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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.<\/jats:p>","DOI":"10.3390\/cells12020312","type":"journal-article","created":{"date-parts":[[2023,1,16]],"date-time":"2023-01-16T03:40:34Z","timestamp":1673840434000},"page":"312","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["PDE6D Mediates Trafficking of Prenylated Proteins NIM1K and UBL3 to Primary Cilia"],"prefix":"10.3390","volume":"12","author":[{"given":"Siebren","family":"Faber","sequence":"first","affiliation":[{"name":"Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stef J. F.","family":"Letteboer","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9681-2908","authenticated-orcid":false,"given":"Katrin","family":"Junger","sequence":"additional","affiliation":[{"name":"Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1527-5029","authenticated-orcid":false,"given":"Rossano","family":"Butcher","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trinadh V. Satish","family":"Tammana","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4552-2908","authenticated-orcid":false,"given":"Sylvia E. C.","family":"van Beersum","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2209-2113","authenticated-orcid":false,"given":"Marius","family":"Ueffing","sequence":"additional","affiliation":[{"name":"Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4347-6503","authenticated-orcid":false,"given":"Rob W. J.","family":"Collin","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2693-689X","authenticated-orcid":false,"given":"Karsten","family":"Boldt","sequence":"additional","affiliation":[{"name":"Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald","family":"Roepman","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/s41580-019-0116-4","article-title":"Establishing and regulating the composition of cilia for signal transduction","volume":"20","author":"Nachury","year":"2019","journal-title":"Nat. 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