Systematic proteomics of the VCP-UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis

Nat Cell Biol. 2015 Oct;17(10):1356-69. doi: 10.1038/ncb3238. Epub 2015 Sep 21.

Abstract

The AAA-ATPase VCP (also known as p97 or CDC48) uses ATP hydrolysis to 'segregate' ubiquitylated proteins from their binding partners. VCP acts through UBX-domain-containing adaptors that provide target specificity, but the targets and functions of UBXD proteins remain poorly understood. Through systematic proteomic analysis of UBXD proteins in human cells, we reveal a network of over 195 interacting proteins, implicating VCP in diverse cellular pathways. We have explored one such complex between an unstudied adaptor UBXN10 and the intraflagellar transport B (IFT-B) complex, which regulates anterograde transport into cilia. UBXN10 localizes to cilia in a VCP-dependent manner and both VCP and UBXN10 are required for ciliogenesis. Pharmacological inhibition of VCP destabilized the IFT-B complex and increased trafficking rates. Depletion of UBXN10 in zebrafish embryos causes defects in left-right asymmetry, which depends on functional cilia. This study provides a resource for exploring the landscape of UBXD proteins in biology and identifies an unexpected requirement for VCP-UBXN10 in ciliogenesis.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism*
  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism*
  • Animals
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism*
  • Cilia / metabolism*
  • Cilia / physiology
  • Cytoskeletal Proteins / genetics
  • Cytoskeletal Proteins / metabolism
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Immunoblotting
  • LLC-PK1 Cells
  • Microscopy, Confocal
  • Microscopy, Fluorescence
  • Morphogenesis / physiology
  • Protein Binding
  • Protein Interaction Mapping / methods
  • Protein Interaction Maps*
  • Proteomics / methods*
  • RNA Interference
  • Swine
  • Tumor Suppressor Proteins / genetics
  • Tumor Suppressor Proteins / metabolism
  • Valosin Containing Protein

Substances

  • Adaptor Proteins, Signal Transducing
  • Cell Cycle Proteins
  • Cytoskeletal Proteins
  • IFT74 protein, human
  • IFT88 protein, human
  • Tumor Suppressor Proteins
  • UBXN10 protein, human
  • Adenosine Triphosphatases
  • VCP protein, human
  • Valosin Containing Protein