IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-64347-5.html
   My bibliography  Save this article

The slit diaphragm in Drosophila exhibits a bilayered, fishnet architecture

Author

Listed:
  • Deborah Moser

    (Goethe University Frankfurt)

  • Konrad Lang

    (Faculty of Medicine and Medical Center - University of Freiburg)

  • Alexandra N. Birtasu

    (Goethe University Frankfurt)

  • Florian Grahammer

    (Martinistraße
    University Medical Center Hamburg-Eppendorf)

  • Martin Helmstädter

    (Faculty of Medicine and Medical Center - University of Freiburg
    Medical Center - University of Freiburg)

  • Margot P. Scheffer

    (Goethe University Frankfurt)

  • Tobias Hermle

    (Faculty of Medicine and Medical Center - University of Freiburg)

  • Achilleas S. Frangakis

    (Goethe University Frankfurt)

Abstract

The kidney relies on the glomerulus to filter large volumes of blood plasma, with the slit diaphragm (SD) as a key structural component of the glomerular filtration barrier. Despite its central role, the molecular architecture of the SD has remained elusive for decades. Using cryo-electron tomography on focused ion beam-milled Drosophila nephrocytes, an invertebrate podocyte model, we show that the SD exhibits a bilayered fishnet architecture. In the cryo-electron tomography map, we observe criss-crossing strands spanning the extracellular space that can be populated with Sns and Kirre, the Drosophila orthologs of nephrin and Neph1, respectively. We show that sns silencing shortens the SD lines until disappearance, linking the fishnet architecture directly to Sns. After Rab5 silencing, which causes Sns mistrafficking and ectopic formation of the SD, the fishnet pattern also appears ectopically. Elucidating the molecular SD architecture establishes a crucial link between the SD organization and its (patho)physiology.

Suggested Citation

  • Deborah Moser & Konrad Lang & Alexandra N. Birtasu & Florian Grahammer & Martin Helmstädter & Margot P. Scheffer & Tobias Hermle & Achilleas S. Frangakis, 2025. "The slit diaphragm in Drosophila exhibits a bilayered, fishnet architecture," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-64347-5
    DOI: 10.1038/s41467-025-64347-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-64347-5
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-64347-5?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Yun-Tao Liu & Heng Zhang & Hui Wang & Chang-Lu Tao & Guo-Qiang Bi & Z. Hong Zhou, 2022. "Isotropic reconstruction for electron tomography with deep learning," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Helen Weavers & Silvia Prieto-Sánchez & Ferdinand Grawe & Amparo Garcia-López & Ruben Artero & Michaela Wilsch-Bräuninger & Mar Ruiz-Gómez & Helen Skaer & Barry Denholm, 2009. "The insect nephrocyte is a podocyte-like cell with a filtration slit diaphragm," Nature, Nature, vol. 457(7227), pages 322-326, January.
    3. Kotaro Kelley & Ashleigh M. Raczkowski & Oleg Klykov & Pattana Jaroenlak & Daija Bobe & Mykhailo Kopylov & Edward T. Eng & Gira Bhabha & Clinton S. Potter & Bridget Carragher & Alex J. Noble, 2022. "Waffle Method: A general and flexible approach for improving throughput in FIB-milling," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Addendum: Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 636(8042), pages 4-4, December.
    5. Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 630(8016), pages 493-500, June.
    6. Georg Dietzl & Doris Chen & Frank Schnorrer & Kuan-Chung Su & Yulia Barinova & Michaela Fellner & Beate Gasser & Kaolin Kinsey & Silvia Oppel & Susanne Scheiblauer & Africa Couto & Vincent Marra & Kry, 2007. "A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila," Nature, Nature, vol. 448(7150), pages 151-156, July.
    7. Liang Xue & Swantje Lenz & Maria Zimmermann-Kogadeeva & Dimitry Tegunov & Patrick Cramer & Peer Bork & Juri Rappsilber & Julia Mahamid, 2022. "Publisher Correction: Visualizing translation dynamics at atomic detail inside a bacterial cell," Nature, Nature, vol. 611(7937), pages 13-13, November.
    8. Liang Xue & Swantje Lenz & Maria Zimmermann-Kogadeeva & Dimitry Tegunov & Patrick Cramer & Peer Bork & Juri Rappsilber & Julia Mahamid, 2022. "Visualizing translation dynamics at atomic detail inside a bacterial cell," Nature, Nature, vol. 610(7930), pages 205-211, October.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Iskander Khusainov & Natalie Romanov & Camille Goemans & Beata Turoňová & Christian E. Zimmerli & Sonja Welsch & Julian D. Langer & Athanasios Typas & Martin Beck, 2024. "Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Nikita Balyschew & Artsemi Yushkevich & Vasilii Mikirtumov & Ricardo M. Sanchez & Thiemo Sprink & Mikhail Kudryashev, 2023. "Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Pantelis Livanos & Choy Kriechbaum & Sophia Remers & Arvid Herrmann & Sabine Müller, 2025. "Kinesin-12 POK2 polarization is a prerequisite for a fully functional division site and aids cell plate positioning," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    4. Justin Riper & Arleth O. Martinez-Claros & Lie Wang & Hannah E. Schneiderman & Sweta Maheshwari & Monica C. Pillon, 2025. "CryoEM structure of the SLFN14 endoribonuclease reveals insight into RNA binding and cleavage," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    5. Xin Yong & Guowen Jia & Qin Yang & Chunzhuang Zhou & Sitao Zhang & Huaqing Deng & Daniel D. Billadeau & Zhaoming Su & Da Jia, 2025. "Cryo-EM structure of the BLOC-3 complex provides insights into the pathogenesis of Hermansky-Pudlak syndrome," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    6. Camille N. Lambert & Vaitea Opuu & Francesco Calvanese & Polina Pavlinova & Francesco Zamponi & Eric J. Hayden & Martin Weigt & Matteo Smerlak & Philippe Nghe, 2025. "Exploring the space of self-reproducing ribozymes using generative models," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    7. Sara Basse Hansen & Sergio G. Bartual & Huijie Yuan & Olawale G. Raimi & Andrii Gorelik & Andrew T. Ferenbach & Kristian Lytje & Jan Skov Pedersen & Taner Drace & Thomas Boesen & Daan M. F. Aalten, 2025. "Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    8. Chongbing Liao & Qihui Liu & Gan Luo & Yinyue Luo & Dan Yao & Qingxia Wang & Jue Zhang & Yang Wu & Jialin Jin & Dan Xu & Wuyuan Lu, 2025. "Human neutrophil α-defensin HNP1 interacts with bacterial OmpA to promote Acinetobacter baumannii biofilm formation," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    9. Jianping Kong & Wanqian Wu & Shiyue Ke & Zihan Zhou & Shenglan Xia & Jianyu Chen & Runyu Zhu & Yijia Hou & Tinashe Makanyire & Xiangru Shan & Zhuyue Zhuo & Keying Li & Hongtao Shen & Pan Yang & Pingpi, 2025. "Molecular mechanisms of CBASS phospholipase effector CapV mediated membrane disruption," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    10. Julian O. Streit & Sammy H. S. Chan & Saifu Daya & John Christodoulou, 2025. "Rational design of 19F NMR labelling sites to probe protein structure and interactions," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    11. FNU Vidya & Youran Luo & Hongwei Wu & Wilfred A. Donk & Andrew C. McShan & Vinayak Agarwal, 2025. "Large protein-like leader peptides engage differently with RiPP halogenases and lanthionine synthetases," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    12. Shuyi Zeng & Xingyu Xiong & Houfang Long & Qianhui Xu & Yifan Yu & Bo Sun & Cong Liu & Zhizhi Wang & Wenqing Xu & Shengnan Zhang & Dan Li, 2025. "Design of Ig-like binders targeting α-synuclein fibril for mitigating its pathological activities," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    13. Yu Zhang & Tingting Zhang & Xue Xiao & Yejun Wang & Adam Kawalek & Jinzhao Ou & Anmin Ren & Wenhao Sun & Vincent Bakker & Yujie Liu & Yuelong Li & Liang Yang & Liang Ye & Ning Jia & Jan-Willem Veening, 2025. "CRISPRi screen identifies FprB as a synergistic target for gallium therapy in Pseudomonas aeruginosa," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    14. Dhana G. Gorasia & Eric Hanssen & Manasi Mudaliyar & Craig J. Morton & Sepideh Valimehr & Christine Seers & Lianyi Zhang & Matthew T. Doyle & Debnath Ghosal & Paul D. Veith & Eric C. Reynolds, 2025. "Insights into type IX secretion from PorKN cogwheel structure bound to PorG and attachment complexes," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    15. Xiaorong Li & Xiaoxu Yang & Xiaoli Lu & Bingqian Lin & Yuanyuan Zhang & Bangdong Huang & Yutong Zhou & Jing Huang & Kun Wu & Qiang Zhou & Ximin Chi, 2025. "Structural basis for substrate recognition mechanism of human SLC26A7," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    16. Ai Tamura & Kazuyuki Yamagata & Takashi Kono & Masanori Fujimoto & Takahiro Fuchigami & Motoi Nishimura & Masataka Yokoyama & Akitoshi Nakayama & Naoko Hashimoto & Ikki Sakuma & Nobuyuki Mitsukawa & Y, 2025. "p53-inducible lncRNA LOC644656 causes genotoxic stress-induced stem cell maldifferentiation and cancer chemoresistance," Nature Communications, Nature, vol. 16(1), pages 1-22, December.
    17. Gašper Šolinc & Marija Srnko & Franci Merzel & Ana Crnković & Mirijam Kozorog & Marjetka Podobnik & Gregor Anderluh, 2025. "Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    18. Minghua Hou & Yuhao Xia & Pengcheng Wang & Zexin lv & Dongliang Hou & Xiaogen Zhou & Jianyang Zeng & Guijun Zhang, 2025. "High-accuracy protein complex structure modeling based on sequence-derived structure complementarity," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    19. Tae-Kyeong Jeong & R. Ciaran MacKenzie Frater & Jongha Yoon & Anja Groth & Ji-Joon Song, 2025. "CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    20. Mike Sleutel & Ravi R. Sonani & Jessalyn G. Miller & Fengbin Wang & Andres Gonzalez Socorro & Yang Chen & Reece Martin & Borries Demeler & Michael J. Rudolph & Vikram Alva & Han Remaut & Edward H. Ege, 2025. "Donor strand complementation and calcium ion coordination drive the chaperone-free polymerization of archaeal cannulae," Nature Communications, Nature, vol. 16(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-64347-5. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.