SCD1 and SCD2 Form a Complex that Functions with the ... · 1 RESEARCH ARTICLE 2 3 SCD1 and SCD2 Form a Complex that Functions with the Exocyst and 4 RabE1 in Exocytosis and Cytokinesis

RESEARCH ARTICLE 1 2

SCD1 and SCD2 Form a Complex that Functions with the Exocyst and 3

RabE1 in Exocytosis and Cytokinesis 4

5 Jonathan Russell Mayersa, Tianwei Hub, Chao Wangb, Jessica J. Cárdenasa Yuqi Tana, 6 Jianwei Panb,c, Sebastian Y. Bednareka* 7 8 a Department of Biochemistry University of Wisconsin-Madison, Madison, Wisconsin 53706 9 b Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life 10 Sciences, Lanzhou University, Lanzhou 730000, China 11 c College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China 12 *Corresponding author: [email protected] 13 14 Short Title: The SCD Complex Functions in Exocytosis 15 16 One-sentence summary: Plants have evolved to utilize the SCD complex, which is 17 architecturally distinct from—but performs similar functions as—the structurally-related exocytic 18 yeast and mammalian Sec2/Rabin8 Rab GEFs. 19 20 The author responsible for distribution of materials integral to the findings presented in this 21 article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) 22 is: Sebastian Y. Bednarek ([email protected]). 23 24 ABSTRACT 25 Although exocytosis is critical for the proper trafficking of materials to the plasma membrane, 26 relatively little is known about the mechanistic details of post-Golgi trafficking in plants. Here we 27 demonstrate that the DENN (Differentially Expressed in Normal and Neoplastic cells) domain 28 protein SCD1 (STOMATAL CYTOKINESIS DEFECTIVE 1) and SCD2 form a previously 29 unknown protein complex, the SCD complex, that functionally interacts with subunits of the 30 exocyst complex and a member of the RabE1 family of GTPases in Arabidopsis thaliana. 31 Consistent with a role in post-Golgi trafficking, scd1 and scd2 mutants display defects in 32 exocytosis and recycling of PIN2-GFP. Perturbation of exocytosis using the small molecule 33 Endosidin2 results in growth inhibition and PIN2-GFP trafficking defects in scd1 and scd2 34 mutants. In addition to the exocyst, the SCD complex binds in a nucleotide state-specific 35 manner with Sec4p/Rab8-related RabE1 GTPases and overexpression of wild-type RabE1 36 rescues scd1 temperature-sensitive mutants. Furthermore, SCD1 colocalizes with the exocyst 37 subunit, SEC15B, and RabE1 at the cell plate and in distinct punctae at or near the plasma 38 membrane. Our findings reveal a mechanism for plant exocytosis, through the identification and 39 characterization of a protein interaction network that includes the SCD complex, RabE1, and the 40 exocyst. 41 42 43

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Plant Cell Advance Publication. Published on September 29, 2017, doi:10.1105/tpc.17.00409

©2017 American Society of Plant Biologists. All Rights Reserved

INTRODUCTION 45

Vesicular trafficking to and from the plasma membrane is paramount to plant 46

growth and development, as it facilitates multiple important processes including cell wall 47

biosynthesis, nutrient uptake, hormone signaling, and pathogen defense (Takano et al., 48

2005; Tanaka et al., 2006; Robatzek, 2007). Similarly, in dividing cells exocytic and 49

endocytic trafficking pathways are essential for the formation of the cytokinetic organelle 50

known as the cell plate. 51

Proper regulation and function of biosynthetic secretory and endocytic 52

membrane trafficking pathways depend on stage-specific Rab GTPases. In their GTP-53

bound form, Rabs recruit divergent effectors to coordinate the formation, transport, 54

tethering and fusion of transport vesicles and organelles. To function properly, Rabs 55

must continually cycle between active and inactive forms through the exchange of GTP 56

and GDP via interactions with Rab GEFs (guanine nucleotide exchange factors) and 57

Rab GAPs (GTPase activating proteins)(Stenmark, 2009). Thus, the association of Rab 58

GTPases with downstream effector proteins is inherently dependent upon their 59

interactions with GEFs and GAPs. Surprisingly, of the 57 Arabidopsis thaliana Rabs, 60

only a few of their GEFs/GAPs and downstream effector proteins are known (Preuss et 61

al., 2006; Goh et al., 2007; Camacho et al., 2009; Thellmann et al., 2010; Qi and Zheng, 62

2011; Fukuda et al., 2013; Singh et al., 2014). Therefore, despite recent advances in 63

our knowledge of Rab function in plants, a significant gap remains in our understanding 64

of the molecular machinery involved in their regulation. 65

In yeast, communication between the GEF Sec2p and the Rab GTPases Ypt32p 66

and Sec4p establishes a functional connection between cargo-containing Golgi-derived 67

exocytic vesicles and the molecular machinery necessary for their targeting and fusion 68

with the plasma membrane (Ortiz et al., 2002). Specifically, Ypt32p recruits Sec2p to 69

the trans-Golgi network which in turn binds and activates the Sec4p, which facilitates 70

interactions with the exocyst complex, an evolutionarily conserved eight-subunit 71

complex consisting of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84, to 72

promote docking with the plasma membrane prior to fusion (Hammer and Sellers, 2012; 73

Wu and Guo, 2015; Vukasinovic and Zarsky, 2016). A similar mechanism occurs in 74

mammalian cells, in which a Rab cascade comprising Rab11, Rab8 and the Rab8 GEF 75

3

Rabin8 promotes exocyst-dependent vesicle targeting to the plasma membrane 76

(Knodler et al., 2010; Westlake et al., 2011; Mizuno-Yamasaki et al., 2012). 77

Similar to its function in yeast and mammalian cells (Heider and Munson, 2012; 78

Wu and Guo, 2015), the exocyst plays an important role in the trafficking of materials to 79

the plasma membrane, and also functions in multiple steps during cytokinesis and cell 80

plate formation in plants (McMichael and Bednarek, 2013; Rybak et al., 2014). 81

Arabidopsis exocyst subunit mutants exhibit developmental phenotypes including 82

dwarfism, improper guard cell cytokinesis, and cell plate maturation defects (Fendrych 83

et al., 2010; Drdova et al., 2013; Rybak et al., 2014; Wu and Guo, 2015). However, 84

although homologs for Ypt32/Rab11, Sec4p/Rab8 and exocyst subunits are known to 85

function in exocytosis and cytokinesis in plants, the molecular details of their 86

interactions are not known. 87

Arabidopsis scd1 (stomatal cytokinesis defective 1) and scd2 mutants exhibit 88

strikingly similar phenotypes to exocyst mutants: plants are dwarfed and have defects in 89

cell division and expansion that result in guard cell cytokinesis and root hair 90

morphogenesis defects (Falbel et al., 2003; Korasick et al., 2010; McMichael et al., 91

2013). In addition, SCD1 and SCD2 genetically interact and are associated with 92

clathrin-coated vesicles (CCVs), suggesting a role for these proteins in membrane 93

trafficking during cytokinesis and cell expansion including endocytosis (McMichael and 94

Bednarek, 2013; McMichael et al., 2013). The SCD1 protein is defined by an N-terminal 95

DENN (Differentially Expressed in Normal and Neoplastic cells) domain that in 96

metazoans has been demonstrated to activate Rab GTPases (Marat and McPherson, 97

2010; Yoshimura et al., 2010; Marat et al., 2012); however, a connection between 98

DENN-domain proteins and Rab GTPases has not been established in plants. 99

Members of the plant RabE1 GTPase (RabE1a-e) family are most closely 100

related to mammalian Rab8 and S. cerevisiae Sec4p (Rutherford and Moore, 101

2002). Live-cell imaging has demonstrated that RabE1d and RabE1c localize to the 102

Golgi stacks, plasma membrane, and the cell plate in dividing cells (Zheng et al., 2005; 103

Chow et al., 2008; Speth et al., 2009). Moreover, functional studies have indicated that 104

RabE1s act in post-Golgi trafficking to the plasma membrane and cell plate (Speth et 105

al., 2009; Ahn et al., 2013). Similar to the scd1 and scd2 mutant phenotypes, silencing 106

4

of RabE1 expression in Nicotiana benthamiana results in defective guard mother cell 107

cytokinesis, and overexpression of dominant-negative mutant RabE1 in plants 108

manifests in shoot and root growth defects (Speth et al., 2009; Ahn et al., 2013). 109

To date, only a few factors that function to regulate the exocyst complex have 110

been identified in plants (Lavy et al., 2007; Hazak et al., 2010). Here we show, through 111

the use of proteomics, in vitro binding studies, cargo trafficking assays, and 112

colocalization analysis, that SCD1 and SCD2 are subunits of a protein complex, which 113

we refer to as the SCD complex, that functions together with RabE1s and the exocyst in 114

a protein interaction network to mediate post-Golgi trafficking to the plasma 115

membrane and cell plate. 116

117

118

5

RESULTS 119

SCD1 and SCD2 are Subunits of an Oligomeric Protein Complex 120

Previously we demonstrated that SCD1 and SCD2 function in membrane 121

transport required for cytokinesis and cell expansion (McMichael et al., 2013). To further 122

define the protein interaction network of SCD1 and SCD2, we generated Arabidopsis 123

cell lines (PSB-d) that express N-terminal G-protein/Streptavidin-binding peptide (GS)-124

tagged SCD1 (GS-SCD1), SCD2 (GS-SCD2), or GFP (GS-GFP) fusion proteins. GS-125

SCD1, GS-SCD2, and GS-GFP were purified from Arabidopsis cell extracts using 126

tandem affinity purification (TAP) chromatography as described (Van Leene et al., 127

2011). TAP elutions were analyzed by SDS-PAGE (Figure 1A, Supplemental Figure 1) 128

and liquid chromatography tandem mass spectrometry (LC/MS/MS) (Figure 1B, 129

Supplemental Data Set 1). The major polypeptides detected in the TAP GS-SCD1 and 130

GS-SCD2 elutions migrated in SDS-PAGE at the expected molecular mass of GS-131

SCD1 (~140 kD) and GS-SCD2 (~70 kD), respectively, with the G-protein removed 132

during purification as described (Van Leene et al., 2011) (Figure 1A). In addition, 133

polypeptides of the expected size for endogenous SCD1 (~132 kD) and SCD2 (~64 kD) 134

were observed in the GS-SCD1 and GS-SCD2 TAP fractions, respectively. LC/MS/MS 135

analysis confirmed that endogenous untagged SCD2 co-purified with GS-SCD1 and 136

vice versa (Figure 1B, Supplemental Data Set 1) indicating that SCD1 and SCD2 137

physically interact. The association of endogenous untagged SCD1 and SCD2 was 138

further analyzed using independent methods. Immunoprecipitation of untransformed 139

Arabidopsis cell lysate using anti-SCD2 antibodies demonstrated co-140

immunoprecipitation of SCD1 with SCD2 under standard (100mM KCl) and higher salt 141

(300mM KCl) conditions, indicating that the association of SCD1 and SCD2 is salt 142

stable (Figure 1D). Furthermore, SCD1 and SCD2 were found to co-fractionate by 143

velocity gradient sedimentation analysis, which separates proteins based on their native 144

molecular mass and hydrodynamic properties (Harding, 1999). Specifically, Arabidopsis 145

cell extracts were fractionated by glycerol gradient sedimentation and analyzed by 146

immunoblotting with antibodies against both SCD1 and SCD2 (Figure 1C). Quantitative 147

analysis of the immunoblots revealed that endogenous SCD1 and SCD2 fractionated in 148

separate slower sedimenting peaks corresponding to their expected monomeric forms 149

6

(molecular masses 132 and 64 kD, respectively), as well as in an overlapping ~17S 150

7

peak with an estimated molecular mass of ~430 kD, which is larger than expected for a 151

complex containing only single copies of SCD1 and SCD2, suggesting that SCD1 and 152

SCD2 are subunits of a multimeric protein complex. In addition, LC/MS/MS analysis of 153

proteins that co-purified with GS-SCD1 and GS-SCD2 identified two SCD2-like 154

polypeptides encoded by At5g23700 and At5g13260, which we have named SCD2c 155

and SCD2b respectively. SCD2c and SCD2b share 75% and 56% amino acid identity 156

with SCD2, respectively (Figure 1B, Supplemental Data Set 1). Similar to SCD2, these 157

two SCD2-like proteins are predicted to contain two centrally located coiled-coil 158

domains as well as a ProDom-defined (Corpet et al., 1998), plant-specific domain of 159

unknown function, PD147848, at their respective carboxyl termini. LC/MS/MS analysis 160

of proteins that co-purified with GS-GFP did not show similar enrichment profiles of 161

interacting proteins (Supplemental Data Set 1, Supplemental Table 1). A small amount 162

of RabE1c co-purified with GS-GFP, but its abundance in the GS-SCD1 and GS-SCD2 163

samples was 9- and 29-fold higher respectively, based on Exponentially Modified 164

Protein Abundance Index (emPAI) as determined by Mascot (Supplemental Table 1). 165

166

scd Mutants Display Post-Golgi Trafficking Defects 167

Arabidopsis scd1 and scd2 mutant plants exhibit cytokinesis and cell expansion 168

defects, including impaired internalization of the endocytic tracer dye, FM4-64, 169

indicative of potential roles in cell plate and plasma membrane trafficking (Falbel et al., 170

2003; McMichael et al., 2013). LC/MS/MS analysis of GS-TAP experiments have 171

identified exocyst subunits (SEC3A, SEC5, SEC6, SEC10, SEC15B, EXO70A1, and 172

EXO84B) as potential interactors with SCD1 and SCD2, suggesting that the SCD 173

complex may function in exocytic vesicle trafficking to the cell plate and plasma 174

membrane (Figure 1B, Supplemental Data Set 1). To test this, we assayed the 175

trafficking of the plant plasma membrane protein PIN-FORMED2 fused to green 176

fluorescent protein (PIN2-GFP) (Xu and Scheres, 2005) in scd1 and scd2 mutants. 177

PIN2 is a member of the PIN family of transport proteins that functions to transport 178

auxin, a crucial developmental hormone, across the plasma membrane (Krecek et al., 179

2009). PIN2-GFP is trafficked from the trans-Golgi network/early endosome to the 180

plasma membrane where it can undergo rounds of constitutive endocytosis and 181

8

recycling from endosomes to the plasma membrane or be transported to the vacuole for 182

9

degradation (Lofke et al., 2013; Wang et al., 2013). To monitor GFP-PIN2 trafficking, 183

wild-type (Col-0) and loss-of-function scd1-2 and scd2-1 mutant plants expressing 184

PIN2-GFP, under control of its native promoter (ProPIN2:PIN2-GFP), were treated with 185

the reversible vesicle trafficking inhibitor Brefeldin A (BFA), which causes formation of 186

intracellular endosomal and trans-Golgi compartment aggregates (BFA bodies) (Rosa et 187

al., 1992; Ritzenthaler et al., 2002; Wang et al., 2013). Following 50 µM BFA treatment 188

for 60 min, de novo synthesized and internalized PIN2-GFP accumulated in 1–2 BFA 189

bodies/root cell in scd1-2, scd2-1, and wild-type plants as monitored by confocal 190

microscopy (Figure 2). Time course assays demonstrated that the levels of intracellular 191

PIN2-GFP decreased upon BFA removal in wild-type, scd1-2, and scd2-1 root cells, 192

indicative of the restoration of protein trafficking to the plasma membrane (Dhonukshe 193

et al., 2007). Relative to wild-type however, scd1-2 and scd2-1 mutants displayed a 194

significant delay in the rate of loss of PIN2-GFP-positive BFA bodies per cell and higher 195

PIN2-GFP fluorescent signal intensity (Figure 2A-2O). 196

To distinguish between the trafficking of de novo synthesized and internalized 197

PIN2-GFP, BFA washout experiments were performed in the presence of cycloheximide 198

(CHX), an inhibitor of eukaryotic translation (Schneider-Poetsch et al., 2010). In the 199

presence of CHX and BFA, the number of PIN2-GFP labeled BFA bodies/cell was found 200

to be reduced in both scd mutants compared to wild type (Figure 2P), indicative of an 201

endocytosis defect and consistent with previous data showing that scd1 and scd2 202

mutants exhibit defects in the uptake of the endocytic tracer dye, FM4-64 (McMichael et 203

al., 2013). In addition to a reduction in endocytosis, recycling of PIN2-GFP from BFA 204

bodies was delayed in scd mutants. As shown in Figure 2P-2Q, after normalization for 205

the initial number of BFA bodies per root cell in the presence of CHX, we observed a 206

decrease in the rate of PIN2-GFP-labeled BFA body disappearance in scd1-2 and scd2-207

1 mutants following removal of BFA. Similarly, scd mutants had increased PIN2-GFP 208

intensity per BFA body area per cell after washout (Figure 2R). Taken together, our 209

analysis of PIN2-GFP trafficking in the scd mutants indicates that the SCD complex 210

functions in exocytosis and endosomal recycling of plasma membrane proteins. 211

212

The SCD Complex Communicates with the Exocyst Complex 213

10

Given that the SCD complex functions in post-Golgi trafficking, and the 214

identification of exocyst subunits as putative SCD complex interactors (Figure 1B, 215

Supplemental Data Set 1), we further explored the relationship between the SCD 216

complex and the exocyst. To determine if SCD complex-mediated post-Golgi trafficking 217

to the plasma membrane is dependent on exocyst function, we performed 218

pharmacological studies with the small molecule Endosidin2 (ES2), which selectively 219

inhibits exocytosis by binding to exocyst subunit Exo70 (Zhang et al., 2016). As 220

previously shown, ES2 treatment of wild-type seedlings expressing PIN2-GFP blocks 221

exocytosis and endosomal recycling, resulting in the intracellular accumulation of PIN2-222

GFP in punctate structures (Figure 3A) that are distinct from BFA bodies (Zhang et al., 223

2016). Interestingly, ES2 was found to enhance the intracellular accumulation of PIN2-224

GFP in both scd1 and scd2 mutants compared to wild-type plants. Specifically, scd1-2 225

and scd2-1 mutant root cells treated with 40 µM ES2 showed 2.3-fold and 2.6-fold 226

elevation, respectively, in the average number of PIN2-GFP labeled-punctae/cell 227

(Figure 3A-3D) relative to ES2-treated wild-type (Col-0) root cells. These intracellular 228

PIN2-GFP punctae were not detectable in untreated Col-0 and scd mutants (Figure 2S-229

U). To confirm the presence of internalized PIN2-GFP in ES2 bodies, experiments were 230

performed with CHX. Treatment with both ES2 and CHX together enhanced intracellular 231

accumulation of PIN2-GFP, likely due to inhibition of recycling PIN2-GFP back to the 232

plasma membrane by ES2 (Supplemental Figure 2). 233

Homozygous temperature-sensitive scd1-1 grown above the permissive 234

temperature of 16°C and loss-of-function scd1-2 and scd2-1 plants are dwarfed and 235

display numerous growth defects including stunted roots (Falbel et al., 2003; McMichael 236

et al., 2013). To assess the effects of ES2 on root growth, wild-type (Col-0) and scd 237

mutant seedlings were germinated and grown for 13 days in the presence of DMSO or 238

30 µM ES2 and root length was measured. Relative to DMSO-treated control seedlings, 239

ES2-treated wild-type (Col-0) seedlings showed a ~10% reduction in root length. By 240

contrast, ES2 inhibited scd1-1, scd1-2 and scd2-1 seedling root growth by ~50%, ~80%, 241

and ~80%, respectively, relative to DMSO-treated scd mutant seedlings (Figure 3E, 3F). 242

The observed enhancement of growth defects observed in ES2-treated scd1 and scd2 243

mutants provides further support for a functional connection between the SCD and 244

11

exocyst protein complexes, and suggests that the SCD complex functions in protein 245

trafficking through downstream interactions with the exocyst. 246

LC/MS/MS analysis of tandem affinity purified GS-SCD2 from Arabidopsis cell 247

extracts identified seven of the eight exocyst subunits, with the notable absence of Sec8 248

(Figure 1B, Supplemental Data Set 1). Interestingly, SEC15 and SEC10, which in yeast 249

act as a linker between transport vesicles and the rest of the exocyst complex (Guo et 250

al., 1999), were the most highly represented exocyst subunits that co-purified with GS-251

SCD2 based on the number of spectral counts. To verify the physical connection 252

between the SCD and exocyst complexes, we chose to further explore the interaction of 253

the SCD complex with SEC15B using in vitro binding and colocalization studies. To 254

determine if SCD1 and SCD2 interact with SEC15B, immobilized GST and GST-255

SEC15B were incubated with Arabidopsis cell extracts. Immunoblot analysis of proteins 256

12

bound to GST and GST-SEC15B demonstrated that SCD1 and SCD2 interacted with 257

GST-SEC15B and not with the GST negative control (Figure 4A). 258

Next, we utilized CLSM to assess whether GFP-SCD1 and red fluorescent 259

protein (RFP)-SEC15B colocalize. As previously shown (Fendrych et al., 2010; Rybak 260

et al., 2014), RFP-SEC15B predominantly localized to the cell plate and to punctate 261

13

structures at or adjacent to the plasma membrane in dividing and non-dividing cells, 262

respectively (Figure 4C, 4F). Similarly, SCD1 was associated with punctae closely 263

associated with the plasma membrane (McMichael et al., 2013) (Figure 4E) as well as 264

the cell plate in dividing cells (Figure 4B), which had previously not been reported. 265

Fluorescence intensity line scans across the cell plate (Figure 4D) and punctate 266

structures (Figure 4G) revealed overlapping intensity profiles of GFP-SCD1 and RFP-267

SEC15B consistent with colocalization (Figure 4H-4J). Furthermore, colocalization was 268

quantitatively verified for image pairs using the Costes randomization test (Costes et al., 269

2004). Images were analyzed with 100 Costes iterations returning a Costes P-Value of 270

1.00 for both punctae and cell plate localization with Pearson’s R values of 0.65 and 271

0.61 respectively. 272

Next, we utilized CLSM to assess whether SCD function is required for the 273

localization of the exocyst. As shown previously (Fendrych et al., 2010), GFP-SEC15B 274

was associated with the plasma membrane in non-dividing cells. However, the 275

subcellular distribution of GFP-SEC15B was altered in scd1-2 mutant root cells 276

compared to wild type (Figure 4K, 4L), with the most dramatic differences seen near the 277

plasma membrane. Line scan intensity measurements also demonstrated an increase in 278

the intracellular levels of GFP-SEC15B in scd1-2 mutants relative to wild type (Figure 279

4M, 4N). These data, together with the ES2 inhibitor and in vitro binding studies, 280

indicate that the SCD complex and exocyst function together to mediate post-Golgi 281

vesicle trafficking to the plasma membrane. 282

283

The SCD Complex Selectively Interacts with RabE1 GTPases 284

Given that SCD1 contains a tripartite DENN domain that has been demonstrated 285

in other systems to function as a GEF for Rab GTPases (Marat and McPherson, 2010; 286

Yoshimura et al., 2010; Marat et al., 2012), the SCD complex may function through 287

interactions with Rab GTPases to regulate exocytic vesicle trafficking. Consistent with 288

this, LC/MS/MS analysis of proteins associated with SCD1 and SCD2 identified all 289

members of the RabE1 family; specifically, RabE1a-e were identified by TAP and Co-IP 290

of GS-tagged and endogenous SCD proteins (Figure 1B, Supplemental Data Set 1). 291

Previously published reports have implicated RabE1 GTPases in post-Golgi trafficking 292

14

to the plasma membrane and cell plate (Zheng et al., 2005; Speth et al., 2009; Ahn et 293

al., 2013), suggesting that the SCD complex’s role in membrane trafficking may be 294

through its interaction with RabE1. We utilized colocalization analysis and in vitro 295

binding studies to validate the interaction of the SCD complex with RabE1 GTPases. 296

CLSM imaging of root cells from Arabidopsis lines that express GFP-SCD1 and 297

mO-RabE1c showed colocalization between GFP-SCD1 and mO-RabE1c at distinct 298

intracellular punctae, some of which appear at or near the plasma membrane, as well 299

as at the cell plate (Figure 5A-5H). Fluorescence intensity line scans across the cell 300

plate (Figure 5C, 5G) and punctate structures (Figure 5F, 5H) revealed overlapping 301

intensity profiles of GFP-SCD1 and mO-RabE1c consistent with colocalization. 302

Additionally, colocalization was quantitatively verified for image pairs as described 303

above, with 100 Costes iterations returning a Costes P-value of 1.00 for both punctae 304

and cell plate localization with Pearson’s R values of 0.50 and 0.61 respectively. 305

To confirm the specificity of RabE1 GTPase interaction with the SCD complex, in 306

vitro binding studies were performed with GST-tagged RabE1 and members of other 307

Arabidopsis Rab GTPase families that function in various stages of the plant 308

biosynthetic secretory and endocytic pathways. Following incubation of immobilized 309

candidate GST-Rab fusion proteins with Arabidopsis cell extracts, bound proteins were 310

eluted and analyzed by immunoblotting. As shown in Figure 5I, SCD1 selectively bound 311

to RabE1c. Binding of SCD1 to GST alone, or to GST-tagged members of other Rab 312

GTPases families including RabA5, A4, A2, C1, D2, G3, and H1, was not detected 313

(Figure 5I, 5J). SCD complex association with any other Rab families was also not 314

detected by LC/MS/MS (Supplemental Data Set 1). Furthermore, both SCD1 and SCD2 315

bound to all RabE1 family members in vitro, (Figure 5J) but not to the GST control. 316

To further define the interaction between RabE1 and the SCD complex, we 317

tested the binding of SCD proteins from Arabidopsis cell extract to nucleotide state-318

specific RabE1c mutants in vitro. SCD1 and SCD2 bound to either wild-type RabE1c or 319

to the S29N mutant RabE1c, RabE1cS29N, which is analogous to dominant inhibitory H-320

rasS17N mutant that displays reduced nucleotide affinity (Farnsworth and Feig, 1991; 321

Nassar et al., 2010). By contrast, no binding was observed to the RabE1cQ74L mutant 322

(Figure 5K), which is predicted to have a reduced intrinsic hydrolysis rate of GTP as 323

15

demonstrated for other Rab proteins (Walworth et al., 1998). These data demonstrate 324

that the SCD1 and SCD2 bind RabE1c in a nucleotide-dependent manner. 325

To test whether the SCD complex functions in the activation of RabE, we 326

determined if overexpression of wild-type RabE1 would rescue the conditional growth 327

and developmental defects of partial loss-of-function scd1-1 mutants. Precedence for 328

this has been established as Rab Sec4p was shown to rescue the temperature-329

sensitive growth defects of mutant alleles of its GEF Sec2p, in S. cerevisiae (Nair et al., 330

16

1990; Walch-Solimena et al., 1997). To determine if RabE1 overexpression rescues the 331

17

scd1 mutant, we generated multiple independent transgenic scd1-1 mutant lines that 332

express wild-type N-terminal mOrange (mO)-tagged RabE1c (mO-RabE1c) under the 333

control of the constitutive 35S-CaMV promoter. Whereas partial loss-of-function scd1-1 334

mutant plants exhibit temperature-sensitive growth and stomatal cytokinesis defects at 335

temperatures at or above 22°C (Falbel et al., 2003; McMichael et al., 2013), scd1-1 336

mO-RabE1c grown at 22°C were found to be phenotypically similar to wild-type (Col-0) 337

plants at various stages of development including leaf expansion, inflorescence growth, 338

and guard cell formation (Figure 6A-6C). By contrast, overexpression of mO-RabD2b 339

(scd1-1 mO-RabD2b), which is involved in ER to Golgi trafficking (Zheng et al., 2005) 340

failed to suppress the growth defects of scd1-1 plants (Supplemental Figure 3A-3B). 341

To determine if RabE1 suppression of the scd1-1 phenotype was dependent on 342

nucleotide state we examined the effect of overexpression of GTPase deficient 343

“constitutively active” RabE1cQ74L and “inactive” RabE1cS29N mutants. Previous studies 344

have reported that expression of GFP-RabE1dQ74L in wild-type plants did not 345

significantly affect plant growth and development (Speth et al., 2009; Ahn et al., 2013). 346

Similar to scd1-1 plants that expressed wild-type mO-RabE1c, the scd1-1 mO-347

RabE1cQ74L lines showed significant rescue of the scd1-1 mutant growth and 348

development defects (Figure 6A-6C). However, whereas bolt height and stomatal 349

development were restored in the scd1 mO-RabE1cQ74L lines, the level of suppression 350

of the scd1-1 phenotype was significantly reduced relative to scd1-1 plants expressing 351

wild-type mO-RabE1c (Figure 6A-6C). In contrast to scd1-1 mO-RabE1c and scd1-1 352

mO-RabE1cQ74L lines, scd1-1 mO-RabE1cS29N plants were phenotypically 353

indistinguishable from the parental scd1-1 lines (Figure 6A-6C). Overexpression of mO-354

RabE1cS29N did not suppress or enhance growth and guard cell cytokinesis defects 355

associated with the scd1-1 mutation, providing further evidence that the scd1-1 356

phenotype is likely due to defects in its nucleotide state-specific interaction with RabE1. 357

Expression of mO-RabD2b, mO-RabE1c, mO-RabE1cQ74L, and mO-RabE1cS29N was 358

confirmed by RT-PCR and immunoblot analysis (Supplemental Figure 3C, 3D). Taken 359

together, the biochemical interaction and genetic suppression studies suggest that the 360

SCD complex is required in some manner for RabE1 activation. 361

362

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363

19

DISCUSSION 364

Here we demonstrate that the SCD1 and SCD2 proteins are members of the 365

SCD complex that functions in concert with the exocyst and RabE1s in post-Golgi 366

trafficking to the plasma membrane and cell plate (Figure 7). This conclusion is 367

supported by the results presented in this work as well as the previous phenotypic 368

characterization of scd, rabE1, and exocyst mutants (Speth et al., 2009; Fendrych et al., 369

2010; Ahn et al., 2013; Drdova et al., 2013; Rybak et al., 2014; Wu and Guo, 2015). 370

Exocyst mutants, including exo84b, sec6, and scd mutants show similar developmental 371

phenotypes including dwarfism, reduced leaf pavement cell expansion, and aberrant 372

guard mother cell cytokinesis (Falbel et al., 2003; Fendrych et al., 2010; McMichael et 373

al., 2013; Wu et al., 2013). At the cellular level, scd1 and scd2 share similar defects as 374

exocyst subunit loss-of-function mutants and ES2-treated cells (Zhang et al., 2016) in 375

exocytosis and endosomal recycling of the plasma membrane protein, PIN2-GFP, in the 376

presence of BFA (Drdova et al., 2013) (Figure 2), and show an accumulation of 377

secretory vesicles, indicating that the SCD and exocyst complexes function in post-378

Golgi vesicle targeting and fusion (Falbel et al., 2003; Fendrych et al., 2010). 379

Importantly, the SCD and exocyst complexes were found to colocalize at the cell plate 380

and in punctae adjacent to the plasma membrane (Figure 4B-4J) and to biochemically 381

interact by proteomic analysis of the SCD complex (Figure 1; Supplemental Data Set 1) 382

and by in vitro binding studies (Figure 4A). The interaction of the SCD and exocyst 383

complexes is further supported by the finding that ES2 inhibition of exocyst function 384

enhances growth and trafficking defects of scd1 and scd2 mutants (Figure 3). Given the 385

large number of EXO70 subunits, 23 in the Arabidopsis genome (Cvrckova et al., 2012), 386

ES2 experiments cannot distinguish whether the SCD complex functions in concert 387

solely with EXO70A1 and/or other EXO70-containing exocyst complexes in the 388

trafficking of proteins to the plasma membrane. 389

In addition to its association with the exocyst, the SCD complex was found to 390

interact with RabE1 GTPases, which have previously been shown to localize to the 391

Golgi, plasma membrane, and the cell plate (Zheng et al., 2005; Chow et al., 2008; 392

Speth et al., 2009). Similar to scd1 and scd2 mutants, silencing of NbRabE1 expression 393

or expression of dominant-negative NbRabE1S29N results in defects in protein trafficking 394

20

from the Golgi to the plasma membrane and inhibition of N. benthamiana plant growth 395

accompanied by defects in guard cell cytokinesis, polarized root hair expansion, and 396

pathogen defense responses (Falbel et al., 2003; Zheng et al., 2005; Speth et al., 2009; 397

21

Korasick et al., 2010; Ahn et al., 2013; McMichael et al., 2013). In this study, we show 398

that RabE1s bind to the SCD complex in a nucleotide-state specific manner and 399

colocalize at the cell plate and in punctae at or near the plasma membrane (Figure 1, 400

Supplemental Data Set 1, and Figure 5). 401

402

The SCD Complex Biochemically and Genetically Interacts with RabE1 403

The SCD1 subunit of the SCD complex contains an N-terminal tripartite DENN 404

domain, which in other systems has been demonstrated to possess GEF activity for 405

specific Rab GTPases (Allaire et al., 2010; Yoshimura et al., 2010), defining the DENN 406

domain as a protein module characteristic of vesicle-trafficking regulators. In particular, 407

DENN-domain-containing proteins connecdenn 1–3 are CCV-associated GEFs for 408

Rab35, which functions in CCV trafficking, endosomal recycling, actin regulation, and 409

cytokinesis in animals (Allaire et al., 2006; Kouranti et al., 2006; Patino-Lopez et al., 410

2008; Allaire et al., 2010; Marat et al., 2012). Our data showing that SCD complex binds 411

to “inactive” RabE1cS29N and not the “constitutively active” RabE1cQ74L (Figure 5K) is 412

intriguing and suggests that the SCD complex functions to activate members of the 413

RabE1 family. This hypothesis is further supported by the genetic evidence that 414

overexpression of wild-type RabE1c and constitutively active RabE1cQ74L, but not the 415

inactive RabE1cS29N mutant protein, suppressed the growth and developmental defects 416

in scd1-1 mutants (Figure 6). In a similar manner, overexpression of Sec4p in S. 417

cerevisiae rescues the temperature-sensitive growth defects of mutant alleles of its 418

GEF, Sec2p (Nair et al., 1990; Walch-Solimena et al., 1997), and expression of 419

“constitutively active” mutant RAB-A1cQ72L partially rescues the growth and 420

development of attrs130 mutant plants (Qi et al., 2011), which have defects in the plant 421

homolog of the yeast and mammalian Ypt32/Rab11 TRAPPII complex. In all these 422

cases, it is likely that when overexpressed the levels of GTP-bound or constitutive-423

active Rab GTPase are sufficient to overcome the need for GEF-catalyzed activation to 424

support vesicle trafficking. 425

In S. cerevisiae and mammalian cells, Sec4p and Rab8 are activated through the 426

structurally related GEFs Sec2p and Rabin8, respectively (Guo et al., 2013). Vesicle-427

associated GTP-bound Sec4p/Rab8 GTPases and their cognate GEFs interact with the 428

22

exocyst Sec15 subunit to promote docking and fusion of exocytic vesicles at the plasma 429

membrane (Huber et al., 1993; Guo et al., 1999; Feng et al., 2012). In contrast to 430

Sec4p- and Rab8-dependent trafficking, our understanding of the effectors involved in 431

RabE1 activation and post-Golgi vesicle docking/fusion is limited and unlike the 432

Sec4p/Rab8 GEFs, Sec2p and Rabin 8, and other DENN GEFs (Dong et al., 2007; 433

Allaire et al., 2010; Yoshimura et al., 2010; Marat et al., 2012; Vetter et al., 2015), the 434

architecture of the multisubunit SCD complex, with the exception of the SCD1 DENN 435

domain, is fundamentally distinct. Of interest are future experiments to determine if the 436

SCD complex functions as a GEF for RabE1. A complication in testing its GEF activity is 437

the multisubunit nature of the SCD complex as we are only able to purify relatively low 438

quantities of the complex from tissue-cultured cells, and individual subunits and 439

domains including the SCD1 DENN domain are not stable when individually purified, 440

thereby necessitating reconstitution of the intact complex. In addition, it will be important 441

to determine the molecular function(s) of the plant-specific protein SCD2. Furthermore, 442

the presence of two SCD2-like proteins (AT5G13260 and AT5G23700) in GS-SCD1, 443

GS-SCD2, and anti-SCD2 Co-IPs provides interesting insight for other subunits in the 444

SCD complex. While more work is required to fully delineate the subunit identity and 445

stoichiometry of the complex, it is tempting to speculate, given the co-fractionation of 446

these two proteins with SCD1 and SCD2, that they may be additional subunits of the 447

SCD complex. 448

Although we favor a model in which the SCD complex functions in the activation 449

of RabE1, we cannot rule out potential alternative roles for the SCD complex in RabE1-450

dependent membrane trafficking. In addition to GEFs and GAPs, Rab GTPases are 451

regulated by other factors including guanine nucleotide release factors, GDP 452

dissociation inhibitors (GDI), and GDI displacement factors (GDF), which serve to 453

deliver Rabs to membranes (Stenmark, 2009). The selective interaction of SCD 454

complex with bacterially expressed (i.e. non-prenylated) RabE1, (Figure 5) however, 455

appears to be distinct from that of GDIs which bind with high affinity exclusively to the 456

prenylated GDP-form of Rabs (Araki et al., 1990; Pylypenko et al., 2006) and display 457

limited specificity in Rab binding (Grosshans et al., 2006). Similarly, the GDF, Yip3 458

(Sivars et al., 2003), and the mammalian guanine-nucleotide release factor MSS4, 459

23

which has been proposed to function as a chaperone for nucleotide-free Rabs (Itzen et 460

al., 2006), bind to a number of distinct Rabs, unlike the SCD complex, which binds 461

selectively to RabE1s but not to other early or late secretory pathway Rabs (Figure 5I; 462

Supplemental Data Set 1). 463

464

The SCD Complex Functions in Exocytosis, Recycling and Endocytosis 465

The highly dynamic process of cell plate formation involves vesicle-mediated 466

delivery and retrieval of membrane from the division plane. Likewise, in non-dividing 467

cells the coordination of exocytosis and endocytosis is critical for polarized cell 468

expansion and the polarized distribution of plasma-membrane proteins. Interestingly, 469

scd1 and scd2 mutants display defects not only in exocytosis but also in the uptake of 470

the endocytic tracer dye FM4-64 (McMichael et al., 2013), and PIN2-GFP endocytosis 471

(Figure 2P, 2R). While the SCD Complex interaction network is composed of proteins 472

involved in exocytosis, scd mutants exhibit defects in both endocytosis and exocytosis 473

(Figure 7). Whether the SCD proteins function directly or indirectly in endocytosis 474

remains to be determined. Consistent with the latter, defects in retrograde trafficking 475

have been demonstrated to affect anterograde trafficking; for example, in human cells, 476

defects in GARP and VAMP4-dependent endosome to trans-Golgi network trafficking 477

result in an inhibition of recycling of factors necessary for the trafficking of proteins to 478

the plasma membrane (Hirata et al., 2015). By contrast, however, treatment of plant 479

cells with the small molecule Endosidin 16 (ES16), which inhibits RabA-dependent 480

exocytosis, does not affect endocytosis (Li et al., 2017). Nevertheless, it cannot be 481

excluded that the SCD/RabE1 and ES16-sensitive/RabA trafficking pathways are 482

distinct and that the SCD-dependent exocytic pathway is responsible for transporting 483

factors required for endocytosis and/or that the SCD complex functions directly in 484

endocytosis (Figure 7). Indeed, in S. cerevisiae, Sec4p and Sec2p have also been 485

shown to function in exocytosis and endocytosis (Riezman, 1985; Johansen et al., 486

2016) and work in diverse systems, including yeast, metazoans, and Trypanosoma 487

brucei has demonstrated a role for the exocyst in endocytosis (Riezman, 1985; Sommer 488

et al., 2005; Jose et al., 2015; Boehm et al., 2017). 489

24

Although scd1 and scd2 mutants exhibit strong growth and developmental 490

defects, PIN2-GFP exocytosis and/or endosomal recycling were found to be only 491

partially impaired in mutant root cells (Figure 2). This may reflect the existence of 492

RabE1 independent post-Golgi trafficking pathways including RabA-dependent 493

pathways that could compensate for the loss, in scd mutants, of RabE1-dependent 494

trafficking to the cell plate and/or plasma membrane. An alternative, but not mutually 495

exclusive, possibility is that the severe developmental defects observed in scd mutants 496

could be due to the lowered efficiency, as opposed to total inhibition, of the trafficking of 497

critical cell-type specific factors necessary at distinct times in plant development. 498

Our work demonstrates that SCD1 and SCD2 form a complex that functions in 499

the post-Golgi trafficking to the plasma membrane and cell plate, a process that is 500

mediated through interactions with RabE1 and the exocyst complex. 501

502

503

25

METHODS 504

505

Plant Materials 506

Columbia-0 lines used in this study were obtained from ABRC. scd1-1, scd1-2, and 507

scd2-1 lines are described in (Falbel et al., 2003; McMichael et al., 2013). PIN2-GFP 508

lines are described in (Xu and Scheres, 2005). 509

510

Transgenic Plants/scd1-1 Mutant Rescue 511

Transgenic plants created in this study were generated using the floral dip method, 512

using Agrobacterium tumefaciens strain EHA105 (Clough and Bent, 1998). Transgenic 513

scd1-1 mutant plants were transformed with the vector 35Spro:mO-RabE1c (or 514

35Spro:mO-RabD2b) (pSITE-II-5c) and the indicated point mutant constructs (Q74L or 515

S29N). Following selection with kanamycin on ½ MS +1% agar (w/v), T3 plants were 516

transferred to soil and grown at 22°C under 16-hour light (T12 fluorescent bulb ~160 517

µmol m-2 s-1) and 8-hour dark cycle and phenotypically analyzed for defects in bolt 518

height 60 days after germination. For the guard cell cytokinesis screen, stomata from 519

seedling leaves were analyzed in 14–20-day-old plants grown under continuous light 520

(T8 fluorescent bulb ~120 µmol m-2 s-1 grown on ½ MS + 0.6% agar (w/v). 521

Measurements included at least three independent transformants for each 522

overexpression line. Overexpression of mO-RabE1c and mutants was confirmed by 523

immunoblot analysis using anti-RabE1 antibodies (Speth et al., 2009), with anti-CDC48 524

served as a loading control (Rancour et al., 2002). 525

For GFP-SCD1 colocalization with RabE1c or SEC15B, scd1-1 ProSCD1:GFP-526

SCD1 (McMichael et al., 2013) lines were transformed as described above with either 527

35Spro:mO-RabE1c or UBQ10pro:RFP-SEC15B. Initial transformants were selected on 528

selective media (Kanamycin or Basta on ½ MS +0.6% agar) and propagated on soil. 529

Imaging of seedling roots was performed as described below. 530

531

Cloning/RT PCR 532

All PCR-generated cloning fragments used in this study were produced using Phusion 533

DNA polymerase (Thermo Fisher). All oligonucleotide primers were synthesized by 534

26

Integrated DNA Technologies. Detailed cloning information and primer sequences can 535

be found in Supplemental Tables 2 and 3. All clones were sequence verified by Sanger 536

Sequencing (UW-Madison Biotech Center). 537

Expression of mOrange-tagged Rabs in scd1-1 lines was verified by RT-PCR 538

with primers JM15 and JM16 specific for the mOrange tag, and isolation of mRNA was 539

verified in each sample using primers against UBQ10 (JM17 and JM18). Briefly, RNA 540

from seedlings was isolated using the RNeasy plant mini kit (Qiagen). Following 541

isolation 1 μg of RNA was used in a reverse transcriptase reaction with M-MuLV reverse 542

transcriptase (New England Biolabs) according to the manufacturer’s instructions. 543

Following RT-PCR, first-strand cDNA was diluted 25-fold in a PCR reaction using 544

primers JM15 and JM16 (mOrange) or JM17 and JM18 (UBQ10). 545

546

GST-Binding Experiments 547

GST-fusion proteins were purified using standard techniques. Briefly, frozen E. coli 548

pellets (containing IPTG induced over-night expression of GST-fusion proteins) were 549

thawed in GST buffer (PBS pH 7.4, 500mM NaCl, 0.1% Tween-20 and 1mM BME) in 550

the presence of 1mM lysozyme plus PMSF (1mM) and Benzamadine (1mM) then 551

subjected to sonication for 2 min of total on time (20sec on, 40sec off). Pellets were 552

clarified by centrifugation at 23,700 g before incubation with glutathione resin for 1 hour 553

at 4°C and batch washed 3x with GST buffer. For GST-pulldown experiments, 554

immobilized GST fusion proteins (50 μL) were incubated with 1.5 mL of T87 tissue 555

culture extract [3-day-old T87 cells were lysed in lysis buffer (50 mM Hepes pH 7.6, 100 556

mM KCl, 0.5 mM EDTA, 0.5 mM MgCl, 0.05% NP-40, and 10% glycerol + protease 557

and/or phosphatase inhibitors) as a 50:50 slurry of pelleted cells to lysis buffer with 558

depressurized nitrogen (1500 psi for 20 min on ice in a cell disruption vessel (Parr 559

Instruments)), and rotated for 15 min at 4°C after addition of 0.5% TX-100 followed by 560

clarification with ultracentrifugation at 134,878 g for 20 min in a TLA100.3 rotor] for 1 561

hour at 4°C then washed with lysis buffer (3x) before elution with 10mM glutathione in 562

elution buffer (50 mM Tris pH 8.1, 150 mM NaCl). Eluants were analyzed via SDS-563

PAGE and immunoblotting as described in figure legends. Affinity purified antibodies 564

27

against SCD1 and SCD2 were generated as described (Falbel et al., 2003; McMichael 565

et al., 2013). 566

567

Co-Immunoprecipitation/TAP Purification 568

Co-IPs were performed from cell extract prepared as described above (for each panel, 569

the same extract is used for each condition). For Co-IP, anti-SCD2 antibodies were 570

covalently linked to Protein A beads (Bio-Rad) using dimethylpimelimidate (Sigma). To 571

covalently link beads, Protein A beads were washed in PBS with 0.1% Tween-20 (PBS-572

t) three times. Beads were then resuspended in PBS-t plus 55 μg of SCD2 antibody 573

(McMichael et al., 2013) and incubated for 1 hour at room temperature. Following 574

incubation, beads were washed 3 times with PBS-t followed by 3 washes with 0.2 M 575

sodium borate pH 9.0. Dimethylpimelimidate (DMP, 22 mM) was added and the beads 576

were incubated for 30 min at room temperature. Beads were then washed 3 times with 577

0.2 M ethanolamine pH 8.5, 200 mM NaCl. For IP, antibody-linked beads (50 μL) were 578

incubated with ~ 1.5 mL of plant cell extract (prepared as described above) and washed 579

with lysis buffer (described above) 3 times, bound proteins were eluted with 100 mM 580

glycine and TCA precipitated. TCA pellets were analyzed using mass spectroscopy 581

(described below) or immunoblot techniques. 582

GS-TAP fusions to SCD1 and SCD2 (or GS-TAP GFP) were generated using 583

gateway cloning techniques into pKNGSTAP (Van Leene et al., 2011). Transgenic 584

PSBd cell lines were generated and TAP of GS-SCD1 and GS-SCD2 was performed as 585

described (Van Leene et al., 2011), with some modifications (see below). Briefly, 6-day-586

old transgenic PSBd cell lines expressing GS-SCD1, GS-SCD2, or GS-GFP were lysed 587

using depressurized nitrogen in lysis buffer (as described in GST-binding experiment 588

above). Following lysis, extracts were incubated with 0.5% TX-100 and clarified (as 589

described in GST-binding experiment above). After clarification, extracts were incubated 590

with human IgG Sepharose 6 (GE healthcare) for 1 hour at 4°C. Following incubation, 591

beads were batch washed with wash buffer (10 mM Tris pH 8.0, 150 mM NaCl, 0.1% 592

(v/v) NP-40, and 5% (v/v) ethylene glycol) 3 times, and incubated with ~200 units of 593

TEV protease for 60 min at 16°C. The supernatant was collected and incubated with 594

pre-equilibrated Streptavidin Sepharose Resin (GE Healthcare) for 1 hour at 4°C. 595

28

Following incubation, beads were batch washed with wash buffer 3x and eluted with 596

desthiobiotin in wash buffer. Eluants were TCA precipitated and analyzed by 597

immunoblot or mass spectroscopy analysis. 598

599

Mass Spectroscopy 600

Enzymatic “In Liquid” Digestion 601

Purified protein samples were TCA/acetone precipitated [10% TCA, 28% acetone final] 602

then pellets re-solubilized and denatured in 7.5 μl of 8M Urea / 50mM NH4HCO3 (pH8.5) 603

/ 1mM TrisHCl for 5 minutes. Samples were subsequently diluted to 30 μl for a reduction 604

step with 1.25 μl of 25 mM DTT, 2.5 μl MeOH, 18.75 μl 25mM NH4HCO3 (pH8.5). 605

Samples were incubated at 50̊C for 15 minutes and cooled on ice to room temperature 606

and then 1.5μl of 55 mM IAA was added for alkylation. Samples were incubated in 607

darkness at room temperature for 15 minutes. Reactions were quenched by adding 4 μl 608

of 25 mM DTT. Subsequently 2 μl of Trypsin/LysC solution (100ng/μl Trypsin/LysC Mix 609

from PROMEGA Corp. in 25mM NH4HCO3) and 12.5 μl of 25 mM NH4HCO3 (pH8.5) 610

were added to generate a 50 µl final volume. Digestion was conducted for 2 hours at 611

42°C then an additional 1 µl of trypsin/LysC solution was added. Digestion proceeded 612

overnight at 37°C. Reactions were terminated by acidification with 2.5% TFA 613

(Trifluoroacetic Acid) added to a 0.3% final concentration. 614

NanoLC-MS/MS 615

Digests were cleaned up using OMIX C18 SPE cartridges (Agilent, Palo Alto, CA) per 616

manufacturer protocol and eluted in 20 µl of 60/40/0.1% ACN/H2O/TFA, dried to 617

completion in the speed-vac and finally reconstituted in 20 µl of 0.1% formic acid. 618

Peptides were analyzed by nanoLC-MS/MS using the Agilent 1100 nanoflow system 619

(Agilent) connected to a new generation hybrid linear ion trap-orbitrap mass 620

spectrometer (LTQ-Orbitrap Elite™, Thermo Fisher Scientific) equipped with an EASY-621

Spray™ electrospray source. Chromatography of peptides prior to mass spectral 622

analysis was accomplished using capillary emitter column (PepMap® C18, 3 µM, 100 Å, 623

150x0.075 mm, Thermo Fisher Scientific) onto which 3 µl of extracted peptides was 624

automatically loaded. The NanoHPLC system delivered solvents A: 0.1% (v/v) formic 625

acid, and B: 99.9% (v/v) acetonitrile, 0.1% (v/v) formic acid, at 0.50 µL/min to load the 626

29

peptides (over a 30 minute period) and 0.2 µl/min to elute peptides directly into the 627

nano-electrospray with gradual gradient from 3% (v/v) B to 30% (v/v) B over 77 minutes 628

and concluded with 5 minute fast gradient from 30% (v/v) B to 50% (v/v) B, at which 629

time a 5 minute flash-out from 50-95% (v/v) B took place. As peptides eluted from the 630

HPLC-column/electrospray source survey MS scans were acquired in the Orbitrap with 631

a resolution of 120,000 followed by MS2 fragmentation of the 20 most intense peptides 632

detected in the MS1 scan from 300 to 2000 m/z; redundancy was limited by dynamic 633

exclusion. 634

Data analysis 635

Raw MS/MS data were converted to mgf file format using MSConvert (ProteoWizard: 636

Open Source Software for Rapid Proteomics Tools Development) for downstream 637

analysis. Resulting mgf files were used to search against Arabidopsis thaliana TAIR10 638

amino acid sequence database with a decoy reverse entries and a list of common 639

contaminants (70,857 total entries) using in-house Mascot search engine 2.2.07 (Matrix 640

Science) with variable Methionine oxidation with Asparagine and Glutamine 641

deamidation. Peptide mass tolerance was set at 15 ppm and fragment mass at 0.6 Da. 642

Protein annotations, significance of identification and spectral-based quantification was 643

done with help of Scaffold software (version 4.3.2, Proteome Software Inc., Portland, 644

OR). Peptide identifications were accepted if they exceeded specific database search 645

engine thresholds. Mascot identifications required that at least ion scores must be 646

greater than both the associated identity scores and 20. Protein identifications were 647

accepted if they contained at least 2 identified peptides. Protein probabilities were 648

assigned by the Protein Prophet algorithm (Nesvizhskii et al., 2003). Proteins that 649

contained similar peptides and could not be differentiated based on MS/MS analysis 650

alone were grouped to satisfy the principles of parsimony. 651

652

Glycerol Gradient Velocity Sedimentation 653

T87 tissue culture extract generated (as described in GST-pulldown above) and then 654

separated on a 10–40% (v/v) glycerol gradient by centrifugation at 35,000 rpm for 16 655

hours at 4°C in an SW 50.1 rotor. Following centrifugation, fractions were collected and 656

analyzed by immunoblot analysis following by SDS-PAGE as described in figure 657

30

legends. Densitometry was measured using Photoshop, graphs were generated in 658

GraphPad Prism. For protein standards, the following proteins were used: ovalbumin 659

(Sigma), bovine serum albumin (Sigma), yeast alcohol dehydrogenase (Sigma), sweet 660

potato beta-amylase (Sigma), catalase (Sigma), apoferritin (MP Biomedicals), 661

thyroglobulin(Sigma). Following centrifugation, SDS-PAGE gels were Coomassie 662

stained and quantified as described above and used to generate standard curves from 663

which experimental S-values were determined to make native molecular weight 664

determinations. 665

666

Microscopy 667

All colocalization experiments, ES2-treated PIN2-GFP experiments, and GFP-SEC15B 668

experiments were conducted on a CLSM (Nikon A1R-Si+). For colocalization studies, 669

roots of 5-day-old seedlings were grown on ½ MS plus 1% agar (continuous light T8 670

fluorescent bulb ~120 µmol m-2 s-1) (w/v) and imaged. For ES2 treatments, 5-day-old 671

seedlings grown on ½ MS 1% agar (w/v) plates were placed in ½ MS plus 40 µM ES2 672

for 2 hours at room temperature, roots were imaged by CLSM. A single focal plane was 673

used to determine the number of punctae per cell. For CHX plus ES2 experiments, 674

seedlings were grown as described above and left untreated, or pretreated with 50 µM 675

CHX for 30 min before additional treatment with 50 µM CHX with and without 40 µM 676

ES2 for 120 min. To verify our colocalization analysis, images were processed using 677

ImageJ Coloc 2 plug-in. Briefly, background subtraction from candidate images was 678

performed using rolling ball subtraction with a 200-pixel ball size. ROIs were selected 679

and run through Coloc 2 plug-in with 100 Costes randomizations using a PSF of 3. All 680

graphs were generated in GraphPad Prism. All line scans were performed using NIS-681

Elements software with a 2-pixel width, intensity over distance of the line scan was 682

plotted using GraphPad Prism. 683

For PIN2-GFP plus BFA trafficking experiments, seedlings were pretreated with 684

BFA for 60 min in ½ MS liquid media, and followed by washout with ½ MS liquid 685

medium for different lengths of time (0, 20, 40, and 60 min). For PIN2-GFP BFA+CHX 686

trafficking experiments, seedlings were pretreated with CHX for 30 min in ½ MS liquid 687

media, followed by washout with CHX and BFA for 60 min in ½ MS liquid media, and/or 688

31

finally by washout with ½ MS liquid medium for different lengths of time (0, 20, 40, and 689

60 min). Following treatment, seedlings were imaged by CLSM (Leica TCS SP5 AOBS). 690

691

Plant Growth with ES2 692

Wild-type (Col-0), scd1-1, scd1-2 and scd 2-1 mutant plants were grown vertically on ½ 693

MS 1% (w/v) agar with either DMSO or 30 µM ES2, under constant light (T8 fluorescent 694

bulb ~120 µmol m-2 s-1) at 22°C. Seedling images were taken using a digital camera 695

(Nikon CoolPix S8100) and the root length of 13-day-old seedlings was measured using 696

available tools in Photoshop. Graphs were generated using GraphPad Prism. 697

698

Quantification and Statistical Analysis 699

All statistically significance calculations were carried out using the Student’s t test using 700

GraphPad Prism software, and are shown in Supplemental Data Set 2. For PIN2-GFP 701

trafficking in the presence of BFA and/or CHX, sample sizes, P values are indicated in 702

the figure legends. For ES2-treated seedling growth experiments, P values are 703

indicated in the figure legend, sample sizes for DMSO treated are: Col-0 (26 roots), 704

scd1-1 (26 roots), scd1-2 (28 roots), scd 2-1 (10 roots). Sample sizes for ES2 treated 705

are: Col-0 (26 roots), scd1-1 (34 roots), scd1-2 (26 roots) and scd2-1 (17 roots). For 706

PIN2-GFP ES2 treatment experiments, the P values are indicated in the figure legends, 707

sample sizes are Col-0 (8 roots, 367 cells), scd1-2 (5 roots, 210 cells), and scd2-1 (4 708

roots, 221 cells). Significance calculations of colocalization experiments are described 709

in the “Microscopy” section. 710

711

Accession Numbers 712

The accession numbers for DNA sequences used in this study are as follows: 713

SCD1: AT1G4940, SCD2: AT3G48860, RabE1a: AT3G53610, RabE1b: AT5G59840, 714

RabE1c: AT3G46060, RabE1d: AT5G03520, RabE1e: AT3G09900, RabA5b: 715

AT3G07410, RabH1c: AT4G98890, RabC1: AT1G43890, RabA5e: AT1G05810, 716

RabA4a: AT5G65270, RabD2b: AT5G47200, SEC15B: AT4G02350. 717

718

Supplemental Data 719

32

Supplemental Figure 1. Tandem Affinity Purified GS-GFP. 720

Supplemental Figure 2. PIN2-GFP Trafficking in the Presence of CHX and ES2. 721

Supplemental Figure 3. RabD2b Overexpression Does Not Rescue scd1-1. 722

Supplemental Table 1. Mascot Protein Scores and Exponentially Modified Protein 723

Abundance Index (emPAI) for GS-TAP purifications. 724

Supplemental Table 2. Constructs Used in This Study 725

Supplemental Table 3. Primers Used in This Study 726

Supplemental Data Set 1. Detailed LC/MS/MS Data Sheet of Proteins Identified with 727

GS-TAP and Co-IP Experiments Performed in This Study. 728

Supplemental Data Set 2. T-test Tables 729

730

AUTHOR CONTRIBUTIONS 731

J.R.M., J.J.C., J.P., and S.Y.B. designed research; J.R.M., T. H., C. W., J.J.C., and732

Y.T., performed experiments; J.R.M., T. H., C. W., Y.T., J.P., and S.Y.B. analyzed data;733

J.R.M., and S.Y.B. wrote the paper.734

735

ACKNOWLEDGMENTS 736

The authors would like to thank members of the Bednarek lab and Richard Amasino for 737

helpful discussions and critically reading the manuscript. We also would like to thank 738

Elle Kielar Grevstad (UW-Madison Biochemistry) for assistance with confocal 739

microscopy and data analysis. We also thank Grzegorz Sabat for performing Mass 740

Spectroscopy (UW-Madison Biotechnology Center) and for help with data analysis. We 741

also like to thank Glenn Hicks for providing ES2 and Christopher Grefen for 742

pUBQN:XFP-Dest vectors. We also thank Sheng Yang He for the kind gift of RabE1 743

antibody. J.M. is supported by a fellowship from the National Institute of Health 744

(F32 GM112446-02). This work was supported by funding to S.Y.B from the UW 745

Madison College of Agriculture and Life Sciences and the National Science Foundation 746

(award No. 1121998 and 1614915), and to J.P. from the National Natural Science 747

Foundation of China (No. 31670283, 31370313, and 91317304). 748

749

750

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DOI 10.1105/tpc.17.00409; originally published online September 29, 2017;Plant Cell

Sebastian BednarekJonathan Russell Mayers, Tianwei Hu, Chao Wang, Jessica J Càrdenas, Yuqi Tan, Jianwei Pan and

CytokinesisSCD1 and SCD2 Form a Complex that Functions with the Exocyst and RabE1 in Exocytosis and

This information is current as of May 20, 2019

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SCD1 and SCD2 Form a Complex that Functions with the ... · 1 RESEARCH ARTICLE 2 3 SCD1 and SCD2 Form a Complex that Functions with the Exocyst and 4 RabE1 in Exocytosis and Cytokinesis