Research groupJunior group

Daniel Roderer

Structure and mechanism of microbiome-driven diseases

Portrait

We are interested in the molecular mechanism of host-microbiome interactions in the human intestinal system, which play important roles in onset and progression of diseases. We therefore apply Cryo-EM to solve the structures of protein complexes that facilitate epithelial adhesion of bacteria.


Profile

We thrive to understand the molecular mechanism underlying the interaction of the intestinal microbiome with the human host. We focus on bacteria that are overrepresented in the microbiome of colorectal cancer (CRC) patients and the interactions of bacterial adhesins with epithelial and immune cells of the intestinal system. Genomic sequencing, big data analysis, and substantial microbial studies in animal models identified important drivers of CRC on the microbial and cellular level, but the underlying mechanistic details are not known. Therefore, we structurally analyze complexes between commensal proteins and human receptors to understand the molecular background of their binding mechanisms. 

We apply cryogenic electron microscopy (Cryo-EM) and single particle analysis to determine the structures of protein complexes that facilitate the host-microbiome interaction, which is a prerequisite for structure-based design of personalized anticancer compounds. In addition, we visualize molecular details of bacteria interacting with the host epithel via cryo-ET to understand their binding mechanisms in a cellular context. Finally, we attempt to identify yet undescribed bacterial adhesins that facilitate epithelial binding in a pathogenic context using genomic and biochemical screening systems. 


The Roderer group

Job Offers

Applications are open for 1 PhD position in the Roderer Group to investigate the structure-function relationship of a transmembrane protease using cryo-EM and single particle analysis. The position is funded by the Einstein Center of Catalysis, please find more information under the link (right side). The application deadline is January 15th, 2023. Please contact Daniel Roderer directly for more details.

Publications

  • Y. Xu*, R. Viswanatha*, O. Sitsel, D. Roderer, H. Zhao, C. Ashwood, C. Voelcker, S. Tian, S. Raunser, N, Perrimon and M. Dong. CRISPR screens in Drosophila cells identify Vsg as a Tc toxin receptor. Nature 610 (349-355), 2022. doi: 10.1038/s41586-022-05250-7.
  • A. Belyy*, F. Lindemann*, D. Roderer, J. Funk, B. Bardiaux, J. Protze, P. Bieling, H. Oschkinat and S. Raunser. Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Nat Comm 13 (4202), 2022. doi: 10.1038/s41467-022-31836-w.
  • E. Mirgorodskaya, E. Dransart, M. Shafaq-Zadah, D. Roderer, C. Sihlbom, H. Leffler and L. Johannes. Site-specific N-glycan profiles of α5β1 integrin from rat liver. Biol. Cell 114 (6), 2022. doi: 10.1111/boc.202200017.
  • D. Roderer, F. Bröcker, O. Sitsel, P. Kaplonek, F. Leidreiter, P. H. Seeberger and S. Raunser. Glycan-dependent two-step cell adhesion mechanism of Tc toxins. Nat Comm 11 (2694), 2020. doi: 10.1038/s41467-020-16536-7.
  • D. Roderer, E. Schubert, O. Sitsel and S. Raunser. Towards the application of Tc toxins as a universal protein translocation system. Nat Comm 10, 5263 (2019). doi: 10.1038/s41467-019-13253-8. 
  • D. Roderer, O. Hofnagel, R. Benz and S. Raunser. Structure of a Tc holotoxin pore provides insights into the translocation mechanism. PNAS 116 (45), 2019. doi: 10.1073/pnas.1909821116.
  • F. Leidreiter*, D. Roderer*, D. Meusch, C. Gatsogiannis and S. Raunser. Common architecture of Tc toxins from human and insect pathogenic bacteria. Science Advances 5 (10), 2019. doi: 10.1126/sciadv.aax6497.
  • D. Roderer and S. Raunser. Tc toxin complexes: Assembly, membrane permeation and protein translocation. Annual Review of Microbiology 73, 2019. doi: 10.1146/annurev-micro-102215-095531. Review.
  • T. Wagner, F. Merino, M. Stabrin, T. Moriya, C. Antoni, A. Apelbaum, P. Hagel, O. Sitsel, T. Raisch, D. Prumbaum, D. Quentin, D. Roderer, S. Tacke, B. Siebolds, E. Schubert, T.R. Shaikh, P. Lill, C. Gatsogiannis and S. Raunser. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biology 2: 218, 2019. doi: 10.1038/s42003-019-0437-z.
  • C. Gatsogiannis*, F. Merino*, D. Roderer*, D. Balchin, E. Schubert, A. Kuhlee, M. Hayer-Hartl and S. Raunser. Tc toxin activation requires unfolding and refolding of a β-propeller. Nature 563 (209-213), 2018. doi: 10.1038/s41586-018-0556-6.
  • D. Roderer and R. Glockshuber. Assembly mechanism of the α-pore-forming toxin cytolysin A from Escherichia coli. Philos Trans R Soc Lond B Biol Sci. 5;372(1726), 2017. doi: 10.1098/rstb.2016.0211. Review.
  • C. Gatsogiannis, F. Merino, D. Prumbaum, D. Roderer, F. Leidreiter, D. Meusch and S. Raunser. Membrane insertion of a Tc toxin in near-atomic detail. Nat Struct Mol Biol 23 (10), 2016. doi: 10.1038/nsmb.3281. 
  • D. Roderer, S. Benke, B. Schuler and R. Glockshuber. Soluble Oligomers of the Pore-forming Toxin Cytolysin A from Escherichia coli Are Off-pathway Products of Pore Assembly. J Biol Chem 291 (11), 2016. doi: 10.1074/jbc.M115.700757. 
  • D. Roderer, R. Glockshuber and M. Rubini. Acceleration of the Rate-Limiting Step of Thioredoxin Folding by Replacement of its Conserved cis-Proline with (4 S)-Fluoroproline. ChemBioChem 16 (15), 2015. doi: 10.1002/cbic.201500342. 
  • D. Roderer*, M Schärer*, M. Rubini and R. Glockshuber. Acceleration of protein folding by four orders of magnitude through a single amino acid substitution. SciRep 5 (11840), 2015. doi: 10.1038/srep11840. 
  • S. Benke, D. Roderer, B. Wunderlich, D. Nettels, R. Glockshuber and B. Schuler. The assembly dynamics of the cytolytic pore toxin ClyA. Nat Comm 6 (6198), 2015. doi: 10.1038/ncomms7198.
  • D. Roderer, S. Benke, M. Müller, H. Fäh-Rechsteiner, N. Ban, B. Schuler and R. Glockshuber. Characterization of variants of the pore-forming toxin ClyA from Escherichia coli controlled by a redox switch. Biochemistry 53 (40), 2014. doi: 10.1021/bi5007578.