2018). p62 filaments capture and present ubiquitinated cargos for autophagy. The EMBO Journal.

2017

Karagöz, GE; Acosta-Alvear, D; Nguyen, HT; Lee, CP; Chu, F; Walter, P (2017). An unfolded protein-induced conformational switch activates mammalian IRE1. eLife. 6.

Tomanov, K., Nehlin, L., Ziba, I., Bachmair, A. (2017). SUMO chain formation relies on the amino-terminal region of SUMO conjugating enzyme and has dedicated substrates in plants. Biochemical J., in press

Nukarinen, E., Tomanov, K., Ziba, I., Weckwerth, W., Bachmair, A. (2017). Protein sumoylation and phosphorylation intersect in Arabidopsis signaling. Plant J. 91:505-517

Haselbach D, Schrader J, Lambrecht F, Henneberg F, Chari A, Stark H (2017). Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs. Nat Commun. 8:15578

Rittinger, K., Ikeda, F. (2017). Linear ubiquitin chains: enzymes, mechanisms and biology. Open Biol. 7(4)

Ebner, P., Versteeg, GA., Ikeda, F. (2017). Ubiquitin enzymes in the regulation of immune responses. Crit Rev Biochem Mol Biol. 52(4):425-460

2016

Trentini, DB., Suskiewicz, MJ., Heuck, A., Kurzbauer, R., Deszcz, L., Mechtler, K., Clausen, T. (2016). Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature. 539(7627):48-53

Suskiewicz, MJ., Clausen, T. (2016). Chemical Biology Interrogates Protein Arginine Phosphorylation. Cell Chem Biol. 23(8):888-90

Gallego, LD., Ghodgaonkar Steger, M., Polyansky, AA., Schubert, T., Zagrovic, B., Zheng, N., Clausen, T., Herzog, F., Köhler, A. (2016). Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1. Proc Natl Acad Sci U S A. 113(38):10553-8

Fracchiolla, D., Sawa-Makarska, J., Zens, B., de Ruiter, A., Zaffagnini, G., Brezovich, A., Romanov, J., Runggatscher, K., Kraft, C., Zagrovic, B., and Martens, S. (2016). Mechanism of cargo-directed Atg8 conjugation during selective autophagy. eLife 5, e18544.

Asaoka, T., Almagro, J., Ehrhardt, C., Tsai, I., Schleiffer, A., Deszcz, L., Junttila, S., Ringrose, L., Mechtler, K., Kavirayani, A., Gyenesei, A., Hofmann, K., Duchek, P., Rittinger, K., Ikeda, F. (2016). Linear ubiquitination by LUBEL has a role in Drosophila heat stress response. EMBO Rep. 17(11):1624-1640

* Heuck, A., Schitter-Sollner, S., Suskiewicz, MJ., Kurzbauer, R., Kley, J., Schleiffer, A., Rombaut, P., Herzog, F., Clausen, T. (2016). Structural basis for the disaggregase activity and regulation of Hsp104. eLife. 5

2015

Schneider, M., Hellerschmied, D., Schubert, T., Amlacher, S., Vinayachandran, V., Reja, R., Pugh, BF., Clausen, T., Köhler, A. (2015). The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell. 162(5):1016-28

Wurzer, B., Zaffagnini, G., Fracchiolla, D., Turco, E., Abert, C., Romanov, J., and Martens, S. (2015). Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy. eLife 4.

Tomanov, K., Bachmair, A. (2015). Expression and purification of the Arabidopsis SUMO E4 ligases PIAL1 and PIAL2. bio-protocol 5:e1544

Martens, S., Bachmair, A. (2015). How cells coordinate waste removal through their major proteolytic pathways. Nat. Cell Biol. 30:841-842

Ikeda, F. (2015). Linear ubiquitination signals in adaptive immune responses. Immunol Rev. 266(1):222-36

2014

*Karagöz, GE; Duarte, AMS; Akoury, E; Ippel, H; Biernat, J; Morán Luengo, T; Radli, M; Didenko, T; Nordhues, BA; Veprintsev, DB; Dickey, CA; Mandelkow, E; Zweckstetter, M; Boelens, R; Madl, T; Rüdiger, SGD (2014). Hsp90-Tau complex reveals molecular basis for specificity in chaperone action. Cell;156:963-74.

Schmidt, A., Trentini, DB., Spiess, S., Fuhrmann, J., Ammerer, G., Mechtler, K., Clausen, T. (2014). Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response. Mol Cell Proteomics. 13(2):537-50

Sawa-Makarska, J., Abert, C., Romanov, J., Zens, B., Ibiricu, I., and Martens, S. (2014). Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane–cargo apposition during selective autophagy. Nat Cell Biol 16, 425-433.

Trentini, DB., Fuhrmann, J., Mechtler, K., Clausen, T. (2014). Chasing phosphoarginine proteins: development of a selective enrichment method using a phosphatase trap. Mol Cell Proteomics. 13: 1953-1964

Tomanov, K., Zeschmann, A., Hermkes, R., Eifler, K., Ziba, I., Grieco, M., Novatchkova, M., Hofmann, K., Hesse, H., Bachmair, A. (2014). Arabidopsis PIAL1 and 2 promote SUMO chain formation as E4 type SUMO ligases, and are involved in stress responses and sulfur metabolism. Plant Cell 26:4547-4560

Tomanov, K., Luschnig, C., Bachmair, A. (2014). Ubiquitin Lys 63 chains – second-most abundant, but poorly understood in plants. Frontiers Plant Sci. 5:15

Kumari, S., Redouane, Y., Lopez-Mosqueda, J., Shiraishi, R., Romanowska, M., Lutzmayer, S., Kuiper, J., Martinez, C., Dikic, I., Pasparakis, M., Ikeda, F. (2014). Sharpin prevents skin inflammation by inhibiting TNFR1-induced keratinocyte apoptosis. Elife. 3