Group Spahn - Nanoscale Bacteriology

The Nanoscale Bacteriology Lab investigates the molecular organization of bacterial cells. We employ diverse microscopy methods, in particluar super-resolution microscopy. This set of microscopy methods allows to visualize biological specimen and structures with a spatial resolution of a few nanometers. Compared to conventional, diffraction-limited microscopy (e.g. widefield or confocal fluorescence microscopy), this represents a resolution increase by a factor of 10 - 30. With this greatly enhanced resolution, we are now able to study proteins, nucleic acids and other biomolecules on the near-molecular scale an in the context of individual, intact cells.

The methods or workflows for multicolor super-resolution imaging in bacteria is nowadays still limited. We thus establish and develop methods that allow the simultaneous visualization of different target molecules. This includes single-molecule based techniques (single-molecule localization microscopy, SMLM), stimulated emission depletion (STED) microscopy and live-cell imaging. Together with artificial intelligence, these imaging methods can provide rich information on diverse biological questions. We are also interested in the development of smart microscopy approaches, which can for example accelerate drug screening at high spatial resolution.

Our biological focus lies on the investigation of the transertion process in gram-negative bacteria. Transertion describes the coupling of transcription, translation and insertion of membrane proteins, which represents a postulated, but still insufficiently studied (an unproven) mechansim that dynamically couples the chromsomal DNA (the so-called nucleoid) to the inner membrane. As bacterial cells are tiny (an E. coli cell in rich medium is ~ 1 µm wide and 3 - 5 µm long), we need high-resolution methods to study the nature of such processes. Using systematic perturbation of cellular processes with drug treatments, we could show that protein biosynthesis strongly contributes to the organization of the E. coli nucleoid. In our ongoing and future work, we want to decipher the molecular mechanisms that mediate bacterial organization, both in our model organism E. coli, as well as in gram-negative pathogens.

Our broad method spectrum allows us to study many more exciting biological questions. This includes:

• Architecture of bacterial biofilms
• Antibiotic resistance mechansims
• Host-pathogen interactions

• Spahn, C., Middlemiss, S., Gómez-de-Mariscal, E., Henriques, R., Bode, H. B., Holden, S., Heilemann, M., “The nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry.” Nat. Commun. 16, 3732 (2025) [link]
• Pandi, A., Adam, D., Zare, A., Trinh, V.T., Schaefer, S.L., Wiegand, M., Klabunde B., Bobkova, E., Kushwaha, M., Foroughijabbari, Y., Braun, P., Spahn, C., Preußer, C., von Strandmann, E.P., Bode, H.B., von Buttlar, H., Bertrams, W., Jung, A.L., Abendroth, F., Schmeck, B., Hummer, G., Vázquez, O., Erb, T.J. “Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides.” Nat. Commun. 14, 7197 (2023) [link]
• Spahn, C., Gómez-de-Mariscal, E., Laine, F.L., Pereira, P. M., von Chamier, L., Condiut, M., Pinho, M.G., Jacquemet, G., Holden, S., Heilemann, M. & Henriques, R., “DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches.” Commun. Biol. 5, 688 (2022) [link]
• Koller, N., Höllthaler, P., Barends, M., Döring, M, Spahn, C., Durán, V., Costa, B., Becker, J., Heilemann, M., Kalinke, U., Tampé, R., “Nanoscale organization of the MHC I peptide-loading complex in human dendritic cells.” Cell. Mol. Life Sci. 79(9):477 (2022) [link]
• Chamier, v.L.^#, Laine^#, R.F., Jukkala, J., Spahn, C., Krentzel, D., Nehme, E., Lerche, M., Hernández-Pérez, S., Mattila, P.K., Karinou, E., Holden, S., Solak, A.C., Krull, A., Buchholz, T.-O., Jones, M.L., Royer, L.A., Leterrier, C., Shechtman, Y., Jug, F., Heilemann, M., Jacquemet, G., Henriques, R., “Democratising deep learning for microscopy with ZeroCostDL4Mic.” Nature Communications 12, 2246 (2021) [link]
• Vo T.D.^#, Spahn, C.^#, Heilemann, M., Bode, H.B., “Microbial cationic peptides as a natural defense mechanism against insect antimicrobial peptides.” ACS Chemical Biology 16(3), pp 447-451 (2021) [link]
• Glogger, M., Spahn, C., Enderlein, J., Heilemann M., “Multi-Color, Bleaching-Resistant Super-Resolution Optical Fluctuation Imaging with Oligonucleotide-Based Exchangeable Fluorophores.” Angewandte Chemie (2020). [link]
• Spahn, C., Hurter, F., Glaesmann, M., Karathanasis, C., Lampe, M., Heilemann, M., “Protein-Specific, Multicolor and 3D STED Imaging in Cells with DNA-Labeled Antibodies.” Angewandte Chemie 58(52), pp 18835-18838 (2019). [link]
• Spahn, C., Grimm, J.B., Lavis, L.D., Lampe, M., Heilemann, M., “Whole-Cell, 3D, and Multicolor STED Imaging with Exchangeable Fluorophores.” Nano Letters 19 (1), pp 500–505 (2018). [link]
• Spahn, C.^#, Glaesmann, M.^#, Grimm, J.B., Ayala, A.X., Lavis, L.D., Heilemann, M., “A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels.” Scientific Reports 8, 14768 (2018). [link]
• Gao, Y.^#, Spahn, C.^#, Heilemann, M., Kenney, L.J., “The Pearling Transition Provides Evidence of Force-Driven Endosomal Tubulation during Salmonella Infection.” mBio 9, e01083-18 (2018). [link]
• Diekmann, R., Wolfson, D.L., Spahn, C., Heilemann, M., Schüttpelz, M. & Huser, T. “Nanoscopy of bacterial cells immobilized by holographic optical tweezers.” Nature Communications 7, 13711 (2016). [link]
• Spahn, C., Herrmannsdӧrfer, F., Kuner, T. & Heilemann, M. “Temporal accumulation analysis provides simplified artifact-free analysis of membrane-protein nanoclusters.” Nature Methods 13, 963–964 (2016). [link]
• Devraj, K., Poznanovic, S., Spahn, C., Schwall, G., Harter, P., Mittelbronn, M., Antoniello, K., Paganetti, P., Muhs, A., Heilemann, M., Hawkins, R.A., Schrattenholz, A. & Liebner, S. “BACE-1 is expressed in the blood-brain barrier endothelium and is upregulated in a murine model of Alzheimer’s disease.” Journal of Cerebral Blood Flow & Metabolism 36, 1281–1294 (2016). [link]
• Foo, Y. H.^#, Spahn, C.^#, Zhang, H., Heilemann, M. & Kenney, L. J. “Single cell super-resolution imaging of E. coli OmpR during environmental stress.” Integr. Biology 7, 1297–1308 (2015). [link]
• Spahn, C., Cella-Zannacchi, F., Endesfelder, U. & Heilemann, M. “Correlative super-resolution imaging of RNA polymerase distribution and dynamics, bacterial membrane and chromosomal structure in Escherichia coli.” Methods and Applications in Fluorescence 3, 014005 (2015). [link]
• Raulf, A., Spahn, C., Zessin, P. & Heilemann, M. “Click chemistry facilitates direct labelling and super-resolution imaging of nucleic acids and proteins.” RSC Advances 4, 30462–30466 (2014). [link]
• Spahn, C., Endesfelder, U. & Heilemann, M. “Super-resolution imaging of Escherichia coli nucleoids reveals highly structured and asymmetric segregation during fast growth.” Journal of Structural Biology 185 (3), 243-249 (2014). [link]
• Klehs, K., Spahn, C., Endesfelder, U., Lee, S.F., Fuerstenberg, A. & Heilemann, M. “Increasing the Brightness of Cyanine Fluorophores for Single-Molecule and Superresolution Imaging.” ChemPhysChem 15, 637–641 (2014). [link]