Jasmonate and Phytochrome A Signaling in ArabidopsisWound and Shade Responses Are Integrated throughJAZ1 Stability C W

Frances Robson,a,1 Haruko Okamoto,b,2 Elaine Patrick,a Sue-Re Harris,b Claus Wasternack,c

Charles Brearley,a and John G. Turnera,3

a School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United KingdombDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdomc Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany

Jasmonate (JA) activates plant defense, promotes pollen maturation, and suppresses plant growth. An emerging theme in

JA biology is its involvement in light responses; here, we examine the interdependence of the JA- and light-signaling

pathways in Arabidopsis thaliana. We demonstrate that mutants deficient in JA biosynthesis and signaling are deficient in a

subset of high irradiance responses in far-red (FR) light. These mutants display exaggerated shade responses to low, but

not high, R/FR ratio light, suggesting a role for JA in phytochrome A (phyA) signaling. Additionally, we demonstrate that the

FR light–induced expression of transcription factor genes is dependent on CORONATINE INSENSITIVE1 (COI1), a central

component of JA signaling, and is suppressed by JA. phyA mutants had reduced JA-regulated growth inhibition and VSP

expression and increased content of cis-(+)-12-oxophytodienoic acid, an intermediate in JA biosynthesis. Significantly,

COI1-mediated degradation of JASMONATE ZIM DOMAIN1-b-glucuronidase (JAZ1-GUS) in response to mechanical

wounding and JA treatment required phyA, and ectopic expression of JAZ1-GUS resulted in exaggerated shade responses.

Together, these results indicate that JA and phyA signaling are integrated through degradation of the JAZ1 protein, and

both are required for plant responses to light and stress.

INTRODUCTION

The group of signaling molecules known collectively as the

jasmonates (JAs) are plant hormones that regulate many phys-

iological processes, including defense, growth, development,

fertility, and senescence, throughout the life cycle of higher

plants (Devoto and Turner, 2003; Wasternack, 2007; Balbi and

Devoto, 2008; Reinbothe et al., 2009). JAs inhibit growth by

suppressing mitosis in apical meristems (Zhang and Turner,

2008), inhibit photosynthesis and energy-generating processes

(Ueda and Kato, 1980; Reinbothe et al., 1993; Jung et al., 2007),

and activate plant defense responses to a variety of biotic and

abiotic stresses (Rao et al., 2000; Glazebrook, 2005; Howe and

Jander, 2008; Frenkel et al., 2009;Clarke et al., 2009), suggesting

that JAs regulate the balance between growth and defense in

response to a dynamic environment.

In response to biotic and abiotic stress, a-linolenic acid is

released from plastid membranes by phospholipases, providing

the precursor for JA synthesis via the octadecanoid pathway

(Mueller et al., 1993). Regulation of JA responses occurs via a

global reprogramming of transcription that results in the up-

regulation of genes involved in defense, secondary metabolism,

hormone biosynthesis, and, in a feedback loop, JA synthesis

(Sasaki et al., 2001; Devoto et al., 2005; Cho et al., 2007;

Dombrecht et al., 2007; Jung et al., 2007; Pauwels et al., 2008;

Wang et al., 2008). Arabidopsis thaliana mutants in JA biosyn-

thesis, allene oxide synthase (aos; Park et al., 2002) and 12-oxo-

phytodienoic acid reductase (opr3; Stintzi and Browse, 2000),

are male sterile, highlighting the role of JAs in fertility.

A number of key players in JA signal transduction have been

identified in Arabidopsis. The gene for the F-box protein COI1

was identified in a mutant screen for plants insensitive to growth

inhibition by the JA analog, coronatine, a phytotoxin produced by

some pathogenic strains of Pseudomonas syringae (Feys et al.,

1994). Mutations in the COI1 gene result in plants that are

compromised in all known JA responses: defense against biotic

and abiotic stresses, growth inhibition, and fertility (Xie et al.,

1998; Zhang and Turner, 2008). COI1 binds to the Arabidopsis

homologs of S-PHASE KINASE-ASSOCIATED PROTEIN1 and

CULLIN to form the SCFCOI1 complex, an E3 ubiquitin ligase that

degrades target proteins in response to JA via the 26S proteo-

some (Devoto et al., 2002; Xu et al., 2002). Targets of SCFCOI1

include the JAZ transcriptional repressors (Chini et al., 2007;

Thines et al., 2007). JAZ proteins interact with and repress

activators of JA gene expression, including a transcription fac-

tor, the Arabidopsis homolog of myelocytomatosis viral onco-

gene (MYC), MYC2 (Boter et al., 2004; Lorenzo et al., 2004). In

1 John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UnitedKingdom.2 School of Pharmacy, Iwate Medical University, Morioka, Iwate 020-8505, Japan.3 Address correspondence to j.g.turner@uea.ac.uk.The author responsible for distribution of materials integral to thefindings presented in this article in accordance with the policy describedin the Instructions for Authors (www.plantcell.org) is: John G. Turner(j.g.turner@uea.ac.uk).CSome figures in this article are displayed in color online but in blackand white in the print edition.WOnline version contains Web-only data.www.plantcell.org/cgi/doi/10.1105/tpc.109.067728

The Plant Cell, Vol. 22: 1143–1160, April 2010, www.plantcell.org ã 2010 American Society of Plant Biologists

response to a JA signal, JAZ proteins bind to COI1 and are

degraded, relieving the repression of MYC2 that leads to ex-

pression of JA-regulated genes (Chini et al., 2007; Thines et al.,

2007). COI1 has been identified as a receptor for the bioactive

JA derivative (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile; Fonseca

et al., 2009; Yan et al., 2009). All interactions of COI1 with JAZ

proteins tested so far are mediated by JA-Ile (Thines et al., 2007;

Katsir et al., 2008; Melotto et al., 2008; Chini et al., 2009). The

amino acid conjugate synthase, JA-RESISTANT1 (JAR1), the

enzyme responsible for conjugating JA to Ile and other amino

acids, is a crucial component of the JA signal transduction

cascade for a subset of JA responses (Staswick et al., 2002;

Staswick and Tiryaki, 2004; Chung et al., 2008).

As well as providing the primary source of energy to support

photosynthesis, light is one of the most important environmental

signals governing the growth and development of plants through-

out their life cycle (Chen et al., 2004). The phytochromes, which

absorb light primarily in the red (R) and far-red (FR) part of the

spectrum (600 to 750 nm), regulate seed germination, seedling

establishment, circadian entrainment, and flowering time (Chory

et al., 1996). Phytochromes are also responsible for monitoring

the change in R/FR ratio that occurs when plants are shaded by

neighbors due to the selective absorbance of red light by

photosynthetic pigments (Ballare et al., 1990). This allows shade-

intolerant plants like Arabidopsis to preempt the threat of crowd-

ing by competitors and initiate escape mechanisms, collectively

known as shade avoidance responses, to reach light and so

maximize photosynthesis. Changes in R/FR ratio light are mainly

detected by phyB that acts to suppress shade avoidance in high

R/FR light (Franklin et al., 2003). Consequently, the phyBmutant

displays a constitutive shade avoidance response and, in all light

conditions, has elongated hypocotyls, petioles, and stems, ele-

vated leaves, and early flowering (Whitelam and Johnson, 1982;

Somers et al., 1991). However, in low R/FR ratio light, such as

occurs under dense canopies, phyA signaling limits excessive

shade avoidance, and plant survival is enhanced. The principal

evidence is that the phyAmutant is impaired in deetiolation under

extreme canopy shade and displays exaggerated shade avoid-

ance responses only in low, but not high, R/FR ratio light (Johnson

et al., 1994; Yanovsky et al., 1995; Smith et al., 1997). Moreover,

that the phyA phyB double mutant displays more exaggerated

shade responses than thephyBmutant alone suggests that in very

low R/FR ratio light, phyA antagonizes phyB.

One of the first indications of a link between JA and phyA

signaling came from the discovery that a mutation in the Arabi-

dopsis gene FAR-RED-INSENSITIVE219, which was originally

identified as a suppressor of the constitutive photomorphogen-

esis1mutation (Hsieh et al., 2000), is allelic to jar1 (Staswick et al.,

2002). Although jar1was at first thought not to have a photomor-

phogenic deficiency, a subsequent investigation reported that

both fin219 and the jar1 alleles are insensitive to FR light with

respect to hypocotyl growth inhibition (Chen et al., 2007). Other

screens have also identified Arabidopsis mutants that are in-

volved in both light and JA signaling. For example, the mutant

jasmonate insensitive1 (jin1) was found to be an allele of MYC2

(Lorenzo et al., 2004), which was also identified as the gene for

Z-BOX BINDING FACTOR1 (ZBF1) on the basis of its binding to

the Z-box of light-regulated promoters (Yadav et al., 2005). Mu-

tations in MYC2/JIN1/ZBF1 lead to hypersensitivity to blue light

with respect to hypocotyl growth inhibition and altered blue and

FR light gene expression. In a screen for mutants with increased

sensitivity to JA, amutation in LONGHYPOCOTYL1 (HY1), which

encodes a plastid heme oxygenase required for phytochrome

chromophore biosynthesis, was recovered. Subsequently, it was

demonstrated that mutations in either HY1 or HY2, which en-

codes a phytochromobilin synthase, cause elevated JA produc-

tion and sensitivity (Zhai et al., 2007). The ecological significance

of an interaction between phytochrome and JA signaling was

revealed in a study ofArabidopsis plants grown at high density or

in illumination supplemented with FR light. In these plants, phyB

signaling led to shade avoidance phenotypes and suppressed

both JA-mediated gene expression and JA-dependent defenses

against an insect herbivore (Moreno et al., 2009).

In rice (Oryza sativa), characterization of the hebiba mutant

provided the first evidence of a link between JA signaling and

photomorphogenesis in monocots (Riemann et al., 2003). This

mutant was isolated in a screen for reduced sensitivity to red

light. Significantly, hebiba is male sterile, compromised in JA

accumulation, and has been reported to map close to a known

JA biosynthesis gene. The light-regulated turnover of the phyA

protein is delayed in hebiba and restored by exogenous JA,

suggesting a specific role for JA in a key facet of phytochrome

A signaling (Sineshchekov et al., 2004; Riemann et al., 2009). In

addition, a knockout mutation in the rice homolog of JAR1 is

insensitive to FR and blue light inhibition of coleoptile elongation

(Riemann, et al., 2008). These two ricemutants point to a key role

for JA biosynthesis and signaling in photomorphogenesis, which

is largely absent from our current understanding of photomor-

phogenesis in Arabidopsis. It is possible that photomorphogenic

phenotypes in Arabidopsis JA mutants have been overlooked

because many of the JA biosynthesis mutants and the JA

receptor coi1 are male sterile and may have been lost during

screens to identify mutants with altered light perception.

We previously noticed that coi1-16 mutants flower early, and

in some growth conditions display elongated, hyponastic peti-

oles, and elongated hypocotyls, phenotypes that are classic

indicators of deficient responses to light quality (Whitelam and

Johnson, 1982). An upright growth habit had also been reported

for the coi1-20mutant that was isolated in a screen for resistance

to P. syringae (Kloek et al., 2001). We have therefore investigated

the interaction of JA and phytochrome signaling in light-

regulated growth responses. We demonstrate that COI1 and

JA signaling is required for some aspects of photomorphogen-

esis and shade avoidance growth responses, that phy A is

required for full sensitivity to growth inhibition by JA, and that

phyA and JA signaling are integrated at the level of degradation

of a target of the COI1 E3 ligase, the JAZ1 protein.

RESULTS

COI1 Modulates Responses to Light

COI1 Regulates Flowering and Shade Responses

The COI1 gene controls most of the known JA responses in

Arabidopsis (Xie et al., 1998). We reasoned that if JA regulates

1144 The Plant Cell

some light responses, then COI1 would be required for at least

some of these. We first compared time to flower in the partial

loss-of-function mutant coi1-16 and its wild-type background

Columbia (Col)-gl1, to which we refer hereafter as the wild type.

In short days (SDs), coi1-16 plants flowered earlier thanwild-type

plants and did so with fewer leaves (Figures 1A and 1C). In long

days (LDs), the coi1-16 mutant also flowered earlier, although

with a similar number of leaves to the wild type (Figure 1B).

However, sensitivity to daylength was retained in respect of both

flowering time and leaf number. In this regard, the coi1-16mutant

displays the early flowering response that is reminiscent of phyB

mutants (Goto et al., 1991).

When Arabidopsis plants are shaded by neighboring vegeta-

tion, the incident light they receive has a reduced ratio of R/FR

because of the selective absorption of red light by the photo-

synthetic pigments of plants forming the canopy (Ballare et al.,

1990). Under these conditions, Arabidopsis displays shade

avoidance responses (Whitelam and Johnson, 1982). To test

whether COI1 is required for these phytochrome-dependent

responses, we compared the shade avoidance phenotypes of

coi1-16 and the wild type. Under low R/FR ratio light, the

hypocotyls of coi1-16 were >30% longer than those of the wild

type (Figures 2A and 2B). By contrast, when plants were grown

under a high R/FR ratio, the hypocotyls of both coi1-16 and the

wild type were shorter than under low R/FR and were not

significantly different in length (Figures 2A and 2B). In this

respect, coi1-16 mutants are reminiscent of phyA mutants,

which, when grown in low, but not high, R/FR, display enhanced

hypocotyl elongation compared with wild-type controls (Figure

2C; Johnson et al., 1994; Yanovsky et al., 1995; Smith et al.,

1997). Our results are consistent with the hypothesis that phy-

tochrome A (phyA) modulates sensitivity to reductions in R/FR

perceived by phyB under FR-enriched light conditions, such as

those found underneath dense canopies. Moreover, that both

coi1-16 and phyA mutants display enhanced shade avoidance

only under low R/FR ratio light further suggests that COI1may be

required for the phyA-mediated antagonism of phyB signaling in

shade responses. In contrast with coi1-16, however, phyA

mutants flower slightly later in LDs and significantly later in SDs

than the wild type (Johnson et al., 1994). This suggests that, in

addition to its role in phyA-mediated shade avoidance, COI1 is

involved in flowering responses mediated by a different mech-

anism, possibly involving phyB.

COI1 Is Required during Early Seedling Development for

Photomorphogenic Responses to FR Light

Light is an important signal during early seedling development,

promoting photomorphogenic responses such as cotyledon

expansion and chloroplast development while inhibiting hypo-

cotyl growth, processes that are collectively referred to as

seedling deetiolation (Chen et al., 2004). We examined these

responses in monochromatic R, FR, and blue (B) light to further

dissect the light responses regulated by COI1.

Elongation ofArabidopsis hypocotyls is inhibited in continuous

FR light (FRc) in a fluence-dependent, high irradiance response

(HIR) mediated by phyA (Whitelam et al., 1993; Shinomura et al.,

2000). The seminal evidence for the role of phyA in this response

is that null mutants, including phyA-211 (Reed et al., 1994), lack

inhibition of hypocotyl elongation in FRc (Whitelam et al., 1993).

We therefore tested whether COI1 is also required for this

phyA-mediated response. coi1-16 seedlings grown under FRc

light (1 mmol m22 s21) had significantly longer hypocotyls than

wild-type seedlings (Figures 3A and 3C). This key observation

indicates that COI1 is necessary for the inhibition of hypocotyl

elongation that occurs in FRc light. However, unlike the phyA

mutants, which are deficient in all seedling deetiolation re-

sponses to FRc light, coi1-16 seedlings, like the wild type, had

open, expanded cotyledons and no apical hook. Thus, COI1 is

not required for all FR responses. To confirm the requirement for

COI1 in the inhibition of hypocotyl elongation, we also tested the

coi1-1 null mutant. This mutant, like coi1-16, is recessive, but in

addition is infertile and therefore can only be maintained in

segregating F2 populations. An F2 population collected from a

COI1/coi1-1 plant was grown in FRc light (1 mmol m22 s21). This

population segregated in a ratio of 18:4 for seedlings with short

(#8 mm) versus long (>8 mm) hypocotyls, whereas wild-type

Figure 1. coi1-16 Mutants Flower Early.

(A) Flowering time in SD.

(B) Flowering time in LD. Days to flowering: number of days from

germination to first appearance of buds. Leaf number: total number of

rosette and cauline leaves on the primary inflorescence, counted after

bolting. The wild type and coi1-16 are significantly different with respect

to the number of days to flowering and the total leaf number in SD and

with respect to days to flowering in LD (Student’s t test; P < 0.01). Total

leaf numbers in LD are not significantly different. n = 20 (mean 6 SE).

(C) Eight-week-old wild type (left) and coi1-16 plants in SD.

[See online article for color version of this figure.]

phyA Regulates JAZ1 Stability 1145

seedlings all had short hypocotyls (#8 mm) under this condition

(Figures 3B and 3C). We presumed that seedlings with the longer

hypocotyls in the segregating population were homozygous

coi1-1 seedlings and that the seedlings with shorter hypocotyls

were heterozygous and wild type. This indicates that the ob-

served phenotypes of the coi1-16 mutants are not allele specific.

Together, these results identify a novel role for COI1 in hypocotyl

growth inhibition in response to FRc light. Like the coi1-16

mutants, coi1-1 mutants displayed wild-type apical hook open-

ing and cotyledon expansion in response to FR light.

We examined the fluence rate dependence of the requirement

for COI1 for inhibition of hypocotyl elongation in the range

previously demonstrated to be regulated by the HIR. As ex-

pected, FRc-grown wild-type seedlings exhibited a fluence-

dependent inhibition of hypocotyl growth, whereas the phyA-211

hypocotyls were the same length as dark-grown hypocotyls at all

fluences tested (Figure 3D). coi1-16 hypocotyls were signifi-

cantly longer (by 10 to 25%) thanwild-type hypocotyls at FR light

fluence rates from 0.01 to 120 mmol m22 s21. However, coi1-16

exhibited only a partial defect in FR hypocotyl responses,

Figure 2. coi1-16 Mutants Display an Exaggerated Shade Avoidance

Response to Low R/FR.

(A) Hypocotyl elongation response to low R/FR ratio light of wild-type

and coi1-16 seedlings. Average hypocotyl lengths of 30 12-d-old seed-

lings per genotype/treatment (mean 6 SD) are shown. Differences

between the wild type and coi1-16 in low R/FR are significant (Student’s

t test; P < 0.0001).

(B) Photographs of representative 10-d-old wild-type and coi1-16 seed-

lings under high and low R/FR ratios. A 10-mm ruler is shown.

(C) Hypocotyl elongation response to low R/FR ratio light of Col-0 and

phyA-211 seedlings. Average hypocotyl lengths of 30 12-d-old seedlings

per genotype/treatment (mean 6 SD) are shown. Differences between

Col-0 and phyA-211 in low R/FR are significant (Student’s t test; P =

0.002).

[See online article for color version of this figure.]Figure 3. coi1 Mutants Are Partially Insensitive to FR Light.

(A) Average hypocotyl lengths of 4-d-old wild-type and coi1-16 seedlings

grown for 2 d in the dark and transferred for 2 d to FRc at 1 mmol m�2 s�1.

n = 10 (mean 6 SD). Differences are significant (Student’s t test; P <

0.0001).

(B) Frequency distribution of hypocotyl lengths of a wild-type population

and a coi1-1+/� segregating population grown as in (A).

(C) Photographs of 4-d-old wild-type, coi1-16, and coi1-1 seedlings

grown as in (A) and (B).

(D) Fluence rate response to FRc light. Average hypocotyl lengths of

6-d-old wild-type, coi1-16, and phyA-211 seedlings grown in difference

fluence rates of FRc light (730 6 10 nm). Forty seedlings per genotype/

treatment were measured (mean 6 SE). The wild type and coi1-16 were

significantly different at all fluences (Student’s t test; P < 0.01). The wild-

type background of phyA-211 (Col-0) was not significantly different from

the wild-type background of the coi1-16 mutant and was omitted for

clarity. Most error bars are smaller than symbols.

1146 The Plant Cell

retaining sensitivity in particular to higher fluences. These results

indicated that COI1 is required for part of the FR- and fluence

rate–dependent inhibition of hypocotyl elongation.

A Role for COI1 in Photomorphogenesis Extends to Red

Light Responses

phyB is the primary photoreceptor for the inhibition of elongation

of hypocotyls of Arabidopsis seedlings exposed to continuous R

(Rc) light (McCormac et al., 1993). To determine whether COI1 is

also required for phyB-mediated seedling responses, we grew

seedlings of coi1-16, wild type, and the loss-of-function phyB

mutant, phyB-9 (Reed et al., 1994) in Rc light at different fluence

rates and compared hypocotyl lengths. Again, as anticipated,

the hypocotyl length of thewild typewas reduced in approximate

proportion to the log of the fluence rate, while at all fluence rates,

hypocotyls of phyB-9 were as fully elongated as those of dark-

grown seedlings. By contrast, coi1-16 hypocotyls were signifi-

cantly longer than those of the wild type at fluence rates >0.3

mmol m22 s21 (Figure 4A). Similar to the responses in FRc, coi1-

16 mutants displayed only partial insensitivity to Rc-mediated

inhibition of hypocotyl growth. Additionally, coi1-16 seedlings,

similar to wild-type seedlings, had open, expanded, and green

cotyledons and no apical hook, indicating that COI1 is not

required for all R light responses. Significantly, hypocotyls of

dark-grown coi1-16 seedlings were not different in length from

those of their wild-type counterparts (Figure 4A), indicating that

the altered hypocotyl length of light-grown seedlings is light

dependent and does not result from a general defect in growth.

These data indicate that COI1 is necessary for light-induced

suppression of hypocotyl elongation in response to both Rc and

FRc light and may therefore be required for both phyA and phyB

signaling during early seedling development. However, coi1-16

was only slightly insensitive to suppression of hypocotyl elon-

gation by continuous blue (Bc) light (see Supplemental Figure

1 online). While the major receptors for blue light responses

are the cryptochromes (Ahmad and Cashmore, 1993), sup-

pression of hypocotyl elongation by Bc light is also partly

mediated by phyA (Johnson et al., 1994). The slight insensitivity

to Bc in coi1-16 could also reflect loss of COI1-dependent

phyA activity.

Low Fluence Responses to Red Light Do Not Involve COI1

We showed in the preceding section that COI1 is required for Rc

light inhibition of hypocotyl elongation, a classic HIRmediated by

phyB. PhyB acts as amolecular switch that is activated by R light

and inactivated by FR light, to regulate R/FR reversible low

fluence responses (Nagatani et al., 1991). We tested whether

COI1 was also required for phyB-mediated low fluence re-

sponses by monitoring the response to end-of-day (EOD) FR.

Wild-type, coi1-16, and phyB-9 seedlings were grown in white

light (SD) and at the end of each day were exposed to FR light for

10 min for three consecutive days. As anticipated, wild-type, but

not phyB-9, seedlings showed FR-mediated elongation of hy-

pocotyls (Nagatani et al., 1991) (Figure 4B). A subsequent 5-min

red light treatment resulted in hypocotyl growth inhibition of wild-

type seedlings similar to that of white light or white light plus

EOD red light–grown control seedlings. Significantly, coi1-16

seedlings responded like wild-type seedlings to the EOD-FR

treatment.

Although the previous section identified a role for COI1 in HIR

to Rc light, our data above show that COI1 is not required for the

R/FR reversible phyB-mediated low fluence EOD-FR response.

Because we show here that COI1 is required for shade re-

sponses to low, but not high, R/FR and additionally for HIR to FRc

light, both of which are mediated by phyA, we investigated

further the interaction of COI1 and phyA signaling.

Figure 4. COI1 Is Required for Hypocotyl Growth Inhibition Responses

to Rc Light but Is Not Required for the phyB-Mediated Low Fluence

Response to EOD-FR.

(A) Fluence rate response to Rc light. Average hypocotyl lengths of 6-d-

old wild-type, coi1-16, and phyB-9 seedlings grown in difference fluence

rates of Rc light (660 6 10 nm). Forty seedlings per genotype/treatment

were measured (mean6 SE). The wild type and coi1-16 were significantly

different at the three highest fluences of red light tested only (45, 13, and

2.3 mmol m�2 s�1; Student’s t test; P < 0.01) but not at the lower fluences

(0.3 and 0.09 mmol m�2 s�1). The wild-type background of phyB-9 (Col-0)

was not significantly different from the wild-type background of the

coi1-16 mutant and was omitted for clarity. Error bars are smaller than

symbols.

(B) EOD-FR hypocotyl response. Hypocotyl lengths of 3-d-old white

light/SD-grown Col-0, phyB-9, wild-type, and coi1-16 plants given 5 min

red, 10 min FR, or 10 min FR followed by 5 min red light at the end of

every light cycle. n = 10 (mean 6 SD).

phyA Regulates JAZ1 Stability 1147

JA Regulates the Expression of the FR-Inducible

Transcription Factors HFR1 and PIL1 in a

COI1-Dependent Manner

We showed in the previous section that COI1 is required for

several FR-dependent responses, including inhibition of hypo-

cotyl elongation and shade avoidance. We reasoned that COI1

might also be required for regulation of expression of genes

involved in FR signaling. FR induces expression of the basic

helix-loop-helix (bHLH) transcription factors encoded by HFR1

and PIL1, which regulate responses to FRc and low R/FR ratio

light (Fairchild et al., 2000; Salter et al., 2003; Sessa et al., 2005),

and the chlorophyll a/b binding protein gene, CAB2, which is

often employed as a marker of light signaling (Karlin-Neumann

et al., 1988). We grew the wild-type and coi1-16 seedlings in the

dark and transferred them to FRc light and used quantitative

RT-PCR (qRT-PCR) to compare levels of transcripts of HFR1,

PIL1, and CAB2 (Figure 5). As expected, the expression of

HFR1, PIL1, and CAB2 was elevated in wild-type seedlings

transferred to FR light, but this induction was significantly atten-

uated in coi1-16 seedlings. Notably, the COI1-dependent FR

induction of HFR1, PIL1, and CAB2 was itself suppressed by JA

treatment. We conclude that COI1 is required for both the FR

induction and for the JA suppression of transcription of HFR1,

PIL1, and CAB2.

COI1 Is Required for the FR Light–Preconditioned Block

of Greening

We examined whether other phyA responses required COI1.

Wild-type Arabidopsis seedlings raised in FRc light and subse-

quently transferred to white light fail to produce chlorophyll and

they die. This preconditioned block of greening by FR (Barnes

et al., 1996) is in part a consequence of the phyA-mediated

repression of the light-dependent NADPH-protochlorophyllide

oxidoreductase A gene (PORA). This repression causes hyper-

accumulation of the chlorophyll precursor, protochlorophyllide-

F632, and irreversible photooxidative damage on transfer of

seedlings to white light (Runge et al., 1996). The phyA mutants

do not exhibit FR repression of PORA and are therefore resistant

to FR-mediated block of greening. To examine whether COI1

was required for this FR response, we raised wild-type, phyA-

211, and coi1-16 seedlings in FRc light (10mmolm22 s21) for 6 d,

transferred these to white light for 2 d, and then measured their

chlorophyll content. Wild-type seedlings had bleached cotyle-

dons at harvest and did not survive, whereas both phyA-211 and

coi1-16 cotyledons were detectably green following transfer

from FR to white light, and their chlorophyll contents were

significantly higher than the wild type (Figures 6A and 6B).

We tested whether the resistance to FR block of greening in

coi1-16 was associated with failure to repress PORA, as it is in

phyA-211. Wild-type, phyA-211, and coi1-16 seedlings were

grown in the dark for 6 d and transferred into FRc light for 4 or

24 h. mRNAwas extracted and PORA expression wasmeasured

by qRT-PCR. As expected, PORA was depleted in wild-type

seedlings illuminatedwith FRc for 4 h andwas undetectable after

24 h (Figure 6C). PORA was not depleted in phyA-211 and was

still detectable after 24 h of FRc light. Significantly, PORA

expression in coi1-16 was higher than in the wild type, both in

the dark and after exposure to FRc light. The elevated basal level

of PORA in coi1-16 may explain its survival of FR light–precondi-

tioned block of greening and indicates that thatCOI1 contributes

to repression of PORA during skotomorphogenesis and during

FR light–mediated photomorphogenesis.

JA Biosynthesis and Signaling Regulate Responses to

FR Light

JA Biosynthesis and Signaling Are Required for

FR-Dependent Photomorphogenesis

In the preceding sections, we showed that COI1 is required for

the phyA-mediated FR-dependent inhibition of hypocotyl elon-

gation. Because COI1 is a component of the JA signal pathway,

we wished to determine whether COI1 in particular, or JA

signaling in general, is required for the inhibition of hypocotyl

elongation by FR. Mutants defective in synthesis of JA (aos and

Figure 5. Light-Regulated Genes Are Induced by FR in a COI1-Depen-

dent Manner and Are Suppressed by Exogenous JA.

Expression of HFR1, PIL1, and CAB2 genes in 6-d-old etiolated wild-

type or coi1-16 seedlings exposed to FR or FR + 20 mM methyl

jasmonate (meJA) for the number of hours indicated. Expression levels

(mean 6 SD) of three technical replicate qRT-PCR reactions are ex-

pressed relative to ACTIN2.

1148 The Plant Cell

opr3) were grown in FRc light (1 mmol m22 s21) and in darkness,

and their hypocotyl lengths were measured. We represent hy-

pocotyl growth as a percentage of dark-grown controls. The

average length of Col-0 wild-type hypocotyls in FRc was 56.5%

(65.2) of that in darkness, while hypocotyls of the phyA-211

mutants in FR light were 98.5% 6 6.3% of their length in

darkness (Figure 7A). The hypocotyls of the aos mutant were

inhibited by FR light to 78.4% (69.4) of their length in darkness,

which was significantly less (P < 0.0001) than the inhibition of

Col-0 wild-type hypocotyls. At variance with this, the null opr3

mutant was not significantly different from its wild type

(Wassilewskija) with respect to percentage of hypocotyl growth

inhibition by FRc light (wild type, 72.9%6 4.6%; opr3, 72.3%64.3%).

We also analyzed the FRc growth phenotype of the mutants

fin219 and jar1-1. Our results are consistent with former studies

(Hsieh et al., 2000; Chen et al., 2007): in FRc light, fin-219

and jar-1 hypocotyl lengths were inhibited 84.3% 6 4.6% and

62.4% 6 4.3%, respectively, of their dark-grown lengths and

significantly less than the inhibition of hypocotyls of their wild

type, Col-0 (fin219, P < 0.0001; jar1-1, P < 0.01).

We investigated the role of signaling components that act

downstream of JA biosynthesis. COI1 is involved in JA percep-

tion, and Figure 3 shows that coi1-16 is less sensitive to FRc

inhibition of hypocotyl length than the wild type. Similarly, Figure

7A shows that in FRc, coi1-16 hypocotyls were 79%of the length

of dark-grown hypocotyls. These results indicate that COI1 is

required for FRc inhibition of hypocotyl elongation. We also

examined the response to FRc of lines with mutations in genes

for negative (JASMONATE INSENSITIVE3 [JAI3]/JAZ3) and pos-

itive (MYC2/JIN1/ZBF1) regulators of JA signaling. Mutants of

these genes, jai3 and jin1-1, respectively, were originally isolated

by virtue of their insensitivity to growth inhibition by JA (Lorenzo

et al., 2004).

In FRc light, wild-type Col-0 hypocotyls were 66.2% (67.5) of

their dark-grown length, but the jai3 and jin1-1mutant hypocotyls

were less strongly inhibited to 78.5% (66.6) and 76.6% (69.1) of

their dark-grown length, respectively (Figure 7B), and the re-

duced sensitivity of themutants comparedwith thewild typewas

significant (P < 0.0001 and P = 0.011, respectively). It was

previously reported that there was no difference between the

hypocotyl growth response of the wild type and myc2 (jin1)

mutants to FRc light (Yadav et al., 2005). The differencewe report

here may be due to the lower fluence rate, 1 mmol m22 s21 we

have used, compared with the 90 mmol m22 s21 fluence rate

employed by Yadav et al. (2005). In support of this explanation,

others (Staswick et al., 2002; Chen et al., 2007) report that

hypocotyl length of jar1-1mutants differ from thewild type in FRc

only at fluences <10 mmol m22 s21. Alternatively, Yadav et al.

(2005) used T-DNA mutants myc2-2 and myc2-3 rather than the

jin1-1 allele, and there may be allele-specific responses that

could explain the difference in our results. Our experiments

demonstrate that wild-type alleles of genes JAI3/JAZ3 and

MYC2/JIN1/ZBF1, whose products act downstream of COI1,

are necessary components of the JA signaling required for FR

light inhibition of hypocotyl elongation. These data indicate that

JA synthesis and signaling contribute to the activation of phyA-

mediated inhibition of hypocotyl elongation by FR light. OPR3,

however, is not required for this response.

Expression of JA Biosynthesis and Signaling Genes Is

Regulated by FR Light

The transcription of JA biosynthesis genes is activated by JA in a

COI1-dependent manner, apparently in a feedback loop (Devoto

et al., 2005).We sought to establishwhether genes involved in JA

biosynthesis and signaling are regulated transcriptionally by FR

light, as has been demonstrated in rice (Haga and Iino, 2004). For

Figure 6. COI1 Is Required for the FR Light–Preconditioned Block of Greening Response.

(A) Wild-type, coi1-16, and phyA-211 seedlings grown in FRc (10 mmol m�2 s�1) for 6 d and transferred to white light/LD (100 mmol m�2 s�1) for 2 d.

(B) Chlorophyll accumulation (mg/mg tissue) in plants grown as in (A).

(C) Expression of the PORA gene in 6-d-old etiolated wild-type, coi1-16, and phyA-211 seedlings exposed to FR (10 mmol m�2 s�1) for the number of

hours indicated. Expression levels (mean 6 SD) of three technical replicate qRT-PCR reactions are expressed relative to ACTIN2.

phyA Regulates JAZ1 Stability 1149

this, seedlings of the wild type and coi1-16 were grown in

darkness and transferred to FRc, and samples taken at intervals

were assayed by qRT-PCR for transcription of the JA biosyn-

thesis gene ALLENE OXIDE CYCLASE1 (AOC1), the signaling

genes JAZ1 and MYC2/JIN1/ZBF1, and the response gene

VEGETATIVE STORAGE PROTEIN1 (VSP1), which is commonly

used as a marker of JA responses (Berger et al., 1995). FR

caused transient induction of all genes, and this induction was

attenuated in the coi1-16 mutants (Figure 7C). Evidently, FRc

induces COI1-dependent transcription of genes involved in JA

biosynthesis and signaling.

JAR1, JAZ3, and MYC2/JIN1/ZBF1 Are Required for

Shade Responses

We show above that JAR1,COI1, JAZ3, andMYC2were required

for the FRc inhibition of hypocotyl elongation by phyA. We there-

fore tested whether these genes were also required for shade

responses in low R/FR ratio light. coi1-16, jar1-1, jin1-1, and jai3

(Figures 8A and 8B), and coi1-1 and fin219 (see Supplemental

Figure 2 online) showed enhance shade avoidance at low, but not

high, R/FR ratio light comparedwith thewild type. Together, these

results indicate that JA biosynthesis and signaling are involved in

the adaptive response of plants to deep canopy shade.

phyA Regulates Sensitivity to JAs

phyA Is Required for JA-Mediated Root Growth Inhibition

The foregoing demonstrates that JA is required for phyA

signaling. We therefore examined whether this is reciprocated

and whether phyA is required for JA signaling. In Arabidopsis,

root growth is inhibited by exogenous JA in a dose-dependent

manner (Staswick et al., 1992; Feys et al., 1994; Lorenzo et al.,

2004). We therefore grew the wild type, coi1-16, Col-0, and

phyA-211 in LD for 8 d on media containing different concentra-

tions of MeJA. As expected, wild-type roots were progressively

inhibited by increasingMeJAconcentration, whereas the coi1-16

mutant was significantly less sensitive to root growth inhibition

by MeJA (Figures 9A and 9B). The phyA-211 mutant was also

significantly less sensitive to root growth inhibition by MeJA than

its wild type (P < 0.001) at all concentrations, though less so than

coi1-16 (Figures 9A and 9C). Col-0 and phyA-211 roots were not

significantly different in length in the absence of JA, indicating

that the altered root phenotype of phyA-211 was JA dependent

and not due to a general defect in root growth. These data

indicate that a functional phyA gene is required for part of the root

growth inhibition by exogenous JA.

phyA Is Required for JA-Mediated Induction of VSP1

Arabidopsis VSP1 is transcriptionally activated by JA and

wounding in a COI1-dependent manner (Benedetti et al., 1995;

Berger et al., 1995). Transcription of VSP1 is transiently induced

by FR light and is COI1 dependent (Figure 7C). We tested

whether phyA was required for the transcription of VSP1. For

this, 6-d-old Col-0 and phyA-211 seedlings were transferred to

media containing 20 mM MeJA or fresh control media and

incubated in the dark or in FRc light for 8 h. RNA was extracted

and VSP1 was measured by qRT-PCR. In Col-0, VSP1 MeJA

treatment increased VSP1 expression over the untreated control

by 226-fold in the dark and 314-fold in FRc light (Figure 9C). By

contrast, MeJA increased VSP1 expression phyA mutants, over

the untreated control, by 3.9-fold in the dark and by 30-fold in FR

light (Figure 9C). Therefore, in young seedlings, transcriptional

activation of VSP1 by MeJA requires phyA.

phyA Mutants Have Altered OPDA Levels

Treatment of etiolated rice seedlings with red light resulted

in accumulation of JA (Riemann et al., 2003). We therefore

Figure 7. JA Biosynthesis and Signaling Genes Are Involved in FR

Responses.

(A) Average percentage of hypocotyl growth inhibition by FR of 4-d-old

(2 d dark, 2 d FR at 1 mmol m�2 s�1) JA and JA-Ile biosynthesis mutants

aos, jar1-1/fin219, and opr3, along with their wild-type parental lines

(Col-0 and Wassilewskija) and the phyA-211 and coi1-16 mutants for

comparison. The aos and opr3 mutants are taller than the wild type in

the dark so bars represent percentage of dark-grown (4 d dark) hypo-

cotyl length. The differences in percentage of growth inhibition between

the wild type and the mutants were tested by Student’s t test, and

the significant results (P < 0.05) are indicated by asterisks. n = 20

(mean 6 SD).

(B) Average percentage of hypocotyl growth inhibition by FR of 4-d-old

(2 d dark, 2 d FR at 1 mmol m�2 s�1) JA signaling mutants jin1-1 and jai3,

the wild type (Col-0), and the phyA-211 mutant.

(C) Expression of AOC1, MYC2/JIN1/ZBF1, JAZ1, and VSP1 genes in

6-d-old wild-type and coi1-16 etiolated seedlings exposed to FR (10

mmol m�2 s�1) for the number of hours indicated. Expression levels

(mean 6 SD) of three technical replicate qRT-PCR reactions are ex-

pressed relative to ACTIN2.

1150 The Plant Cell

investigated whether in Arabidopsis FRc treatments that pro-

mote photomorphogenesis also result in accumulation of JA or

its derivatives. We grew the wild type, coi1-16, Col-0, and phyA-

211 for 3 d in the dark or 2 d dark followed by 24 h of FR light (10

mmol m22 s21). Seedlings were flash-frozen and analyzed for JA

content. JA and JA-Ile were undetectable in two independent

experiments in both dark and FR, in all genotypes and all

replicates. Cis-(+)-12-oxophytodienoic acid (OPDA), however,

was abundant in both dark-grown and FR-treated seedlings

(Figure 9D), consistent with a former study (Brux et al., 2008). FRc

treatment did not affect the OPDA content of seedlings, but the

OPDA content of phyA-211 (400 to 500 pmol/g fresh weight) was

significantly higher than that of Col-0 (235 to 240 pmol/g fresh

weight, P < 0.01). Interestingly, the coi1-16 plants had signif-

icantly reduced OPDA content, supporting the hypothesis that

there is feedback regulation of oxylipin biosynthesis downstream

of JA perception (Stintzi and Browse, 2000).

phyA Is Not Required for Wound- and JA-Mediated Aerial

Growth Inhibition, Anthocyanin Accumulation, or

Chlorophyll Degradation

Responses of wild-type Arabidopsis to exogenous JA include

inhibition of root growth, inhibition of aerial growth, accumulation

of anthocyanin, and degradation of chlorophyll, and these re-

sponses are absent from coi1mutants (Feys et al., 1994; Ellis and

Turner, 2002; He et al., 2002). To establish whether phyA in-

volvement in JA signaling is specific to particular JA-mediated

processes, we examined additional JA responses in phyA-221.

There were no significant differences between MeJA-treated

phyA-211 and the wild type with respect to aerial growth inhibi-

tion, anthocyanin accumulation, or chlorophyll degradation, in-

dicating that phyA is not required for these responses to JA (see

Supplemental Figure 3 online).

Exogenous and wound-induced JAs inhibit mitosis, resulting

in growth inhibition (Zhang and Turner, 2008). To test whether

phyA was required for wound-induced growth inhibition, we

repeatedly wounded wild-type, coi1-16, and phyA-211 plants

over 10 d and recorded their size. Both the wild type and phyA-

211 showed a similar level of growth inhibition, whereas coi1-16

was not significantly inhibited, indicating that growth inhibition by

endogenous wound-induced JA does not require phyA (see

Supplemental Figure 3 online).

Light and JA Pathways Converge at JAZ1

phyA Regulates Wound- and JA-Mediated

JAZ1 Degradation

The JAZ proteins are repressors of JA-responsive gene expres-

sion, and a critical step in JA signaling is their COI1-mediated

degradation (Chini et al., 2007; Thines et al., 2007). We show that

JAZ1 transcription is enhanced by FR light (Figure 7C) and that

the jai3mutant hypocotyl was insensitive to inhibition by FRc and

by low R/FR ratio light (Figures 7C and 8), demonstrating a role

for JAZ genes in phyA-mediated responses. We therefore inves-

tigated whether phyA was required for JAZ degradation. The

35S:JAZ1-b-glucuronidase (GUS) transgene (Thines et al., 2007)

was introduced into the phyA-211mutant by crossing. Seedlings

containing 35S:JAZ1-GUS in the wild type, in plants segregating

for COI1/coi1-1, and in phyA-211 were grown in axenic culture

for 10 d. In control plants, GUS activity was detected in all

genotypes (Figure 10A, left panel). A single wound to a leaf

caused the disappearance within 1 h of JAZ1-GUS from the

aerial parts and roots of wild-type plants, as previously reported

(Zhang and Turner, 2008) but not from one-quarter of the

segregating COI1/coi1-1 population, which we predict to be

coi1-1 homozygotes (Figure 10A, middle panel). Significantly,

JAZ1-GUS was not degraded in the aerial parts of phyA-211

mutants, which resembled coi1-1 mutants in this respect. JAZ1-

GUS was degraded, however, in the roots of phyA-211 plants.

The same genotypes were grown for 10 d onmedia containing

50 mM MeJA. Wild-type plants were very stunted, as expected,

and JAZ1-GUS was completely degraded in these conditions

(Figure 10A, right panel). The coi1-1 homozygotes showed

complete insensitivity to growth inhibition as expected for the

null allele, and JAZ1-GUS was not degraded in this genotype,

as was shown previously (Thines et al., 2007). phyA-211 was as

stunted as the wild type at this concentration of MeJA, as

previously found (Figures 9A and 9B; see Supplemental Figure 3

online). However, similar to phyA-211 wounded plants, JAZ1-

GUS was not degraded in the aerial parts but was degraded in

the roots (Figure 10A, right panel). These results indicate that

both phyA and COI1 are required for JAZ1 degradation in green

tissues of wounded or MeJA-treated plants but that phyA is not

required for JAZ1 destabilization in the root. Significantly, the

Figure 8. JA Biosynthesis and Response Mutants Show Exaggerated

Shade Responses to Low R/FR.

(A) Photographs of representative 10-d-old wild-type, jin1-1, jai3, and

jar1-1 seedlings grown in high (left) and low (right) R/FR. Arrows denote

the ends of the hypocotyls.

(B) Average percentage of increase in hypocotyl length (mm) by low R/FR

compared with high R/FR of seedlings grown as in (A). The differences

between the wild type and the mutants were tested by Student’s t test

and are significant (P < 0.05). n = 20 (mean 6 SD).

phyA Regulates JAZ1 Stability 1151

strongGUS activity in the green tissues of theMeJA-treated, and

severely stunted, phyA-211 mutants indicates that stabilization

of JAZ1 does not result in insensitivity to growth inhibition by

MeJA.

The preceding wound and JA experiments were on seedlings

grown in standard experimental axenic conditions on sucrose-

containing media in LDs. We previously noticed that JAZ1-GUS

is less stable in seedlings raise in conditions we typically use for

R/FR light experiments: media without sucrose and in continu-

ous light. Consequently, we grew lines containing 35S:JAZ1-

GUS in the wild type and in phyA backgrounds in media lacking

sucrose, in continuous light, and comparedGUS expressionwith

lines containing 35S:GUS as control. In these conditions, JAZ-

GUSwas destabilized in the aerial parts of wild-type plants in the

absence of any deliberate stress or JA, and GUS activity was

detectable, although at reduced level, in roots (Figure 10B). In the

phyA background, however, JAZ-GUS was present at high level

in the aerial parts but was undetectable in roots, suggesting that

phyA regulates JAZ1 stability differently in the shoot and the root.

Figure 9. phyA Mutants Display Altered JA-Related Phenotypes.

(A) From the left: 8-d-old white light–grown wild type, coi1-16, Col-0, and

phyA-211 plants grown on media containing 0, 10, or 50 mM MeJA.

(B) Dose–response curves. Root lengths of 8-d-old wild-type and coi1-

16 plants (left) and Col-0 and phyA-211 plants (right) grown on different

MeJA concentrations. n = 20 (mean 6 SE). Col-0 and phyA-211 are not

significantly different from each other in the absence of MeJA (Student’s

t test; P = 0.77) but are significantly different at all concentrations of

MeJA (1, 5, 10, and 25 mM; Student’s t test; P < 0.01, 50 mM; P < 0.05).

Error bars are smaller than symbols.

(C) Fold induction of VSP1 in wild-type (Col-0) and phyA seedlings in

response to treatment for 8 h with 20 mM MeJA. Expression levels

(mean 6 SD) of three technical replicate qRT-PCR reactions are ex-

pressed relative to ACTIN2.

(D) OPDA content of 3-d-old (2 d dark, 1 d FRc 10 mmol m�2 s�1 or 3 d

dark) phyA-211, coi1-16, and control seedlings. phyA-211 seedlings

contain significantly more OPDA than Col-0 in both growth conditions

(Student’s t test; P < 0.01). n = 4 (mean 6 SD).

[See online article for color version of this figure.]

Figure 10. phyA Is Required for JA- and Wound-Mediated JAZ1 Deg-

radation.

(A) Photographs of representative control, wounded (1 h), and 50 mM

MeJA-grown 10-d-old seedlings of Col-gl1/35S:JAZ1-GUS (wild type),

35S:JAZ1-GUS/phyA-211, and 35S:JAZ1-GUS/coi1. Seedlings were

grown on sucrose-containing media in LD conditions.

(B) On media lacking sucrose, JAZ1 is stabilized in aerial parts and

degraded in roots of phyA-211 seedlings in the absence of any delib-

erately applied stress or hormone treatment. Photographs of 12-d-old

seedlings of 35S:GUS, 35S:JAZ-GUS, and 35S:JAZ-GUS/phyA-211.

(C) Hypocotyl elongation response to low R/FR ratio light in 35S:JAZ1-

GUS and control 35:GUS seedlings. Hypocotyl lengths (mean 6 SD)

of $15 seedlings per genotype/treatment are shown. Differences in low

R/FR are significant (Student’s t test; P < 0.0001).

1152 The Plant Cell

JAZ1 Plays a Role in Shade Responses

Having established that JAZ1 stability is in part governed by

phyA, we examined the shade response of 35S:JAZ1-GUS

seedlings. We previously noted that, like most JA loss-of-

function mutants, this line in which JAZ-GUS is expressed

ectopically had elongated petioles in low light (H. Whitfield and

J.G. Turner, unpublished data). Therefore, we grew seedlings

containing 35S:JAZ1-GUS and control 35S:GUS seedlings in

high or low R/FR ratio light as before. 35S:JAZ1-GUS seed-

lings, like coi1 and other JA mutants, and phyA had exagger-

ated shade responses in low, but not high, R/FR ratio light

(Figure 10C). Therefore, the 35S:JAZ1-GUS seedlings had an

exaggerated shade avoidance phenotype similar to that of the

JA and FR light mutants, including jar1, fin219, coi1-16, coi1-1,

jai3, jin1-1, and phyA.

DISCUSSION

We demonstrate roles for JA signaling in phyA-regulated hypo-

cotyl growth inhibition and chlorophyll biosynthesis in Arabidop-

sis during FR-induced photomorphogenesis and in suppression

of elongation growth in low R/FR ratio light when shade avoid-

ance responses are attenuated. The JA receptor COI1 was

required for the FR-induced expression of the light-regulated

genes HFR1, PIL1, and CAB2, and exogenous JA suppressed

this process. The influence of JA signaling on phyA-mediated

responses was reciprocated: phyA was partially insensitive to

JA-induced root growth inhibition and had altered oxylipin con-

tent and attenuated induction of the JA response gene VSP1.

Therefore, our work supports previous reports that Arabidop-

sis mutants defective in JA signaling (fin219/jar1, Hsieh et al.,

2000; Staswick et al., 2002; Chen et al., 2007;myc2/jin1, Lorenzo

et al., 2004; Yadav et al., 2005) express an altered light pheno-

type and that Arabidopsis mutants defective in light signaling

(hy1/hy2, Zhai et al., 2007; det3, Brux et al., 2008; phyB, Moreno

et al., 2009) display JA-related phenotypes. In this context, we

show that FR light regulated the expression of the JA-induced

genes AOC1, JIN1, JAZ1, and VSP1. Crucially, integration of the

JA and phyA signal pathways was at the level of JAZ1 stability:

phyA was required for JAZ1 destabilization by wounding or

exogenous JA. The photodestruction of phyA is in part controlled

by JA, as was demonstrated in the hebiba mutant of rice

(Sineshchekov et al., 2004; Riemann et al., 2009). Together, our

results establish that the control of protein stability is central to

the integration of these two signal pathways.

JA Signaling Regulates Diverse phyA Responses

phyA has a profound influence on seedling development, par-

ticularly in adverse environmental conditions. Thus, phyA seed-

lings exhibit exaggerated elongation growth under increasing

canopy density of wheat (Triticum aestivum; Yanovsky et al.,

1995). In extreme conditions, seedlings fail to deetiolate properly

and show reduced survival rates. phyA therefore suppresses

exaggerated growth responses in conditions in which a plant

must balance limited resource between extension growth and

physiological and developmental processes such as photosyn-

thesis and seed production that allow survival.

Our work shows that JA mutants, similar to phyA, display

exaggerated shade responses in low, but not high, R/FR ratio

light. JAs also downregulate photosynthetic gene expression

(Ueda and Kato, 1980; Reinbothe et al., 1993; Jung et al., 2007).

We speculate that plants growing in photosynthetically poor

radiation regulate JA action through the phyA photoreceptor.

They do so to prevent inappropriate extension growth, decrease

energy-costly defense mechanisms, and increase photosyn-

thetic output.

coi1 mutant seedlings were also compromised in a subset of

FR light–mediated HIRs during photomorphogenesis, including

hypocotyl growth inhibition and the preconditioned block of

greening. However, they showed normal responses with respect

to opening of the apical hook and cotyledon expansion. Like

coi1, most of the JA biosynthesis and response mutants dis-

played reduced sensitivity to FR light especially in hypocotyl

growth inhibition. The opr3 mutant, which is blocked in JA

biosynthesis (Stintzi and Browse, 2000; Stintzi et al., 2001),

displayed a wild-type response to FR light. This observation may

instead implicate an intermediate in the JA biosynthesis pathway

as the oxylipin(s) directly responsible for hypocotyl growth inhi-

bition, as was suggested by Brux et al. (2008). Exogenous JA in

growth media has a dramatic effect on growth inhibition of roots

and aerial parts of light-grown plants, but the effect on hypocotyl

growth is mild (Brux et al., 2008). This suggests the possibility

that the JA component of hypocotyl growth inhibition is regulated

downstream of biosynthesis and perception of JA. In that case,

the role of COI1 and the downstream signaling components in

phyA-mediated hypocotyl deetiolation might be in regulating a

feedback loop for JA synthesis.

JA responses extend also to phyB signaling in Arabidopsis

(Moreno et al., 2009) and in rice, as demonstrated by the hebiba

mutant, which is compromised in red light coleoptile growth

responses (Riemann et al., 2003). We show that coi1mutants are

partially insensitive to red light–mediated hypocotyl growth inhi-

bition. Thus, JA signaling contributes to all major phytochrome

responses during seedling deetiolation.

Chlorophyll Biosynthesis Is Suppressed by COI1

JAs downregulate expression of genes involved in photosyn-

thesis and reduce photosynthetic output (Ueda and Kato, 1980;

Reinbothe et al., 1993; Jung et al., 2007). They also promote

turnover of proteins involved in light capture and energy-

generating processes during dark-induced senescence

(Tsuchiya et al., 1999; He et al., 2002). We show that COI1

suppresses chlorophyll biosynthesis: PORA gene expression is

higher in the coi1-16 mutant, and coi1 seedlings, like phyA, are

resistant to the FR preconditioned block of greening. Intriguingly,

coi1 seedlings also accumulate higher levels of chlorophyll on

transfer from dark to white light (F. Robson and J.G. Turner,

unpublished data). The hebibamutant seedlings also have higher

levels of active protochlorophyllide than their wild-type counter-

parts in the dark and in FR (Sineshchekov et al., 2004). This

indicates that JA signaling regulates chlorophyll biosynthesis

phyA Regulates JAZ1 Stability 1153

during skotomorphogenesis and during photomorphogenesis in

FR-enriched light, in both monocots and dicots.

phyA Controls JA Sensitivity and Response to

Mechanical Wounding

phyA mutants had reduced JA-mediated root growth inhibition.

The phenotype was mild, however, and only apparent at low

concentrations of JA, which may explain why phyA has not been

identified in previous screens for JA-insensitive root growth.

Interestingly, we demonstrate that OPDA is increased in phyA

mutants and markedly reduced in coi1-16 mutants. We interpret

this in terms of feedback regulation of oxylipin biosynthesis

downstream of JA perception (Stintzi and Browse, 2000; Sasaki

et al., 2001).

phyA mutants also displayed reduced JA induction of VSP1

(Figure 9C). VSP proteins are acid phosphatases (Thaller et al.,

1998) that may have a role in defense against herbivores (Berger

et al., 2002; Liu et al., 2005). phyB signaling suppresses re-

sponses to herbivory (Ballare, 2009; Moreno et al., 2009). Addi-

tionally, plants exposed to low R/FR have reduced resistance to

insect pests, suggesting that in light conditions that favor exten-

sion growth, defenses may be compromised (Izaguirre et al.,

2006). The phytochromes are known also to modulate the SA

pathway. For example, the phyA phyB double mutant was

compromised in its defense response to the bacterial pathogen

P. syringae (Genoud et al., 2002); moreover, full activation of

systemic acquired resistance was dependent on a prolonged

light period during the early stage of plant–pathogen interaction

(Griebel and Zeier, 2008).

phyA regulates transcription in response to FR light

(Tepperman et al., 2001; Wang et al., 2002; Devlin et al., 2003).

The defense-related genes Thionin2.2 and PR5 and a disease

resistance protein of the TIR-NBS-LRR class are regulated by

phyA during shade responses (Devlin et al., 2003). It will be

interesting, therefore, to compare the transcript profiles of phyA

and the wild type with respect to responses to mechanical

wounding, herbivory, or plant diseases.

We observed altered JA-regulated VSP1 expression and al-

tered OPDA content of phyAmutants in the light and in the dark.

The latter is at odds with conventional understanding that light is

a requirement for phyA action. The most likely explanation of

phyA activity in our dark-grown seedlings is that phyA protein is

reporting a very low fluence response to our green safelight.

The Role of JAZ1

We show that JAZ1 destabilization requires signals from the

phyA and JA signal pathways. A crucial question arises: What is

the role of JAZ1 in phytochrome and JA signaling? Most knock-

out mutations in JAZ genes do not manifestly show JA-regulated

growth inhibition phenotypes, suggesting that there is functional

redundancy among genes in this family (Chini et al., 2007; Thines

et al., 2007). The functions of JAZ proteins are revealed in the

phenotypes of a dominant JAZ mutant (jai3/jaz3; Lorenzo et al.,

2004) or from transgenic plants (35S:JAZ3D and 35S:JAZ1D) that

express JAZ proteins lacking the C-terminal motif required for

JAZ destabilization (Chini et al., 2007; Thines et al., 2007; Yan

et al., 2007; Chung et al., 2008). It is proposed that these gain-of-

function mutant proteins interfere with COI1 signaling by block-

ing the degradation of other JAZ proteins (Chini et al., 2009;

Chung and Howe, 2009). Although it is difficult to attribute

particular phenotypes to individual JAZ proteins, dominant

35S:JAZ1D transgenic plants display a range of JA-related

phenotypes: they are male sterile, have reduced defense against

P. syringae, and show altered JA-mediated root growth inhibition

and gene expression (Thines et al., 2007; Melotto et al., 2008).

They also display reduced resistance to the generalist herbivore

Spodoptera exigua (Chung et al., 2008). Transgenic lines that

have reduced JAZ1 expression have increased sensitivity to root

growth inhibition by MeJA (Grunewald et al., 2009). This is

consistent with JAZ1 suppressing JA-mediated root growth

inhibition. The phyA mutant also displayed slightly reduced

sensitivity to JA-mediated root growth inhibition. However, in

this mutant, JAZ1-GUS was constitutively degraded in the roots

(Figures 10A and 10B). Although phyA clearly regulates JAZ1

stability, phyA may also regulate other components of JA sig-

naling that contribute to the overall mutant phenotype.

The most striking effect of the phyA mutation was that JAZ1-

GUS was stabilized in green tissues of seedlings that had either

been wounded or grown on 50mMMeJA for an extended period.

JAZ1-GUS is degraded in wild-type plants by these treatments

within 1 h (Thines et al., 2007; Zhang and Turner, 2008). Signif-

icantly, the aerial parts of the phyA mutant displayed wild-type

sensitivity to JA-mediated growth inhibition, despite JAZ1-GUS

stabilization. This suggests that JAZ1 destabilization is not

Figure 11. Model Showing the Proposed Integration of JA and Phyto-

chrome Signaling in Shade and Defense Responses.

(A) In high R/FR light, phyB suppresses the shade avoidance syndrome

(SAS) and enhances sensitivity to JA.

(B) In low R/FR light, phyB is inactivated, the suppression of shade

responses is released, and sensitivity to JA is reduced (Moreno et al.,

2009).

(C) In very low or extended R/FR light, phyA signaling suppresses

exaggerated shade responses by recruiting a JA signal. Some responses

to a JA signal in photosynthetic tissues require phyA.

1154 The Plant Cell

required for JA-mediated inhibition of growth of green tissues.

The 35S:JAZ1-GUS transgenic plants had exaggerated shade

avoidance responses in low, but not high, R/FR ratio light (Figure

10C), similar to that of coi1-16, other JA mutants, and phyA

mutants. Similar phenotypes have been reported in plants over-

expressing members of a JAZ-related family of proteins: the

Arabidopsis ZIM/TIFYs (Shikata et al., 2004). These results, taken

together with our findings, highlight a role for the JAZ and related

ZIM/TIFY families of transcriptional repressors in shade re-

sponses. Looking ahead, it is possible that JAZ proteins regulate

responses beyond those presently associated with JA or phyto-

chromes revealed here.

Integration of Signal Pathways through Common bHLH

Transcription Factors

Shade and defense responses involve a common set of bHLH

transcription factors.MYC2 is a bHLH transcription factor that is

induced by JA in a COI1-dependent manner and regulates a

diverse set of JA responses (Dombrecht et al., 2007). HFR1,

another bHLH transcription factor, is a negative master regulator

of shade responses. HFR1 attenuates elongation growth re-

sponses and flowering of plants that have been unsuccessful in

escaping canopy shade (Sessa et al., 2005). The hfr1 mutant is

remarkably similar to phyA and coi1 in that it displayed an

exaggerated shade response only in low R/FR ratio light, for

which it is known as slender in canopy shade1. With regard to

shade, we have found thatHFR1, and the positive regulatorPIL1,

are both, in part at least, under the control ofCOI1. Paradoxically,

JA suppressed this FR induction, suggesting thatCOI1 either up-

or downregulates individual genes depending on the environ-

mental signal. The involvement of COI1 in positive (FR) and

negative (JA) regulation of the same target demonstrates that

shade and defense pathways may share common components

and are integrative rather than mutually exclusive. We propose a

regulatory pathway by which phyA and COI1 control the stability

of negative regulators, the JAZ proteins, depending on the input

signal and that the JAZ proteins dictate the specificity of the

response by regulating a set of bHLH transcription factor genes,

including MYC2, HFR1, and PIL1 (Figure 11).

To Grow or Defend?

Our study adds to the literature that describes the physiological

and ecological implications of neighbor competition and re-

sponses to canopy shade on the one hand and defense re-

sponses to herbivores or other biotic and abiotic stresses on the

other (Herms and Mattson, 1992; Izaguirre et al., 2006; Ballare,

2009; Moreno et al., 2009). Modern agriculture requires both

efficient land use and defense against pests and diseases.

Dense sowing of crops can lead to reduced productivity due to

neighbor competition that reduces plant yield and increased

susceptibility to herbivory and mechanical damage. Elucidation

of the molecular mechanisms that control the balance of these

processes may benefit agriculture.

We propose that phyA and JA signaling cooperate to regulate

the balance between shade avoidance responses in FR-

enriched light and defense responses to mechanical damage

or herbivores. Our work indicates that the interaction is at the

level of degradation of JAZ proteins that are targets of both

signaling pathways. These two signaling pathways are inte-

grated, mutually dependent and reciprocal in their influence on

the developmental processes that formerly have been assigned

to each other.

METHODS

Plant Materials

The coi1-16 and coi1-1 mutants were identified in this lab (Feys et al.,

1994; Ellis and Turner, 2002). coi1-16 is in a transgenic Col-gl1 back-

ground containing the VSP1:luciferase reporter gene. The coi1-16 pa-

rental line is referred to as the wild type in this article. coi1-16 seeds were

propagated by maintenance of flowering plants at 168C. coi1-1 is in the

Col-gl1 background and is maintained as a heterozygous segregating

population. Seeds of the aos-TJ1180, phyA-211, and phyB-9 mutants

were obtained from the Nottingham Arabidopsis Stock Centre (Reed

et al., 1994; Park et al., 2002). The opr3mutant (Stintzi and Browse, 2000),

the 35S-JAZ1-GUS line in COI1/coi1-1 (Thines et al., 2007), jai3, jin1-1,

(Lorenzo et al., 2004), cry1-304 (Bruggemann et al., 1996), fin219 (Hsieh

et al., 2000), and jar1-1 (Staswick et al., 2002) were gifts from the author

labs stated here. All mutants are in Col-0 except for aos-TJ1180, which is

in Col-gl1, and opr3, which is in Wassilewskija. Aos and opr3 seeds were

propagated by repeatedly dipping inflorescences in 500 mM MeJA

throughout the flowering period.

Growth Conditions

For flowering time experiments, wound-mediated growth inhibition, gen-

eral propagation, crossing, and genetic analysis of plants, seeds were

planted on damp soil (Levington’s F2 compost plus fine grit at a ratio of

6:1), incubated at 48C in the dark for 48 h to synchronize germination, and

then transferred to growth chambers set at long (16 h light/8 h dark) or

short (8 h light/16 h dark) days as appropriate, at 228C with a 3/2 mix of

cool white/gro-lux fluorescent bulbs (100 mmol m22 s21).

Seeds for axenic growth were surface sterilized by incubating in 70%

ethanol for 2 min and then 10% bleach/0.01% triton for 10 min followed

by five washes with sterilized deionized water. For seedling morpholog-

ical and gene expression responses to specific light regimes, sterilized

seeds were sown on 0.8% plant agar plates containing half-strength

Murashige and Skoog salts plus vitamins and 0.5 g/L MES buffer, pH 5.7.

For the analysis of seedling JA responses, seeds were sown on the

same media plus 2% sucrose. MeJA (Sigma-Aldrich; 100 mM stock in

ethanol) was added to cooled molten media to the required final con-

centration as appropriate. All plated seeds were stratified at 48C in the

dark for 72 h followed by 24 h white light (cool white fluorescent bulbs,

70 mmol m22 s21) at 228C to synchronize germination. All subsequent

manipulations were done in an inner dark roomwith a dim green safe light

obtained by wrapping a fluorescent lamp (Sylvania standard white;

OSRAM-Sylvania) with two layers of green filters (LEE Filters).

For hypocotyl length measurements, seeds prepared as above were

transferred into the dark for 24 h at 228C by which time the radicles had

emerged. Germinated seedlings were then exposed to FRc, Rc, or Bc

light for 2 to 6 d (see below for light sources). Control plates were kept in

the dark.

For gene expression, seeds prepared as above were transferred into

the dark for 6 d. The seedlings were then exposed to FRc for the required

length of time before harvesting into liquid N2.

For seedling responses to high and low R/FR light, see below for

light sources and ratios. Seeds prepared as above were transferred to a

Sanyo growth cabinet (cool white fluorescent bulbs, 70 mmol m22 s21,

phyA Regulates JAZ1 Stability 1155

continuous light, high R/FR) for 3 d before being transferred into low R/FR

conditions for a further 9 d. Control plants were kept in high R/FR for a

further 9 d.

For EOD-FR, seeds prepared as above were transferred to SD (cool

white fluorescent bulbs, 70mmol m22 s21) for 3 d with a 10-min FR and/or

5-min R treatment at the end of every light cycle.

For seedling JA responses, seeds prepared as above were

transferred to LD growth cabinets with cool white fluorescent bulbs

(70 mmol m22 s21) for the required number of days. Seedlings for root

growth inhibition measurements were grown vertically.

Light Sources

Plants examined for their responses to continuous monochromatic FR

(730 nm6 10 nm), R (660 nm6 10 nm), or B (470 nm6 10 nm) light were

grown in a growth chamber equipped with light emitting diodes (E30-

LED; Percival Scientific) at 218C. FR light was filtered through a layer each

of #116 and #172 (LEE Filters) to cut off wavelengths shorter than 700 nm.

This cabinet was also used for EOD-FR and R light treatments.

High and low R/FR experiments were conducted essentially as

described by Keiller and Smith (1989) and Devlin et al. (1999) where

continuous high R/FR light was provided by cool white fluorescent bulbs

in a Sanyo growth cabinet (W) and low R/FR light was provided by adding

supplementary FR light (W + FR; see Supplemental Figure 4 online). The

high R/FR cabinet provided a photon irradiance, 400 to 700 nm, of 70

mmol m22 s21 and a R/FR of 10.8. The low R/FR cabinet provided the

same photon irradiance but an R/FR of 0.068. The supplementary FR light

was provided by prototype LED arrays (G.Whitelam, Leicester University)

and was filtered through one layer of 0.3-mm black plexiglass to remove

wavelengths lower than 700 nm. Light intensities and qualities were

measured using a spectrometer (USB2000; Ocean Optics; see Supple-

mental Figure 4 online) and a SKP 200 photometer (Sky Instruments).

Measurement of Hypocotyls and Roots

Seedlings were placed flat on agar plates and scanned using a flatbed

scanner. Hypocotyls and roots from scanned images were measured

using the ImageJ program (Abramoff et al., 2004).

Flowering Time

Flowering time of soil-grown plants in LD and SD was scored as the

number of days from germination to the first appearance of buds in

the rosette center. The total number of rosette and cauline leaves on the

primary inflorescence was counted after bolting.

RNA Extraction and Real-Time PCR

Total RNA was extracted from frozen plant material using an RNeasy

plant mini kit (Qiagen). An RNase-free DNase step was incorporated

according to the manufacturer’s protocol for preparation of RNA for real-

time PCR expression analysis. RNA was quantified using a NanoDrop

1000 (Thermo Scientific). A total of 1 mg of RNA was used per sample for

cDNA synthesis using random hexamer primers and Superscript II

reverse transcriptase (Invitrogen) according to the manufacturer’s pro-

tocol. Real-time PCR was performed to quantify cDNA using either

inventoried small-scale TaqMan gene expression assays, each contain-

ing a FAM dye-labeled TaqMan MGB probe and a PCR primer pair

(Applied Biosystems), or manually designed PCR primers and FAM/

TAMRA probes (Sigma-Genosys). Each reaction was performed in 25 mL

and contained the equivalent of 5 ng of reverse transcribed RNA, 33%

TaqMan PCR Master Mix (Applied Biosystems), 200 nM each of the

forward and reverse primer, and 100 nM of probe using the ABI Prism

7900 Fast real-time PCR system (Applied Biosystems), according to the

manufacturer’s protocol. To determine relative RNA levels within the

samples, standard curves for the PCRwere prepared using amix of cDNA

from all samples and making twofold serial dilutions covering the range

equivalent to 20 to 0.625 ng RNA. All expression levels were quantified

relative to the housekeeping geneACTIN2, and reactionswere performed

in triplicate for each cDNA sample. Details of the TaqMan Gene Expres-

sion Assays and manually designed primers and probes used are in

Supplemental Tables 1 and 2 online.

Histochemical GUS Assay

Seedlings were incubated in ice-cold 90% acetone for 20 min. The

solution was changed to GUS staining solution (100 mM sodium phos-

phate buffer, 20% methanol, 5% Triton X-100, 10 mM EDTA, 500 mM

potassium ferrocyanide, 500 mM potassium ferricyanide, and 500 mg/mL

X-Gluc). The seedlings were infiltrated on ice by briefly applying and

releasing a vacuum twice and then incubated overnight at 378C in the dark

followed by destaining and clearing in several changes of 70% ethanol.

Chlorophyll Extraction and Measurement

Approximately 3 to 5mg tissue per samplewas extracted overnight in 800

mL dimethylformamide at 48C in the dark. Absorbance at 664 and 647 nm

was measured in a SmartSpec Plus spectrophotometer (Bio-Rad) and

total chlorophyll content determined in mg/mg tissue according to the

extinction coefficients calculated by Porra et al. (1989).

Anthocyanin Extraction and Measurement

Anthocyanin was extracted and measured according to Neff and Chory

(1998) with the following modifications. Approximately 20 mg frozen and

ground plant tissue per sample was incubated overnight in 300 mL

methanol:HCl (99:1) at 48C in the dark. After addition of 200 mL deionized

waterd, anthocyaninswere separated fromchlorophylls by the addition of

500 mL chloroform. Total anthocyanins were determined by measuring

the absorbance at 530 and 657 nm using a spectrophotometer. Relative

anthocyanin levels (abs 530 to abs 657) were calculated per milligram of

tissue.

JA, JA-Ile, and OPDA Extraction and Measurement

Frozen plant tissue sampleswere extractedwithmethanol and acetylated

before preparative HPLC (Miersch et al., 2008). Fractions obtained were

analyzed by gas chromatography–mass spectrometry. JA and OPDA

were analyzed as pentafluorobenzyl esters on an Rtx-5ms column in

chemical ionization mode with NH3 as collision gas (Miersch et al., 2008).

JA-Ile was quantified by gas chromatography–mass spectrometry

on a DB-5ht column after derivitization with (trimethylsilyl)diazomethane

(Guranowski et al., 2007).

Accession Numbers

Sequence data from this article can be found in the Arabidopsis Ge-

nome Initiative database under the following accession numbers: COI1

(At2G39940), phyA (At1G09570), phyB (At2G18790), CRY1 (At4G08920),

JAZ1 (At1G19180), MYC2 (At1G32640), FIN219/JAR1 (At2G46370), JAI3/

JAZ3 (At3G17860), AOS (At5G42650), and OPR3 (At2G06050). Accession

numbers for genes used in qPCRare listed in Supplemental Tables 1 and 2

online.

Supplemental Data

The following materials are available in the online version of this article.

1156 The Plant Cell

Supplemental Figure 1. coi1-16 Mutants Are Slightly Insensitive to

Blue Light.

Supplemental Figure 2. coi1-1 and fin219 Mutants Show Exagger-

ated Shade Responses to Low R/FR.

Supplemental Figure 3. phyA Mutants Have Wild-Type Responses

to JA and Wounding with Respect to Aerial Growth Inhibition,

Anthocyanin Accumulation, and Chlorophyll Degradation.

Supplemental Figure 4. Light Conditions of Sanyo Growth Cabinet

Supplemented (Red and Yellow Traces) or Not (Black Trace) with FR.

Supplemental Table 1. Taqman Gene Expression Assays Used for

Real-Time qPCR.

Supplemental Table 2. Sequences of Manually Designed Primers

and Probes Used for qPCR.

ACKNOWLEDGMENTS

This article is dedicated to the memory of the late Garry Whitelam to

acknowledge his enormous contribution to the field of phytochrome

biology and his enthusiasm for science. Garry also generously lent us his

hand-built prototype FR, red, and blue LED arrays that allowed us to

perform light experiments at the University of East Anglia. We thank the

following people: Birgit Ortel for oxylipin measurements, John Baker for

photography, Caroline Pennington for help with real-time qRT-PCR,

John Browse, Roberto Solano, Chentao Lin, Paul Staswick, and Xing

Wang Deng, and their colleagues for gifts of seeds, and Andrew Mayes

for assistance with spectrum measurements in high/low R/FR growth

conditions. F.R. is funded by Biotechnology and Biological Science

Research Council (BBSRC) Grant BBD013429/1; H.O. is a BBSRC

David Phillips Research Fellow (43JF20606); and S.-R.H. is funded by

the Electro Magnetic Field Biological Trust.

Received April 8, 2009; revised March 2, 2010; accepted April 7, 2010;

published April 30, 2010.

REFERENCES

Abramoff, M.D., Magelhaes, P.J., and Ram, S.J. (2004). Image Pro-

cessing with ImageJ. Biophotonics International 11: 36–42.

Ahmad, M., and Cashmore, A.R. (1993). HY4 gene of A. thaliana

encodes a protein with characteristics of a blue-light photoreceptor.

Nature 366: 162–166.

Balbi, V., and Devoto, A. (2008). JA signalling network in Arabidopsis

thaliana: Crucial regulatory nodes and new physiological scenarios.

New Phytol. 177: 301–318.

Ballare, C.L. (2009). Illuminated behavior. Phytochrome as a key reg-

ulator of light foraging and plant anti-herbivore defense. Plant Cell

Environ. 32: 713–725.

Ballare, C.L., Scopel, A.L., and Sanchez, R.A. (1990). Far-red radiation

reflected from adjacent leaves: An early signal of competition in plant

canopies. Science 247: 329–332.

Barnes, S.A., Nishizawa, N.K., Quaggio, R.B., Whitelam, G.C., and

Chua, N.H. (1996). Far-red light blocks greening of Arabidopsis

seedlings via a phytochrome A-mediated change in plastid develop-

ment. Plant Cell 8: 601–615.

Benedetti, C.E., Xie, D., and Turner, J.G. (1995). COI1-dependent

expression of an Arabidopsis vegetative storage protein in flowers

and siliques and in response to coronatine or methyl JA. Plant Physiol.

109: 567–572.

Berger, S., Mitchell-Olds, T., and Stotz, H.U. (2002). Local and

differential control of vegetative storage protein expression in re-

sponse to herbivore damage in Arabidopsis thaliana. Physiol. Plant.

114: 85–91.

Berger, S., Bell, E., Sadka, A., and Mullet, J.E. (1995). Arabidopsis

thaliana Atvsp is homologous to soybean VspA and VspB, genes

encoding vegetative storage protein acid phosphatases, and is reg-

ulated similarly by methyl JA, wounding, sugars, light and phosphate.

Plant Mol. Biol. 27: 933–942.

Boter, M., Ruiz-Rivero, O., Abdeen, A., and Prat, S. (2004). Conserved

MYC transcription factors play a key role in JA signaling both in

tomato and Arabidopsis. Genes Dev. 18: 1577–1591.

Bruggemann, E., Handwerger, K., Essex, C., and Storz, G. (1996).

Analysis of fast neutron-generated mutants at the Arabidopsis thaliana

HY4 locus. Plant J. 10: 755–760.

Brux, A., Liu, T.-Y., Krebs, M., Stierhof, Y.-D., Lohmann, J.U., Miersch,

O., Wasternack, C., and Schumacher, K. (2008). Reduced V-ATPase

activity in the trans-Golgi network causes oxylipin-dependent hypocotyl

growth inhibition in Arabidopsis. Plant Cell 20: 1088–1100.

Chen, I.-C., Huang, I.C., Liu, M.-J., Wang, Z.-G., Chung, S.-S., and

Hsieh, H.-L. (2007). Glutathione S-transferase interacting with far-red

insensitive 219 is involved in phytochrome A-mediated signaling in

Arabidopsis. Plant Physiol. 143: 1189–1202.

Chen, M., Chory, J., and Fankhauser, C. (2004). Light signal trans-

duction in higher plants. Annu. Rev. Genet. 38: 87–117.

Chini, A., Fonseca, S., Chico, J.M., Fernandez-Calvo, P., and

Solano, R. (2009). The ZIM domain mediates homo- and heteromeric

interactions between Arabidopsis JAZ proteins. Plant J. 59: 77–87.

Chini, A., Fonseca, S., Fernandez, G., Adie, B., Chico, J.M., Lorenzo,

O., Garcia-Casado, G., Lopez-Vidriero, I., Lozano, F.M., Ponce,

M.R., Micol, J.L., and Solano, R. (2007). The JAZ family of repressors

is the missing link in JA signalling. Nature 448: 666–671.

Cho, K., Agrawal, G.K., Shibato, J., Jung, Y.-H., Kim, Y.-K., Nahm,

B.H., Jwa, N.-S., Tamogami, S., Han, O., Kohda, K., Iwahashi, H.,

and Rakwal, R. (2007). Survey of differentially expressed proteins and

genes in jasmonic acid treated rice seedling shoot and root at the

proteomics and transcriptomics levels. J. Proteome Res. 6: 3581–

3603.

Chory, J., Chatterjee, M., Cook, R.K., Elich, T., Fankhauser, C., Li, J.,

Nagpal, P., Neff, M., Pepper, A., Poole, D., Reed, J., and Vitart, V.

(1996). From seed germination to flowering, light controls plant

development via the pigment phytochrome. Proc. Natl. Acad. Sci.

USA 93: 12066–12071.

Chung, H.S., and Howe, G.A. (2009). A critical role for the TIFY motif in

repression of jasmonate signaling by a stabilized splice variant of the

JASMONATE ZIM-domain protein JAZ10 in Arabidopsis. Plant Cell

21: 131–145.

Chung, H.S., Koo, A.J.K., Gao, X., Jayanty, S., Thines, B., Jones,

A.D., and Howe, G.A. (2008). Regulation and function of Arabidopsis

JA ZIM-domain genes in response to wounding and herbivory. Plant

Physiol. 146: 952–964.

Clarke, S.M., Cristescu, S.M., Miersch, O., Harren, F.J., Wasternack,

C., and Mur, L.A. (2009). JAs act with salicylic acid to confer basal

thermotolerance in Arabidopsis thaliana. New Phytol. 182: 175–187.

Devlin, P.F., Robson, P.R., Patel, S.R., Goosey, L., Sharrock, R.A.,

and Whitelam, G.C. (1999). Phytochrome D acts in the shade-

avoidance syndrome in Arabidopsis by controlling elongation growth

and flowering time. Plant Physiol. 119: 909–915.

Devlin, P.F., Yanovsky, M.J., and Kay, S.A. (2003). A genomic analysis

of the shade avoidance response in Arabidopsis. Plant Physiol. 133:

1617–1629.

Devoto, A., Ellis, C., Magusin, A., Chang, H.-S., Chilcott, C., Zhu, T.,

and Turner, J. (2005). Expression profiling reveals COI1 to be a key

phyA Regulates JAZ1 Stability 1157

regulator of genes involved in wound- and methyl JA-induced sec-

ondary metabolism, defence, and hormone interactions. Plant Mol.

Biol. 58: 497–513.

Devoto, A., Nieto-Rostro, M., Xie, D.X., Ellis, C., Harmston, R.,

Patrick, E., Davis, J., Sherratt, L., Coleman, M., and Turner, J.G.

(2002). COI1 links JA signalling and fertility to the SCF ubiquitin-ligase

complex in Arabidopsis. Plant J. 32: 457–466.

Devoto, A., and Turner, J.G. (2003). Regulation of JA-mediated plant

responses in Arabidopsis. Ann. Bot. (Lond.) 92: 329–337.

Dombrecht, B., Xue, G.P., Sprague, S.J., Kirkegaard, J.A., Ross,

J.J., Reid, J.B., Fitt, G.P., Sewelam, N., Schenk, P.M., Manners,

J.M., and Kazan, K. (2007). MYC2 differentially modulates diverse

JA-dependent functions in Arabidopsis. Plant Cell 19: 2225–2245.

Ellis, C., and Turner, J. (2002). A conditionally fertile coi1 allele indicates

cross-talk between plant hormone signalling pathways in Arabidopsis

thaliana seeds and young seedlings. Planta 215: 549–556.

Fairchild, C.D., Schumaker, M.A., and Quail, P.H. (2000). HFR1

encodes an atypical bHLH protein that acts in phytochrome A signal

transduction. Genes Dev. 14: 2377–2391.

Feys, B.J.F., Benedetti, C.E., Penfold, C.N., and Turner, J.G. (1994).

Arabidopsis mutants selected for resistance to the phytotoxin coro-

natine are male-sterile, insensitive to methyl JA, and resistant to a

bacterial pathogen. Plant Cell 6: 751–759.

Fonseca, S., Chini, A., Hamberg, M., Adie, B., Porzel, A., Kramell, R.,

Miersch, O., Wasternack, C., and Solano, R. (2009). (+)-7-Iso-

jasmonoyl-L-isoleucine is the endogenous bioactive jasmonate. Nat.

Chem. Biol. 5: 344–350.

Franklin, K.A., Praekelt, U., Stoddart, W.M., Billingham, O.E., Halliday,

K.J., and Whitelam, G.C. (2003). Phytochromes B, D, and E act

redundantly to control multiple physiological responses in Arabidop-

sis. Plant Physiol. 131: 1340–1346.

Frenkel, M., Kulheim, C., Jankanpaa, H., Skogstrom, O., Dall’Osto,

L., Agren, J., Bassi, R., Moritz, T., Moen, J., and Jansson, S.

(2009). Improper excess light energy dissipation in Arabidopsis results

in a metabolic reprogramming. BMC Plant Biol. 9: 12.

Genoud, T., Buchala, A.J., Chua, N.H., and Metraux, J.P. (2002).

Phytochrome signalling modulates the SA-perceptive pathway in

Arabidopsis. Plant J. 31: 87–95.

Glazebrook, J. (2005). Contrasting mechanisms of defense against

biotrophic and necrotrophic pathogens. Annu. Rev. Phytopathol. 43:

205–227.

Goto, N., Kumagai, T., and Koornneef, M. (1991). Flowering responses

to light-breaks in photomorphogenic mutants of Arabidopsis thaliana,

a long-day plant. Physiol. Plant. 83: 209–215.

Griebel, T., and Zeier, J. (2008). Light regulation and daytime depen-

dency of inducible plant defenses in Arabidopsis: Phytochrome

signaling controls systemic acquired resistance rather than local

defense. Plant Physiol. 147: 790–801.

Grunewald, W., Vanholme, B., Pauwels, L., Plovie, E., Inze, D.,

Gheysen, G., and Goossens, A. (2009). Expression of the Arabidop-

sis jasmonate signalling repressor JAZ1/TIFY10A is stimulated by

auxin. EMBO Rep. 10: 923–928.

Guranowski, A., Miersch, O., Staswick, P.E., Suza, W., andWasternack,

C. (2007). Substrate specificity and products of side-reactions cata-

lyzed by JA:amino acid synthetase (JAR1). FEBS Lett. 581: 815–820.

Haga, K., and Iino, M. (2004). Phytochrome-mediated transcriptional

up-regulation of ALLENE OXIDE SYNTHASE in rice seedlings. Plant

Cell Physiol. 45: 119–128.

He, Y., Fukushige, H., Hildebrand, D.F., and Gan, S. (2002). Evidence

supporting a role of jasmonic acid in Arabidopsis leaf senescence.

Plant Physiol. 128: 876–884.

Herms, D.A., and Mattson, W.J. (1992). The dilemma of plants: To

grow or defend. Q. Rev. Biol. 67: 283.

Howe, G.A., and Jander, G. (2008). Plant immunity to insect herbivores.

Annu. Rev. Plant Biol. 59: 41–66.

Hsieh, H.-L., Okamoto, H., Wang, M., Ang, L.-H., Matsui, M., Goodman,

H., and Deng, X.W. (2000). FIN219, an auxin-regulated gene, defines

a link between phytochrome A and the downstream regulator COP1 in

light control of Arabidopsis development. Genes Dev. 14: 1958–1970.

Izaguirre, M.M., Mazza, C.A., Biondini, M., Baldwin, I.T., and Ballare,

C.L. (2006). Remote sensing of future competitors: Impacts on plant

defenses. Proc. Natl. Acad. Sci. USA 103: 7170–7174.

Johnson, E., Bradley, M., Harberd, N.P., and Whitelam, G.C. (1994).

Photoresponses of light-grown phyA mutants of Arabidopsis (phyto-

chrome A is required for the perception of daylength extensions).

Plant Physiol. 105: 141–149.

Jung, C., Lyou, S., Yeu, S., Kim, M., Rhee, S., Kim, M., Lee, J., Choi,

Y., and Cheong, J.-J. (2007). Microarray-based screening of JA-

responsive genes in Arabidopsis thaliana. Plant Cell Rep. 26: 1053–

1063.

Karlin-Neumann, G.A., Sun, L., and Tobin, E.M. (1988). Expression of

light-harvesting chlorophyll a/b-protein genes is phytochrome-

regulated in etiolated Arabidopsis thaliana seedlings. Plant Physiol.

88: 1323–1331.

Katsir, L., Schilmiller, A.L., Staswick, P.E., He, S.Y., and Howe, G.A.

(2008). COI1 is a critical component of a receptor for JA and the

bacterial virulence factor coronatine. Proc. Natl. Acad. Sci. USA 105:

7100–7105.

Keiller, D., and Smith, H. (1989). Control of carbon partitioning by light

quality mediated by phytochrome. Plant Sci. 63: 25–29.

Kloek, A.P., Verbsky, M.L., Sharma, S.B., Schoelz, J.E., Vogel, J.,

Klessig, D.F., and Kunkel, B.N. (2001). Resistance to Pseudomonas

syringae conferred by an Arabidopsis thaliana coronatine-insensitive

(coi1) mutation occurs through two distinct mechanisms. Plant J. 26:

509–522.

Liu, Y., Ahn, J.-E., Datta, S., Salzman, R.A., Moon, J., Huyghues-

Despointes, B., Pittendrigh, B., Murdock, L.L., Koiwa, H., and

Zhu-Salzman, K. (2005). Arabidopsis vegetative storage protein is an

anti-insect acid phosphatase. Plant Physiol. 139: 1545–1556.

Lorenzo, O., Chico, J.M., Sanchez-Serrano, J.J., and Solano, R.

(2004). JA-INSENSITIVE1 encodes a MYC transcription factor essen-

tial to discriminate between different JA-regulated defense responses

in Arabidopsis. Plant Cell 16: 1938–1950.

McCormac, A.C., Wagner, D., Boylan, M.T., Quail, P.H., Smith, H.,

Garry, C., and Whitelam, G.C. (1993). Photoresponses of transgenic

Arabidopsis seedlings expressing introduced phytochrome

B-encoding cDNAs: Evidence that phytochrome A and phytochrome

B have distinct photoregulatory functions. Plant J. 4: 19–27.

Melotto, M., Mecey, C., Niu, Y., Chung, H.S., Katsir, L., Yao, J., Zeng,

W., Thines, B., Staswick, P., Browse, J., Howe, G.A., and He, S.Y.

(2008). A critical role of two positively charged amino acids in the Jas

motif of Arabidopsis JAZ proteins in mediating coronatine- and

jasmonoyl isoleucine-dependent interactions with the COI1 F-box

protein. Plant J. 55: 979–988.

Miersch, O., Neumerkel, J., Dippe, M., Stenzel, I., and Wasternack,

C. (2008). Hydroxylated JAs are commonly occurring metabolites of

jasmonic acid and contribute to a partial switch-off in JA signaling.

New Phytol. 177: 114–127.

Moreno, J.E., Tao, Y., Chory, J., and Ballare, C.L. (2009). Ecological

modulation of plant defense via phytochrome control of JA sensitivity.

Proc. Natl. Acad. Sci. USA 106: 4935–4940.

Mueller, M.J., Brodschelm, W., Spannagl, E., and Zenk, M.H. (1993).

Signaling in the elicitation process is mediated through the octade-

canoid pathway leading to jasmonic acid. Proc. Natl. Acad. Sci. USA

90: 7490–7494.

Nagatani, A., Chory, J., and Furuya, M. (1991). Phytochrome B is not

1158 The Plant Cell

detectable in the hy3 mutant of Arabidopsis, which is deficient in

responding to end-of-day far-red light treatments. Plant Cell Physiol.

32: 1119–1122.

Neff, M.M., and Chory, J. (1998). Genetic interactions between phyto-

chrome A, phytochrome B, and cryptochrome 1 during Arabidopsis

development. Plant Physiol. 118: 27–35.

Park, J.-H., Halitschke, R., Kim, H.B., Baldwin, I.T., Feldmann, K.A.,

and Feyereisen, R. (2002). A knock-out mutation in allene oxide

synthase results in male sterility and defective wound signal trans-

duction in Arabidopsis due to a block in jasmonic acid biosynthesis.

Plant J. 31: 1–12.

Pauwels, L., Morreel, K., De Witte, E., Lammertyn, F., Van Montagu,

M., Boerjan, W., Inze, D., and Goossens, A. (2008). Mapping methyl

JA-mediated transcriptional reprogramming of metabolism and cell

cycle progression in cultured Arabidopsis cells. Proc. Natl. Acad. Sci.

USA 105: 1380–1385.

Porra, R.J., Thompson, W.A., and Kriedemann, P.E. (1989). Determi-

nation of accurate extinction coefficients and simultaneous equations

for assaying chlorophylls a and b extracted with four different sol-

vents: Verification of the concentration of chlorophyll standards by

atomic absorption spectroscopy. Biochim. Biophys. Acta 975: 384–394.

Rao, M.V., Lee, H.-i., Creelman, R.A., Mullet, J.E., and Davis, K.R.

(2000). Jasmonic acid signaling modulates ozone-induced hypersen-

sitive cell death. Plant Cell 12: 1633–1646.

Reed, J.W., Nagatani, A., Elich, T.D., Fagan, M., and Chory, J. (1994).

Phytochrome A and phytochrome B have overlapping but distinct

functions in Arabidopsis development. Plant Physiol. 104: 1139–1149.

Reinbothe, S., Reinbothe, C., and Parthier, B. (1993). Methyl JA-

regulated translation of nuclear-encoded chloroplast proteins in barley

(Hordeum vulgare L. cv. salome). J. Biol. Chem. 268: 10606–10611.

Reinbothe, C., Springer, A., Samol, I., and Reinbothe, S. (2009). Plant

oxylipins: Role of jasmonic acid during programmed cell death,

defence and leaf senescence. FEBS J. 276: 4666–4681.

Riemann, M., Bouyer, D., Hisada, A., Muller, A., Yatou, O., Weiler, E.,

Takano, M., Furuya, M., and Nick, P. (2009). Phytochrome A

requires JA for photodestruction. Planta 229: 1035–1045.

Riemann, M., Muller, A., Korte, A., Furuya, M., Weiler, E.W., and

Nick, P. (2003). Impaired induction of the JA pathway in the rice

mutant hebiba. Plant Physiol. 133: 1820–1830.

Riemann, M., Riemann, M., and Takano, M. (2008). Rice JA RESIS-

TANT 1 is involved in phytochrome and JA signalling. Plant Cell

Environ. 31: 783–792.

Runge, S., Sperling, U., Frick, G., Apel, K., and Armstrong, G.A.

(1996). Distinct roles for light-dependent NADPH:protochlorophyllide

oxidoreductases (POR) A and B during greening in higher plants.

Plant J. 9: 513–523.

Salter, M.G., Franklin, K.A., and Whitelam, G.C. (2003). Gating of the

rapid shade-avoidance response by the circadian clock in plants.

Nature 426: 680–683.

Sasaki, Y., et al. (2001). Monitoring of methyl JA-responsive genes in

Arabidopsis by cDNA macroarray: Self-activation of jasmonic acid

biosynthesis and crosstalk with other phytohormone signaling path-

ways. DNA Res. 8: 153–161.

Sessa, G., Carabelli, M., Sassi, M., Ciolfi, A., Possenti, M., Mittempergher,

F., Becker, J., Morelli, G., and Ruberti, I. (2005). A dynamic balance

between gene activation and repression regulates the shade avoid-

ance response in Arabidopsis. Genes Dev. 19: 2811–2815.

Shikata, M., Matsuda, Y., Ando, K., Nishii, A., Takemura, M., Yokota,

A., and Kohchi, T. (2004). Characterization of Arabidopsis ZIM, a

member of a novel plant-specific GATA factor gene family. J. Exp.

Bot. 55: 631–639.

Shinomura, T., Uchida, K., and Furuya, M. (2000). Elementary pro-

cesses of photoperception by phytochrome A for high-irradiance

response of hypocotyl elongation in Arabidopsis. Plant Physiol. 122:

147–156.

Sineshchekov, V.A., Loskovich, A.V., Riemann, M., and Nick, P.

(2004). The JA-free rice mutant hebiba is affected in the response of

phyA’/phyA’’ pools and protochlorophyllide biosynthesis to far-red

light. Photochem. Photobiol. Sci. 3: 1058–1062.

Smith, H., Xu, Y., and Quail, P.H. (1997). Antagonistic but comple-

mentary actions of phytochromes A and B allow optimum seedling

de-etiolation. Plant Physiol. 114: 637–641.

Somers, D.E., Sharrock, R.A., Tepperman, J.M., and Quail, P.H.

(1991). The hy3 long hypocotyl mutant of Arabidopsis is deficient in

phytochrome B. Plant Cell 3: 1263–1274.

Staswick, P.E., Su, W., and Howell, S.H. (1992). Methyl JA inhibition of

root growth and induction of a leaf protein are decreased in an

Arabidopsis thalianamutant. Proc. Natl. Acad. Sci. USA 89: 6837–6840.

Staswick, P.E., and Tiryaki, I. (2004). The oxylipin signal jasmonic acid

is activated by an enzyme that conjugates it to isoleucine in Arabi-

dopsis. Plant Cell 16: 2117–2127.

Staswick, P.E., Tiryaki, I., and Rowe, M.L. (2002). JA response locus

JAR1 and several related Arabidopsis genes encode enzymes of the

firefly luciferase superfamily that show activity on jasmonic, salicylic,

and indole-3-acetic acids in an assay for adenylation. Plant Cell 14:

1405–1415.

Stintzi, A., and Browse, J. (2000). The Arabidopsis male-sterile mutant,

opr3, lacks the 12-oxophytodienoic acid reductase required for JA

synthesis. Proc. Natl. Acad. Sci. USA 97: 10625–10630.

Stintzi, A., Weber, H., Reymond, P., Browse, J., and Farmer, E.E.

(2001). Plant defense in the absence of jasmonic acid: The role of

cyclopentenones. Proc. Natl. Acad. Sci. USA 98: 12837–12842.

Tepperman, J.M., Zhu, T., Chang, H.-S., Wang, X., and Quail, P.H.

(2001). Multiple transcription-factor genes are early targets of phyto-

chrome A signaling. Proc. Natl. Acad. Sci. USA 98: 9437–9442.

Thaller, M.C., Schippa, S., and Rossolini, G.M. (1998). Conserved

sequence motifs among bacterial, eukaryotic, and archaeal phospha-

tases that define a new phosphohydrolase superfamily. Protein Sci. 7:

1647–1652.

Thines, B., Katsir, L., Melotto, M., Niu, Y., Mandaokar, A., Liu, G.,

Nomura, K., He, S.Y., Howe, G.A., and Browse, J. (2007). JAZ

repressor proteins are targets of the SCFCOI1 complex during JA

signalling. Nature 448: 661–665.

Tsuchiya, T., Ohta, H., Okawa, K., Iwamatsu, A., Shimada, H.,

Masuda, T., and Takamiya, K. (1999). Cloning of chlorophyllase,

the key enzyme in chlorophyll degradation: Finding of a lipase motif

and the induction by methyl jasmonate. Proc. Natl. Acad. Sci. USA 96:

15362–15367.

Ueda, J., and Kato, J. (1980). Isolation and identification of a senes-

cence-promoting substance from wormwood (Artemisia absinthium

L.). Plant Physiol. 66: 246–249.

Wang, H., Ma, L., Habashi, J., Li, J., Zhao, H., and Deng, X.W. (2002).

Analysis of far-red light-regulated genome expression profiles of

phytochrome A pathway mutants in Arabidopsis. Plant J. 32: 723–733.

Wang, Z., Cao, G., Wang, X., Miao, J., Liu, X., Chen, Z., Qu, L.-J., and

Gu, H. (2008). Identification and characterization of COI1-dependent

transcription factor genes involved in JA-mediated response to

wounding in Arabidopsis plants. Plant Cell Rep. 27: 125–135.

Wasternack, C. (2007). JAs: An update on biosynthesis, signal trans-

duction and action in plant stress response, growth and development.

Ann. Bot. (Lond.) 100: 681–697.

Whitelam, G.C., Johnson, E., Peng, J.R., Carol, P., Anderson, M.L.,

Cowl, J.S., and Harberd, N.P. (1993). Phytochrome-a null mutants of

Arabidopsis display a wild-type phenotype in white light. Plant Cell 5:

757–768.

Whitelam, G.C., and Johnson, C.B. (1982). Photomorphogenesis in

phyA Regulates JAZ1 Stability 1159

Impatiens parviflora and other plant species under simulated natural

canopy radiations. New Phytol. 90: 611–618.

Xie, D.-X., Feys, B.F., James, S., Nieto-Rostro, M., and Turner, J.G.

(1998). COI1: An Arabidopsis gene required for JA-regulated defense

and fertility. Science 280: 1091–1094.

Xu, L.H., Liu, F.Q., Lechner, E., Genschik, P., Crosby, W.L., Ma, H.,

Peng, W., Huang, D.F., and Xie, D.X. (2002). The SCFCOl1 ubiquitin-

ligase complexes are required for JA response in Arabidopsis. Plant

Cell 14: 1919–1935.

Yadav, V., Mallappa, C., Gangappa, S.N., Bhatia, S., and

Chattopadhyay, S. (2005). A basic helix-loop-helix transcription

factor in Arabidopsis, MYC2, acts as a repressor of blue light-

mediated photomorphogenic Growth. Plant Cell 17: 1953–1966.

Yan, Y., Stolz, S., Chetelat, A., Reymond, P., Pagni, M., Dubugnon,

L., and Farmer, E.E. (2007). A downstream mediator in the growth

repression limb of the JA pathway. Plant Cell 19: 2470–2483.

Yan, J., Zhang, C., Gu, M., Bai, Z., Zhang, W., Qi, T., Cheng, Z., Peng,

W., Luo, H., Nan, F., Wang, Z., and Xie, D. (2009). The Arabidopsis

CORONATINE INSENSITIVE1 protein is a jasmonate receptor. Plant

Cell 21: 2220–2236.

Yanovsky, M.J., Casal, J.J., and Whitelam, G.C. (1995). Phytochrome

A, phytochrome B and HY4 are involved in hypocotyl growth re-

sponses to natural radiation in Arabidopsis: Weak de-etiolation of

the phyA mutant under dense canopies. Plant Cell Environ. 18:

788–794.

Zhai, Q.Z., Li, C.B., Zheng, W.G., Wu, X.Y., Zhao, J.H., Zhou, G.X.,

Jiang, H.L., Sun, J.Q., Lou, Y.G., and Li, C.Y. (2007). Phytochrome

chromophore deficiency leads to overproduction of jasmonic acid

and elevated expression of JA-responsive genes in Arabidopsis. Plant

Cell Physiol. 48: 1061–1071.

Zhang, Y., and Turner, J.G. (2008). Wound-induced endogenous JAs

stunt plant growth by inhibiting mitosis. PLoS One 3: e3699.

1160 The Plant Cell

DOI 10.1105/tpc.109.067728; originally published online April 30, 2010; 2010;22;1143-1160Plant Cell

and John G. TurnerFrances Robson, Haruko Okamoto, Elaine Patrick, Sue-Ré Harris, Claus Wasternack, Charles Brearley

Integrated through JAZ1 Stability Wound and Shade Responses AreArabidopsisJasmonate and Phytochrome A Signaling in

 This information is current as of July 28, 2018

 

Supplemental Data /content/suppl/2010/04/12/tpc.109.067728.DC1.html

References /content/22/4/1143.full.html#ref-list-1

This article cites 101 articles, 50 of which can be accessed free at:

Permissions https://www.copyright.com/ccc/openurl.do?sid=pd_hw1532298X&issn=1532298X&WT.mc_id=pd_hw1532298X

eTOCs http://www.plantcell.org/cgi/alerts/ctmain

Sign up for eTOCs at:

CiteTrack Alerts http://www.plantcell.org/cgi/alerts/ctmain

Sign up for CiteTrack Alerts at:

Subscription Information http://www.aspb.org/publications/subscriptions.cfm

is available at:Plant Physiology and The Plant CellSubscription Information for

ADVANCING THE SCIENCE OF PLANT BIOLOGY © American Society of Plant Biologists