Abstract

The transition zone (TZ) ciliary subcompartment is thought to control cilium composition and signalling by facilitating a protein diffusion barrier at the ciliary base. TZ defects cause ciliopathies such as Meckel–Gruber syndrome (MKS), nephronophthisis (NPHP) and Joubert syndrome1 (JBTS). However, the molecular composition and mechanisms underpinning TZ organization and barrier regulation are poorly understood. To uncover candidate TZ genes, we employed bioinformatics (coexpression and co-evolution) and identified TMEM107 as a TZ protein mutated in oral–facial–digital syndrome and JBTS patients. Mechanistic studies in Caenorhabditis elegans showed that TMEM-107 controls ciliary composition and functions redundantly with NPHP-4 to regulate cilium integrity, TZ docking and assembly of membrane to microtubule Y-link connectors. Furthermore, nematode TMEM-107 occupies an intermediate layer of the TZ-localized MKS module by organizing recruitment of the ciliopathy proteins MKS-1, TMEM-231 (JBTS20) and JBTS-14 (TMEM237). Finally, MKS module membrane proteins are immobile and super-resolution microscopy in worms and mammalian cells reveals periodic localizations within the TZ. This work expands the MKS module of ciliopathy-causing TZ proteins associated with diffusion barrier formation and provides insight into TZ subdomain architecture.

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Acknowledgements

This work was financially supported via the European Community’s Seventh Framework Programme FP7/2009 (SYSCILIA grant agreement 241955 to O.E.B., M.A.H., R.H.G. and C.A.J., and Gencodys to M.A.H.), Science Foundation Ireland (11/PI/1037 to O.E.B.), the Dutch Kidney Foundation CP11.18 ‘KOUNCIL’ (to R.H.G.), the GIS-Institut des Maladies Rares (HTS to C.T.-R.), the French Fondation for Rare Disease (to C.T.-R.), the Virgo consortium (FES0908 to M.A.H.), the Netherlands Genomics Initiative (050-060-452, RvdL to M.A.H.), the French Ministry of Health (PHRC national 2010-A01014-35 and 2013 to C.T.-R.), the Fondation pour la Recherche Médicale (DEQ20130326532 to S.S.), the Regional Council of Burgundy (to C.T.-R.), a Sir Jules Thorn Award for Biomedical Research (JTA/09 to C.A.J.), and the UK Medical Research Council (MR/K011154/1 to C.A.J., and MR/K015613/1 to M.P.). We thank the patients and their families for their participation. We also thank the NHLBI GO Exome Sequencing Project and its ongoing studies that produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Broad GO Sequencing Project (HL-102925), the Seattle GO Sequencing Project (HL-102926) and the Heart GO Sequencing Project (HL-103010). We thank M. Leroux (Simon Fraser University, Canada), B. Yoder (University of Alabama, USA), the Caenorhabditis elegans Genetics Center (Minnesota, USA), the National Bioresource project (Tokyo, Japan), the International C. elegans gene knockout consortium, and the C. elegans Million Mutation Project for nematode reagents. We are grateful to C. Eggeling and C. Lagerholm (Weatherall Institute of Molecular Medicine and the Wolfson Imaging Center, Oxford, UK) for assistance with STED microscopy, D. Scholz and T. Toivonen (UCD Conway Institute imaging facility, Dublin, IRL) for imaging support, and R. Dijkstra (Scientific Volume Imaging bv, Hilversum, NL) for assistance with STED image deconvolution. We also thank A. Cleasby (Faculty of Biological Sciences, University of Leeds, Leeds, UK) for help with developing the dSTORM technique, B. Chih (Genentech, South San Francisco, CA, USA) for the kind gift of polyclonal anti-TMEM17 and TMEM231 antibodies, and T. McMorrow (University College Dublin, Dublin, Ireland) for the generous gift of the RPTEC/TERT1 cells. We thank D. Rodriguez (Trousseau hospital, Paris) for assistance with analysis of brain MRIs. The dSTORM microscope was generously funded by alumnus M. Beverly, in support of the University of Leeds ‘making a world of difference campaign’.

Author information

Author notes

    • Nils J. Lambacher
    • , Ange-Line Bruel
    •  & Teunis J. P. van Dam

    These authors contributed equally to this work.

Affiliations

  1. School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

    • Nils J. Lambacher
    • , Stefanie Kuhns
    • , Julie E. Kennedy
    • , Karl Gaff
    •  & Oliver E. Blacque
  2. EA4271 GAD, Genetics of Development Abnormalities, Burgundy University, 21078 Dijon, France

    • Ange-Line Bruel
    • , Jean-Baptiste Rivière
    • , Laurence Faivre
    •  & Christel Thauvin-Robinet
  3. Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA Nijmegen, Netherlands

    • Teunis J. P. van Dam
    • , Robin van der Lee
    •  & Martijn A. Huynen
  4. Section of Ophthalmology and Neurosciences, Leeds Institute of Biomolecular & Clinical Sciences, University of Leeds, Leeds LS9 7TF, UK

    • Katarzyna Szymańska
    •  & Colin A. Johnson
  5. Department of Nephrology and Hypertension, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands

    • Gisela G. Slaats
    • , Ka Man Wu
    •  & Rachel H. Giles
  6. School of Biochemistry and Immunology, Microscopy Facility, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland

    • Gavin J. McManus
  7. Centre de référence des malformations et maladies congénitales du cervelet et Service de Génétique, APHP, Hôpital Trousseau, 75012 Paris, France

    • Lydie Burglen
    •  & Diane Doummar
  8. INSERM U1141, 75019 Paris, France

    • Lydie Burglen
  9. FHU TRANSLAD, CHU Dijon, 21079 Dijon, France

    • Jean-Baptiste Rivière
    • , Laurence Faivre
    •  & Christel Thauvin-Robinet
  10. INSERM UMR1163, Hôpital Necker-Enfants Malades, 75015 Paris, France

    • Tania Attié-Bitach
    •  & Sophie Saunier
  11. Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France

    • Tania Attié-Bitach
    •  & Sophie Saunier
  12. Institut IMAGINE, 75015 Paris, France

    • Tania Attié-Bitach
    •  & Sophie Saunier
  13. Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France

    • Tania Attié-Bitach
  14. School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK

    • Alistair Curd
    •  & Michelle Peckham

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Contributions

N.J.L., J.E.K., K.G. and O.E.B. performed and interpreted experiments with C. elegans. T.J.P.v.D., R.v.d.L. and M.A.H. performed all bioinformatics analyses. A.-L.B., L.B., D.D., T.A.-B., S.S. and C.T.-R. collected and purified patient samples, performed exome sequencing and analysed sequencing data. N.J.L., S.K. and G.J.M. performed the STED imaging. A.C., M.P. and C.A.J. conducted the dSTORM imaging and processing. K.S., S.K., G.G.S., K.M.W. and R.H.G. conducted transfection and immunofluorescence microscopy in mammalian cells. K.S. and C.A.J. contributed the co-immunoprecipitation experiments. J.-B.R., L.F. and C.T.-R. diagnosed and referred patients. The co-corresponding authors shared supervision of the work. M.A.H. uncovered TMEM107 as a candidate ciliary gene, and directed the bioinformatics work. C.T.-R. collated JBTS and OFD patient samples, performed clinical characterization and directed the sequencing. O.E.B. directed research, analysed and collated data for the manuscript. O.E.B., M.A.H., R.H.G. and C.A.J. conceived and executed the study, and O.E.B., N.J.L., T.J.v.D. and M.A.H. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Martijn A. Huynen or Christel Thauvin-Robinet or Oliver E. Blacque.

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  1. 1.

    Electron Tomogram of the C. elegans TZ.

    Reconstruction derived from a 200 nm section of a C. elegans amphid channel ciliary TZ. Arrow denotes a Y-link density throughout the tomogram, indicating that the Y-link structures are continuous sheets along the axial plane. Bar; 100 nm.

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DOI

https://doi.org/10.1038/ncb3273

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