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Cryo-EM elucidates the uroplakin complex structure within liquid-crystalline lipids in the porcine urothelial membrane
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Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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Research works printed but not linked: 76
- Deng, F. M., Ding, M., Lavker, R. M. & Sun, T. T. Urothelial function reconsidered: a new role in urinary protein secretion. Urology 57, 117 (2001). · DOI
- Wu, X. R., Kong, X. P., Pellicer, A., Kreibich, G. & Sun, T. T. Uroplakins in urothelial biology, function, and disease. Kidney Int. 75, 1153–1165 (2009). · DOI
- Apodaca, G. The uroepithelium: not just a passive barrier. Traffic 5, 117–128 (2004). · DOI
- Khandelwal, P., Abraham, S. N. & Apodaca, G. Cell biology and physiology of the uroepithelium. Am. J. Physiol. Renal Physiol. 297, F1477–F1501 (2009). · DOI
- Hu, P. et al. Ablation of uroplakin III gene results in small urothelial plaques, urothelial leakage, and vesicoureteral reflux. J. Cell Biol. 151, 961–972 (2000). · DOI
- Jenkins, D. & Woolf, A. S. Uroplakins: new molecular players in the biology of urinary tract malformations. Kidney Int. 71, 195–200 (2007). · DOI
- Lee, G. Uroplakins in the lower urinary tract. Int. Neurourol. J. 15, 4–12 (2011). · DOI
- Yu, J., Lin, J. H., Wu, X. R. & Sun, T. T. Uroplakins Ia and Ib, two major differentiation products of bladder epithelium, belong to a family of four transmembrane domain (4TM) proteins. J. Cell Biol 125, 171–182 (1994). · DOI
- Hu, C. C. et al. Assembly of urothelial plaques: tetraspanin function in membrane protein trafficking. Mol. Biol. Cell 16, 3937–3950 (2005). · DOI
- Tu, L., Sun, T. T. & Kreibich, G. Specific heterodimer formation is a prerequisite for uroplakins to exit from the endoplasmic reticulum. Mol. Biol. Cell 13, 4221–4230 (2002). · DOI
- Liang, F. X. et al. Organization of uroplakin subunits: transmembrane topology, pair formation and plaque composition. Biochem. J. 355, 13–18 (2001). · DOI
- Min, G., Wang, H., Sun, T. T. & Kong, X. P. Structural basis for tetraspanin functions as revealed by the cryo-EM structure of uroplakin complexes at 6-A resolution. J. Cell Biol. 173, 975–983 (2006). · DOI
- Min, G., Zhou, G., Schapira, M., Sun, T. T. & Kong, X. P. Structural basis of urothelial permeability barrier function as revealed by Cryo-EM studies of the 16 nm uroplakin particle. J. Cell Sci. 116, 4087–4094 (2003). · DOI
- Min, G. et al. Localization of uroplakin Ia, the urothelial receptor for bacterial adhesin FimH, on the six inner domains of the 16 nm urothelial plaque particle. J. Mol. Biol. 317, 697–706 (2002). · DOI
- Walz, T. et al. Towards the molecular architecture of the asymmetric unit membrane of the mammalian urinary bladder epithelium: a closed “twisted ribbon” structure. J. Mol. Biol. 248, 887–900 (1995). · DOI
- Wang, H., Min, G., Glockshuber, R., Sun, T. T. & Kong, X. P. Uropathogenic E. coli adhesin-induced host cell receptor conformational changes: implications in transmembrane signaling transduction. J. Mol. Biol. 392, 352–361 (2009). · DOI
- Hultgren, S. J. et al. Pilus and nonpilus bacterial adhesins: assembly and function in cell recognition. Cell 73, 887–901 (1993). · DOI · Paper page
- Hooton, T. M. & Stamm, W. E. Diagnosis and treatment of uncomplicated urinary tract infection. Infect. Dis. Clin. North Am. 11, 551–581 (1997). · DOI
- Zhou, G. et al. Uroplakin Ia is the urothelial receptor for uropathogenic Escherichia coli: evidence from in vitro FimH binding. J. Cell Sci. 114, 4095–4103 (2001). · DOI
- Thumbikat, P. et al. Bacteria-induced uroplakin signaling mediates bladder response to infection. PLoS Pathog. 5, e1000415 (2009). · DOI
- Sorzano et al. Cryo-EM and the elucidation of new macromolecular structures: random conical tilt revisited. Sci. Rep. 5, 14290 (2015). · DOI
- Frank, J., Goldfarb, W., Eisenberg, D. & Baker, T. S. Reconstruction of glutamine synthetase using computer averaging. Ultramicroscopy 3, 283–290 (1978). · DOI
- Righetto, R. D., Biyani, N., Kowal, J., Chami, M. & Stahlberg, H. Retrieving high-resolution information from disordered 2D crystals by single-particle cryo-EM. Nat. Commun. 10, 1722 (2019). · DOI
- Radermacher, M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J. Electron Microsc. Tech. 9, 359–394 (1988). · DOI
- Liang, F. et al. Urothelial hinge as a highly specialized membrane: detergent-insolubility, urohingin association, and in vitro formation. Differentiation 65, 59–69 (1999). · DOI
- Oda, T., Yanagisawa, H., Shinmori, H., Ogawa, Y. & Kawamura, T. Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation. Elife 11, e79990 (2022). · DOI · Paper page
- Dutka, P. et al. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Biophys. J. 122, 40A (2023). · DOI
- Zhao, P. et al. Structure and activation mechanism of the hexameric plasma membrane H(+)-ATPase. Nat. Commun. 12, 6439 (2021).
- Ghysels, A. et al. Permeability of membranes in the liquid ordered and liquid disordered phases. Nat. Commun. 10, 5616 (2019). · DOI · Paper page
- Ulmschneider, M. B. & Sansom, M. S. Amino acid distributions in integral membrane protein structures. Biochim. Biophys. Acta 1512, 1–14 (2001). · DOI
- Simons, K. & Ehehalt, R. Cholesterol, lipid rafts, and disease. J. Clin. Invest. 110, 597–603 (2002). · DOI
- Kusumi, A. et al. Defining raft domains in the plasma membrane. Traffic 21, 106–137 (2020). · DOI
- Liu, S. L. et al. Orthogonal lipid sensors identify transbilayer asymmetry of plasma membrane cholesterol. Nat. Chem. Biol. 13, 268–274 (2017). · DOI · Paper page
- Lin, J. H., Wu, X. R., Kreibich, G. & Sun, T. T. Precursor sequence, processing, and urothelium-specific expression of a major 15-kDa protein subunit of asymmetric unit membrane. J. Biol. Chem. 269, 1775–1784 (1994). · DOI
- Kanik-Prastowska, I., Lis, J. & Matejuk, A. Glycosylation of uroplakins. Implications for bladder physiopathology. Glycoconj. J. 31, 623–636 (2014). · DOI
- Wu, X. R., Medina, J. J. & Sun, T. T. Selective interactions of UPIa and UPIb, two members of the transmembrane 4 superfamily, with distinct single transmembrane-domained proteins in differentiated urothelial cells. J. Biol. Chem. 270, 29752–29759 (1995). · DOI
- Xie, B. et al. Distinct glycan structures of uroplakins Ia and Ib: structural basis for the selective binding of FimH adhesin to uroplakin Ia. J. Biol. Chem. 281, 14644–14653 (2006). · DOI
- El, Mazouni, D. & Gros, P. Cryo-EM structures of peripherin-2 and ROM1 suggest multiple roles in photoreceptor membrane morphogenesis. Sci. Adv. 8, eadd3677 (2022). · DOI
- Hicks, R. M., Ketterer, B. & Warren, R. C. The ultrastructure and chemistry of the luminal plasma membrane of the mammalian urinary bladder: a structure with low permeability to water and ions. Philos. Trans. R. Soc. Lond. B Biol. Sci. 268, 23–38 (1974). · DOI
- Stubbs, C. D., Ketterer, B. & Hicks, R. M. The isolation and analysis of the luminal plasma membrane of calf urinary bladder epithelium. Biochim. Biophys. Acta 558, 58–72 (1979). · DOI
- Watanabe, T. et al. The urinary bladder is rich in glycosphingolipids composed of phytoceramides. J. Lipid Res. 63, 100303 (2022). · DOI
- Lee, J. H., de, Val, N., Lyumkis, D. & Ward, A. B. Model building and refinement of a natively glycosylated HIV-1 Env protein by high-resolution cryoelectron microscopy. Structure 23, 1943–1951 (2015). · DOI
- Prestegard, J. H. A perspective on the PDB’s impact on the field of glycobiology. J. Biol. Chem. 296, 100556 (2021). · DOI
- Sauer, M. M. et al. Catch-bond mechanism of the bacterial adhesin FimH. Nat. Commun. 7, 10738 (2016). · DOI
- Desai, A. J. & Miller, L. J. Changes in the plasma membrane in metabolic disease: impact of the membrane environment on G protein-coupled receptor structure and function. Br. J. Pharmacol. 175, 4009–4025 (2018). · DOI
- Los, D. A. & Murata, N. Membrane fluidity and its roles in the perception of environmental signals. Biochim. Biophys. Acta 1666, 142–157 (2004). · DOI · Paper page
- Balogh, G. et al. The hyperfluidization of mammalian cell membranes acts as a signal to initiate the heat shock protein response. FEBS J. 272, 6077–6086 (2005). · DOI
- Zhang, T., Hu, W. & Chen, W. Plasma membrane integrates biophysical and biochemical regulation to trigger immune receptor functions. Front. Immunol. 12, 613185 (2021). · DOI
- Ord, M., Faustova, I. & Loog, M. The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV. Sci. Rep. 10, 16944 (2020).
- Negrete, H. O., Lavelle, J. P., Berg, J., Lewis, S. A. & Zeidel, M. L. Permeability properties of the intact mammalian bladder epithelium. Am. J. Physiol. 271, F886–F894 (1996).
- Lavelle, J. P., Apodaca, G., Meyers, S. A., Ruiz, W. G. & Zeidel, M. L. Disruption of guinea pig urinary bladder permeability barrier in noninfectious cystitis. Am. J. Physiol. 274, F205–F214 (1998).
- Hu, P. et al. Role of membrane proteins in permeability barrier function: uroplakin ablation elevates urothelial permeability. Am. J. Physiol. Renal Physiol. 283, F1200–F1207 (2002). · DOI
- Huang, H. W., Goldberg, E. M. & Zidovetzki, R. Ceramide induces structural defects into phosphatidylcholine bilayers and activates phospholipase A2. Biochem. Biophys. Res. Commun. 220, 834–838 (1996). · DOI
- Grassme, H., Schwarz, H. & Gulbins, E. Molecular mechanisms of ceramide-mediated CD95 clustering. Biochem. Biophys. Res. Commun. 284, 1016–1030 (2001). · DOI
- Grassme, H. et al. CD95 signaling via ceramide-rich membrane rafts. J. Biol. Chem. 276, 20589–20596 (2001). · DOI
- Sodt, A. J., Pastor, R. W. & Lyman, E. Hexagonal substructure and hydrogen bonding in liquid-ordered phases containing palmitoyl sphingomyelin. Biophys. J. 109, 948–955 (2015). · DOI
- Gensure, R. H., Zeidel, M. L. & Hill, W. G. Lipid raft components cholesterol and sphingomyelin increase H+/OH- permeability of phosphatidylcholine membranes. Biochem. J. 398, 485–495 (2006). · DOI
- Pellecchia, M., Sebbel, P., Hermanns, U., Wüthrich, K. & Glockshuber, R. Pilus chaperone FimC-adhesin FimH interactions mapped by TROSY-NMR. Nat. Struct. Biol. 6, 336–339 (1999). · DOI
- Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005). · DOI
- Hagen, W. J. H., Wan, W. & Briggs, J. A. G. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197, 191–198 (2017). · DOI
- Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996). · DOI
- Nicastro, D. et al. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313, 944–948 (2006). · DOI
- Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
- Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022). · DOI · Paper page
- Evans, R., et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022). · DOI · Paper page
- Kwon, D. N. et al. Characterization of a putative cis-regulatory element that controls transcriptional activity of the pig uroplakin II gene promoter. Biochem. Biophys. Res. Commun. 410, 264–269 (2011). · DOI
- Visnjar, T. et al. Uroplakin traffic through the Golgi apparatus induces its fragmentation: new insights from novel in vitro models. Sci. Rep. 7, 12842 (2017). · DOI
- Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019). · DOI · Paper page
- Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018). · DOI
- Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010). · DOI · Paper page
- Emsley, P. & Crispin, M. Structural analysis of glycoproteins: building N-linked glycans with Coot. Acta Crystallogr. D Struct. Biol. 74, 256–263 (2018). · DOI
- Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI
- Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI
- Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). · DOI · Paper page
- Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018). · DOI
- Tsugawa, H. et al. A lipidome atlas in MS-DIAL 4. Nat. Biotechnol. 38, 1159–1163 (2020). · DOI
Metadata
- Authors
- Yanagisawa, H., Kita, Y., Oda, T., & Kikkawa, M.
- Affiliations
- The University of Tokyo (JP)
- University of Yamanashi (JP)
- Corresponding author
- Oda, Toshiyuki
- Kikkawa, Masahide
- Venue
- Communications Biology
- Published
- 2023-10-07
- Volume
- 6
- Issue
- 1
- Pages
- 1018-1018
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC10560298
- OpenAlex
- W4387425865
- Cited by
- 13
- References
- 2
- Citations by year
- 2026: 2 · 2025: 9 · 2024: 2
- FWCI
- 1.32
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- MEXT | Japan Society for the Promotion of Science (JP21H02654, JP22H05538, JP21H05248)
- Takeda Science Foundation
- Daiichi Sankyo Foundation of Life Science
- Naito Foundation
- Japan Agency for Medical Research and Development (JP22ama121002, JP23ama121002)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Skin and Cellular Biology Research
- Keywords
- urothelium, hexosylceramide, urinary tract infection, permeability barrier, membrane protein structure
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