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Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases
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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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 measuredpRab10 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 measuredSeveral 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 measuredRab10 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.”
From Cellular and subcellular localization of Rab10 and phospho-T73 Rab10 in the mouse and human brain (2023) · cites this paper as [79]
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].”
From Cellular and subcellular localization of Rab10 and phospho-T73 Rab10 in the mouse and human brain (2023) · cites this paper as [79]
Rab10 was identified as phosphorylated by LRRK2 combining two independent genetic and chemical phosphoproteomic screens and has been validated in subsequent studies.
“Rab10 specifically was identified as phosphorylated by LRRK2 combining two independent genetic and chemical phosphoproteomic screens and has been validated in subsequent studies [19, 28, 32, 34, 35, 41, 79].”
From Cellular and subcellular localization of Rab10 and phospho-T73 Rab10 in the mouse and human brain (2023) · cites this paper as [79]
LRRK2 phosphorylates Rab10 at threonine 73 (pT73Rab10).
“Rab10 in particular has been validated in multiple studies as a substrate for LRRK2 which phosphorylates threonine 73 (pT73Rab10) in the switch II domain involved in effector binding [78, 79].”
From Cellular and subcellular localization of Rab10 and phospho-T73 Rab10 in the mouse and human brain (2023) · cites this paper as [79]
Rab10 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]
LRRK2 phosphorylates RAB proteins on their switch II regions, interfering with their binding to most regulatory and effector proteins.
“LRRK2 phosphorylates the RAB proteins on their switch II regions, which consequently interferes with their binding to most regulatory and effector proteins [12,18,19].”
From Distinct Roles for RAB10 and RAB29 in Pathogenic LRRK2-Mediated Endolysosomal Trafficking Alterations (2020) · cites this paper as [18]
RAB7A does not serve as a substrate for the LRRK2 kinase activity in vitro or in intact cells.
“RAB7A does not serve as a substrate for the LRRK2 kinase activity in vitro or in intact cells [12,18,31]”
From Distinct Roles for RAB10 and RAB29 in Pathogenic LRRK2-Mediated Endolysosomal Trafficking Alterations (2020) · cites this paper as [18]
RAB10 serves as a prominent LRRK2 kinase substrate in all cell lines and tissues analyzed.
“RAB10 serves as a prominent LRRK2 kinase substrate in all cell lines and tissues analyzed [12,18,32,33,34,35].”
From Distinct Roles for RAB10 and RAB29 in Pathogenic LRRK2-Mediated Endolysosomal Trafficking Alterations (2020) · cites this paper as [18]
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Rab GTPases as coordinators of vesicle traffic
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International Parkinson's Disease Genomics Consortium (IPDGC), Nalls, M. A., Parkinson's Study Group (PSG) Parkinson's Research: The Organized GENetics Initiative (PROGENI), 23andMe, GenePD, NeuroGenetics Research Consortium (NGRC), Hussman Institute of Human Genomics (HIHG), Investigator, T. A. J. D., (CHARGE), C. F. H. A. A. R. I. G. E., North American Brain Expression Consortium (NABEC), et al. (2014) · Nature Genetics · doi:10.1038/ng.3043 · Cited by 1,895
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Metadata
- 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
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2016-01-29
- Volume
- 5
- ISSN
- 2050-084X
- PMC
- PMC4769169
- Cited by
- 1,042
- References
- 4
- Language
- en
- Licence
- 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)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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