2 running title - github pages

1

1

Running title: Retrograde coordinates light and hormone signals 2

3

Corresponding Author: 4

Katayoon Dehesh 5

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, 6

University of California Riverside, CA, 92521, USA. 7

Tel: 951-827-6370 8

E-Mail: [email protected] 9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

Plant Physiology Preview. Published on May 19, 2020, as DOI:10.1104/pp.20.00090

Copyright 2020 by the American Society of Plant Biologists

www.plantphysiol.orgon May 25, 2020 - Published by Downloaded from Copyright © 2020 American Society of Plant Biologists. All rights reserved.

http://www.plantphysiol.org

2

Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate 29

growth 30

Jishan Jiang1+, Yanmei Xiao2, Hao Chen1,Wei Hu2 , Liping Zeng1, Haiyan Ke1, Franck 31

A.Ditengou4, Upendra Devisetty3,5, Klaus Palme4, Julin Maloof 3, Katayoon Dehesh1* 32

33

Affiliations 34

1Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, 35

University of California, Riverside, CA, 92521, USA. 36

2Department of Molecular and Cellular Biology, University of California, Davis, CA 37

95616, USA. 38

3Department of Plant Biology, University of California, Davis, CA, 95616, USA. 39

4 University of Freiburg, Faculty of Biology; BIOSS Centre for Biological Signaling 40

Studies and ZBSA Centre for Biosystems Studies, Schänzler str.1, 79104 Freiburg, 41

Germany. 42

5Current address: Thomas W. Keating Bioresearch Building, University of Arizona, 43

Tucson, Arizona, 85721, USA. 44

+ Current address: College of Grassland Science and Technology, China Agricultural 45

University, Beijing, China. 46

*To whom correspondence should be addressed 47

One-sentence summary: The plastidial retrograde metabolite MEcPP orchestrates 48

coordination of light and hormonal signaling cascade by inducing phytochrome B 49

abundance and modulating auxin and ethylene levels. 50

Author Contributions 51

J.J. and K.D. designed the study, J.J., Y.X., H.C. W.H., U.D., H.K., and F.D. 52

performed the experiments, L.Z performed the bioinformatics analyses, J.M. and K.P. 53

provided experimental tools and K.D. wrote the manuscript. 54

55

Financial source: This work was supported by National Institute of Health 56

(R01GM107311) grant awarded to KD. 57



3

The author responsible for distribution of materials integral to the findings presented 58

in this article is Katayoon Dehesh ([email protected]). 59

Abstract 60

Exquisitely regulated plastid-to-nucleus communication by retrograde signaling 61

pathways is essential for fine-tuning of responses to the prevailing environmental 62

conditions. The plastidial retrograde signaling metabolite methylerythritol 63

cyclodiphosphate (MEcPP) has emerged as a stress signal transduced into a diverse 64

ensemble of response outputs. Here we demonstrate enhanced phytochrome B protein 65

abundance in red light–grown MEcPP-accumulating ceh1 mutant plants relative to 66

wild-type seedlings. We further establish MEcPP-mediated coordination of 67

phytochrome B with auxin and ethylene signaling pathways and uncover differential 68

hypocotyl growth of red light–grown seedlings in response to these phytohormones. 69

Genetic and pharmacological interference with ethylene and auxin pathways outline 70

the hierarchy of responses, placing ethylene epistatic to the auxin signaling pathway. 71

Collectively, our findings establish a key role of a plastidial retrograde metabolite in 72

orchestrating the transduction of a repertoire of signaling cascades. This work 73

positions plastids at the zenith of relaying information coordinating external signals 74

and internal regulatory circuitry to secure organismal integrity. 75

76

77

78

79

80

81

82

83

84

85

86

87



4

88

89

Introduction 90

Dynamic alignment of internal and external cues through activation of corresponding 91

signal transduction pathways is a defining characteristic of organisms essential for 92

fitness and the balancing act of metabolic investment in growth versus adaptive 93

responses. The integrity of these responses is achieved through finely controlled 94

communication circuitry, notably retrograde (organelle-to-nucleus) signaling cascades. 95

Despite the central role of retrograde signaling in regulation and coordination of 96

numerous adaptive processes, the nature and the operational mode of action of 97

retrograde signals have remained poorly understood. 98

Through a forward-genetic screen, we identified a bifunctional plastid-produced 99

metabolite methylerythritol cyclodiphosphate (MEcPP) that serves as a precursor of 100

isoprenoids produced by the plastidial methylerythritol phosphate (MEP) pathway and 101

functions as a stress-specific retrograde signaling metabolite (Xiao et al., 2012). We 102

further demonstrated that stress-induced MEcPP accumulation leads to growth 103

retardation and induction of selected nuclear-encoded, stress-response genes (Xiao et 104

al., 2012; Walley et al., 2015; Lemos et al., 2016; Wang et al., 2017a). We specifically 105

established that regulation of growth is in part via MEcPP-mediated modulation of 106

levels and distribution patterns of auxin (IAA) through dual transcriptional and 107

post-translational regulatory inputs (Jiang et al., 2018). 108

Auxin functions as a key hormone regulating a repertoire of plant development 109

processes including hypocotyl growth (J. Jensen et al., 1998; De Grauwe et al., 2005). 110

The auxin biosynthesis pathway that converts tryptophan (Trp) to IAA in plants is 111

established to be through conversion of Trp to indole-3-pyruvate (IPA) by the TAA 112

family of amino transferases and subsequent production of IAA from IPA by the YUC 113

family, a family of flavin monooxygenases (Zhao, 2012). Subsequently, establishment 114

of auxin gradient is achieved by transporters such as the auxin-efflux carrier 115

PIN-FORMED1 (PIN1) (Galweiler et al., 1998; Geldner et al., 2001). Interestingly, 116

IAA biosynthesis, transport, and signaling during light–mediated hypocotyl growth 117



5

are in turn regulated by ethylene (Liang et al., 2012), and conversely ethylene is 118

regulated by auxin (Vandenbussche et al., 2003; Ruzicka et al., 2007; Stepanova et 119

al., 2007; Swarup et al., 2007; Negi et al., 2010). As such, auxin-ethylene crosstalk 120

inserts an additional layer of complexity to the already intricate and multifaceted 121

growth regulatory mechanisms. 122

Ethylene in plants is derived from conversion of S-adenosyl-L-methionine (AdoMet) 123

to 1-aminocyclopropane-1-carboxylate (ACC) by ACC synthase (ACS) (Yang and 124

Hoffman, 1984), followed by conversion of ACC to ethylene catalyzed by ACC 125

oxidase (L.-C. Wang et al., 2002). Ethylene stimulates hypocotyl growth in the light 126

but inhibits it in the dark (Smalle et al., 1997; J. Jensen et al., 1998; Vandenbussche et 127

al., 2012). 128

Light signaling is a common environmental stimulus controlling developmental 129

processes through hormonal modulation, such as regulation of auxin biosynthesis and 130

signaling genes by phytochrome B (phyB) (Morelli and Ruberti, 2002; Tanaka et al., 131

2002b; Tian et al., 2002; Nozue et al., 2011; Hornitschek et al., 2012a; de Wit et al., 132

2014; Leivar and Monte, 2014). PhyB is the main photoreceptor mediating red-light 133

photomorphogenesis; phyB is activated by red light and imported into the nucleus 134

where it forms phyB-containing nuclear bodies (phyB-NBs) (Nagy and Schafer, 2002; 135

Quail, 2002). Formation of phyB-NBs depends on binding to and sequestration of the 136

basic helix-loop-helix (bHLH) transcription factors, Phytochrome Interacting Factor 1 137

(PIF1), PIF3, PIF4, PIF5, and PIF7 (Rausenberger et al., 2010; Leivar and Quail, 138

2011). The prominent role of phyB in auxin regulation is best displayed by simulation 139

of shade avoidance responses (SAR) through exogenous application of auxin or via 140

genetic manipulation of auxin (Tanaka et al., 2002a; Hornitschek et al., 2012b). In 141

addition, PIFs, specifically PIF4, PIF5, and PIF7, play a major role in regulating auxin 142

by targeting promoter elements of multiple auxin biosynthetic and signal transduction 143

genes (Franklin et al., 2011; Nozue et al., 2011; Leivar et al., 2012; Sellaro et al., 144

2012; Leivar and Monte, 2014). Moreover, the ethylene–promoted hypocotyl 145

elongation in light is regulated by the PIF3-dependent, growth-promoting pathway 146



6

activated transcriptionally by EIN3, whereas under dark conditions, ethylene inhibits 147

growth by destabilizing the ethylene response factor 1 (ERF1) (Zhong et al., 2012). 148

Here, we identify MEcPP as a retrograde signaling metabolite that coordinates 149

internal and external cues, and we further delineate light and hormonal signaling 150

cascades that elicit adaptive responses to ultimately drive growth-regulating processes 151

tailored to the prevailing environment. 152

153



7

Results 154

Elevated phyB abundance suppresses hypocotyl growth in ceh1 155

Given the stunted hypocotyl phenotype of the high MEcPP–accumulating mutant 156

ceh1, we explored the nature of the photoreceptors involved by examining hypocotyl 157

length of seedlings grown in the dark and under various monochromatic light 158

conditions. The analyses showed comparable hypocotyl lengths of dark-grown ceh1 159

and control seedlings (WT) (Fig. 1A). However, under continuous red light (Rc; 15 160

μE m-2sec-1), ceh1 seedlings displayed notably shorter hypocotyls than those of WT 161

plants (Fig. 1A). This data led us to question the role of phyB, the prominent red-light 162

photoreceptor, in regulating ceh1 hypocotyl growth. To answer this question, we 163

generated a ceh1/phyB-9 double-mutant line, and subsequently compared seedling 164

hypocotyl length with WT, ceh1, and phyB-9 seedlings grown under continuous dark 165

and Rc conditions (Fig. 1A & B). The data clearly demonstrated phyB-dependent 166

suppression of hypocotyl growth in ceh1 under Rc, as evidenced by the recovery of 167

ceh1 retarded hypocotyl growth in ceh1/phyB-9 to lengths comparable to those of 168

phyB-9 seedlings. 169

Hypocotyl growth of the aforementioned four genotypes was also examined under 170

continuous blue (Bc) and far-red (FRc) light conditions. The reduced hypocotyl 171

growth of the ceh1 mutant grown under Bc, albeit not as severe as those grown under 172

Rc, further implicate blue light–receptor cytochromes (Yu et al., 2010) in regulating 173

growth of these seedlings (Fig. S1A & B). Additionally, ceh1 and ceh1/phyB-9 174

seedlings grown under Bc exhibited equally shortened hypocotyls, and under FRc 175

light hypocotyl growth was almost similarly retarded in all genotypes (Fig. S1A & B). 176

Collectively, these results support the involvement of cryptochromes as well as phyB 177

in ceh1 hypocotyl growth, albeit to different degrees. However, the more drastic effect 178

of phyB in regulating hypocotyl growth of Rc-grown, high MEcPP–accumulating 179

seedlings, in conjunction with the supporting evidence from earlier data using white 180

light–grown ceh1 seedlings (Jiang et al., 2019), led us to primarily focus on the role of 181

phyB. 182

Next, we measured MEcPP levels in the four genotypes grown in the dark and in 183



8 various monochromatic wavelengths to examine a potential correlation between 184



9

growth phenotypes and altered levels of the retrograde signaling metabolite (Fig. 1C 185

& S1C). The analyses showed almost undetectable MEcPP levels in dark-grown 186

plants of all the genotypes, and low levels of the metabolite in Rc-grown WT and 187

phyB-9 seedlings. By contrast, ceh1 seedlings grown in Rc accumulated high MEcPP 188

levels, a phenotype that was partially (~10-fold) suppressed in ceh1/phyB-9 seedlings. 189

This reduction was not unexpected since phyB-controlled PIF regulates the expression 190

of DXS, the first MEP-pathway gene encoding the flux determinant enzyme 191

(Chenge-Espinosa et al., 2018). It is noteworthy that despite this significant reduction, 192

the MEcPP content of ceh1/phyB-9 seedlings remained ~100-fold above those of WT 193

or phyB-9 plants grown simultaneously and under the same conditions. This reduction 194

of MEcPP in ceh1/phyB-9 also occurred in seedlings grown in Bc (Fig. S1C), likely 195

because of the direct interaction between PIFs and blue light–receptor cryptochromes 196

(Pedmale et al., 2016). However, in spite of reduced MEcPP levels in Rc- or 197

Bc-grown ceh1/phyB-9 seedlings, the hypocotyl growth recovery is exclusive to 198

mutant seedlings grown in Rc (Fig. 1A-C & S1A-C), leading to the conclusion that 199

there is also a blue light–dependent pathway that regulates ceh1 hypocotyl growth in 200

Bc. Moreover, hypocotyls of all genotypes, regardless of their MEcPP levels, 201

remained stunted in FRc, a light condition known to inactivate phyB. Collectively, the 202

results further verify the function of phyB in altering the observed growth phenotype 203

of ceh1 mutant seedlings. 204

To examine the correlation between accumulation of MEcPP and alteration of growth 205

in response to red-light treatment, we further examined the hypocotyl length of Col-0 206

ecotype, Col-0 transformed with HPL:LUC construct (WT), ceh1, and complemented 207

ceh1 (CP) seedlings (Fig. 2A-B). In contrast to the stunted hypocotyl growth of ceh1, 208

these data clearly showed recovery of hypocotyl growth in CP to lengths comparable 209

to Col-0 and WT seedlings (Fig. 2A-B). 210

Next, we questioned whether phyB transcript and/or protein levels are altered in ceh1 211

mutants grown in Rc. The expression data analyses revealed similar PHYB transcript 212

levels in ceh1 and WT seedlings (Fig. S1D). To determine the hyB protein levels, we 213

performed immunoblot analyses using proteins isolated from the aforementioned 214



10

genotypes (Fig. 2C). The data showed higher PhyB levels in ceh1 versus other 215

genotypes specifically as compared with the complemented line (CP), supporting 216

conclusion that MEcPP mediates enhanced abundance of phyB. 217

To further examine the potential role of MEcPP in ceh1 in reducing growth and 218

altering phyB levels, we employed a pharmacological approach using fosmidomycin 219

(FSM), a MEP-pathway inhibitor (Fig. 2D-F). This inhibitor interferes with and 220

highly reduces the flux through the pathway and abolishes MEcPP-mediated actions 221

such as formation of otherwise stress–induced subcellular structures known as ER 222



11

bodies or furthering the reduced auxin levels in ceh1 mutant plants 223

(Gonzalez-Cabanelas et al., 2015; Wang et al., 2017b; Jiang et al., 2018). We 224

examined hypocotyl growth of red light–grown 7-day-old seedlings that were treated 225

with FSM for 3 days. These data showed enhanced hypocotyl growth of FSM-treated 226

ceh1 compared to non-treated seedlings (Fig. 2D-E). It is of note that the length of 227

FSM-treated ceh1 hypocotyls did not recover to that of the WT seedlings, suggesting 228

an inefficiency of FSM treatment and/or the presence of other regulatory factors. In 229

addition, immunoblot analysis showed a very slight reduction in phyB abundance in 230

FSM-treated ceh1 compared to non-treated seedling (Fig. 2F). There may be two 231

reasons for not detecting an overall stronger response to FSM treatment. One is the 232

very high MEcPP levels in the ceh1 mutant, and the other the degree of FSM 233

penetration. However, the clearly higher PhyB levels in the ceh1 mutant compared to 234

CP, WT, and Col lines supports the notion of MEcPP-mediated increase of phyB 235

abundance, verifying the earlier report using white light–grown seedlings (Jiang et al., 236

2019). 237

In addition to MEcPP, the ceh1 mutant accumulates substantial amounts of the 238

defense hormone salicylic acid (SA) (Xiao et al., 2012; Bjornson et al., 2017). The 239

reported involvement of phyB in SA accumulation and signaling (Chai et al., 2015; 240

Nozue et al., 2018) prompted us to examine the potential role of this defense hormone 241

in regulating ceh1 hypocotyl growth. For these experiments, we employed the 242

previously generated SA-deficient double-mutant line ceh1/eds16 (Xiao et al., 2012). 243

All four genotypes (WT, ceh1, ceh1/eds16, and eds16) displayed similar hypocotyl 244

length when grown in the dark, whereas in Rc both ceh1 and ceh1/eds16 seedlings 245

displayed equally reduced hypocotyl lengths as compared to their respective control 246

backgrounds (Fig. S1G). These results illustrate SA-independent regulation of ceh1 247

hypocotyl growth in Rc. 248

Given the well-established role of PIFs in transduction of phyB signals, we examined 249

PIFs expression levels and found significantly reduced PIF4 and -5 transcripts in 250

Rc-grown ceh1 compared to WT seedlings (Fig. S2). These data led us to genetically 251

investigate the potential role of PIFs in regulating hypocotyl length of Rc-grown ceh1 252



12 seedlings. For these experiments, we quantified hypocotyl growth of pifq (pif1, -3, -4, 253



13

and -5) alone and in lines introgressed into the ceh1 mutant background. The results 254

revealed similarly dwarf hypocotyls in ceh1/pifq and pifq backgrounds, which were 255

slightly but significantly shorter than that of ceh1 seedlings (Fig. 3A). Furthermore, 256

equally reduced hypocotyl growth in ceh1/pifq and pifq suggest that PIFs are the 257

predominant growth regulators in ceh1 under the experimental conditions employed. 258

The role of PIFs in determining hypocotyl growth was further tested by examining 259

ceh1 seedlings overexpressing PIF4 and -5 grown in Rc (Fig. 3B). The data showed 260

the expected enhanced hypocotyl growth of PIF overexpressors compared to WT 261

seedlings and recovery of the retarded growth observed in ceh1 in ceh1/PIF4 and -5 262

overexpression lines. 263

Collectively, these data illustrate growth regulatory function of PIFs, and identify 264

MEcPP–mediated transcriptional regulation of PIF4 and -5 as an integral regulatory 265

circuit controlling ceh1 hypocotyl growth. 266

Reduced expression of auxin biosynthesis and response genes in ceh1 267

To identify the downstream components of the MEcPP–mediated phyB signaling 268

cascade, we performed RNAseq profiling of WT and ceh1 seedlings grown in the 269

dark and in Rc. A multi-dimensional scaling (MDS) plot revealed significant overlap 270

between expression profiles of WT and ceh1 seedlings grown in the dark, in contrast 271

to their distinct expression profiles when grown in Rc (Fig. S3). GO-term analyses 272

identified over-representations of auxin signaling and response genes amongst the 273

significantly (≥2-fold) altered transcripts (Fig. S4). Confirmation of the data through 274

RT-qPCR identified auxin biosynthesis (YUC3 and -8) and response genes (IAA6 and 275

-19) as the most significantly differentially expressed genes under Rc conditions (Fig. 276

4A-B). We further quantified the IAA content in plants and found similar auxin levels 277

in dark-grown plans of all genotypes in contrast to significantly reduced auxin levels 278

(50%) in Rc-grown ceh1 versus WT plants (Fig. 4C). We validated this finding by 279

testing Rc-grown WT and ceh1 lines expressing the auxin signaling reporter 280

DR5-GFP (Jiang et al., 2018). The reduced GFP signal in ceh1 was on par with lower 281

IAA levels in the mutant compared to the WT seedling (Fig. 4D). 282

Next, we examined possible modulation of other phytohormones such as abscisic acid 283



14 (ABA) and jasmonic acid (JA) in response to high MEcPP levels in ceh1 seedlings 284



15

(Fig. S5). Similar ABA and JA levels found in WT and ceh1 plants grown in the dark 285

and in Rc strongly support the specificity of MEcPP-mediated regulation of auxin. 286

Enhanced tolerance of ceh1 to auxin and auxinole 287

Reduced IAA levels in ceh1 led us to examine whether external application of this 288

hormone could rescue the retarded hypocotyl growth in ceh1 seedlings. The analyses 289

showed longer hypocotyls in ceh1 seedlings treated with IAA at concentrations (10 290

and 100 M) that inhibited growth in WT seedlings (Fig. 5A-B). Interestingly, ceh1 291

and WT hypocotyls displayed similar lengths when treated with the highest IAA 292

concentration used here (100 M), albeit through two opposing responses, namely 293

growth suppression in WT and induction in ceh1. 294

This finding led to the hypothesis that the enhanced tolerance of ceh1 to auxin 295

treatment is not solely the result of reduced auxin levels in the mutant, but also a 296

consequence of modified auxin signaling in the mutant. To address this possibility, we 297

treated WT and ceh1 seedlings with auxinole, an auxin signaling inhibitor that 298

functions as an auxin antagonist for TIR1/AFB receptors (Hayashi et al., 2008; 299

Hayashi et al., 2012). The analyses showed clear dose-dependent suppression of 300

hypocotyl growth of WT seedlings in response to auxinole treatment, in contrast to 301

the unresponsiveness of ceh1 seedlings at all concentrations examined (Fig. 5C-D). 302

Collectively, the data indicated enhanced tolerance of ceh1 to otherwise inhibitory 303

concentrations of auxin and auxinole, likely stemming from reduced auxin levels and 304

compromised signaling in the mutant line. 305

Altered auxin transport in ceh1 306

We have previously established that MEcPP-mediated modulation of levels and 307

distribution patterns of auxin (IAA) is via dual transcriptional and post-translational 308

regulatory inputs (Jiang et al., 2018). We specifically demonstrated reduced transcript 309

and protein levels of auxin efflux transporter PIN-FORMED 1 (PIN1) in ceh1 310

seedlings grown in white light. Here, we extended these analyses to Rc-grown 311

seedlings, initially by expression analyses of PIN1 in WT and ceh1. The analyses 312

showed similar PIN1 transcript levels in ceh1 and the WT seedlings (Fig. 6A). By 313

contrast, the combined approaches of immunoblot and immunolocalization analyses 314



16 confirmed a significant reduction in PIN1 protein levels in ceh1 compared to WT 315



17 seedlings (Fig. 6B-C). Specifically, immunolocalization clearly showed reduced PIN1 316



18

protein abundance in plasma membranes of xylem parenchyma cells (along tracheids), 317

most notably in the meristems of ceh1 compared to WT seedlings, albeit with an 318

unchanged polarity (Fig. 6C). These data support the earlier finding establishing the 319

role of MEcPP in modulating PIN1 protein abundance both in Rc- and white light–320

grown seedlings (Jiang et al., 2018). 321

The reduced levels of the major auxin transporter PIN1 led us to examine the impact 322

of varying concentrations of a general auxin polar transport inhibitor, specifically 323

1-naphthylphthalamic acid (NPA) (Scanlon, 2003), on the hypocotyl growth of WT 324

and ceh1 seedlings grown in Rc (Fig. 6D-E). As expected, NPA application reduced 325

WT hypocotyl growth in a dose-dependent manner, which contrasts the lack of 326

detectable response in ceh1, thereby confirming compromised auxin transport in the 327

mutant. 328

Ethylene regulates hypocotyl growth in ceh1 329

Comparative transcriptomic profiling of WT and ceh1 seedlings grown in Rc revealed 330

reduced levels of ethylene biosynthesis genes, ACSs (Table S1), in the mutant. This 331

observation, in conjunction with the established crosstalk between ethylene and auxin 332

(Yu et al., 2013; Sun et al., 2015; Das et al., 2016), prompted us to further investigate 333

the potential function of ethylene in regulating ceh1 hypocotyl growth. Initially, we 334

performed RT-qPCR analyses on ethylene biosynthesis genes to validate the original 335

transcriptomic profile data (Table S1, and Fig. S4). The data showed that compared to 336

WT seedlings, there is a prominent reduction in the transcript levels of ACS4 in dark- 337

and Rc-grown ceh1 seedlings (≥2-fold and ~60-fold, respectively), as well as a 338

notable (3–10-fold depending on the gene) reduced expression of ACS5, -6, and -8, 339

albeit solely in Rc-grown ceh1 (Fig. 7A). 340

Measurements of ethylene in these seedlings confirmed reduced levels (~80%) of the 341

hormone in Rc-grown ceh1 compared to WT seedlings (Fig. 7B). This led us to 342

examine hypocotyl growth of seedlings grown in the presence of varying 343

concentrations of ethylene precursor, ACC (Fig. 7C-D). The data show suppression of 344

WT hypocotyl growth at all concentrations examined, as opposed to equally enhanced 345

hypocotyl growth in ceh1 at both ACC concentrations (10 and 20 M), an indication 346



19 of saturation of growth response. Altogether, the data support MEcPP-mediated 347



20

coordination of red-light signaling cascades with ethylene levels and ethylene 348

regulation of hypocotyl growth. 349

Hierarchy of ethylene and auxin signaling pathways 350

The partial recovery of ceh1 hypocotyl growth by external application of auxin and 351

ethylene, albeit to varying degrees, prompted us to genetically explore their potential 352

interdependency and hierarchy of their respective growth regulatory actions in 353

Rc-grown seedlings. To address this, we applied ACC and IAA independently to 354

mutant lines ceh1; ceh1 introgressed into auxin receptor mutant tir1-1 (ceh1/tir1-1); 355

and ceh1 introgressed into single ethylene-signaling mutants ein3 and eil1 (ceh1/ein3, 356

ceh1/eil1) and the double mutant ein3 eil1 (ceh1/ein3 eil1). 357

Analyses of hypocotyl lengths of Rc-grown WT, ceh1, ceh1/tir1-1, and tir1-1 358

seedlings in the absence and presence of ACC demonstrated TIR1-dependent 359

growth-promoting action of ACC in tir1-1 and ceh1/tir1-1 (Fig. 8A-B). We furthered 360

these studies by applying ACC alone or together with NPA (Fig. 8C-D). Consistent 361

with the earlier data, ACC treatment promoted ceh1 hypocotyl growth, but less 362

effectively when combined with the auxin polar transport inhibitor NPA (Fig. 8C-D). 363

In parallel, we examined hypocotyl growth of Rc-grown WT, ceh1, ein3, ceh1/ein3, 364

eil1, ceh1/eil1, ein3/eil1, and ceh1/ein3eil1 seedlings in the presence and absence of 365

externally applied IAA (Fig. 8E-F). Enhanced growth of ceh1 hypocotyls in the 366

presence of IAA irrespective of mutant backgrounds (single or double ein3/eil1) 367

reaffirmed the growth-promoting function of auxin even in lines perturbed in ethylene 368

signaling. 369

This finding establishes the dependency of ethylene function on auxin signaling, 370

delineating the hierarchy of responses and positioning ethylene as epistatic to the 371

auxin signaling pathway. 372

373



21 Discussion 374



22

An inherent feature of plant growth and development is the capacity to coordinate and 375

integrate external cues with endogenous regulatory pathways through tightly 376

regulated signaling cascades. Recent studies have identified retrograde signaling as a 377

quintessential mode of cellular communication required for optimal organismal 378

response to prevailing conditions. Here, we provide a coherent picture of how the 379

stress-specific plastidial retrograde signaling metabolite (MEcPP) coordinates light 380

and hormonal signaling circuitries to adjust growth to the most prevalent 381

environmental cue, light conditions. 382

Our simplified schematic model (Fig. 9) depicts MEcPP as the upstream signal 383

coordinating and modulating drivers of growth, specifically through enhancing phyB 384

protein abundance and the consequential reduction of auxin levels and distribution in 385

conjunction with diminished ethylene content. 386

The degradation of phyB is established to be through intermolecular transaction of 387

this photoreceptor with PIF transcription factors (Ni et al., 2013), thereby supporting 388

the prospect of significantly reduced PIF4 and -5 transcript levels as the likely cause 389

of enhanced phyB protein abundance in ceh1 seedlings grown in Rc. Furthermore, 390

reversion of ceh1 stunted hypocotyls in ceh1/phyB-9 confirms the key role of 391

enhanced phyB protein abundance in growth retardation of the mutant, confirming the 392

earlier finding using white light–grown seedlings (Jiang et al., 2019) 393

The role of phyB in regulating growth is reported to be through repressing 394

auxin-response genes (Devlin et al., 2003; Halliday et al., 2009). The red light–395

mediated reduction of auxin biosynthesis and signaling together with decreased 396

hormone levels in ceh1 supports phyB function in auxin regulation. In addition, 397

reduced levels of PIN1 protein abundance as evidenced by immunoblot and 398

immunolocalization assays suggest the regulatory role of phyB in controlling auxin 399

transport via modulation of PIN1 protein levels. This notion is supported by the 400

ineffectiveness of auxin transport inhibitor in modulating hypocotyl growth of 401

Rc-grown ceh1 seedlings. 402

Similar to auxin, reduction of ethylene levels, partly due to decreased transcript levels 403

of the respective biosynthesis genes in Rc-grown ceh1, strongly supports the 404



23

regulatory role of MEcPP-mediated induction of phyB in the process. Partial and 405

differential recovery of ceh1 hypocotyl growth under Rc in the presence of external 406

auxin or ACC identifies auxin as the key growth-regulating hormone under these 407

experimental conditions. Moreover, measurement of hypocotyl growth of ceh1 408

seedlings introgressed into auxin and ethylene signaling receptor mutants, places 409

ethylene epistatic to auxin, and supports a one-directional control mechanism of 410

ethylene-auxin interaction under Rc conditions. 411

Conclusions 412

Here, we revealed MEcPP-mediated enhanced abundance of PhyB, in part via 413

suppression of PIF4 and -5 expression levels, and the resulting reduced hypocotyl 414



24

growth. We further established MEcPP-mediated coordination of phytochrome B with 415

auxin and ethylene signaling pathways, and the function of the collective signaling 416

circuitries in the regulation of hypocotyl growth of red light–grown seedlings. In 417

addition, hormonal applications and pharmacological treatments support hierarchical 418

functions of auxin and ethylene in regulating growth, with ethylene being epistatic to 419

auxin. 420

In summary, this finding illustrates MEcPP-mediated coordination of light and 421

hormonal signaling cascades to ultimately reprogram plant growth in responses to the 422

light environment and further provides information on the functional hierarchy of 423

these growth regulatory inputs. As such, this finding identifies plastids as the control 424

hub of growth plasticity in response to environmental cues. 425

MATERIALS AND METHODS 426

Plant materials 427

The wild-type seedlings used here are the earlier-reported Col-0 ecotype transformed 428

with HPL:LUC constructs and used as the parent (WT) for isolation of the ceh1 429

mutant (Xiao et al., 2012). All experiments were performed with 7-day-old seedlings 430

grown in 15 μE m-2 sec-1 continuous monochromatic light at 22°C, unless specified 431

otherwise. The ein3/eil1 double mutant is provided by Hongwei Guo (Southern 432

University of Science and Technology); DR5-GFP is a gift from Mark Estelle 433

(University of California, San Diego); and tir1-1 (CS3798) was ordered from ABRC. 434

Light treatment 435

Surface-sterilized seeds were planted on half-strength Murashige and Skoog medium 436

(1/2 MS: 2.2 g/L Murashige and Skoog salts, 1 g/L MES (2-(N-morpholino) 437

ethanesulfonic acid, pH 5.7, and 8 g/L agar), stratified at 4°C for 5 days, grown in 15 438

μE m-2 sec-1 of monochromatic red, far-red, and blue LEDs (Quantum Devices 439

Snap-Lite) in a custom chamber at ~ 22°C for 7 days prior to hypocotyl measurement. 440

Dark control experiments were performed by exposing seedlings to white light for 3 441

hours after stratification, and then wrapping the plates with 3 layers of aluminum foil, 442

and growing seedlings for 7 days before quantification of hypocotyl length. Each 443

treatment was performed on three biological replicates, each replicate with 15 444



25

seedlings. 445

Hypocotyl length measurement 446

Seven-day-old seedlings were scanned with an Epson flatbed scanner, hypocotyl 447

length was measured using Image J. 448

RNA isolation and RNA-Seq library construction 449

Total RNA was isolated using TRIzol (Life Technologies) from 7-day-old seedlings 450

grown in the dark and in Rc. The RNA quality and quantity were assessed by 451

Nanodrop ND 1000 (Nanodrop technologies), 4 µg of qualified total RNA was used 452

for RNA-Seq library preparation using Illumina’s TruSeq v1 RNA sample Preparation 453

kit (RS-930-2002) with a low-throughput protocol following manufacturer’s 454

instructions with modifications as described (Devisetty et al., 2014). Illumina’s 12 455

indices were used during adaptor ligation and library construction. The constructed 456

libraries were size-selected using 1:1 volume of AMPure XP beads (Beckman Coulter, 457

Brea CA). Size and quality of libraries were examined using Bioanalyzer 2100 458

(Agilent, Santa Clara, CA). The 12 libraries were quantified using Quant-iT™ 459

PicoGreen® ds DNA Assay Kit (Invitrogen) and equally pooled in 1 lane of 460

single-end 50-bp sequencing in HiSeq 2000 machine (Illumina, San Diego, CA) at the 461

QB3 facility at UC Berkeley. 462

Quality filtering and alignment of RNA-Seq data 463

To ensure good read quality for downstream analysis, raw reads were pre-processed 464

using FastX-tool kit software (http://hannonlab.cshl.edu/fastx_toolkit/) and custom 465

Perl scripts. First, the de-multiplexed raw reads were filtered with fastq_quality_filter, 466

parameters (−q 20, minimum quality score to keep: 20; −p 95, minimum percent of 467

bases that must satisfy the quality score cut-off: 95). Next, reads with custom adapters 468

were removed using a custom script. Quality of reads was examined before and after 469

quality control with FastQC quality assessment software 470

(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Then Reads (1x50 bp) 471

were mapped against the Arabidopsis representative_gene_model (TAIR10) using 472

BWA v0.6.1-r104 (Li and Durbin, 2009) with parameters (-l 20) and SAMtools (Li et 473

al., 2009). The resulting BAM files were used to calculate the read counts using a 474



26

custom R script, and then the counts were used for differential gene expression 475

analysis. 476

Differential expression analysis of RNA-Seq data 477

The EdgeR Bioconductor package implemented in R was used to generate the 478

pseudo-normalized counts for visualization and to carry out differential gene 479

expression analysis (Robinson et al., 2010). Genes were kept for further analysis if 480

read counts were greater than 1 count per million (cpm) in at least 3 of the 12 libraries. 481

The EdgeR Generalized linear models (GLM) framework with explanatory variables 482

of genotype and treatment allowed us to specify a design matrix estimating the effect 483

of run number (batch) as a nuisance parameter. After fitting the model for our 484

experiment, we defined contrasts between parent lines (WT) and mutant (ceh1) in red 485

light and tested for significant expression differences using a likelihood ratio test 486

(‘glmLRT’). P-values for the remaining genes were adjusted using 487

Benjamini-Hochberg method for false discovery correction. Genes with an 488

FDR-adjusted P-value less than or equal to 0.01 were identified as differentially 489

expressed. 490

Multi-dimensional scaling (MDS) plot 491

A multi-dimensional scaling (MDS) plot was generated in edgeR to analyze 492

relationship between samples. Distance between each pair of RNA-seq profiles 493

corresponded to the average (root-mean-square) of absolute logFC between each pair 494

of samples. 495

GO Term enrichment 496

Goseq package in R (Young et al., 2010) was used to identify enriched Gene 497

Ontology (GO) terms (mainly biochemical process) in the differentially expressed 498

gene list. 499

Hormones and chemical treatments 500

Surface-sterilized seeds were planted on 1/2 MS, stratified at 4°C for 3 days, 501

germinated under continuous red light at 15 μmol m-2 sec-1 for 2 days and 502

subsequently transformed to 1/2 MS medium with 1 g/L MES (2-(N-morpholino) 503

ethanesulfonic acid) in combination with hormones or chemicals. These plates were 504



27

vertically placed in continuous red light for 5 extra days before hypocotyl 505

measurements. IAA, ACC, auxinole, and NPA were dissolved in ethanol, water, 506

DMSO, and DMSO, respectively. The corresponding solvents were used as control 507

treatment (mock) for the respective experiments. 508

MEcPP and hormone measurements 509

Quantification of SA, JA, ABA, and IAA was carried out by gas 510

chromatography-mass spectrometry (GC-MS), using dihydro-JA, deuterated SA, 511

ABA, and IAA as internal standard, respectively, as previously described (Savchenko 512

et al., 2010). MEcPP extraction and quantification was performed as previously 513

described (Jiang et al., 2019). 514

Microscopy 515

Confocal fluorescence imaging was performed using Zeiss LSM 710. GFP signal was 516

examined in 7-day-old DR5-GFP and ceh1/DR5-GFP seedlings grown on 1/2 MS in 517

Rc (15 μE m-2sec-1). 518

Immunolocalization of PIN1 519

Immunolocalization of PIN1 was performed using anti-PIN1 monoclonal primary 520

antibody and FITC anti mouse secondary antibody as previously described (Jiang et 521

al., 2018). 522

Reverse Transcription Quantitative PCR 523

Total RNA was isolated from 7-day-old seedlings grown in the Rc using TRIzol (Life 524

Technologies) and treated with DNase to eliminate DNA contamination. 1 μg total 525

RNA was reverse transcribed into cDNA using SuperScript III (Invitrogen). 526

At4g26410 was used to normalize target gene expressions. Gene-specific primers 527

were designed using QuantPrime qPCR primer design tool 528

(http://www.quantprime.de/) and are listed (Supplemental Table S2). Each experiment 529

was performed with three biological replicates and three technical replicates. 530

Protein extraction and immunoblot analyses 531

For protein extraction 7-day-old seedlings were collected, ground with liquid nitrogen, 532

homogenized in extraction buffer (10 mM Hepes, pH 7.6, 1 M Sucrose, 5 mM KCl, 5 533

mM MgCl2, 5 mM EDTA, 14 mM 2-ME, 0.4% (W/V) Triton X-100, 0.4 mM PMSF, 534



28

20 μM MG132, 20 μM MG115, and Proteinase Inhibitor), centrifuged at 1X10-5G 535

for 10 min at 4°C, after which supernatants were transferred to new tubes as total 536

proteins. Then the proteins were separated on 7.5% SDS-PAGE gel and transferred to 537

PVDF membranes. Blots were probed with B1+B7 (1:500) primary antibodies 538

obtained from Peter Quail lab. The secondary was anti-mouse horseradish peroxidase 539

(HRP) (KPL, catalog no. 074-1806) (1:10000). Immunoblots for PIN1 protein were 540

performed as previously described (Jiang et al., 2018) using anti PIN1 monoclonal 541

antibody (1:100) primary antibody and secondary anti-mouse Horseradish peroxidase 542

(HRP) (1:3000). Chemiluminescent reactions were performed using the Pierce ECL 543

Western Blotting Substrate following the manufacturer’s instructions. Excess 544

substrate was removed from membranes before placing them between two plastic 545

sheets to develop with X-ray, and subsequently scanned with Epson Perfection V600 546

Photo Scanner. 547

Statistical analyses 548

All experiments were performed with at least three biological replicates. Data are 549

mean ± standard deviation (SD). The statistical analyses were performed using library 550

agricolae, Tukey’s HSD test method in R with a significance of P < 0.05 (Bunn, 2008). 551

We have specified the method we used for statistical analysis in all figure legends. 552

The names and accession numbers of all genes named in the paper are presented in 553

Table S1. 554

Accession Numbers 555

Sequence data from this article can be found in the GenBank/EMBL data libraries 556

under accession numbers PRJNA601482. 557

558

Supplemental Data 559

Supplemental Figure S1. Hypocotyl growth of ceh1 in continuous blue and far-red 560

light is phyB-independent. 561

Supplemental Figure S2. Expression levels of PIF1, -3, -4, and -5 in WT and ceh1 562

seedlings grown in the dark and Rc (15 μEm-2sec-1). 563

Supplemental Figure S3. MDS plot of sequencing data from 7-day-old WT and ceh1 564

seedlings grown in the dark and Rc (15 μEm-2sec-1). 565



29

Supplemental Figure S4. Heatmap of Top 50 significantly enriched Go terms of 566

down-regulated genes in ceh1/WT under continuous Rc (15 μEm-2sec-1). 567

in ceh1/WT under continuous Rc (15 μEm-2sec-1). 568

Supplemental Figure S5. Similar ABA and JA levels in WT and ceh1 seedlings 569

grown in the dark and in Rc (15 μEm-2sec-1). 570

Supplemental Table S1. List of differentially expressed genes. 571

Supplemental Table S2. List of primers used in RT-qPCR analyses. 572

573

574

Acknowledgements 575

We would like to thank Mr. Derrick R. Hicks (University of Washington) for 576

providing images of ethylene, IAA and MEcPP stick chemical structures depicted in 577

our model. We also would like to thank Prof. Meng Chen and Dr. Yongjian Qiu for 578

providing the red-light chamber and reagents for our experiments, and Dr. Peter Quail 579

for generously providing us with the phyB antibody. We would like to thank Jacob 580

North for all his efforts towards seedling preparation. We are thankful to Dr. Geoffrey 581

Benn for performing the statistical analyses using R program. 582

583

584

585

586

Figure legends 587

Fig. 1. Ceh1 hypocotyl growth in red light is phyB-dependent 588

(A) Representative images of 7-day-old WT, ceh1, ceh1/phyB-9 and phyB-9 589

seedlings grown in the dark and continuous red light (Rc: 15 μEm-2sec-1). (B) 590

Quantification of hypocotyl lengths from aforementioned genotypes shown in Fig.1A. 591

(C) MEcPP levels of samples from Fig.1A. The break indicates a change of scale on 592

the y axis. Statistical analyses were performed using Tukey’s HSD method (n≥45), 593

different letters indicate significant difference (P < 0.05). Scale bars: 1cm. 594

595



30

Fig. 2. MEcPP induction of phyB results in stunted ceh1 hypocotyl growth 596

(A) Representative images of 7-day-old Col-0, WT, ceh1 and complementation line 597

(CP) seedlings grown in Rc15 (15 μEm-2sec-1). Scale bars: 1 cm. (B) & (E) 598

Quantification of hypocotyl length of seedlings from panel (A) and (D), respectively. 599

Data are presented with 45 seedlings. Statistical analyses were carried out using 600

Tukey’s HSD method, different letters indicate significant difference (P < 0.05). (C) 601

& (F) Immunoblots of phyB protein abundance, using RPN6 antibody a loading 602

control. (D) Representative images of 7-day-old WT and ceh1 seedlings grown in 603

Rc15 (15 μEm-2sec-1) in the absence (-) and presence (+) of fosmidomycin (20 μM). 604

605

Fig. 3. Overexpression of PIF4 and PIF5 recover stunted hypocotyl growth of ceh1 606

(A) Quantification of hypocotyl lengths of 7-day-old WT, ceh1, ceh1/pifq, and pifq 607

grown in Rc (15 μEm-2sec-1). (B) Quantification of hypocotyl lengths from 608

7-day-old WT, ceh1, ceh1/PIF4-OX, PIF4-OX, ceh1/PIF5-OX and PIF5-OX grown in 609

Rc (15 μEm-2sec-1). Data are presented with n≥20 for the pif mutant backgrounds 610

and n≥30 for the experiments containing PIF-OX seedlings. The break indicates a 611

change of scale on the y axis. Statistical analyses were carried out using Tukey’s HSD 612

method, different letters indicate significant difference. 613

614

Fig. 4. Auxin is reduced in ceh1 615

Expression levels of YUC3, 8 (A) and IAA6, 19 (B) in WT and ceh1 seedlings. RNAs 616

were extracted from 7-day-old WT and ceh1seedlings grown in the dark and Rc (15 617

μEm-2sec-1). Transcript levels of target genes were normalized to the levels of 618

At4g26410 (M3E9). Data are presented with three biological replicates and three 619

technical replicates. Statistical analyses were determined by a two-tailed Student’s t 620

tests with a significance of P < 0.05 *, P < 0.01 **. (C) IAA levels in 7-day-old WT 621

and ceh1 seedlings grown in the dark and Rc (15 μEm-2sec-1). Data are presented 622

with three biological replicates. The break indicates a change of scale on the y axis. 623

Statistical analyses were carried out by a two-tailed Student’s t tests with a 624

significance of P < 0.05. (D) Representative images of DR5-GFP signal intensity in 625



31

7-day hypocotyls of Rc (15 μEm-2sec-1) grown WT and ceh1 seedlings. DR5-GFP 626

(green), chloroplast fluorescence (red) and merged images. 627

628

Fig. 5. Enhanced tolerance of ceh1 to auxin and auxinole 629

(A) & (C) Representative images of 7-day-old WT and ceh1 seedlings in the absence 630

(0) and presence of IAA and auxinole grown under Rc (15 μEm-2sec-1), respectively. 631

(B) & (D) Quantification of hypocotyl lengths of seedlings from panel (A) & (C), 632

respectively. Data are presented with 45 seedlings. The break indicates a change of 633

scale on the y axis. Statistical analyses were carried out using Tukey’s HSD method, 634

different letters indicate significant difference (P < 0.05). Scale bars: 1cm. 635

636

Fig. 6. Altered auxin transport in ceh1 637

(A) PIN1 expression levels in 7-day-old WT and ceh1 seedlings grown in Rc (15 638

μEm-2sec-1). Experiment was performed as described in Fig. 4A. Data are presented 639

with three biological replicates and three technical replicates. (B) Immunoblots of 640

PIN1 and ATPase as the protein loading control, and signal intensity quantification of 641

the PIN1/ATPase protein abundance in 7-day-old WT and ceh1 seedlings grown 642

under Rc (15 μEm-2sec-1) with two biological replicates. Asterisk denotes significant 643

difference as determined by a two-tailed Student’s t tests. (C) Immunolocalization of 644

PIN1 in the hypocotyls of 7-day-old WT and ceh1 seedlings grown under Rc (15 645

μEm-2sec-1). Scale bar: 20 μm. (D) Representative images of 7-day-old WT and ceh1 646

seedlings grown under Rc (15 μEm-2sec-1) in the absence (0) and presence of 647

NPA. Scale bar: 1cm. (E) Quantification of hypocotyl length of seedlings from panel 648

(D).Data are presented with 45 seedlings. Statistical analyses were carried out using 649

Tukey’s HSD method. Data are means ± SD and different letters indicate significant 650

difference (P < 0.05). 651

652

Fig. 7. Ethylene regulates hypocotyl growth in ceh1 653

(A) Expression levels of ACS4, 5, 6 and 8 in 7-day-old WT and ceh1seedlings grown 654

in the dark and Rc (15 μEm-2sec-1). Experiment was performed as described in Fig. 655



32

4A. Data are presented with three biological replicates and three technical replicates. 656

Statistical analyses were determined by a two-tailed Student’s t tests with a 657

significance of P < 0.05 *, P < 0.01 **. (B) Ethylene levels in samples used in panel 658

(A). (C) Representative images of 7-day-old WT and ceh1 seedlings grown in the 659

absence (0) and presence of ACC in the Rc (15 μEm-2sec-1). Scale bar: 1cm. (D) 660

Quantification of hypocotyl length of seedlings from panel (C). Data are presented 661

with 45 seedlings. The break indicates a change of scale on the y axis. Statistical 662

analyses were carried out using Tukey’s HSD method, different letters indicate 663

significant difference (P < 0.05). 664

665

Fig. 8. Ethylene is epistatic to auxin 666

(A) Representative images of 7-day-old WT, ceh1, ceh1/tir1-1 and tir1-1 seedlings 667

grown in the Rc (15 μEm-2sec-1) in the absence (-) and presence (+) of ACC. (C) 668

Representative images of 7-day-old WT and ceh1 seedlings grown in the Rc (15 669

μEm-2sec-1) in the absence (-) and presence (+) of ACC/NPA alone or in 670

combination. (E) Representative images of 7-day-old WT, ceh1, ein3, ceh1/ein3, 671

eil1, ceh1/eil1, ein3/eil1, ceh1/ein3eil1 seedlings grown in the Rc (15 μEm-2sec-1) in 672

the absence (-) and presence (+) of IAA. (B) & (D) & (F) Quantification of hypocotyl 673

length of seedlings from panel (A) & (C) & (E), respectively. Data are presented with 674

45 seedlings. The break indicates a change of scale on the y axis. Statistical analyses 675

were carried out using Tukey’s HSD method, different letters indicate significant 676

difference (P < 0.05). Scale bars: 1cm. 677

678

Fig.9. Schematic model depicting MEcPP as the integrator of growth regulating 679

pathways. Stress induction of MEcPP accumulation reduces expression of PIF 4 and 680

5 and enhances abundance of phyB protein and the consequential orchestration of 681

ethylene-auxin hierarchy to regulate growth. 682

683

684

685



33

686



Parsed CitationsBjornson, M., Balcke, G.U., Xiao, Y., de Souza, A., Wang, J.Z., Zhabinskaya, D., Tagkopoulos, I., Tissier, A., and Dehesh, K. (2017).Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata. Plant J 91, 70-84.

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

Bunn, A.G. (2008). A dendrochronology program library in R (dplR). Dendrochronologia 26, 115-124.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Chai, T., Zhou, J., Liu, J., and Xing, D. (2015). LSD1 and HY5 antagonistically regulate red light induced-programmed cell death inArabidopsis. Front Plant Sci 6, 292.


Chenge-Espinosa, M., Cordoba, E., Romero-Guido, C., Toledo-Ortiz, G., and Leon, P. (2018). Shedding light on the methylerythritolphosphate (MEP)-pathway: long hypocotyl 5 (HY5)/phytochrome-interacting factors (PIFs) transcription factors modulating key limitingsteps. Plant J 96, 828-841.


Das, D., St Onge, K.R., Voesenek, L.A., Pierik, R., and Sasidharan, R. (2016). Ethylene- and shade-induced hypocotyl elongation sharetranscriptome patterns and functional regulators. Plant Physiol.


De Grauwe, L., Vandenbussche, F., Tietz, O., Palme, K., and Van Der Straeten, D. (2005). Auxin, ethylene and brassinosteroids:tripartite control of growth in the Arabidopsis hypocotyl. Plant & cell physiology 46, 827-836.


de Wit, M., Lorrain, S., and Fankhauser, C. (2014). Auxin-mediated plant architectural changes in response to shade and hightemperature. Physiologia plantarum 151, 13-24.


Devisetty, U.K., Covington, M.F., Tat, A.V., Lekkala, S., and Maloof, J.N. (2014). Polymorphism identification and improved genomeannotation of Brassica rapa through Deep RNA sequencing. G3 (Bethesda) 4, 2065-2078.


Devlin, P.F., Yanovsky, M.J., and Kay, S.A. (2003). A genomic analysis of the shade avoidance response in Arabidopsis. Plant physiology133, 1617-1629.


Franklin, K.A., Lee, S.H., Patel, D., Kumar, S.V., Spartz, A.K., Gu, C., Ye, S., Yu, P., Breen, G., Cohen, J.D., Wigge, P.A., and Gray, W.M.(2011). Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature. Proceedings of the National Academyof Sciences of the United States of America 108, 20231-20235.


Galweiler, L., Guan, C., Muller, A., Wisman, E., Mendgen, K., Yephremov, A., and Palme, K. (1998). Regulation of polar auxin transport byAtPIN1 in Arabidopsis vascular tissue. Science 282, 2226-2230.


Geldner, N., Friml, J., Stierhof, Y.D., Jurgens, G., and Palme, K. (2001). Auxin transport inhibitors block PIN1 cycling and vesicletrafficking. Nature 413, 425-428.


Gonzalez-Cabanelas, D., Wright, L.P., Paetz, C., Onkokesung, N., Gershenzon, J., Rodriguez-Concepcion, M., and Phillips, M.A. (2015).The diversion of 2-C-methyl-D-erythritol-2,4-cyclodiphosphate from the 2-C-methyl-D-erythritol 4-phosphate pathway to hemiterpeneglycosides mediates stress responses in Arabidopsis thaliana. The Plant journal : for cell and molecular biology 82, 122-137.


Halliday, K.J., Martinez-Garcia, J.F., and Josse, E.M. (2009). Integration of light and auxin signaling. Cold Spring Harbor perspectives inbiology 1, a001586.



https://www.ncbi.nlm.nih.gov/pubmed?term=Bjornson%2C M%2E%2C Balcke%2C G%2EU%2E%2C Xiao%2C Y%2E%2C de Souza%2C A%2E%2C Wang%2C J%2EZ%2E%2C Zhabinskaya%2C D%2E%2C Tagkopoulos%2C I%2E%2C Tissier%2C A%2E%2C and Dehesh%2C K%2E %282017%29%2E Integrated omics analyses of retrograde signaling mutant delineate interrelated stress%2Dresponse strata%2E Plant J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bjornson,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata&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

https://scholar.google.com/scholar?as_q=Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bjornson,&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Bunn%2C A%2EG%2E %282008%29%2E A dendrochronology program library in R %28dplR%29%2E Dendrochronologia&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bunn,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=A dendrochronology program library in R (dplR)&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

https://scholar.google.com/scholar?as_q=A dendrochronology program library in R (dplR)&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bunn,&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Chai%2C T%2E%2C Zhou%2C J%2E%2C Liu%2C J%2E%2C and Xing%2C D%2E %282015%29%2E LSD1 and HY5 antagonistically regulate red light induced%2Dprogrammed cell death in Arabidopsis%2E Front Plant Sci&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Chai,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=LSD1 and HY5 antagonistically regulate red light induced-programmed cell death in Arabidopsis&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

https://scholar.google.com/scholar?as_q=LSD1 and HY5 antagonistically regulate red light induced-programmed cell death in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Chai,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Chenge%2DEspinosa%2C M%2E%2C Cordoba%2C E%2E%2C Romero%2DGuido%2C C%2E%2C Toledo%2DOrtiz%2C G%2E%2C and Leon%2C P%2E %282018%29%2E Shedding light on the methylerythritol phosphate %28MEP%29%2Dpathway%3A long hypocotyl 5 %28HY5%29%2Fphytochrome%2Dinteracting factors %28PIFs%29 transcription factors modulating key limiting steps%2E Plant J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Chenge-Espinosa,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Shedding light on the methylerythritol phosphate (MEP)-pathway: long hypocotyl 5 (HY5)/phytochrome-interacting factors (PIFs) transcription factors modulating key limiting steps&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

https://scholar.google.com/scholar?as_q=Shedding light on the methylerythritol phosphate (MEP)-pathway: long hypocotyl 5 (HY5)/phytochrome-interacting factors (PIFs) transcription factors modulating key limiting steps&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Chenge-Espinosa,&as_ylo=2018&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Das%2C D%2E%2C St Onge%2C K%2ER%2E%2C Voesenek%2C L%2EA%2E%2C Pierik%2C R%2E%2C and Sasidharan%2C R%2E %282016%29%2E Ethylene%2D and shade%2Dinduced hypocotyl elongation share transcriptome patterns and functional regulators%2E Plant Physiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Das,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene- and shade-induced hypocotyl elongation share transcriptome patterns and functional regulators.&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

https://scholar.google.com/scholar?as_q=Ethylene- and shade-induced hypocotyl elongation share transcriptome patterns and functional regulators.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Das,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=De Grauwe%2C L%2E%2C Vandenbussche%2C F%2E%2C Tietz%2C O%2E%2C Palme%2C K%2E%2C and Van Der Straeten%2C D%2E %282005%29%2E Auxin%2C ethylene and brassinosteroids%3A tripartite control of growth in the Arabidopsis hypocotyl%2E Plant %26 cell physiology&dopt=abstract

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

https://scholar.google.com/scholar?as_q=Auxin, ethylene and brassinosteroids: tripartite control of growth in the Arabidopsis hypocotyl&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

https://scholar.google.com/scholar?as_q=Auxin, ethylene and brassinosteroids: tripartite control of growth in the Arabidopsis hypocotyl&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=De&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=de Wit%2C M%2E%2C Lorrain%2C S%2E%2C and Fankhauser%2C C%2E %282014%29%2E Auxin%2Dmediated plant architectural changes in response to shade and high temperature%2E Physiologia plantarum&dopt=abstract

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

https://scholar.google.com/scholar?as_q=Auxin-mediated plant architectural changes in response to shade and high temperature&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

https://scholar.google.com/scholar?as_q=Auxin-mediated plant architectural changes in response to shade and high temperature&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=de&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Devisetty%2C U%2EK%2E%2C Covington%2C M%2EF%2E%2C Tat%2C A%2EV%2E%2C Lekkala%2C S%2E%2C and Maloof%2C J%2EN%2E %282014%29%2E Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing%2E G3 %28Bethesda&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Devisetty,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing&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

https://scholar.google.com/scholar?as_q=Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Devisetty,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Devlin%2C P%2EF%2E%2C Yanovsky%2C M%2EJ%2E%2C and Kay%2C S%2EA%2E %282003%29%2E A genomic analysis of the shade avoidance response in Arabidopsis%2E Plant physiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Devlin,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=A genomic analysis of the shade avoidance response in Arabidopsis&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

https://scholar.google.com/scholar?as_q=A genomic analysis of the shade avoidance response in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Devlin,&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Franklin%2C K%2EA%2E%2C Lee%2C S%2EH%2E%2C Patel%2C D%2E%2C Kumar%2C S%2EV%2E%2C Spartz%2C A%2EK%2E%2C Gu%2C C%2E%2C Ye%2C S%2E%2C Yu%2C P%2E%2C Breen%2C G%2E%2C Cohen%2C J%2ED%2E%2C Wigge%2C P%2EA%2E%2C and Gray%2C W%2EM%2E %282011%29%2E Phytochrome%2Dinteracting factor 4 %28PIF4%29 regulates auxin biosynthesis at high temperature%2E Proceedings of the National Academy of Sciences of the United States of America&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Franklin,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature&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

https://scholar.google.com/scholar?as_q=Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Franklin,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Galweiler%2C L%2E%2C Guan%2C C%2E%2C Muller%2C A%2E%2C Wisman%2C E%2E%2C Mendgen%2C K%2E%2C Yephremov%2C A%2E%2C and Palme%2C K%2E %281998%29%2E Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue%2E Science&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Galweiler,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue&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

https://scholar.google.com/scholar?as_q=Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Galweiler,&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Geldner%2C N%2E%2C Friml%2C J%2E%2C Stierhof%2C Y%2ED%2E%2C Jurgens%2C G%2E%2C and Palme%2C K%2E %282001%29%2E Auxin transport inhibitors block PIN1 cycling and vesicle trafficking%2E Nature&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Geldner,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Auxin transport inhibitors block PIN1 cycling and vesicle trafficking&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

https://scholar.google.com/scholar?as_q=Auxin transport inhibitors block PIN1 cycling and vesicle trafficking&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Geldner,&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Gonzalez%2DCabanelas%2C D%2E%2C Wright%2C L%2EP%2E%2C Paetz%2C C%2E%2C Onkokesung%2C N%2E%2C Gershenzon%2C J%2E%2C Rodriguez%2DConcepcion%2C M%2E%2C and Phillips%2C M%2EA%2E %282015%29%2E The diversion of 2%2DC%2Dmethyl%2DD%2Derythritol%2D2%2C4%2Dcyclodiphosphate from the 2%2DC%2Dmethyl%2DD%2Derythritol 4%2Dphosphate pathway to hemiterpene glycosides mediates stress responses in Arabidopsis thaliana%2E The Plant journal %3A for cell and molecular biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Gonzalez-Cabanelas,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=&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

https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Gonzalez-Cabanelas,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Halliday%2C K%2EJ%2E%2C Martinez%2DGarcia%2C J%2EF%2E%2C and Josse%2C E%2EM%2E %282009%29%2E Integration of light and auxin signaling%2E Cold Spring Harbor perspectives in biology 1%2C a&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Halliday,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Integration of light and auxin signaling&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

https://scholar.google.com/scholar?as_q=Integration of light and auxin signaling&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Halliday,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1


Hayashi, K., Tan, X., Zheng, N., Hatate, T., Kimura, Y., Kepinski, S., and Nozaki, H. (2008). Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling. Proceedings of the National Academy of Sciences of the UnitedStates of America 105, 5632-5637.


Hayashi, K., Neve, J., Hirose, M., Kuboki, A., Shimada, Y., Kepinski, S., and Nozaki, H. (2012). Rational design of an auxin antagonist ofthe SCF(TIR1) auxin receptor complex. ACS Chem Biol 7, 590-598.


Hornitschek, P., Kohnen, M.V., Lorrain, S., Rougemont, J., Ljung, K., Lopez-Vidriero, I., Franco-Zorrilla, J.M., Solano, R., Trevisan, M.,Pradervand, S., Xenarios, I., and Fankhauser, C. (2012a). Phytochrome interacting factors 4 and 5 control seedling growth in changinglight conditions by directly controlling auxin signaling. Plant J 71, 699-711.


Hornitschek, P., Kohnen, M.V., Lorrain, S., Rougemont, J., Ljung, K., Lopez-Vidriero, I., Franco-Zorrilla, J.M., Solano, R., Trevisan, M.,Pradervand, S., Xenarios, I., and Fankhauser, C. (2012b). Phytochrome interacting factors 4 and 5 control seedling growth in changinglight conditions by directly controlling auxin signaling. The Plant journal : for cell and molecular biology 71, 699-711.


J. Jensen, P., P. Hangarter, R., and Estelle, M. (1998). Auxin Transport Is Required for Hypocotyl Elongation in Light-Grown but NotDark-Grown Arabidopsis. plant Physiol 116, 455-462.


Jiang, J., Zeng, L., Ke, H., De La Cruz, B., and Dehesh, K. (2019). Orthogonal regulation of phytochrome B abundance by stress-specificplastidial retrograde signaling metabolite. Nature communications 10, 2904.


Jiang, J., Rodriguez-Furlan, C., Wang, J.Z., de Souza, A., Ke, H., Pasternak, T., Lasok, H., Ditengou, F.A., Palme, K., and Dehesh, K.(2018). Interplay of the two ancient metabolites auxin and MEcPP regulates adaptive growth. Nature communications 9, 2262.


L.-C. Wang, K., Li, H., and R.Ecker, J. (2002). Ethylene Biosynthesis and Signaling Networks. The plant cell, 131-151.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Leivar, P., and Quail, P.H. (2011). PIFs: pivotal components in a cellular signaling hub. Trends in plant science 16, 19-28.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Leivar, P., and Monte, E. (2014). PIFs: Systems Integrators in Plant Development. Plant Cell 26, 56-78.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Leivar, P., Monte, E., Cohn, M.M., and Quail, P.H. (2012). Phytochrome signaling in green Arabidopsis seedlings: impact assessment ofa mutually negative phyB-PIF feedback loop. Molecular plant 5, 734-749.


Lemos, M., Xiao, Y., Bjornson, M., Wang, J.Z., Hicks, D., Souza, A., Wang, C.Q., Yang, P., Ma, S., Dinesh-Kumar, S., and Dehesh, K.(2016). The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk.J Exp Bot 67, 1557-1566.


Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Genome Project DataProcessing, S. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.


Liang, X., Wang, H., Mao, L., Hu, Y., Dong, T., Zhang, Y., Wang, X., and Bi, Y. (2012). Involvement of COP1 in ethylene- and light-regulated hypocotyl elongation. Planta 236, 1791-1802.



https://www.ncbi.nlm.nih.gov/pubmed?term=Hayashi%2C K%2E%2C Tan%2C X%2E%2C Zheng%2C N%2E%2C Hatate%2C T%2E%2C Kimura%2C Y%2E%2C Kepinski%2C S%2E%2C and Nozaki%2C H%2E %282008%29%2E Small%2Dmolecule agonists and antagonists of F%2Dbox protein%2Dsubstrate interactions in auxin perception and signaling%2E Proceedings of the National Academy of Sciences of the United States of America&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hayashi,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling&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

https://scholar.google.com/scholar?as_q=Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hayashi,&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Hayashi%2C K%2E%2C Neve%2C J%2E%2C Hirose%2C M%2E%2C Kuboki%2C A%2E%2C Shimada%2C Y%2E%2C Kepinski%2C S%2E%2C and Nozaki%2C H%2E %282012%29%2E Rational design of an auxin antagonist of the SCF%28TIR1%29 auxin receptor complex%2E ACS Chem Biol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hayashi,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Rational design of an auxin antagonist of the SCF(TIR1) auxin receptor complex&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

https://scholar.google.com/scholar?as_q=Rational design of an auxin antagonist of the SCF(TIR1) auxin receptor complex&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hayashi,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Hornitschek%2C P%2E%2C Kohnen%2C M%2EV%2E%2C Lorrain%2C S%2E%2C Rougemont%2C J%2E%2C Ljung%2C K%2E%2C Lopez%2DVidriero%2C I%2E%2C Franco%2DZorrilla%2C J%2EM%2E%2C Solano%2C R%2E%2C Trevisan%2C M%2E%2C Pradervand%2C S%2E%2C Xenarios%2C I%2E%2C and Fankhauser%2C C%2E %282012a%29%2E Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling%2E Plant J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hornitschek,&hl=en&c2coff=1


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hornitschek,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Hornitschek%2C P%2E%2C Kohnen%2C M%2EV%2E%2C Lorrain%2C S%2E%2C Rougemont%2C J%2E%2C Ljung%2C K%2E%2C Lopez%2DVidriero%2C I%2E%2C Franco%2DZorrilla%2C J%2EM%2E%2C Solano%2C R%2E%2C Trevisan%2C M%2E%2C Pradervand%2C S%2E%2C Xenarios%2C I%2E%2C and Fankhauser%2C C%2E %282012b%29%2E Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling%2E The Plant journal %3A for cell and molecular biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hornitschek,&hl=en&c2coff=1


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hornitschek,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=J%2E Jensen%2C P%2E%2C P%2E Hangarter%2C R%2E%2C and Estelle%2C M%2E %281998%29%2E Auxin Transport Is Required for Hypocotyl Elongation in Light%2DGrown but Not Dark%2DGrown Arabidopsis%2E plant Physiol&dopt=abstract

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

https://scholar.google.com/scholar?as_q=Auxin Transport Is Required for Hypocotyl Elongation in Light-Grown but Not Dark-Grown Arabidopsis&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

https://scholar.google.com/scholar?as_q=Auxin Transport Is Required for Hypocotyl Elongation in Light-Grown but Not Dark-Grown Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=J.&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Jiang%2C J%2E%2C Zeng%2C L%2E%2C Ke%2C H%2E%2C De La Cruz%2C B%2E%2C and Dehesh%2C K%2E %282019%29%2E Orthogonal regulation of phytochrome B abundance by stress%2Dspecific plastidial retrograde signaling metabolite%2E Nature communications&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jiang,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Orthogonal regulation of phytochrome B abundance by stress-specific plastidial retrograde signaling metabolite&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

https://scholar.google.com/scholar?as_q=Orthogonal regulation of phytochrome B abundance by stress-specific plastidial retrograde signaling metabolite&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jiang,&as_ylo=2019&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Jiang%2C J%2E%2C Rodriguez%2DFurlan%2C C%2E%2C Wang%2C J%2EZ%2E%2C de Souza%2C A%2E%2C Ke%2C H%2E%2C Pasternak%2C T%2E%2C Lasok%2C H%2E%2C Ditengou%2C F%2EA%2E%2C Palme%2C K%2E%2C and Dehesh%2C K%2E %282018%29%2E Interplay of the two ancient metabolites auxin and MEcPP regulates adaptive growth%2E Nature communications&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jiang,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Interplay of the two ancient metabolites auxin and MEcPP regulates adaptive growth&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

https://scholar.google.com/scholar?as_q=Interplay of the two ancient metabolites auxin and MEcPP regulates adaptive growth&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jiang,&as_ylo=2018&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=L%2E%2DC%2E Wang%2C K%2E%2C Li%2C H%2E%2C and R%2EEcker%2C J%2E %282002%29%2E Ethylene Biosynthesis and Signaling Networks%2E The plant cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=L.-C.&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene Biosynthesis and Signaling Networks.&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

https://scholar.google.com/scholar?as_q=Ethylene Biosynthesis and Signaling Networks.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=L.-C.&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Leivar%2C P%2E%2C and Quail%2C P%2EH%2E %282011%29%2E PIFs%3A pivotal components in a cellular signaling hub%2E Trends in plant science&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Leivar,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=PIFs: pivotal components in a cellular signaling hub&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

https://scholar.google.com/scholar?as_q=PIFs: pivotal components in a cellular signaling hub&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Leivar,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Leivar%2C P%2E%2C and Monte%2C E%2E %282014%29%2E PIFs%3A Systems Integrators in Plant Development%2E Plant Cell&dopt=abstract


https://scholar.google.com/scholar?as_q=PIFs: Systems Integrators in Plant Development&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

https://scholar.google.com/scholar?as_q=PIFs: Systems Integrators in Plant Development&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Leivar,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Leivar%2C P%2E%2C Monte%2C E%2E%2C Cohn%2C M%2EM%2E%2C and Quail%2C P%2EH%2E %282012%29%2E Phytochrome signaling in green Arabidopsis seedlings%3A impact assessment of a mutually negative phyB%2DPIF feedback loop%2E Molecular plant&dopt=abstract


https://scholar.google.com/scholar?as_q=Phytochrome signaling in green Arabidopsis seedlings: impact assessment of a mutually negative phyB-PIF feedback loop&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

https://scholar.google.com/scholar?as_q=Phytochrome signaling in green Arabidopsis seedlings: impact assessment of a mutually negative phyB-PIF feedback loop&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Leivar,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Lemos%2C M%2E%2C Xiao%2C Y%2E%2C Bjornson%2C M%2E%2C Wang%2C J%2EZ%2E%2C Hicks%2C D%2E%2C Souza%2C A%2E%2C Wang%2C C%2EQ%2E%2C Yang%2C P%2E%2C Ma%2C S%2E%2C Dinesh%2DKumar%2C S%2E%2C and Dehesh%2C K%2E %282016%29%2E The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk%2E J Exp Bot&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lemos,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk&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

https://scholar.google.com/scholar?as_q=The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lemos,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Li%2C H%2E%2C and Durbin%2C R%2E %282009%29%2E Fast and accurate short read alignment with Burrows%2DWheeler transform%2E Bioinformatics&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Li,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Fast and accurate short read alignment with Burrows-Wheeler transform&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

https://scholar.google.com/scholar?as_q=Fast and accurate short read alignment with Burrows-Wheeler transform&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Li,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Li%2C H%2E%2C Handsaker%2C B%2E%2C Wysoker%2C A%2E%2C Fennell%2C T%2E%2C Ruan%2C J%2E%2C Homer%2C N%2E%2C Marth%2C G%2E%2C Abecasis%2C G%2E%2C Durbin%2C R%2E%2C and Genome Project Data Processing%2C S%2E %282009%29%2E The Sequence Alignment%2FMap format and SAMtools%2E Bioinformatics&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Li,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The Sequence Alignment/Map format and SAMtools&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

https://scholar.google.com/scholar?as_q=The Sequence Alignment/Map format and SAMtools&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Li,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Liang%2C X%2E%2C Wang%2C H%2E%2C Mao%2C L%2E%2C Hu%2C Y%2E%2C Dong%2C T%2E%2C Zhang%2C Y%2E%2C Wang%2C X%2E%2C and Bi%2C Y%2E %282012%29%2E Involvement of COP1 in ethylene%2D and light%2Dregulated hypocotyl elongation%2E Planta&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Liang,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Involvement of COP1 in ethylene- and light-regulated hypocotyl elongation&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

https://scholar.google.com/scholar?as_q=Involvement of COP1 in ethylene- and light-regulated hypocotyl elongation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Liang,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1


Morelli, G., and Ruberti, I. (2002). Light and shade in the photocontrol of Arabidopsis growth. Trends in plant science 7, 399-404.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Nagy, F., and Schafer, E. (2002). Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathwaysin higher plants. Annual review of plant biology 53, 329-355.


Negi, S., Sukumar, P., Liu, X., Cohen, J.D., and Muday, G.K. (2010). Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato. Plant J 61, 3-15.


Ni, W., Xu, S.L., Chalkley, R.J., Pham, T.N., Guan, S., Maltby, D.A., Burlingame, A.L., Wang, Z.Y., and Quail, P.H. (2013). Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negativefeedback modulation of photoreceptor phyB levels in Arabidopsis. The Plant cell 25, 2679-2698.


Nozue, K., Harmer, S.L., and Maloof, J.N. (2011). Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes RevealsPHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis. Plant Physiol 156, 357-372.


Nozue, K., Devisetty, U.K., Lekkala, S., Mueller-Moule, P., Bak, A., Casteel, C.L., and Maloof, J.N. (2018). Network Analysis Reveals aRole for Salicylic Acid Pathway Components in Shade Avoidance. Plant Physiol 178, 1720-1732.


Pedmale, U.V., Huang, S.C., Zander, M., Cole, B.J., Hetzel, J., Ljung, K., Reis, P.A.B., Sridevi, P., Nito, K., Nery, J.R., Ecker, J.R., andChory, J. (2016). Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell 164, 233-245.


Quail, P.H. (2002). Photosensory perception and signalling in plant cells: new paradigms? Current opinion in cell biology 14, 180-188.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Rausenberger, J., Hussong, A., Kircher, S., Kirchenbauer, D., Timmer, J., Nagy, F., Schafer, E., and Fleck, C. (2010). An IntegrativeModel for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology. Plos One 5.


Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digitalgene expression data. Bioinformatics 26, 139-140.


Ruzicka, K., Ljung, K., Vanneste, S., Podhorska, R., Beeckman, T., Friml, J., and Benkova, E. (2007). Ethylene regulates root growththrough effects on auxin biosynthesis and transport-dependent auxin distribution. The Plant cell 19, 2197-2212.


Savchenko, T., Walley, J.W., Chehab, E.W., Xiao, Y., Kaspi, R., Pye, M.F., Mohamed, M.E., Lazarus, C.M., Bostock, R.M., and Dehesh, K.(2010). Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks. The Plant cell 22,3193-3205.


Scanlon, M.J. (2003). The polar auxin transport inhibitor N-1-naphthylphthalamic acid disrupts leaf initiation, KNOX protein regulation,and formation of leaf margins in maize. Plant Physiol 133, 597-605.


Sellaro, R., Pacin, M., and Casal, J.J. (2012). Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock,and light signaling. Molecular plant 5, 619-628.


Smalle, J., Haegman, M., Kurepa, J., Van Montagu, M., and Van Der Straeten, D. (1997). Ethylene can stimulate Arabidopsis hypocotylelongation in the light. P Natl Acad Sci USA 94, 2756-2761.



https://www.ncbi.nlm.nih.gov/pubmed?term=Morelli%2C G%2E%2C and Ruberti%2C I%2E %282002%29%2E Light and shade in the photocontrol of Arabidopsis growth%2E Trends in plant science&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Morelli,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Light and shade in the photocontrol of Arabidopsis growth&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

https://scholar.google.com/scholar?as_q=Light and shade in the photocontrol of Arabidopsis growth&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Morelli,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Nagy%2C F%2E%2C and Schafer%2C E%2E %282002%29%2E Phytochromes control photomorphogenesis by differentially regulated%2C interacting signaling pathways in higher plants%2E Annual review of plant biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nagy,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants&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

https://scholar.google.com/scholar?as_q=Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nagy,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Negi%2C S%2E%2C Sukumar%2C P%2E%2C Liu%2C X%2E%2C Cohen%2C J%2ED%2E%2C and Muday%2C G%2EK%2E %282010%29%2E Genetic dissection of the role of ethylene in regulating auxin%2Ddependent lateral and adventitious root formation in tomato%2E Plant J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Negi,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato&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

https://scholar.google.com/scholar?as_q=Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Negi,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ni%2C W%2E%2C Xu%2C S%2EL%2E%2C Chalkley%2C R%2EJ%2E%2C Pham%2C T%2EN%2E%2C Guan%2C S%2E%2C Maltby%2C D%2EA%2E%2C Burlingame%2C A%2EL%2E%2C Wang%2C Z%2EY%2E%2C and Quail%2C P%2EH%2E %282013%29%2E Multisite light%2Dinduced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis%2E The Plant cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ni,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis&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

https://scholar.google.com/scholar?as_q=Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ni,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Nozue%2C K%2E%2C Harmer%2C S%2EL%2E%2C and Maloof%2C J%2EN%2E %282011%29%2E Genomic Analysis of Circadian Clock%2D%2C Light%2D%2C and Growth%2DCorrelated Genes Reveals PHYTOCHROME%2DINTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis%2E Plant Physiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nozue,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes Reveals PHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis&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

https://scholar.google.com/scholar?as_q=Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes Reveals PHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nozue,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Nozue%2C K%2E%2C Devisetty%2C U%2EK%2E%2C Lekkala%2C S%2E%2C Mueller%2DMoule%2C P%2E%2C Bak%2C A%2E%2C Casteel%2C C%2EL%2E%2C and Maloof%2C J%2EN%2E %282018%29%2E Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance%2E Plant Physiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nozue,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance&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

https://scholar.google.com/scholar?as_q=Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nozue,&as_ylo=2018&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Pedmale%2C U%2EV%2E%2C Huang%2C S%2EC%2E%2C Zander%2C M%2E%2C Cole%2C B%2EJ%2E%2C Hetzel%2C J%2E%2C Ljung%2C K%2E%2C Reis%2C P%2EA%2EB%2E%2C Sridevi%2C P%2E%2C Nito%2C K%2E%2C Nery%2C J%2ER%2E%2C Ecker%2C J%2ER%2E%2C and Chory%2C J%2E %282016%29%2E Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light%2E Cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Pedmale,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light&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

https://scholar.google.com/scholar?as_q=Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Pedmale,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Quail%2C P%2EH%2E %282002%29%2E Photosensory perception and signalling in plant cells%3A new paradigms%3F Current opinion in cell biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Quail,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Photosensory perception and signalling in plant cells: new paradigms&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

https://scholar.google.com/scholar?as_q=Photosensory perception and signalling in plant cells: new paradigms&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Quail,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Rausenberger%2C J%2E%2C Hussong%2C A%2E%2C Kircher%2C S%2E%2C Kirchenbauer%2C D%2E%2C Timmer%2C J%2E%2C Nagy%2C F%2E%2C Schafer%2C E%2E%2C and Fleck%2C C%2E %282010%29%2E An Integrative Model for Phytochrome B Mediated Photomorphogenesis%3A From Protein Dynamics to Physiology%2E Plos One&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Rausenberger,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=An Integrative Model for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology.&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

https://scholar.google.com/scholar?as_q=An Integrative Model for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Rausenberger,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Robinson%2C M%2ED%2E%2C McCarthy%2C D%2EJ%2E%2C and Smyth%2C G%2EK%2E %282010%29%2E edgeR%3A a Bioconductor package for differential expression analysis of digital gene expression data%2E Bioinformatics&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Robinson,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=edgeR: a Bioconductor package for differential expression analysis of digital gene expression data&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

https://scholar.google.com/scholar?as_q=edgeR: a Bioconductor package for differential expression analysis of digital gene expression data&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Robinson,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ruzicka%2C K%2E%2C Ljung%2C K%2E%2C Vanneste%2C S%2E%2C Podhorska%2C R%2E%2C Beeckman%2C T%2E%2C Friml%2C J%2E%2C and Benkova%2C E%2E %282007%29%2E Ethylene regulates root growth through effects on auxin biosynthesis and transport%2Ddependent auxin distribution%2E The Plant cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ruzicka,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution&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

https://scholar.google.com/scholar?as_q=Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ruzicka,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Savchenko%2C T%2E%2C Walley%2C J%2EW%2E%2C Chehab%2C E%2EW%2E%2C Xiao%2C Y%2E%2C Kaspi%2C R%2E%2C Pye%2C M%2EF%2E%2C Mohamed%2C M%2EE%2E%2C Lazarus%2C C%2EM%2E%2C Bostock%2C R%2EM%2E%2C and Dehesh%2C K%2E %282010%29%2E Arachidonic acid%3A an evolutionarily conserved signaling molecule modulates plant stress signaling networks%2E The Plant cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Savchenko,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks&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

https://scholar.google.com/scholar?as_q=Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Savchenko,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Scanlon%2C M%2EJ%2E %282003%29%2E The polar auxin transport inhibitor N%2D1%2Dnaphthylphthalamic acid disrupts leaf initiation%2C KNOX protein regulation%2C and formation of leaf margins in maize%2E Plant Physiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Scanlon,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The polar auxin transport inhibitor N-1-naphthylphthalamic acid disrupts leaf initiation, KNOX protein regulation, and formation of leaf margins in maize&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

https://scholar.google.com/scholar?as_q=The polar auxin transport inhibitor N-1-naphthylphthalamic acid disrupts leaf initiation, KNOX protein regulation, and formation of leaf margins in maize&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Scanlon,&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Sellaro%2C R%2E%2C Pacin%2C M%2E%2C and Casal%2C J%2EJ%2E %282012%29%2E Diurnal dependence of growth responses to shade in Arabidopsis%3A role of hormone%2C clock%2C and light signaling%2E Molecular plant&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Sellaro,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling&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

https://scholar.google.com/scholar?as_q=Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sellaro,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Smalle%2C J%2E%2C Haegman%2C M%2E%2C Kurepa%2C J%2E%2C Van Montagu%2C M%2E%2C and Van Der Straeten%2C D%2E %281997%29%2E Ethylene can stimulate Arabidopsis hypocotyl elongation in the light%2E P Natl Acad Sci USA&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Smalle,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene can stimulate Arabidopsis hypocotyl elongation in the light&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

https://scholar.google.com/scholar?as_q=Ethylene can stimulate Arabidopsis hypocotyl elongation in the light&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Smalle,&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1


Stepanova, A.N., Yun, J., Likhacheva, A.V., and Alonso, J.M. (2007). Multilevel interactions between ethylene and auxin in Arabidopsisroots. Plant Cell 19, 2169-2185.


Sun, J., Ma, Q., and Mao, T. (2015). Ethylene Regulates the Arabidopsis Microtubule-Associated Protein WAVE-DAMPENED2-LIKE5 inEtiolated Hypocotyl Elongation. Plant Physiol 169, 325-337.


Swarup, R., Perry, P., Hagenbeek, D., Van Der Straeten, D., Beemster, G.T.S., Sandberg, G., Bhalerao, R., Ljung, K., and Bennett, M.J.(2007). Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell 19,2186-2196.


Tanaka, S., Nakamura, S., Mochizuki, N., and Nagatani, A. (2002a). Phytochrome in cotyledons regulates the expression of genes in thehypocotyl through auxin-dependent and -independent pathways. Plant & cell physiology 43, 1171-1181.


Tanaka, S.I., Nakamura, S., Mochizuki, N., and Nagatani, A. (2002b). Phytochrome in cotyledons regulates the expression of genes inthe hypocotyl through auxin-dependent and -independent pathways. Plant and Cell Physiology 43, 1171-1181.


Tian, Q., Uhlir, N.J., and Reed, J.W. (2002). Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression. The Plant cell 14, 301-319.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Vandenbussche, F., Vaseva, I., Vissenberg, K., and Van Der Straeten, D. (2012). Ethylene in vegetative development: a tale with ariddle. The New phytologist 194, 895-909.


Vandenbussche, F., Smalle, J., Le, J., Saibo, N.J., De Paepe, A., Chaerle, L., Tietz, O., Smets, R., Laarhoven, L.J., Harren, F.J., VanOnckelen, H., Palme, K., Verbelen, J.P., and Van Der Straeten, D. (2003). The Arabidopsis mutant alh1 illustrates a cross talk betweenethylene and auxin. Plant Physiol 131, 1228-1238.


Walley, J., Xiao, Y., Wang, J.Z., Baidoo, E.E., Keasling, J.D., Shen, Z., Briggs, S.P., and Dehesh, K. (2015). Plastid-producedinterorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum. Proceedingsof the National Academy of Sciences of the United States of America 112, 6212-6217.


Wang, J.Z., Li, B., Xiao, Y., Ni, Y., Ke, H., Yang, P., de Souza, A., Bjornson, M., He, X., Shen, Z., Balcke, G.U., Briggs, S.P., Tissier, A.,Kliebenstein, D.J., and Dehesh, K. (2017a). Initiation of ER Body Formation and Indole Glucosinolate Metabolism by the PlastidialRetrograde Signaling Metabolite, MEcPP. Molecular plant 10, 1400-1416.


Wang, J.Z., Li, B.H., Xiao, Y.M., Ni, Y., Ke, H.Y., Yang, P.Y., de Souza, A., Bjornson, M., He, X., Shen, Z.X., Balcke, G.U., Briggs, S.P.,Tissier, A., Kliebenstein, D.J., and Dehesh, K. (2017b). Initiation of ER Body Formation and Indole Glucosinolate Metabolism by thePlastidial Retrograde Signaling Metabolite, MEcPP. Molecular plant 10, 1400-1416.


Xiao, Y., Savchenko, T., Baidoo, E.E., Chehab, W.E., Hayden, D.M., Tolstikov, V., Corwin, J.A., Kliebenstein, D.J., Keasling, J.D., andDehesh, K. (2012). Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes.Cell 149, 1525-1535.


Yang, S.F., and Hoffman, N.E. (1984). Ethylene Biosynthesis and Its Regulation in Higher-Plants. Annu Rev Plant Phys 35, 155-189.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Young, M.D., Wakefield, M.J., Smyth, G.K., and Oshlack, A. (2010). Gene ontology analysis for RNA-seq: accounting for selection bias.Genome Biol 11, R14.



https://www.ncbi.nlm.nih.gov/pubmed?term=Stepanova%2C A%2EN%2E%2C Yun%2C J%2E%2C Likhacheva%2C A%2EV%2E%2C and Alonso%2C J%2EM%2E %282007%29%2E Multilevel interactions between ethylene and auxin in Arabidopsis roots%2E Plant Cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Stepanova,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Multilevel interactions between ethylene and auxin in Arabidopsis roots&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

https://scholar.google.com/scholar?as_q=Multilevel interactions between ethylene and auxin in Arabidopsis roots&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Stepanova,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Sun%2C J%2E%2C Ma%2C Q%2E%2C and Mao%2C T%2E %282015%29%2E Ethylene Regulates the Arabidopsis Microtubule%2DAssociated Protein WAVE%2DDAMPENED2%2DLIKE5 in Etiolated Hypocotyl Elongation%2E Plant Physiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Sun,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene Regulates the Arabidopsis Microtubule-Associated Protein WAVE-DAMPENED2-LIKE5 in Etiolated Hypocotyl Elongation&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

https://scholar.google.com/scholar?as_q=Ethylene Regulates the Arabidopsis Microtubule-Associated Protein WAVE-DAMPENED2-LIKE5 in Etiolated Hypocotyl Elongation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sun,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Swarup%2C R%2E%2C Perry%2C P%2E%2C Hagenbeek%2C D%2E%2C Van Der Straeten%2C D%2E%2C Beemster%2C G%2ET%2ES%2E%2C Sandberg%2C G%2E%2C Bhalerao%2C R%2E%2C Ljung%2C K%2E%2C and Bennett%2C M%2EJ%2E %282007%29%2E Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation%2E Plant Cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Swarup,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation&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

https://scholar.google.com/scholar?as_q=Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Swarup,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Tanaka%2C S%2E%2C Nakamura%2C S%2E%2C Mochizuki%2C N%2E%2C and Nagatani%2C A%2E %282002a%29%2E Phytochrome in cotyledons regulates the expression of genes in the hypocotyl through auxin%2Ddependent and %2Dindependent pathways%2E Plant %26 cell physiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tanaka,&hl=en&c2coff=1


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tanaka,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Tanaka%2C S%2EI%2E%2C Nakamura%2C S%2E%2C Mochizuki%2C N%2E%2C and Nagatani%2C A%2E %282002b%29%2E Phytochrome in cotyledons regulates the expression of genes in the hypocotyl through auxin%2Ddependent and %2Dindependent pathways%2E Plant and Cell Physiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tanaka,&hl=en&c2coff=1


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tanaka,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Tian%2C Q%2E%2C Uhlir%2C N%2EJ%2E%2C and Reed%2C J%2EW%2E %282002%29%2E Arabidopsis SHY2%2FIAA3 inhibits auxin%2Dregulated gene expression%2E The Plant cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tian,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression&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

https://scholar.google.com/scholar?as_q=Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tian,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Vandenbussche%2C F%2E%2C Vaseva%2C I%2E%2C Vissenberg%2C K%2E%2C and Van Der Straeten%2C D%2E %282012%29%2E Ethylene in vegetative development%3A a tale with a riddle%2E The New phytologist&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vandenbussche,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene in vegetative development: a tale with a riddle&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

https://scholar.google.com/scholar?as_q=Ethylene in vegetative development: a tale with a riddle&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vandenbussche,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Vandenbussche%2C F%2E%2C Smalle%2C J%2E%2C Le%2C J%2E%2C Saibo%2C N%2EJ%2E%2C De Paepe%2C A%2E%2C Chaerle%2C L%2E%2C Tietz%2C O%2E%2C Smets%2C R%2E%2C Laarhoven%2C L%2EJ%2E%2C Harren%2C F%2EJ%2E%2C Van Onckelen%2C H%2E%2C Palme%2C K%2E%2C Verbelen%2C J%2EP%2E%2C and Van Der Straeten%2C D%2E %282003%29%2E The Arabidopsis mutant alh1 illustrates a cross talk between ethylene and auxin%2E Plant Physiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vandenbussche,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The Arabidopsis mutant alh1 illustrates a cross talk between ethylene and auxin&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

https://scholar.google.com/scholar?as_q=The Arabidopsis mutant alh1 illustrates a cross talk between ethylene and auxin&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vandenbussche,&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Walley%2C J%2E%2C Xiao%2C Y%2E%2C Wang%2C J%2EZ%2E%2C Baidoo%2C E%2EE%2E%2C Keasling%2C J%2ED%2E%2C Shen%2C Z%2E%2C Briggs%2C S%2EP%2E%2C and Dehesh%2C K%2E %282015%29%2E Plastid%2Dproduced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum%2E Proceedings of the National Academy of Sciences of the United States of America&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Walley,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum&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

https://scholar.google.com/scholar?as_q=Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Walley,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wang%2C J%2EZ%2E%2C Li%2C B%2E%2C Xiao%2C Y%2E%2C Ni%2C Y%2E%2C Ke%2C H%2E%2C Yang%2C P%2E%2C de Souza%2C A%2E%2C Bjornson%2C M%2E%2C He%2C X%2E%2C Shen%2C Z%2E%2C Balcke%2C G%2EU%2E%2C Briggs%2C S%2EP%2E%2C Tissier%2C A%2E%2C Kliebenstein%2C D%2EJ%2E%2C and Dehesh%2C K%2E %282017a%29%2E Initiation of ER Body Formation and Indole Glucosinolate Metabolism by the Plastidial Retrograde Signaling Metabolite%2C MEcPP%2E Molecular plant&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wang,&hl=en&c2coff=1


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang,&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wang%2C J%2EZ%2E%2C Li%2C B%2EH%2E%2C Xiao%2C Y%2EM%2E%2C Ni%2C Y%2E%2C Ke%2C H%2EY%2E%2C Yang%2C P%2EY%2E%2C de Souza%2C A%2E%2C Bjornson%2C M%2E%2C He%2C X%2E%2C Shen%2C Z%2EX%2E%2C Balcke%2C G%2EU%2E%2C Briggs%2C S%2EP%2E%2C Tissier%2C A%2E%2C Kliebenstein%2C D%2EJ%2E%2C and Dehesh%2C K%2E %282017b%29%2E Initiation of ER Body Formation and Indole Glucosinolate Metabolism by the Plastidial Retrograde Signaling Metabolite%2C MEcPP%2E Molecular plant&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wang,&hl=en&c2coff=1


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang,&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Xiao%2C Y%2E%2C Savchenko%2C T%2E%2C Baidoo%2C E%2EE%2E%2C Chehab%2C W%2EE%2E%2C Hayden%2C D%2EM%2E%2C Tolstikov%2C V%2E%2C Corwin%2C J%2EA%2E%2C Kliebenstein%2C D%2EJ%2E%2C Keasling%2C J%2ED%2E%2C and Dehesh%2C K%2E %282012%29%2E Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress%2Dresponse genes%2E Cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xiao,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes&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

https://scholar.google.com/scholar?as_q=Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Xiao,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Yang%2C S%2EF%2E%2C and Hoffman%2C N%2EE%2E %281984%29%2E Ethylene Biosynthesis and Its Regulation in Higher%2DPlants%2E Annu Rev Plant Phys&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yang,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Ethylene Biosynthesis and Its Regulation in Higher-Plants&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

https://scholar.google.com/scholar?as_q=Ethylene Biosynthesis and Its Regulation in Higher-Plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yang,&as_ylo=1984&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Young%2C M%2ED%2E%2C Wakefield%2C M%2EJ%2E%2C Smyth%2C G%2EK%2E%2C and Oshlack%2C A%2E %282010%29%2E Gene ontology analysis for RNA%2Dseq%3A accounting for selection bias%2E Genome Biol 11%2C R&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Young,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Gene ontology analysis for RNA-seq: accounting for selection bias&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

https://scholar.google.com/scholar?as_q=Gene ontology analysis for RNA-seq: accounting for selection bias&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Young,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1


Yu, X., Liu, H., Klejnot, J., and Lin, C. (2010). The Cryptochrome Blue Light Receptors. The arabidopsis book 8, e0135.Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Yu, Y., Wang, J., Zhang, Z., Quan, R., Zhang, H., Deng, X.W., Ma, L., and Huang, R. (2013). Ethylene promotes hypocotyl growth and HY5degradation by enhancing the movement of COP1 to the nucleus in the light. PLoS genetics 9, e1004025.


Zhao, Y. (2012). Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants. Mol Plant 5, 334-338.


Zhong, S., Shi, H., Xue, C., Wang, L., Xi, Y., Li, J., Quail, P.H., Deng, X.W., and Guo, H. (2012). A molecular framework of light-controlledphytohormone action in Arabidopsis. Curr Biol 22, 1530-1535.



https://www.ncbi.nlm.nih.gov/pubmed?term=Yu%2C X%2E%2C Liu%2C H%2E%2C Klejnot%2C J%2E%2C and Lin%2C C%2E %282010%29%2E The Cryptochrome Blue Light Receptors%2E The arabidopsis book 8%2C e&dopt=abstract

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

https://scholar.google.com/scholar?as_q=The Cryptochrome Blue Light Receptors&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

https://scholar.google.com/scholar?as_q=The Cryptochrome Blue Light Receptors&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yu,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Yu%2C Y%2E%2C Wang%2C J%2E%2C Zhang%2C Z%2E%2C Quan%2C R%2E%2C Zhang%2C H%2E%2C Deng%2C X%2EW%2E%2C Ma%2C L%2E%2C and Huang%2C R%2E %282013%29%2E Ethylene promotes hypocotyl growth and HY5 degradation by enhancing the movement of COP1 to the nucleus in the light%2E PLoS genetics 9%2C e&dopt=abstract

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

https://scholar.google.com/scholar?as_q=Ethylene promotes hypocotyl growth and HY5 degradation by enhancing the movement of COP1 to the nucleus in the light&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

https://scholar.google.com/scholar?as_q=Ethylene promotes hypocotyl growth and HY5 degradation by enhancing the movement of COP1 to the nucleus in the light&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yu,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Zhao%2C Y%2E %282012%29%2E Auxin biosynthesis%3A a simple two%2Dstep pathway converts tryptophan to indole%2D3%2Dacetic acid in plants%2E Mol Plant&dopt=abstract

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

https://scholar.google.com/scholar?as_q=Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants&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

https://scholar.google.com/scholar?as_q=Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhao,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Zhong%2C S%2E%2C Shi%2C H%2E%2C Xue%2C C%2E%2C Wang%2C L%2E%2C Xi%2C Y%2E%2C Li%2C J%2E%2C Quail%2C P%2EH%2E%2C Deng%2C X%2EW%2E%2C and Guo%2C H%2E %282012%29%2E A molecular framework of light%2Dcontrolled phytohormone action in Arabidopsis%2E Curr Biol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhong,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=A molecular framework of light-controlled phytohormone action in Arabidopsis&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

https://scholar.google.com/scholar?as_q=A molecular framework of light-controlled phytohormone action in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhong,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1


2 running title - github pages

Documents