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

Steger, Martin, Tonelli, Francesca, Ito, Genta, Davies, Paul, Trost, Matthias, Vetter, Melanie, Wachter, Stefanie, Lorentzen, Esben, Duddy, Graham, Wilson, Stephen, Baptista, Marco AS, Fiske, Brian K, Fell, Matthew J, Morrow, John A, Reith, Alastair D, Alessi, Dario R, Mann, Matthias·2016·eLife

Abstract

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.

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Crossref · 10.7554/elife.12813

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  • Most mutations in LRRK2 increase its kinase activity, increasing phosphorylation of a broad subset of Rab GTPases.

    “Most mutations in LRRK2 increase its kinase activity, increasing phosphorylation of a broad subset of Rab GTPases [79].”

    From Cellular and subcellular localization of Rab10 and phospho-T73 Rab10 in the mouse and human brain (2023) · cites this paper as [79]

    The Introduction says that PD-associated LRRK2 mutations increase phosphorylation of at least three Rab GTPases, supporting increased phosphorylation of a subset, but not characterizing that subset as broad. The Results section on pathogenic mutations distinguishes kinase-domain mutations that augment kinase activity from the ROC-COR mutation R1441C, which increased Rab phosphorylation in cells without directly enhancing kinase activity. The paper therefore does not support the claim that most mutations increase kinase activity as the mechanism. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • pRab10 likely plays a role in neurodegenerative diseases including Parkinson's and Alzheimer's diseases.

    “Rab10 and its phosphorylated form, pRab10 likely play a role in neurodegenerative diseases including Parkinson’s and Alzheimer’s diseases [64, 79, 94].”

    From Cellular and subcellular localization of Rab10 and phospho-T73 Rab10 in the mouse and human brain (2023) · cites this paper as [79]

    The Results section, “Parkinson’s disease-associated pathogenic mutations modulate Rab GTPase phosphorylation levels” (page unavailable), reports that PD-associated LRRK2 mutations increased phosphorylated Rab10 in cells, supporting a possible Parkinson’s link. Our copy does not connect Rab10 or pRab10 to Alzheimer’s disease, so it does not support that part of the claim. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • Several RABs identified as being controlled by Retromer are substrates for LRRK2-mediated phosphorylation in response to disrupted lysosomal homoeostasis.

    “several RABs identified as being controlled by Retromer are substrates for LRKK2-mediated phosphorylation in response to disrupted lysosomal homoeostasis127–129.”

    From Mapping of endosomal proximity proteomes reveals Retromer as a hub for RAB GTPase regulation (2025) · cites this paper as [129]

    The Results section, “Direct in vitro phosphorylation of Rab isoforms by LRRK2” (page unavailable), shows that LRRK2 phosphorylates several Rab GTPases, and the physiological-substrates section finds that only a subset are targets in cells. Our copy does not establish that these Rabs are controlled by Retromer or that disrupted lysosomal homeostasis triggers their phosphorylation; the Discussion mentions lysosomal-pathway defects in LRRK2-knockout animals but does not make that causal claim. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • Rab10 is a LRRK2 kinase substrate.

    “Rab10 is a LRRK2 kinase substrate [79], therefore, immunofluorescence was performed to see if Rab10 and pRab10 are present in SPNs.”
  • Multiple studies show that a subset of Rab GTPases are LRRK2 kinase substrates, and LRRK2 can phosphorylate these Rab GTPases in vivo and in vitro.

    “Multiple studies show that a subset of Rab GTPases are LRRK2 kinase substrates, and LRRK2 can phosphorylate these Rab GTPases in vivo and in vitro [41, 79].”

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Authors
Steger, M., Tonelli, F., Ito, G., Davies, P., Trost, M., Vetter, M., Wachter, S., Lorentzen, E., Duddy, G., Wilson, S., Baptista, M. A., Fiske, B. K., Fell, M. J., Morrow, J. A., Reith, A. D., Alessi, D. R., & Mann, M.
Venue
eLife
Published
2016-01-29
Volume
5
ISSN
2050-084X
Cited by
1,042
References
4
Language
en
Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (P2ZHP3_151580)
  • Michael J. Fox Foundation for Parkinson's Research (6986)
  • Max-Planck-Gesellschaft
  • Medical Research Council (MC_UU_12016/3)

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