Short title: TARK1 regulates pre-invasion defense 2 Corresponding … · 8 Authors: Andrew R. Guzman, Jung-Gun Kim, Kyle W. Taylor, Daniel Lanver and Mary 9 Beth Mudgett 10 11 Affiliations:

1

Short title: TARK1 regulates pre-invasion defense 1

2

Corresponding Author: Professor Mary Beth Mudgett ([email protected]) 3

4

Title: Tomato Atypical Receptor Kinase1 is involved in the regulation of pre-invasion 5

defense 6

7

Authors: Andrew R. Guzman, Jung-Gun Kim, Kyle W. Taylor, Daniel Lanver and Mary 8

Beth Mudgett 9

10

Affiliations: Department of Biology, Stanford University, Stanford, CA 94305-5020, 11

USA 12

13

One sentence summary: A Leucine Rich Repeat Receptor-like pseudokinase is 14

involved in the regulation of stomatal movement in response to bacteria and biotic 15

elicitors, affecting resistance to bacterial invasion. 16

17

Author Contributions 18

A.R.G., K.W.T., M.B.M. and J-G.K. designed the research; A.R.G., J-G.K., K.W.T. and 19

D.L. performed the experiments; A.R.G., J-G.K. and K.W.T. analyzed the data; A.R.G., 20

J-G.K., K.W.T. and M.B.M interpreted data; and A.R.G. and M.B.M wrote the 21

manuscript. 22

Plant Physiology Preview. Published on May 12, 2020, as DOI:10.1104/pp.19.01400

Copyright 2020 by the American Society of Plant Biologists

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2

Present address: Stanford University, 371 Jane Stanford Way, 228A Gilbert 23

Biosciences, Stanford, CA 94305-5020 24

25

Abstract 26

27

Tomato Atypical Receptor Kinase 1 (TARK1) is a pseudokinase required for post-28

invasion immunity. TARK1 was originally identified as a target of the Xanthomonas 29

euvesicatoria effector protein Xanthomonas outer protein N (XopN), a suppressor of 30

early defense signaling. How TARK1 participates in immune signal transduction is not 31

well understood. To gain insight into TARK1’s role in tomato (Solanum lycopersicum) 32

immunity, we used a proteomics approach to isolate and identify TARK1-associated 33

immune complexes formed during infection. We found that TARK1 interacts with 34

proteins predicted to be associated with stomatal movement. TARK1 CRISPR mutants 35

and overexpression (OE) lines did not display differences in light-induced stomatal 36

opening or abscisic acid-induced stomatal closure; however, they did show altered 37

stomatal movement responses to bacteria and biotic elicitors. Notably, we found that 38

TARK1 CRISPR plants were resistant to Pst WT (Pseudomonas syringae pathovar 39

tomato strain DC300)-induced stomatal reopening, and TARK1 OE plants were 40

insensitive to Pst COR- (Pst strain DC3118, coronatine deficit)-induced stomatal closure. 41

We also found that TARK1 OE in leaves resulted in increased susceptibility to bacterial 42

invasion. Collectively, our results indicate that TARK1 functions in stomatal movement 43

only in response to biotic elicitors and support a model in which TARK1 regulates 44

stomatal opening post-elicitation. 45

46



3

Introduction 47

Pathogens have developed a number of different strategies to invade and multiply 48

within host plant tissues and plants have evolved countermeasures to combat 49

encroaching pathogens. One of the first stages dictating antagonistic interactions 50

between host and pathogen begins with the perception of microbial patterns called 51

microbe-associated molecular patterns (MAMPs), which are detected by cell surface 52

localized pattern recognition receptors (PRRs) (Jones and Dangl, 2006). This response 53

initiates signaling cascades that generate reactive oxygen species (ROS), activate 54

mitogen-activated protein kinases (MAPKs), and transcribe defense related genes 55

aimed to limit pathogen growth and host invasion. 56

57

For leaf-associated bacteria, early recognition events often occur at the surface of the 58

leaf and ports of entry into leaf tissue. Bacteria gain access to the nutrient rich 59

extracellular spaces within leaf tissue (the apoplast) by invading wounds and natural 60

openings. One of the primary structures that gate access to the apoplast and restrict 61

pathogen invasion are guard cell pores called stomata. Given that a primary role of 62

stomata is to exchange CO2 and water with the environment (Kim et al., 2010), leaf 63

tissues are vulnerable to microbial invasion during periods of transpiration and 64

photosynthesis. Detection of bacterial MAMPs by PRRs within leaves ultimately leads to 65

stomatal closure, a defense response referred to as stomatal immunity (Melotto et al., 66

2006; Zeng and He, 2010). 67

68

Most of the molecular mechanisms describing stomatal immunity against 69

phytopathogenic bacteria come from the studies using Arabidopsis thaliana and 70

Pseudomonas syringae as a model host-pathogen system. For example, PRR protein 71

complexes in Arabidopsis have been shown to be of particular importance in stomatal 72

immunity especially in the context of ROS production and signaling. The NADPH 73

oxidase RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) plays a critical role 74

in ROS production in leaves (Nühse et al., 2007; Zhang et al., 2007; Mersmann et al., 75

2010). RBOHD has also shown to be required for MAMP-induced stomatal closure 76

(Mersmann et al., 2010; Macho et al., 2012). RBOHD is part of an important PRR 77



4

complex involving the flagellin receptor FLAGELLIN SENSING2 (FLS2) and the 78

receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE1 (BIK1) (Li et al., 2014). 79

MAMP perception through FLS2, as well as the EF-TU RECEPTOR (EFR), leads to 80

RBOHD phosphorylation by BIK1 and this regulation of RBOHD activity induces 81

stomatal closure and contributes to resistance to surface inoculated bacteria (Kadota et 82

al., 2014; Li et al., 2014). These studies highlight core Arabidopsis protein complexes 83

involved in regulation of stomatal movement. By contrast, there is limited data 84

describing protein complexes involved in this process outside of the Brassicaceae. 85

86

In addition to MAMP perception, the plant hormones abscisic acid (ABA), salicylic acid 87

(SA) and jasmonic acid isoleucine (JA-Ile) play integral roles in regulating stomatal 88

immunity. ABA is known to induce stomatal closure and is required for Pseudomonas 89

syringae pathovar (pv.) tomato strain DC3000 (Pst) and MAMP induced stomatal 90

closure in multiple plant species (Melotto et al., 2006; Du et al., 2014). In Arabidopsis, 91

ABA deficient mutant aba3-1 does not close stomata in response to Pst, or the bacterial 92

elicitors flagellin (Flg22) and lipopolysaccharide (LPS) (Melotto et al., 2006). A similar 93

response has been observed with the tomato ABA biosynthesis mutant notabilis (not), 94

where Pst-induced stomatal closure is not observed (Du et al., 2014). Treatment with 95

the defense hormone SA has also been shown to induce stomatal closure (Khokon et 96

al., 2011; Zeng et al., 2011). Arabidopsis mutants defective in SA biosynthesis (ics1 and 97

eds5/sid1/scord3) and SA signaling (npr1) are compromised in bacterial- and MAMP-98

induced stomatal closure (Melotto et al., 2006; Zeng and He, 2010; Zeng et al., 2011). 99

By contrast, JA-Ile, the most active form of jasmonic acid produced in plants in 100

response to wounding, promotes stomatal opening. Direct application of JA-Ile to dark 101

treated Ipomea tricolor stomata induced stomatal opening (Okada et al., 2009). 102

Arabidopsis coronatine insensitve1 (coi1) mutants which lack the JA-Ile receptor have 103

constitutively smaller stomata apertures (Sheard et al., 2010; Panchal et al., 2016a). 104

These pharmacological and genetic studies highlight the importance of ABA and SA as 105

positive regulators of stomatal immunity, and JA-Ile as a negative regulator. 106

107



5

Pathogen manipulation of stomata has been most extensively shown with Pst through 108

the secretion of small molecules and delivery of effector proteins into host plant cells 109

(Melotto et al., 2017). The Pst small molecule coronatine (COR) has been well 110

characterized for its role in inducing stomatal reopening. COR is a hormone mimic that 111

closely resembles JA-Ile (Krumm et al., 1995; Staswick and Tiryaki, 2004; Melotto et al., 112

2006; Okada et al., 2009). Both JA-Ile and COR have been shown to bind to the 113

Arabidopsis jasmonic acid co-receptor COI1 (Katsir et al., 2008). When COR binds to 114

COI1, downstream signaling leads to the induction of NAC transcription factors which 115

repress SA biosynthesis genes and induce SA metabolism genes thereby suppressing 116

SA accumulation and promoting stomatal opening (Zheng et al., 2012; Du et al., 2014; 117

Gimenez-Ibanez et al., 2017). Thus, COR functions as a bacterial virulence factor by 118

interfering with stomatal immunity and SA-dependent defense responses. 119

120

In this work, we investigated the role of the pseudokinase TARK1 (Tomato Atypical 121

Receptor Kinase1) in the regulation of stomatal movements and pre-invasion immune 122

responses in tomato plants in response to pathogen challenge. TARK1 is a leucine-rich 123

repeat receptor-like kinase (LRR-RLK) belonging to the LRR XIIb RLK subfamily 124

(Sakamoto et al., 2012). TARK1 was originally identified in a screen to identify targets of 125

XopN, a Xanthomonas euvesicatoria (Xe) virulence factor secreted by the type III 126

secretion system. TARK1 was shown to be required for tomato immunity and leaf 127

symptom development in response to Xe infection. While the function of TARK1 has 128

remained elusive, it is known to be localized to the plasma membrane and possess a 129

pseudokinase domain (Kim et al., 2009). 130

131

Pseudokinases like TARK1 are prevalent in many plant species representing 13% of all 132

Arabidopsis kinases and 20% of Arabidopsis RLKs (Castells and Casacuberta, 2007). 133

There is growing evidence that pseudokinases in plants and animals play important 134

roles in signaling cascades and can serve as scaffolding proteins that either directly or 135

indirectly regulate protein-protein interactions (Langeberg and Scott, 2015). In plants, 136

multiple pseudokinases have been associated with diverse biological processes ranging 137

from the regulation of immune complex formation and signaling, to modulation of ABA-138



6

based signaling during seedling development (Lewis et al., 2013; Blaum et al., 2014; 139

Halter et al., 2014a; Halter et al., 2014b; Kumar et al., 2017). Recent work has also 140

shown that the LRR-RLK pseudokinase GUARD CELL HYDROGEN PEROXIDE-141

RESISTANT1 (GHR1) plays an important role in stomatal closure (Hua et al., 2012; 142

Sierla et al., 2018). 143

144

Here we provide evidence linking TARK1 to stomatal immunity in tomato. Using a 145

proteomics approach, we discovered that TARK1 interacts with tomato proteins 146

predicted to be associated with stomatal movement and disease resistance signaling. 147

Analysis of transgenic tomato mutant lines with altered TARK1 levels revealed that 148

TARK1 is required for stomatal responses triggered by biotic elicitors, supporting a 149

model in which TARK1 regulates stomata opening post-elicitation. Our findings 150

implicate TARK1 in both pre- and post-invasion immunity in tomato and describe 151

components of putative TARK1-associated complexes operating during pathogen-152

triggered immunity. 153

154

155



7

Results 156

157

TARK1 interacts with proteins associated with stomatal movement 158

Previously, it was shown that TARK1 is involved in tomato disease resistance in 159

response to Xanthomonas euvesicatoria (Xe) pathogenesis. Reduction in TARK1 160

mRNA expression using a hairpin RNA construct led to enhanced susceptibility to Xe 161

infection in post-invasion immunity assays (Kim et al., 2009). TARK1-silenced plants 162

also presented less disease symptoms in response to Xe infection, indicating that 163

TARK1 plays a role not only in immune signaling in response to Xe but also disease 164

symptom development. Considering that TARK1 plays a role in tomato immunity but 165

lacks any detectible kinase activity in vitro (Kim et al., 2009), we hypothesized that 166

TARK1 interacts with plasma membrane proteins, potentially PRRs, or other 167

membrane-associated proteins to regulate and/or amplify immune signal transduction 168

post-bacterial invasion. 169

170

To test this hypothesis, we used an immunoprecipitation-proteomics approach to purify 171

and identify TARK1-associated protein complexes. In service to this, we generated 172

TARK1 transgenic overexpression (OE) lines by transforming VF36 tomato plants with a 173

P35S::TARK1-GFP construct containing the 35S Cauliflower Mosaic Virus promoter 174

constitutively expressing TARK1 with a C-terminal green fluorescent protein (GFP) 175

epitope tag (i.e. TARK1-GFP; Fig. 1A). The TARK1 OE line used in this study 176

constitutively expresses TARK1-GFP in uninfected leaves (Fig. 1B). 177

178

To identify TARK1 immune complexes formed during pathogen-triggered immunity (PTI), 179

TARK1 OE leaves were inoculated with a high dose of the Xe type-3 secretion system 180

(T3SS) mutant Xe ∆hrcV. This strain lacks a key structural component necessary for the 181

T3SS to deliver effector proteins from the pathogen to the host (Rossier et al., 1999). Xe 182

∆hrcV infection represents activation of PTI because tomato plants susceptible to WT 183

Xe are now able to detect Xe PAMPs in the absence of Xe effector proteins and mount 184

a stronger basal tomato defense response (Taylor et al., 2012). Notably, we detected 185

more TARK1-GFP protein in TARK1 OE leaves infected with Xe ∆hrcV (Fig. 1B) using 186



8

polyclonal peptide antibodies that recognizes the putative juxtamembrane domain 187



9

(amino acids 295-312), the region N-terminal to the pseudokinase domain (Fig. 1A). We 188

also detected the accumulation of the endogenous TARK1 protein in WT and TARK1 189

OE leaves infected with Xe ∆hrcV, but not in uninfected leaf tissue (Fig. 1B). These data 190

reveal that TARK1 protein levels are regulated in tomato leaves in response to biotic 191

stress. 192

193

Twenty-four hours following Xe ∆hrcV inoculation, TARK1-GFP was purified from 194

infected TARK1 OE tomato leaves using GFP magnetic agarose beads. WT or leaves 195

overexpressing GFP alone were used as controls. After isolation of TARK1-associated 196

complexes, protein samples were analyzed using liquid chromatography and mass 197

spectrometry analysis (LC-MS/MS). Of the peptides detected, we selected for candidate 198

proteins that were enriched in the TARK1-GFP immunoprecipitation (IP) over the GFP 199

control IP. We then selected for proteins whose mRNA abundance had increased 200

during PTI (greater than 1.8-fold increase). We determined this by utilizing a tomato 201

RNAseq data set that compared a high dose Xe ∆hrcV infection to mock treatment 202

(Stork, 2014). We also excluded proteins with known or proposed functions (Gene 203

Ontology designations, (Ashburner et al., 2000; The Gene Ontology Consortium, 2019)) 204

linked to chloroplast function and photosynthesis. Using these criteria, we identified 17 205

candidate proteins that associated with TARK1 during PTI (Supplemental Table S1). 206

207

Gene ontology enrichment analysis of the candidate tomato proteins did not reveal a 208

significant enrichment in any biological process. When we ran the same analysis using 209

the closest Arabidopsis homologs of the candidate proteins, there was a substantial 210

enrichment in proton transmembrane transport. To expand our search, we 211

bioinformatically mined available online datasets and literature to uncover potential 212

biological functions associated with each tomato candidate and its closest Arabidopsis 213

homolog. From these analyses, we found that the 17 candidates fell into 3 major 214

categories – defense, membrane and vesicle transport, and mitochondrial function 215

(Supplemental table S1). 216



10

Of the defense related candidates, three proteins (plasma membrane H+-ATPase HA4 217

(Solyc07g017780), lipoxygenase LOX8 (Solyc08g029000) and LRR-RLK 218

(Solyc04g074000; herein referred to as RLK15)) share homology with Arabidopsis 219

proteins that regulate stomatal functions (Fig 1C). Previous phylogenetic analysis 220

utilizing tomato and Arabidopsis H+-ATPase sequences found that tomato HA4 clusters 221

closest with Arabidopsis AHA1 and AHA2 (Liu et al., 2016), which are known to play 222

important roles in guard cell movement during pathogen attack. Mutant Arabidopsis 223

leaves with constitutively active AHA1 possess open stomata that do not close in 224

response to ABA or PTI induced stomatal closure (Merlot et al., 2007; Liu et al., 2009). 225

LOX8’s closest homolog in Arabidopsis is LIPOXYGENASE1 (LOX1) based on Basic 226

Local Alignment protein (BLASTp; (Altschul et al., 1997)) and phylogenetic analysis, 227

which places tomato LOX8 and Arabidopsis LOX1 in the 9-LOX subfamily (Upadhyay 228

and Mattoo, 2018). Studies of Arabidopsis LOX1 indicate that it is required for 229

resistance to Pst spray inoculation and MAMP induced stomatal closure (Montillet et al., 230

2013). Tomato RLK15’s closest homolog in Arabidopsis is MDS1-INTERACTING 231

RECEPTOR LIKE KINASE2 (MIK2). RLK15 and MIK2 are found within LRR-RLK 232

subfamily XIIb as determined by sequence alignment of all tomato and Arabidopsis 233

LRR-RLK kinase domain sequences (Sakamoto et al., 2012). In Arabidopsis, MIK2 has 234

been shown to interact with the heteromeric guanine nucleotide-binding (G) protein β-235

subunit AGB1, which is required for RAPID ALKALINIZATION FACTOR1 (RALF1) 236

induced stomatal closure (Yu et al., 2018). In addition to interaction with MIK2, AGB1 237

was also shown to interact with RECEPTOR-LIKE KINASE1 (RKL1), the closest 238

Arabidopsis homolog of TARK1. 239

To confirm interaction between TARK1 and HA4, RLK15 or LOX8, we fused the HA 240

epitope to TARK1 (TARK1-3xHA) and GFP to the candidate interactors (GFP-HA4, 241

RLK15-GFP, LOX8-GFP) and then overexpressed pairs of proteins in Nicotiana 242

benthamiana using Agrobacterium tumefaciens–mediated transient expression. Co-IP 243

assays were then performed using GFP magnetic agarose beads. A homologous LRR-244

RLK to TARK1 (referred to as TARK1-Like or TARK1L; Solyc11g011020) was tagged 245

and used as a control to assess specificity of the interactions. TARK1L is predicted to 246



11

encode a RLK that shares 67% similarity to TARK1 at the amino acid level. It has 5 247

LRRs and the same sequence variation as TARK1 for the conserved catalytic residue in 248

subdomain VIb in the kinase domain, indicating that it may be a pseudokinase (Kim et 249

al., 2009). TARK1-3xHA was enriched in the co-IPs with GFP-HA4 or RLK15-GFP 250

compared to the co-IPs with TARK1L-3xHA (Fig. 1D). LOX8 interaction with TARK1 251

however was not detected using this assay (Fig 1D). 252

253

Collectively, our biochemical studies suggest that TARK1 associates with multiple 254

proteins during PTI (Supplemental table S1). Confirmation of TARK1 interaction with 255

HA4 and RLK15 provides additional evidence for complex formation inside plant cells 256

and reveals a potential functional link between TARK1 and stomatal movement. 257

258

TARK1 is not required for light induced opening or ABA induced closure of 259

stomata 260

To investigate TARK1’s potential role in stomatal movement, we generated transgenic 261

tark1 mutant tomato lines in the VF36 background using CRISPR Cas9 mediated 262

genome editing. Mutants were produced using a single guide RNA targeting nucleotides 263

94 to 113 of TARK1. The mutant allele used in this study has a 1 bp insertion after 264

nucleotide 109 in the coding region of TARK1 which results in a predicted premature 265

stop after amino acid 42 (Fig. 1A). This tark1 mutant is herein referred to as TARK1 CR. 266

We were unable to detect the accumulation of the full-length TARK1 protein in TARK1 267

CR leaves inoculated with Xe ∆hrcV using polyclonal antibodies recognizing a TARK1 268

peptide located in the juxtamembrane domain (Fig. 1B). These data suggest that this 269

TARK1 CR is a loss-of-function mutant line. 270

271

Following the generation of the TARK1 CR lines, we determined if TARK1 was involved 272

in light induced stomatal opening. We adapted an established leaf imaging assay that is 273

used for Arabidopsis (Chitrakar and Melotto, 2010) to monitor stomatal apertures in 274

intact tomato leaf tissue. Leaf pieces of WT, TARK1 CR and TARK1 OE lines were 275

floated on control buffer and then stomatal apertures were measured every hour for 6 276

hours after the transition from the dark to the light. At 1 hour post-light exposure, all 277



12

genotypes had closed stomata (Supplemental Fig. S1A), indicating that neither TARK1 278

CR or OE had constitutively open stomata. Maximal stomata apertures were similar 279

between genotypes and this was reached after 3-4 hours post-light exposure 280

(Supplemental Fig. S1A). These data suggest that there is no difference in maximal 281

stomata aperture or light induced stomatal opening among the genotypes. 282

283

We then treated leaves with ABA to determine if there was a difference in stomatal 284

closure responses. ABA is a key signaling hormone associated with both abiotic and 285

biotic stress responses and induces stomatal closure (Zhang, 2014). We first 286

determined the dose response of tomato stomata to ABA treatment to find the optimal 287

concentration for our stomatal assays to capture hypo- or hyper- closure responses 288

(Supplemental Fig. S2A). Following this, leaf pieces were floated on control buffer or 289

buffer containing 10 µM ABA and stomatal apertures were measured 4 hours post-290

treatment (Supplemental Fig. S1B). No significant differences in the extent of stomatal 291

closure were detected, indicating that TARK1 is not involved in ABA-induced stomatal 292

closure. 293

294

TARK1 CR mutants are more sensitive to SA and Flg22 295

Considering TARK1 was previously shown to be a positive regulator of tomato immunity 296

in association with bacterial infection (Kim et al., 2009), we examined stomatal 297

movements in response to the defense hormone SA and two MAMPs, the bacterial 298

flagellin peptide Flg22 and the fungal polysaccharide chitin. We chose chitin to 299

determine if TARK1 could be involved in general defense rather than bacteria specific 300

responses. Dose response assays were performed with WT stomata to optimize 301

effective concentrations of elicitors for these assays (Supplemental Fig. S2B-D). 302

Following this, leaf pieces of WT, TARK1 CR and TARK1 OE lines were floated on 303

control buffer, 100 µM SA, 10 µM Flg22 or 10 µg/mL chitin and stomatal apertures were 304

measured 4 hours post-treatment. TARK1 CR stomata were significantly more closed in 305

response to both SA and Flg22 when compared to WT and TARK1 OE stomata (Fig. 306

2A,B). Chitin induced stomatal closure in all three genotypes and apertures were not 307

significantly different (Fig. 2C). These data indicate that the TARK1 CR mutant is more 308



13

sensitive to SA and Flg22, and chitin perception is unaffected. Moreover, they suggest 309



14

that TARK1 is involved in stomatal movement that occurs in response to elicitors 310

detected during bacterial infection. 311

312

Pst-induced stomatal reopening is affected in both TARK1 CR and OE plants 313

To determine if TARK1 is involved in bacterial induced stomatal closure, leaf pieces of 314

WT, TARK1 CR and TARK1 OE lines were floated on stomatal buffer (control) or a 315

1x108 CFU/mL suspension of Pst WT or Pst DC3118 (COR-) in water. This Pst COR- 316

strain is commonly used to assay for defects in stomatal immunity because Pst COR- is 317

unable to produce coronatine, which is required for Pst WT to reopen stomata after their 318

closure in response to Pst invasion (Melotto et al., 2006). In our assay system, we found 319

that WT stomata typically close by 1 hour post-Pst treatment and reopen 4 hours post-320

Pst treatment in a COR-dependent manner (Fig. 3A,B), consistent with previous reports 321

(Melotto et al., 2006; Zhang et al., 2008; Montillet et al., 2013; Panchal et al., 2016b). 322

TARK1 CR stomata closed in response to both Pst WT and Pst COR- at 1 hour post-323

treatment; however, stomata apertures were significantly smaller at 4 hours post-324

treatment compared to the 1 hour timepoint (Fig 3B). Response to bacteria delivered 325

COR was impaired for TARK1 CR stomata. At both timepoints, TARK1 OE stomata 326

treated with Pst WT or Pst COR- were more open than WT stomata (Fig. 3A,B), 327

indicating that TARK1 OE stomata are not responsive to either treatment (Fig. 3A). To 328

support these findings, we repeated the pathogen assays with two additional tomato 329

lines – a TARK1 CR mutant line that is predicted to produce a premature stop after 88 330

amino acids referred to as TARK1 CR line 2 and a TARK1 OE line that constitutively 331

expresses TARK1-HA (Supplemental Fig. S3A)(Taylor et al., 2012). TARK1 CR line 2 332

plants produced no detectible TARK1 protein while TARK1-HA plants produced a 333

greater amount of TARK1-HA than endogenous TARK1 protein (Supplemental Fig. S3 334

B-C). The stomatal responses for TARK1 CR line 2 and TARK1-HA OE leaves 335

(Supplemental Fig. S3D-G) were similar to those obtained for TARK1 CR line 1 and 336

TARK1-GFP OE leaves, respectively (Fig. 3). Collectively, our stomatal assays using 337

WT and four mutant tomato lines indicate that TARK1 plays a role in stomatal opening 338

or regulating stomatal closure in response to Pst treatment. 339

340



15

Stomata in tomato lines close in response to COR and JA-Ile 341

To further investigate the COR insensitive phenotype in the TARK1 CR line, we treated 342

leaf pieces with a commercially available source of COR from Sigma. Apertures of 343



16

stomata for all three genotypes treated with 0.1 ng/µL of COR were significantly smaller 344

than those treated with control buffer (Fig. 3C), suggesting that COR treatment alone 345

induces stomatal closing in tomato. This finding was unexpected as COR treatment (0.1 346

- 2.5 ng/µL) did not cause stomatal closing in Arabidopsis (Melotto et al., 2006). We 347

tested different concentrations of COR (0.01 - 1 ng/µL) and detected COR-dependent 348

stomatal closing 2 to 4 hours post-treatment (Supplemental Fig. S4A). We also tested a 349

preparation of COR from Carol Bender Consulting LLC. This source of COR also 350

induced stomatal closure (Supplemental Fig. S4B). These data suggest that tomato 351

response to exogenous application of COR is different from those reported in 352

Arabidopsis. 353

354

In addition, both sources of COR did not reopen stomata in response to ABA-induced 355

closure (Supplemental Fig. S4B). Considering that COR is a JA-Ile mimic, we also 356

tested if JA-Ile caused stomatal closure. WT stomatal apertures treated with 1, 10 or 357

100 µM JA-Ile were significantly smaller than control at 4 hours post-treatment 358

(Supplemental Fig. S4C). These assays show that WT tomato stomata are sensitive to 359

COR or JA-Ile elicitation and result in stomatal closure under the conditions tested. 360

361

Despite these findings, we attempted to test if COR treatment could induce stomatal 362

reopening in WT stomata treated with Pst COR- in our assay. Previous studies in 363

Arabidopsis have shown that exogenous application of COR is sufficient to complement 364

the Pst COR- mutation (Panchal et al., 2016b; Ishiga et al., 2018). We confirmed this 365

using COR from Sigma. Stomatal apertures in Arabidopsis leaves treated with Pst 366

COR- were significantly smaller compared to those in leaves treated with Pst COR- plus 367

exogenous COR (Supplemental Fig. S4D), consistent with previous results (Panchal et 368

al., 2016b; Ishiga et al., 2018). By contrast, we found that exogenous application of 369

COR of tomato leaves was unable to complement the Pst COR- mutation in our 370

stomatal assays (Fig. 3D). In addition, we found that COR application suppressed 371

stomatal reopening mediated by Pst WT (Fig. 3D). Our data thus indicate that 372

exogenous application of COR produces a different and distinct phenotype in tomato 373

compared to those established for Arabidopsis (Melotto et al., 2006; Desclos-Theveniau 374



17

et al., 2012; Panchal et al., 2016b; Ishiga et al., 2018). It should be noted however that 375

Pst delivered COR induces stomatal re-opening in tomato (Fig. 3B), which is consistent 376

with previous studies. 377

378

Collectively, these data reveal that COR and (±)-JA-Ile both trigger stomata closing in 379

VF36 tomato plants. The fact that stomata from WT, TARK1 CR and TARK1 OE plants 380

all close in response to exogenous COR treatment suggests that all genotypes are 381

sensitive to COR. However, because we were unable to observe COR induced stomatal 382

opening in our assays, we cannot rule out the possibility that TARK1 CR plants are 383

resistant to COR-induced stomatal opening during Pst invasion. 384

385

Role of TARK1 in pre- and post-invasion defenses against Pseudomonas 386

We next determined if the differences in stomatal movement responses impacted 387

bacterial invasion by assessing pre- and post-invasion infection outcomes. To study 388

bacterial invasion of leaf tissue, we spray-inoculated individual leaves of WT, TARK1 389

CR and TARK1 OE plants with a 1x108 CFU/mL suspension of Pst WT or Pst COR-. 390

Bacterial growth and disease symptoms were monitored for multiple leaflets from a 391

single leaf of the same age on different plants to control for variation in disease 392

progression dependent on leaf development. TARK1 OE leaflets infected with Pst WT 393

had a significantly higher number of bacteria and greater disease symptom 394

development when compared to similarly infected WT leaflets at 4 days post-inoculation 395

(DPI) (Fig. 4A,B). TARK1 CR leaflets infected with Pst WT had similar titers of bacteria 396

and extent of symptom development to infected WT leaflets at 2 and 4 days post-spray 397

(Fig. 4A,B; Supplemental Fig. S5). TARK1 OE leaflets also harbored significantly more 398

Pst COR- bacteria at 4 DPI when compared to WT leaflets. These data indicate that 399

overexpression of TARK1 enhances susceptibility to Pst epiphytic growth and/or 400

invasion. 401

402

We also utilized the TARK1 CR and OE lines to study post-invasion defense in tomato 403

leaves following Pst challenge. Individual leaflets of WT, TARK1 CR and TARK1 OE 404

leaves of the same age were hand-inoculated with a 1x104 CFU/mL suspension of Pst 405



18

WT and Pst COR- and then bacterial titers were measured 4 DPI. For hand-inoculated 406

leaves, both TARK1 OE and CR leaflets harbored similar titers of Pst WT and Pst COR- 407

at 4 DPI when compared to infected WT (Supplemental Fig. S6A). These data indicate 408

TARK1 does not affect resistance to Pst infection within the apoplast. 409

410

Role of TARK1 in pre- and post-invasion defense against Xanthomonas 411



19

Considering that TARK1 is involved in resistance to Xe infection (Kim et al., 2009), we 412

determined if TARK1 plays a role in pre-invasion resistance to Xe infection. WT, TARK1 413

CR and TARK1 OE plants were infected with Xe using similar spray- and hand-414

inoculation procedures described for Pst infections above. For spray-inoculated leaves, 415

only TARK1 OE leaflets sprayed with Xe WT had a significantly higher number of 416

bacteria at 12 DPI when compared to similarly infected WT leaflets (Fig. 4C). In terms of 417

disease symptoms, WT leaves sprayed with Xe WT developed more evenly distributed 418

bacterial spot symptoms (i.e. necrotic lesions) compared to TARK1 CR leaves (Fig. 4D) 419

despite both genotypes having similar bacteria titers (Fig. 4C). By contrast, the TARK1 420

OE leaves containing the highest titer of Xe WT (Fig. 4C) developed bacterial spot 421

lesions in dense clusters which were not uniformly distributed (Fig. 4D). These data 422

indicate that reducing or overexpressing TARK1 protein levels in tomato leaves impacts 423

the development and severity of bacterial spot disease symptoms. 424

425

For hand-inoculated leaves, individual leaflets of WT, TARK1 CR and TARK1 OE 426

leaves of the same age were hand-inoculated with a 1x105 CFU/mL suspension of Xe 427

WT or Xe ∆xopN and then bacterial titers were measured 12 DPI. The titer of Xe WT 428

was significantly higher than the titer Xe ∆xopN in WT (Supplemental Fig. S6B), 429

consistent with our prior work demonstrating that XopN is a virulence factor required for 430

maximal Xe growth in VF36 tomato leaves (Roden et al., 2004; Kim et al., 2009; Taylor 431

et al., 2012). Notably, the titer of Xe ∆xopN was significantly higher in TARK1 CR 432

leaflets, but not the TARK1 OE leaflets, compared to similarly infected WT leaflets 433

(Supplemental Fig. S6B). These data show that TARK1 is required to restrict Xe ∆xopN 434

growth in the extracellular spaces of leaf tissue (i.e. post-invasion or apoplastic 435

immunity) and that overexpression of TARK1 does not enhance this resistance under 436

the conditions tested. These pre- and post-invasion studies reveal that overexpression 437

of TARK1 leads to enhanced Xe invasion and loss of TARK1 function impairs apoplastic 438

immunity in the absence of the XopN. 439

440

441



20

Discussion 442

443

The goal of this study was to further investigate the role of the pseudokinase TARK1 in 444

tomato immunity. Previous work uncovered a role for TARK1 in the positive regulation 445

of post-invasion immunity (also referred to as apoplastic immunity) in tomato leaves in 446

response to bacterial infection (Kim et al., 2009). We hypothesized that TARK1 might 447

interact with PRRs or other membrane-associated proteins in leaf cells to regulate 448

and/or amplify defense signal transduction during PTI. By purifying TARK1 complexes 449

formed during PTI (Fig. 1C), we were able to identify several TARK1 interacting proteins 450

and link TARK1 function to pre-invasion immunity. Two of the proteins confirmed to 451

interact with TARK1 are predicted to be involved in stomatal function: plasma 452

membrane H+-ATPase HA4 and LRR-RLK RLK15 (Fig. 1D). By using loss-of-function 453

and TARK1 overexpression lines, we now provide evidence that, in addition to 454

apoplastic immunity, TARK1 plays a role in the regulation of stomatal movement during 455

bacterial infection. 456

457

While TARK1 is not required for light induced stomatal opening or ABA induced 458

stomatal closure in tomato leaves (Supplemental Fig. S1), it is required for stomatal 459

movement in response to bacterial invasion. TARK1 CR stomata are hypersensitive to 460

Flg22 and SA induced stomatal closure (Fig. 2A,B). Moreover, TARK1 CR stomata 461

close in response to Pst but do not reopen in response to Pst delivered COR (Fig. 2B). 462

This suggests that TARK1 CR stomata are either insensitive or resistant to COR. 463

TARK1 CR leaves were not altered in their susceptibility to Pst at 2 or 4 days post-spray 464

inoculation (Figure 4A, Supplement Fig. S5), indicating that the reduction in stomata 465

apertures measured during elicitation did not change infection outcomes. This suggests 466

that reduced stomatal apertures triggered by Pst are not narrow enough to restrict 467

bacterial entry over the course of the infection. By contrast, overexpression of TARK1 468

enhances Pst invasion, in a COR-independent manner, resulting in higher titers within 469

the leaf tissue and, as a consequence, more disease symptoms (Fig. 4,B). These latter 470

results indicate that lack of stomata closure in response to Pst or Pst COR- treatment 471

(Fig. 3B) impacts the host’s ability to resist bacterial invasion. Our data suggest that 472



21

TARK1 functions either as a positive regulator of stomatal opening or a negative 473

regulator of stomatal closure. 474

475

We were unable to test the possibility that TARK1 may be involved in COR or JA-Ile 476

induced stomatal reopening. We found that tomato stomata close in response to both 477

COR and JA-Ile which is contradictory to what others have shown in Arabidopsis and 478

tomato (Melotto et al., 2006; Okada et al., 2009; Ortigosa et al., 2019). We confirmed 479

that our COR stock elicited the expected stomatal responses in Arabidopsis 480

(Supplemental Fig. S4D), validating that our elicitation conditions and imaging methods 481

captured known stomatal aperture changes reported in the literature. It is important to 482

note that there is controversy in field whether or not the JA pathway promotes stomatal 483

opening or closure (Suhita et al., 2004; Munemasa et al., 2007; Speth et al., 2009; 484

Montillet et al., 2013). Although there is one study showing that JA-Ile treatment causes 485

stomatal opening (Okada et al., 2009), we were unable to reproduce this finding using 486

similar concentrations of JA-Ile (Supplemental Fig. S4). A major difference in our 487

stomatal assay is that we image tissue directly and do not perform epidermal leaf peels. 488

It is possible that differences in stomatal phenotypes may be dependent on the growth 489

conditions, species, and/or cultivars tested. 490

While the regulation of stomatal closing in response to biotic and abiotic stresses is well 491

understood (Murata et al., 2015), less is known about the regulation of stomata opening. 492

Most of our knowledge comes from the study of blue light induced stomatal opening. 493

Blue light perception by phototropin receptors leads to the initiation of signaling 494

cascades that eventually lead to the activation of the plasma membrane H+-ATPase 495

AHA1 via the phosphorylation of key residues and the interaction with a 14-3-3 protein 496

(Shimazaki et al., 2007; Hayashi et al., 2010; Yamauchi et al., 2016). Activation of 497

AHA1 causes membrane hyperpolarization (Shimazaki et al., 2007; Marten et al., 2010) 498

and activation of K+ channels which alters ion levels within the cell (Lebaudy et al., 2008; 499

Kim et al., 2010). This causes a decrease in water potential and water uptake triggering 500

stomatal opening (Inoue et al., 2010; Marten et al., 2010). Considering that TARK1 501

interacts with the putative H+-ATPase HA4, we hypothesize that TARK1 may be 502



22

regulating HA4 activity or interaction with other HA4-associated proteins at the plasma 503

membrane to regulate stomatal apertures in response to bacteria invasion. 504

For biotic interactions, the L-type lectin receptor kinase-V.5 (LecRK-V.5) was shown to 505

be a negative regulator of stomatal closure (Desclos-Theveniau et al., 2012), revealing 506

that plants possess mechanisms to reverse bacteria-induced stomatal closure to 507

maintain homeostasis. Genetic evidence indicates that LecRK-V.5 regulates stomatal 508

immunity upstream of ROS production. LecRK-V.5 mutants have constitutively smaller 509

stomatal apertures in the absence of elicitation. Also, LecRK-V.5 OE stomata close in 510

response to Pst COR- and then reopen (Desclos-Theveniau et al., 2012). While both 511

LecRK-V.5 and TARK1 mutants are affected in stomatal opening in response to 512

bacteria; the phenotypes are distinct. This indicates that TARK1’s role in the regulation 513

of stomatal movement is likely operating via a different mechanism. 514

How TARK1 functions as a pseudokinase to participate in defense signaling is not yet 515

clear. A few plant pseudokinases have been shown to serve as decoy substrates for 516

pathogen enzymes playing key roles in pathogen recognition and activation of effector 517

triggered immunity (ETI) (Lewis et al., 2013; Wang et al., 2015). Other pseudokinases 518

serve as scaffolding proteins to mediate protein-protein interactions. Interestingly, LRR-519

RLK pseudokinase GHR1 is required for stomatal closure through the activation of 520

SLAC1 (Hua et al., 2012), which is thought to occur via GHR1-mediated protein 521

interactions (Sierla et al., 2018). It is possible that TARK1 may be serving as a scaffold 522

to recruit other proteins at the plasma membrane that have a more direct influence over 523

the regulation of stomatal movement. For the instance, TARK1 may function as a 524

scaffold that facilitates the interaction of the H+-ATPase HA4 with another protein that 525

either activates or inhibits HA4’s activity. One candidate may be TFT1, a 14-3-3 protein, 526

that was previously shown to be a target of the Xanthomonas effector protein XopN. 527

Based on in vitro biochemical data, Taylor et al. (2012) proposed that XopN promotes 528

interaction between TARK1 and TFT1 to interfere with one or both of their functions. 529

Alternatively, but not mutually exclusive, TARK1 could serve as a substrate for kinases 530

like the LRR-RLK RLK15. Differential phosphorylation of TARK1 could facilitate the 531

assembly or disassembly of TARK1 protein complexes involved in pre- and post-532



23

invasion immunity. Future work will be aimed to elucidate the role(s) of the TARK1-533

associated complexes identified in this work to understand the underlying mechanisms 534

by which this pseudokinase coordinates immune signaling in tomato. 535

536

Taken together, our findings establish a role of TARK1 in both pre- and post-invasion 537

immunity. For pre-invasion immunity, overexpression of TARK1 in tomato leaves affects 538

stomatal immunity and leads to enhanced bacterial invasion. This phenotype does not 539

require bacterial delivered COR. In the absence of TARK1, stomata are more sensitive 540

to biotic elicitors, resulting in reduced stomatal apertures with no change in stomatal 541

immunity impacting bacterial titers. For post-invasion immunity, overexpression of 542

TARK1 in tomato leaves does not enhance disease resistance in the apoplast to either 543

Pst or Xe. However, loss of TARK1 impairs post-invasion defense to Xe strains lacking 544

the effector XopN, implying that XopN functions to suppress TARK1-mediated defense 545

after bacterial invasion (Supplemental Fig. S6). This is consistent with post-invasions 546

studies previously reported by Kim et al. (2009). 547

548

In conclusion, we provide evidence that TARK1 is required for stomatal responses 549

triggered by biotic elicitors and plays a role in pre-invasion defense triggered in 550

response to bacterial infection. This work provides avenues to elucidate the role of this 551

pseudokinase in the regulation of stomatal opening during pathogen triggered immunity. 552

553

Materials and Methods 554

555

Plant constructs, transformation and mutagenesis 556

To generate TARK1-GFP and GFP overexpression transgenic lines, pGWB5(TARK1-557

GFP) (Kim et al., 2009) and pGWB5(GFP) (Nakagawa et al., 2007) were mobilized into 558

A. tumefaciens strain LBA4404 and then strains were used to transform VF36 tomato 559

line using standard methods (McCormick, 1991). TARK1-HA overexpression lines were 560

previously published (Taylor et al., 2012). 561

562



24

To generate TARK1 CRISPR mutant, CRISPR/Cas9 sites were selected by CRISPR-P 563

2.0 (http://cbi.hzau.edu.cn/CRISPR2/) (Liu et al., 2017). To generate sgRNA constructs 564

for TARK1, sgRNAs were PCR amplified from pDONR207(AtU6p-sgRNA with attL1 and 565

attL2; from Jeffery L. Dangl) using primer sets sgRNAfor/sgRNArev. PCR products were 566

self-ligated and recombined into pMDC83(2x35Sp-Cas9-HA-NLS with Gateway 567

cassette) (Jeon et al., 2020) using LR clonase II (ThermoFisher). Final plasmids were 568

transformed into A. tumefaciens LBA4404 and then strains were used for tomato 569

transformations (McCormick, 1991). Homozygous mutant T1 plants were selected by 570

using PAGE-based genotyping (Zhu et al., 2014). To confirm mutations, CRISPR/Cas9 571

target sites were PCR amplified from genomic DNA using primer set TARK1for/rev and 572

products were sequenced by Sanger method (Genewiz). 573

For transient protein overexpression, TARK1 interacting proteins were amplified by PCR 574

using their respective primer sets (Supplemental Table S2) and cloned into pENTR/D-575

TOPO, and then recombined into the pEAQ-GWB5 or pEAQ-GWB6 destination vector 576

via a Gateway LR reaction creating pEAQ-GWB6(HA4), pEAQ-GWB5(RLK15) and 577

pEAQ-GWB5(LOX8). To make GFP fusion constructs in pEAQ vector (Sainsbury et al., 578

2009), gateway cassette-GFP or GFP-gateway cassette regions were PCR amplified 579

from pGWB5 or pGWB6 (Nakagawa et al., 2007) using PCR primer sets 580

GWB5for/GWB5rev or GWB6for/GWB6rev, respectively. PCR products were digested 581

with EcoRV or NruI + EcoRV, respectively, and cloned into NruI + StuI sites in pEAQ-582

HT to generate pEAQ-GWB5 or pEAQ-GWB6. 583

TARK1 peptide antibody production 584

A synthetic peptide (ATENHDIEDVFSDKKVRV) corresponding to residues 295-312 in 585

the juxtamembrane domain of TARK1 was synthesized and conjugated to keyhole 586

limpet hemocyanin carrier protein and used to generate polyclonal antisera from rabbits 587

(Covance). 588

589

Bacterial strains and culture conditions 590

Strains used in this study were as follows: Pseudomonas syringae pathovar tomato 591

strain DC3000 (Pst WT), strain Pst DC3118 (coronatine deficient mutant, COR-), 592



25

Xanthomonas euvesicatoria 85-10 (Xe WT), Xe ∆hrcV (type-3 secretion deficient 593

mutant), Xe ∆hrpF (type-3 secretion deficient mutant) and Xe ∆xopN. Pst and Xe strains 594

were grown on nutrient yeast glycerol agar (NYGA) (Turner et al., 1984) at 28°C. Pst 595

DC3000, Xe WT, Xe ∆hrcV and Xe ∆hrpF antibiotic selection was 100 µg/mL rifampicin 596

(Rif) while Pst DC3118 was 100 µg/mL Rif + 50 µg/mL kanamycin (Km) and Xe ∆xopN 597

was 100 µg/mL Rif + 50 µg/mL spectinomycin (Sp). 598

599

Bacterial infection assays 600

For spray inoculation assays, a 1x108 CFU/mL suspension of Pst WT or COR- (in 1 mM 601

MgCl2) or Xe (in 10 mM MgCl2) with 0.02% v/v silwet L-77 (Helena Chemical Company, 602

TN) was sprayed on leaves until dripping and then plants were placed in chambers at 603

high humidity (>95%) for 48 hours. Plants were kept in a glasshouse under 16 hours of 604

light/day at 28°C. Leaflets from the same leaf were used for each experiment. For each 605

strain analyzed, four leaf discs (0.5 cm2) per treatment per time point were collected 606

from one leaflet, pooled, ground in 1 mM or 10 mM MgCl2, and then spotted on NYGA 607

plates in triplicate to determine bacterial titer in each sprayed leaflet. Three biological 608

replicates (i.e. two leaflets per plant and three plants per genotype) were used per 609

experiment. 610

For hand-inoculation assays, leaves were hand-inoculated with either Pst strains (1x104 611

CFU/mL in 1 mM MgCl2) or Xe strains (1x105 CFU/mL in 10 mM MgCl2) using a 612

needless syringe. Infected plants were kept in glasshouse under 16 hours of light/day at 613

28°C. Bacterial growth was measured as described above. 614

Transient protein expression in N. benthamiana 615

A. tumefaciens strains C58C1 pCH32 transformed with binary vectors were grown 616

overnight on Luria agar containing 100 µg/mL Rif + 50 µg/mL Km + 5 µg/mL tetracycline 617

at 28°C, collected, suspended in Agrobacterium induction media (10 mM MES, pH 5.6, 618

10 mM MgCl2, and 150 mM acetosyringone; Acros Organics) and then incubated for 2 619

hours at room temperature (Mudgett et al., 2000). N. benthamiana leaves were hand-620

inoculated with a suspension (0.8x108 cells/mL) of two strains in induction media. Plants 621

were incubated at room temperature under continuous low light for 2 days. 622



26

623

Co-immunoprecipitation assays 624

Immunoprecipitation (IP) of TARK1-GFP or GFP tagged TARK1 interacting proteins 625

was performed as described with modifications (Kadota et al., 2016). Tomato TARK1-626

GFP and GFP OE leaves were hand-inoculated with a suspension (1x108 CFU/mL) of 627

Xe ∆hrcV in 10 mM MgCl2. Tissue was collected 24 hours later, frozen and ground in 628

liquid N2. Ground tissue was added to extraction buffer at a 3:1 buffer to tissue ratio. 629

Final concentrations of buffer components were: 150 mM Tris-HCl pH 7.5, 150 mM 630

NaCl, 10% v/v glycerol, 1.5 mM Na3VO4, 10 mM DTT, 1 mM Na2MoO4, 1.5 mM NaF, 1 631

mM EDTA, 1 mM protease inhibitor cocktail (Sigma), 0.5% v/v IGEPAL (detergent) and 632

1 mM PMSF. Tissue was solubilized in buffer at 4°C with rotation for 1 hour. Samples 633

were spun down at 15,000 g at 4°C for 20 min. The supernatant was filtered and 634

incubated with 50 µL of GFP TRAP magnetic agarose beads (Chromotek) for 1.5 635

hours at 4°C with rotation. Beads were removed and washed with extraction buffer 636

lacking detergent. Proteins were eluted with 0.2 M glycine pH 2.5. Experiments were 637

performed in triplicate. WT plants were used as a control in TARK1-GFP IP #1-2 and 638

GFP OE plants were used as controls for TARK1-GFP IP #3. 639

For validation of TARK1 interaction with candidate proteins, TARK1-3xHA or 640

TARK1Like-3xHA (control) were transiently expressed with GFP-HA4, RLK15-GFP or 641

LOX8-GFP in N. benthamiana leaves and then purified as described above. 642

643

Mass spectrometry 644

Mass spectrometry (MS) was performed at the Stanford University MS Facility 645

(http://mass-spec.stanford.edu). Protein was precipitated using four volumes of cold 646

acetone at -80°C overnight. The supernatant was removed, and the resulting pellet was 647

reconstituted and reduced with 10 mM DTT at 55°C for 30 minutes. Proteins were 648

alkylated with 30 mM acrylamide for 30 minutes at room temperature. Digestion was 649

performed using Trypsin/LysC (Promega) overnight at 37°C, and the resulting peptides 650

desalted, dried and then reconstituted. 651

652



27

Peptides were analyzed by liquid chromatography (LC) using a Nanoacquity UPLC 653

(Waters Corporation, Milford, MA) followed by MS using an Orbitrap Elite MS (Thermo 654

Scientific, San Jose, CA) equipped with a captive spray emitter source (Michrom 655

Bioresources, Auburn, CA). For a typical LC/MS experiment, a flow rate of 450 nL/min 656

was used, where mobile phase A was 0.2% v/v formic acid in water and mobile phase B 657

was 0.2% v/v formic acid in acetonitrile. Analytical columns were prepared in-house with 658

an I.D. of 100 microns packed with Dr. Maisch 1.8 micron C18 stationary phase to a 659

length of ~20 cm. Peptides were directly injected onto the analytical column using a 660

gradient (2-45% B, followed by a high-B wash) of 80 minutes. MS was operated in a 661

data-dependent fashion using CID fragmentation for MS/MS spectra generation 662

collected in the ion trap. 663

664

For data analysis, the .RAW data files were checked using Preview (Protein Metrics) to 665

verify success of injection and sample quality. They were then processed using Byonic 666

v2.6.49 (Protein Metrics) to identify peptides and infer proteins using Solanum 667

lycopersicum database from Uniprot including isoforms. Proteolysis with Trypsin/LysC 668

was assumed to be fully specific with up to two missed cleavage sites. Precursor mass 669

accuracies were held within 12 ppm with fragment ions held within 0.4 Da. Proteins 670

were held to a false discovery rate of 1%, using standard approaches as described 671

previously (Elias and Gygi, 2007). 672

673

Stomatal assays 674

Leaf pieces were cut from leaflets of fully expanded leaves of 4-5 week old tomato 675

plants and floated on stomatal buffer (25 mM 2-(N-morpholino)ethanesulfonic acid 676

(MES)-KOH pH 6.15, 10 mM KCl) for 3 hours under light to allow stomata to fully open 677

as described (Melotto et al., 2006; Chitrakar and Melotto, 2010). Leaf pieces were then 678

floated on 10 µM abscisic acid (ABA, Sigma), 100 µM sodium salicylate (SA, Sigma), 10 679

µM Flg22 peptide (Protein and Nucleic Acid Facility, Stanford University, CA), 680

coronatine (COR; Sigma purified from Pseudomonas syringae pathovar glycinea and 681

Carol Bender, Consulting LLC) or (±)-jasmonic acid isoleucine ((±)-JA-Ile, Cayman 682

Chemical) in stomatal buffer or 1x108 CFU/mL of Pst DC3000 or Pst DC3118 (Zhao et 683



28

al., 2003) in water (Melotto et al., 2006). (±)-JA-Ile is a mixture containing two of four 684

possible stereoisomers of JA-Ile: (1R,2R) and (1S,2S). All treatments involving ABA 685

contained 0.65% v/v EtOH and COR contained 0.00025% v/v MeOH. At indicated time 686

points, leaf pieces were removed to a microscope slide containing sterilized water and 687

observed under a fluorescent microscope (Leica DM5000 B). Widths of stomatal 688

apertures were measured using ImageJ software (Tsai et al., 2010). Completely closed 689

stomata were reported as a value of 1 µm. 690

691

Statistical Analysis 692

Each experiment was conducted at least two times unless stated otherwise. Statistical 693

significances were based on One-way ANOVA followed by Tukey’s multiple 694

comparisons test using SPSS Statistics for Macintosh Version 25.0 (IBM Corp. Armonk, 695

NY). 696

Accession Numbers 697

Sequence data from this article can be found in the GenBank/EMBL data libraries under 698

accession numbers: TARK1 (NM_001247651.2), HA4 (NM_001324146.1), NRC4a 699

(NM_001372087.1), RLK15 (XM_010321865.3), GAPDH (NM_001279325.2), Heat 700

shock protein (XM_004234937.4), LOX8 (XM_004244842.4), Calnexin-like 701

protein(NM_001247200.2), Coatomer subunit protein 1 (XM_004238268.4), Coatomer 702

subunit protein 2 (XM_004230813.4), Mitochondrial phosphate carrier protein 703

(NM_001279338.2), ATP synthase subunit beta (XM_004236916.3), Mitochondrial 704

ADP/ATP carrier protein (NM_001306138.1), Alpha/beta hydrolase fold protein 705

(XM_004235953.4), Cysteine synthase protein (NM_001321342.1), Ubiquinol-706

cytochrome c reductase iron-sulfur subunit (XM_004250642.4) and Glutarhione S-707

transferase (XM_004246336.4)._ 708

709

Supplemental Data 710 711 Supplemental Figure S1. Light induced stomatal opening and ABA induced stomatal 712 closure in WT, TARK1 CRISPR (CR) and TARK1 overexpression (OE) leaves. 713 714



29

Supplemental Figure S2. Characterization of abscisic acid (ABA), salicylic acid (SA), 715 flagellin peptide (Flg22) and chitin induced stomatal closure in WT tomato leaves. 716 717 Supplemental Figure S3. Stomatal movements in TARK1 CRISPR mutant line 2 (line 2) 718 and TARK1 overexpression (TARK1-HA) leaves behave similarly to TARK1 CRISPR 719 mutant line 1 and TARK1 OE (Fig. 3) leaves. 720 721 Supplemental Figure S4. Characterization of the effects of coronatine (COR) treatment 722 on stomatal apertures in tomato and Arabidopsis leaves. 723 724 Supplemental Figure S5. Phenotypes of WT, TARK1 CRISPR (CR) and TARK1 725 overexpression (OE) plants following bacterial spray inoculation 2 days post-spray. 726 727 Supplemental Figure S6. Apoplastic immunity in WT, TARK1 CRISPR (CR) and 728 TARK1 overexpression (OE) plants. 729 730 Supplemental Table S1 List of candidate TARK1 interacting proteins identified by 731 mass spectrometry. 732 733

Supplemental Table S2 Primer sequences used in this study related to Experimental 734

Procedures. 735

Supplemental Table S3. Number of stomata apertures measured for each figure 736 737

Acknowledgements 738

We would like to thank George Lomonossoff (John Innes Center) for providing the 739

pEAQ plasmid. We would like to thank the Vincent Coates Foundation Mass 740

Spectrometry Laboratory, Stanford University Mass Spectrometry for processing 741

and analysis of proteomic samples. We also thank Maeli Melotto and members of the 742

Mudgett laboratory for critical discussion. This work is supported by the Agriculture and 743

Food Research Initiative grant 2018-67011-28034 from the USDA National Institute of 744

Food and Agriculture given to A.G. The National Institute of General Medical Sciences 745

of the National Institutes of Health award number: T32GM007276 given to A.G. The 746

Binational Science Foundation grant 2011069 given M.B.M. This work was supported 747

in part by NIH P30 CA124435 utilizing the Stanford Cancer Institute 748

Proteomics/Mass Spectrometry Shared Resource. This work utilized the LTQ-749



30

Orbitrap mass spectrometer system that was purchased with funding from National 750

Institutes of Health Shared Instrumentation grant S10RR027425. 751

752

Figure Legends 753

Figure 1. Isolation and validation of TARK1 interacting proteins. A, Diagram of TARK1 754 and TARK-GFP proteins and their predicted domains: SP, signal peptide; LRR, leucine 755 rich repeats; TM, transmembrane; JM, juxtamembrane and PK, pseudokinase domain. 756 Predicted protein molecular weights: TARK1 = 66 kDa; TARK1-GFP = 92 kDa. Arrow = 757 Site of CRISPR (CR) mutation. Bar = Peptide used for antibody (Ab) production. B, 758 Immunoblot analysis showing TARK1 and TARK1-GFP protein levels in untreated (-) 759 and Xe ∆hrcV (+) infected leaves 24 hours post-inoculation using a TARK1 peptide 760 antibody (αTARK1 Ab). C, Table of TARK1 interacting proteins that are associated with 761 stomatal function. (*) = Closest Arabidopsis homolog using best BLAST P (Altschul et 762 al., 1997). Protein name and/or gene locus is listed. (**) = Number of unique peptides 763 identified in TARK1-GFP immunoprecipitation (IP) samples (n = 3 biological replicates) 764 using LC-MS/MS. D, Co-immunoprecipitation using GFP magnetic agarose beads with 765 candidates that have N (GFP-) or C (-GFP) terminal tag and TARK1-3xHA or 766 TARK1Like-3xHA. 767 768 Figure 2. Stomatal apertures of leaf pieces from WT, TARK1 CRISPR (CR) and TARK1 769 overexpression (OE) plants treated with biotic elicitors. Leaf pieces were floated on 2-770 (N-morpholino)ethanesulfonic acid (MES) buffer (control) or A 100 µM salicylic acid (SA) 771 in MES buffer, B 10 µM Flg22 in MES buffer and C 10 µg/mL chitin in MES buffer and 772 then apertures were measures at 4 hours post-treatment. For A-C, approximately 60-773 100 apertures were measured from an individual plant from the indicated genotypes per 774 independent experiment. Box and whisker plots represent data aggregated from 3 775 independent experiments (n=255-300 apertures, see Supplemental Table S3 for exact 776 n). Whiskers represent the range, boxes represent interquartile range split by the 777 median, circles represent individual data points and letters above bars represent 778 statistical significance (Oneway ANOVA, P<0.05). 779 780

Figure 3. Stomatal movements in leaves of WT, TARK1 CRISPR (CR) and TARK1 781 overexpression (OE) plants in response to Pst and coronatine treatment. Stomatal 782 apertures of leaf pieces from WT, TARK1 CR, and OE plants floated on water (control), 783 Pst DC3000 (Pst WT) or the coronatine deficient strain Pst DC3118 (Pst COR-) in water 784 at A 1 and B 4 hours post-treatment. C, Stomatal apertures of leaf pieces floated on 785 MES buffer, pH 6.15 (control) or 0.1 ng/µL coronatine (COR) in MES buffer 4 hours 786 post-treatment. D, Control (MES; black), COR (Sigma; blue), Pst WT (in water; red), Pst 787 WT + COR (0.5ng/μL; orange), Pst COR- (in water; grey), Pst COR- + COR (purple) 4 788 hours post-treatment. For A-D, approximately 60-100 apertures were measured from an 789 individual plant from the indicated genotypes per independent experiment. Box and 790 whisker plots represent data aggregated from 3 independent experiments (n=247-300 791



31

apertures, see Supplemental Table S3 for exact n). Whiskers represent the range, 792 boxes represent interquartile range split by the median, circles represent individual data 793 points and letters above bars represent statistical significance (Oneway ANOVA, 794 P<0.05). 795

796 Figure 4. Phenotypes of WT, TARK1 CRISPR (CR), and TARK1 overexpression (OE) 797 plants following bacterial spray inoculation. A, Number of Pst (log(CFU/cm2)) in WT, CR, 798 and OE leaflets 4 days post-inoculation (DPI). B, Disease symptoms in WT, CR and OE 799 leaflets infected with Pst WT 4 DPI. C, Number of Xe WT (log(CFU/cm2)) in WT, CR and 800 OE leaflets 12 days post inoculation. D, Disease symptoms in WT, CR and OE leaflets 801 infected with Xe WT 16 DPI. For A-D, assays were performed with one leaf from each 802 plant genotype in triplicate (n=3). For A and C, circles on bar graphs represent bacterial 803 number in each leaflet analyzed. 2 leaflets were assayed per leaf. Letters above the 804 bars represent statistical significance (Oneway ANOVA, P<0.05, n=6). 805 806

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https://www.ncbi.nlm.nih.gov/pubmed?term=McCormick S %281991%29 Transformation of tomato with Agrobacterium tumefaciens%2E In Plant Tissue Culture Manual%2E Springer%2C Dordrecht%2C Dordrecht%2C pp 311%26%23x&dopt=abstract

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https://www.ncbi.nlm.nih.gov/pubmed?term=Taylor KW%2C Kim J%2DG%2C Su XB%2C Aakre CD%2C Roden JA%2C Adams CM%2C Mudgett MB %282012%29 Tomato TFT1 is required for PAMP%2Dtriggered immunity and mutations that prevent T3S effector XopN from binding to TFT1 attenuate Xanthomonas virulence%2E PLoS Pathog 8%3A e&dopt=abstract

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https://www.ncbi.nlm.nih.gov/pubmed?term=Turner P%2C Barber C%2C Daniels M %281984%29 Behaviour of the transposons Tn 5 and Tn 7 in Xanthomonas campestris pv%2E campestris%2E MGG Molecular %26 General Genetics 195%3A 101%26%23x&dopt=abstract

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https://scholar.google.com/scholar?as_q=The Plasma Membrane H+-ATPase AHA1 Plays a Major Role in Stomatal Opening in Response to Blue Light.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yamauchi&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

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https://scholar.google.com/scholar?as_q=A genetic screen reveals Arabidopsis stomatal and/or apoplastic defenses against Pseudomonas syringae pv.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zeng&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Zeng W%2C He SY %282010%29 A prominent role of the flagellin receptor FLAGELLIN%2DSENSING2 in mediating stomatal response to Pseudomonas syringae pv tomato DC3000 in Arabidopsis%2E Plant Physiol 153%3A 1188%26%23x&dopt=abstract

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https://scholar.google.com/scholar?as_q=A prominent role of the flagellin receptor FLAGELLIN-SENSING2 in mediating stomatal response to Pseudomonas syringae pv tomato DC3000 in Arabidopsis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zeng&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

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https://scholar.google.com/scholar?as_q=A Pseudomonas syringae effector inactivates MAPKs to suppress PAMP-induced immunity in plants.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Zhang W%2C He SY%2C Assmann SM %282008%29 The plant innate immunity response in stomatal guard cells invokes G%2Dprotein%2Ddependent ion channel regulation%2E Plant J 56%3A 984%26%23x&dopt=abstract


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https://scholar.google.com/scholar?as_q=The plant innate immunity response in stomatal guard cells invokes G-protein-dependent ion channel regulation.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Zhao Y%2C Thilmony R%2C Bender CL%2C Schaller A%2C He SY%2C Howe GA %282003%29 Virulence systems of Pseudomonas syringae pv%2E tomato promote bacterial speck disease in tomato by targeting the jasmonate signaling pathway%2E Plant J 36%3A 485%26%23x&dopt=abstract

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Zhu X, Xu Y, Yu S, Lu L, Ding M, Cheng J, Song G, Gao X, Yao L, Fan D, et al (2014) An Efficient Genotyping Method for Genome-modified Animals and Human Cells Generated with CRISPR/Cas9 System. Sci Rep 4: 957–8



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