PDE6D Mediates Trafficking of Prenylated Proteins NIM1K and UBL3 to Primary Cilia
Siebren Faber,
Stef J. F. Letteboer,
Katrin Junger,
Rossano Butcher,
Trinadh V. Satish Tammana,
Sylvia E. C. van Beersum,
Marius Ueffing,
Rob W. J. Collin,
Qin Liu,
Karsten Boldt,
Ronald Roepman
Affiliations
Siebren Faber
Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
Stef J. F. Letteboer
Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
Katrin Junger
Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
Rossano Butcher
Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
Trinadh V. Satish Tammana
Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
Sylvia E. C. van Beersum
Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
Marius Ueffing
Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
Rob W. J. Collin
Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
Qin Liu
Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
Karsten Boldt
Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
Ronald Roepman
Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
Mutations in PDE6D impair the function of its cognate protein, phosphodiesterase 6D (PDE6D), in prenylated protein trafficking towards the ciliary membrane, causing the human ciliopathy Joubert Syndrome (JBTS22) and retinal degeneration in mice. In this study, we purified the prenylated cargo of PDE6D by affinity proteomics to gain insight into PDE6D-associated disease mechanisms. By this approach, we have identified a specific set of PDE6D-interacting proteins that are involved in photoreceptor integrity, GTPase activity, nuclear import, or ubiquitination. Among these interacting proteins, we identified novel ciliary cargo proteins of PDE6D, including FAM219A, serine/threonine-protein kinase NIM1 (NIM1K), and ubiquitin-like protein 3 (UBL3). We show that NIM1K and UBL3 localize inside the cilium in a prenylation-dependent manner. Furthermore, UBL3 also localizes in vesicle-like structures around the base of the cilium. Through affinity proteomics of UBL3, we confirmed its strong interaction with PDE6D and its association with proteins that regulate small extracellular vesicles (sEVs) and ciliogenesis. Moreover, we show that UBL3 localizes in specific photoreceptor cilium compartments in a prenylation-dependent manner. Therefore, we propose that UBL3 may play a role in the sorting of proteins towards the photoreceptor outer segment, further explaining the development of PDE6D-associated retinal degeneration.
