Molecular definition of the endogenous Toll-like receptor signalling pathways – Nature

    0


  • Janeway, C. A. Approaching the asymptote? Evolution and revolution in immunology. Cold Spring Harb. Symp. Quant. Biol. 54, 1–13 (1989).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kawai, T. & Akira, S. TLR signaling. Cell Death Differ. 13, 816–825 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kawai, T. & Akira, S. The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat. Immunol. 11, 373–384 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Motshwene, P. G. et al. An oligomeric signaling platform formed by the toll-like receptor signal transducers MyD88 and IRAK-4. J. Biol. Chem. 284, 25404–25411 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bonham, K. S. et al. A promiscuous lipid-binding protein diversifies the subcellular sites of Toll-like receptor signal transduction. Cell 156, 705–716 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, S.-C., Lo, Y.-C. & Wu, H. Helical assembly in the MyD88–IRAK4–IRAK2 complex in TLR/IL-1R signalling. Nature 465, 885–890 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Deguine, J. & Barton, G. M. MyD88: a central player in innate immune signaling. F1000Prime Rep. 6, 97 (2014).

  • Medzhitov, R. et al. MyD88 is an adaptor protein in the hToll/IL-1 receptor family signaling pathways. Mol. Cell 2, 253–258 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liu, T., Zhang, L., Joo, D. & Sun, S.-C. NF-κB signaling in inflammation. Signal Transduct. Target. Ther. 2, 17023 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kawai, T., Adachi, O., Ogawa, T., Takeda, K. & Akira, S. Unresponsiveness of MyD88-deficient mice to endotoxin. Immunity 11, 115–122 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Strickson, S. et al. Roles of the TRAF6 and Pellino E3 ligases in MyD88 and RANKL signaling. Proc. Natl Acad. Sci. USA 114, E3481–E3489 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cohen, P. & Strickson, S. The role of hybrid ubiquitin chains in the MyD88 and other innate immune signalling pathways. Cell Death Differ. 24, 1153–1159 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Arthur, J. S. C. & Ley, S. C. Mitogen-activated protein kinases in innate immunity. Nat. Rev. Immunol. 13, 679–692 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fitzgerald, K. A. et al. IKKε and TBK1 are essential components of the IRF3 signaling pathway. Nat. Immunol. 4, 491–496 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tan, Y. & Kagan, J. C. Innate immune signaling organelles display natural and programmable signaling flexibility. Cell 177, 384–398 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Du, X., Poltorak, A., Silva, M. & Beutler, B. Analysis of Tlr4-mediated LPS signal transduction in macrophages by mutational modification of the receptor. Blood Cells Mol. Dis. 25, 328–338 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kagan, J. C. et al. TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-β. Nat. Immunol. 9, 361–368 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pandey, S., Kawai, T. & Akira, S. Microbial sensing by Toll-like receptors and intracellular nucleic acid sensors. Cold Spring Harb. Perspect. Biol. 7, a016246 (2015).

    Article 
    PubMed Central 

    Google Scholar
     

  • Fitzgerald, K. A. & Kagan, J. C. Toll-like receptors and the control of immunity. Cell 180, 1044–1066 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • O’Neill, L. A. J., Golenbock, D. & Bowie, A. G. The history of Toll-like receptors—redefining innate immunity. Nat. Rev. Immunol. 13, 453–460 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • West, A. P., Koblansky, A. A. & Ghosh, S. Recognition and signaling by Toll-like receptors. Annu. Rev. Cell Dev. Biol. 22, 409–437 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lam, S. S. et al. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat. Methods 12, 51–54 (2015).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Zacharias, D. A., Violin, J. D., Newton, A. C. & Tsien, R. Y. Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 296, 913–916 (2002).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • De Nardo, D. et al. Interleukin-1 receptor–associated kinase 4 (IRAK4) plays a dual role in myddosome formation and Toll-like receptor signaling. J. Biol. Chem 293, 15195–15207 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hornung, V. et al. Quantitative expression of Toll-like receptor 1–10 mRNA in cellular subsets of human peripheral blood mononuclear cells and sensitivity to CpG oligodeoxynucleotides. J. Immunol. 168, 4531–4537 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Alexopoulou, L., Holt, A. C., Medzhitov, R. & Flavell, R. A. Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature 413, 732–738 (2001).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Powers, E. T. & Powers, D. L. The kinetics of nucleated polymerizations at high concentrations: amyloid fibril formation near and above the “supercritical concentration”. Biophys. J. 91, 122–132 (2006).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cushing, L. et al. IRAK4 kinase activity controls Toll-like receptor–induced inflammation through the transcription factor IRF5 in primary human monocytes. J. Biol. Chem. 292, 18689–18698 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moncrieffe, M. C. et al. MyD88 death-domain oligomerization determines myddosome architecture: implications for Toll-like receptor signaling. Structure 28, 281–289 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Suzuki, N. et al. Severe impairment of interleukin-1 and Toll-like receptor signalling in mice lacking IRAK-4. Nature 416, 750–754 (2002).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Pereira, M. et al. The IRAK4 scaffold integrates TLR4-driven TRIF and MYD88 signaling pathways. Cell Rep. 40, 111225 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, K. L. et al. Discovery of clinical candidate 1-{[(2S,3S,4S)−3-ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}−7-methoxyisoquinoline-6-carboxamide (PF-06650833), a potent, selective inhibitor of interleukin-1 receptor associated kinase 4 (IRAK4), by fragment-based drug design. J. Med. Chem. 60, 5521–5542 (2017).

  • Cao, Z., Xiong, J., Takeuchi, M., Kurama, T. & Goeddel, D. V. TRAF6 is a signal transducer for interleukin-1. Nature 383, 443–446 (1996).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Pomerantz, J. L. & Baltimore, D. NF‐κB activation by a signaling complex containing TRAF2, TANK and TBK1, a novel IKK‐related kinase. EMBO J. 18, 6694–6704 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, Z. J., Parent, L. & Maniatis, T. Site-specific phosphorylation of IκBα by a novel ubiquitination-dependent protein kinase activity. Cell 84, 853–862 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • DiDonato, J. A., Hayakawa, M., Rothwarf, D. M., Zandi, E. & Karin, M. A cytokine-responsive IκB kinase that activates the transcription factor NF-κB. Nature 388, 548–554 (1997).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Yamaoka, S. et al. Complementation cloning of NEMO, a component of the IκB kinase complex essential for NF-κB activation. Cell 93, 1231–1240 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rothwarf, D. M., Zandi, E., Natoli, G. & Karin, M. IKK-γ is an essential regulatory subunit of the IκB kinase complex. Nature 395, 297–300 (1998).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Mercurio, F. et al. IκB kinase (IKK)-associated protein 1, a common component of the heterogeneous IKK complex. Mol. Cell. Biol. 19, 1526–1538 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Q. et al. Enhanced NF-κB activation and cellular function in macrophages lacking IκB kinase 1 (IKK1). Proc. Natl Acad. Sci. USA 102, 12425–12430 (2005).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gerondakis, S. et al. Unravelling the complexities of the NF-κB signalling pathway using mouse knockout and transgenic models. Oncogene 25, 6781–6799 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kang, Y. J. et al. Macrophage deletion of p38α partially impairs lipopolysaccharide-induced cellular activation. J. Immunol. 180, 5075–5082 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Alberti-Segui, C., Goeden, K. R. & Higgins, D. E. Differential function of Listeria monocytogenes listeriolysin O and phospholipases C in vacuolar dissolution following cell-to-cell spread. Cell. Microbiol. 9, 179–195 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ngo, V. N. et al. Oncogenically active MYD88 mutations in human lymphoma. Nature 470, 115–119 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Treon, S. P. et al. MYD88 L265P somatic mutation in Waldenström’s macroglobulinemia. N. Engl. J. Med. 367, 826–833 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Balka, K. R. & De Nardo, D. Understanding early TLR signaling through the Myddosome. J. Leukoc. Biol. 105, 339–351 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schmid-Burgk, J. L., Höning, K., Ebert, T. S. & Hornung, V. CRISPaint allows modular base-specific gene tagging using a ligase-4-dependent mechanism. Nat. Commun. 7, 12338 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fazal, F. M. et al. Atlas of subcellular rna localization revealed by APEX-Seq. Cell 178, 473–490 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fisch, D. et al. Human GBP1 is a microbe‐specific gatekeeper of macrophage apoptosis and pyroptosis. EMBO J. 38, e100926 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kremers, G.-J., Hazelwood, K. L., Murphy, C. S., Davidson, M. W. & Piston, D. W. Photoconversion in orange and red fluorescent proteins. Nat. Methods 6, 355–358 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanjabi, S. et al. A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. Genes Dev. 19, 2138–2151 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bindels, D. S. et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 14, 53–56 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fisch, D. et al. Human GBP1 differentially targets Salmonella and Toxoplasma to license recognition of microbial ligands and caspase-mediated death. Cell Rep. 32, 108008 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tan, Y. & Kagan, J. C. Biochemical isolation of the myddosome from murine macrophages. Methods Mol. Biol. 1714, 79–95 (2018).

  • Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mellacheruvu, D. et al. The CRAPome: a contaminant repository for affinity purification–mass spectrometry data. Nat. Methods 10, 730–736 (2013). 2013 108.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Berthold, M. R. et al. in Data Analysis, Machine Learning and Applications. Studies in Classification, Data Analysis, and Knowledge Organization 319–326 (Springer, 2008); https://doi.org/10.1007/978-3-540-78246-9_38.

  • Szklarczyk, D. et al. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49, D605–D612 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kang, M., Andreani, M. & Kenworthy, A. K. Validation of normalizations, scaling, and photofading corrections for FRAP data analysis. PLoS ONE 10, e0127966 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Miura, K. Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences. F1000Res. 9, 1494 (2020).

  • Laine, R. F. et al. NanoJ: a high-performance open-source super-resolution microscopy toolbox. J. Phys. Appl. Phys. 52, 163001 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Krull, A., Buchholz, T.-O. & Jug, F. Noise2Void—learning denoising from single noisy images. In Proc. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (ed. O’Conner, L.) 2124–2132 (IEEEComputer Society, 2019).

  • Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat. Methods https://doi.org/10.1038/s41592-022-01663-4 (2022).

  • Cutler, K. J. et al. Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation. Nat. Methods 19, 1438–1448 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schmidt, U., Weigert, M., Broaddus, C. & Myers, G. Cell detection with star-convex polygons. Lect. Notes Comput. Sci. 11071, 265–273 (2018).

  • Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ershov, D. et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat. Methods 19, 829–832 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fisch, D. et al. Defining host–pathogen interactions employing an artificial intelligence workflow. eLife 8, e40560 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fisch, D. et al. PIM1 controls GBP1 activity to limit self-damage and to guard against pathogen infection. Science 382, eadg2253 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Magupalli, V. G. et al. HDAC6 mediates an aggresome-like mechanism for NLRP3 and pyrin inflammasome activation. Science 369, eaas8995 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Clough, B. et al. K63-linked ubiquitination targets Toxoplasma gondii for endo-lysosomal destruction in IFNγ-stimulated human cells. PLoS Pathog. 12, e1006027 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     



  • Source link