CoChat
Sign Up
Cited by 3Neuroscience and Neuropharmacology ResearchProtein Structure and DynamicsRNA Research and Splicing

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Coordinated phase separation and phase transition underlie synaptic ribbon condensate formation and plasticity

Open access
Liu, Yang, Wang, Xu, Zheng, Tianyu, Niu, Fengfeng, Sun, Ruiyi, Yang, Chao, Xu, Shun, Zhao, Zhipeng, Shen, Zeyu, Huang, Weilin, Wang, Xuejie, Liu, Kai, Cai, Shujun, Zhang, Mingjie, Wei, Zhiyi·2026·Vita
DOI 10.15302/vita.2026.05.0033

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Mesoscale molecular apparatuses with diverse functions are widespread in cells. How mesoscale cellular apparatuses are formed and regulated is poorly understood. The synaptic ribbon in sensory neurons, which can dynamically adjust its size and shape in response to light or sound, is a mesoscale molecular assembly. In this study, we demonstrate that RIBEYE, the backbone protein of synaptic ribbons, via combined ordered and disordered interactions, forms micron-sized dynamic molecular assemblies. Integrated cryo-electron microscopy and tomography studies revealed that the N-terminal SAM domain and the C-terminal B domain of RIBEYE form distinct nanoscale filaments and further assemble into ribbon-like architectures via phase transition. Unexpectedly, the N-terminal intrinsically disordered region of RIBEYE softens the solid mesoscale ribbon structures via phase separation. The mesoscale size and shape of the RIBEYE condensate are bidirectionally tuned by physiological modulators such as Piccolino and CtBP1, linking synaptic ribbon structural plasticity to functional adaptability. Thus, our study demonstrates that combined phase transition and phase separation of nanoscale protein oligomers can build mesoscale functional cellular apparatuses.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.15302/vita.2026.05.0033

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 73

  1. Shibata, Y., Hu, J.J., Kozlov, M.M. & Rapoport, T.A. Mechanisms shaping the membranes of cellular organelles. Annu. Rev. Cell Dev. Biol. 25, 329–354 (2009). · DOI
  2. Westrate, L.M., Lee, J.E., Prinz, W.A. & Voeltz, G.K. Form follows function: the importance of endoplasmic reticulum shape. Annu. Rev. Biochem. 84, 791–811 (2015). · DOI
  3. Altan-Bonnet, N., Sougrat, R. & Lippincott-Schwartz, J. Molecular basis for Golgi maintenance and biogenesis. Curr. Opin. Cell Biol. 16, 364–372 (2004). · DOI
  4. Wei, J.H. & Seemann, J. Golgi ribbon disassembly during mitosis, differentiation and disease progression. Curr. Opin. Cell Biol. 47, 43–51 (2017). · DOI
  5. Schmitz, F. The making of synaptic ribbons: how they are built and what they do. Neuroscientist 15, 611–624 (2009). · DOI
  6. Voorn, R.A. & Vogl, C. Molecular assembly and structural plasticity of sensory ribbon synapses—A presynaptic perspective. Int. J. Mol. Sci. 21, 8758 (2020). · DOI
  7. Ackermann, F., Waites, C.L. & Garner, C.C. Presynaptic active zones in invertebrates and vertebrates. EMBO Rep. 16, 923–938 (2015). · DOI · Paper page
  8. Huang, C.Y.M. & Rasband, M.N. Axon initial segments: structure, function, and disease. Ann. N.Y. Acad. Sci. 1420, 46–61 (2018). · DOI
  9. Fréal, A. & Hoogenraad, C.C. The dynamic axon initial segment: from neuronal polarity to network homeostasis. Neuron 113, 649–669 (2025). · DOI
  10. Broussard, J.A., Webb, D.J. & Kaverina, I. Asymmetric focal adhesion disassembly in motile cells. Curr. Opin. Cell Biol. 20, 85–90 (2008). · DOI
  11. Schachtner, H., Calaminus, S.D.J., Thomas, S.G. & Machesky, L.M. Podosomes in adhesion, migration, mechanosensing and matrix remodeling. Cytoskeleton 70, 572–589 (2013). · DOI
  12. Weber, K., Hey, S., Cervero, P. & Linder, S. The circle of life: phases of podosome formation, turnover and reemergence. Eur. J. Cell Biol. 101, 151218 (2022). · DOI
  13. Geiger, B., Bershadsky, A., Pankov, R. & Yamada, K.M. Transmembrane crosstalk between the extracellular matrix and the cytoskeleton. Nat. Rev. Mol. Cell Biol. 2, 793–805 (2001). · DOI
  14. Samarel, A.M. Costameres, focal adhesions, and cardiomyocyte mechanotransduction. Am. J. Physiol. Heart Circ. Physiol. 289, H2291–H2301 (2005). · DOI
  15. Frank, D., Kuhn, C., Katus, H.A. & Frey, N. The sarcomeric Z-disc: a nodal point in signalling and disease. J. Mol. Med. 84, 446–468 (2006). · DOI · Paper page
  16. Zhang, J., Herrera, A.M., Paré, P.D. & Seow, C.Y. Dense-body aggregates as plastic structures supporting tension in smooth muscle cells. Am. J. Physiol. Lung Cell. Mol. Physiol. 299, L631–L638 (2010). · DOI
  17. Zhu, J.W. et al. GIT/PIX condensates are modular and ideal for distinct compartmentalized cell signaling. Mol. Cell 79, 782–796.e6 (2020). · DOI
  18. Case, L.B., De Pasquale, M., Henry, L. & Rosen, M.K. Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation. eLife 11, e72588 (2022). · DOI
  19. Liang, P.G. et al. Paxillin phase separation promotes focal adhesion assembly and integrin signaling. J. Cell Biol. 223, e202209027 (2024). · DOI
  20. Sponga, A. et al. Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin. Sci. Adv. 7, eabg7653 (2021). · DOI
  21. Sjöstrand, F.S. Ultrastructure of retinal rod synapses of the guinea pig eye as revealed by three-dimensional reconstructions from serial sections. J. Ultrastruct. Res. 2, 122–170 (1958). · DOI
  22. Stevens-Sostre, W.A. & Hoon, M. Cellular and molecular mechanisms regulating retinal synapse development. Annu. Rev. Vis. Sci. 10, 377–402 (2024). · DOI
  23. Safieddine, S., El-Amraoui, A. & Petit, C. The auditory hair cell ribbon synapse: from assembly to function. Annu. Rev. Neurosci. 35, 509–528 (2012). · DOI
  24. Moser, T., Grabner, C.P. & Schmitz, F. Sensory processing at ribbon synapses in the retina and the cochlea. Physiol. Rev. 100, 103–144 (2020). · DOI
  25. Spiwoks-Becker, I., Glas, M., Lasarzik, I. & Vollrath, L. Mouse photoreceptor synaptic ribbons lose and regain material in response to illumination changes. Eur. J. Neurosci. 19, 1559–1571 (2004). · DOI
  26. Fuchs, M., Sendelbeck, A., Atorf, J., Kremers, J. & Brandstätter, J.H. Strain differences in illumination-dependent structural changes at mouse photoreceptor ribbon synapses. J. Comp. Neurol. 521, 69–78 (2013). · DOI
  27. Mehta, B., Snellman, J., Chen, S., Li, W. & Zenisek, D. Synaptic ribbons influence the size and frequency of miniature-like evoked postsynaptic currents. Neuron 77, 516–527 (2013). · DOI
  28. Maxeiner, S., Luo, F.J., Tan, A., Schmitz, F. & Südhof, T.C. How to make a synaptic ribbon: RIBEYE deletion abolishes ribbons in retinal synapses and disrupts neurotransmitter release. EMBO J. 35, 1098–1114 (2016). · DOI
  29. Lv, C.X. et al. Synaptic ribbons require ribeye for electron density, proper synaptic localization, and recruitment of calcium channels. Cell Rep. 15, 2784–2795 (2016). · DOI
  30. Schmitz, F., Königstorfer, A. & Südhof, T.C. RIBEYE, a component of synaptic ribbons: a protein’s journey through evolution provides insight into synaptic ribbon function. Neuron 28, 857–872 (2000). · DOI · Paper page
  31. Jecrois, A.M. et al. Cryo-EM structure of CtBP2 confirms tetrameric architecture. Structure 29, 310–319.e5 (2021). · DOI
  32. Bellesis, A.G., Jecrois, A.M., Hayes, J.A., Schiffer, C.A. & Royer, W.E. Assembly of human C-terminal binding protein (CtBP) into tetramers. J. Biol. Chem. 293, 9101–9112 (2018). · DOI
  33. Shankhwar, S. et al. RIBEYE B-domain is essential for RIBEYE A-domain stability and assembly of synaptic ribbons. Front. Mol. Neurosci. 15, 838311 (2022). · DOI
  34. Magupalli, V.G. et al. Multiple RIBEYE-RIBEYE interactions create a dynamic scaffold for the formation of synaptic ribbons. J. Neurosci. 28, 7954–7967 (2008). · DOI
  35. Papadopoulos, S., Tinschert, R., Papadopoulos, I., Gerloff, X. & Schmitz, F. Analytical post-embedding immunogold-electron microscopy with direct gold-labelled monoclonal primary antibodies against RIBEYE A- and B-domain suggests a refined model of synaptic ribbon assembly. Int. J. Mol. Sci. 25, 7443 (2024). · DOI
  36. Müller, T.M. et al. A multiple piccolino-RIBEYE interaction supports plate-shaped synaptic ribbons in retinal neurons. J. Neurosci. 39, 2606–2619 (2019). · DOI
  37. Turner, J. & Crossley, M. The CtBP family: enigmatic and enzymatic transcriptional co-repressors. BioEssays 23, 683–690 (2001). · DOI
  38. Nardini, M. et al. CtBP/BARS: a dual-function protein involved in transcription co-repression and Golgi membrane fission. EMBO J. 22, 3122–3130 (2003). · DOI
  39. Quinlan, K.G.R. et al. Specific recognition of ZNF217 and other zinc finger proteins at a surface groove of C-terminal binding proteins. Mol. Cell. Biol. 26, 8159–8172 (2006). · DOI
  40. Schmitz, F. Presynaptic [Ca 2+ ] and GCAPs: aspects on the structure and function of photoreceptor ribbon synapses. Front. Mol. Neurosci. 7, 3 (2014). · DOI
  41. Regus-Leidig, H. et al. Identification and immunocytochemical characterization of Piccolino, a novel Piccolo splice variant selectively expressed at sensory ribbon synapses of the eye and ear. PLoS One 8, e70373 (2013). · DOI
  42. Regus-Leidig, H. et al. In vivo knockdown of Piccolino disrupts presynaptic ribbon morphology in mouse photoreceptor synapses. Front. Cell. Neurosci. 8, 259 (2014). · DOI
  43. Michanski, S. et al. Piccolino is required for ribbon architecture at cochlear inner hair cell synapses and for hearing. EMBO Rep. 24, e56702 (2023). · DOI
  44. Sheets, L., Hagen, M.W. & Nicolson, T. Characterization of Ribeye subunits in zebrafish hair cells reveals that exogenous Ribeye B-domain and CtBP1 localize to the basal ends of synaptic ribbons. PLoS One 9, e107256 (2014). · DOI
  45. Schmitz, F. & Drenckhahn, D. Intermediate stages in the disassembly of synaptic ribbons in cone photoreceptors of the crucian carp, Carassius carassius . Cell Tissue Res. 272, 487–490 (1993). · DOI
  46. Hilbert, B.J., Grossman, S.R., Schiffer, C.A. & Royer, W.E. Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design. FEBS Lett. 588, 1743–1748 (2014). · DOI
  47. Ray, S. et al. α-Synuclein aggregation nucleates through liquid-liquid phase separation. Nat. Chem. 12, 705–716 (2020). · DOI · Paper page
  48. Patel, A. et al. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 162, 1066–1077 (2015). · DOI
  49. De Pascalis, C. & Etienne-Manneville, S. Single and collective cell migration: the mechanics of adhesions. Mol. Biol. Cell 28, 1833–1846 (2017). · DOI
  50. Gardel, M.L., Schneider, I.C., Aratyn-Schaus, Y. & Waterman, C.M. Mechanical integration of actin and adhesion dynamics in cell migration. Annu. Rev. Cell Dev. Biol. 26, 315–333 (2010). · DOI
  51. Litschel, T. et al. Membrane-induced 2D phase separation of the focal adhesion protein Talin. Nat. Commun. 15, 4986 (2024). · DOI
  52. Kanchanawong, P. et al. Nanoscale architecture of integrin-based cell adhesions. Nature 468, 580–584 (2010). · DOI
  53. Stutchbury, B., Atherton, P., Tsang, R., Wang, D.Y. & Ballestrem, C. Distinct focal adhesion protein modules control different aspects of mechanotransduction. J. Cell Sci. 130, 1612–1624 (2017). · DOI
  54. Lange, S., Ehler, E. & Gautel, M. From A to Z and back? Multicompartment proteins in the sarcomere. Trends Cell Biol. 16, 11–18 (2006). · DOI
  55. Faulkner, G. et al. FATZ, a filamin-, actinin-, and telethonin-binding protein of the Z-disc of skeletal muscle. J. Biol. Chem. 275, 41234–41242 (2000). · DOI
  56. Moser, T., Brandt, A. & Lysakowski, A. Hair cell ribbon synapses. Cell Tissue Res. 326, 347–359 (2006). · DOI
  57. Nouvian, R., Beutner, D., Parsons, T.D. & Moser, T. Structure and function of the hair cell ribbon synapse. J. Membr. Biol. 209, 153–165 (2006). · DOI
  58. Regus-Leidig, H., tom Dieck, S. & Brandstätter, J.H. Absence of functional active zone protein Bassoon affects assembly and transport of ribbon precursors during early steps of photoreceptor synaptogenesis. Eur. J. Cell Biol. 89, 468–475 (2010). · DOI
  59. Tom Dieck, S. et al. Molecular dissection of the photoreceptor ribbon synapse: physical interaction of Bassoon and RIBEYE is essential for the assembly of the ribbon complex. J. Cell Biol. 168, 825–836 (2005). · DOI
  60. Schorb, M., Haberbosch, I., Hagen, W.J.H., Schwab, Y. & Mastronarde, D.N. Software tools for automated transmission electron microscopy. Nat. Methods 16, 471–477 (2019). · DOI
  61. 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
  62. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). · DOI
  63. Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021). · DOI
  64. Pettersen, E.F. et al. UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI
  65. Casañal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo-microscopy and crystallographic data. Protein Sci. 29, 1055–1064 (2020). · DOI
  66. Adams, P.D. et al. PHENIX : a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). · DOI · Paper page
  67. 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
  68. Zheng, S.Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). · DOI
  69. Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). · DOI
  70. 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
  71. Zheng, S. et al. AreTomo: an integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. J. Struct. Biol. X 6, 100068 (2022). · DOI
  72. Hunter, J.D. Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 9, 90–95 (2007). · DOI · Paper page
  73. Waskom, M.L. seaborn: statistical data visualization. J. Open Source Softw. 6, 3021 (2021). · DOI · Paper page

Metadata

Authors
Liu, Y., Wang, X., Zheng, T., Niu, F., Sun, R., Yang, C., Xu, S., Zhao, Z., Shen, Z., Huang, W., Wang, X., Liu, K., Cai, S., Zhang, M., & Wei, Z.
Affiliations
  • Southern University of Science and Technology (CN)
  • Hong Kong University of Science and Technology (HK)
ORCID
Venue
Vita
Publisher
China Engineering Science Press Co. Ltd.
Published
2026
ISSN
2097-7468 (ISSN-L)
DOI
10.15302/vita.2026.05.0033
OpenAlex
W7161540635
Cited by
3
References
2
Citations by year
2026: 3
FWCI
7.43
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Vita (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • National Natural Science Foundation of China (32471250, 32400784, 32470576, 32471262, (82188101)
  • Ministry of Education of the People's Republic of China (JYB2025XDXM505)
  • Southern University of Science and Technology
  • National Key Research and Development Program of China (2025YFA1308800)
  • Basic and Applied Basic Research Foundation of Guangdong Province (2024A1515012651, 2024A1515010742, 2023A1515030232)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
synaptic ribbons, ribeye, phase separation, phase transitions, intrinsically disordered regions, SAM domain, B domain, condensate, synaptic plasticity, sensory neurons, CtBP1

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review