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

doi:10.3390/cells12020312

PDE6D Mediates Trafficking of Prenylated Proteins NIM1K and UBL3 to Primary Cilia

Cells. 2023 Jan 13;12(2):312. doi: 10.3390/cells12020312.

Affiliations

¹ Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.
² Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany.
³ Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA.
⁴ Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.

Abstract

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.

Keywords: FAM219A; NIM1K; PDE6D; UBL3; cilium; photoreceptor; prenylation; protein trafficking.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cilia* / metabolism
Cyclic Nucleotide Phosphodiesterases, Type 6 / metabolism
Humans
Mice
Protein Transport
Proteins / metabolism
Retina / metabolism
Retinal Degeneration* / metabolism

Substances

Proteins
PDE6D protein, human
Cyclic Nucleotide Phosphodiesterases, Type 6

Grants and funding

This research was funded by the Landelijke Stichting voor Blinden en Slechtzienden, Stichting Retina Nederland Fonds, Stichting Beheer Het Schild, Stichting Blinden-Penning, and Stichting Steunfonds Uitzicht via Uitzicht 2016/2017-22, together with the Gelderse Blindenstichting, Rotterdamse Stichting Blindenbelangen, Stichting tot Verbetering van het Lot der Blinden ‘Het Lot’, the Stichting voor gehandicapte kinderen Dowilvo, the Netherlands Organisation for Health Research and Development (ZonMW, #91216051), and the Foundation Fighting Blindness, USA (PPA-0717-0719-RAD and BR-CMM-0720-0789-RAD) to R.R.