Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis

Elife. 2017 Nov 10;6:e31012. doi: 10.7554/eLife.31012.

Abstract

We previously reported that Parkinson's disease (PD) kinase LRRK2 phosphorylates a subset of Rab GTPases on a conserved residue in their switch-II domains (Steger et al., 2016) (PMID: 26824392). Here, we systematically analyzed the Rab protein family and found 14 of them (Rab3A/B/C/D, Rab5A/B/C, Rab8A/B, Rab10, Rab12, Rab29, Rab35 and Rab43) to be specifically phosphorylated by LRRK2, with evidence for endogenous phosphorylation for ten of them (Rab3A/B/C/D, Rab8A/B, Rab10, Rab12, Rab35 and Rab43). Affinity enrichment mass spectrometry revealed that the primary ciliogenesis regulator, RILPL1 specifically interacts with the LRRK2-phosphorylated forms of Rab8A and Rab10, whereas RILPL2 binds to phosphorylated Rab8A, Rab10, and Rab12. Induction of primary cilia formation by serum starvation led to a two-fold reduction in ciliogenesis in fibroblasts derived from pathogenic LRRK2-R1441G knock-in mice. These results implicate LRRK2 in primary ciliogenesis and suggest that Rab-mediated protein transport and/or signaling defects at cilia may contribute to LRRK2-dependent pathologies.

Keywords: LRRK2; Parkinson's disease; Rab GTPases; biochemistry; ciliogenesis; human; mass spectrometry; mouse; proteomics.

MeSH terms

  • Animals
  • Carrier Proteins / metabolism
  • Cells, Cultured
  • Cilia / metabolism*
  • Fibroblasts / physiology
  • Gene Knock-In Techniques
  • Humans
  • Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 / metabolism*
  • Low Density Lipoprotein Receptor-Related Protein-1 / metabolism
  • Mass Spectrometry
  • Mice
  • Organelle Biogenesis*
  • Phosphorylation
  • Protein Binding
  • Protein Interaction Mapping
  • Proteomics
  • rab GTP-Binding Proteins / metabolism*

Substances

  • Carrier Proteins
  • LRP1 protein, human
  • LRP2BP protein, human
  • Low Density Lipoprotein Receptor-Related Protein-1
  • Leucine-Rich Repeat Serine-Threonine Protein Kinase-2
  • rab GTP-Binding Proteins