1. Biochemistry and Chemical Biology
  2. Cell Biology

A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation

  1. Edmundo G Vides
  2. Ayan Adhikari
  3. Claire Y Chiang
  4. Pawel Lis
  5. Elena Purlyte
  6. Charles Limouse
  7. Justin L Shumate
  8. Elena Spinola-Lasso
  9. Herschel S Dhekne
  10. Dario R Alessi
  11. Suzanne R Pfeffer  Is a corresponding author
  1. Stanford University, United States
  2. University of Dundee, United Kingdom
  3. Universidad de Las Palmas de Gran Canaria, Spain
https://doi.org/10.7554/eLife.79771
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  1. Edmundo G Vides
  2. Ayan Adhikari
  3. Claire Y Chiang
  4. Pawel Lis
  5. Elena Purlyte
  6. Charles Limouse
  7. Justin L Shumate
  8. Elena Spinola-Lasso
  9. Herschel S Dhekne
  10. Dario R Alessi
  11. Suzanne R Pfeffer
(2022)
A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation
eLife 11:e79771.
https://doi.org/10.7554/eLife.79771
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Abstract

Activating mutations in the Leucine Rich Repeat Kinase 2 (LRRK2) cause Parkinson's disease and previously we showed that activated LRRK2 phosphorylates a subset of Rab GTPases (Steger et al., 2017). Moreover, Golgi-associated Rab29 can recruit LRRK2 to the surface of the Golgi and activate it there for both auto- and Rab substrate phosphorylation. Here we define the precise Rab29 binding region of the LRRK2 Armadillo domain between residues 360-450 and show that this domain, termed 'Site #1', can also bind additional LRRK2 substrates, Rab8A and Rab10. Moreover, we identify a distinct, N-terminal, higher affinity interaction interface between LRRK2 phosphorylated Rab8 and Rab10 termed 'Site #2', that can retain LRRK2 on membranes in cells to catalyze multiple, subsequent phosphorylation events. Kinase inhibitor washout experiments demonstrate that rapid recovery of kinase activity in cells depends on the ability of LRRK2 to associate with phosphorylated Rab proteins, and phosphorylated Rab8A stimulates LRRK2 phosphorylation of Rab10 in vitro. Reconstitution of purified LRRK2 recruitment onto planar lipid bilayers decorated with Rab10 protein demonstrates cooperative association of only active LRRK2 with phospho-Rab10-containing membrane surfaces. These experiments reveal a feed-forward pathway that provides spatial control and membrane activation of LRRK2 kinase activity.

Data availability

All primary data associated with each figure has been deposited in a repository and can be found at https://doi.org/10.5061/dryad.3tx95x6j7; quantitation data of the blots in Figure 3--Fig. Supp. 4 (for the bar graphs in Figures 3C and 3D) can be found at doi (10.5281/zenodo.7057419).

The following data sets were generated

Article and author information

Author details

  1. Edmundo G Vides

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  2. Ayan Adhikari

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  3. Claire Y Chiang

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  4. Pawel Lis

    MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4978-7671

  5. Elena Purlyte

    MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
    Competing interests
    No competing interests declared.

  6. Charles Limouse

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  7. Justin L Shumate

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  8. Elena Spinola-Lasso

    Departamento de Bioquímica y Biología Molecular, Universidad de Las Palmas de Gran Canaria, Gran Canaria, Spain
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2207-5786

  9. Herschel S Dhekne

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2240-1230

  10. Dario R Alessi

    MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2140-9185

  11. Suzanne R Pfeffer

    Department of Biochemistry, Stanford University, Stanford, United States
    For correspondence
    pfeffer@stanford.edu
    Competing interests
    Suzanne R Pfeffer, Senior editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6462-984X

Funding

Aligning Science Across Parkinson's Disease (ASAP-000463)

  • Dario R Alessi
  • Suzanne R Pfeffer

Michael J Fox Foundation (17298)

  • Dario R Alessi
  • Suzanne R Pfeffer

Michael J Fox Foundation (6986)

  • Dario R Alessi
  • Suzanne R Pfeffer

Medical Research Council (MC_UU_00018/1)

  • Dario R Alessi

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Wade Harper, Harvard Medical School, United States

Version history

  1. Preprint posted: April 25, 2022 (view preprint)
  2. Received: April 26, 2022
  3. Accepted: September 22, 2022
  4. Accepted Manuscript published: September 23, 2022 (version 1)
  5. Version of Record published: October 17, 2022 (version 2)

Copyright

© 2022, Vides et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Edmundo G Vides
  2. Ayan Adhikari
  3. Claire Y Chiang
  4. Pawel Lis
  5. Elena Purlyte
  6. Charles Limouse
  7. Justin L Shumate
  8. Elena Spinola-Lasso
  9. Herschel S Dhekne
  10. Dario R Alessi
  11. Suzanne R Pfeffer
(2022)
A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation
eLife 11:e79771.
https://doi.org/10.7554/eLife.79771

Share this article

https://doi.org/10.7554/eLife.79771

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Further reading

    1. Cell Biology

    Genome-wide screen reveals Rab12 GTPase as a critical activator of Parkinson’s disease-linked LRRK2 kinase

    Herschel S Dhekne, Francesca Tonelli ... Suzanne R Pfeffer
    Research Advance Updated

    Activating mutations in the leucine-rich repeat kinase 2 (LRRK2) cause Parkinson’s disease. LRRK2 phosphorylates a subset of Rab GTPases, particularly Rab10 and Rab8A, and we showed previously that these phosphoRabs play an important role in LRRK2 membrane recruitment and activation (Vides et al., 2022). To learn more about LRRK2 pathway regulation, we carried out an unbiased, CRISPR-based genome-wide screen to identify modifiers of cellular phosphoRab10 levels. A flow cytometry assay was developed to detect changes in phosphoRab10 levels in pools of mouse NIH-3T3 cells harboring unique CRISPR guide sequences. Multiple negative and positive regulators were identified; surprisingly, knockout of the Rab12 gene was especially effective in decreasing phosphoRab10 levels in multiple cell types and knockout mouse tissues. Rab-driven increases in phosphoRab10 were specific for Rab12, LRRK2-dependent and PPM1H phosphatase-reversible, and did not require Rab12 phosphorylation; they were seen with wild type and pathogenic G2019S and R1441C LRRK2. As expected for a protein that regulates LRRK2 activity, Rab12 also influenced primary cilia formation. AlphaFold modeling revealed a novel Rab12 binding site in the LRRK2 Armadillo domain, and we show that residues predicted to be essential for Rab12 interaction at this site influence phosphoRab10 and phosphoRab12 levels in a manner distinct from Rab29 activation of LRRK2. Our data show that Rab12 binding to a new site in the LRRK2 Armadillo domain activates LRRK2 kinase for Rab phosphorylation and could serve as a new therapeutic target for a novel class of LRRK2 inhibitors that do not target the kinase domain.

    1. Biochemistry and Chemical Biology

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

    Martin Steger, Federico Diez ... Matthias Mann
    Research Advance Updated

    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.

    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases

    Martin Steger, Francesca Tonelli ... Matthias Mann
    Research Article Updated

    Mutations in Park8, encoding for the multidomain Leucine-rich repeat kinase 2 (LRRK2) protein, comprise the predominant genetic cause of Parkinson's disease (PD). G2019S, the most common amino acid substitution activates the kinase two- to threefold. This has motivated the development of LRRK2 kinase inhibitors; however, poor consensus on physiological LRRK2 substrates has hampered clinical development of such therapeutics. We employ a combination of phosphoproteomics, genetics, and pharmacology to unambiguously identify a subset of Rab GTPases as key LRRK2 substrates. LRRK2 directly phosphorylates these both in vivo and in vitro on an evolutionary conserved residue in the switch II domain. Pathogenic LRRK2 variants mapping to different functional domains increase phosphorylation of Rabs and this strongly decreases their affinity to regulatory proteins including Rab GDP dissociation inhibitors (GDIs). Our findings uncover a key class of bona-fide LRRK2 substrates and a novel regulatory mechanism of Rabs that connects them to PD.