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

Martin Steger1, Francesca Tonelli2, Genta Ito2, Paul Davies2, Matthias Trost2, Melanie Vetter3, Stefanie Wachter3, Esben Lorentzen3, Graham Duddy4,ǂ, Stephen Wilson5, Marco A. S. Baptista6, Brian K. Fiske6, Matthew J. Fell7, John A. Morrow8, Alastair D. Reith9, Dario R. Alessi2,* and Matthias Mann1,*

1Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany 2Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK 3Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany 4Molecular Discovery Research, GlaxoSmithKline Pharmaceuticals R&D, New Frontiers Science Park, Harlow, Essex CM19 5AD, UK 5RD Platform Technology & Science, GlaxoSmithKline Pharmaceuticals R&D, Medicines Research Centre, Stevenage, UK 6The Michael J. Fox Foundation for Parkinson’s Research, Grand Central Station, P.O. Box 4777, New York, NY 10163, USA 7Merck Research Laboratories, Early Discovery Neuroscience, Boston, MA, 02115 USA 8Merck Research Laboratories, Neuroscience, West Point, PA, 19486 USA 9Neurodegeneration Discovery Performance Unit, RD Neurosciences, GlaxoSmithKline Pharmaceuticals R&D, Stevenage, UK ǂPresent address: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

* Correspondence to D.R.A. ([email protected]) or M.M. ([email protected])

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1 Abstract

2 Mutations in Park8, encoding for the multidomain Leucine-rich repeat kinase 2

3 (LRRK2) protein, comprise the predominant genetic cause of Parkinson’s disease (PD).

4 G2019S, the most common amino acid substitution activates the kinase two to three-

5 fold. This has motivated the development of LRRK2 kinase inhibitors; however, poor

6 consensus on physiological LRRK2 substrates has hampered clinical development of

7 such therapeutics. We employ a combination of phosphoproteomics, genetics and

8 pharmacology to unambiguously identify a subset of Rab GTPases as key LRRK2

9 substrates. LRRK2 directly phosphorylates these both in vivo and in vitro on an

10 evolutionary conserved residue in the switch II domain. Pathogenic LRRK2 variants

11 mapping to different functional domains increase phosphorylation of Rabs and this

12 strongly decreases their affinity to regulatory proteins including Rab GDP dissociation

13 inhibitors (GDIs). Our findings uncover a key class of bona-fide LRRK2 substrates and

14 a novel regulatory mechanism of Rabs that connects them to PD.

15

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16 Introduction

17 Parkinson’s disease (PD) is the second most common neurodegenerative disease, affecting 1–

18 2% of the elderly population (1). Environmental and genetic factors contribute to the

19 development of the disease, but its precise etiology still remains elusive (2). Genome-wide

20 association studies (GWAS) have related 28 genetic risk variants at 24 loci with nonfamilial

21 PD (3). Among those, mutations in LRRK2 (Park8) are also found in hereditary forms,

22 pinpointing a shared molecular pathway driving pathogenesis in both familial and non-

23 familial PD and comprising the most common cause of the disease (4, 5). LRRK2 encodes a

24 large protein composed of central kinase and GTPase (ROC-COR) domains that are

25 surrounded by multiple protein-protein interaction regions. PD pathogenic LRRK2 mutations

26 map predominantly to the kinase (G2019S, I2020T) and the ROC-COR domains

27 (R1441C/G/H, Y1699C), implying that these enzymatic activities are crucial for

28 pathogenesis (6). Presently it is unclear how LRRK2 mutations occurring in different

29 functional domains all predispose to PD. The most common PD-associated LRRK2 mutation

30 is the G2019S amino acid substitution, which activates the kinase two to three-fold (7-9).

31 Since protein kinases are attractive pharmacological targets, this finding has raised hopes that

32 selective LRRK2 inhibition can prevent or delay the onset of PD (10).

33 Extensive studies of LRRK2 have associated it with diverse cellular processes such as Wnt

34 signaling, mitochondrial disease, cytoskeleton remodeling, vesicular trafficking, autophagy

35 and protein translation (11-14). Moreover, several LRRK2 substrates have been reported

36 previously, however, evidence that they are phosphorylated by LRRK2 in a physiological

37 context is generally lacking and proofs are confined to in vitro approaches or to cellular

38 systems using overexpressed kinase (9, 15-30). Significant off-target effects for LRRK2

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39 compounds that have been used previously further complicate interpretation of the data (13).

40 Overall, there is little consensus on the cellular roles of LRRK2, thus identification of

41 definitive and verifiable physiological LRRK2 substrates is considered to be one of the

42 greatest challenges in the field (31).

43 Besides mutations in LRRK2, other genetic risk variants for PD map to the Park16 locus.

44 Among the five genes within this locus is Rab7L1 (also known as Rab29), which together

45 with LRRK2 increases nonfamilial PD risk. Depletion of Rab7L1 recapitulates the

46 dopaminergic neuron loss observed with LRRK2-G2019S expression and its overexpression

47 rescues mutant LRRK2 phenotypes (32). Rab GTPases comprise about 70 family members in

48 humans and they are key players in all forms of intracellular vesicular trafficking events (33,

49 34). Apart from Rab7L1, several other family members have been associated with PD

50 pathogenesis. For example, mutations in Rab39b (Park21 locus) predispose to PD in humans

51 (35, 36). Moreover, overexpression of Rab8a, Rab1 and Rab3a attenuate α-synclein-induced

52 cytotoxicity in cellular and animal models of PD, suggesting a functional interplay between

53 Rab GTPases and known PD factors (37, 38). Despite these intriguing links, it is presently

54 unclear, whether LRRK2 directly or indirectly modulates Rab GTPases at the molecular level

55 and if so, by which mechanism.

56 High-resolution, quantitative mass spectrometry (MS) has become the method of choice for

57 confident identification of in vitro and in vivo phosphorylation events (39-41). With current

58 MS instrumentation, proteomics can identify tens of thousands of phosphosites (42, 43).

59 However, challenges in the phosphoproteomic approaches are to determine functionally

60 relevant residues from these large datasets and to establish direct kinase-substrate

61 relationships.

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62 As such, we complement the power of modern phosphoproteomics with parallel genetic,

63 biochemical and pharmacological approaches to establish direct, in vivo LRRK2 substrates.

64 Using fibroblasts derived from two different LRRK2 knock-in mouse lines we identify a

65 subset of Rab GTPases as bona-fide LRRK2 targets. LRRK2 phosphorylates these substrates

66 on an evolutionarily conserved residue situated in their switch II domain both in human and

67 murine cells and in mouse brain. The phosphorylation of Rabs by LRRK2 is direct and

68 strikingly all LRRK2 missense mutations that contribute to PD pathogenesis increase the

69 phosphorylation of at least three Rab GTPases. Further, we establish that different PD

70 pathogenic mutations modulate the interaction with a number of regulatory proteins

71 including guanine dissociation inhibitors (GDI1/2). In this way, LRRK2 regulates the

72 specific insertion of Rab GTPases into target membranes thereby altering their membrane-

73 cytosol equilibrium.

74 Results

75 Identification of LRRK2 substrates in mouse embryonic fibroblasts (MEFs)

76 To search for bona-fide physiological LRRK2 substrates, we performed a dual-

77 phosphoproteomic screening approach using knock-in lines harboring either hyperactive

78 LRRK2 or a LRRK2 variant with wild-type activity but insensitive to a highly selective,

79 newly developed LRRK2 compound. For our first screen (PS1), we generated a mouse model

80 harboring the LRRK2-G2019S substitution that increases kinase activity two to three-fold

81 (Figure 1B). We derived fibroblasts from these animals and treated them with two

82 structurally different LRRK2 inhibitors, GSK2578215A (44) or HG-10-102-01 (45) (Figure

83 1A and Figure 1-figure supplement 1A). This screening modality offers three major

84 advantages; first, increased activity of the G2019S-LRRK2 kinase amplifies the chance of

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85 finding bona-fide substrates, second, using an isogenic system excludes that measured

86 phosphoproteome changes are due to differences in the genetic background and third,

87 considering only the overlapping population of significantly modulated phosphopeptides of

88 two structurally distinct inhibitors constitutes a very stringent criterion for specifically

89 pinpointing LRRK2 substrates.

90 The second screen (PS2) added another layer of specificity by combining phosphoproteomics

91 with genetics and chemical biology. For this, we used fibroblasts derived from either wt or

92 A2016T-LRRK2 knock-in mice and treated them with the newly developed, highly potent

93 and selective LRRK2 compound MLI-2 (46). The A2016T substitution does not change basal

94 LRRK2 activity but decreases sensitivity to MLI-2 about ten-fold (Figure 1C,D and Figure 1-

95 figure supplement 1B). At a dose of 10 nM, we observed a substantial decrease in

96 phosphorylation of LRRK2-pS935, which is associated with LRRK2 kinase activity (47), in

97 wt but not in A2016T cells (Figure 1E and Figure 1-figure supplement 1C). Under these

98 conditions, the phosphoproteome of wt MEFs includes both LRRK2-specific and off-target

99 sites, whereas A2016T (which is resistant to MLI-2), only includes off-targets. Therefore,

100 direct quantitative comparison should reveal true LRRK2 substrates (Figure 1C).

101 Using a state of the art workflow for phosphopeptide enrichment, label-free LC-MS/MS and

102 the MaxQuant environment for stringent statistical data evaluation (48-50), we quantified

103 over 9,000 high confidence phosphosites in each replicate in both screens (median R=0.80

104 and 0.89 in PS1 and PS2, respectively), (Figure 1-figure supplement 1D-G and

105 Supplementary File 1). Independently acquired proteome measurements verified that the

106 detected phosphorylation changes in PS2 were not due to altered protein abundances

107 (changes as determined by label-free quantification in MaxQuant (51) were less than two-

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108 fold (Supplementary File 2)).

109 Next, we determined how many of the identified sites were significantly and robustly

110 modulated. As we were interested in capturing the most strongly regulated sites, we required

111 that the fold change had to be at least as strong as pS935-LRRK2. In PS1, we thus found 234

112 significantly regulated sites after treatment with each of the two LRRK2 compounds

113 GSK2578215A and HG-10-102-01 (ANOVA, p<0.005), with 78 sites regulated by both

114 (Figure 1-figure supplement 2A). Hierarchical clustering divided them into several subgroups

115 (Figure 1-figure supplement 2B-C and Supplementary File 3A). Besides revealing potential

116 off-target sites of the two LRRK2 inhibitors, this identified a particularly interesting cluster

117 containing 47 sites that were downregulated after treatment with both compounds (Figure 1-

118 figure supplement 2C, cluster 5).

119 In PS2, we identified 204 significantly regulated sites (two sample t-test, FDR=0.01,

120 S0=0.2), when comparing wild-type and inhibitor-resistant LRRK2 fibroblasts, with 128 sites

121 specifically downregulated in the wild type, thus excluding off target effects (Figure 1G,

122 Figure 1-figure supplement 2D and Supplementary File 3B).

123 Finally, to stringently define LRRK2 substrates, we overlapped the results of the two

124 orthogonal screens. Remarkably, only two phosphosites passed these stringent filtering

125 criteria, our positive control pS935-LRRK2 and the conserved T73 residue of the small

126 GTPase Rab10 (Figure 1H).

127 Direct in vitro phosphorylation of Rab isoforms by LRRK2

128 Rab10 belongs to the Ras family of small GTPases that regulate intracellular vesicular

129 transport, with approximately 70 members in human. They function as molecular switches in

130 the tethering, docking, fusion and motion of intracellular membranes (33, 52). The T73

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131 residue of Rab10 is located in the switch II domain, which is characteristic of Rab GTPases

132 (Figure 2A). This region changes conformation upon nucleotide binding and regulates the

133 interaction with multiple regulatory proteins (53). Sequence alignment revealed that the

134 equivalent site to T73-Rab10 is highly conserved in more than 40 human Rab-family

135 members, indicating strong functional relevance (Figure 2B). Moreover, superposing the

136 crystal structures of multiple Rab GTPases localizes the equivalent residues to T73-Rab10 in

137 nearly the same position (Figure 2-figure supplement 1A). To investigate whether the

138 phosphorylation of Rab10 by LRRK2 is direct, we performed an in vitro kinase assay using

139 recombinant components. Notably, we found that both wt and LRRK2-G2019S, but neither

140 kinase inactive D1994A mutant nor small molecule-inhibited LRRK2, efficiently

141 phosphorylated Rab10, proving a direct kinase-substrate relationship (Figure 2C).

142 Furthermore, incubation of Rab10 with LRRK2 followed by tryptic digestion and mass

143 spectrometry analysis unambiguously identified T73 as the major phosphorylation site

144 (Figure 2-figure supplement 1B). Given the high conservation of T73-Rab10, we investigated

145 whether other Rab GTPases were also phosphorylated by LRRK2 in vitro. Therefore, we first

146 measured LRRK2-mediated phosphorylation of Rab8a, Rab1a and Rab1b, all of which

147 contain a Thr at the site equivalent to T73-Rab10, by MS or 32P incorporation followed by

148 Edman sequencing. Remarkably, all proteins were rapidly phosphorylated on the predicted

149 LRRK2 phosphorylation site in the switch II domain (Figure 2D-F and Figure 2-figure

150 supplement 1C-E). Next, we compared Rab family members containing Thr sites in the

151 switch II region with those containing a Ser in the equivalent position. Interestingly, while

152 Rabs with threonines (Rab1b, Rab8a and Rab10) were efficiently phosphorylated, those with

153 the equivalent serine sites (Rab5b, Rab7a, Rab7L1, Rab12 and Rab39b) were phosphorylated

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154 to a drastically lower extent (Figure 2G). This confirms the previously reported in vitro

155 preference for threonines by LRRK2 (54). Finally, we performed a side by side comparison

156 of the phosphorylation efficiencies of recombinant Rab8a and Rab7L1 against two

157 previously reported substrates, moesin (Msn) and Rps15 (9, 19). Msn is a cytoskeletal protein

158 and a well-known in vitro LRRK2 substrate, whereas Rps15 is part of the 40S ribosomal

159 subunit and its phosphorylation on Thr136 has been reported to regulate protein translation in

160 D. melanogaster (19). In accordance with our previous observations (Figure 2G),

161 phosphorylation levels of RAB7L1 were barely detectable, and even lower than those of Msn

162 and Rps15. Strikingly, levels of pRab8a were about ten times higher as compared to Rps15

163 and Msn, two of the best in vitro LRRK2 substrates known to date, demonstrating that Rabs

164 with Thr sites in the switch II domain are primary LRRK2 targets (Figure 2H,I).

165 A subset of Rabs are physiological LRRK2 substrates

166 Because of the high conservation of T73-Rab10 (Figure 2B) and the ability of LRRK2 to

167 phosphorylate multiple Rabs in vitro, we inspected our quantitative MS data further to

168 determine whether all sequence and structurally equivalent sites are targets of LRRK2. This

169 turned out not to be the case as pS72-Rab7a was not regulated in either of our screens.

170 LRRK2 thus phosphorylates only a subset of Rab GTPases in mouse fibroblasts.

171 Surprisingly, we noticed that pS105-Rab12, which is not phosphorylated by LRRK2 in vitro

172 (Figure 2G), was among the significantly-modulated sites in PS1 and also downregulated

173 upon MLI-2 treatment in wt cells as compared to the inhibitor-resistant A2016T mutant in

174 PS2 (Figure 3A,B). However, because of elevated intergroup variability and stringent FDR

175 cut-offs, it was not selected in our first analysis. LRRK2 is found also in lower eukaryotes

176 such as C. elegans and D. melanogaster (55) and T73-Rab10 is conserved in these organisms

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177 as well. Also S105-Rab12 is present throughout the vertebrates (Figure 3A,B). We identified

178 both pT73-Rab10 and pS105-Rab12 multiple times with high identification and phosphosite

179 localization scores (Supplementary File 1) and the MS/MS fragmentation spectra of the

180 corresponding synthetic peptides independently validated the MS results (Figure 3-figure

181 supplement 1A,B). Total protein levels of Rab10 and Rab12 did not change appreciably in

182 the A2016T knock-in model as judged by quantitative MS analysis, ruling out that that the

183 observed phospho-level changes are due to differential protein expression (Figure 3-figure

184 supplement 2A).

185 To extend the analysis of LRRK2-mediated phosphorylation of Rab10, we used human

186 embryonic kidney cells harboring doxycycline-dependent gene expression of LRRK2-

187 G2019S (HEK293-t-rex-flpIn). Expression of the kinase, treatment with either

188 GSK2578215A or HG-10-102-01 and enrichment of Rab10 by immunoprecipitation

189 followed by quantitative MS analysis confirmed a strong, LRRK2-dependent decrease of

190 pT73-Rab10 peptide levels (Figure 3-figure supplement 2B). Polyclonal antibodies

191 recognizing pT73-Rab10 and pS106-Rab12 (note that the equivalent site is S105 in mouse)

192 independently verified LRRK2-dependent phosphorylation of both Rab isoforms in HEK293

193 cells (Figure 3C,D).

194 Next, we evaluated whether more Rab isoforms can be phosphorylated in a LRRK2-

195 dependent manner in human cells, focusing on Rab1a, Rab3a and Rab8a, all of which contain

196 Thr as predicted LRRK2 phosphorylation site (Figure 2B). Therefore, we first ectopically

197 expressed LRRK2 along with either Rab1a or Rab3a, in presence or absence of HG-10-102-

198 01 and quantified pT75-Rab1a and pT86-Rab3a peptide levels by MS. Whereas T86-Rab3a

199 is clearly a LRRK2 target, Rab1a is not, indicating that overexpression of LRRK2 is not

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200 sufficient to phosphorylate all Rabs in cells (Figure 3-figure supplement 2C,D). Next, we

201 inhibited LRRK2 in HEK293-t-rex-flpIn cells expressing LRRK2-G2019S and quantified

202 pT72-Rab8. Again, we found a strong decrease of pT72 peptide levels upon LRRK2

203 inhibition with both GSK2578215A and HG-10-102-01 (Figure 3-figure supplement 2E). An

204 antibody raised for specific detection for pT72-Rab8 confirmed these results further (Figure

205 2E).

206 To analyze LRRK2-dependent phosphorylation of Rabs in an endogenous context, we

207 quantified pT72-Rab8 and pT73-Rab10 peptide levels in MEFs derived from LRRK2

208 knockout, wt or G2019SGSK animals. In the knock-out, the decrease was only about two-fold

209 compared to wt, implying a very low intrinsic LRRK2 activity in cells. Consistent with the

210 two to three-fold increased in vitro activity of MEFs-extracted LRRK2-G2019SGSK (Figure

211 1B), our quantitative MS analysis revealed a three-fold increase in both pT72-Rab8 and

212 pT73-Rab10, which was restored to near wt levels by selective LRRK2 kinase inhibition

213 (Figure 3-figure supplement 2F-I). Finally, we globally measured the brain phosphoproteome

214 of LRRK2-G2019SLilly mice injected with vehicle (40% HPβCD) or with MLI-2 (3 mg/kg).

215 Levels of pT72-Rab8 and pS105-Rab12 were decreased more than two-fold upon LRRK2

216 inhibition, validating our findings in the context of a LRRK2 pathogenic mouse model

217 (Figure 3F,G).

218 Having identified Rabs as physiological substrates of LRRK2, we next asked if kinase and

219 substrate also stably interact. Indeed, affinity-purification mass-spectrometry (AP-MS)

220 showed that transiently expressed epitope-tagged LRRK2 and Rab8a efficiently associated

221 with each other, demonstrating that LRRK2 is able to form stable complexes with Rab

222 GTPases in cells (Figure 3H and Figure 3-figure supplement 3A,B). Similarly, Rab10 as well

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223 as Rab12 associate with LRRK2 when transiently overexpressed in HEK293 cells (Figure3-

224 figure supplement 3C-E).

225 Parkinson’s disease associated pathogenic mutations modulate Rab GTPase

226 phosphorylation levels

227 Pathogenic PD LRRK2 mutations predominantly map to the kinase and the ROC-COR

228 (GTPase) domains and a PD risk factor coding mutation is also found in the WD-40 domain

229 (56, 57) (Figure 4A). Because it is presently unclear how mutations occurring in distinct

230 LRRK2 functional domains lead to similar disease phenotypes, we decided to investigate if

231 different LRRK2 pathogenic mutations might impact on the phosphorylation status of Rab

232 GTPases. For this, we expressed different disease causing LRRK2 variants along with either

233 Rab8a or Rab10 in HEK293 cells. This revealed that besides PD-associated mutations

234 located in the kinase domain that augment LRRK2 kinase activity, those occurring in the

235 GTPase (ROC-COR) or the WD-40 domains also increased pT72-Rab8a and pT73-Rab10

236 levels in cells (Figure 4B-E).

237 To determine whether this interplay between different functional domains was direct we next

238 tested whether pathogenic LRRK2 mutations which lie outside the kinase domain also

239 increase Rab phosphorylation in vitro. As expected, compared to wt, the G2019S mutation

240 resulted in a two to three-fold increase in Rab8a phosphorylation. However, the ROC-COR

241 domain R1441C mutation failed to do so, indicating that its effect on Rab8a phosphorylation

242 levels is mediated by accessory factors in cells (Figure 4F,G).

243 LRRK2 controls the interaction of Rabs with regulatory proteins

244 Rab GTPases consist of a similar core structure comprising highly conserved P-loop, switch I

245 and switch II regions (53). They cycle between the cytosol, in which they are GDP bound

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246 and inactive and specific membrane compartments, where they are activated by GDP/GTP

247 exchange (58). In the crystal structure of Rab8a (59), the LRRK2 mediated phosphorylation

248 site is in the switch II region (Figure 2A), which regulates hydrolysis of GTP and coordinates

249 the binding to various regulatory proteins (53). We therefore tested whether the

250 phosphomimetic T72E substitution would modulate GDP/GTP binding or interfere with

251 Rab8a protein interactions. Binding affinities of wt and the TE mutant, determined with

252 fluorescently-labeled (N-Methylanthraniloyl, mant) GDP and non-hydrolysable GTP

253 analogue GMPPNP, did not differ (Figure 5-figure supplement 1). In contrast, AP-MS

254 revealed that a number of proteins preferentially bind to non-phosphorylatable T72A-Rab8a

255 compared to the T72E phosphomimetic protein (Figure 5A,B). These were Rab GDP

256 dissociation inhibitors α and β (GDI1 and GDI2), Rab geranyltransferase complex members

257 (CHM, CHML and RabGGTA/RabGGTB), the Rab8a guanine nucleotide exchange factor

258 (GEF) Rabin8 (Rab3IP), a guanine nucleotide activating protein TBC1D15 and the inositol

259 phosphatase INPP5B (Figure 5C).

260 Rabin8 interacts with membrane-bound Rab8a and activates it by catalyzing the exchange of

261 GDP to GTP (60). This in turn triggers retention of Rab effector proteins that mediate

262 downstream vesicular trafficking events. Rabin8 binds to the switch II domain of Rab8a and

263 contacts the conserved, phosphorylatable T72 residue (Figure 5-figure supplement 2A) (59).

264 We found that compared to wt, the T72E phosphomimetic substitution decreased the level of

265 Rabin8-catalyzed mant-GDP displacement from a Rab8-GDP complex (Figure 5-figure

266 supplement 2B-D). To further substantiate this finding, we phosphorylated purified Rab8a

267 using LRRK2, which resulted in approximately 60% of T72-phosphorylated protein as

268 determined by total protein MS and LC-MS/MS after tryptic digestion (Figure 5-figure

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269 supplement 2E,F). Further enrichment by ion-exchange chromatography yielded a highly

270 enriched (~100%) fraction of pT72-Rab8a (Figure 5-figure supplement 2E). Loading of non-

271 phosphorylated and phosphorylated Rab8a with mant-GDP following incubation with Rabin8

272 revealed that LRRK2-induced phosphorylation of T72-Rab8a inhibits rates of Rabin8-

273 catalyzed GDP exchange 4-fold and decreases Rab8a-Rabin8 interaction (Figures 5D and

274 Figure 5-figure supplement 2G). Both λ-phosphatase treatment of LRRK2-phosphorylated

275 Rab8a and pharmacological inhibition of LRRK2 prevented the decreased GEF activity of

276 Rabin8 towards pT72-Rab8a (Figure 5E and Figure 5-figure supplement 2H). Thus

277 phosphorylation of Rab8a by LRRK2 can limit its activation by Rabin8.

278 PD pathogenic LRRK2 mutations interfere with Rab-GDI1/2 association

279 GDI1 and GDI2, along with CHM and CHML (also known as Rab escorting proteins REP1

280 and REP2) form the GDI superfamily and are essential regulators of the Rab cycle. GDIs

281 extract inactive, prenylated Rabs from membranes and bind them with high affinity in the

282 cytosol (61). The regulatory mechanism by which Rabs are displaced from GDIs to facilitate

283 their insertion into specific target membranes is unknown. The co-crystal structure of GDI1

284 with the yeast Rab homologue Ypt1 shows that GDIs closely contact the switch II region

285 (62), which explains why phosphorylation in this domain interferes with the Rab-GDI

286 interaction. Since GDIs are not specific to one Rab isoform (63), we reasoned that

287 phosphorylation of the switch II domain could be a general mechanism of Rab-GDI

288 dissociation. We therefore substituted S106-Rab12 and T73-Rab10 with non-

289 phosphorylatable Ala or phosphomimetic Glu residues and tested their capacity to form

290 complexes with GDIs by immunoprecipitation followed by mass spectrometry or western

291 blotting. As compared to non-phosphorylatable Rab10 and Rab12, neither S106E-Rab12 nor

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292 T73E-Rab10 were able to bind GDIs, demonstrating the functional importance of these

293 residues (Figure 6A,B and Figure 6-figure supplement 1A,B).

294 To further analyze the effect of Rab phosphorylation and GDI dissociation in the context of

295 PD, we expressed LRRK2 variants harboring various pathogenic mutations along with Rab8a

296 in cells and assessed Rab-GDI complex formation by immunoprecipitation. Strikingly, the

297 level of Rab8a-GDI interaction closely correlated with the degree of T72-Rab8a

298 phosphorylation (Figure 6C,D). Similarly, LRRK2-mediated phosphorylation of S106-Rab12

299 diminished the interaction with GDIs, confirming that the effect is not specific to one Rab

300 isoform (Figure 6E,F). All tested LRRK2 pathogenic mutations that affect kinase activity

301 thus control the interaction of Rabs with GDIs. Finally, to directly test whether disruption of

302 the Rab-GDI interaction results in an altered subcellular distribution of Rabs, we

303 quantitatively determined T72A-Rab8 and T72E-Rab8 protein abundances in SILAC (64)

304 labeled HEK293 cells. This revealed a 2-fold increase of non-phosphorylatable T72A mutant

305 in the cytosol. Consistently, we detected a significant (p= 2.58*10-3) increase of T72E-Rab8

306 protein levels in the membrane fraction, demonstrating that interference with the Rab-GDI

307 interaction results in an unbalanced membrane-cytosol distribution of Rabs (Figure 6G,H).

308 Discussion

309 Here, we used a state of art MS-based phosphoproteomics workflow in combination with

310 cells of two genetically engineered mouse models as well as a mixture of selective LRRK2

311 compounds to define LRRK2 targets with high stringency. Starting with almost 30,000

312 identified phosphosites, our screens rapidly narrowed down the candidates to a small number

313 that were consistently and strongly regulated with all tested compounds and genetic models.

314 Only the known phosphorylation site pS935 on LRRK2 itself and a specific residue in the

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315 Rab10 GTPase (T73) fulfilled our most specific criteria. LRRK2 kinase is conserved also in

316 flies and worms and this is true of the T73-Rab10 substrate site as well. Further experiments

317 with diverse model systems and techniques all verified the T73-Rab10 site as well as the

318 equivalent sites on many but not all other Rab family members. These include the threonine

319 sites on Rab8a and Rab3a (T72 and T86, respectively), as well as S106-Rab12. Rab7a is an

320 important component of the endocytic pathway (52) and phosphorylation on S72 has recently

321 been shown to play a functional role in B-cell signaling (65). While our data clearly show

322 that this site is not regulated by LRRK2 in mouse fibroblasts, its regulation by LRRK2 in B

323 cells remains possible, given the high expression levels of LRRK2 in those cell types (66). In

324 vitro experiments proved that LRRK2 directly phosphorylates Thr but not the Ser sites in

325 Rab isoforms, in line with its well established in vitro preference (9, 19, 54). We found that

326 Ser sites on Rabs were hardly phosphorylated in vitro but S105-Rab12 (S106 in human) was

327 clearly regulated in cells and brain tissue, establishing that accessory factors are required in

328 this case. Consistent with this finding, the major characterized in vivo LRRK2

329 autophosphorylation site is a Ser residue (Ser1292) (67). Our observation of residual Thr72-

330 Rab8 phosphorylation in LRRK2-/- mice implies that one or more other kinase(s) are able to

331 act upon this residue.

332 Besides defining Rab GTPases as LRRK2 targets, our screens identified a number of

333 phosphosites as potential LRRK2 targets. However, these were validated by only one of the

334 screens, their regulation was weaker and for many of them regulation may reflect indirect

335 modulation by the LRRK2 kinase. This is likely to account for the difficulty in identifying

336 substrates of this kinase. In a direct comparison of threonine Rab phosphorylation it was

337 much stronger than the known in vitro LRRK2 targets we tested. Overall, the relatively small

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338 number of regulated sites in our screens, suggest that LRRK2 is a very specific or low

339 activity kinase. LRRK2 is ubiquitously expressed, but highly abundant in kidney, lungs,

340 pancreas and certain cell types of the immune system (31). Therefore, it is possible that

341 different LRRK2 substrates, including Rab isoforms, are phosphorylated in a cell- or tissue

342 specific manner. Further phosphoproteomic research should shed more light on this open

343 question. We conclude that the threonine sites on Rab family members identified here may

344 not be the only functional ones in the context of LRRK2, but that they are the most

345 prominent ones.

346 In searching for a functional role for LRRK2 mediated Rab phosphorylation, we noted that it

347 maps onto the switch II region, which is known to mediate GDP/GTP exchange as well as

348 interaction with regulatory proteins. Results from nucleotide affinity measurements make the

349 former mechanism unlikely but AP-MS established phosphorylation-dependent binding of

350 several proteins involved in regulating their cycling between cytosol and membrane

351 compartments. This indicates that direct phosphorylation of Rabs on a conserved residue

352 situated in the switch II domain regulates their movement by controlling the interaction with

353 numerous regulatory proteins. The affinities of GDIs for Rabs are vastly decreased in a

354 manner correlating with the phosphorylation levels induced by different LRRK2 pathogenic

355 variants. Our data thus establish that LRRK2 is an important regulator of Rab homeostasis

356 which is likely contributing to PD development (Figure 7A). Overactive LRRK2, which

357 results in increased Rab phosphorylation, promotes dissociation from GDIs in the cytosol

358 with concomitant membrane insertion (Figure 7B). In this way, the relative pool of

359 membrane bound and cytosolic Rab is altered, disturbing intracellular trafficking. In

360 particular, PD-associated LRRK2 mutations would shift the membrane-cytosol balance of

17

361 Rabs towards the membrane compartment, thereby causing accumulation of inactive Rabs in

362 the membranes (Figure 7B). The subtle increase in Rab phosphorylation in cells derived from

363 LRRK2-G2019S knock-in mice is consistent with the long time needed for PD to manifest in

364 humans.

365 Intriguingly, our results show that pathogenic LRRK2 mutations outside the kinase domain

366 can also increase Rab phosphorylation. Although our in vitro data clearly shows that this

367 mechanism is indirect, they will still act on the same pathway as kinase domain mutants.

368 Therefore the same model would also be applicable in this case.

369 Independent evidence that Rabs are likely to be primary LRRK2 substrates comes from

370 LRRK2 knockout animal studies. LRRK2-/- mice and rats have deformed kidneys and lungs,

371 indicative of defects in the autophagosome/lysosome pathway, which depend on properly

372 tuned Rab activity (68-70). Moreover, it was recently reported that LRRK2 and Rab2a

373 regulate Paneth cell function, which is compromised in Crohn’s disease (71). In this context

374 it is interesting that we found pS70-Rab2a/b to be regulated in our second screen, although

375 it’s very low abundance impeding meaningful statistical interpretation. Taken together these

376 observations make it plausible that LRRK2 regulates Rab2a by direct phosphorylation of S70

377 in specialized cell types.

378 In conclusion, we prove that LRRK2 induces phosphorylation of Rabs and provide evidence

379 that it deregulates cycling between cytosol and target membrane compartments. It will be

380 interesting to investigate whether the Rab regulatory mechanism uncovered here is of key

381 importance in vesicular trafficking in general. Discovery of a key physiological LRRK2

382 substrate should inform and accelerate research into Parkinson’s disease, including

383 monitoring the efficacy of therapeutic intervention.

18

384

385 Materials and Methods

386 Reagents

387 MLI-2 (72) was obtained from Merck, GSK2578215A (44) from Tocris or GlaxoSmithKline.

388 HG-10-102-01 was custom synthesized by Natalia Shapiro (University of Dundee) as

389 described previously (45). Doxycycline, ATP and trypsin were from Sigma. LysC was

390 obtained from Wako. 32P-γATP was from Perkin Elmer. GST-LRRK2 (residues 960-2527

391 wild type, G2019S, D1994A), full-length wild type flag-LRRK2 from Invitrogen and

392 MANT-GDP (2'-(or-3')-O-(N-Methylanthraniloyl) Guanosine 5'-Diphosphate, Disodium

393 Salt) and MANT-GMPPNP from Jena Bioscience. GFP beads for affinity purification were

394 from Chromotek. Recombinant Rab10 and Rab1a (Figures 3A and 3C) were purchased from

395 mybiosource.

396 Antibodies

397 Anti-Rab10 and Rab8 were from Cell Signaling Technologies, anti-GFP from Invitrogen,

398 anti-HA high affinity from Roche, anti-GDI1/2 from Sigma and anti-pS1292-LRRK2 from

399 Abcam. Rabbit monoclonal antibodies for total LRRK2 and pS935-LRRK2 were purified at

400 the University of Dundee (73). Antibodies against Rab8a phospho-Thr72 (S874D), Rab10

401 phospho-Thr73 (S873D) and Rab12 phospho-Ser106 (S876D) were generated by injection of

402 the KLH (keyhole limpet hemocyanin)-conjugated phospho-peptides

403 AGQERFRpTITTAYYR (Rab8a), AGQERFHpTITTSYYR (Rab10),

404 AGQERFNpSITSAYYR (Rab12) and IAGQERFpTSMTRLYYR (where pS/T is phospho-

405 serine/threonine) into sheep and affinity purified using the phosphopeptides. Antibodies were

19

406 used at final concentrations of 1 μg/ml in the presence of 10 μg/ml of non-phosphorylated

407 peptide.

408 Plasmids

409 The following constructs were used: 6His-SUMO-Rab8a wt/T72A/T72E (DU47363,

410 DU47433, DU47436), HA-Rab8 wt/T72A/T72E (DU35414, DU47360), 6His-SUMO-Rab5b

411 (DU26116), 6-His-SUMO-Rab7a (DU24781), 6-His-SUMO-Rab7L1 (DU50261). 6-HIS-

412 SUMO-Rab10 (DU51062), HA-Rab10 wt/T73A/T73E (DU44250, DU51006, DU51007), 6-

413 His-SUMO-Rab12 (DU52221), HA-Rab12 wt/S106A/S106E (DU48963, DU48966,

414 DU48967), 6-His-SUMO-Rab39b (DU43869). Full datasheets are available on

415 https://mrcppureagents.dundee.ac.uk/.

416 Protein purification

417 Purification of Rabs and Rabin8 (Figures 2D, 2G, and 5E): Buffer A: 50 mM HEPES pH

418 8.0, 500 mM LiCl, 1 mM MgCl2, 10 μM GDP, 2 mM beta-mercaptoethanol; Elution buffer:

419 buffer A + 500 mM imidazole; Lysis buffer: buffer A + 1 mM PMSF and Roche Complete

420 protease inhibitor cocktail (EDTA-free); Gel-filtration buffer: 20 mM HEPES pH 8.0, 50

421 mM NaCl, 1 mM MgCl2, 10 μM GDP, 25 μM ATP, 2 mM DTT.

422 Rab isoforms and Rabin8 (153-237) were expressed as N-terminal His-Sumo fusion proteins

423 in E. coli as described previously (74). The His-Sumo tag was removed using SENP1

424 protease (75). Transformed BL21 (DE3) harboring the GroEL/S plasmid (74) were grown at

425 37 °C to a OD 600 of 0.8, then shifted to 19°C and protein expression induced with Isopropyl

426 β-D-1-thiogalactopyranoside (0.5 mM) for 16 h. Cells were pelleted at 5000 g (4°C for 20

427 min) and lysed by sonication (45% amplitude, 20 sec pulse, 1 min pause, total of 10 min

428 pulse) in lysis buffer. Lysates were clarified by centrifugation at 30,000 g for 20 min at 4°C

20

429 followed by incubation with 1 ml of Nickel-NTA agarose/l culture for 1 h at 4°C. The resin

430 was equilibrated on an AKTA FPLC with buffer A, and bound proteins eluted with imidazole

431 gradient (25 mM-500 mM). Fractions containing the protein of interest were identified by

432 SDS-PAGE and pooled. 10 µg/ml His-SENP1 catalytic domain (residues 415–643) was used

433 to cleave the His tag (16 h at 4 oC). Imidazole was removed by buffer exchange gel filtration

434 on a G25 column equilibrated in Buffer A plus 20 mM Imidazole. His-SENP1 protease was

435 removed using Nickel-NTA agarose. Proteins were concentrated to a maximum of 10 mg/ml

436 using a Vivaspin 10 kDa cut centricon and 0.5 ml samples were resolved on a high resolution

437 Superdex 200, 24 ml gel-filtration column equilibrated with gel filtration buffer and 0.2 ml

438 fractions were collected. Peak fractions containing recombinant protein were pooled. Identity

439 and purity of proteins were assessed by Maldi-TOF MS and SDS-PAGE.

440 Purification of Rab8a and Rabin8 (Figures 5D): Human Rab8a (wt, T72E, T72A, residues 1-

441 183) and human Rabin8 constructs (144-460 and 144-245) containing tobacco etch virus

442 (TEV) cleavable N-terminal 6-HIS tag were expressed in E.coli BL21 (DE3). Cells were

443 lysed by sonication in a buffer containing 50 mM phosphate pH 7.5, 150 mM NaCl, 10%

444 glycerol. For Rab8a proteins 5 mM MgCl2 was added. Proteins were purified by Ni-NTA

445 affinity chromatography. To remove the N-terminal HIS tag, proteins were incubated with

446 TEV protease overnight. Further purification was done by ion-exchange chromatography (Q-

447 Sepharose) followed by size exclusion chromatography (SEC) in a buffer of 10 mM HEPES

448 pH 7.5, 150 mM NaCl and 2 mM DTT using a HiLoad Superdex 75 column. For Rab8a

449 proteins 5 mM MgCl2 was added to the SEC buffer.

450 Mice

21

451 Mice were maintained under specific pathogen-free conditions at the University of Dundee

452 (UK). All animal studies were ethically reviewed and carried out in accordance with Animals

453 (Scientific Procedures) Act 1986, the GSK Policy on the Care, Welfare and Treatment of

454 Animals, regulations set by the University of Dundee and the U.K. Home Office. Animal

455 studies and breeding were approved by the University of Dundee ethical committee and

456 performed under a U.K. Home Office project license.

457 The LRRK2-G2019SGSK knock-in mouse line was generated by a targeting strategy devised

458 to introduce the point mutation G2019S into exon 41 of the LRRK2 gene by homologous

459 recombination in mouse embryonic stem cells. 5’ & 3’ homology arms (approx. 4.8 & 3.8kb

460 respectively) flanking exon 41 were generated using Phusion High-Fidelity DNA Polymerase

461 (New England BioLabs) on a C57BL/6J genomic DNA template. Similarly a 739 bp

462 fragment carrying exon 41 lying between these two homology arms was isolated and

463 subjected to site-directed mutagenesis with the QuickChangeII site-directed mutagenesis kit

464 (Stratagene) to introduce the appropriate point mutation (GG to TC mutation at bps 107/8).

465 The 5’ & 3’ homology arms and the mutated exon 41 fragments were subcloned into a

466 parental targeting vector to achieve the positioning of the loxP & FRT sites and PGKneo

467 cassette. Gene targeting was performed in de novo generated C57BL/6J-derived ES cells.

468 The targeting construct was linearized and electroporated into ES cells according to standard

469 methods. ES cells correctly targeted at the 3’end were identified by Southern blot analysis of

470 EcoRV digested genomic DNA using a PCR-derived external probe. Correct gene targeting

471 at the 5’end and presence of the point mutation was confirmed by sequencing of a ~6 kb PCR

472 product. High-fidelity PCR of ES cell clone-derived genomic DNA using primers spanning

473 the 5’ homology arm generated the latter. Correctly targeted ES cell clones were injected into

22

474 BALB/c blastocysts and implanted into foster mothers according to standard procedures.

475 Male chimaeras resulting from the G2019S targeted ES cells were bred with C57BL/6J

476 female mice, and germline transmission of the targeted allele was confirmed by PCR. The

477 PGKneo cassette was subsequently removed by breeding germline mice to FLPeR(76) mice

478 expressing Flp recombinase from the Rosa26 locus (C57BL/6J genetic background).

479 Absence of the PGKneo cassette in offspring was confirmed by PCR and subsequent

480 breeding to C57BL/6J mice removed the Flper locus (confirmed by PCR). The line was

481 maintained by breeding with C57BL/6J, and crossing mice heterozygous for the point

482 mutation generated homozygous mice. Standard genotyping which distinguishes wild type

483 from point mutation knock-in alleles was used throughout.

484 The Michael J. Fox Foundation for Parkinson’s Research generated the A2016T knock-in

485 mice. A targeting vector was designed to introduce an alanine to threonine (A2016T)

486 substitution at codon 2016 in exon 41 of the endogenous locus. In addition, an FRT-flanked

487 neomycin resistance (neo) cassette was introduced 400 bp downstream of exon 41. The

488 construct was electroporated into C57BL/6N-derived JM8 embryonic stem (ES) cells.

489 Correctly targeted ES cells were injected into blastocysts and chimeric mice were bred to

490 B6.Cg-Tg (ACTFLPe)9205Dym/J (JAX stock No. 005703) to remove the neo cassette and

491 leave a silent FRT site. The resulting animals were crossed to C57BL/6NJ inbred mice (JAX

492 stock No. 005304) for one generation. These mice are available from The Jackson

493 Laboratory and for further information see http://jaxmice.jax.org/strain/021828.html. The

494 LRRK2-G2019SLilly were generated by Ely Lilly and maintained on a C57BL/6J background.

495 Genotyping of mice was performed by PCR using genomic DNA isolated from ear biopsies.

496 For LRRK2-G2019SGSK knock-in mice, Primer 1 (5′-CCGAGCCAAAAACTAAGCTC -3′)

23

497 and Primer 2 (5′-CCATCTTGGGTACTTGACC-3′) were used to detect the wild-type and

498 knock-in alleles. For LRRK2-G2019SLilly knock-in mice Primer 1 (5′-

499 CATTGCGAAGATTGCGGACTACTCAATT-3′) and Primer 2 (5′-

500 AAACAGTAACTATTTCCGTCGTGATCCG-3′) were used to detect the wild-type and

501 knock-in alleles. For LRRK2-A2016T Primer 1 (5′-TTGCCTGTGAGTGTCTCTGG-3′) and

502 Primer 2 (5′-AGGAAATGTGGTTCCGACAC-3′) were used to detect the wild-type and

503 knock-in alleles. The PCR program consisted of 5 min at 95°C, then 35 cycles of 30 s at

504 95°C, 30 s at 60°C and 30 s at 72°C, and 5 min at 72°C. DNA sequencing was used to

505 confirm the knock-in mutation and performed by DNA Sequencing & Services (MRC–PPU;

506 http://www.dnaseq.co.uk) using Applied Biosystems Big-Dye version 3.1 chemistry on an

507 Applied Biosystems model 3730 automated capillary DNA sequencer.

508 For experiments shown in Figure 3F-G, homozygous LRRK2-G2019SLilly mice (3 months of

509 age) were injected subcutaneously with vehicle (40% Hydroxypropyl-β-Cyclodextran) or

510 MLI-2 (3 mg/kg of body mass dissolved in 40% Hydroxypropyl-β-Cyclodextran) and

511 euthanized by cervical dislocation one hour after treatment. Brains were rapidly isolated and

512 snap frozen in liquid nitrogen. No specific randomization method or blinding was applied to

513 experiments.

514 Generation of mouse embryonic fibroblasts (MEFs)

515 Littermate matched wild type and homozygous LRRK2-A2016T mouse embryonic

516 fibroblasts (MEFs) were isolated from mouse embryos at day E12.5 resulting from crosses

517 between heterozygous LRRK2-A2016T/WT mice using a previously described protocol (77).

518 Cells were genotyped as described above for mice and wild type and homozygous A2016T

519 knock-in cells generated from the same littermate selected for subsequent experiments. Cells

24

520 cultured in parallel at passage 4 were used for mass spectrometry and immunoblotting

521 experiments.

522 Littermate matched wild type and homozygous LRRK2-G2019SGSK MEFs were isolated

523 from mouse embryos at day E12.5 resulting from crosses between heterozygous LRRK2-

524 G2019SGSK/WT mice as described previously (77). Wild type and homozygous LRRK2-

525 G2019SGSK/G2019SGSK MEFs were continuously passaged in parallel for at least 15 passages

526 before being used for mass spectrometry and immunoblotting experiments. All cells were

527 cultured in DMEM containing 10% FBS, 2 mM L-glutamine, 50 units/ml penicillin, 50

528 μg/ml streptomycin and non-essential amino acids (Life Technologies). Littermate matched

529 wild type and homozygous knock-out MEFs were isolated from LRRK2 knock-out mice (73)

530 as described previously (78). All knock-in and knock-out cell lines were verified by allelic

531 sequencing.

532 Culture and transfection of cells

533 HEK293 were purchased from ATCC and cultured in Dulbecco’s modified Eagle medium

534 (Glutamax, Gibco) supplemented with 10% fetal calf serum, 100 U/ml penicillin and 100

535 µg/ml streptomycin. The HEK293-t-rex-flpIn stable cell lines with doxycycline-inducible

536 wild type and mutant forms of LRRK2 have been described previously (79). Transient

537 transfections were performed 36-48 h prior to cell lysis using Lipofectamine 2000 (Life

538 Technologies) or FuGene HD (Promega). LRRK2 expression in HEK293-t-rex-flpIn was

539 induced by doxycycline (1 μg/ml, 24 h). All cells were tested for mycoplasma contamination

540 and overexpressing lines were verified by western blot analysis.

541 Immunoprecipitations, pull-downs and subcellular fractionation

25

542 For HA-Rab immunoprecipitations, HA-agarose (Sigma) was washed 3 times with PBS and

543 incubated with lysates at a concentration of 25 μl of resin/mg lysate for 1 h. Beads were then

544 washed twice with 1 ml PBS and samples eluted in 2 x LDS (50 µl per 25 μl of resin) and

545 centrifuged through a 0.22 μm Spinex filter, 2-mercpatoethanol added to 2% (v/v) and heated

546 to 70oC for 5 min prior to SDS-PAGE. For GFP pulldowns and immunoprecipitations, cells

547 were lysed in ice-cold NP-40 extraction buffer (50 mM Tris-HCl, pH 7.5, 120 mM NaCl, 1

548 mM EDTA, 6 mM EGTA, 15 mM sodium pyrophosphate and 1 % NP-40 supplemented with

549 protease and phosphatase inhibitors (Roche) and clarified by centrifugation at 14000 rpm.

550 Supernatants were incubated over night with Rab8 or Rab10 antibodies and bound complexes

551 recovered using agarose protein A/G beads (Pierce). For GFP pulldowns, lysates were

552 incubated with GFP beads for 2 h (Chromotek). On bead digestion of protein complexes used

553 for MS analysis was performed as described previously (80).

554 For subcellular fractionation, SILAC (64) labeled HEK293 cells were counted and mixed in a

555 1:1 ratio after harvesting in PBS, spun at 1000 rpm at 4oC for 5 min and then resuspended in

556 subcellular fractionation buffer (250 mM sucrose, 20 mM HEPES pH 7.4, 10 mM KCl, 1.5

557 mM MgCl2, 1 mM EDTA, 1 mM EGTA and protease/phosphatase inhibitor cocktail

558 (Roche)). Cells were then Dounce homogenized, left on ice for 20 min and spun at 750 g for

559 5 min. The supernatant spun in an ultracentrifuge (100,000 g) for 45 min to obtain cytosolic

560 (supernatant) and membrane (pellet) fractions.

561 Phos-tag SDS-PAGE

562 Phos-tag acrylamide and MnCl2 were added to a standard gel solution at a final concentration

563 of 50 μM and 100 μM, respectively. After degassing for 10 minutes, gels were polymerized

564 by ammonium persulfate and TEMED. Cell lysates used for Phos-tag SDS-PAGE were

26

565 supplemented with MnCl2 at 10 mM to mask the effect of EDTA in the lysates. After SDS-

566 PAGE, gels were washed trice with transfer buffer containing 10 mM EDTA followed by a

567 wash with transfer buffer (10 min each). Blotting to nitrocellulose membranes was carried

568 out according to a standard protocol.

569 Total proteome and phosphoproteome sample preparation and MS analyses 570 All samples were lysed in SDS lysis buffer (4% SDS, 10 mM DTT, 10 mM Tris pH 7.5),

571 boiled and sonicated, and precipitated over-night using ice-cold acetone (v/v= 80%). After

572 centrifugation (4000 g) the pellet was washed at least two times with 80% ice-cold acetone

573 before air drying and resuspension (sonication) in either urea (6 M urea, 2 M thiorurea, 50

574 mM Tris pH 8) or TFE buffer (10% 2-2-2-trifluorethanol, 100 mM ammonium bicarbonate

575 (ABC)). Proteins were digested using LysC and trypsin (1:100), over-night at 37°C. Peptides

576 for total proteome measurements were desalted on C18 StageTips and phosphopeptides were

577 enriched as described previously (48).

578 LC-MS/MS measurements 579 Peptides were loaded on a 50 cm reversed phase column (75 µm inner diameter, packed in-

580 house with ReproSil-Pur C18-AQ 1.9 µm resin [Dr. Maisch GmbH]). Column temperature

581 was maintained at 50°C using a homemade column oven. An EASY-nLC 1000 system

582 (Thermo Fisher Scientific) was directly coupled online with a mass spectrometer (Q

583 Exactive, Q Exactive Plus, Q Exactive HF, LTQ Orbitrap, Thermo Fisher Scientific) via a

584 nano-electrospray source, and peptides were separated with a binary buffer system of buffer

585 A (0.1% formic acid (FA)) and buffer B (80% acetonitrile plus 0.1% FA), at a flow rate of

586 250nl/min. Peptides were eluted with a gradient of 5% - 30% buffer B over 30, 95, 155 or

587 240 minutes followed by 30% - 95% buffer B over 10 minutes, resulting in approximately 1,

27

588 2, 3 or 4 h gradients respectively. The mass spectrometer was programmed to acquire in a

589 data-dependent mode (Top5–Top15) using a fixed ion injection time strategy. Full scans

590 were acquired in the Orbitrap mass analyzer with resolution 60,000 at 200 m/z (3E6 ions

591 were accumulated with a maximum injection time of 25 ms). The top intense ions (N for

592 TopN) with charge states ≥2 were sequentially isolated to a target value of 1E5 (maximum

593 injection time of 120 ms, 20% underfill), fragmented by HCD (NCE 25%, Q Exactive) or

594 CID (NCE 35%, LTQ Orbitrap) and detected in the Orbitrap (Q Exactive, R= 15,000 at m/z

595 200) or the Ion trap detector (LTQ Orbitrap).

596 Data processing and analysis 597 Raw mass spectrometry data were processed using MaxQuant version 1.5.1.6 or 1.5.3.15 (49,

598 50) with an FDR < 0.01 at the level of proteins, peptides and modifications. Searches were

599 performed against the Mouse or Human UniProt FASTA database (September 2014).

600 Enzyme specificity was set to trypsin, and the search included cysteine

601 carbamidomethylation as a fixed modification and N-acetylation of protein, oxidation of

602 methionine, and/or phosphorylation of Ser, Thr, Tyr residue (PhosphoSTY) as variable

603 modifications. Up to 2 missed cleavages were allowed for protease digestion, and peptides

604 had to be fully tryptic. Quantification was performed by MaxQuant, ‘match between runs’

605 was enabled, with a matching time window of 0.5-0.7 min. Bioinformatic analyses were

606 performed with Perseus (www.perseus-framework.org) and Microsoft Excel and data

607 visualized using Graph Prism (GraphPad Software Inc) or R studio

608 (https://www.rstudio.com/). Hierarchical clustering of phosphosites was performed on

609 logarithmized (Log2) intensities. Significance was assessed using one sample t-test, two-

610 sample student’s t-test and ANOVA analysis, for which replicates were grouped, and

28

611 statistical tests performed with permutation-based FDR correction for multiple hypothesis

612 testing. Missing data points were replaced by data imputation after filtering for valid values

613 (all valid values in at least one experimental group). Error bars are mean ± SEM or mean ±

614 SD.

615 LRRK2 inhibitor IC50 LRRK2 kinase assay

616 LRRK2 kinase activity was assessed in an in vitro kinase reaction performed as described

617 previously (54). For IC50 determination of LRRK2 inhibitor, peptide kinase assays were set

618 up in a total volume of 30 μl with recombinant wild type GST-LRRK2-(1326-2527) or

619 mutant GST-LRRK2[A2016T]-(1326-2527) (6 nM) in 50 mM Tris-HCl pH 7.5, 0.1 mM

620 EGTA, 10 mM MgCl2, 0.1 mM [γ-32P]ATP (~300-600 cpm/pmol) and 20 μM Nictide

621 LRRK2 substrate peptide substrate, in the presence of indicated concentration of MLI-2.

622 After incubation for 20 minutes at 30°C, reactions were terminated by applying 25 μl of the

623 reaction mixture onto P81 phosphocellulose papers and immersion in 50 mM phosphoric

624 acid. After extensive washing, reaction products were quantified by Cerenkov counting. IC50

625 values were calculated using non-linear regression analysis using GraphPad Prism (GraphPad

626 Software Inc). The IC50s for GSK2578215A (44) against wild type GST-LRRK2-(1326-

627 2527) or mutant GST-LRRK2[A2016T]-(1326-2527) are 10.9 nM and 81.1 nM respectively

628 and the IC50s for HG-10-102-01 (45) vs LRRK2 WT and A2016T are 20.3 nM and 153.7

629 nM respectively. The IC50 of MLI-2 against wild type GST-LRRK2-(1326-2527) or mutant

630 GST-LRRK2[A2016T]-(1326-2527) are 0.8 nM and 7.2 nM (see Extended Data Figure 1a).

631 As MLI-2 displayed greater potency as well as a higher degree of resistance between wild

632 type and A2016T mutation (9-fold compared to 7.4-fold for GSK2578215A and 7.6-fold for

29

633 HG-10-102-01), we used MLI-2 for mass spectrometry studies employing LRRK2[A2016T]

634 knock-in MEFs.

635 In vitro kinase assays

636 Phosphorylation of Rab isoforms (Figures 2D, 2G, 2H and 4F): LRRK2 kinase assays were

637 performed using purified recombinant GST-tagged LRRK2 (960-2527, wt, D1994A,

638 G2019S, Invitrogen) incubated with recombinant Rab isoform (1 μM). Proteins were

639 incubated in kinase assay buffer (20 mM Tris pH 7.5, 1 mM EGTA, 5 mM β-

640 glycerophosphate, 5 mM NaF, 10 mM MgCl2, 2 mM DTT, 10 μM ATP and 0.5 μCi of γ-

641 32P-ATP) at a combined volume of 30 μL. The reaction mixture was incubated at 30°C for

642 30 min, or as indicated. Reactions were quenched by the addition of SDS-sample loading

643 buffer, heated to 70°C for 10 min and then separated on SDS-PAGE. Following

644 electrophoresis, gels were fixed (50% (v/v) methanol, 10% (v/v) acetic acid), stained in

645 Coomassie brilliant blue, dried and exposed to a phospho-imaging screen for assessing

646 radioactive 32P incorporation. For MS analysis, 100 μM of ATP was used and the reaction

647 was stopped by addition of 2 M urea buffer (2 M urea in 50 mM Tris pH 7.5) containing

648 LRRK2 inhibitor HG-10-102-01 (2 μM).

649 Phosphorylation of Rab isoforms (Figures 2C and 2F): Assays were set up in a total volume

650 of 25 μl with recombinant full-length Flag-LRRK2 (100 ng, Invitrogen) in 50 mM Tris-HCl

32 651 pH 7.5, 0.1 mM EGTA, 10 mM MgCl2, 0.1 mM [γ- P]ATP (~300-600 cpm/pmol), with

652 recombinant Rab isoform (1.5 µg) in the presence or absence of the LRRK2 inhibitor HG-10-

653 102-01 (2 μM). After incubation for 30 min at 30 °C, reactions were stopped by the addition

654 of Laemmli sample buffer and reaction products resolved on SDS-PAGE. The incorporation

655 of phosphate into protein substrates was determined by autoradiography. For phosphorylation

30

656 of Rab8a or Nictide (Figure 1B) LRRK2 was immunoprecipitated from MEFs and kinase

657 activity was assessed in an in vitro kinase reaction as described previously (78).

658 Phosphosite identification by MS and Edman sequencing (Figure 2-figure supplement

659 1)

660 Purified Rab1b and Rab8a (5 μg) were phosphorylated using recombinant full-length wild

661 type Flag-LRRK2 (0.2 μg; Invitrogen) in a buffer containing 50 mM Tris-HCl pH 7.5, 0.1

662 mM EGTA, 10 mM MgCl2, 0.1 mM [γ-32P]ATP (~3000 Ci/pmol) for one hour at 30°C. The

663 reactions were stopped by the addition of SDS sample buffer and reaction products were

664 resolved by electrophoresis on SDS-PAGE gels that were stained with Coomassie blue. The

665 band corresponding to Rab1b/Rab8a was excised and digested overnight with trypsin at

666 30°C. and the peptides were separated on a reverse-phase HPLC Vydac C18 column

667 (Separations Group) equilibrated in 0.1% (v/v) trifluoroacetic acid, and the column

668 developed with a linear acetonitrile gradient at a flow rate of 0.2 ml/min. Fractions (0.1 ml

669 each) were collected and analyzed for 32P radioactivity by Cerenkov counting.

670 Phosphopeptides were analyzed by liquid chromatography (LC)-MS/MS using a Thermo

671 U3000 RSLC nano liquid chromatography system (Thermo Fisher Scientific) coupled to a

672 Thermo LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific). Data files were

673 searched using Mascot (www.matrixscience.com) run on an in-house system against a

674 database containing the appropriate Rab sequences, with a 10 ppm mass accuracy for

675 precursor ions, a 0.6 Da tolerance for fragment ions, and allowing for Phospho (ST), Phospho

676 (Y), Oxidation (M), and Dioxidation (M) as variable modifications. Individual MS/MS

677 spectra were inspected using Xcalibur 2.2 (Thermo Fisher Scientific), and Proteome

678 Discoverer with phosphoRS 3.1 (Thermo Fisher Scientific) was used to assist with

31

679 phosphosite assignment. The site of phosphorylation of 32P-labeled peptides was determined

680 by solid-phase Edman degradation on a Shimadzu PPSQ33A Sequencer of the peptide

681 coupled to Sequelon-AA membrane (Applied Biosystems) as described previously (81).

682 Phosphorylation of Rab8a (Figure 5D)

683 Rab8a was phosphorylated using LRRK2-G2019S (see ‘in vitro kinase assays’ section). Non

684 phosphorylated and phosphorylated Rab8a proteins were separated using ion-exchange

685 chromatography (Mono S 4.6/100; GE Healthcare) with a linear salt gradient from buffer A

686 (20 mM Tris/HCl pH 7.5, 50 mM NaCl, 10% (v/v) glycerol) to buffer B (as buffer A, but

687 with 1000 mM NaCl). The successful enrichment of phosphorylated Rab8a was confirmed

688 by ESI-TOF mass spectrometry.

689 Rab8a nucleotide binding experiments 690 Rab8a (1-183, wt and T72E) were subjected to HPLC revealing that the purified proteins

691 were (>90%) in the nucleotide-free form. To determine affinities for G-nucleotides,

692 fluorescence measurements were carried out at 20°C in a buffer containing 50 mM Tris pH

693 7.5, 100 mM NaCl and 5 mM MgCl2. Spectra were measured with a Perkin Elmer LS50B

694 fluorescence spectrophotometer. 1 µM of methylanthraniloyl (mant) labeled GMPPNP and

695 GDP was incubated with increasing concentrations of wild type and T72E Rab8a in 60 µl

696 volumes. Fluorescence of mant-nucleotides was excited at 355 nm and emission spectra

697 monitored from 400 to 500 nm, with emission maxima detected at 448 nm. Intrinsic protein

698 fluorescence and mant-nucleotide background fluorescence was subtracted from the curves.

699 Data collection was performed with the program FL WinLab (Perkin Elmer), while further

700 analysis, curve fitting and dissociation constant (Kd) determination was done using GraphPad

701 Prism (GraphPad Software Inc).

32

702 Guanine exchange factor (GEF) assays 703 Figure 5E: Purified Rab8a (100 μg) was phosphorylated using LRRK2 G2019S (1.5 μg) in a

704 buffer containing 50 mM Tris-HCl pH 7.5, 0.1 mM EGTA, 10 mM MgCl2, 2 mM DTT, 1

705 mM ATP (18 h, room temperature) in a Dispo-Biodialyzer MWCO 1 kDa (Sigma-Aldrich)

706 and incubated in 2 l of the same Buffer to allow for ADP exchange. The buffer was

707 subsequently exchanged to a GDP dissociation assay buffer containing 20 mM HEPES-

708 NaOH pH 7.5, 50 mM NaCl, 2 mM DTT, 1 mM MnCl2, 0.01% (w/v) Brij-35 using Zeba

709 Spin desalting columns (Invitrogen). Phosphorylated Rab8a (50 μg) was treated with lambda

710 phosphatase (5 μg) for 30 minutes at 30 °C where indicated. To load mant-GDP, Rab8a was

711 incubated with 40 μM mant-GDP in the presence of 5 mM EDTA at 30°C for 30 minutes.

712 After adding MgCl2 at 10 mM, in order to remove unbound mant-GDP, the buffer was

713 exchanged to a buffer containing 10 mM HEPES-NaOH pH 7.5, 50 mM NaCl, 5 mM DTT, 1

714 mM MgCl2 using Zeba Spin desalting columns. GDP dissociation reactions were set up in a

715 total volume of 50 μl with 1 μM Rab8a:mant-GDP in 20 mM HEPES-NaOH pH 7.5, 50 mM

716 NaCl, 2 mM DTT, 1 mM MgCl2, 0.1 mM GDP and the reaction was started by adding the

717 indicated concentration of Rabin8 (residues 153-237) (59). Kinetic measurement of the mant

718 fluorescence was carried out in a black half-area 96-well plate with PHERAStar FS (BMG

719 Labtech) at room temperature using a set of filters (excitation: 350 nm, emission: 460 nm).

720 The observed rate constant (kobs) and the catalytic efficiency (kcat/Km) were calculated as

721 described previously (82). Phosphorylation stoichiometry (63%) was calculated by digestion

722 of the protein with trypsin and analyzing the fragments by Orbitrap mass spectrometry.

723 Figure 5D: Phosphorylated Rab8a was obtained as described in section ‘Phosphorylation of

724 Rab8a’. GEF assays were performed as described previously (83). Loading of purified

725 nucleotide-free (both phosphorylated and non-phosphorylated) Rab8a (1-183) with 2’(3’)-O-

33

726 (N-methylanthraniloyl)-GDP (mantGDP) was achieved by incubation with an 1.5 molar

727 excess of mantGDP for 2 h at RT. Unbound mantGDP was removed using a size-exclusion

728 chromatography column. (Micro Bio-Spin® column, Bio-RAD). The nucleotide exchange

729 reactions were set up in a total volume of 50 μl in a quartz-glass cuvette (Hellma® Analytics)

730 with 0.5 μM mantGDP-bound Rab8a (non-phosphorylated or phosphorylated) using a GEF

731 buffer containing 30 mM Tris pH 7.5, 5 mM MgCl2, 3 mM DTT and 10 mM KH2PO4, pH

732 7.4. Purified Rabin8 (144-245, GEF domain) was subjected to size exclusion

733 chromatography prior to GEF activity assay to ensure no loss of GEF activity due to storage.

734 Rabin8 was added to a final concentration of 2 μM and incubated for 30 min at 20°C. The

735 reactions were initiated by addition of GTP (1 mM cf). The dissociation of mant-GDP from

736 Rab8a was monitored every 2s for a total of 300s at 20°C using a fluorescence spectrometer

737 (PerkinElmer, 366nm excitation and 450nm emission). The observed rate constants (kobs)

738 were calculated by fitting the data into a one-phase exponential decay equation without

739 constraints using nonlinear regression in GraphPad Prism (GraphPad Software Inc).

740 Ni2+-NTA Rabin8 pull-down 741 Ni2+-NTA beads were pre-equilibrated with buffer containing PBS pH 7.4, 30 mM imidazole

742 and 5 mM MgCl2. Purified HIS-tagged Rabin8 (residues 144-460) and untagged Rab8a (1-

743 183) WT or quantitatively phosphorylated pT72 were mixed at equal molar ratios. Individual

744 proteins and a mixture of the proteins were incubated with Ni2+-NTA beads for 1.5 h at 4°C.

745 Beads were washed 3 times with PBS, bound proteins eluted with 500mM imidazole

746 followed by SDS–PAGE and western blot analysis.

Acknowledgements

This work was supported by the Max-Planck Society for the Advancement of Science, The

Michael J. Fox Foundation for Parkinson’s Research (grant ID 6986), the Swiss National

34

Science Foundation (to M.S., P2ZHP3_151580) and the Medical Research Council (to

D.R.A.).We thank S. Suppmann, S. Uebel and E. Weyher-Stingl from the MPIB

Biochemistry Core Facility and G. Sowa, S. Kroiss, K. Mayr and I. Paron from the

department of Proteomics and Signal Transduction for providing technical assistance. M.

Raeschle, F. Sacco, J. Liu and M. Murgia for critical reading and commenting on the

manuscript. A. Itzen (TUM Munich) provided GroEL/ES chaperone plasmids. H. Cai (NIH

Bethesda) provided LRRK2-/- mice. We thank T. Hochdorfer for protein purification and

technical support of the MRC-Protein Phosphorylation and Ubiquitylation Unit, the

management of mouse colony service, genotyping and DNA Sequencing Service

(coordinated by Nicholas Helps), the tissue culture team (coordinated by K. Airey and J.

Stark) and the protein production and antibody purification teams (coordinated by H.

McLauchlan and J. Hastie). Eli Lilly provided the LRRK2-G2019SLilly knock-in mice. We

acknowledge K. Basu, M. Miller and J. Scott from the chemistry department at Merck

Research Laboratories and the Merck LRRK2 program team for their contributions leading to

the discovery of MLI-2.

747 Author contributions

748 M.S., F.T., G.I., P.D., E.L., D.R.A. and M.M. designed the experiments. M.S., F.T., G.I.,

749 M.T., M.V. and S.W. performed the experiments. M.S. conducted all global MS experiments

750 and bioinformatic analyses of MS data and discovered the regulated Rab phosphorylation.

751 M.A.S.B. and B.K.F. generated A2016T knock-in mice and supported the project. A.D.R.,

752 G.D. and S.W. generated the G2019SGSK knock-in mouse line. A.D.R. provided

753 GSK2578215A and supported the project from conception. M.J.F. and J.A.M. provided MLI-

754 2. M.S., P.D., D.R.A. and M.M. wrote the manuscript. All authors discussed the results and

35

755 approved the manuscript. Requests for LRRK2 G2019SGSK mice should be directed to:

756 [email protected]

757 Competing financial interests

758 M.S., F.T., G.I., P.D., M.T., M.V., S.W., E.L., M.A.S.B., B.K.F., D.R.A. and M.M. declare

759 no competing financial interests.

760 S.W. and A.D.R. are employees of GlaxoSmithKline, a global healthcare company that may

761 conceivably benefit financially through this publication.

762 M.J.F. and J.A.M. are employees of Merck Research Laboratories.

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936 60. Westlake CJ, Baye LM, Nachury MV, Wright KJ, Ervin KE, Phu L, et al. Primary cilia membrane 937 assembly is initiated by Rab11 and transport protein particle II (TRAPPII) complex-dependent trafficking 938 of Rabin8 to the centrosome. Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2759-64. PMID: 21273506. 939 doi: 10.1073/pnas.1018823108. 940 61. Pylypenko O, Rak A, Reents R, Niculae A, Sidorovitch V, Cioaca MD, et al. Structure of Rab escort 941 protein-1 in complex with Rab geranylgeranyltransferase. Mol Cell. 2003 Feb;11(2):483-94. PMID: 942 12620235. 943 62. Rak A, Pylypenko O, Durek T, Watzke A, Kushnir S, Brunsveld L, et al. Structure of Rab GDP- 944 dissociation inhibitor in complex with prenylated YPT1 GTPase. Science. 2003 Oct 24;302(5645):646-50. 945 PMID: 14576435. doi: 10.1126/science.1087761. 946 63. Seabra MC, Wasmeier C. Controlling the location and activation of Rab GTPases. Curr Opin Cell 947 Biol. 2004 Aug;16(4):451-7. PMID: 15261679. doi: 10.1016/j.ceb.2004.06.014. 948 64. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, et al. Stable isotope 949 labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression 950 proteomics. Molecular & cellular proteomics : MCP. 2002 May;1(5):376-86. PMID: 12118079. 951 65. Satpathy S, Wagner SA, Beli P, Gupta R, Kristiansen TA, Malinova D, et al. Systems-wide analysis 952 of BCR signalosomes and downstream phosphorylation and ubiquitylation. Mol Syst Biol. 953 2015;11(6):810. PMID: 26038114. doi: 10.15252/msb.20145880. 954 66. Gardet A, Benita Y, Li C, Sands BE, Ballester I, Stevens C, et al. LRRK2 is involved in the IFN- 955 gamma response and host response to pathogens. Journal of immunology. 2010 Nov 1;185(9):5577-85. 956 PMID: 20921534. doi: 10.4049/jimmunol.1000548. 957 67. Sheng Z, Zhang S, Bustos D, Kleinheinz T, Le Pichon CE, Dominguez SL, et al. Ser1292 958 autophosphorylation is an indicator of LRRK2 kinase activity and contributes to the cellular effects of PD 959 mutations. Sci Transl Med. 2012 Dec 12;4(164):164ra1. PMID: 23241745. doi: 960 10.1126/scitranslmed.3004485. 961 68. Herzig MC, Kolly C, Persohn E, Theil D, Schweizer T, Hafner T, et al. LRRK2 protein levels are 962 determined by kinase function and are crucial for kidney and lung homeostasis in mice. Hum Mol Genet. 963 2011 Nov 1;20(21):4209-23. PMID: 21828077. doi: 10.1093/hmg/ddr348. 964 69. Hinkle KM, Yue M, Behrouz B, Dachsel JC, Lincoln SJ, Bowles EE, et al. LRRK2 knockout mice have 965 an intact dopaminergic system but display alterations in exploratory and motor co-ordination behaviors. 966 Mol Neurodegener. 2012;7:25. PMID: 22647713. doi: 10.1186/1750-1326-7-25. 967 70. Baptista MA, Dave KD, Frasier MA, Sherer TB, Greeley M, Beck MJ, et al. Loss of leucine-rich 968 repeat kinase 2 (LRRK2) in rats leads to progressive abnormal phenotypes in peripheral organs. PLoS 969 One. 2013;8(11):e80705. PMID: 24244710. doi: 10.1371/journal.pone.0080705. 970 71. Zhang Q, Pan Y, Yan R, Zeng B, Wang H, Zhang X, et al. Commensal bacteria direct selective 971 cargo sorting to promote symbiosis. Nat Immunol. 2015 Sep;16(9):918-26. PMID: 26237551. doi: 972 10.1038/ni.3233. 973 72. Fell MJ, Mirescu C, Basu K, Cheewatrakoolpong B, DeMong DE, Ellis JM, et al. MLi-2, a potent, 974 selective and centrally active compound for exploring the therapeutic potential and safety of LRRK2 975 kinase inhibition. J Pharmacol Exp Ther. 2015 Sep 25. PMID: 26407721. doi: 10.1124/jpet.115.227587. 976 73. Dzamko N, Inesta-Vaquera F, Zhang J, Xie C, Cai H, Arthur S, et al. The IkappaB kinase family 977 phosphorylates the Parkinson's disease kinase LRRK2 at Ser935 and Ser910 during Toll-like receptor 978 signaling. PloS one. 2012;7(6):e39132. PMID: 22723946. doi: 10.1371/journal.pone.0039132. 979 74. Bleimling N, Alexandrov K, Goody R, Itzen A. Chaperone-assisted production of active human 980 Rab8A GTPase in Escherichia coli. Protein expression and purification. 2009 Jun;65(2):190-5. PMID: 981 19116169. doi: 10.1016/j.pep.2008.12.002.

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982 75. Chaugule VK, Burchell L, Barber KR, Sidhu A, Leslie SJ, Shaw GS, et al. Autoregulation of Parkin 983 activity through its ubiquitin-like domain. The EMBO journal. 2011 Jul 20;30(14):2853-67. PMID: 984 21694720. doi: 10.1038/emboj.2011.204. 985 76. Farley FW, Soriano P, Steffen LS, Dymecki SM. Widespread recombinase expression using FLPeR 986 (flipper) mice. Genesis. 2000 Nov-Dec;28(3-4):106-10. PMID: 11105051. 987 77. Wiggin GR, Soloaga A, Foster JM, Murray-Tait V, Cohen P, Arthur JS. MSK1 and MSK2 are 988 required for the mitogen- and stress-induced phosphorylation of CREB and ATF1 in fibroblasts. 989 Molecular and cellular biology. 2002 Apr;22(8):2871-81. PMID: 11909979. 990 78. Davies P, Hinkle KM, Sukar NN, Sepulveda B, Mesias R, Serrano G, et al. Comprehensive 991 characterization and optimization of anti-LRRK2 (leucine-rich repeat kinase 2) monoclonal antibodies. 992 Biochem J. 2013 Jul 1;453(1):101-13. PMID: 23560750. doi: 10.1042/BJ20121742. 993 79. Nichols RJ, Dzamko N, Morrice NA, Campbell DG, Deak M, Ordureau A, et al. 14-3-3 binding to 994 LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic 995 localization. The Biochemical journal. 2010 Sep 15;430(3):393-404. PMID: 20642453. doi: 996 10.1042/BJ20100483. 997 80. Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, et al. Quantitative proteomics 998 combined with BAC TransgeneOmics reveals in vivo protein interactions. The Journal of cell biology. 999 2010 May 17;189(4):739-54. PMID: 20479470. doi: 10.1083/jcb.200911091. 1000 81. Campbell DG, Morrice NA. Identification of protein phosphorylation sites by a combination of 1001 mass spectrometry and solid phase Edman sequencing. Journal of biomolecular techniques : JBT. 2002 1002 Sep;13(3):119-30. PMID: 19498976. 1003 82. Delprato A, Merithew E, Lambright DG. Structure, exchange determinants, and family-wide rab 1004 specificity of the tandem helical bundle and Vps9 domains of Rabex-5. Cell. 2004 Sep 3;118(5):607-17. 1005 PMID: 15339665. doi: 10.1016/j.cell.2004.08.009. 1006 83. Eberth A, Ahmadian MR. In vitro GEF and GAP assays. Current protocols in cell biology / editorial 1007 board, Juan S Bonifacino [et al]. 2009 Jun;Chapter 14:Unit 14 9. PMID: 19499504. doi: 1008 10.1002/0471143030.cb1409s43. 1009 84. Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, et al. ProteomeXchange 1010 provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014 1011 Mar;32(3):223-6. PMID: 24727771. doi: 10.1038/nbt.2839.

1012

1013

1014

41

1015 Figure legends

1016 Figure 1. Two unbiased phosphoproteomic screens identify physiological LRRK2

1017 targets.

1018 (A) Experimental setup of PS1. LRRK2-G2019SGSK mouse embryonic fibroblasts (MEFs,

1019 n=5) were treated with DMSO or each of two structurally distinct LRRK2 inhibitors

1020 GSK2578215A or HG-10-102-01 (1 µM for 90 minutes). (B) LRRK2 immunoprecipitated

1021 from either knockout (-/-), wild type (wt) or LRRK2-G2019SGSK (G2019S) knock-in or

1022 MEFs was assessed for phosphorylation of Nictide (54) peptide substrate in absence or

1023 presence of GSK2578215A (2 μM). Western blot below shows that similar levels of LRRK2

1024 were immunoprecipitated. Error bars are mean ± SD (n=3). (C) Scheme of PS2. The higher

1025 affinity of MLI-2 towards wt-LRRK2 allows specific pinpointing of LRRK2 substrates when

1026 comparing the phosphoproteomes of wt and A2016T MEFs. (D) Kinase activities of wt

1027 (closed circles) and A2016T (open circles) GST-LRRK2 [1326-2527] purified from HEK293

1028 cells were assayed in the presence of the indicated concentration of MLI-2 (n=3). (E)

1029 Decreased levels of pS935-LRRK2 in wt MEFs after treatment with 10 nM MLI-2. (F) Heat

1030 map cluster of phosphopeptides in PS1 (p<0.005) which are downregulated after treatment

1031 with both GSK2578215A and HG-10-102-01. (G) Heat map cluster of downregulated

1032 (FDR=0.01, S0=0.2) phosphopeptides in PS2. (H) Venn diagram of overlapping

1033 downregulated phosphosites in PS1 and PS2. (Biorep= biological replicate).

1034

42

1035 Figure1-figure supplement 1. Two unbiased phosphoproteomic screens identify

1036 physiological LRRK2 targets.

1037 (A) Western blot analysis of wild type (wt) and LRRK2-G2019SGSK (G2019S) mouse

1038 embryonic fibroblasts, treated with DMSO (-) or 1 µM of GSK2578215A or HG-10-102-01

1039 for 90 minutes. (B) In vitro kinase assay using LRRK2 immunoprecipitated from MEFs (wt

1040 and A2016T) in the presence of various concentrations of MLi-2. Phosphorylation of Nictide

1041 was quantified by liquid scintillation counting. The Western blot below shows that similar

1042 levels of LRRK2 were used. Error bars are mean ± SD (n=3). (C) Western blot analysis of

1043 pS935-LRRK2 and total LRRK2 levels in wt-LRRK2 MEFs and A2016T-LRRK2 MEFs

1044 treated for 60 minutes with the indicated concentrations of MLI-2. (D) Number of quantified

1045 class I phosphorylation sites of PS1 in five biological replicates (Biorep) per phenotype

1046 analyzed. (E) More than 9,000 phosphorylation sites are identified in each of the four

1047 biological replicates (Biorep) of wild type and A2016T MEFs (PS2). (F) Pearson correlations

1048 for the phosphoproteomes of PS1 and PS2 (G).

1049

43

1050 Figure1-figure supplement 2. Two unbiased phosphoproteomic screens identify

1051 physiological LRRK2 targets.

1052 (A) Venn diagram of significantly-regulated (ANOVA, p<0.005) sites with GSK2578215A

1053 and HG-10-102-01 in PS1 (B) Heat map of regulated phosphosites identified in 5 biological

1054 replicates of MEFs (LRRK2-G2019SGSK (DMSO), LRRK2-G2019SGSK+ GSK2578215A and

1055 LRRK2-G2019SGSK + HG-10-102-01). (C) Clusters identified in (B). (D) Volcano plot of all

1056 phosphosites of PS2. Significant sites are in blue and pS935 is indicated.

1057

44

1058 Figure 2. Phosphorylation of Rab GTPases by LRRK2 in vitro.

1059 (A) Position of threonine 72 in the switch II region of Rab8a (PDB: 4HLY). (B) Sequence

1060 alignment of Rab10 and other indicated Rab-family members. (C) Phosphorylation of Rab10

1061 (1 µM) by wt-, G2019S- or kinase inactive LRRK2-D1994A. Inhibition of LRRK2-G2019S

1062 by GSK2578215A or HG-10-102-01 prevents phosphorylation. (D) Time course of LRRK2

1063 (wt) mediated Rab8a (4 µM) phosphorylation and (E) quantification of phosphorylation

1064 stoichiometry (n=3). (F) Time course of LRRK2-wt-mediated pT75-Rab1a phosphorylation

1065 and MS-based label-free quantification (n=3). (G) In vitro phosphorylation of recombinant

1066 Rab proteins (4 µM) by LRRK2-wt. (H) Phosphorylation of recombinant Rab7L1, Rab8a,

1067 moesin and Rps15 by LRRK2 and (I) quantification of the signals. For all reactions LRRK2

1068 inhibitors= 2 µM and LRRK2= 100 ng. Error bars indicate mean ± SEM of replicates.

1069

45

1070 Figure 2-figure supplement 1. Phosphorylation of Rab GTPases by LRRK2 in vitro.

1071 (A) Superposition of the crystal structures of 14 Rab isoforms (Rab1a, 1b, 2, 3, 4, 6, 7, 9, 12,

1072 18, 27, 30, 31, 43). All potential LRRK2 phosphorylation sites (in grey) cluster in the same

1073 region. (B) MS analysis of in vitro phosphorylated Rab10 identified three LRRK2-specific

1074 sites (note that phosphorylation is prevented completely by HG-10-102-01) and pT73 as the

1075 one with the highest intensity. The CID fragmentation spectrum and the Andromeda score

1076 (score) for the tryptic pT73-Rab10 peptide are shown. (C) Phosphorylation of Rab8a and

1077 Rab1b by LRRK2-wt. Inhibition of LRRK2 by HG-10-102-01 prevents phosphorylation. (D)

1078 HPLC trace of tryptic peptides of Rab8a and Rab1b (E) after in vitro phosphorylation by

1079 LRRK2-wt and sequence analysis of tryptic peptides. Y axis units are relative Cherenkov

1080 counts per minute.

1081

46

1082 Figure 3. A number of Rab GTPases are physiological LRRK2 substrates.

1083 (A) MS-quantified pT73-Rab10 peptide intensities in PS1 and PS2. Sequence alignment of

1084 the T73-Rab10 region is shown below. (B) Same as (A) with pS106-Rab12. Western blots

1085 illustrating phosphorylation of T73-HA-Rab10 (C), S106-HA-Rab12 (D) and T72-Rab8 (E)

1086 after induction of LRRK2 expression by doxycycline (1µg/ml). HG-10-102-01 (1µM) was

1087 added prior to lysis (F) Western blot of homogenized brain lysates from LRRK2-G2019SLilly

1088 mice injected with vehicle (40% HPβCD) or with 3 mg/kg MLI-2 (Biorep= biological

1089 replicate) and (G) MS-based quantification of pT72-Rab8 and pS105-Rab12 peptides. (H)

1090 Cytoscape network analysis of Rab8a interacting proteins determined by affinity-purification

1091 mass spectrometry (AP-MS). LRRK2 is in purple and dashed lines in grey show

1092 experimentally-determined interactions from string database (http://string-db.org/).

1093

47

1094 Figure 3-figure supplement 1. HCD MS/MS spectra of synthetic Rab peptides

1095 (A) HCD MS/MS spectra of the pT73-Rab10 peptide identified in PS2. The spectrum of the

1096 corresponding synthetic peptide is shown below. (B) Same as (A) but pS105-Rab12.

1097

48

1098 Figure 3-figure supplement 2. Quantification of Rab phosphorylation by mass

1099 spectrometry

1100 (A) MS-based label-free quantification (MaxLFQ) of the Rab10 and Rab12 protein

1101 intensities in PS2. (B) MS-based quantification of pT73-Rab10 (left) and total Rab10 (right)

1102 derived from HEK293 (trex flpIn) cells expressing GFP-LRRK2-G2019S after LRRK2

1103 inhibition (n=4). (C) MS-quantified Rab3-pT86 peptide levels of ectopically expressed

1104 Rab3a alone or in combination with LRRK2-G2019S, in presence or absence of HG-10-102-

1105 01 (3µM, 3h, n=3). A western blot of the same samples is shown below. (D) Same as (C) but

1106 Rab1a was expressed and pT75-Rab1a quantified. (E) Same as (B) with pT72-Rab8 (left) and

1107 total Rab8a (right). (F) Label-free quantification of pT73-Rab10 and (G) pT72-Rab8a from

1108 knockout, wt, G2019S or G2019S treated with HG-10-102-01 (3 µM, 3 h) MEFs. Total

1109 Rab10 and Rab8 protein levels were also quantified (n=3). (H) and (I) Western blot analyses

1110 of samples used in (F) and (G). Open circles indicate imputed values.

1111

49

1112 Figure 3-figure supplement 3. Several Rabs stably associate with LRRK2 in cells.

1113 (A) Western blot of HEK293 cells expressing flag-LRRK2-G2019S, either alone or in

1114 combination with HA-Rab8a (B) Volcano plot of MS-quantified Rab8a interactors (n=4). (C)

1115 Same as (A) with HA-Rab10 or HA-Rab12. (D) and (E) Volcano plots of MS-quantified

1116 Rab10 and Rab12 interactors.

1117

50

1118 Figure 4. LRRK2 pathogenic variants increase phosphorylation of Rab GTPases.

1119 (A) Scheme of LRRK2 and common PD-associated amino acid substitutions (in red). (B)

1120 Different LRRK2 versions were co-expressed with Rab8a in HEK293 cells, lysates subjected

1121 to immunoblot analysis and (C) indicated signals quantified. (D) and (E) Same as (B) but

1122 HA-Rab10 was used. (F) In vitro phosphorylation of recombinant Rab8a (4 µM) by indicated

1123 LRRK2 variants (100 ng) and (G) quantification of the signals. HG-10-102-01= 2 µM. Error

1124 bars indicate mean ± SEM of replicates (n=3).

1125

51

1126 Figure 5. LRRK2 controls the interaction of Rabs with regulatory proteins.

1127 (A) Volcano plots showing interactors of GFP-Rab8a (T72A) transiently expressed in

1128 HEK293 cells and (B) Proteins differentially binding to T72A as compared to T72E. (C)

1129 Fold changes (T72A/T72E, n=4) of regulated proteins shown in (B). (D) Kinetic

1130 measurements of the dissociation of mant-GDP from non-phosphorylated and T72

1131 phosphorylated Rab8a by Rabin8. Observed rate constants (kobs) are indicated for each

1132 reaction and data points represent mean (n=3). (E) Measurements of mant-GDP dissociation

1133 from LRRK2 phosphorylated Rab8a by Rabin8 in absence or presence of λ-phosphatase (λ-

1134 PPase) or MLI-2 (1 µM). Error bars are mean ± SD of replicates.

1135

52

1136 Figure 5-figure supplement 1. Rab8a nucleotide binding experiments.

1137 Titration experiment using Rab8a (wt and T72E) and fluorescently labeled non-hydrolysable

1138 GTP analog (mant-GMPPNP) or GDP (mant-GDP). The fluorescence signal is plotted as a

1139 function of Rab8a concentration. The dissociation constants (Kd) ± SD are indicated. Error

1140 bars are mean ± SD (n=3).

1141

53

1142 Figure 5-figure supplement 2. Rab8a guanine nucleotide exchange assays.

1143 (A) Ribbon structure of Rab8a in complex with Rabin8 (PDB: 4LHY). The LRRK2

1144 phosphorylation site (T72) situated in the switch II region and forming close contact with

1145 Rabin8 is indicated. (B) Kinetics of mant-GDP dissociation from Rab8a (wt, T72A and

1146 T72E) by Rabin8. (C) and (D) Representation of the observed rate constants (kobs) and

1147 catalytic efficiencies (kcat/Km) for the same reactions. (E) ESI-TOF mass determination of

1148 Rab8a after in vitro phosphorylation by LRRK2-G2019S (left) and after enrichment of

1149 phosphorylated Rab8a by ion-exchange chromatography (right). (F) CID fragmentation

1150 spectrum of the tryptic pT72-Rab8a peptide, which was identified after phosphorylation of

1151 Rab8a by LRRK2 followed by enrichment of the phosphorylated form by ion exchange

1152 chromatography. (G) Ni2+-NTA pull-down of Rab8a (non-phosphorylated or phosphorylated

1153 on T72) by HIS-tagged Rabin8 using purified components. (H) Representation of the

1154 observed rate constants (kobs) and catalytic efficiencies (kcat/Km) for the indicated reactions.

1155 Error bars are mean ± SD (n=3)

1156

54

1157 Figure 6. PD pathogenic LRRK2 mutations interfere with Rab-GDI1/2 association.

1158 (A) Fold changes (T73A/T73E, n=3) of indicated MS-quantified Rab10 interactors. (B) Same

1159 as (A) but S106A-Rab12 and S106E-Rab12 (n=4). (C) Different LRRK2 versions were co-

1160 expressed with Rab8a in HEK293 cells, lysates subjected to immunoblot analysis or

1161 immunoprecipitation using α-HA antibodies and indicated signals quantified (D). (E) and (F)

1162 Same as (C) with Rab12 expression. (G) Scheme for analyzing T72A-Rab8a and T72E-

1163 Rab8a subcellular protein distributions in a SILAC experiment. (H) SILAC ratios (Log2) of

1164 T72E-Rab8a/T72A-Rab8a proteins in the cytosolic and membrane fraction of HEK293 cells.

1165

55

1166 Figure 6-figure supplement 1. Rab10/12-GDI interactions. 1167 (A) HA-Rab10 constructs (wt, T73A, T73E) were expressed in HEK293 cells and lysates

1168 subjected to α-HA immunoprecipitation before western blotting. (B) Same as (A) using HA-

1169 Rab12 (wt, S106A, S106E).

1170

56

1171 Figure 7 Model of Rab GTPase phosphorylation by LRRK2 and its outcome

1172 (A) Rab GTPases (Rabs) cycle between an inactive (GDP-bound) and an active state (GTP-

1173 bound) between cytosol and membranes, respectively. Geranyl-geranyl-modified Rab

1174 GTPases in their GDP-bound state are tightly bound by guanine dissociation inhibitors

1175 (GDIs) in the cytosol. LRRK2 aids the insertion of Rabs in their specific target membrane.

1176 After removal of the LRRK2 phosphorylation site, guanine exchange factors (GEFs)

1177 facilitate exchange of GDP to GTP. This in turn allows binding to effector proteins and

1178 membrane trafficking events. Next, a Rab-specific GTPase activating protein (GAP) assists

1179 in the hydrolysis of GTP followed by removal of the Rab GTPase from the target membrane

1180 by GDIs. (B) In pathogenic conditions, in which LRRK2 is hyperactive, RabGTPases have

1181 strongly diminished affinities for GDIs. As a result, the equilibrium between membrane-

1182 bound and cytosolic Rabs is disturbed, which may contribute to LRRK2 mutant carrier

1183 disease phenotypes. Model adapted and modified from (58).

1184

57

1185 Supplementary File 1 | All phosphosites quantified in the phosphoproteomic screens one

1186 (PS1, LRRK2-G2019SGSK MEFs and two (PS2, wt and LRRK2-A2016T MEFs).

1187 Supplementary File 2 | All quantified proteins of wt and LRRK2-A2016T MEFs.

1188 Supplementary File 3A | Significantly modulated sites of PS1

1189 Supplementary File 3B | Significantly modulated sites of PS2

1190

58

1191 Proteomics raw data have been deposited to the ProteomeXchange Consortium (84)via the

1192 PRIDE partner repository with the data set identifier PXD003071.

1193 The reviewer account details for accessing this data are as follows: 1194 Username: [email protected] 1195 Password: Kr4Fj1US

59

Figure 1 A C PhosphoproteomicPhosphoproteomic screen 1 ((PS1)PS1) PhosphoproteomicPhosphoproPhospho otteomicmmicmic screen 2 (PS2)(PS

LRRK2LRRK2 LRRK2LRRK2 LRRK2LRRK2 G2019SG2019S G2019SG2019S G2019SG2019S Off TarTargetget Off TargetTarget

MLI-2 MLI-2

LRRK2LRRRRK2 LRRK2LRRRK2 wildwild ttypeype AA2016T2010 6TT Off TaTarget r g et Off TargetTa r g et MLI-2M

LI-2I2 LI-2I2 MLI-2MLI MLI-2MLI MLI-2

DDMSOMSO GSK2578215AGSK2578215A HG-10-102-01HG-10-102-01

B D WT IC50 = 0.8 nM 10000 100 A2016T IC50 = 7.2 nM

8000

50 6000 Activity (%) 4000 relative to DMSO 0 DMSO -11 -10 -9 -8 -7 -6 Cherenkov counts 2000 MLI-2 [log(M)]

0 E LRRK2-A2016T wild type Rep.: 12341234 LRRK2: -/- wt wt G2019S G2019S GSK2578215A: - --++ DLRRK2 (pS935)

DLRRK2 F G

G2019S +MLI-2 DMSO GSK2578215A HG-10-102-01 A2016T wild type Biorep: 123451234512345 Biorep: 12341234 Lrrk2 (S935)

Rab10 (T73) Rab10 (T73)

Lrrk2 (S935)

z-score z-score low high low high

H LRRK2 (pS935) Rab10 (pT73)

PS1 45 2 PS2 126 Figure 2 A B Thr72 P61026 Rab10 _ 54 Q-GKKIKLQIWDTAGQERFHTITTSYYRGAMGIMLV 88 P61006 Rab8A _ 53 D-GKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLV 87 switch II Q92930 Rab8B _ 53 D-GKKIKLQIWDTAGQERFRTITTAYYRGAMGIMLV 87 P20339 Rab5A _ 65 D-DTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVV 99 Q6IQ22 Rab12 _ 87 R-GKKIRLQIWDTAGQERFNSITSAYYRSAKGIILV 121 switch I P51153 Rab13 _ 53 E-GKKIKLQVWDTAGQERFKTITTAYYRGAMGIILV 87 P62820 Rab1A _ 56 D-GKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVV 90 Q9H0U4 Rab1B _ 56 D-GKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVV 90 Q92928 Rab1C _ 56 D-GKTIKLQIWDTAGQERFWTITSSYYRGAHGFLVV 90 Q86YS6 Rab43 _ 63 Q-GKRVKLQIWDTAGQERFRTITQSYYRSANGAILA 97 A4D1S5 Rab19 _ 62 D-GKKVKMQVWDTAGQERFRTITQSYYRSAHAAIIA 96 Q15286 Rab35 _ 53 N-GEKVKLQIWDTAGQERFRTITSTYYRGTHGVIVV 87 GTP P20336 Rab3A _ 67 N-DKRIKLQIWDTAGQERYRTITTAYYRGAMGFILM 101 P20337 Rab3B _ 67 H-EKRVKLQIWDTAGQERYRTITTAYYRGAMGFILM 101 Q96E17 Rab3C _ 75 N-EKRIKLQIWDTAGQERYRTITTAYYRGAMGFILM 109 O95716 Rab3D _ 75 H-DKRIKLQIWDTAGQERYRTITTAYYRGAMGFLLM 109 Q15771 Rab30 _ 54 N-GEKVKLQIWDTAGQERFRSITQSYYRSANALILT 88 C Q9NP72 Rab18 _ 53 D-GNKAKLAIWDTAGQERFRTLTPSYYRGAQGVILV 87 Q14964 Rab39A_ 58 EPGKRIKLQLWDTAGQERFRSITRSYYRNSVGGFLV 92 P59190 Rab15 _ 53 D-GIKVRIQIWDTAGQERYQTITKQYYRRAQGIFLV 87 LRRK2 (960-2527): - - Q96DA2 Rab39B_ 53 EPGKRIKLQIWDTAGQERFRSITRAYYRNSVGGLLL 88 D1994A D1994A G2019S G2019S G2019S G2019S D1994A D1994A G2019S G2019S G2019S G2019S wild-type wild-type wild-type wild-type GSK2578215A: ------P20338 Rab4A _ 58 G-GKYVKLQIWDTAGQERFRSVTRSYYRGAAGALLV 92 + + P61019 Rab2B _ 51 D-GKTILVDFWDTAGQERFQSMHASYYHKAHACIMV 85 HG-10-102-01: ------+ ------+ - Q8WUD1 Rab2A _ 51 D-GKQIKLQIWDTAGQESFRSITRSYYRGAAGALLV 85 Rab10: + --- +++ ++ + --- +++ ++ Q96AX2 Rab37 _ 75 D-GVRVKLQIWDTAGQERFRSVTHAYYRDAQALLLL 109 Q9ULW5 Rab26 _ 109 D-GVKVKLQMWDTAGQERFRSVTHAYYRDAHALLLL 143 LRRK2 191kDa 97kDa Q8IZ41 Rab45 _ 586 D-GERTVLQLWDTAGQERFRSIAKSYFRKADGVLLL 620 Q13636 Rab31 _ 50 G-NELHKFLIWDTAGQERFHSLAPMYYRGSAAAVIV 84 Q5JT25 Rab41 _ 76 E-DQIVQLQLWDTAGQERFHSLIPSYIRDSTIAVVV 110 64kDa P51159 Rab27A_ 64 R-GQRIHLQLWDTAGQERFRSLTTAFFRDAMGFLLL 98 51kDa O00194 Rab27B_ 64 K-AFKVHLQLWDTAGQERFRSLTTAFFRDAMGFLLM 98 P61020 Rab5B _ 65 D-DTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVV 99 39kDa P51148 Rab5C _ 66 D-DTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVV 100 P51151 Rab9A _ 52 D-GHFVTMQIWDTAGQERFRSLRTPFYRGSDCCLLT 86 28kDa Rab10 Q9NP90 Rab9B _ 52 D-GRFVTLQIWDTAGQERFKSLRTPFYRGADCCLLT 86 19kDa Q7Z6P3 Rab44 _ 581 D-NKCFVLQLWDTAGQERYHSMTRQLLRKADGVVLM 615 14kDa    P20340 Rab6A _ 58 E-DRTIRLQLWDTAGQERFRSLIPSYIRDSAAAVVV 92 Q9NRW1 Rab6B _ 58 E-DRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVV 92 Coomassie Autoradiograph Q9H0N0 Rab6C _ 58 E-DGTIGLRLWDTAGQERLRSLIPRYIRDSAAAVVV 92 P51149 Rab7A _ 53 D-DRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLV 87 Q96AH8 Rab7B _ 53 G-DTTLKLQIWDTGGQERFRSMVSTFYKGSDGCILA 87 D O14966 Rab7L1 _ 52 SDYEIVRLQLWDIAGQERFTSMTRLYYRDASACVIM 87 Rab8a Rab8a HG-10-102-01: ------+ ------+ - LRRK2: + + + + + + + + + - + + + + + + + + + - E Time (min): 0 1 2 5 10 20 40 80 80 80 0 1 2 5 10 20 40 80 80 80 250kDa 0.20 LRRK2 150kDa

100kDa 0.15

75kDa 0.10 50kDa

37kDa 0.05

25kDa pmol(ATP)/pmol(Rab8) Rab8a 0.00 20kDa 0 20406080       Time (min) Coomassie Autoradiograph FG - Rab1b Rab5b Rab7a Rab7L1 Rab8a Rab10 Rab12 Rab39b HG-10-102-01: --+--+--+--+--+--+ --+--+--+ MS-based quantification LRRK2-wt: -++-++-++-++-++ -++ -++-++-++ 250kDa LRRK2 Rab1a-pT75 150kDa -FRpTITSSYYR- 100kDa 6 75kDa

50kDa

37kDa 4 25kDa 20kDa Rabs 15kDa

250kDa 2 150kDa 100kDa

Log2 peptide intensity 75kDa (relative to HG-10-102-01) 0 50kDa Time (sec): [150] 30 60 90 120 150 HG-10-102-01 (2PM): +- - - - - 37kDa Autoradiograph Coomassie 25kDa 20kDa 15kDa 123456789101112131415161718 123456789

H I HG-10-102-01: -- -- -+-+-+ - + ------+-+-+ - + - LRRK2-wt: -- -- ++++++ + + + -- -- ++++++ + + + Msn: -- -+ ------++ - -- -+ ------++ - Rps15: --+- -- --++-- - --+- -- --++-- - 700 Rab8a: -+ -- - - -++ ---- -+ -- - - -++ ---- Rab7L1: +- -- ++------+- -- ++------600 LRRK2 250kDa 500 150kDa 100kDa 400 75kDa 300 50kDa GST-Mns (400-577) GST-Rps15 200 37kDa Cherenkov counts Rab8a 100 25kDa 20kDa Rab7L1 0 1 2 3 4 5678910111213 1 2 3 4 5678910111213 Rab7L1 Rab8a Rps15 Msn Coomassie Autoradiograph Figure 3 AB Rab10-pT73 Rab12-pS105 -FHpTITTSYYR- -FNpSITSAYYR- PS1 PS2 PS1 PS2 2 p= 8.91*10-6 3 p= 2.75*10-3 3 p= 7.24*10-6 3 p= 0.026

2 2 2

0 1 1 1

0 0 0

-2 -1 -1 -1

-2 -2 -2 -4 Log2 Intensity (relative to DMSO) Log2 Intensity (relative to DMSO) Log2 Intensity (relative to wild type) Log2 Intensity (relative to wild type) -3 -3 -3 G2019S: DMSOGSK2578215A HG-10-102-01 wild type+MLI2 A2016T+MLI2 G2019S: DMSOGSK2578215A HG-10-102-01 wild type+MLI2 A2016T+MLI2

P61026 H.SAPIENS 65 WDTAGQERFHTITTSYYRGAM 85 P61027 M.MUSCULUS 65 WDTAGQERFHTITTSYYRGAM 85 Q6IQ22 H.SAPIENS 96 WDTAGQERFNSITSAYYRSAK 116 P35281 R.NORVEGICUS 65 WDTAGQERFHTITTSYYRGAM 85 P35283 M.MUSCULUS 95 WDTAGQERFNSITSAYYRSAK 115 P24409 C.FAMILIARIS 65 WDTAGQERFHTITTSYYRGAM 85 P35284 R.NORVEGICUS 95 WDTAGQERFNSITSAYYRSAK 115 A6QLS9 B.TAURUS 65 WDTAGQERFHTITTSYYRGAM 85 P51152 C.FAMILIARIS Q6DGV5 D.RERIO 65 WDTAGQERFHTITTSYYRGAM 85 60 WDTAGQERFNSITSAYYRSAK 80 Q5ZIT5 G.GALLUS 65 WDTAGQERFHTITTSYYRGAM 85 A6QPX8 B.TAURUS 94 WDTAGQERFNSITSAYYRSAK 116 Q94148 C.ELEGANS 65 WDTAGQERFHTITTSYYRGAM 85 Q502Q0 D.RERIO 89 WDTAGQERFNSITSAYYRGAK 109 O15971 D.MELANOGASTER 65 WDTAGQERFHTITTSYYRGAM 85 R4GIH4 G.GALLUS 102 WDTAGQERFNSITSAYYRSAK 122

CDE

HEK293 (flpIn-trex HEK293 (flpIn-trex HEK293 (flpIn-trex GFP-LRRK2-G2019S) GFP-LRRK2-G2019S) GFP-LRRK2-G2019S) Doxycycline: -+++ Doxycycline: -+ + + Doxycycline: -++ + HG-10-102-01: --+- HG-10-102-01: -- + - HG-10-102-01: --+ - HA-Rab10: wt wt wt T73A HA-Rab12: wt wt wt S106A HA-Rab8a: wt wt wt T72A DLRRK2 DLRRK2 DLRRK2 lysates lysates lysates DLRRK2-pS935 DLRRK2-pS935 DLRRK2-pS935

DHA-Rab10 DHA-Rab12 DHA-Rab8a IP-HA IP-HA IP-HA DRab10-pT73 DRab12-pS106 DRab8-pT72

F G Mouse brain Rab8-pT72 Rab12-pS105 vehicle MLI-2 -FRpTITTAYYR- -FNpSITSAYYR- 123123 -3 2 p= 4.07*10 2 p= 0.047 D-LRRK2 (pS935)

D-LRRK2

D-Tubulin-E 1 1

0 0 H

WDR81 -1 -1 WDR91 ERLIN2 ARF3

MICALL2 ARF1 Log2 Intensity (relative to vehicle) -2 LRRK2 ARF5 -2 vehicle MLI-2 vehicle MLI-2 MICALL1 RAB39A

INPP5B RABIF DVL2

CHM OCRL GBF1 Rab8A DVL3 RAB8B RABGGTA

RAB6A GDI1

TBC1D15 MICAL1 RAB1A GDI2 MICAL3 RAB18 TBC1D9B

ARL1 RAB6B

SYTL4

known interactions low enrichment this study known interactions found also in this study high enrichment Figure 4 A T2031S R1728H G2019S R1441C/G/H Y1699C I2020T G2385R

1 ARM ANK LRR ROCOCC COR KINASEE WD40 2527 660 702 822 983 1319 1335 1515 1845 1859 2138 2142 2498

B C HA-Rab8a 25

LRRK2: - wt D2017A R1441C R1441G R1441H Y1699C R1728H I2020T G2019S T2031S G2385R 20 DLRRK2 15 DRab8-pT72 10 DHA-Rab8 5 DTubulin-E (relative to D2017A) ROC COR KINASE WD40 pT72-Rab8a/total Rab8a 0 wt I2020T T2031S T2385R Y1699C D2017A R1441C R1441H R1728H G2019S R1441G

D E HA-Rab10 18 16 LRRK2: - wt D2017A R1441C R1441G R1441H Y1699C R1728H I2020T G2019S T2031S G2385R 14 DLRRK2 12 DRab10-pT73 10 8 DHA-Rab10 6 4

DTubulin-E (relative to D2017A) 2 pT73-Rab10/total Rab10 0

ROC COR KINASE WD40 wt I2020T T2031S T2385R Y1699C D2017A R1441C R1441H R1728H G2019S R1441G

F G

LRRK2: - 800 R1441C G2019S R1441C G2019S R1441C G2019S wild-type wild-type wild-type HG-10-102-01: ------+++ 700 Rab8a: +--- ++ ++ ++ 600 250kDa 500 150kDa 100kDa 400 75kDa 300

50kDa Cherenkov counts 200 37kDa 100 25kDa 20kDa 0 HG-10-102-01: - + - + - + wild-typeR1441C G2019S 250kDa 150kDa 100kDa 75kDa

50kDa

37kDa Autoradiograph Coomassie 25kDa 20kDa 1 234 567 8910 Figure 5 A B

Decreasing affinity for Rab8a-T72E Rab8a(T72A)-specific interactors

10 RABIF GDI1 8

MICALL2 GDI2 9 7

GDI2 8

GDI1 6 RAB6C 7 WDR81 RAB8A TBC1D15 WDR91 RABGGTA ERLIN2 DVL2 VAPA 5 6 MICALL1 MICAL3 CHML CHML TBC1D8B CHM ARF1 TBC1D9B

5 INPP5B 4 ARL8B RAB39A RAB18 INPP5B /RJ SYDOXH /RJ SYDOXH ARF4 ESYT1 4 CHM RAB3IP RABGGTB RAB3IP

TBC1D15 OCRL 3 GBF1 SYTL4 ERLIN1 3 RAB8B MICAL1 RABGGTA 2

2 RABGGTB Bait Bait ARF5 ARL1 Rab GTPases Rab GTPases RabGTPase inhibitors 1 RabGTPase inhibitors

1 RAB1A RAB11A GEFs GEFs GAPs GAPs Rab GGT complex Rab GGT complex Others RAB8A

0 Others 0 -2 0 2 4 6 8 10 -2 0 2 4 6 8 10 /RJ 5DE7$EHDGV /RJ 5DE7$5DE7(

C 12 D

10 1.0

8 0.8

6 0.6 Log2 -1 pT72-Rab8 kobs (s ) = 0.001 4 -1 Rab8 kobs (s ) = 0.002 0.4 -1 pT72-Rab8 + Rabin8 kobs (s ) = 0.009 -1 2 Rab8 WT + Rabin8 kobs (s ) = 0.034 (Fold change T72A vs T72E) (Fold change T72A

relative fluorescence 0.2 0 0 CHM GDI1 GDI2 0 50 100 150 200250 300 CHML RAB3IP INPP5B time (s) TBC1D15 RABGGTA RABGGTB

E Rab8a Rab8a+ȜPPase Rab8a+LRRK2 1.0 1.0 1.0 no Rabin8 0.2 ȝM Rabin8 0.9 0.9 0.9 0.5 ȝM Rabin8 1 ȝM Rabin8 0.8 0.8 0.8

0.7 0.7 0.7 relative fluorescence relative fluorescence 0.6 relative fluorescence 0.6 0.6 0 100 200 300 0 100 200 300 0 100 200 300 time [sec] time [sec] time [sec] Rab8A+LRRK2+ȜPPase Rab8A+LRRK2+MLI-2 1.0 1.0 no Rabin8 0.2 ȝM Rabin8 0.9 0.9 0.5 ȝM Rabin8 1 ȝM Rabin8 0.8 0.8

0.7 0.7 relative fluorescence 0.6 relative fluorescence 0.6 0 100 200 300 0 100 200 300 time [sec] time [sec] Figure 6 A C 20 HA-Rab8a Rab10 LRRK2: - wt D2017A R1441C R1441G R1441H Y1699C R1728HG2019S I2020T T2031S G2385R DLRRK2-pS1292 15 DLRRK2

DRab8-pT72 10 lysates DHA-Rab8

DGDI1/2 (T73A vs T73E) (T73A

Log2 fold change 5 DTubulin-E

DGDI1/2 0 CHM CHML GDI1 GDI2 DHA-Rab8 IP-HA

B DHA-Rab8 Rab12 Phos-tag 15 ROC COR KINASE WD40 D 1.4

10 1.2 1 0.8 0.6 5

GDI1/2/Rab8 0.4 (S106A vs S106E) (S106A Log2 fold change 0.2 (relative to D2017A) 0

0 wt GDI1 GDI2 I2020T T2031S T2385R Y1699C D2017A R1441C R1441H R1728H G2019S R1441G

E HA-Rab12

LRRK2: - wt D2017A R1441C R1441G R1441H Y1699C R1728HG2019S I2020T T2031S G2385R DLRRK2

DGDI1/2 DTubulin-E

lysates DHA-Rab12-pS106

DHA-Rab12

DGDI1/2

IP-HA DHA-Rab12 ROC COR KINASE WD40

F G H Rab8 1.2 0.5 1 SILAC light SILAC heavy Rab8-T72A Rab8-T72E 0.8 mix 1:1 0 0.6

0.4

GDI1/2/Rab12 fractionate 0.2 (relative to D2017A) membranes/cytosol -0.5 0 wt I2020T Log2 (SILAC ratio T72E/T72A)

T2031S LC-MS/MS T2385R Y1699C D2017A

R1441C R1441H R1728H G2019S -1 R1441G cytosol membrane Figure 7 A

GDI GDI

GDI Rabs ŝŶĂĐƟǀĞ Rabs ŝŶĂĐƟǀĞ GDP Rabs GDP ŝŶĂĐƟǀĞ GDI GDP GDI GDI GDI >ZZ<ϮͲǁƚ + P Rabs ŝŶĂĐƟǀĞ Rabs GDP ŝŶĂĐƟǀĞ

GDP

P Rabs Rabs ŝŶĂĐƟǀĞ Regulated distribution of Rabs between ŝŶĂĐƟǀĞ cytosol and membranes GDP GDP

WŚŽƐƉŚĂƚĂƐĞy GTP ? GTP P GEF i GAP

GDP GDP

Rabs ĂĐƟǀĞ

GTP īĞĐƚŽƌ īĞĐƚŽƌ

B

GDI GDI

Rabs ŝŶĂĐƟǀĞ Rabs ŝŶĂĐƟǀĞ GDI GDP

GDP GDI Rabs GDI ŝŶĂĐƟǀĞ LRRK2 + P 'ϮϬϭϵ^ͬ GDP R1441G

Shifted balance towards P P P Rabs Rabs Rabs Rabs ŝŶĂĐƟǀĞ ŝŶĂĐƟǀĞ ŝŶĂĐƟǀĞ phosphorylated Rabs-accumulation ŝŶĂĐƟǀĞ in membranes GDP GDP GDP GDP

WŚŽƐƉŚĂƚĂƐĞy GTP ? GTP P GEF i GAP

GDP GDP

Rabs ĂĐƟǀĞ

GTP īĞĐƚŽƌ īĞĐƚŽƌ