1 short title: new bri1 mutations - plant physiology · 65 last two decades, over 20 different bri1...

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Short title: New BRI1 mutations 1

Corresponding author: Jia Li 2

Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, 3

School of Life Sciences, Lanzhou University, Lanzhou 730000, China 4

+86 931 8915662 5

Email: [email protected] 6

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Plant Physiology Preview. Published on May 1, 2017, as DOI:10.1104/pp.17.00118

Copyright 2017 by the American Society of Plant Biologists

www.plantphysiol.orgon March 19, 2020 - Published by Downloaded from Copyright © 2017 American Society of Plant Biologists. All rights reserved.

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Scanning for new BRI1 receptor mutations via TILLING analysis 31

Chao Sun1, Kan Yan1, Jian-Ting Han1, Liang Tao1, Ming-Hui Lv1, Tao Shi1, 32

Yong-Xing He1, Michael Wierzba2, Frans E. Tax2, Jia Li1,* 33

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1Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, 35

School of Life Sciences, Lanzhou University, Lanzhou 730000, China 36

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2Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 38

85721, USA 39

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*Corresponding author: Jia Li, [email protected] 41

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Present address of Kan Yan: School of Chemical and Biological Engineering, 43

Lanzhou Jiaotong University, Lanzhou 730000, China 44

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One sentence summary: Nine morphologically altered new BRI1 mutants were identified 46

from 83 independent TILLING mutations in Arabidopsis thaliana. 47

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List of author contributions: J. L. and F. E. T. conceived the research plans, 49

supervised the experiments and edited the manuscript; C. S. designed the experiments, 50

analyzed the data and prepared the draft of the article; C. S. and K. Y. performed most 51

of the experiments; L. T., M-H. L. and M. W. performed part of the experiments; J-T. 52

H. and Y-X. H. performed the molecular dynamic simulation analysis; T. S. helped 53

with the sequence analysis. 54

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Funding information: This project is supported by the National Natural Science 56

Foundation of China (31470380 and 31530005 to Jia Li) 57

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ABSTRACT 60

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Identification and characterization of a mutational spectrum for a specific protein can 62

help to elucidate its detailed cellular functions. BRI1, a multidomain transmembrane 63

receptor-like kinase, is a major receptor of brassinosteroids in Arabidopsis. Within the 64

last two decades, over 20 different bri1 mutant alleles have been identified, which 65

helped to determine the significance of each domain within BRI1. To further 66

understand molecular mechanisms of BRI1, we tried to identify additional alleles via 67

TILLING. Here we report our identification of 83 new point mutations in BRI1, 68

including 9 mutations that exhibit an allelic series of typical bri1 phenotypes, from 69

subtle to severe morphological alterations. We carried out biochemical analyses to 70

investigate possible mechanisms of these mutations in affecting BR signaling. A 71

number of interesting mutations have been isolated via this study. For example, 72

bri1-702, the only weak allele identified so far with a mutation in the activation loop, 73

showed reduced autophosphorylation activity. bri1-705, a subtle allele with a 74

mutation in the extracellular portion, disrupts the interaction of BRI1 with its ligand 75

brassinolide (BL) and co-receptor BAK1. bri1-706, with a mutation in the 76

extracellular portion, is a subtle defective mutant. Surprisingly, root inhibition 77

analysis indicated that it is largely insensitive to exogenous BL treatment. In this study, 78

we found bri1-301 possess kinase activity in vivo, clarified a previous report arguing 79

that kinase activity may not be necessary for the function of BRI1. These data provide 80

additional insights into our understanding of the early events in the BR signaling 81

pathway. 82

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INTRODUCTION 90

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Brassinosteroids (BRs) are known to play critical roles in regulating many aspects of 92

plant growth and development, including germination, cell elongation, flowering time 93

control, reproduction, photomorphogenesis, and skotomorphogenesis (Clouse and 94

Sasse, 1998; Gudesblat and Russinova, 2011; Wang et al., 2012; Zhu et al., 2013). 95

Recent studies revealed that BRs are also involved in many additional physiological 96

processes, such as root meristem maintenance (Gonzalez-Garcia et al., 2011; Hacham 97

et al., 2011; Vilarrasa-Blasi et al., 2014; Chaiwanon and Wang, 2015; Wei and Li, 98

2016), stomatal development (Gudesblat et al., 2012; Kim et al., 2012), root hair 99

differentiation (Cheng et al., 2014), leaf angle regulation in monocots (Zhang et al., 100

2012), shoot branching control (Wang et al., 2013), and organ boundary determination 101

(Bell et al., 2012; Gendron et al., 2012). 102

In Arabidopsis, BRs are perceived by their major receptor BRASSINOSTEROID 103

INSENSITIVE 1 (BRI1) and co-receptor BRI1-ASSOCIATE RECEPTOR KINASE 1 104

(BAK1), both of which are single-pass transmembrane leucine-rich repeat 105

receptor-like protein kinases (LRR-RLKs) (Li and Chory, 1997; Li et al., 2002; Nam 106

and Li, 2002; Gou et al., 2012). There are 25 total extracellular LRRs in BRI1. 107

Between 21st and 22nd LRR, there is an amino acid sequence containing 68 residues 108

named as an “island”. Genetic and structural analyses indicated that the “island” and 109

the 22nd LRR are directly involved in BR binding. In the absence of BRs, the kinase 110

activity of BRI1 is inhibited by its carboxyl terminus (Wang et al., 2005) and by its 111

associated inhibitory protein named as BRI1 KINASE INHIBITOR 1 (BKI1) (Wang 112

and Chory, 2006). When BRs are present, on the other hand, they can directly interact 113

with the extracellular pocket of BRI1, causing BKI1 to dissociate from the complex 114

(Wang and Chory, 2006; Hothorn et al., 2011; She et al., 2011; Wang et al., 2014). The 115

newly formed BRI1-BL surface can directly interact with the extracellular residues of 116

BAK1 via several hydrogen bonds (Santiago et al., 2013; Sun et al., 2013). The 117

BRI1-BL-BAK1 complex can then initiate early BR signaling events and activate its 118

downstream signaling cascade (Wang et al., 2008). Genetic and structural analyses 119



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demonstrated the essential roles of both BRI1 and BAK1 in controlling BR signal 120

transduction (Clouse et al., 1996; Li and Chory, 1997; Hothorn et al., 2011; She et al., 121

2011; Gou et al., 2012; Santiago et al., 2013; Sun et al., 2013). 122

During the past two decades, over 20 unique bri1 alleles have been isolated 123

(Clouse et al., 1996; Li and Chory, 1997; Noguchi et al., 1999; Friedrichsen et al., 124

2000; Xu et al., 2008; Belkhadir et al., 2010; Shang et al., 2011; Gou et al., 2012). 125

Analyses of these mutants have contributed significantly to our better understanding 126

of BRI1 in regulating plant growth and development (Vert et al., 2005). These alleles 127

share similar phenotypes in various degrees, including dwarfism, dark-green, compact 128

rosette leaves with short petioles, delayed flowering time and senescence, reduced 129

male fertility, and altered both photomorphogenesis and skotomorphogenesis (Clouse, 130

1996; Kwon and Choe, 2005). Most alleles exhibiting the strongest morphological 131

defects contain point mutations in the “island” or kinase domain (Friedrichsen et al., 132

2000). BRI1 was first cloned via a map based strategy (Li and Chory, 1997). Many of 133

the early isolated bri1 alleles are strong alleles with largely reduced male sterility, 134

preventing their use in large scale genetic transformation assays. Fertile weak bri1 135

alleles, such as bri1-5 and bri1-9, on the other hand, are excellent genetic tools used 136

for characterizing the entire BR signaling pathway via extragenic modifier screens 137

(Noguchi et al., 1999). For example, several key components regulating BR signal 138

transduction or BR homeostasis were identified via activation tagging genetic screens 139

using bri1-5 as background, including BRS1 (Li et al., 2001), BAK1 (Li et al., 2002), 140

BSU1 (Mora-Garcia et al., 2004), BRL1 (Zhou et al., 2004), BEN1 (Yuan et al., 2007), 141

and TCP1 (Guo et al., 2010). EBS1 to EBS7, a series of functionally related proteins 142

mediating endoplasmic reticulum (ER) quality control, were isolated via a suppressor 143

screen from ethylmethanesulfonate (EMS) mutagenized bri1-9 (Jin et al., 2007; Jin et 144

al., 2009; Su et al., 2011; Hong et al., 2012; Su et al., 2012; Liu et al., 2015). BES1, a 145

key downstream transcription factor in the BR signaling pathway, was identified via a 146

suppressor screen utilizing an EMS mutagenized bri1-119 library (Yin et al., 2002). 147

Identification of these key regulatory components by using weak bri1 mutants has 148

contributed significantly to our current knowledge of the BR signaling pathway, from 149



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BR perception to downstream responsive gene regulation. 150

In order to deeply understand the molecular mechanisms of BRI1 in regulating 151

the BR signaling pathway, we analyzed all BRI1 point mutations generated from a 152

Targeted Induced Local Lesions IN Genomes (TILLING) project (McCallum et al., 153

2000). Among 83 total BRI1 point mutations isolated, we identified 9 mutants, 154

including 4 subtle, 1 weak, and 4 strong alleles. For example, bri1-702 is a new weak 155

allele with a mutation in the activation loop of the BRI1 kinase domain. Several 156

previously identified bri1 activation loop point mutants are all strong alleles. 157

Therefore, bri1-702 represents the first weak allele bearing a point mutation in the 158

activation loop. bri1-705 is a new subtle allele containing a point mutation in the 159

extracellular portion. Structural analysis suggests that this mutation likely disrupts the 160

formation of hydrogen bonds among BRI1, brassinolide (BL), and BAK1. A third 161

interesting mutant is bri1-706, containing a point mutation in the 8th LRR of the 162

extracellular portion of BRI1. bri1-706 shows a subtle aerial part defective phenotype 163

compared to wild-type (WT) plants, but its root growth is largely insensitive to 164

exogenously applied BL. The new mutants identified from these studies can be used 165

as genetic tools for further dissecting the functions of BRI1, as well as utilizing as 166

references for studying the biological functions of other RLKs in plants. 167

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RESULTS 169

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A series of new bri1 alleles were identified via TILLING analyses 171

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BRI1, the major receptor of brassinosteroids in Arabidopsis, contains multiple 173

functional domains (Li and Chory, 1997; Friedrichsen et al., 2000). Mutational 174

analyses have helped to characterize the biological significance of each of these 175

domains. To further dissect the roles of BRI1 in the BR signaling pathway, we tried to 176

identify all possible BRI1 mutations and identify the mutants with altered phenotypes. 177

TILLING is a reverse genetic method using a high-throughput screening 178

technology to detect point mutations from an EMS mutagenized library (McCallum et 179



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al., 2000). Using this approach, a large number of mutations can be isolated for a 180

specific target gene. TILLING has been used to generate mutations for a number of 181

important genes including BRI1 in Arabidopsis (Till et al., 2003). All 87 BRI1 182

TILLING mutations were obtained from the Arabidopsis Biological Resource Center 183

(ABRC) and 83 mutations were confirmed by a dCAPs method (Neff et al., 1998). 184

These mutations are distributed throughout the entire BRI1 sequence, especially in 185

LRR1-10 of its extracellular portion, “island” and kinase domain (Supplemental 186

Figure S1). These mutations were generated in Columbia (Col-0) background 187

containing an er mutation. A high dose of EMS could introduce mutations in other 188

genes that could result in BRI1-unrelated phenotypes. In order to remove those 189

additional mutations, we backcrossed the mutants with Col-0 for at least three 190

generations. Offspring plants containing BRI1 mutations were selected by using the 191

dCAPs approach (Neff et al., 1998). After backcrossing three times, most mutations 192

were found to exhibit no morphological differences from wild-type plants. Only 9 193

mutations consistently exhibit typical bri1-like phenotypes. These mutants were 194

named in the order of their identification, from bri1-702 to bri1-711 (Figure 1, Table 195

1). 196

To further confirm their bri1-related phenotypes, we carried out additional two 197

backcrosses for the 9 new mutants isolated via TILLING. In the F2 generation of the 198

third backcrossing, the phenotypes of bri1-702, bri1-705, bri1-706, bri1-710 and 199

bri1-711 were segregated out as single recessive alleles with a ratio close to 3:1. 200

However, for strong alleles, the ratio is less than 4:1, which might be caused by lower 201

germination rates as observed previously (Steber and McCourt, 2001). Thus, the 202

phenotype appears to be caused by a single locus for all 9 different mutants. bri1-702 203

shows a weak bri1 phenotype similar to bri1-5, bri1-9 and bri1-301 (Figure 2A) 204

(Noguchi et al., 1999; Xu et al., 2008). In comparison, bri1-705, bri1-706, bri1-710 205

and bri1-711 show even weaker phenotypes than bri1-702, which were therefore 206

named as subtle alleles in this study. Whereas bri1-703, bri1-704, bri1-708, and 207

bri1-709 show severe phenotypes similar to a previously reported bri1 null allele, 208

bri1-701 (Figure 2A) (Gou et al., 2012). Interestingly, bri1-707 and bri1-301 both 209



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have mutations in Gly989, but with different amino acid substitutions. As a 210

consequence, bri1-301 shows a weak bri1 phenotype (Xu et al., 2008), whereas 211

bri1-707 does not show any defective phenotypes. Similarly, bri1-708 and 212

bri1-8/108-112 bear different mutations at the same residue. While bri1-8/108-112 are 213

intermediate bri1 mutants (Noguchi et al., 1999), bri1-708 shows a null bri1 214

phenotype (Figure 2A). Statistically, all these 9 new bri1 mutants show significantly 215

reduced growth (Figure 2B). 216

To exclude the possibility that the phenotypes are caused by mutations of other 217

genes closely linked to BRI1, which are not easily segregated out by backcrossing, we 218

crossed these mutants with a number of known bri1 weak alleles. If the phenotype is 219

caused by a mutation in a different gene, the F1 seedlings should show a wild-type 220

phenotype due to functional complementation. All the obtained F1 seedlings show 221

bri1 like phenotypes (Figure 3A). In addition, we transformed the wild-type BRI1 222

sequence driven by its native promoter into these 9 different bri1 mutant alleles. The 223

transgenic plants showed BRI1-overexpressing phenotypes in WT background (Figure 224

3B) (Wang et al., 2001; Nam and Li, 2002). We next transformed the genomic DNA 225

sequences (containing BRI1 promoter and its coding sequences) of bri1-702 and 226

bri1-705 to the null mutant, bri1-701. The resulting transgenic plants resembled the 227

phenotypes of bri1-702 and bri1-705, respectively (Figure 3C). These genetic and 228

transgenic results demonstrated that all 9 new mutants are truly allelic to bri1. 229

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Characterization of newly identified bri1 mutants 231

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Root inhibition analysis indicated that bri1-702 and bri1-705 are less sensitive to 233

exogenously applied BL (Figure 4A). It is interesting that the rosette of bri1-706 is 234

significantly bigger than bri1-702 and bri1-705 (Figure 2A), but its root growth is 235

almost completely insensitive to BL treatment, similar to that of null bri1 mutants 236

(Figure 4A and 4D). bri1-707, bri1-710 and bri1-711 show slightly reduced 237

sensitivity to BL compared to Col-0 (Figure 4B). All new bri1 strong mutants, 238

including bri1-703, bri1-704, bri1-708 and bri1-709, are insensitive to BL similar to 239



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bri1-701 (Figure 4C) (Gou et al., 2012). Previous studies indicated that bri1 weak 240

mutant show reduced sensitivity to BL but increased sensitivity to brassinazole (BRZ), 241

a specific BR biosynthetic inhibitor (Asami et al., 2000; Yin et al., 2002). We 242

therefore tested the sensitivity of these new bri1 alleles to BRZ under darkness. As 243

expected, the hypocotyl growth of weak and subtle alleles exhibited hypersensitivity 244

to BRZ, whereas all strong alleles are insensitive to the BRZ treatment (Figure 4E). 245

These data indicated the new bri1 alleles exhibit typical bri1 phenotypes and reduced 246

sensitivity to exogenously applied BL. 247

Previous studies also indicated that, upon application of exogenous BL, the 248

expression of the BR biosynthesis gene CPD is down-regulated and the expression of 249

a BR response gene, SAUR-AC1, is up-regulated (Li et al., 2001; Yin et al., 2005). In 250

addition, the phosphorylation status of BES1 also can be used as an indicator of 251

downstream signaling response to the BL treatment (Yin et al., 2002; Sun et al., 2010; 252

Yu et al., 2011). Quantitative real-time PCR was performed to examine the expression 253

levels of CPD and SAUR-AC1 in WT and newly identified bri1 mutants treated with 254

or without 1 μM BL (Figure 5A and 5B). Similar to previous reports, the expression 255

of SAUR-AC1 was increased dramatically in Col-0 but had no significant change in 256

bri1-701 after the BL treatment. The expression of SAUR-AC1 in the newly identified 257

weak and subtle bri1 alleles exhibited reduced sensitivity to the BL treatment, 258

whereas in newly identified strong bri1 alleles, the expression of SAUR-AC1 is 259

insensitive to the treatment of BL and remained at a lower level of expression with or 260

without the treatment (Figure 5A). Similar to the SAUR-AC1 response, the CPD 261

responses of bri1-702 and bri1-705 showed reduced sensitivity to the BL treatment 262

(Figure 5B). Although the expression levels of CPD in BR-treated bri1-706, bri1-707, 263

bri1-710, and bri1-711 decreased relatively to the same degree compared to Col-0, 264

basal expression levels of CPD without BL treatment were higher than WT, 265

suggesting that the BR signaling is indeed partially altered in these mutants (Figure 266

5B). 267

We next investigated the phosphorylation status of BES1 in WT and in the newly 268

identified bri1 mutants with or without 1 μM BL application (Figure 5C and 5D). In 269



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Col-0, two almost equal intensity bands, representing phosphorylated and 270

unphosphorylated forms of BES1 were detected without the treatment of BL. After 271

the BL treatment, phosphorylated BES1 was greatly reduced and unphosphorylated 272

BES1 was significantly accumulated in Col-0, suggesting that the BR signaling 273

pathway is functional. In bri1-702 and bri1-705, only a small amount of 274

unphosphorylated BES1 was detected after the BL treatment. In the strong bri1 alleles 275

bri1-701, bri1-703, bri1-704, bri1-708, and bri1-709, the accumulation of 276

unphosphorylated BES1 could not be easily observed after the treatment of BL. In 277

subtle alleles, bri1-711, bri1-710, and bri1-706, the accumulation of 278

unphosphorylated BES1 is similar to that in Col-0 upon the treatment of 1μM BL. It is 279

intriguing that bri1-301 and bri1-707 contain different missense mutations at the same 280

residue, but the BES1 response to BL is totally different. bri1-301 remains partial 281

sensitivity while bri1-707 is completely sensitive to the treatment of BL (Figure 5C 282

and 5D). These molecular and biochemical results confirmed that bri1-706, bri1-710, 283

and bri1-711 are subtle alleles of bri1. 284

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bri1-702, with a point mutation in the activation loop of BRI1, shows reduced 286

autophosphorylation activity 287

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Autophosphorylation, especially the ‘pocket opening’ of the activation loop, is a 289

common activation mechanism for protein kinases (Oh et al., 2000). In order to 290

understand whether the mutations in the newly identified bri1 mutants affect the 291

kinase activity of BRI1, we used the phospho-amino acid stain Pro-Q Diamond to 292

detect the autophosphorylation activity of E. coli expressed mutant BRI1 cytoplasmic 293

domain (CD) fused with a maltose binding protein (MBP-BRI1-CD) (Figure 6A and 294

6B). After sequential staining with the Pro-Q Diamond and Coomassie blue silver, the 295

E. coli cell lysate which contains the expressed bri1-301-CD, exhibited an 296

undetectable kinase activity in vitro, similar to the results from a previous report (Xu 297

et al., 2008). However, bri1-707-CD, which bears a different substitution at the same 298

residue with bri1-301-CD, showed reduced but detectable autophosphorylation 299



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activity (Figure 6A and 6B). Interestingly, compared to the undetectable kinase 300

activities of other intracellular bri1 mutants, bri1-702, a weak allele with a mutation 301

in the activation loop, still shows autophosphorylation activity, although it is partially 302

reduced compared to WT (Figure 6A and 6B). This result indicated that mutation of 303

bri1-702 leads to reduced kinase activity of BRI1 and therefore attenuated BR signal 304

transduction. 305

To confirm these results in vivo, we generated transgenic plants overexpressing 306

BAK1-GFP in Col-0 and various genotypic backgrounds. A phosphothreonine 307

antibody was used to detect the phosphorylation on threonine residues of 308

immunoprecipitated BAK1-GFP from different backgrounds applied with or without 309

BL (Figure 6C). Similar to a previous report (Wang et al., 2008), the phosphorylation 310

level of BAK1 was strongly enhanced by the BL treatment or by overexpressing BRI1 311

in Col-0. The phosphorylation of BAK1 was reduced to an almost undetectable level 312

and exhibited no response to BL treatment in bri1 null alleles. In bri1-702 and 313

bri1-301, the phosphorylation level of BAK1 was slightly induced by exogenously 314

applied BL. Interestingly, without BL, the phosphorylation level of BAK1 was much 315

higher in these two weak alleles than even in WT (Figure 6C). These results suggested 316

that bri1-702, the only weak allele in activation loop identified so far, exhibited not 317

only a reduced autophosphorylation activity of BRI1 in vitro but also a reduced 318

sensitivity of BAK1 phosphorylation response to exogenously applied BL in vivo. 319

Even though in vitro bri1-301 autophosphorylation could not be detected as 320

previously reported (Xu et al., 2008), BAK1 phosphorylation in bri1-301 background 321

is much higher than that in bri1-701 and is induced by the addition of BL. This result 322

suggests that bri1-301 is indeed partially functional towards its substrate in vivo, 323

clarifying a previous argument regarding whether the kinase activity of BRI1 is even 324

critical to the BR signaling transduction (Xu et al., 2008). 325

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Overexpression of mBAK1 failed to generate a dominant negative phenotype in 330

bri1-705 331

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Structural analysis suggested the extracellular portions of BRI1 and BAK1 can form a 333

BL-induced complex (Santiago et al., 2013; Sun et al., 2013). Several crucial surfaces 334

for the interaction of BRI1 and BAK1 were also identified, among which were two 335

residues of BRI1 (Thr726 and Met727) directly associated with BAK1 via 336

hydrophobic interactions (Santiago et al., 2013; Sun et al., 2013). Coincidentally, 337

bri1-705, a new subtle allele with a typical BR-deficient phenotype, contained a 338

nearby mutation at Pro719 to Leu which may affect interaction between BRI1 and 339

BAK1. In order to test this hypothesis, a series of transgenic analyses were carried out. 340

Based on previous studies, overexpression of BAK1 can suppress the phenotype of 341

bri1-5, while overexpression of a kinase-inactive version of BAK1 (mBAK1), in 342

which a point mutation is introduced on a conserved lysine residue within the ATP 343

binding site, results in a dominant negative phenotype (Li et al., 2002; Gou et al., 344

2012). Both genetic suppression and dominant negative phenotypes rely on 345

interactions between the extracellular portion of BRI1 and BAK1. If a mutation in 346

BRI1 disrupts the interaction with BAK1 or mBAK1, overexpression of mBAK1 may 347

not dramatically alter the phenotype of the bri1 mutant. BAK1-GFP and mBAK1-GFP 348

were transformed to a series of weak bri1 alleles. Consistent with previous reports (Li 349

et al., 2002), the defective phenotype of bri1-5 was partially rescued by 350

overexpressing BAK1 but greatly enhanced by overexpressing mBAK1 (Supplemental 351

Figure S2). Overexpression of BAK1 or mBAK1 in bri1-301 and bri1-702 resulted in 352

phenotypes similar to those in bri1-5 (Figure 7) (Li et al., 2002). However, 353

overexpression of BAK1 or mBAK1 failed to dramatically alter the phenotype of 354

bri1-705 (Figure 7), suggesting the mutation in bri1-705 may interfere with the 355

interaction between bri1-705 and BAK1 or mBAK1. These genetic data demonstrated 356

that the BL-dependent extracellular heterodimerization of BRI1 and BAK1 is an 357

important step in the initiation of BR signaling. 358

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To further confirm this notion, we performed a molecular dynamic simulation 360

(MD) analysis of the BRI1-BL-BAK1 structure. The fluctuation of 120 ns MD 361

trajectories obtained from two simulation systems (the wild-type complex and 362

BRI1-Pro719Leu complex) were monitored by using the root mean square deviation 363

(RMSD) of the backbone atoms of BRI1, BAK1 and BL (Supplemental Figure S3). It 364

can be clearly seen that the RMSD values of both BRI1-Pro719Leu and wild-type 365

BRI1 oscillate at ~ 4 Å after 20 ns whereas the structural fluctuations of BAK1 and 366

BL are significantly higher in the BRI1-Pro719Leu complex compared to the 367

wild-type complex, implying that the Pro719Leu mutation of BRI1 may destabilize 368

the interactions of BRI1-BL and BRI1-BAK1. The simulation analysis also showed 369

that the mutation leads to significant conformation alterations of Arg717, which 370

precedes Pro719 and has the propensity to change from a random coil to a β-turn in 371

the mutant complex. Meanwhile, the β-turn structure formed by Asn705 and Ile706 in 372

the wild-type complex seems to be destabilized and prone to show a random coil 373

conformation in the mutant complex (Figure 8A). Analysis of the interaction 374

interfaces revealed the hydrogen bonding of the residue Asn705, which bridges the 375

side-chain of His61 from BAK1 and the hydroxyl group of BL, was continuously 376

interrupted in the BRI1-Pro719Leu complex during the last 20 ns simulation (Figure 377

8B). Additionally, the hydrogen bond between the main-chain oxygen atom of His61 378

from BAK1 and the hydroxyl group of BL also breaks up more frequently in the 379

BRI1-Pro719Leu complex compared to the wild-type complex (Figure 8B). Taken 380

together, these results suggest the mutation in bri1-705 results in significant local 381

conformational changes involving the residue Asn705 that interacts with both BAK1 382

and BL, thus destabilizing the pairwise interactions among BRI1, BAK1 and BL 383

(Figure 8C). 384

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bri1 point mutants exhibiting defective phenotypes all bear point mutations 386

within conserved residues among BRI1s and BRLs 387

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Eighty-three missense mutations of BRI1 were isolated in this study, among which 9 389



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point mutations resulted in typical bri1 phenotypes including one mutation that 390

generated a premature stop codon, and 74 point mutations did not show any 391

significant phenotypes in normal laboratory growing conditions. There were 16 392

different bri1 point mutants identified in previous reports (premature stop mutants are 393

not included). Altogether, 98 point mutations of BRI1 have been found so far. We 394

were curious whether these 24 bri1 point mutants (16 previously identified plus 8 395

newly identified) with mutant phenotypes all contain point mutations in conserved 396

residues. We thus carried out a sequence alignment among 70 BRI1s or BRLs from 18 397

sequenced flowering plant species (Figure 9A). As expected, all of these mutants are 398

mutated at conserved residues, but their phenotypes are not positively related to the 399

degree of conservation. Surprisingly, not all mutations of conserved residues exhibit 400

defective phenotypes (Figure 9A). As BRI1 is a typical LRR-RLK with multiple 401

functional domains, we also performed sequence analysis among all LRR-RLKs from 402

Arabidopsis thaliana (Figure 9B). These results indicated that not all mutation 403

residues of 24 bri1mutants are conserved among all LRR-RLKs. These residues may 404

be particularly important for specific BRI1 functions which have been evolutionarily 405

selected. We also found that not all mutations of conserved residues among all 406

LRR-RLKs exhibit defective phenotypes (Figure 9B). 407

408

DISCUSSION 409

410

The activation loop is a crucial region for protein kinase activity (Oh et al., 2000). 411

Sequence analysis indicated most residues in the activation loop are extremely 412

conserved in 70 BRI1s/BRLs obtained from 18 sequenced flowering plant species 413

(Supplemental Figure S4A). Besides, there are several residues in the activation loop 414

of BRI1 that are also conserved in all Arabidopsis LRR-RLKs (Supplemental Figure 415

S4B). Two new bri1 strong alleles, bri1-703 and bri1-704, contain mutations in the 416

last and first residues of the BRI1 activation loop respectively, and both of which are 417

extremely conserved not only in BRI1s or BRLs but also in all other Arabidopsis 418

LRR-RLKs. Two previously reported alleles, bri1-103/104 and bri1-115, with 419



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mutations on extremely conserved residues among BRI1s or BRLs but less conserved 420

among all other LRR-RLKs, also show strong bri1 phenotypes (Supplemental Figure 421

S4) (Li and Chory, 1997; Friedrichsen et al., 2000). We found that bri1-702, the only 422

weak allele in the activation loop of BRI1, contains a mutation in Pro1050 which is 423

extremely conserved in BRI1s or BRLs but not conserved in all other LRR-RLKs 424

(Supplemental Figure S4). However, there is also a mutation found via TILLING in 425

Arg1032Lys which has the same degree of conservation with bri1-103/104 among 426

BRI1s or BRLs but showed no defective phenotypes, possibly because it is mutated to 427

lysine, which shows similar degree of conservation with arginine in other LRR-RLKs 428

(Supplemental Figure S4). Among all Arabidopsis LRR-RLKs, several residues 429

mutated in bri1 alleles are not even conserved. We suggest that these mutation 430

residues may be related to the specificity of the BRI1-mediated signaling pathway 431

(Figure 9B). 432

In previous studies, the importance of the BRI1 kinase activity was questioned 433

because bri1-301-KD showed no kinase activity in vitro, either via an 434

autophosphorylation assay or an analysis for its phosphorylation activity towards 435

BAK1, but exhibits a weak bri1 phenotype (Xu et al., 2008). In our studies, 436

bri1-301-CD fusion protein extracted from E. coli also could not be stained by 437

phosphoprotein diamond Pro-Q (Figure 6A and 6B). However, we noticed that unlike 438

a bri1 null allele, the BAK1 phosphorylation level in bri1-301 is even higher than that 439

of wild-type as detected by immunoblotting using a phosphothreonine antibody 440

(Figure 6C). This is possibly caused by higher endogenous levels of BL in bri1-301 as 441

was found in other bri1 mutants (Noguchi et al., 1999). The phosphorylation level of 442

BAK1 in bri1-301 can be significantly induced by BL in vivo (Figure 6C). This result 443

indicated bri1-301-CD possesses kinase activity for its substrate BAK1 in vivo. The 444

undetectable autophosphorylation of bri1-301-CD in vitro may be caused by protein 445

misfolding when expressed in E. coli. 446

In this study, we also have some interesting findings from analyzing new bri1 447

mutant alleles. For example, bri1-707 (Gly989Glu, Col-0 accession) contains the 448

same mutation as bri1-301 (Gly989Ile, Col-0 accession) but with a different amino 449



16

acid substitution. As a result, bri1-707 shows a WT-like phenotype (Figure 2). 450

Actually, the change of Gly to Glu is predicted to substitute a larger side chain than 451

Gly to Ile because of an additional carboxyl group in Glu. Similarly, the new strong 452

allele bri1-708 (Arg983Gly, Col-0 accession) also bears a point mutation at the same 453

residue as bri1-8 (Arg983Gln, WS2 accession) and bri1-108-112 (Arg983Gln, Col-0 454

accession). However, the Arg to Gly substitution causes a greater phenotypical 455

alteration than the Arg to Gln substitution. These results indicated that the 456

mechanisms of point mutation are complicated and may involve in structural changes. 457

We identified an extracellular subtle mutant bri1-705, which has an amino acid 458

substitution close to the BRI1-BAK1 interaction surface. Unlike other weak alleles, 459

such as bri1-5, bri1-702 and bri1-301, overexpression of mBAK1 in bri1-705 failed to 460

generate a dominant negative phenotype (Figure 7). This result suggested that the 461

mutation in bri1-705 may affect the interaction between the extracellular portions of 462

BRI1 and BAK1. This is further supported by the MD simulation results, indicating 463

that the mutation in bri1-705 results in significant local conformational changes, 464

causing the disruption of three pairs of hydrogen bonds formed between 465

BRI1-Asn705 and BAK1-His61, BRI1-Asn705 and BL, and BAK1-His61 and BL. 466

Alterations of this hydrogen bonding network could potentially destabilize the 467

pairwise interactions among BRI1, BAK1 and BL and lead to decreased binding 468

affinity of the BRI1-BAK1 extracellular portions. Our data therefore provide 469

additional genetic and structural evidence for the crucial role of BL-dependent 470

BRI1-BAK1 heterodimerization in the early events of BR signaling. 471

During our study, we identified another surprising bri1 mutant, bri1-706. 472

bri1-706 only shows a subtle morphological phenotype compared to other weak 473

alleles isolated so far (Figure 2). However, root inhibition and hypocotyl promotion 474

assays showed that bri1-706 is greatly insensitive to the treatment of BL (Figure 4A, 475

Supplemental Figure S5A). When pBRI1::BRI1 was introduced in bri1-706, both the 476

phenotype and insensitivity to BL were completely restored (Figure 3B, Supplemental 477

Figure S5B). Endo H analyses indicated that bri1-706 proteins are partially retained in 478

ER in 10-day-old seedlings, in which roots and shoots of the seedlings showed no 479



17

significant differences (Supplementation Figure S5C-D and S6). But CPD 480

down-regulation and unphosphorylated BES1 accumulation in response to exogenous 481

BL in bri1-706 are similar to those of wild-type seedlings (Supplemental Figure 482

S5E-G). This is the first bri1 mutant showing that phenotypic severity is not 483

positively correlated to the degree of insensitivity to exogenous BL application. These 484

data suggest that the specific mutation found in bri1-706 may have destructed the 485

interaction of bri1-706 with an unknown protein which may regulate a branch of the 486

BR signaling pathway. Detailed molecular mechanisms regarding how bri1-706 487

affects root growth sensitivity to BL need to be further investigated in the near future. 488

We identified a strong allele, bri1-709, in which a point mutation results in a 489

premature stop codon within the juxtamembrane region (Supplemental Figure S7A). 490

Interestingly, a specific band which is smaller than that in Col-0 can be detected by an 491

immunoblotting assay using total proteins from bri1-709 plants with an anti-BRI1 492

antibody (Supplemental Figure S7B). This result suggests that the early stop codon of 493

bri1-709 did not disrupt the protein transport of BRI1, and that a partial BRI1 protein 494

without the kinase domain and the carboxyl terminus is expressed in bri1-709. This 495

mutant can be used for future genetic and biochemical analyses. 496

In previous studies, two extracellular weak alleles, bri1-5 and bri1-9, were found 497

to be retained in the endoplasmic reticulum (ER), because the mutational BRI1 498

proteins interact with ER chaperones and fail to pass the ER quality control system 499

(Jin et al., 2007; Hong et al., 2008; Jin et al., 2009). In order to test whether BRI1 is 500

retained in the ER for our newly identified extracellular mutation alleles, we 501

performed an Endo H analysis (Supplemental Figure S6). The results indicated that 502

BRI1 is not retained on ER in bri1-710 and bri1-711, and partially retained on ER in 503

bri1-705 and bri1-706. In bri1-705 and bri1-706, there is still a considerable amount 504

of BRI1 which is resistant to Endo H cleavage, suggesting partially retained bri1-705 505

or bri1-706 on ER may not be the main reason causing their defective phenotypes. 506

507

508

509



18

CONCLUSIONS 510

511

In this study, we analyzed 83 BRI1 point mutations generated by TILLING, among 512

which 9 mutants showed typical bri1 mutant phenotypes. bri1-702 is a weak allele. 513

bri1-705, bri1-706, bri1-710, and bri1-711, are subtle alleles. bri1-703, bri1-704, 514

bri1-708, and bri1-709 are strong alleles, similar to bri1-701 (Figure 1, Table 1). 515

bri1-702, the first weak allele in the activation loop of BRI1 identified so far, 516

exhibited not only reduced autophosphorylation activity of BRI1 in vitro but also 517

reduced sensitivity of BAK1 phosphorylation response to exogenously applied BL in 518

vivo (Figure 6). bri1-705, a new subtle allele in the extracellular portion, contains a 519

BRI1 mutation that may disrupts the formation of hydrogen bonds among BRI1, BL, 520

and BAK1 (Figure 8). Surprisingly, bri1-706, a subtle morphological mutant with a 521

mutation in the extracellular portion of BRI1, showed insensitive root growth 522

inhibition to exogenously applied BL which is similar to the null bri1 mutants (Figure 523

2A and 4A). Identification of unexpected characteristics of bri1-706 suggests there are 524

still many unknown aspects in the early events of the BR signaling pathway waiting to 525

be elucidated in the future. 526

527

MATERIALS AND METHODS 528

529

Plant materials, growth conditions and mutants detection 530

531

Original bri1 TILLING seeds obtained from ABRC are all in Col-0 accession which 532

contains an er mutation. After er and additional mutations were segregated out via 533

backcrossing for at least three generations, each homozygous bri1 was isolated and 534

used for phenotypic determination and detailed analyses. Other known bri1 mutants 535

used in this study include bri1-5 (WS2 background), bri1-9 (Col-0 background)， 536

bri1-301 (Col-0 background) and bri1-701 (SALK_116202). All plants were grown in 537

a greenhouse under a long-day lighting condition (16 h light and 8 h dark) or under 538

darkness at 22˚C. Seedlings were grown in 1/2 MS agar plates or liquid media 539



19

supplemented with 1% (w/v) sucrose. 540

dCAPs approach was used for confirming the point mutations (Neff et al., 1998). 541

dCAPS Finder 2.0 (http://helix.wustl.edu/dcaps/dcaps.html) was used for designing 542

mismatched PCR primers to generate or disrupt a restriction enzyme recognition site 543

relative to the mutation (Neff et al., 2002). All primers and enzymes used in this study 544

for genotyping bri1 TILLING mutations are listed in Supplemental Table S1. 545

546

Root inhibition and hypocotyl growth assays 547

548

Seeds were surface sterilized with 75% (w/v) ethanol for 30 seconds, followed by 1% 549

NaClO for additional 7 min, and washed with desterilized water for 5 times. The 550

seeds were then placed on 1/2 MS plates with 0.8% (w/v) agar, 1% (w/v) sucrose, and 551

different concentrations of 24-epiBL (Sigma, St. Louis, MO) or brassinazole (Santa 552

Cruz Biotechnology). The seeds were vernalized at 4˚C for 3 days and transferred to 553

different growth conditions as indicated in the figure legends. Before placed in the 554

dark, plates were exposed to white light for 6 hours to induce germination. All 555

measurements were carried out using ImageJ (http://rsb.info.nih.gov/ij/). 556

557

Vector construction and transgenic plants generation 558

559

Gateway technology (Invitrogen, Life Technologies) was used in cloning all genes 560

into expression vectors in this study. The full-length CDS fragments of BRI1, 561

BRI1-CD and BAK1 were amplified and cloned into a pDONR/Zeo entry clone vector. 562

Site-directed mutagenesis was carried out for generating mutated entry clones of BRI1, 563

BRI1-CD and BAK1 based on the method described previously (Gou et al., 2010). All 564

the cloned genes were sequence verified. Genes in the entry clone vectors were then 565

cloned into various destination vectors for different purposes such as 566

pBRI1-GWR-Flag, pBIB-BASTA-35s-GWR-Flag and pBIB-HYG-35s-GWR-GFP. All 567

expression constructs were transferred into appropriate plant materials by a floral dip 568

method (Clough and Bent, 1998). 569



20

RNA extraction and quantitative Real-time PCR 570

571

Seven-day-old seedlings of Col-0 and bri1 mutants grown on 1/2 MS plates were 572

collected and then grown with or without 1 μM 24-epiBL in liquid media for 4 hours. 573

Total RNAs were extracted using an RNA simple total RNA kit (Tiangen, China) and 574

reverse transcribed to total cDNAs utilizing M-MLV a reverse transcriptase 575

(Invitrogen, Life Technologies). The quantitative Real-time PCR was performed by a 576

StepOnePlus Real-Time PCR System (Applied Biosystems) utilizing SYBR Green 577

reagent (Takara, Japan). Detailed experimental procedures were the same as 578

previously reported (Zhao et al., 2016). 579

580

Membrane protein isolation, immunoprecipitation, Western blotting and 581

phosphoprotein staining 582

583

Ten-day-old seedlings of 35S::BAK1-GFP 35S::BRI1-FLAG, Col-0 35S::BAK1-GFP, 584

bri1-702 35S::BAK1-GFP, bri1-301 35S::BAK1-GFP, or bri1-701 35S::BAK1-GFP 585

were treated with or without 100 nM 24-epiBL for 1.5 hours and then grounded to 586

fine powder in liquid N2. The membrane protein isolation procedure was the same as 587

previously reported (Li et al., 2002). The soluble protein samples were 588

immunoprecipitated utilizing an anti-GFP antibody (Invitrogen, Carlsbad, CA) 589

combined with Protein A/G Plus-Sefinose Resin (BBI, Canada). The 590

immunoprecipitated proteins were separated on 10% SDS-PAGE and tested by 591

Western analyses with anti-GFP and anti-phosphothreonine antibodies. 592

The same plant materials used for quantitative Real-time PCR were also used in 593

detection of BES1 phosphorylation status. Total proteins were separated on 12% 594

SDS-PAGE and detected via a specific anti-BES1 antibody (made by Jia Li’s lab). 595

The transgenetic plants in Figure 7 were identified by detecting their GFP tag utilizing 596

an anti-GFP antibody (Invitrogen, Carlsbad, CA). The Endo H analyses shown in 597

Supplemental Figure S5 and S6 were performed as previously described (Hong et al., 598

2008). The total proteins of WT and mutants in Supplemental Figure S7 were 599



21

separated on 8% SDS-PAGE and detected via a specific anti-BRI1 antibody (Agrisera, 600

A177246, Sweden). Horseradish peroxidase-linked anti-rabbit or anti-mouse antibody 601

was used as a secondary antibody, and the signal was detected by Western Lightning 602

Chemiluminescence Reagent Plus (Perkin-Elmer, Waltham, MA) in all Western blot 603

experiments. 604

For the phosphoprotein staining assay, the cytoplasmic domain sequences of WT 605

BRI1 and mutated BRI1 (residues 815–1196) were cloned into the expression vector 606

pMAL-cRI-MBP-GWR. The recombinant proteins were expressed in E. coli and 607

induced by 0.1mM IPTG for 6 hours at 18˚C. The cell lysates were boiled and 608

centrifuged. The supernatant was separated on 10% SDS-PAGE and sequentially 609

stained with Pro-Q Diamond (Invitrogen, Carlsbad, CA) and Coomassie blue silver as 610

previously described (Taylor et al., 2013). 611

612

Molecular dynamics simulation analysis 613

614

The initial complex coordinates of BRI1-BAK1-BL were retrieved from the PDB 615

database (http://www.rcsb.org) under the accession code 4M7E (Sun et al., 2013). MD 616

simulations were carried out using the AMBER 10 software package (Case et al., 617

2005) to check the stability of the BRI1 and BAK1 in complex with BL. We used the 618

AMBER ff12SB (Hornak et al., 2006) force field for the protein and water and the 619

general AMBER force field (GAFF) (Wang et al., 2004) for the BL molecule. Atom 620

types and AM1-BCC atomic charges were generated for BL using the Antechamber 621

module. The LEaP module of the AMBER10 software package was used to prepare 622

the protein-ligand complex. The complex was solvated using the explicit TIP3P 623

(Jorgensen et al., 1983) water model, which extended a minimum 10 Å distance from 624

the box surface to any atom of the solute. Two consecutive steps of minimization were 625

carried out. All bond lengths were constrained using the SHAKE algorithm (Ryckaert 626

et al., 1977), and the equations of motion were integrated with 2 fs time step using the 627

Verlet leapfrog algorithm. To eliminate possible bumps between the solute and the 628

solvent, the entire system was minimized in two steps. First, the complex was 629



22

restrained with a harmonic potential with a force constant k=50 kcal mol-1Å-2. The 630

water molecules and counter ions were optimized using the steepest descent method 631

of 1,000 steps, followed by the conjugate gradient method for 2,000 steps. Second, the 632

entire system was optimized using the first step method without any constraints. 633

Subsequently, the entire system was heated gradually in the NVT ensemble from 0 to 634

300k over 400ps, with a weak restraint (k=5 kcal mol-1Å-2) for the complex (Wu et al., 635

2016). The final coordinates obtained after the temperature equilibration simulation 636

were used for a 120 ns MD simulation during which the temperature was kept by the 637

Langevin thermostat with a collision frequency of 2 ps-1. A constant pressure periodic 638

boundary was used to maintain the pressure of the system using an isotropic position 639

scaling algorithm with a relaxation time of 2 ps. After MD simulation, distances 640

between two atoms were calculated using the cpptraj program, and the dictionary of 641

secondary structure of protein (DSSP) program developed by Kabsch and Sander was 642

used to assign the secondary structures of the BRI1-BAK1-BL complex (Kabsch and 643

Sander, 1983). All the structure figures were prepared using PyMol (www.pymol.org). 644

645

Sequence analysis 646

647

For sequence analysis, the sequences of 70 BRI1s or BRLs from 18 flowering plants, 648

and 223 LRR-RLK sequences from Arabidopsis were downloaded and analyzed in 649

software Mega (http://www.megasoftware.net/), the final alignment data was 650

generated to a logo (Figure 9 and Supplemental Figure S4) on a website 651

(http://weblogo.berkeley.edu/logo.cgi). 652

653

SUPPLEMENTAL MATERIALS 654

655

Supplemental Table S1. List of primers and enzymes used in this study for 656

genotyping bri1 TILLING mutations. 657

Supplemental Figure S1. Eighty-three total mutations of BRI1 identified in this study 658

and 22 previously reported bri1 mutants. 659



23

Supplemental Figure S2. Overexpression of mBAK1 in bri1-5 resulted in a dominant 660

negative phenotype. 661

Supplemental Figure S3. Monitoring of the equilibration of the MD trajectories of 662

the wild-type complex (colored in black) and BRI1-Pro719Leu complex (colored in 663

red). 664

Supplemental Figure S4. Sequence analyses of the BRI1 activation loop. 665

Supplemental Figure S5. Endo H cleavage of BRI1, responses of BES1 666

phosphorylation and CPD expression to BL treatment showed no significant 667

differences between shoots and roots of bri1-706 seedlings. 668

Supplemental Figure S6. Endo H analysis indicated that BRI1 is not retained in the 669

endoplasmic reticulum (ER) in bri1-710 and bri1-711, and partially retained in the ER 670

in bri1-705 and bri1-706. 671

Supplemental Figure S7. In bri1-709, the mutation results in a premature stop 672

codon. 673

674

ACKNOWLEDGMENTS 675

676

We thank Jia Li lab member, Yao Xiao, for generating the BES1 antibody. We also 677

thank Steven Henikoff and his team for their hard work on the 678

Arabidopsis TILLING Project. All the seeds were purchased from ABRC. 679

680

681

682

683

684

685

686

687

688



24

Table 1. bri1 alleles (For references, please see Figure 1)

Allele Base pair change

AccessionAllelic strength

Possible mechanism

bri1-1 G2725A Col-0 Strong unknown

bri1-3 4-bp deletion after 2745

WS2 Strong Premature stop

bri1-4 10-bp deletion after 459

WS2 Strong Premature stop

bri1-5 G206A WS2 Weak ER retention

bri1-5R1 G260A bri1-5 Weak Partially restore ER retention of bri1-5

bri1-6/119 G1931A En-2 Weak unknown

bri1-7 G1838A WS2 Weak unknown

bri1-8/108 -112

G2948A WS2/ Col-0

Inter- mediate

Autophosphorylation cannot be detected in vitro

bri1-9 C1985T WS2 Weak ER retention

bri1-101 G3232A Col-0 Strong Autophosphorylation cannot be detected in vitro

bri1-102 C2249T Col-0 Strong unknown

bri1-103/ 104

G3091A Col-0 Strong unknown

bri1-105- 107

C3175T Col-0 Strong unknown


bri1-114/ 116

C1747T Col-0 Strong unknown


bri1-117/ 118

G3415A Col-0 Strong unknown

bri1-120 T1196C Ler Weak unknown



25

bri1-201 G1831A WS2 Strong unknown

bri1-202 C2854T WS2 Strong unknown

bri1-301 GG2965/6AT Col-0 Weak

Autophosphorylation of bri1-301 cannot be detected in vitro but transphosphorylation of BAK1 can be detected in vivo

bri1-701 T-DNA insertion

Col-0 Strong Knock-out of BRI1

bri1-702 C3148T Col-0 Weak Reduced autophosphorylation in vitro



bri1-705 C2156T Col-0 Subtle Disrupt the formation of hydrogen bonds among BRI1, BL, and BAK1

bri1-706 C758T Col-0 Subtle unknown

bri1-708 C2947G Col-0 Strong Autophosphorylation cannot be detected in vitro

bri1-709 G2543A Col-0 Strong Premature stop

bri1-710 G1858A Col-0 Subtle unknown

bri1-711 G2236A Col-0 Subtle unknown

689

690

691

692

693

694

695

696

697



26

FIGURE LEGENDS 698

699

Figure 1. Diagram showing all bri1 mutants identified thus far, including 9 new 700

alleles identified by this study. New mutants are labeled in red and known mutants 701

are labeled in black. Known bri1 mutants include bri1-1 (Clouse et al., 1996; 702

Friedrichsen et al., 2000), bri1-3, bri1-4, bri1-5, bri1-6, bri1-7, bri1-8, bri1-9 703

(Noguchi et al., 1999), bri1-5R1 (Belkhadir et al., 2010), bri1-101, bri1-102 704

bri1-103/104, bri1-105-107, bri1-108-112, bri1-113, bri1-114/116, bri1-115, 705

bri1-117/118, bri1-119 (Li and Chory, 1997; Friedrichsen et al., 2000), bri1-120 706

(Shang et al., 2011), bri1-201, bri1-202 (Domagalska et al., 2007), bri1-301 (Xu et al., 707

2008), and bri1-701 (Gou et al., 2012). 708

709

Figure 2. New bri1 mutants identified in this study and their phenotypes. (A) 710

Phenotypes of mutants and wild-type seedlings. The picture was taken 3 weeks after 711

germination. (B) Rosette width and height of the mutants and wild-type seedlings. 712

Rosette width was measured 3 weeks after germination. Height was measured when 713

growth was completely finished. T-tests were carried out to show the significance 714

between each allele and Col-0. Each data shown is the average and SD (n≥20). ***, 715

P<0.001. ns, not significant. 716

717

Figure 3. Complementation analyses confirm that all mutants are alleles of bri1. 718

(A) The phenotypes of new bri1 weak or subtle alleles cannot be complemented by 719

other bri1 weak alleles. (B) BRI1 driven by its native promoter can completely rescue 720

the phenotypes of new bri1 weak or subtle alleles. (C) The phenotypes of bri1-702 721

and bri1-705 can be recapitulated by expressing their corresponding genomic DNA in 722

a null BRI1 mutant allele, bri1-701. Pictures were taken 4 weeks after germination. 723

724

Figure 4. All mutants show either insensitive or reduced sensitivity to 725

exogenously applied BL. (A to C) Response of root growth to the treatment of BL. 726

Seven-day-old seedlings grown on 1/2 MS media supplemented with different 727



27

concentrations of BL. (D) bri1-706 is almost completely insensitive to BL. 728

Seven-day-old seedlings grown on 1/2 MS media supplemented with or without 1μM 729

BL. The seedlings were grown under long-day light conditions in a 22˚C growth 730

chamber for A to D. (E) Response of hypocotyl growth to the treatment of BRZ. 731

Four-day-old seedlings were grown on 1/2 MS media with or without BRZ 732

application under darkness in a 22˚C growth chamber. T-tests were performed to show 733

significance between each allele and Col-0. Each data represents average and SD 734

(n≥20). ***, P<0.001. 735

736

Figure 5. Responses of downstream BR signaling components of the new mutants 737

to BL. (A and B) Transcriptional responses of SAUR-AC1 and CPD to the treatment 738

of BL. ACTIN2 was used as a reference gene. Error bars represent SD (n= 3). (C) 739

Response of BES1 phosphorylation status to the treatment of BL. Total protein was 740

extracted and immuno-blotted with an anti-BES1 antibody. (D) Coomassie blue 741

staining showing equal loading between each pair of samples in C. Seven-day-old 742

long-day grown seedlings treated with or without 1 μM BL for 4 h were used in A-D. 743

-, without BL treatment; +, with BL treatment; *, non-specific band. BES1-P, 744

phosphorylated BES1; BES1, unphosphorylated BES1. 745

746

Figure 6. In vitro and in vivo phosphorylation analyses of the BRI1, bri1, and 747

BAK1. (A) Pro-Q diamond analyses of BRI1 and various bri1 cytoplasmic domains. 748

The recombinant proteins were expressed in E. coli and total protein extracts were 749

separated on 10% SDS-PAGE. The gel was stained by Pro-Q diamond. (B) Coomassie 750

blue silver staining to show equal loading of the samples. mBRI1 contains a mutation 751

within the ATP binding site (Lys911Glu). (C) In vivo phosphorylation analyses of 752

BAK1-GFP from various bri1 mutants in response to the treatment of BL. Membrane 753

proteins were extracted from 10-day-old long-day grown seedlings treated with or 754

without 100 nM BL for 1.5h. BAK1-GFP proteins from different bri1 alleles were 755

immunoprecipitated with an anti-GFP antibody. The phosphorylation levels of BAK1 756

were detected with a phosphothreonine antibody. The immunoprecipitated 757



28

BAK1-GFP was immuno-blotted with an anti-GFP antibody to show equal loading. -, 758

without BL treatment; +, with BL treatment. 759

760

Figure 7. Overexpression of mBAK1 in bri1-301 and bri1-702 but not in bri1-705 761

resulted in dominant negative phenotypes. (A) Phenotypes of the transgenic plants 762

and their backgrounds. The pictures were taken 3 weeks after germination. (B) 763

Western blotting analyses showing the expressed BAK1-GFP and mBAK1-GFP 764

fusion proteins in transgenic plants. Total proteins from rosette leaves were extracted 765

and immuno-blotted with an anti-GFP antibody. mBAK1 contains a mutation within 766

the ATP binding site (Lys317Glu). 767

768

Figure 8. Conformational changes monitored during the last 20 ns MD 769

simulation. (A) Time evolution of the secondary structures of residue 703-721 of 770

BRI1 in the wild-type complex (left) and mutant complex (right). Compared with the 771

wild-type complex, the residue Arg717 preceding Pro719 has the propensity to change 772

from a random coil to a β-turn while Asn705 and Ile706 seem to be destabilized and 773

prone to adopt a random coil conformation in the mutant complex. (B) Monitoring 774

time evolution of the distances between the atom OD1 of BRI1-Asn 705 and ND1 of 775

BAK1-His61 (upper left panel), atom OD1 of BRI1-Asn 705 and O02 from C2 of BL 776

(upper right panel) and atom ND1 of BAK1-His61 and O03 from C3 of BL (lower 777

panel) , respectively. The distances in the wild-type complex and mutant complex are 778

colored in black and red, respectively. (C) The interaction modes of BRI1-Asn705 779

(cyan), BAK1-His61 (purple) and BL (yellow). At 110 ns, as shown in upper right 780

inset, Asn705, His61 and BL form pairwise hydrogen bonds, indicated by the close 781

distances of 2.91, 2.81 and 3.03 Å between Asn705, His61 and BL, respectively. 782

However, in the bri1-705 mutant complex shown in the lower right inset, these 783

hydrogen bonds are disrupted as evidenced by the much larger pairwise distances 784

between Asn705, His61 and BL. 785

786

787



29

Figure 9. Sequence analyses of all 98 BRI1 point mutations. (A) Sequence 788

analyses among 70 BRI1s or BRLs from 18 sequenced flowering plant species. 789

Mutants showing defective phenotypes all result from mutations of conserved 790

residues. But not all mutations in the conserved residues show defective phenotypes. 791

(B) Sequence analyses among all 223 LRR-RLKs of Arabidopsis thaliana. Not all 792

mutation sites from mutants with defective phenotypes are conserved, and vice versa. 793

Only the amino acid sites with mutations are shown. New mutants from this study are 794

labeled in red. Previously known mutants are labeled in black. New mutations without 795

significant phenotypes are labeled in grey. The size of the logo is positively correlated 796

to the degree of conservation. 797

798

799

800

801

802

803

804

805

806

807

808

809

810

811

812

813

814

815

816

817



30

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819

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Parsed CitationsAsami T, Min YK, Nagata N, Yamagishi K, Takatsuto S, Fujioka S, Murofushi N, Yamaguchi I, Yoshida S (2000) Characterization ofbrassinazole, a triazole-type brassinosteroid biosynthesis inhibitor. Plant Physiol 123: 93-99

Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Belkhadir Y, Durbak A, Wierzba M, Schmitz RJ, Aguirre A, Michel R, Rowe S, Fujioka S, Tax FE (2010) Intragenic Suppression of aTrafficking-Defective Brassinosteroid Receptor Mutant in Arabidopsis. Genetics 185: 1283-1296


Bell EM, Lin WC, Husbands AY, Yu L, Jaganatha V, Jablonska B, Mangeon A, Neff MM, Girke T, Springer PS (2012) ArabidopsisLATERAL ORGAN BOUNDARIES negatively regulates brassinosteroid accumulation to limit growth in organ boundaries. Proc NatlAcad Sci U S A 109: 21146-21151


Case DA, Cheatham TE, Darden TA, Gohlke H, Luo R, Merz KM, Onufriev AV, Simmerling C, Wang B, Woods RJ (2005) The Amberbiomolecular simulation programs. J Comput Chem 26: 1668-1688


Chaiwanon J, Wang ZY (2015) Spatiotemporal brassinosteroid signaling and antagonism with auxin pattern stem cell dynamics inArabidopsis roots. Curr Biol 25: 1031-1042


Cheng Y, Zhu W, Chen Y, Ito S, Asami T, Wang X (2014) Brassinosteroids control root epidermal cell fate via direct regulation of aMYB-bHLH-WD40 complex by GSK3-like kinases. Elife 02525


Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. PlantJ 16: 735-743


Clouse SD (1996) Molecular genetic studies confirm the role of brassinosteroids in plant growth and development. Plant J 10: 1-8Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Clouse SD, Langford M, McMorris TC (1996) A brassinosteroid-insensitive mutant in Arabidopsis thaliana exhibits multiple defectsin growth and development. Plant Physiol 111: 671-678


Clouse SD, Sasse JM (1998) Brassinosteroids: Essential regulators of plant growth and development. Annu Rev of Plant PhysiolPlant Mol Biol 49: 427-451


Domagalska MA, Schomburg FM, Amasino RM, Vierstra RD, Nagy F, Davis SJ (2007) Attenuation of brassinosteroid signalingenhances FLC expression and delays flowering. Development 134: 2841-2850


Friedrichsen DM, Joazeiro CA, Li J, Hunter T, Chory J (2000) Brassinosteroid-insensitive-1 is a ubiquitously expressed leucine-rich repeat receptor serine/threonine kinase. Plant Physiol 123: 1247-1256


Gendron JM, Liu JS, Fan M, Bai MY, Wenkel S, Springer PS, Barton MK, Wang ZY (2012) Brassinosteroids regulate organboundary formation in the shoot apical meristem of Arabidopsis. Proc Natl Acad Sci U S A 109: 21152-21157



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http://www.ncbi.nlm.nih.gov/pubmed?term=Gonzalez%2DGarcia M%2DP%2C Vilarrasa%2DBlasi J%2C Zhiponova M%2C Divol F%2C Mora%2DGarcia S%2C Russinova E%2C Cano%2DDelgado AI %282011%29 Brassinosteroids control meristem size by promoting cell cycle progression in Arabidopsis roots%2E Development 138%3A 849%2D859&dopt=abstract

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Noguchi T, Fujioka S, Choe S, Takatsuto S, Yoshida S, Yuan H, Feldmann KA, Tax FE (1999) Brassinosteroid-insensitive dwarfmutants of Arabidopsis accumulate brassinosteroids. Plant Physiol 121: 743-752


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http://scholar.google.com/scholar?as_q=A Putative Leucine-Rich Repeat Receptor Kinase Involved in Brassinosteroid Signal Transduction&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A Putative Leucine-Rich Repeat Receptor Kinase Involved in Brassinosteroid Signal Transduction&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Li&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

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http://scholar.google.com/scholar?as_q=Brassinosteroid signaling network and regulation of photomorphogenesis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wang ZY%2C Seto H%2C Fujioka S%2C Yoshida S%2C Chory J %282001%29 BRI1 is a critical component of a plasma%2Dmembrane receptor for plant steroids%2E Nature 410%3A 380%2D383&dopt=abstract

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http://scholar.google.com/scholar?as_q=BRI1 is a critical component of a plasma-membrane receptor for plant steroids&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wei Z%2C Li J %282016%29 Brassinosteroids Regulate Root Growth%2C Development%2C and Symbiosis%2E Mol Plant 9%3A 86%2D100&dopt=abstract

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http://scholar.google.com/scholar?as_q=Brassinosteroids Regulate Root Growth, Development, and Symbiosis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wei&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wu D%2C Tao X%2C Chen Z%2C Han J%2C Jia W%2C Zhu N%2C Li X%2C Wang Z%2C He Y %282016%29 The environmental endocrine disruptor p %2Dnitrophenol interacts with FKBP51%2C a positive regulator of androgen receptor and inhibits androgen receptor signaling in human cells%2E J Hazard Mater 307%3A 193%2D201&dopt=abstract

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http://scholar.google.com/scholar?as_q=A new class of transcription factors mediates brassinosteroid-regulated gene expression in arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yin&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

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http://scholar.google.com/scholar?as_q=BES1 Accumulates in the Nucleus in Response to Brassinosteroids to Regulate Gene Expression and Promote Stem Elongation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yin&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1


Yu X, Li L, Zola J, Aluru M, Ye H, Foudree A, Guo H, Anderson S, Aluru S, Liu P, Rodermel S, Yin Y (2011) A brassinosteroidtranscriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J 65: 634-646


Yuan T, Fujioka S, Takatsuto S, Matsumoto S, Gou X, He K, Russell SD, Li J (2007) BEN1, a gene encoding a dihydroflavonol 4-reductase (DFR)-like protein, regulates the levels of brassinosteroids in Arabidopsis thaliana. Plant J 51: 220-233


Zhang C, Xu Y, Guo S, Zhu J, Huan Q, Liu H, Wang L, Luo G, Wang X, Chong K (2012) Dynamics of brassinosteroid responsemodulated by negative regulator LIC in rice. PLoS Genet 8: e1002686


Zhao B, Lv M, Feng Z, Campbell T, Liscum E, Li J (2016) TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1to Regulate Early Events of the Brassinosteroid Signaling Pathway. Mol Plant 9: 582-592


Zhou A, Wang HC, Walker JC, Li J (2004) BRL1, a leucine-rich repeat receptor-like protein kinase, is functionally redundant withBRI1 in regulating Arabidopsis brassinosteroid signaling. Plant J 40: 399-409


Zhu JY, Sae-Seaw J, Wang ZY (2013) Brassinosteroid signalling. Development 140: 1615-1620Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title


http://www.ncbi.nlm.nih.gov/pubmed?term=Yu X%2C Li L%2C Zola J%2C Aluru M%2C Ye H%2C Foudree A%2C Guo H%2C Anderson S%2C Aluru S%2C Liu P%2C Rodermel S%2C Yin Y %282011%29 A brassinosteroid transcriptional network revealed by genome%2Dwide identification of BESI target genes in Arabidopsis thaliana%2E Plant J 65%3A 634%2D646&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yu X, Li L, Zola J, Aluru M, Ye H, Foudree A, Guo H, Anderson S, Aluru S, Liu P, Rodermel S, Yin Y (2011) A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J 65: 634-646

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yu&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yu&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Yuan T%2C Fujioka S%2C Takatsuto S%2C Matsumoto S%2C Gou X%2C He K%2C Russell SD%2C Li J %282007%29 BEN1%2C a gene encoding a dihydroflavonol 4%2Dreductase %28DFR%29%2Dlike protein%2C regulates the levels of brassinosteroids in Arabidopsis thaliana%2E Plant J 51%3A 220%2D233&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yuan T, Fujioka S, Takatsuto S, Matsumoto S, Gou X, He K, Russell SD, Li J (2007) BEN1, a gene encoding a dihydroflavonol 4-reductase (DFR)-like protein, regulates the levels of brassinosteroids in Arabidopsis thaliana. Plant J 51: 220-233

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yuan&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yuan&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhang C%2C Xu Y%2C Guo S%2C Zhu J%2C Huan Q%2C Liu H%2C Wang L%2C Luo G%2C Wang X%2C Chong K %282012%29 Dynamics of brassinosteroid response modulated by negative regulator LIC in rice%2E PLoS Genet 8%3A e1002686&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang C, Xu Y, Guo S, Zhu J, Huan Q, Liu H, Wang L, Luo G, Wang X, Chong K (2012) Dynamics of brassinosteroid response modulated by negative regulator LIC in rice. PLoS Genet 8: e1002686

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhang&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Dynamics of brassinosteroid response modulated by negative regulator LIC in rice.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Dynamics of brassinosteroid response modulated by negative regulator LIC in rice.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhao B%2C Lv M%2C Feng Z%2C Campbell T%2C Liscum E%2C Li J %282016%29 TWISTED DWARF 1 Associates with BRASSINOSTEROID%2DINSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway%2E Mol Plant 9%3A 582%2D592&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhao B, Lv M, Feng Z, Campbell T, Liscum E, Li J (2016) TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway. Mol Plant 9: 582-592

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhao&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhao&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhou A%2C Wang HC%2C Walker JC%2C Li J %282004%29 BRL1%2C a leucine%2Drich repeat receptor%2Dlike protein kinase%2C is functionally redundant with BRI1 in regulating Arabidopsis brassinosteroid signaling%2E Plant J 40%3A 399%2D409&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhou A, Wang HC, Walker JC, Li J (2004) BRL1, a leucine-rich repeat receptor-like protein kinase, is functionally redundant with BRI1 in regulating Arabidopsis brassinosteroid signaling. Plant J 40: 399-409

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhou&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhou&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhu JY%2C Sae%2DSeaw J%2C Wang ZY %282013%29 Brassinosteroid signalling%2E Development 140%3A 1615%2D1620&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhu JY, Sae-Seaw J, Wang ZY (2013) Brassinosteroid signalling. Development 140: 1615-1620

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhu&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Brassinosteroid signalling&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Brassinosteroid signalling&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhu&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1


1 short title: new bri1 mutations - plant physiology · 65 last two decades, over 20 different bri1...

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