{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:56:09Z","timestamp":1790776569062,"version":"4.1.0"},"reference-count":138,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                    is an obligate intracellular bacterial pathogen and a leading cause of sexually transmitted infections worldwide. During its biphasic developmental cycle, infectious, non-replicative elementary bodies alternate with replicative reticulate bodies within a membrane-bound intracellular niche known as the inclusion.\n                    <jats:italic>C. trachomatis<\/jats:italic>\n                    relies heavily on host-derived metabolites, including sphingolipids, which are essential for inclusion integrity, bacterial growth and production of infectious progeny. Here, using expansion microscopy, we uncover an unexpected localization of sphingolipid derivatives within the highly condensed DNA nucleoids of elementary bodies. These sphingolipids are released from nucleoids prior to DNA decondensation during the elementary-to-reticulate body transition, the earliest phenotypic event in the complex developmental cycle of these bacteria. Thereafter, nucleoids undergo a characteristic DNA decondensation process that we visualized by expansion microscopy. By combining super-resolution imaging with a FRET-based metabolic tracking approach and lipidomics, we identified sphingomyelin derived from the sphingolipid analogues as the sphingolipid species predominantly associated with the condensing nucleoids of elementary bodies. Notably, reticulate bodies arrested in their developmental stage fail to accumulate sphingomyelin, suggesting a potential role for this lipid in stage-specific DNA condensation.\n                  <\/jats:p>","DOI":"10.1038\/s41467-026-77974-3","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T11:12:50Z","timestamp":1790766770000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Sphingolipids associate with the chlamydial nucleoid and mark developmental transitions in Chlamydia trachomatis"],"prefix":"10.1038","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4757-5014","authenticated-orcid":false,"given":"Marcel","family":"R\u00fchling","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-7828-026X","authenticated-orcid":false,"given":"Fabienne","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5931-4897","authenticated-orcid":false,"given":"Till","family":"Epprecht","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7029-1111","authenticated-orcid":false,"given":"Paul F.","family":"K\u00f6hling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8703-3275","authenticated-orcid":false,"given":"Fabian","family":"Schumacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Sachs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louise","family":"Kersting","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian","family":"Fink","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lina","family":"Girndt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1888-9595","authenticated-orcid":false,"given":"Burkhard","family":"Kleuser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1692-3219","authenticated-orcid":false,"given":"Markus","family":"Sauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8036-4853","authenticated-orcid":false,"given":"J\u00fcrgen","family":"Seibel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2132-670X","authenticated-orcid":false,"given":"Gregor L.","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4740-6991","authenticated-orcid":false,"given":"Thomas","family":"Rudel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"77974_CR1","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/nrm.2017.107","volume":"19","author":"YA Hannun","year":"2018","unstructured":"Hannun, Y. A. & Obeid, L. M. Sphingolipids and their metabolism in physiology and disease. Nat. Rev. Mol. Cell Biol. 19, 175\u2013191 (2018).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"77974_CR2","doi-asserted-by":"publisher","first-page":"1552","DOI":"10.1126\/science.279.5356.1552","volume":"279","author":"MJ Lee","year":"1998","unstructured":"Lee, M. J. et al. Sphingosine-1-phosphate as a ligand for the G protein-coupled receptor EDG-1. Science 279, 1552\u20131555 (1998).","journal-title":"Science"},{"key":"77974_CR3","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/S0163-7827(00)00007-2","volume":"39","author":"N Aug\u00e9","year":"2000","unstructured":"Aug\u00e9, N., N\u00e8gre-Salvayre, A., Salvayre, R. & Levade, T. Sphingomyelin metabolites in vascular cell signaling and atherogenesis. Prog. Lipid Res. 39, 207\u2013229 (2000).","journal-title":"Prog. Lipid Res."},{"key":"77974_CR4","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/42408","volume":"387","author":"K Simons","year":"1997","unstructured":"Simons, K. & Ikonen, E. Functional rafts in cell membranes. Nature 387, 569\u2013572 (1997).","journal-title":"Nature"},{"key":"77974_CR5","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.chemphyslip.2018.08.003","volume":"216","author":"E Bieberich","year":"2018","unstructured":"Bieberich, E. Sphingolipids and lipid rafts: Novel concepts and methods of analysis. Chem. Phys. Lipids 216, 114\u2013131 (2018).","journal-title":"Chem. Phys. Lipids"},{"key":"77974_CR6","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1083\/jcb.200307087","volume":"162","author":"EC Lai","year":"2003","unstructured":"Lai, E. C. Lipid rafts make for slippery platforms. J. Cell Biol. 162, 365\u2013370 (2003).","journal-title":"J. Cell Biol."},{"key":"77974_CR7","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1194\/jlr.TR120000658","volume":"61","author":"D Sviridov","year":"2020","unstructured":"Sviridov, D., Mukhamedova, N. & Miller, Y. I. Lipid rafts as a therapeutic target. J. Lipid Res. 61, 687\u2013695 (2020).","journal-title":"J. Lipid Res."},{"key":"77974_CR8","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.ymgme.2016.12.008","volume":"120","author":"EH Schuchman","year":"2017","unstructured":"Schuchman, E. H. & Desnick, R. J. Types A and B Niemann-Pick disease. Mol. Genet. Metab. 120, 27\u201333 (2017).","journal-title":"Mol. Genet. Metab."},{"key":"77974_CR9","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1016\/j.ejim.2006.07.005","volume":"17","author":"A Mehta","year":"2006","unstructured":"Mehta, A. Epidemiology and natural history of Gaucher\u2019s disease. Eur. J. Intern. Med. 17, S2\u2013S5 (2006).","journal-title":"Eur. J. Intern. Med."},{"key":"77974_CR10","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1016\/j.plipres.2013.05.001","volume":"52","author":"JP Slotte","year":"2013","unstructured":"Slotte, J. P. Biological functions of sphingomyelins. Prog. Lipid Res. 52, 424\u2013437 (2013).","journal-title":"Prog. Lipid Res."},{"key":"77974_CR11","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/0009-8981(75)90220-X","volume":"59","author":"RE De Rooij","year":"1975","unstructured":"De Rooij, R. E., Liem, K. O., Brouwer-Schipper, J. W., Husmann, G. G. & Hooghwinkel, G. J. A method for the determination of sphingomyelinase activity. Clin. Chim. Acta 59, 71\u201379 (1975).","journal-title":"Clin. Chim. Acta"},{"key":"77974_CR12","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/S0022-2275(20)40138-5","volume":"8","author":"PB Schneider","year":"1967","unstructured":"Schneider, P. B. & Kennedy, E. P. Sphingomyelinase in normal human spleens and in spleens from subjects with Niemann-Pick disease. J. Lipid Res. 8, 202\u2013209 (1967).","journal-title":"J. Lipid Res."},{"key":"77974_CR13","doi-asserted-by":"publisher","first-page":"3884","DOI":"10.1016\/S0021-9258(19)69540-2","volume":"256","author":"T Yamanaka","year":"1981","unstructured":"Yamanaka, T., Hanada, E. & Suzuki, K. Acid sphingomyelinase of human brain. Improved purification procedures and characterization. J. Biol. Chem. 256, 3884\u20133889 (1981).","journal-title":"J. Biol. Chem."},{"key":"77974_CR14","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/0005-2760(95)00245-6","volume":"1300","author":"L Nyberg","year":"1996","unstructured":"Nyberg, L., Duan, R. D., Axelson, J. & Nilsson, A. Identification of an alkaline sphingomyelinase activity in human bile. Biochim. Biophys. Acta 1300, 42\u201348 (1996).","journal-title":"Biochim. Biophys. Acta"},{"key":"77974_CR15","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1093\/cvr\/cvp030","volume":"82","author":"C Pavoine","year":"2009","unstructured":"Pavoine, C. & Pecker, F. Sphingomyelinases: their regulation and roles in cardiovascular pathophysiology. Cardiovasc. Res. 82, 175\u2013183 (2009).","journal-title":"Cardiovasc. Res."},{"key":"77974_CR16","doi-asserted-by":"crossref","unstructured":"Breiden, B. & Sandhoff, K. Acid Sphingomyelinase, a Lysosomal and Secretory Phospholipase C, Is Key for Cellular Phospholipid Catabolism. Int. J. Mol. Sci. 22, (2021).","DOI":"10.3390\/ijms22169001"},{"key":"77974_CR17","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1016\/S0092-8674(00)80448-1","volume":"91","author":"H Grassme","year":"1997","unstructured":"Grassme, H. et al. Acidic sphingomyelinase mediates entry of N. gonorrhoeae into nonphagocytic cells. Cell 91, 605\u2013615 (1997).","journal-title":"Cell"},{"key":"77974_CR18","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.chom.2015.06.006","volume":"18","author":"S Luisoni","year":"2015","unstructured":"Luisoni, S. et al. Co-option of Membrane Wounding Enables Virus Penetration into Cells. Cell Host Microbe 18, 75\u201385 (2015).","journal-title":"Cell Host Microbe"},{"key":"77974_CR19","doi-asserted-by":"crossref","unstructured":"Peters, S. et al. Neisseria meningitidis Type IV Pili Trigger Ca(2+)-Dependent Lysosomal Trafficking of the Acid Sphingomyelinase To Enhance Surface Ceramide Levels. Infect. Immun. 87, (2019).","DOI":"10.1128\/IAI.00410-19"},{"key":"77974_CR20","doi-asserted-by":"crossref","unstructured":"R\u00fchling, M. et al. A Novel Rapid Host Cell Entry Pathway Determines Intracellular Fate of Staphylococcus aureus. eLife (2024).","DOI":"10.7554\/eLife.102810.1"},{"key":"77974_CR21","doi-asserted-by":"publisher","first-page":"e1004574","DOI":"10.1371\/journal.ppat.1004574","volume":"10","author":"N Mueller","year":"2014","unstructured":"Mueller, N., Avota, E., Collenburg, L., Grassm\u00e9, H. & Schneider-Schaulies, S. Neutral Sphingomyelinase in Physiological and Measles Virus Induced T Cell Suppression. PLoS Pathog. 10, e1004574 (2014).","journal-title":"PLoS Pathog."},{"key":"77974_CR22","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/1981091a0","volume":"198","author":"HM Doery","year":"1963","unstructured":"Doery, H. M., Magnusson, B. J., Cheyne, I. M. & Gulasekharam, J. A Phospholipase in Staphylococcal Toxin which hydrolyses Sphingomyelin. Nature 198, 1091\u20131092 (1963).","journal-title":"Nature"},{"key":"77974_CR23","doi-asserted-by":"publisher","first-page":"412827","DOI":"10.1155\/2014\/412827","volume":"2014","author":"TA Pe\u00f1ate Medina","year":"2014","unstructured":"Pe\u00f1ate Medina, T. A. et al. Identification of Sphingomyelinase on the Surface of Chlamydia pneumoniae: Possible Role in the Entry into Its Host Cells. Interdiscip. Perspect. Infect. Dis. 2014, 412827 (2014).","journal-title":"Interdiscip. Perspect. Infect. Dis."},{"key":"77974_CR24","unstructured":"Mohseni, M., Sung, S. & Takov, V. in StatPearls (StatPearls Publishing Copyright \u00a92025, StatPearls Publishing LLC., Treasure Island (FL); 2025)."},{"key":"77974_CR25","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1038\/s41579-023-00860-y","volume":"21","author":"K Stelzner","year":"2023","unstructured":"Stelzner, K., Vollmuth, N. & Rudel, T. Intracellular lifestyle of Chlamydia trachomatis and host\u2013pathogen interactions. Nat. Rev. Microbiol. 21, 448\u2013462 (2023).","journal-title":"Nat. Rev. Microbiol."},{"key":"77974_CR26","doi-asserted-by":"publisher","first-page":"7451","DOI":"10.1073\/pnas.0400754101","volume":"101","author":"NA Grieshaber","year":"2004","unstructured":"Grieshaber, N. A., Fischer, E. R., Mead, D. J., Dooley, C. A. & Hackstadt, T. Chlamydial histone-DNA interactions are disrupted by a metabolite in the methylerythritol phosphate pathway of isoprenoid biosynthesis. Proc. Natl. Acad. Sci. USA 101, 7451\u20137456 (2004).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"77974_CR27","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1111\/cmi.12310","volume":"16","author":"A Nans","year":"2014","unstructured":"Nans, A., Saibil, H. R. & Hayward, R. D. Pathogen-host reorganization during Chlamydia invasion revealed by cryo-electron tomography. Cell. Microbiol. 16, 1457\u20131472 (2014).","journal-title":"Cell. Microbiol."},{"key":"77974_CR28","doi-asserted-by":"publisher","first-page":"e00034","DOI":"10.1128\/mmbr.00034-23","volume":"87","author":"EA Rucks","year":"2023","unstructured":"Rucks, E. A. Type III Secretion in Chlamydia. Microbiol. Mol. Biol. Rev. 87, e00034\u201300023 (2023).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"77974_CR29","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1111\/cmi.12549","volume":"18","author":"S Stallmann","year":"2016","unstructured":"Stallmann, S. & Hegemann, J. H. The Chlamydia trachomatis Ctad1 invasin exploits the human integrin \u03b21 receptor for host cell entry. Cell. Microbiol. 18, 761\u2013775 (2016).","journal-title":"Cell. Microbiol."},{"key":"77974_CR30","doi-asserted-by":"publisher","first-page":"e1004846","DOI":"10.1371\/journal.ppat.1004846","volume":"11","author":"P Subbarayal","year":"2015","unstructured":"Subbarayal, P. et al. EphrinA2 receptor (EphA2) is an invasion and intracellular signaling receptor for Chlamydia trachomatis. PLoS Pathog. 11, e1004846 (2015).","journal-title":"PLoS Pathog."},{"key":"77974_CR31","doi-asserted-by":"publisher","first-page":"5289","DOI":"10.1128\/JB.00526-06","volume":"188","author":"NA Grieshaber","year":"2006","unstructured":"Grieshaber, N. A., Sager, J. B., Dooley, C. A., Hayes, S. F. & Hackstadt, T. Regulation of the Chlamydia trachomatis histone H1-like protein Hc2 is IspE dependent and IhtA independent. J. Bacteriol. 188, 5289\u20135292 (2006).","journal-title":"J. Bacteriol."},{"key":"77974_CR32","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1111\/j.1365-2958.2005.04949.x","volume":"59","author":"NA Grieshaber","year":"2006","unstructured":"Grieshaber, N. A., Grieshaber, S. S., Fischer, E. R. & Hackstadt, T. A small RNA inhibits translation of the histone-like protein Hc1 in Chlamydia trachomatis. Mol. Microbiol. 59, 541\u2013550 (2006).","journal-title":"Mol. Microbiol."},{"key":"77974_CR33","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1126\/science.256.5055.377","volume":"256","author":"CE Barry","year":"1992","unstructured":"Barry, C. E., Hayes, S. F. & Hackstadt, T. Nucleoid Condensation in Escherichia coli That Express a Chlamydial Histone Homolog. Science 256, 377\u2013379 (1992).","journal-title":"Science"},{"key":"77974_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02432-0","volume":"9","author":"JK Lee","year":"2018","unstructured":"Lee, J. K. et al. Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis. Nat. Commun. 9, 45 (2018).","journal-title":"Nat. Commun."},{"key":"77974_CR35","doi-asserted-by":"publisher","first-page":"1390","DOI":"10.1038\/s41564-020-0762-5","volume":"5","author":"K Rajeeve","year":"2020","unstructured":"Rajeeve, K. et al. Reprogramming of host glutamine metabolism during Chlamydia trachomatis infection and its key role in peptidoglycan synthesis. Nat. Microbiol. 5, 1390\u20131402 (2020).","journal-title":"Nat. Microbiol."},{"key":"77974_CR36","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1128\/mr.55.1.143-190.1991","volume":"55","author":"JW Moulder","year":"1991","unstructured":"Moulder, J. W. Interaction of chlamydiae and host cells in vitro. Microbiol. Rev. 55, 143\u2013190 (1991).","journal-title":"Microbiol. Rev."},{"key":"77974_CR37","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1101\/gr.7020108","volume":"18","author":"NR Thomson","year":"2008","unstructured":"Thomson, N. R. et al. Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates. Genome Res. 18, 161\u2013171 (2008).","journal-title":"Genome Res."},{"key":"77974_CR38","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1111\/j.1365-2958.1993.tb01655.x","volume":"8","author":"G Tipples","year":"1993","unstructured":"Tipples, G. & McClarty, G. The obligate intracellular bacterium Chlamydia trachomatis is auxotrophic for three of the four ribonucleoside triphosphates. Mol. Microbiol. 8, 1105\u20131114 (1993).","journal-title":"Mol. Microbiol."},{"key":"77974_CR39","doi-asserted-by":"publisher","first-page":"7233","DOI":"10.1128\/jb.179.23.7233-7242.1997","volume":"179","author":"JL Wylie","year":"1997","unstructured":"Wylie, J. L., Hatch, G. M. & McClarty, G. Host cell phospholipids are trafficked to and then modified by Chlamydia trachomatis. J. Bacteriol. 179, 7233\u20137242 (1997).","journal-title":"J. Bacteriol."},{"key":"77974_CR40","doi-asserted-by":"publisher","first-page":"e1000664","DOI":"10.1371\/journal.ppat.1000664","volume":"5","author":"DK Robertson","year":"2009","unstructured":"Robertson, D. K., Gu, L. & Rowe, R. K. & Beatty, W. L. Inclusion Biogenesis and Reactivation of Persistent Chlamydia trachomatis Requires Host Cell Sphingolipid Biosynthesis. PLoS Pathog. 5, e1000664 (2009).","journal-title":"PLoS Pathog."},{"key":"77974_CR41","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1046\/j.1462-5822.2000.00077.x","volume":"2","author":"C Van Ooij","year":"2000","unstructured":"Van Ooij, C. et al. Host cell-derived sphingolipids are required for the intracellular growth of Chlamydia trachomatis. Cell. Microbiol. 2, 627\u2013637 (2000).","journal-title":"Cell. Microbiol."},{"key":"77974_CR42","doi-asserted-by":"publisher","first-page":"4877","DOI":"10.1073\/pnas.92.11.4877","volume":"92","author":"T Hackstadt","year":"1995","unstructured":"Hackstadt, T., Scidmore, M. A. & Rockey, D. D. Lipid metabolism in Chlamydia trachomatis-infected cells: directed trafficking of Golgi-derived sphingolipids to the chlamydial inclusion. Proc. Natl. Acad.Sci. USA 92, 4877\u20134881 (1995).","journal-title":"Proc. Natl. Acad.Sci. USA"},{"key":"77974_CR43","doi-asserted-by":"publisher","first-page":"e1002198","DOI":"10.1371\/journal.ppat.1002198","volume":"7","author":"CA Elwell","year":"2011","unstructured":"Elwell, C. A. et al. Chlamydia trachomatis Co-opts GBF1 and CERT to Acquire Host Sphingomyelin for Distinct Roles during Intracellular Development. PLoS Pathog. 7, e1002198 (2011).","journal-title":"PLoS Pathog."},{"key":"77974_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19897-1","volume":"11","author":"R Gotz","year":"2020","unstructured":"Gotz, R. et al. Nanoscale imaging of bacterial infections by sphingolipid expansion microscopy. Nat. Commun. 11, 6173 (2020).","journal-title":"Nat. Commun."},{"key":"77974_CR45","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51874-w","volume":"15","author":"M R\u00fchling","year":"2024","unstructured":"R\u00fchling, M. et al. Trifunctional sphingomyelin derivatives enable nanoscale resolution of sphingomyelin turnover in physiological and infection processes via expansion microscopy. Nat. Commun. 15, 7456 (2024).","journal-title":"Nat. Commun."},{"key":"77974_CR46","doi-asserted-by":"crossref","unstructured":"Moldovan, A. et al. Chlamydia trachomatis exploits sphingolipid metabolic pathways during infection of phagocytes. mBio, e0398124 (2025).","DOI":"10.1128\/mbio.03981-24"},{"key":"77974_CR47","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1002\/j.1460-2075.1996.tb00433.x","volume":"15","author":"T Hackstadt","year":"1996","unstructured":"Hackstadt, T., Rockey, D. D., Heinzen, R. A. & Scidmore, M. A. Chlamydia trachomatis interrupts an exocytic pathway to acquire endogenously synthesized sphingomyelin in transit from the Golgi apparatus to the plasma membrane. EMBO J. 15, 964\u2013977 (1996).","journal-title":"EMBO J."},{"key":"77974_CR48","doi-asserted-by":"crossref","unstructured":"Kumagai, K. et al. Chlamydial Infection-Dependent Synthesis of Sphingomyelin as a Novel Anti-Chlamydial Target of Ceramide Mimetic Compounds. Int. J. Mol. Sci. 23 (2022).","DOI":"10.3390\/ijms232314697"},{"key":"77974_CR49","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1002\/1873-3468.13632","volume":"594","author":"Y Tachida","year":"2020","unstructured":"Tachida, Y. et al. Chlamydia trachomatis-infected human cells convert ceramide to sphingomyelin without sphingomyelin synthases 1 and 2. FEBS Lett. 594, 519\u2013529 (2020).","journal-title":"FEBS Lett."},{"key":"77974_CR50","doi-asserted-by":"publisher","first-page":"7686","DOI":"10.1074\/jbc.RA119.012325","volume":"295","author":"R Verhaegh","year":"2020","unstructured":"Verhaegh, R., Becker, K. A., Edwards, M. J. & Gulbins, E. Sphingosine kills bacteria by binding to cardiolipin. J. Biol. Chem. 295, 7686\u20137696 (2020).","journal-title":"J. Biol. Chem."},{"key":"77974_CR51","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/j.ijfoodmicro.2005.05.007","volume":"105","author":"S Possemiers","year":"2005","unstructured":"Possemiers, S., Van Camp, J., Bolca, S. & Verstraete, W. Characterization of the bactericidal effect of dietary sphingosine and its activity under intestinal conditions. Int. J. Food Microbiol. 105, 59\u201370 (2005).","journal-title":"Int. J. Food Microbiol."},{"key":"77974_CR52","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1007\/BF02956173","volume":"9","author":"EBeitr\u00e4ge Abbe","year":"1873","unstructured":"Abbe, E. Beitr\u00e4ge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung. Arch. Mikrosk. Anat. 9, 413\u2013468 (1873).","journal-title":"Arch. Mikrosk. Anat."},{"key":"77974_CR53","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1126\/science.1260088","volume":"347","author":"F Chen","year":"2015","unstructured":"Chen, F., Tillberg, P. W. & Boyden, E. S. Optical imaging. Expansion microscopy. Science 347, 543\u2013548 (2015).","journal-title":"Science"},{"key":"77974_CR54","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1038\/nmeth.3833","volume":"13","author":"TJ Chozinski","year":"2016","unstructured":"Chozinski, T. J. et al. Expansion microscopy with conventional antibodies and fluorescent proteins. Nat. Methods 13, 485\u2013488 (2016).","journal-title":"Nat. Methods"},{"key":"77974_CR55","doi-asserted-by":"publisher","first-page":"e73775","DOI":"10.7554\/eLife.73775","volume":"11","author":"HGJ Damstra","year":"2022","unstructured":"Damstra, H. G. J. et al. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 11, e73775 (2022).","journal-title":"eLife"},{"key":"77974_CR56","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1038\/nbt.3641","volume":"34","author":"T Ku","year":"2016","unstructured":"Ku, T. et al. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol. 34, 973\u2013981 (2016).","journal-title":"Nat. Biotechnol."},{"key":"77974_CR57","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17523-8","volume":"11","author":"O M\u2019Saad","year":"2020","unstructured":"M\u2019Saad, O. & Bewersdorf, J. Light microscopy of proteins in their ultrastructural context. Nat. Commun. 11, 3850 (2020).","journal-title":"Nat. Commun."},{"key":"77974_CR58","doi-asserted-by":"publisher","first-page":"18212","DOI":"10.1021\/jacs.2c03743","volume":"144","author":"BM White","year":"2022","unstructured":"White, B. M., Kumar, P., Conwell, A. N., Wu, K. & Baskin, J. M. Lipid Expansion Microscopy. J. Am. Chem. Soc. 144, 18212\u201318217 (2022).","journal-title":"J. Am. Chem. Soc."},{"key":"77974_CR59","doi-asserted-by":"crossref","unstructured":"Sachs, S., Reinhard, S., Eilts, J., Sauer, M. & Werner, C. Visualizing the trans-synaptic arrangement of synaptic proteins by expansion microscopy. Front. Cell. Neurosci. 18 (2024).","DOI":"10.3389\/fncel.2024.1328726"},{"key":"77974_CR60","doi-asserted-by":"publisher","first-page":"644750","DOI":"10.3389\/fcimb.2021.644750","volume":"11","author":"Kunz","year":"2021","unstructured":"Kunz et al. The Expandables: Cracking the Staphylococcal Cell Wall for Expansion Microscopy. Front. Cell. Infect. Microbiol. 11, 644750 (2021).","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"77974_CR61","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56641-z","volume":"16","author":"TW Shin","year":"2025","unstructured":"Shin, T. W. et al. Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues. Nat. Commun. 16, 1579 (2025).","journal-title":"Nat. Commun."},{"key":"77974_CR62","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1046\/j.1365-2958.1997.4591832.x","volume":"25","author":"JD Clausen","year":"1997","unstructured":"Clausen, J. D., Christiansen, G., Holst, H. U. & Birkelund, S. Chlamydia trachomatis utilizes the host cell microtubule network during early events of infection. Mol. Microbiol. 25, 441\u2013449 (1997).","journal-title":"Mol. Microbiol."},{"key":"77974_CR63","doi-asserted-by":"publisher","first-page":"3793","DOI":"10.1242\/jcs.00695","volume":"116","author":"SS Grieshaber","year":"2003","unstructured":"Grieshaber, S. S., Grieshaber, N. A. & Hackstadt, T. Chlamydia trachomatis uses host cell dynein to traffic to the microtubule-organizing center in a p50 dynamitin-independent process. J. Cell Sci. 116, 3793\u20133802 (2003).","journal-title":"J. Cell Sci."},{"key":"77974_CR64","doi-asserted-by":"publisher","first-page":"9869","DOI":"10.1021\/jp034463d","volume":"107","author":"JJ McManus","year":"2003","unstructured":"McManus, J. J., R\u00e4dler, J. O. & Dawson, K. A. Does Calcium Turn a Zwitterionic Lipid Cationic? J. Phys. Chem. B 107, 9869\u20139875 (2003).","journal-title":"J. Phys. Chem. B"},{"key":"77974_CR65","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1007\/s00249-006-0086-2","volume":"36","author":"D Uhr\u00edkov\u00e1","year":"2007","unstructured":"Uhr\u00edkov\u00e1, D., Lengyel, A., Hanulov\u00e1, M., Funari, S. S. & Balgav\u00fd, P. The structural diversity of DNA-neutral phospholipids-divalent metal cations aggregates: a small-angle synchrotron X-ray diffraction study. Eur. Biophys. J. 36, 363\u2013375 (2007).","journal-title":"Eur. Biophys. J."},{"key":"77974_CR66","doi-asserted-by":"publisher","first-page":"13203","DOI":"10.1021\/jp062713v","volume":"110","author":"M Pisani","year":"2006","unstructured":"Pisani, M., Bruni, P., Caracciolo, G., Caminiti, R. & Francescangeli, O. Structure and Phase Behavior of Self-Assembled DPPC\u2212DNA\u2212Metal Cation Complexes. J. Phys. Chem. B 110, 13203\u201313211 (2006).","journal-title":"J. Phys. Chem. B"},{"key":"77974_CR67","doi-asserted-by":"publisher","first-page":"15966","DOI":"10.1021\/ja046105+","volume":"126","author":"JJ McManus","year":"2004","unstructured":"McManus, J. J., R\u00e4dler, J. O. & Dawson, K. A. Observation of a Rectangular Columnar Phase in a DNA\u2212Calcium\u2212Zwitterionic Lipid Complex. J. Am. Chem. Soc. 126, 15966\u201315967 (2004).","journal-title":"J. Am. Chem. Soc."},{"key":"77974_CR68","doi-asserted-by":"publisher","first-page":"011904","DOI":"10.1103\/PhysRevE.67.011904","volume":"67","author":"O Francescangeli","year":"2003","unstructured":"Francescangeli, O. et al. Structure of self-assembled liposome-DNA-metal complexes. Phys. Rev. E 67, 011904 (2003).","journal-title":"Phys. Rev. E"},{"key":"77974_CR69","doi-asserted-by":"publisher","first-page":"12277","DOI":"10.1021\/jp904986j","volume":"113","author":"DH Mengistu","year":"2009","unstructured":"Mengistu, D. H., Bohinc, K. & May, S. Binding of DNA to Zwitterionic Lipid Layers Mediated by Divalent Cations. J. Phys. Chem. B 113, 12277\u201312282 (2009).","journal-title":"J. Phys. Chem. B"},{"key":"77974_CR70","doi-asserted-by":"publisher","first-page":"8930","DOI":"10.1021\/jp982413g","volume":"102","author":"MS Malghani","year":"1998","unstructured":"Malghani, M. S. & Yang, J. Stable Binding of DNA to Zwitterionic Lipid Bilayers in Aqueous Solutions. J. Phys. Chem. B 102, 8930\u20138933 (1998).","journal-title":"J. Phys. Chem. B"},{"key":"77974_CR71","doi-asserted-by":"publisher","first-page":"6293","DOI":"10.1021\/la0531796","volume":"22","author":"S Gromelski","year":"2006","unstructured":"Gromelski, S. & Brezesinski, G. DNA Condensation and Interaction with Zwitterionic Phospholipids Mediated by Divalent Cations. Langmuir 22, 6293\u20136301 (2006).","journal-title":"Langmuir"},{"key":"77974_CR72","doi-asserted-by":"publisher","first-page":"223","DOI":"10.3389\/fcell.2019.00223","volume":"7","author":"S Banhart","year":"2019","unstructured":"Banhart, S., Sch\u00e4fer, E. K., Gensch, J. M. & Heuer, D. Sphingolipid Metabolism and Transport in Chlamydia trachomatis and Chlamydia psittaci Infections. Front. Cell. Dev. Biol. 7, 223 (2019).","journal-title":"Front. Cell. Dev. Biol."},{"key":"77974_CR73","doi-asserted-by":"publisher","first-page":"e0086422","DOI":"10.1128\/mbio.00864-22","volume":"13","author":"K Wang","year":"2022","unstructured":"Wang, K. et al. A Reverse Genetic Approach for Studying sRNAs in Chlamydia trachomatis. mBio 13, e0086422 (2022).","journal-title":"mBio"},{"key":"77974_CR74","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/0005-2787(72)90405-4","volume":"277","author":"FA Manzoli","year":"1972","unstructured":"Manzoli, F. A., Muchmore, J. H., Bonora, B., Sabioni, A. & Stefoni, S. Interaction between sphingomyelin and DNA. Biochim. Biophys. Acta 277, 251\u2013255 (1972).","journal-title":"Biochim. Biophys. Acta"},{"key":"77974_CR75","doi-asserted-by":"publisher","first-page":"e2400103","DOI":"10.1111\/boc.202400103","volume":"117","author":"A Sayed","year":"2025","unstructured":"Sayed, A., Eswara, K., Teles, K., Boudellioua, A. & Fischle, W. Nuclear lipids in chromatin regulation: Biological roles, experimental approaches and existing challenges. Biol. Cell 117, e2400103 (2025).","journal-title":"Biol. Cell"},{"key":"77974_CR76","doi-asserted-by":"publisher","first-page":"3727","DOI":"10.1242\/jcs.114.20.3727","volume":"114","author":"Y Mizutani","year":"2001","unstructured":"Mizutani, Y. et al. Nuclear localization of neutral sphingomyelinase 1: biochemical and immunocytochemical analyses. J. Cell Sci. 114, 3727\u20133736 (2001).","journal-title":"J. Cell Sci."},{"key":"77974_CR77","doi-asserted-by":"publisher","first-page":"46832","DOI":"10.1074\/jbc.M306577200","volume":"278","author":"N Igarashi","year":"2003","unstructured":"Igarashi, N. et al. Sphingosine kinase 2 is a nuclear protein and inhibits DNA synthesis. J. Biol. Chem. 278, 46832\u201346839 (2003).","journal-title":"J. Biol. Chem."},{"key":"77974_CR78","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/S0014-5793(99)01378-2","volume":"460","author":"E Albi","year":"1999","unstructured":"Albi, E. & Magni, M. V. Sphingomyelin synthase in rat liver nuclear membrane and chromatin. FEBS Lett. 460, 369\u2013372 (1999).","journal-title":"FEBS Lett."},{"key":"77974_CR79","doi-asserted-by":"publisher","first-page":"R470","DOI":"10.1016\/j.cub.2015.04.004","volume":"25","author":"M Welte","year":"2015","unstructured":"Welte, M. ichaelA. Expanding Roles for Lipid Droplets. Curr. Biol. 25, R470\u2013R481 (2015).","journal-title":"Curr. Biol."},{"key":"77974_CR80","first-page":"2013","volume":"327\u2013340","author":"JP Layerenza","year":"1831","unstructured":"Layerenza, J. P. et al. Nuclear lipid droplets: A novel nuclear domain. Biochim Biophys Acta Mol. Cell Biol. Lipids 327\u2013340, 2013 (1831).","journal-title":"Biochim Biophys Acta Mol. Cell Biol. Lipids"},{"key":"77974_CR81","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0500-6-386","volume":"6","author":"R Uzbekov","year":"2013","unstructured":"Uzbekov, R. & Roingeard, P. Nuclear lipid droplets identified by electron microscopy of serial sections. BMC Res. Notes 6, 386 (2013).","journal-title":"BMC Res. Notes"},{"key":"77974_CR82","doi-asserted-by":"publisher","first-page":"1254","DOI":"10.1126\/science.1176709","volume":"325","author":"NC Hait","year":"2009","unstructured":"Hait, N. C. et al. Regulation of histone acetylation in the nucleus by sphingosine-1-phosphate. Science 325, 1254\u20131257 (2009).","journal-title":"Science"},{"key":"77974_CR83","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s42003-025-08697-2","volume":"8","author":"C Conte","year":"2025","unstructured":"Conte, C. et al. Sphingomyelin regulates the transcriptional machinery in nuclear lipid microdomains. Commun. Biol. 8, 1303 (2025).","journal-title":"Commun. Biol."},{"key":"77974_CR84","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1194\/jlr.M074997","volume":"58","author":"ITG Silva","year":"2017","unstructured":"Silva, I. T. G., Fernandes, V., Souza, C., Treptow, W. & Santos, G. M. Biophysical studies of cholesterol effects on chromatin[S]. J. Lipid Res. 58, 934\u2013940 (2017).","journal-title":"J. Lipid Res."},{"key":"77974_CR85","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/0005-2760(75)90080-6","volume":"409","author":"SK Erickson","year":"1975","unstructured":"Erickson, S. K., Da Vison, A. M. & Gould, R. G. Correlation of rat liver chromatin-bound free and esterified cholesterol with the circadian rhythm of cholesterol biosynthesis in the rat. Biochim. Biophys. Acta Lipids Lipid Metab. 409, 59\u201367 (1975).","journal-title":"Biochim. Biophys. Acta Lipids Lipid Metab."},{"key":"77974_CR86","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.plipres.2018.04.003","volume":"70","author":"V Fernandes","year":"2018","unstructured":"Fernandes, V., Teles, K., Ribeiro, C., Treptow, W. & Santos, G. Fat nucleosome: Role of lipids on chromatin. Prog. Lipid Res. 70, 29\u201334 (2018).","journal-title":"Prog. Lipid Res."},{"key":"77974_CR87","doi-asserted-by":"publisher","first-page":"1645","DOI":"10.1128\/jb.175.6.1645-1655.1993","volume":"175","author":"AS Lynch","year":"1993","unstructured":"Lynch, A. S. & Wang, J. C. Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I. J. Bacteriol. 175, 1645\u20131655 (1993).","journal-title":"J. Bacteriol."},{"key":"77974_CR88","doi-asserted-by":"crossref","unstructured":"Leibowitz, P. J. & Schaechter, M. in Int. Rev. Cytol. 41, (eds. Bourne, G. H. Danielli, J. F. & Jeon, K. W.) 1\u201328 (Academic Press, 1975).","DOI":"10.1016\/S0074-7696(08)60964-X"},{"key":"77974_CR89","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1111\/j.1365-2958.1995.tb02330.x","volume":"16","author":"V Norris","year":"1995","unstructured":"Norris, V. Hypothesis: chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation. Mol. Microbiol. 16, 1051\u20131057 (1995).","journal-title":"Mol. Microbiol."},{"key":"77974_CR90","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1146\/annurev-genet-112414-054958","volume":"49","author":"M Roggiani","year":"2015","unstructured":"Roggiani, M. & Goulian, M. Chromosome-Membrane Interactions in Bacteria. Annu. Rev. Genet. 49, 115\u2013129 (2015).","journal-title":"Annu. Rev. Genet."},{"key":"77974_CR91","doi-asserted-by":"publisher","first-page":"7445","DOI":"10.1073\/pnas.1109479109","volume":"109","author":"EA Libby","year":"2012","unstructured":"Libby, E. A., Roggiani, M. & Goulian, M. Membrane protein expression triggers chromosomal locus repositioning in bacteria. Proc. Natl. Acad. Sci. USA 109, 7445\u20137450 (2012).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"77974_CR92","doi-asserted-by":"publisher","first-page":"685687","DOI":"10.3389\/fmicb.2021.685687","volume":"12","author":"C Gogou","year":"2021","unstructured":"Gogou, C., Japaridze, A. & Dekker, C. Mechanisms for Chromosome Segregation in Bacteria. Front. Microbiol. 12, 685687 (2021).","journal-title":"Front. Microbiol."},{"key":"77974_CR93","doi-asserted-by":"publisher","first-page":"3074","DOI":"10.1194\/jlr.D008532","volume":"51","author":"SM Hammad","year":"2010","unstructured":"Hammad, S. M. et al. Blood sphingolipidomics in healthy humans: impact of sample collection methodology. J. Lipid Res. 51, 3074\u20133087 (2010).","journal-title":"J. Lipid Res."},{"key":"77974_CR94","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.plipres.2011.11.001","volume":"51","author":"S Gr\u00f6sch","year":"2012","unstructured":"Gr\u00f6sch, S., Schiffmann, S. & Geisslinger, G. Chain length-specific properties of ceramides. Prog. Lipid Res. 51, 50\u201362 (2012).","journal-title":"Prog. Lipid Res."},{"key":"77974_CR95","doi-asserted-by":"publisher","first-page":"8840","DOI":"10.1021\/bi970145r","volume":"36","author":"J Bai","year":"1997","unstructured":"Bai, J. & Pagano, R. E. Measurement of Spontaneous Transfer and Transbilayer Movement of BODIPY-Labeled Lipids in Lipid Vesicles. Biochemistry 36, 8840\u20138848 (1997).","journal-title":"Biochemistry"},{"key":"77974_CR96","doi-asserted-by":"publisher","first-page":"13318","DOI":"10.1021\/bi00211a045","volume":"32","author":"JR Silvius","year":"1993","unstructured":"Silvius, J. R. & Leventis, R. Spontaneous interbilayer transfer of phospholipids: dependence on acylchain composition. Biochemistry 32, 13318\u201313326 (1993).","journal-title":"Biochemistry"},{"key":"77974_CR97","doi-asserted-by":"publisher","first-page":"3892","DOI":"10.1021\/bi00468a015","volume":"29","author":"JD Jones","year":"1990","unstructured":"Jones, J. D., Almeida, P. F. & Thompson, T. E. Spontaneous interbilayer transfer of hexosylceramides between phospholipid bilayers. Biochemistry 29, 3892\u20133897 (1990).","journal-title":"Biochemistry"},{"key":"77974_CR98","doi-asserted-by":"publisher","first-page":"e00358","DOI":"10.1128\/msphere.00358-26","volume":"11","author":"Y Wang","year":"2026","unstructured":"Wang, Y. et al. Chlamydial histone homologs control developmental fitness in the next infection cycle. mSphere 11, e00358\u201300326 (2026).","journal-title":"mSphere"},{"key":"77974_CR99","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1046\/j.1365-2958.2000.02057.x","volume":"37","author":"EI Shaw","year":"2000","unstructured":"Shaw, E. I. et al. Three temporal classes of gene expression during the Chlamydia trachomatis developmental cycle. Mol. Microbiol. 37, 913\u2013925 (2000).","journal-title":"Mol. Microbiol."},{"key":"77974_CR100","doi-asserted-by":"publisher","first-page":"2936","DOI":"10.1128\/jb.175.10.2936-2942.1993","volume":"175","author":"DG Wichlan","year":"1993","unstructured":"Wichlan, D. G. & Hatch, T. P. Identification of an early-stage gene of Chlamydia psittaci 6BC. J. Bacteriol. 175, 2936\u20132942 (1993).","journal-title":"J. Bacteriol."},{"key":"77974_CR101","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.1128\/iai.56.12.3021-3025.1988","volume":"56","author":"MR Plaunt","year":"1988","unstructured":"Plaunt, M. R. & Hatch, T. P. Protein synthesis early in the developmental cycle of Chlamydia psittaci. Infect. Immun. 56, 3021\u20133025 (1988).","journal-title":"Infect. Immun."},{"key":"77974_CR102","first-page":"1","volume":"282","author":"RJ Botelho","year":"2004","unstructured":"Botelho, R. J., Scott, C. C. & Grinstein, S. Phosphoinositide involvement in phagocytosis and phagosome maturation. Curr. Top. Microbiol. Immunol. 282, 1\u201330 (2004).","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"77974_CR103","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1128\/IAI.74.1.73-80.2006","volume":"74","author":"DE Nelson","year":"2006","unstructured":"Nelson, D. E. et al. Inhibition of chlamydiae by primary alcohols correlates with the strain-specific complement of plasticity zone phospholipase D genes. Infect. Immun. 74, 73\u201380 (2006).","journal-title":"Infect. Immun."},{"key":"77974_CR104","doi-asserted-by":"publisher","first-page":"2379","DOI":"10.1128\/IAI.68.4.2379-2385.2000","volume":"68","author":"K Wolf","year":"2000","unstructured":"Wolf, K., Fischer, E. & Hackstadt, T. Ultrastructural Analysis of Developmental Events inChlamydia pneumoniae-Infected Cells. Infect. Immun. 68, 2379\u20132385 (2000).","journal-title":"Infect. Immun."},{"key":"77974_CR105","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1139\/m76-003","volume":"22","author":"JW Costerton","year":"1976","unstructured":"Costerton, J. W., Poffenroth, L., Wilt, J. C. & Kordov\u00e1, N. Ultrastructural studies of the nucleoids of the pleomorphic forms of Chlamydia psittaci 6BC: a comparison with bacteria. Can. J. Microbiol. 22, 16\u201328 (1976).","journal-title":"Can. J. Microbiol."},{"key":"77974_CR106","doi-asserted-by":"crossref","unstructured":"Wagner, F. et al. Monitoring Sphingomyelin Biosynthesis at Nanoscale Resolution by Expansion Microscopy. bioRxiv, 2026.2005.2027.726241 (2026).","DOI":"10.64898\/2026.05.27.726241"},{"key":"77974_CR107","doi-asserted-by":"publisher","first-page":"25811","DOI":"10.1074\/jbc.M412052200","volume":"280","author":"I L\u00f3pez-Montero","year":"2005","unstructured":"L\u00f3pez-Montero, I. et al. Rapid Transbilayer Movement of Ceramides in Phospholipid Vesicles and inHumanErythrocytes*. J. Biol. Chem. 280, 25811\u201325819 (2005).","journal-title":"J. Biol. Chem."},{"key":"77974_CR108","doi-asserted-by":"publisher","first-page":"e1002092","DOI":"10.1371\/journal.ppat.1002092","volume":"7","author":"I Derr\u00e9","year":"2011","unstructured":"Derr\u00e9, I., Swiss, R. & Agaisse, H. The Lipid Transfer Protein CERT Interacts with the Chlamydia Inclusion Protein IncD and Participates to ER-Chlamydia Inclusion Membrane Contact Sites. PLoS Pathog. 7, e1002092 (2011).","journal-title":"PLoS Pathog."},{"key":"77974_CR109","doi-asserted-by":"publisher","first-page":"e12752","DOI":"10.1111\/cmi.12752","volume":"19","author":"S Koch-Edelmann","year":"2017","unstructured":"Koch-Edelmann, S. et al. The cellular ceramide transport protein CERT promotes Chlamydia psittaci infection and controls bacterial sphingolipid uptake. Cell. Microbiol. 19, e12752 (2017).","journal-title":"Cell. Microbiol."},{"key":"77974_CR110","doi-asserted-by":"crossref","unstructured":"R\u00fchling, M. et al. A Novel Rapid Host Cell Entry Pathway Determines Intracellular Fate of Staphylococcus aureus. eLife (2026).","DOI":"10.7554\/eLife.102810.4"},{"key":"77974_CR111","doi-asserted-by":"publisher","first-page":"6438","DOI":"10.1074\/jbc.M708422200","volume":"283","author":"N Paland","year":"2008","unstructured":"Paland, N. et al. Reduced display of tumor necrosis factor receptor I at the host cell surface supports infection with Chlamydia trachomatis. J. Biol. Chem. 283, 6438\u20136448 (2008).","journal-title":"J. Biol. Chem."},{"key":"77974_CR112","doi-asserted-by":"publisher","first-page":"e4698","DOI":"10.21769\/BioProtoc.4698","volume":"13","author":"HGJ Damstra","year":"2023","unstructured":"Damstra, H. G. J. et al. Ten-fold Robust Expansion Microscopy. Bio Protoc. 13, e4698 (2023).","journal-title":"Bio Protoc."},{"key":"77974_CR113","doi-asserted-by":"crossref","unstructured":"Damstra, H. G. J. et al. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). bioRxiv, 2021.2002.2003.428837 (2021).","DOI":"10.1101\/2021.02.03.428837"},{"key":"77974_CR114","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"77974_CR115","doi-asserted-by":"crossref","unstructured":"Wickham, H. ggplot2 Elegant Graphics for Data Analysis, Edn. 2. (Springer Cham, 2016).","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"77974_CR116","unstructured":"RStudioTeam RStudio: Integrated Development for R. RStudio,. PBC (2020)."},{"key":"77974_CR117","unstructured":"Cordeli\u00e8res, F. P. & Bolte, S. (2008)."},{"key":"77974_CR118","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1111\/j.1365-2818.2006.01706.x","volume":"224","author":"S Bolte","year":"2006","unstructured":"Bolte, S. & Cordeli\u00e8res, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213\u2013232 (2006).","journal-title":"J. Microsc."},{"key":"77974_CR119","doi-asserted-by":"crossref","unstructured":"Weiss, G. L., Medeiros, J. M. & Pilhofer, M. in Bacterial Protein Secretion Systems: Methods and Protocols. (eds. Journet, L. & Cascales, E.) 353\u2013375 (Springer New York, New York, NY; 2017).","DOI":"10.1007\/978-1-4939-7033-9_27"},{"key":"77974_CR120","doi-asserted-by":"publisher","first-page":"e52286","DOI":"10.7554\/eLife.52286","volume":"9","author":"T Zachs","year":"2020","unstructured":"Zachs, T. et al. Fully automated, sequential focused ion beam milling for cryo-electron tomography. eLife 9, e52286 (2020).","journal-title":"eLife"},{"key":"77974_CR121","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.jsb.2005.07.007","volume":"152","author":"DN Mastronarde","year":"2005","unstructured":"Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36\u201351 (2005).","journal-title":"J. Struct. Biol."},{"key":"77974_CR122","doi-asserted-by":"publisher","first-page":"1612","DOI":"10.1038\/s41592-024-02373-9","volume":"21","author":"F Eisenstein","year":"2024","unstructured":"Eisenstein, F., Fukuda, Y. & Danev, R. Smart parallel automated cryo-electron tomography. Nat. Methods 21, 1612\u20131615 (2024).","journal-title":"Nat. Methods"},{"key":"77974_CR123","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1006\/jsbi.1996.0013","volume":"116","author":"JR Kremer","year":"1996","unstructured":"Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer Visualization of Three-Dimensional Image Data Using IMOD. J. Struct. Biol. 116, 71\u201376 (1996).","journal-title":"J. Struct. Biol."},{"key":"77974_CR124","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1111\/j.1365-2818.2008.01977.x","volume":"230","author":"DN Mastronarde","year":"2008","unstructured":"Mastronarde, D. N. Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package. J. Microsc. 230, 212\u2013217 (2008).","journal-title":"J. Microsc."},{"key":"77974_CR125","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51438-y","volume":"15","author":"S Wiedemann","year":"2024","unstructured":"Wiedemann, S. & Heckel, R. A deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography. Nat. Commun. 15, 8255 (2024).","journal-title":"Nat. Commun."},{"key":"77974_CR126","doi-asserted-by":"crossref","unstructured":"Heebner, J. E. et al. Deep Learning-Based Segmentation of Cryo-Electron Tomograms. JoVE, e64435 (2022).","DOI":"10.3791\/64435-v"},{"key":"77974_CR127","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1002\/pro.3943","volume":"30","author":"EF Pettersen","year":"2021","unstructured":"Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70\u201382 (2021).","journal-title":"Protein Sci."},{"key":"77974_CR128","doi-asserted-by":"publisher","first-page":"e4472","DOI":"10.1002\/pro.4472","volume":"31","author":"UH Ermel","year":"2022","unstructured":"Ermel, U. H., Arghittu, S. M. & Frangakis, A. S. ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Protein Sci. 31, e4472 (2022).","journal-title":"Protein Sci."},{"key":"77974_CR129","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.jsb.2011.12.017","volume":"178","author":"D Casta\u00f1o-D\u00edez","year":"2012","unstructured":"Casta\u00f1o-D\u00edez, D., Kudryashev, M., Arheit, M. & Stahlberg, H. Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J. Struct. Biol. 178, 139\u2013151 (2012).","journal-title":"J. Struct. Biol."},{"key":"77974_CR130","doi-asserted-by":"publisher","first-page":"100631","DOI":"10.1016\/j.jlr.2024.100631","volume":"65","author":"A Prell","year":"2024","unstructured":"Prell, A., Wigger, D., Huwiler, A., Schumacher, F. & Kleuser, B. The sphingosine kinase 2 inhibitors ABC294640 and K145 elevate (dihydro)sphingosine 1-phosphate levels in various cells. J. Lipid Res. 65, 100631 (2024).","journal-title":"J. Lipid Res."},{"key":"77974_CR131","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/0378-1119(85)90120-9","volume":"33","author":"C Yanisch-Perron","year":"1985","unstructured":"Yanisch-Perron, C., Vieira, J. & Messing, J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors. Gene 33, 103\u2013119 (1985).","journal-title":"Gene"},{"key":"77974_CR132","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1007\/978-1-4939-9694-0_11","volume":"2042","author":"K Wolf","year":"2019","unstructured":"Wolf, K., Rahnama, M. & Fields, K. A. Genetic Manipulation of Chlamydia trachomatis: Chromosomal Deletions. Methods Mol. Biol. 2042, 151\u2013164 (2019).","journal-title":"Methods Mol. Biol."},{"key":"77974_CR133","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.chroma.2016.12.033","volume":"1481","author":"C Muhle","year":"2017","unstructured":"Muhle, C. & Kornhuber, J. Assay to measure sphingomyelinase and ceramidase activities efficiently and safely. J. Chromatogr. A 1481, 137\u2013144 (2017).","journal-title":"J. Chromatogr. A"},{"key":"77974_CR134","doi-asserted-by":"crossref","unstructured":"Krones, D. et al. Staphylococcus aureus \u03b1-Toxin Induces Acid Sphingomyelinase Release From a Human Endothelial Cell Line. Front. Microbiol. 12 (2021).","DOI":"10.3389\/fmicb.2021.694489"},{"key":"77974_CR135","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","volume":"25","author":"KJ Livak","year":"2001","unstructured":"Livak, K. J. & Schmittgen, T. D. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2\u2212\u0394\u0394CT Method. Methods 25, 402\u2013408 (2001).","journal-title":"Methods"},{"key":"77974_CR136","doi-asserted-by":"publisher","first-page":"D640","DOI":"10.1093\/nar\/gkad1045","volume":"52","author":"O Yurekten","year":"2024","unstructured":"Yurekten, O. et al. MetaboLights: open data repository for metabolomics. Nucleic Acids Res. 52, D640\u2013d646 (2024).","journal-title":"Nucleic Acids Res."},{"key":"77974_CR137","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.mimet.2017.04.010","volume":"139","author":"R Butcher","year":"2017","unstructured":"Butcher, R. et al. Reduced-cost Chlamydia trachomatis-specific multiplex real-time PCR diagnostic assay evaluated for ocular swabs and use by trachoma research programmes. J. Microbiol. Methods 139, 95\u2013102 (2017).","journal-title":"J. Microbiol. Methods"},{"key":"77974_CR138","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1007\/s10616-011-9383-4","volume":"63","author":"SL Chua","year":"2011","unstructured":"Chua, S. L., See Too, W. C., Khoo, B. Y. & Few, L. L. UBC and YWHAZ as suitable reference genes for accurate normalisation of gene expression using MCF7, HCT116 and HepG2 cell lines. Cytotechnology 63, 645\u2013654 (2011).","journal-title":"Cytotechnology"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77974-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77974-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77974-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:03:35Z","timestamp":1790773415000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77974-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":138,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["77974"],"URL":"https:\/\/doi.org\/10.1038\/s41467-026-77974-3","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]},"assertion":[{"value":"19 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interest.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"10367"}}