Nature

Profiling phagosome proteins identifies PD-L1 as a fungal-binding receptor

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  • Li, K. & Underhill, D. M. C-type lectin receptors in phagocytosis. Curr. Top. Microbiol. Immunol. 429, 1–18 (2020).

    PubMed 

    Google Scholar
     

  • Underhill, D. M. & Goodridge, H. S. Information processing during phagocytosis. Nat. Rev. Immunol. 12, 492–502 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stafford, C. A. et al. Phosphorylation of muramyl peptides by NAGK is required for NOD2 activation. Nature 609, 590–596 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wolf, A. J. et al. Hexokinase is an innate immune receptor for the detection of bacterial peptidoglycan. Cell 166, 624–636 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Faro-Trindade, I. et al. Characterisation of innate fungal recognition in the lung. PLoS ONE 7, e35675 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goldmann, M. et al. The lipid raft-associated protein stomatin is required for accumulation of dectin-1 in the phagosomal membrane and for full activity of macrophages against Aspergillus fumigatus. mSphere 8, e0052322 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Husebye, H. et al. The Rab11a GTPase controls Toll-like receptor 4-induced activation of interferon regulatory factor-3 on phagosomes. Immunity 33, 583–596 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kagan, J. C. & Iwasaki, A. Phagosome as the organelle linking innate and adaptive immunity. Traffic 13, 1053–1061 (2012).

    Article 
    CAS 
    PubMed 
    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
     

  • Goodridge, H. S. et al. Activation of the innate immune receptor dectin-1 upon formation of a ‘phagocytic synapse’. Nature 472, 471–475 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martell, J. D. et al. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat. Biotechnol. 30, 1143–1148 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hung, V. et al. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat. Protoc. 11, 456–475 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kang, M. G. & Rhee, H. W. Molecular spatiomics by proximity labeling. Acc. Chem. Res. 55, 1411–1422 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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
     

  • Boder, E. T. & Wittrup, K. D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15, 553–557 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Francisco, J. A., Earhart, C. F. & Georgiou, G. Transport and anchoring of β-lactamase to the external surface of Escherichia coli. Proc. Natl Acad. Sci. USA 89, 2713–2717 (1992).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fridy, P. C., Thompson, M. K., Ketaren, N. E. & Rout, M. P. Engineered high-affinity nanobodies recognizing staphylococcal protein A and suitable for native isolation of protein complexes. Anal. Biochem. 477, 92–94 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shui, W. et al. Membrane proteomics of phagosomes suggests a connection to autophagy. Proc. Natl Acad. Sci. USA 105, 16952–16957 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guo, M. et al. High-resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages. Proteomics 15, 3169–3174 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pauwels, A. M. et al. Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation. Mol. Cell. Proteomics 18, 909–922 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stuart, L. M. et al. A systems biology analysis of the Drosophila phagosome. Nature 445, 95–101 (2007).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Dong, H., Zhu, G., Tamada, K. & Chen, L. B7-H1, a third member of the B7 family, co-stimulates T-cell proliferation and interleukin-10 secretion. Nat. Med. 5, 1365–1369 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, L. Co-inhibitory molecules of the B7-CD28 family in the control of T-cell immunity. Nat. Rev. Immunol. 4, 336–347 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doroshow, D. B. et al. PD-L1 as a biomarker of response to immune-checkpoint inhibitors. Nat. Rev. Clin. Oncol. 18, 345–362 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Upadhaya, S. et al. Combinations take centre stage in PD1/PDL1 inhibitor clinical trials. Nat. Rev. Drug Discov. 20, 168–169 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liang, S. C. et al. Regulation of PD-1, PD-L1, and PD-L2 expression during normal and autoimmune responses. Eur. J. Immunol. 33, 2706–2716 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Graham, L. M. et al. Soluble dectin-1 as a tool to detect β-glucans. J. Immunol. Methods 314, 164–169 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stark, S., Flaig, R. M., Sandusky, M. & Watzl, C. The use of trimeric isoleucine-zipper fusion proteins to study surface-receptor-ligand interactions in natural killer cells. J. Immunol. Methods 296, 149–158 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zak, K. M. et al. Structural biology of the immune checkpoint receptor PD-1 and its ligands PD-L1/PD-L2. Structure 25, 1163–1174 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Micic, J. et al. Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly. Nat. Commun. 11, 3751 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Halbeisen, R. E., Scherrer, T. & Gerber, A. P. Affinity purification of ribosomes to access the translatome. Methods 48, 306–310 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zgadzay, Y. et al. E-site drug specificity of the human pathogen Candida albicans ribosome. Sci. Adv. 8, eabn1062 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, D. Y. et al. The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proc. Natl Acad. Sci. USA 105, 3011–3016 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Steffen, K. K. et al. Ribosome deficiency protects against ER stress in Saccharomyces cerevisiae. Genetics 191, 107–118 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hartley, G. P., Chow, L., Ammons, D. T., Wheat, W. H. & Dow, S. W. Programmed cell death ligand 1 (PD-L1) signaling regulates macrophage proliferation and activation. Cancer Immunol. Res. 6, 1260–1273 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hudson, K., Cross, N., Jordan-Mahy, N. & Leyland, R. The extrinsic and intrinsic roles of PD-L1 and its receptor PD-1: implications for immunotherapy treatment. Front. Immunol. 11, 568931 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yesbolatova, A. et al. The auxin-inducible degron 2 technology provides sharp degradation control in yeast, mammalian cells, and mice. Nat. Commun. 11, 5701 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ene, I. V., Cheng, S. C., Netea, M. G. & Brown, A. J. Growth of Candida albicans cells on the physiologically relevant carbon source lactate affects their recognition and phagocytosis by immune cells. Infect. Immun. 81, 238–248 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nieto, C. et al. The programmed death ligand 1 interactome demonstrates bidirectional signaling coordinating immune suppression and cancer progression in head and neck squamous cell carcinoma. J. Natl Cancer Inst. 115, 1392–1403 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schafer, J. B., Lucas, E. D., Dzieciatkowska, M., Forward, T. & Tamburini, B. A. J. Programmed death ligand 1 intracellular interactions with STAT3 and focal adhesion protein paxillin facilitate lymphatic endothelial cell remodeling. J. Biol. Chem. 298, 102694 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lucas, E. D. et al. PD-L1 reverse signaling in dermal dendritic cells promotes dendritic cell migration required for skin immunity. Cell Rep. 33, 108258 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, Y. et al. PD-L1 negatively regulates antifungal immunity by inhibiting neutrophil release from bone marrow. Nat. Commun. 13, 6857 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kagan, J. C. Infection infidelities drive innate immunity. Science 379, 333–335 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Oldenburg, M. et al. TLR13 recognizes bacterial 23S rRNA devoid of erythromycin resistance-forming modification. Science 337, 1111–1115 (2012).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, X. D. & Chen, Z. J. Sequence specific detection of bacterial 23S ribosomal RNA by TLR13. eLife 1, e00102 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nishiura, H. et al. Monocyte chemotactic factor in rheumatoid arthritis synovial tissue. Probably a cross-linked derivative of S19 ribosomal protein. J. Biol. Chem. 271, 878–882 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Filip, A. M. et al. Ribosomal protein S19 interacts with macrophage migration inhibitory factor and attenuates its pro-inflammatory function. J. Biol. Chem. 284, 7977–7985 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zapatero-Belinchon, F. J., Carriqui-Madronal, B. & Gerold, G. Proximity labeling approaches to study protein complexes during virus infection. Adv. Virus Res. 109, 63–104 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dickinson, M. S. et al. Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites. PLoS Pathog. 15, e1007698 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Olson, M. G. et al. Proximity labeling to map host–pathogen interactions at the membrane of a bacterium-containing vacuole in Chlamydia trachomatis-infected human cells. Infect. Immun. https://doi.org/10.1128/IAI.00537-19 (2019).

  • Yan, Y. et al. Receptor-interacting protein kinase 2 (RIPK2) stabilizes c-Myc and is a therapeutic target in prostate cancer metastasis. Nat. Commun. 13, 669 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Szklarczyk, D. et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638–D646 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hill, B. D., Prabhu, P., Rizvi, S. M. & Wen, F. Yeast intracellular staining (yICS): enabling high-throughput, quantitative detection of intracellular proteins via flow cytometry for pathway engineering. ACS Synth. Biol. 9, 2119–2131 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Harnpicharnchai, P. et al. Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol. Cell 8, 505–515 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bernstein, F. C. et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542 (1977).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lyskov, S. et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS ONE 8, e63906 (2013).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Morin, A. et al. Collaboration gets the most out of software. eLife 2, e01456 (2013).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marze, N. A., Roy Burman, S. S., Sheffler, W. & Gray, J. J. Efficient flexible backbone protein–protein docking for challenging targets. Bioinformatics 34, 3461–3469 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cravener, M. V. & Mitchell, A. P. Candida albicans culture, cell harvesting, and total RNA extraction. Bio Protoc. 10, e3803 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).

    Article 

    Google Scholar
     

  • Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Horwitz, A. A. et al. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR–Cas. Cell Syst. 1, 88–96 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ewels, P. A. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 38, 276–278 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Korotkevich, G., Sukhov, V. & Sergushichev, A. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2019).

  • Gantner, B. N., Simmons, R. M., Canavera, S. J., Akira, S. & Underhill, D. M. Collaborative induction of inflammatory responses by dectin-1 and Toll-like receptor 2. J. Exp. Med. 197, 1107–1117 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     



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