Research Projects

Current Research

Bacterial Disease and Host-Pathogen Interactions

Manipulation of human host cells is a fundamental challenge for all pathogens. To understand host-pathogen interaction and pathogenesis, we examine the characteristics, functionalities and interactions of molecular structures involved in the survival and multiplication of bacteria within the host. One example of such nanomachine is the type III secretion system (T3SS), a membrane-embedded nanosyringe-like complex that allows the direct delivery of proteins, known as effectors, into the cytosol of human cells. The T3SS is a highly conserved virulence machinery of Gram-negative bacteria, and thus it represents an attractive target for novel anti-infectives. The structural core of the T3SS is a ~3.5 multi-megadalton complex assembled from more than fifteen different proteins that spans the two lipid bilayers of Gram-negative bacteria. The current challenge we face is to understand how structural switches in this bacterial secretion apparatus allow the recognition and secretion of effectors in a hierarchical manner and what kind of protein-protein interactions can drive bacterial invasion. We integrate high-end technologies like X-ray lasers and electron cryo-microscopes with other biophysical methodologies to study the functional dependence of structural determinants in T3SSs from water-borne bacterial pathogens and investigate the rules for effector protein secretion, transport dynamics and regulation of the T3SS.

In addition, we have a strong interest in uncovering the strategies used by Gram-negative organisms to subvert the antibacterial response of human cells. Components of the tip of the T3SS apparatus interact with host membranes to allow the translocation of effectors directly to the human cell cytosol. How the translocon components assemble and insert into host membranes to form pores are under investigation. We also focus on the molecular interactions of T3SS effector proteins with host components and their signaling cascade that drives cellular subversion. Shigella, the causative agent of diarrhoea and other gut-associated diseases, invades the human colonic epithelium and avoids clearance by promoting cell death of resident immune cells in the gut. Different modalities of cell death (pyroptosis, necroptosis and cell death programs involving alternative caspases) have been linked to the killing mechanism. Although these modalities may not be mutually exclusive and may progress simultaneously, we evaluate the contribution of each program in dying cells with special focus on the T3SS dependency.

Pseudomonas aeruginosa is an adaptive environmental bacterium and an important opportunistic pathogen, which causes devastating acute as well as chronic, persistent infections. Due to its high ability of adaptation to different adverse environmental settings and multidrug resistance, this opportunistic pathogen poses a particular threat in public health and thus the urgency of developing new antibiotics is critical. To bypass drug resistance, we are interested in finding novel molecular mechanisms underlying virulence in P. aeruginosa. For this, we combine multiple omics data of clinical isolates with microbiological, biophysical and structural biology methodologies to elucidate structure-function relationships of novel proteins associated with virulence in P. aeruginosa.

We integrate interdisciplinary approaches to advance our understanding of the assembly and three dimensional structure of key bacterial components involved in virulence pathways and their interaction with the host responses to allow us the design of molecular drugs for the treatment of Gram-negative bacterial infections.

Future projects and goals

Our underlying biological goal is to understand in-depth the process by which Type 3 Secretion Systems orchestrate the sequential order of effector translocation and trigger controlled subversion of a target cell. In addition, we aim to identify novel bacterial protein complexes essential for P. aeruginosa infections. For this, we will combine high precision imaging technologies with microbiological and biophysical methodologies to examine the dynamic process of a bacterial infection at sub-nanoscale resolution.

Research Team

17

Group Leader

Prof. Dr. Michael Kolbe
Phone:+49 40 8998 87550

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Group Assistant
Phone:+49 40 8998 87549

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PhD Student

Wajeeha Abid

PhD Student

Rizvee Ahmad

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PhD Student

Baptiste Baudu
Phone:+49 40 8998 87557

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PhD Student

Julius Bochert
Phone:+49 40 8998 87557

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Intern

Laura Boskova

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Postdoc

Dr. Spyros Chatziefthymiou
Phone:+49 40 8998 87551

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Bachelor Student

Amelie Geuer
Phone:+49 40 8998 8755

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PhD Student

Fereshta Hafizi
Phone:+49 40 8998 87560

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PhD Student

Jelena Jeremic
Phone:+49 40 8998 87552

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Master Student

Amin Khorasani Asl

Intern

Ronja Leichert

Postdoctoral Scientist

Dr. Vahid Lohrasbi
Phone:+49 40 8998 87554

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PhD Student

Maryam Manouchehri

PostDoc

Nissi Marapatla
Phone:+49 40 8998 87558

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Postdoctoral Scientist

Dr. Sukrit Srivastava

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Publications

2023

Srivastava S, Kolbe M (2023) Novel "GaEl Antigenic Patches" Identified by a "Reverse Epitomics" Approach to Design Multipatch Vaccines against NIPAH Infection, a Silent Threat to Global Human Health. ACS Omega. 2023 Aug 22;8(35):31698-31713. doi: 10.1021/acsomega.3c01909.

Srivastava S, Verma S, Kamthania M, Saxena AK, Pandey KC, Pande V, Kolbe M. (2023) Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health. PLoS One. 2023 Mar 15;18(3):e0282580. doi: 10.1371/journal.pone.0282580.

Flacht L, Lunelli M, Kaszuba K, Chen ZA, O' Reilly FJ, Rappsilber J, Kosinski J, Kolbe M (2023) Integrative structural analysis of the type III secretion system needle complex from Shigella flexneri. Protein Sci.e4595. doi: 10.1002/pro.4595

2021

Srivastava S, Verma S, Kamthania M, Kaur R, Badyal RK, Saxena AK, Shin HJ, Kolbe M, Pandey KC (2021) Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation. JMIR Bioinform Biotech 1(1):e19371. doi: 10.2196/19371.

Srivastava S, Chatziefthymiou SD, Kolbe M. (2021) Vaccines Targeting Numerous Coronavirus Antigens, Ensuring Broader Global Population Coverage: Multi-epitope and Multi-patch Vaccines. Methods Mol Biol. 2410:149-175. doi: 10.1007/978-1-0716-1884-4_7

Wang C, Nehls C, Baabe D, Burghaus O, Hurwitz R, Gutsmann T, Bröring M, Kolbe M. (2021) Flagellin lysine methyltransferase FliB catalyzes a [4Fe-4S] mediated methyl transfer reaction. PLoS Pathog.17(11):e1010052. doi: 10.1371/journal.ppat.1010052

Strahlberg D, Kolbe M, Pagnini G (2021) Antibiotics Resistance Forecasting: A Comparison of Two Time Series Forecast Models. SIAM Undergraduate Research Online

Kotov V, Lunelli M, Wald J, Kolbe M, Marlovits TC (2021) Helical reconstruction of Salmonella and Shigella needle filaments attached to type 3 basal bodies. Biochemistry and Biophysics Reports 27:101039. https://doi.org/10.1016/j.bbrep.2021.101039

Stinn A , Furkert J, Kaufmann Stefan H E, Moura-Alves P, Kolbe M  (2021) Novel Method for Quantifying AhR-Ligand Binding Affinities Using Microscale Thermophoresis: In biosensors-1106567. doi: 10.3390/bios11030060

2020

Srivastava S, Verma S, Kamthania M, Agarwal D, Saxena AK, Kolbe M, Singh S, Kotnis A, Rathi B, Nayar SA, Shin H-J, Vashisht K & Pandey KC (2020) Computationally validated SARS-CoV-2CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide, Journal of Biomolecular Structureand Dynamics, doi: 10.1080/07391102.2020.1838329

Srivastava S, Verma S, Kamthania M, Kaur R, Badyal R K, Saxena A K, Shin H J, Kolbe M, Pandey KC (2020) Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation JMIR Bioinformatics Biotechnol: 1(1):e19371. doi: 10.2196/19371

Horstmann JA, Lunelli M, Cazzola H, Heidemann J, Kühne C, Steffen P, Szefs S, Rossi C, Lokareddy RK, Wang C, Lemaire L, Hughes KT, Uetrecht C, Schlüter H, Grassl GA, Stradal TEB, Rossez Y, Kolbe M, Erhardt M (2020) Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion. Nat Commun: 11(1):2013. doi: 10.1038/s41467-020-15738-3.

Lunelli M, Kamprad A, Bürger J, Mielke T, Spahn CMT, Kolbe M (2020) Cryo-EM structure of the Shigella type III needle complex. PLoS Pathog:16(2):e1008263. doi: 10.1371/journal.ppat.1008263.

2019

Moura-Alves P, Puyskens A, Stinn A, Klemm M, Guhlich-Bornhof U, Dorhoi A, Furkert J, Kreuchwig A, Protze J, Lozza L, Pei G, Saikali P, Perdomo C, Mollenkopf HJ, Hurwitz R, Kirschhoefer F, Brenner-Weiss G, Weiner J, Oschkinat H, Kolbe M, Krause G, Kaufmann SHE (2019) Host monitoring of quorum sensing during Pseudomonas aeruginosa infection. Science: 366(6472). pii: eaaw1629. doi: 10.1126/science.aaw1629

Wang C, Lunelli M, Zschieschang E, Bosse J, Thuenauer R, Kolbe M (2019) Role of flagellar hydrogen bonding in Salmonella motility and flagellar polymorphic transition. Mol Microbiol: ahead of print doi: 10.1111/mmi.14377

Bernal I, Römermann J, Flacht L, Lunelli M, Uetrecht C, Kolbe M (2019) Structural analysis of ligand-bound states of the Salmonella type III secretion system ATPase InvC. Protein Sci 2019: 1-14. doi: 10.1002/pro.3704

Bernal I, Börnicke J, Heidemann J, Svergun D, Horstmann JA, Erhardt M, Tuukkanen A, Uetrecht C, Kolbe M (2019) Molecular organization of soluble type III secretion system sorting platform complexes. J Mol Biol pii: S0022-2836(19)30425-5    doi: 10.1016/j.jmb.2019.07.004

Liu H, Moura-Alves P, Pei G, Mollenkopf H-J, Hurwitz R, Wu X, Wang F, Liu S, Ma M, Fei Y, Zhu C, Koehler A-B, Oberbeck-Mueller D, Hahnke K, Klemm M, guhlich-Bornhof U, Ge B, Tuukkanen A, Kolbe M, Dorhoi A, Kaufmann SHE (2019) cGAS facilitates sensing of extracellular cyclic dinucleotides to activate innate immunity. EMBO Rep 20: e46293  doi: 10.15252/embr.201846293

2017

Horstmann J A, Zschieschang E, de Diego J, Lunelli M, Rohde M, May T, Strowig T, Stradal T, Kolbe M, Erhardt M (2017) Flagellin phasedependent swimming on epithelial cell surfaces contributes to productive Salmonella gut colonisation. Cell Microbiol. e12739.

2016

Senerovic L, Brotcke-Zumsteg A, Kolbe M (2016) IpaB ion channels induce pyroptosis in macrophages, Shigella: Molecular and Cellular Biology, edited by Bill Picking.

2014

Moura-Alves P, Faé K, Houthuys E, Dorhoi A, Kreuchwig A, Furkert J, Barison N, Diehl A, Munder A, Constant P, Skrahina T, Guhlich-Bornhof U, Klemm M, Koehler A B, Bandermann S, Goosmann C, Mollenkopf H J, Hurwitz R, Brinkmann V, Fillatreau S, Daffe M, Tümmler B, Kolbe M, Oschkinat H, Krause G, Kaufmann S H (2014) AhR sensing of bacterial pigments regulates antibacterial defence. Nature, 512: 387-92.

Dohlich K, Brotcke-Zumsteg A, Goosmann C, Kolbe M (2014) A Substrate-Fusion Protein is Trapped inside the Type III Secretion System Channel in Shigella flexneri. PLoS Pathogens, e003881.

2013

Barison N, Gupta R, Kolbe M (2013) A sophisticated multi-step secretion mechanism: how the type 3 secretion system is regulated. Cellular Microbiology, 15: 1809-1817.

Demers J P, Sgourakis N G, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A (2013) The Common Structural Architecture of Shigella flexneri and Salmonella typhimurium Type Three Secretion Needles. PLoS Pathogens, e100324.

2012

Senerovic L, Tsunoda SP, Gossmann C, Brinkmann V, Zychlinsky A, Meissner F, Kolbe M (2012) Spontaneous formation of IpaB ion channels in host cell membranes reveals how Shigella induces pyroptosis in macrophages. Cell Death & Disease, e384.

Mounier J, Boncompain G, Senerovic L, Lagache T, Chrétien F, Perez F, Kolbe M, Olivo-Marin JC, Sansonetti P J, Sauvonnet N (2012) Shigella Effector IpaB-Induced Cholesterol Relocation Disrupts the Golgi Complex and Recycling Network to Inhibit Host Cell Secretion. Cell Host & Microbe, 12: 381-389.

Loquet A, Sgourakis N G, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A (2012) Atomic model of the type III secretion system needle. Nature, 486: 276-279

Barison N, Lambers J, Hurwitz R, Kolbe M (2012) Interaction of MxiG with the Cytosolic Complex of the Type III Secretion System Controls Shigella Virulence. FASEB J, 26:1717-1726.

2011

Lunelli M, Hurwitz R, Lambers J, Kolbe M (2011) Crystal Structure of SipD-PrgI: Insight into the Open State of the Type Three Secretion System Needle Tip and its Interaction with Host Ligands. PLoS Pathogens, 7: 1-12.

2010

Lokareddy R K, Lunelli M, Eilers B, Wolter V, Kolbe M (2010) Combination of Two Separate Binding Domains Defines Stoichiometry between Type III Secretion System Chaperone IpgC and Translocator Protein IpaB. J. Biol. Chem., 285: 39965-39975.

Poyraz O, Schmidt H, Seidel K, Delissen F, Ader C, Tenenboim H, Goosmann C, Laube B, Thünemann A F, Zychlinsky A, Baldus M, Lange A, Griesinger C, Kolbe M (2010) Protein refolding is required for assembly of the type three secretion needle. Nat. Struct. Mol. Biol., 17: 788-792.

2009

Lunelli M, Lokareddy R K, Zychlinsky A, Kolbe M (2009) IpaB-IpgC interaction defines binding motif for type III secretion translocator. Proc. Natl. Acad. Sci., 106: 9661-9666.

2008

Averhoff P, Kolbe M, Zychlinsky A, Weinrauch Y (2008) Single residue determines the specificity of neutrophil elastase for Shigella virulence factors. J. Mol. Biol., 377: 1053-1066.

2007

Ernst O P, Gramse V, Kolbe M, Hofmann K P, Heck M (2007) Monomeric G protein-coupled receptor rhodopsin in solution activates its G protein transducin at the diffusion limit. Proc. Natl. Acad. Sci., 104: 10859- 10864.

2006

Blasig I E, Winkler L, Lassowski B, Mueller S L, Zuleger N, Krause E, Krause G, Gast K, Kolbe M, Piontek J (2006) On the self-association potential of transmembrane tight junction proteins. Cell. Mol. Life Sci., 63: 505- 514.

Schubert M, Kolbe M, Kessler B, Oesterhelt D, Schmieder P (2002) Heteronuclear multidimensional NMR spectroscopy of solubilized membrane proteins: resonance assignment of native bacteriorhodopsin. Chembiochem, 4: 1019-1023.

2002

Kolbe M (2002) Röntgenographische und spektroskopische Charakterisierung der lichgetriebenen Ionenpumpe Halorhodopsin aus Halobacterium salinarum.

2000

Paula S, Tittor J, Kolbe M, Oesterhelt D (2000) Spectroscopic studies on crystals from bacterio- and halorhodopsin. Biophys. J., 78: 286.

Kolbe M, Besir H, Essen L O, Oesterhelt D (2000) Structure of the Light- Driven Chloride Pump Halorhodopsin at 1.8 Å Resolution. Science, 288: 1390– 1396

Links

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