First published online February 27, 2003; 10.1104/pp.102.015487
Plant Physiol, March 2003, Vol. 131, pp. 1340-1346
Phytochromes B, D, and E Act Redundantly to Control Multiple
Physiological Responses in Arabidopsis
Keara A.
Franklin,*
Uta
Praekelt,
Wendy M.
Stoddart,
Olivia E.
Billingham,
Karen J.
Halliday, and
Garry C.
Whitelam
Department of Biology, University of Leicester, United
Kingdom LE1 7RH (K.A.F., U.P., W.M.S., G.C.W.), and School of
Biological Sciences, University of Bristol, United Kingdom BS8 1U6
(O.E.B., K.J.H.)
 |
ABSTRACT |
Phytochrome-mediated perception of the ratio of red
to far-red wavelengths in the ambient light environment is
fundamental to plant growth and development. Such monitoring
enables plants to detect neighboring vegetation and initiate avoidance
responses, thus conferring considerable selective advantage. The shade
avoidance syndrome in plants is characterized by elongation growth and
early flowering, responses that are fully induced by end-of-day far-red light treatments. Elucidating the roles of individual phytochromes in
mediating responses to red to far-red has however always been confounded by synergistic and mutually antagonistic coactions between
family members. The creation of triple and quadruple mutants in
Arabidopsis, deficient in multiple phytochromes, has revealed functional redundancy between phyB, D, and E in controlling flowering time, leaf development, and regulation of the homeobox gene,
ATHB-2. In addition, mutant analysis suggests a possible
novel role for phyC in suppressing ATHB-2 transcription
in the light.
 |
INTRODUCTION |
In addition to its role
as an energy source, light signals serve to provide plants with
information about the surrounding environment. The efficient
perception, interpretation, and transduction of such signals allow
plants to synchronize their development with seasonal
changes and to minimize the adverse effects of environmental perturbations. The ability to monitor the intensity, quality, and
direction of incident light enables plants to modulate a number of
physiological responses, including seed germination, shoot architecture, and the onset of flowering. Three principle families of
photoreceptors have been identified for light perception in higher
plant tissues, the red/far-red (R/FR) light-absorbing phytochromes (PHY) and the UV-A/blue light (B)-absorbing cryptochromes and phototropins (for review, see Quail, 2002 ).
PHY exist as a homodimer of two independently reversible subunits. Each
subunit consists of a polypeptide (approximately 124 kD) attached to a
linear tetrapyrrole via a thioether linkage. In Arabidopsis, five
discrete apo-PHY-encoding genes, PHYA-PHYE, have
been isolated and sequenced (Mathews and Sharrock,
1997 ). PHY A, B, C, and E are evolutionarily divergent
proteins, sharing only 46% to 53% sequence identity, whereas
PHYD encodes an apoprotein that shares 80% sequence
identity with PHYB (Clack et al., 1994 ). Molecular
phylogenetic analysis supports the occurrence of four major duplication
events in the evolution of PHY genes. An initial duplication
is believed to have separated PHYA (light labile in the FR
light-absorbing [Pfr] form) and PHYC (light stable in the Pfr form) from PHYB/D/E (all light
stable in the Pfr form). The subsequent separation of PHYA
from PHYC and PHYB/D from
PHYE resulted in three subfamilies:
A/C, B/D, and E
(Smith, 2000 ).
PHY regulate two principle adaptive phenomena in light-grown plants.
These are proximity perception, leading to shade avoidance responses,
and photoperiodic perception, leading to floral induction in some
species. Fluctuations in the spectral quality of daylight are detected
via perception of the ratio of R to FR wavelengths (R:FR). Such
fluctuations can occur daily (dusk and dawn) and under vegetation
canopies. Early reaction to the threat of impending shade is triggered
by the localized drop in R:FR, reflected from surrounding vegetation
(Ballare et al., 1990 ). Selective attenuation of R
wavelengths by chlorophyllous tissue results in a significant decrease
in the R:FR quantum ratio of reflected light detected by plants lower
in the canopy. Neighbor detection initiates shade avoidance responses,
enabling plants to compete for light. Such responses include enhanced
internode and petiole extension growth, increased apical dominance,
retarded leaf development, and an acceleration of flowering
(Halliday et al., 1994 ; Smith and Whitelam, 1997 ). These physiological adaptations are accompanied by
changes in the distribution of assimilates between leaves, stems, and roots (Keiller and Smith, 1989 ), and confer a
considerable selective advantage. The ability to respond to the
perceived threat of shading and therefore initiate responses before
canopy closure is a crucial competitive strategy in rapidly growing
populations (Ballare et al., 1990 ).
The roles of individual PHY in regulating these responses have
been largely inferred from studies of mutant plants. Mutants of tomato
(Lycopersicon esculentum) and Arabidopsis, deficient in phyA, display a phenotype almost indistinguishable from wild-type (WT) plants when grown in white light (Whitelam et al.,
1993 ; van Tuinen et al., 1995 ). Such phenotypes
suggest that multiple PHY regulate mature plant morphology in a
functionally redundant manner. Deficiency of phyB has been shown to
result in plants displaying phenotypes comparable with those of the
shade avoidance syndrome (Robson et al., 1993 ;
Whitelam and Devlin, 1997 ). Reduction of Pfr by an
end-of-day (EOD) FR treatment results in a qualitatively similar
response to lowering of the Pfr level during the light period by
reduction of the R:FR photon ratio. The retention of shade avoidance
and EOD FR responses in Arabidopsis phyB null mutants suggested the
involvement of other PHY in mediating responses to R:FR, roles
subsequently assigned to phyD and E (Robson et al.,
1993 ; Devlin et al., 1998 ,
1999 ).
The molecular mechanisms underlying physiological responses to
perceived R:FR are poorly understood. Identification of the homeobox
gene ATHB-2 (also known as HAT4; Ruberti
et al., 1991 ; Schena and Davis, 1992 ) provided
the first evidence of a gene reversibly regulated by changes in R:FR
(Carabelli et al., 1993 , 1996 ).
Overexpression of ATHB-2 has been shown to result in a pleiotropic phenotype, some aspects of which resemble the shade avoidance phenotype in Arabidopsis (Steindler et al.,
1997 , 1999 ). Expression analysis revealed
transcript abundance to be controlled by phyA and phyB in addition to
another, as yet unidentified, PHY (Steindler et al.,
1997 ). The synergistic, and in some cases mutually
antagonistic, action of phytochrome species in multiple physiological
responses has made elucidation of the roles of individual family
members problematic in existing mutants. Therefore, the creation of
triple and quadruple mutant combinations has provided a unique insight
into functional redundancy between PHY in mediating responses to R:FR.
In addition, the creation of a phyABDE quadruple mutant has
revealed a unique function for the least well characterized of the PHY, phyC.
 |
RESULTS |
Effect of EOD FR and Reduced R:FR on Internode
Elongation
The promotion of internode elongation after growth under low R:FR
and EOD FR treatment is well documented in Arabidopsis grown at
temperatures above 21°C (Robson et al., 1993 ;
Devlin et al., 1996 , 1998 ). When grown
under low R:FR at 16°C, such responses were absent in WT,
phyBDE triple and phyABDE quadruple mutants (Fig.
1.). A similar lack of response was
observed in WT and phyBDE triple mutant plants grown under
8-h light/16-h dark cycles, with and without EOD FR treatment. However,
elongation of internodes and loss of a rosette habit were clearly
visible in phyABDE quadruple mutants grown under identical
conditions. Such elongation was displayed in control and EOD FR-treated
plants, suggesting an important role for phyA in maintaining rosette
habit in Arabidopsis.

View larger version (44K):
[in this window]
[in a new window]
|
Figure 1.
La-er, phyBDE, and phyABDE
mutants (in La-er background) were grown for 36 d at
16°C under 8-h light and 16-h dark cycles (control), the same
conditions with 15-min EOD FR treatments (+EOD FR), and under
continuous irradiation of high and low R:FR.
|
|
Effect of EOD FR and Reduced R:FR on Leaf Morphology
In response to EOD FR light, WT plants displayed increased petiole
elongation and reduced leaf area, phenotypes consistent with the
characterized shade avoidance syndrome (Fig. 1; Smith and
Whitelam, 1997 ). However, when grown under continuous light of
low R:FR, an increased leaf area was observed in WT and
phyBDE triple mutant plants (Fig. 1). Consonant with visible
changes in leaf morphology, WT plants treated with EOD FR displayed an increase in leaf length/width ratio (Fig.
2). This response was severely reduced in
the phyB mutant and was absent in the phyBD double mutant, phyBE double mutant, phyBDE triple
mutant, and the phyABDE quadruple mutant, all of which
displayed an elongated leaf phenotype under control conditions. A
pronounced increase in leaf length/width ratio was observed in
phyABDE mutant plants compared with phyBDE plants
grown under 8-h light/16-h dark cycles (Fig. 2). A similar increase was
recorded in plants grown under continuous irradiation (high and low
R:FR, data not shown), suggesting a significant role for phyA in the
regulation of leaf morphology.

View larger version (32K):
[in this window]
[in a new window]
|
Figure 2.
Length/width ratios of rosette leaf 11 in
La-er, phyB, phyBD, phyBE,
phyBDE, and phyABDE mutants (in La-er
background) at flowering. Plants were grown at 16°C under 8-h light
and 16-h dark cycles (control) and under the same conditions with
15-min EOD FR treatments (+EOD FR).
|
|
PHY Regulation of Cotyledon Development
When grown under Rc, sequential removal of PHY
species resulted in reduced cotyledon area (Fig.
3A). Monogenic mutants for phyA, phyD, and phyE displayed no such
reduction (data not shown). However, the considerable reduction
observed in phyB mutants suggests a significant role for
this PHY in cotyledon expansion. The additional removal of
phyD and E resulted in further decreases in
cotyledon area, suggesting interactions between PHY family members in
regulating cotyledon size. The smallest cotyledons were observed in the
phyABDE quadruple mutant, confirming, as with leaf
morphology, a role for phyA. The observation that phyABDE
quadruple mutants displayed some cotyledon unfolding and expansion
under Rc provides the first evidence that phyC can function as a weak
red light sensor independently from other PHY. Such data is supported
by the R/FR reversible promotion of cotyledon opening observed in
phyABDE mutants (Fig. 3B). Cotyledon opening was not
observed in plants treated with pulses of R (data not shown).

View larger version (22K):
[in this window]
[in a new window]
|
Figure 3.
A, Cotyledon areas in La-er,
phyB, phyBD, phyBE, phyBDE,
and phyABDE mutants (in La-er background) grown
for 5 d in the dark and Rc at a fluence rate of 50 µmol
m 2 s 1. B, Cotyledon
angles in WT (La-er) and phyABDE mutants grown in
the dark, Rc (10 µmol m 2
s 1) and Rc + FRc (50:50, 20 µmol
m 2 s 1) for 5 d.
|
|
Effect of EOD FR and Reduced R:FR on Flowering Time
An acceleration of flowering (as measured by number of
rosette leaves at bolting) in response to growth under low R:FR and EOD
FR treatment is a well-characterized component of the shade avoidance
syndrome (Smith and Whitelam, 1997 ). The early flowering response of phyB mutants grown at temperatures above 21°C
mimics that of shade-avoiding plants and has resulted in phyB being
universally regarded as a repressor of flowering (Simpson et
al., 1999 ). Observations that phyBD and
phyBE double mutants flower earlier than either monogenic
mutant infer additional roles for phyD and E in the control of
flowering time in Arabidopsis (Devlin et al., 1998 , 1999 ). A retention of flowering response to EOD FR
treatment in phyABD, but not phyABE triple
mutants suggested that phyE performs a more dominant role than phyD
(Devlin et al., 1998 ). The work described here
investigates the interaction of phyB, D, and E in regulating flowering
response to R:FR in multiple PHY mutant combinations grown at
16°C.
As described previously under long- and short-day conditions
(Halliday et al., 2002 ), when grown at 16°C under
continuous irradiation, the phyB mutant flowers with the
same number of leaves as WT (Fig. 4A).
However, an acceleration of flowering was observed in phyBD
and phyBE double mutants grown under continuous irradiation and short days, with a further acceleration being observed in phyBDE triple mutants (Fig. 4, A and B). Such data suggest
repression of flowering to be mediated by phyB, D, and E in a
functionally redundant manner. An acceleration of flowering was
observed in monogenic phyB mutants grown under low R:FR or
treated with EOD FR. This acceleration was reduced in phyBD
and phyBE double mutants and was absent in phyBDE
triple mutants, suggesting functional redundancy between phyB, D, and E
in regulating flowering response to R:FR. A quantitatively similar
response was observed in phyBDE triple and
phyABDE quadruple mutants, proposing little role for phyA in
mediating flowering response to R:FR under these conditions.

View larger version (30K):
[in this window]
[in a new window]
|
Figure 4.
Rosette leaf number in La-er,
phyB, phyBD, phyBE, phyBDE,
and phyABDE mutants (in La-er background) at
bolting. Plants were grown at 16°C under a) Continuous irradiation of
high and low R:FR and b) 8 h light/16 h dark cycles, with and without
EOD FR treatments.
|
|
Phytochrome Regulation of ATHB-2 Transcript
Abundance
Previous observations suggest transcript abundance of the homeobox
gene ATHB-2 to be regulated by several members of the PHY family (Carabelli et al., 1996 ). Transcript levels of
ATHB-2 are low in tissues that have been maintained in white
light, but are rapidly elevated in response to EOD FR treatment before
transfer to darkness (Fig. 5A). Response
to EOD FR was retained in phyABD triple mutant plants,
suggesting the additional action of phyC and/or phyE in mediating this
phenomenon. Analysis of phyABE triple and phyABDE
quadruple mutants revealed a significant increase in ATHB-2
transcript upon transfer from white light to darkness (Fig. 5A). This
increase was not affected by EOD FR treatment, suggesting regulation of
ATHB-2 transcript by EOD FR to be mediated by phyB and phyE
in a functionally redundant manner. Further investigation of the
phyABDE quadruple mutant showed significant repression of
ATHB-2 transcript abundance upon transfer of dark-adapted
plants to white light. The partial repression observed upon transfer to
R light suggests a novel role for phyC. Because of the rapid accumulation of ATHB-2 transcript in darkness, the
reversibility of R-mediated repression was demonstrated by irradiating
plants simultaneously with R and FR. The subsequent attenuation of the response suggests that phyC can, at least, partially mediate repression of ATHB-2 transcript abundance in an R/FR reversible manner.
No effects on transcript accumulation were observed after 2 h of FR (data not shown).

View larger version (41K):
[in this window]
[in a new window]
|
Figure 5.
PHY regulation of ATHB-2 expression. A,
RNA gel-blot showing ATHB-2 transcript accumulation in
La-er, phyABD, phyABE,
phyBDE, and phyABDE mutant plants grown under
continuous white light (Wc) for 3 weeks, then transferred to white
light (W) for 1 h, dark (D) for 1 h, or EOD FR (15 min) and
then dark (45 min; labeled FR). B, RNA gel-blot showing
ATHB-2 transcript accumulation in phyABDE mutant
plants grown under Wc for 3 weeks, then transferred to different light
regimes. W, White light; D, dark. Repeated experiments showed identical
results.
|
|
 |
DISCUSSION |
PHY B, D, and E Act Redundantly to Control Leaf Morphology and
Flowering Time in Response to R:FR
The ability to modulate plant architecture and flowering time in
response to perceived threat of shading remains one of the most radical
adaptive strategies available to higher plants. The most pronounced
phenotypes of the shade avoidance syndrome are extension of internode
and leaf growth and an acceleration of flowering (Smith and
Whitelam, 1997 ). Such adaptations are believed to elevate
leaves to a better-lit stratum in the canopy and promote seed set at a
time when resources may be limiting. Anticipatory avoidance responses
upon perception of neighboring vegetation also represent a crucial
survival strategy, particularly in fast-developing stands
(Ballare et al., 1990 ). The analysis of PHY-deficient
mutants has been fundamental to the elucidation of roles for individual PHY in these responses. Studies have revealed that different PHY play
distinct and overlapping roles within the spectrum of plant photomorphogenesis (McCormac et al., 1993 ;
Whitelam et al., 1993 ; Whitelam and Harberd,
1994 ; Smith, 1995 ; Whitelam and
Devlin, 1997 ). The involvement of phyB in mediating
responses to R:FR is widely documented in a variety of species
(Somers et al., 1991 ; Devlin et al.,
1992 ; López-Juez et al., 1992 ; Reed
et al., 1993 ), although the detection of shade avoidance
responses in phyB null mutants have indicated the involvement of
additional PHY (Whitelam and Smith, 1991 ; Robson
et al., 1993 ; Halliday et al., 1994 ). Subsequent
investigations have revealed the involvement of phyD and phyE,
although, until now, a functional role for other phytochromes could not
be unequivocally excluded (Devlin et al., 1996 ,
1998 , 1999 ).
The work described here shows leaf elongation and acceleration of
flowering in response to low R:FR and EOD FR (i.e. perceived threat of
shading) to be mediated solely by phyB, D, and E in a functionally
redundant manner. These represent the most recently evolved members of
the PHY family, forming a distinct subgroup (Mathews and
Sharrock, 1997 ). It has been previously speculated that shade
avoidance may have provided the selective pressure for the evolution of
these PHY (Devlin et al., 1998 ). Earlier studies have
reported an EOD FR flowering response in phyABD triple but
not phyABE triple mutants, thus implicating a greater role for phyE in mediating this response (Devlin et al.,
1998 ). The apparent discrepancy between previous and current
data may reflect the higher growth temperatures used by other authors.
Growth at 16°C also results in a surprising increase in leaf area in
WT plants grown under low R:FR. Such a response is in apparent
contradiction to previously described shade avoidance phenotypes.
Together with emerging data showing aberrant developmental responses in
phy mutants grown at lower temperatures
(Halliday et al., 2003 ), it must be questioned
whether laboratory experiments using temperatures in excess of 21°C
truly represent the adaptive phenomena of plants grown natively in more
temperate conditions. Such observations question the true nature of the
shade avoidance syndrome and will require further investigation.
PHY A Plays a Predominant Role in Modulating Internode and Leaf
Elongation Growth in Light-Grown Plants
The role of phyA, a light-labile phytochrome, in modulating mature
plant architecture was indicated in earlier studies after an observed
reduction in biomass in the phyAB double mutant compared with either monogenic mutant (Devlin et al., 1996 ).
Internode elongation and loss of rosette habit has been previously
observed in phyAB double and phyABD triple mutant plants after EOD FR
treatment (Devlin et al., 1996 , 1999 ).
The constitutive elongation phenotype observed in phyABE
mutants grown under control conditions was the basis on which the
mutant was isolated and led to the proposal that inhibition of
internode elongation in mature plants is regulated, redundantly, by
phyA, B, and E (Devlin et al., 1998 ). The caulescent appearance of phyABDE quadruple mutants grown under short
days, a phenotype not displayed in phyBDE triple mutants,
thereby supports such a proposal. In addition, the pronounced increase
in leaf length/width ratio in phyABDE quadruple mutants
grown under short days (Fig. 2) and continuous irradiation (data not
shown) suggests a significant role for phyA in inhibiting leaf
elongation in light-grown plants, independent of R:FR ratio.
PHY A, B, C, D, and E Act Redundantly to Modulate Cotyledon
Development under Rc.
The synergistic coactions between phyA and phyB in regulating
cotyledon expansion have been previously recorded (Neff and Vanvolkenburgh, 1994 ; Reed et al., 1994 ;
Neff and Chory, 1998 ). Through the creation of triple
and quadruple mutant combinations, additional roles for phyD and phyE
have been revealed in this study. The partial cotyledon opening and
expansion, observed in Rc-grown phyABDE quadruple mutant
seedlings, also suggest that phyC can weakly mediate these responses in
isolation. The reversibility of cotyledon opening by FR provides
support for such a conclusion. Reporter gene studies by Tóth et
al. (2001) revealed significant PHYC promoter
activity in light-grown cotyledons. Therefore, it can be speculated
that the weak response observed in phyABDE quadruple mutants
does not result from reduced PHYC transcription in cotyledon tissue.
However, it is plausible that the phyABDE quadruple mutant contains reduced levels of phyC, a phenotype previously observed in
phyB-deficient plants (Hirschfeld et al., 1998 ). Such a
deficiency would exacerbate an already reduced response and will be
investigated in future experiments. Taken together, the data presented
here reveal functionally redundant roles for all five PHY in regulating cotyledon development under Rc. In addition, cotyledon opening experiments have provided the first evidence of a R/FR reversible function for phyC.
PHY C Mediates the Repression of ATHB-2 Transcript in the
Light
The ATHB-2 gene encodes a homeodomain-Leu zipper
protein thought to be involved in cotyledon expansion, growth of the
vascular system, and lateral root formation (Steindler et al.,
1999 ). The light-regulation of ATHB-2 transcript
abundance is well documented and is believed to be predominantly
controlled by changes in R:FR (Carabelli et al., 1993 ,
1996 ). Mutant studies have suggested the involvement of
a PHY other than phyA or phyB in mediating this response
(Steindler et al., 1997 ). This work reveals regulation of ATHB-2 transcript abundance in response to EOD FR to be
mediated redundantly by phyB and phyE. However, analysis of the
phyABDE quadruple mutant has revealed a possible function
for phyC in the partial suppression ATHB-2 transcription in
the light. Future experiments should ascertain whether the increased
repression in white light results from the increased fluence rate used
or represents an additional cryptochrome-mediated repression of gene expression. The reduced repression of ATHB-2 transcription
observed by supplementing R with FR provides evidence of another R:FR
reversible function for phyC, although future mutant analyses will
ultimately be required to ascertain whether phyC performs a similar
function in planta.
The creation of mutants in Arabidopsis, null for multiple PHY, has
provided new insights into functional redundancy between family members
in controlling responses to R:FR. Analysis has revealed phyB, D, and E,
the most recently evolved group of phytochromes, to solely mediate leaf
elongation and flowering responses to R:FR ratio in a functionally
redundant manner. The creation of a quadruple mutant, possessing only a
functional phyC, has exposed significant roles for phyA in controlling
internode elongation and leaf morphology in mature plants, independent
of R:FR. Analysis of cotyledon development in phyABDE
quadruple mutants has also provided the first evidence of a
R/FR-reversible phyC function. Growth of plants at 16°C has revealed
leaf phenotypes at variance with the characterized shade avoidance
syndrome, implicating the interaction of light- and temperature-sensing
mechanisms. Regulation of the homeobox gene, ATHB-2, by EOD
FR treatment has been shown to be mediated redundantly by phyB and E,
with a possible role for phyC in suppressing transcript abundance in
the light. Redundant interplay between PHY B and E has been previously
observed in R/FR-reversible seed germination (Hennig et al.,
2002 ) and maintenance of rosette habit (Devlin et al.,
1998 ), responses with no identifiable role for phyD. However, functional interaction with cryptochrome 1 has been shown to be mediated redundantly by phyB and D, with no apparent role for phyE
(Hennig et al., 1999 ). Therefore, it can be concluded
that phyB, D, and E are functionally unique photoreceptors, but act redundantly to regulate multiple responses during Arabidopsis development. Taken together, the data presented here have confirmed previously speculated functional divisions between PHY groups in
addition to revealing new roles for family members and casting incertitude on the true nature of the shade avoidance syndrome under
natural conditions.
 |
MATERIALS AND METHODS |
Plant Material
All experiments were performed using Arabidopsis, ecotype
La-er. The phytochrome mutant alleles used in this study
were phyB-1 (Koornneef et al.,
1980 ), phyBD (Devlin et al.,
1999 ), phyBE (Devlin et al.,
1998 ), phyABD (Devlin et al.,
1999 ), phyABE (Devlin et al.,
1998 ), and phyBDE (Shalitin et al.,
2002 ). The phyABDE quadruple mutant was created
from existing mutants using standard screening procedures.
Growth Conditions
Seeds were surface sterilized in 10% (v/v) commercial
bleach and were sown directly onto Lehle media (Lehle Seeds, Round Rok, TX) supplemented with 0.8% (w/v) agar. After 4 d of
stratification in darkness at 4°C, germination was synchronized by
treating seeds with a light pulse and returning to the dark for 24 h. Seedlings were germinated under 8-h light/16-h-dark cycles at
16°C. After an additional 9 d, uniformly sized seedlings were
transplanted to 5- × 5- × 5-cm pots containing a 3:1 mixture of
compost:horticultural silver sand. After an additional 12 d of
growth under the same conditions, plants were transferred to
experimental light regimes at 16°C. For cotyledon area measurements,
seeds were germinated on Hoagland no. 2 basal salt mixture
(0.8% [w/v] agar) as above before transfer to Rc at a fluence rate
of 50 µmol m 2 s 1 at 22°C. Cotyledons
were excised after 5 d of growth and were measured using scan pro5
(SPSS UK, Surrey, UK). For cotyledon angle measurements, seeds were
germinated as above before transfer to Rc at a fluence rate of 10 µmol m 2 s 1 or Rc + FRc (50:50) at a
fluence rate of 20 µmol m 2 s 1, both at
22°C. Seedlings were photographed and angles were measured with a protractor.
Light Sources
For R:FR ratio experiments, plants were grown under continuous
irradiation in controlled cabinets described previously (Keiller and Smith, 1989 ). The high R:FR cabinet provided a photon
irradiance, 400 to 700 nm, of 130 µmol m 2
s 1 and an R:FR of 4.7. The low R/FR cabinet provided the
same photon irradiance, but an R:FR of 0.089. EOD FR experiments were
carried out under controlled conditions comprising of 8 h of
warm-white fluorescent light (photon irradiance 400-700 nm, 100 µmol
m 2 s 1). Plants treated with EOD FR received
15 min of FR light (photon irradiance 700-800 nm, 57 µmol
m 2 s 1) obtained by filtering the output of
500-W tungsten halogen lamps (Haloline; Osram-Sylvania, Towanda, PA)
through 10 mm of flowing water and one layer of black Plexiglas (FRF
700; West Lakes Plastics, Lenni, PA). R and FR light was provided by
light-emitting diodes at max665 and 735 nm,
respectively. All light measurements were performed using a photosystem
II spectroradiometer (LI-3000; LI-COR, Lincoln, NE).
Leaf and Flowering Measurements
All physiological measurements were performed after bolting.
Data represent the means ± SE from at least 10 plants. Leaf measurements were determined using a ruler. Flowering time
was recorded as the number of rosette leaves present when plants
displayed a 1-cm inflorescence stem.
RNA Gel-Blot Analysis
Seeds were germinated as described previously, and plants
were grown under white light (8-h day and 16-h night cycles) at 16°C
for 3 weeks. Plants were then transferred to continuous white light at
22°C for 24 h before experimental light treatments, all at
22°C. R and R:FR (50:50) were provided by light-emitting diodes at a
fluence rate of 6 and 12 µmol m 2 s 1,
respectively. Total RNA was extracted from whole plants using the
method of Logemann et al. (1987) . Samples of 20 µg of RNA were heat denatured (65°C for 15 min) in the presence of
50% (w/v) formamide, separated on a denaturing 1.5% (w/v) agarose gel
(Sambrook et al., 1989 ), and blotted
onto Hybond-N nylon membrane (Amersham Pharmacia Biotech,
Buckinghamshire, UK). Equal loadings of RNA were confirmed by ethidium
bromide staining of gels before blotting. Prehybridization and
hybridization were performed in the presence of 50% (w/v) formamide at
42°C (Sambrook et al., 1989 ). Washings were
carried out to a final stringency of 0.2× SSC and 0.1% (w/v) SDS at
42°C. An ATHB-2 fragment was isolated by PCR amplification of
La-er genomic DNA using the following primers: forward:
5'-GAAAGACGATCTGGGTCTAAGCTTAGG-3' and reverse:
5'-CAACCTCAGGCTGCTACGTCAGCG-3'. Probes were labeled with
[ -32P] dCTP using random hexanucleotide priming
(Rediprime; Amersham Pharmacia Biotech), and blots were exposed onto
x-ray film (Kodak Biomax MS; Amersham Pharmacia Biotech).
 |
FOOTNOTES |
Received October 1, 2002; returned for revision November 24, 2002; accepted December 25, 2002.
*
Corresponding author; e-mail kaf5{at}le.ac.uk; fax
44-0116-252-3330.
1
This work was supported by the Biotechnology and
Biological Sciences Research Council (UK) (grant no. 91/P15700 to
K.A.F., 91/P08472 to U.P., and 91/P09944 to K.J.H.).
Article, publication date, and citation information can be found at
www.plantphysiol.org/cgi/doi/10.1104/pp.102.015487.
 |
LITERATURE CITED |
-
Ballare CL, Scopel AL, Sanchez RA
(1990)
Far-red radiation reflected from adjacent leaves: an early signal of competition in plant canopies.
Science
247: 329-332[Abstract/Free Full Text]
-
Carabelli M, Morelli G, Whitelam GC, Ruberti I
(1996)
Twilight-zone and canopy shade induction of the ATHB-2 homeobox gene in green plants.
Proc Natl Acad Sci USA
93: 3530-3535[Abstract/Free Full Text]
-
Carabelli M, Sessa G, Ruberti I, Morelli G
(1993)
The Arabidopsis ATHB-2 and -4 genes are strongly induced by far-red-rich light.
Plant J
4: 469-479[CrossRef][ISI][Medline]
-
Clack T, Mathews S, Sharrock RA
(1994)
The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE.
Plant Mol Biol
25: 413-427[CrossRef][ISI][Medline]
-
Devlin PF, Halliday KJ, Harberd NP, Whitelam GC
(1996)
The rosette habit of Arabidopsis thaliana is dependent upon phytochrome action: novel phytochromes control internode elongation and flowering time.
Plant J
10: 1127-1134[CrossRef][ISI][Medline]
-
Devlin PF, Patel SR, Whitelam GC
(1998)
Phytochrome E influences internode elongation and flowering time in Arabidopsis.
Plant Cell
10: 1479-1487[Abstract/Free Full Text]
-
Devlin PF, Robson PRH, Patel SR, Goosey L, Sharrock RA, Whitelam GC
(1999)
Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation and flowering time.
Plant Physiol
119: 909-915[Abstract/Free Full Text]
-
Devlin PF, Rood SB, Somer SE, Quail PH, Whitelam GC
(1992)
Photophysiology of the elongated internode (ein) mutant of Brassica rapa: The ein mutant lacks a detectable phytochrome B-like polypeptide.
Plant Physiol
100: 1442-1447[Abstract/Free Full Text]
-
Halliday KJ, Koorneef M, Whitelam GC
(1994)
Phytochrome B and at least one other phytochrome mediate the accelerated flowering response of Arabidopsis thaliana to low red/far-red ratio.
Plant Physiol
104: 1311-1315[Abstract]
-
Halliday KJ, Salter MG, Thingnaes MG, Whitelam GC (2003) The
phyB-controlled flowering pathway is temperature sensitive and is
mediated by the floral integrator FT. Plant J (in press)
-
Hennig L, Funk M, Whitelam GC, Schäfer E
(1999)
Functional interaction of cryptochrome 1 and phytochrome D.
Plant J
20: 289-294[ISI][Medline]
-
Hennig L, Stoddart WM, Dieterle M, Whitelam GC, Schäfer E
(2002)
Phytochrome E controls light-induced germination of Arabidopsis.
Plant Physiol
128: 194-200[Abstract/Free Full Text]
-
Hirschfeld M, Tepperman JM, Clack T, Quail PH, Sharrock RA
(1998)
Coordination of phytochrome levels in phy B mutants of Arabidopsis as revealed by apoprotein specific monoclonal antibodies.
Genetics
149: 523-535[Abstract/Free Full Text]
-
Keiller D, Smith H
(1989)
Control of carbon partitioning by light quality mediated by phytochrome.
Plant Sci
63: 25-29[CrossRef]
-
Koornneff M, Rolff E, Spruitt CJP
(1980)
Genetic control of light-inhibited hypocotyl elongation in Arabidopsis thaliana L Heynh.
Z Pflanzenphysiol
100: 147-160
-
Logemann J, Schell J, Willmitzer L
(1987)
Improved method for the isolation of RNA from plant tissues.
Anal Biochem
163: 16-20[CrossRef][ISI][Medline]
-
López-Juez E, Nagatani A, Tomizawa K-I, Deak M, Kern R, Kendrick RE, Furuya M
(1992)
The cucumber long hypocotyl mutant lacks a light-stable PHYB-like phytochrome.
Plant Cell
4: 241-251[Abstract/Free Full Text]
-
McCormac A, Wagner D, Boylan MT, Quail PH, Whitelam GC
(1993)
Photoresponses of transgenic Arabidopsis seedlings expressing introduced phytochrome B-encoding cDNAs: evidence that PHYA and PHYB have distinct photoregulatory functions.
Plant J
4: 19-27[CrossRef][ISI]
-
Mathews S, Sharrock RA
(1997)
Phytochrome gene diversity.
Plant Cell Environ
20: 666-671[CrossRef]
-
Neff MM, Chory J
(1998)
Genetic interaction between phytochrome A, phytochrome B and cryptochrome 1 during Arabidopsis development.
Plant Physiol
118: 27-36[Abstract/Free Full Text]
-
Neff MM, Vanvolkenburgh E
(1994)
Light-stimulated cotyledon expansion in Arabidopsis seedlings: the role of phytochrome B.
Plant Physiol
104: 1027-1032[Abstract]
-
Quail PH
(2002)
Photosensory perception and signalling in plant cells: new paradigms?
Curr Opin Plant Biol
14: 180-188
-
Reed JW, Nagatani A, Elich T, Fagan M, Chory J
(1994)
Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development.
Plant Physiol
104: 1139-1149[Abstract]
-
Reed JW, Nagpal P, Poole DS, Furuya M, Chory J
(1993)
Mutations in the gene for red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development.
Plant Cell
5: 147-157[Abstract]
-
Robson PRH, Whitelam GC, Smith H
(1993)
Selected components of the shade-avoidance syndrome are displayed in a normal manner in mutants of Arabidopsis thaliana and Brassica rapa deficient in phytochrome B.
Plant Physiol
102: 1179-1184[Abstract]
-
Ruberti I, Sessa G, Lucchetti S, Morelli G
(1991)
A novel class of plant proteins containing a homeodomain with a closely linked leucine zipper motif.
EMBO J
10: 1787-1791[ISI][Medline]
-
Sambrook J, Frisch EF, Maniatis F
(1989)
Molecular Cloning: A Laboratory Manual, Ed 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
-
Schena M, Davis RW
(1992)
HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily.
Proc Natl Acad Sci USA
89: 3894-3898[Abstract/Free Full Text]
-
Shalitin D, Yang H, mockler TC, Maymon M, Guo H, Whitelam GC, Lin C
(2002)
Regulation of Arabidopsis cryptochrome 2 by blue-light-dependent phosphorylation.
Nature
417: 763-767[CrossRef][Medline]
-
Simpson GG, Gendall AR, Dean C
(1999)
When to switch to flowering.
Annu Rev Cell Dev Biol
99: 519-550[CrossRef]
-
Smith H
(1995)
Physiological and ecological function within the phytochrome family.
Annu Rev Plant Physiol Plant Mol Biol
46: 289-315[CrossRef][ISI]
-
Smith H
(2000)
Phytochromes and light signal perception by plants: an emerging synthesis.
Nature
407: 585-591[CrossRef][Medline]
-
Smith H, Whitelam GC
(1997)
The shade avoidance syndrome: multiple responses mediated by multiple phytochromes.
Plant Cell Environ
20: 840-844[CrossRef]
-
Somers DE, Sharrock RA, Tepperman JM, Quail PH
(1991)
The hy3 long hypocotyl mutant of Arabidopsis is deficient in phytochrome B.
Plant Cell
3: 1263-1274[Abstract/Free Full Text]
-
Steindler C, Carabelli M, Borello U, Morelli G, Ruberti I
(1997)
Phytochrome A, phytochrome B and other phytochromes regulate ATHB-2 expression in etiolated and green Arabidopsis plants.
Plant Cell Environ
20: 759-763
-
Steindler C, Matteucci A, Sessa G, Weimar T, Ohgishi M, Aoyama T, Morelli G, Ruberti I
(1999)
Shade avoidance responses are mediated by the ATHB-2 HD-zip protein, a negative regulator of gene expression.
Development
126: 4235-4245[Abstract]
-
Tóth R, Hall A, Miller AJ, Nagy F, Kozma-Bognár L
(2001)
Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis.
Plant Physiol
127: 1607-1616[Abstract/Free Full Text]
-
van Tuinen A, Kerckhoffs LHJ, Nagatani A, Kendrick RE, Koorneef M
(1995)
Far-red light insensitive, phytochrome A-deficient mutants of tomato.
Mol Gen Genet
246: 133-141[CrossRef][ISI][Medline]
-
Whitelam GC, Devlin PF
(1997)
Roles for different phytochromes in Arabidopsis photomorphogenesis.
Plant Cell Environ
20: 752-758[CrossRef]
-
Whitelam GC, Harberd NP
(1994)
Action and function of phytochrome family members revealed through the study of mutant and transgenic plants.
Plant Cell Environ
17: 615-625[CrossRef]
-
Whitelam GC, Johnson E, Peng J, Carol P, Anderson MC, Cowl JS, Harberd NP
(1993)
Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light.
Plant Cell
5: 757-768[Abstract/Free Full Text]
-
Whitelam GC, Smith H
(1991)
Retention of phytochrome-mediated shade avoidance responses in phytochrome-deficient mutants of Arabidopsis, cucumber and tomato.
J Plant Physiol
139: 119-125
© 2003 American Society of Plant Biologists
This article has been cited by other articles:

|
 |

|
 |
 
A. C. Wollenberg, B. Strasser, P. D. Cerdan, and R. M. Amasino
Acceleration of Flowering during Shade Avoidance in Arabidopsis Alters the Balance between FLOWERING LOCUS C-Mediated Repression and Photoperiodic Induction of Flowering
Plant Physiology,
November 1, 2008;
148(3):
1681 - 1694.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
M. A. Beilstein, I. A. Al-Shehbaz, S. Mathews, and E. A. Kellogg
Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited
Am. J. Botany,
October 1, 2008;
95(10):
1307 - 1327.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
H.-J. Park, L. Ding, M. Dai, R. Lin, and H. Wang
Multisite Phosphorylation of Arabidopsis HFR1 by Casein Kinase II and a Plausible Role in Regulating Its Degradation Rate
J. Biol. Chem.,
August 22, 2008;
283(34):
23264 - 23273.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
D. L. Filiault, C. A. Wessinger, J. R. Dinneny, J. Lutes, J. O. Borevitz, D. Weigel, J. Chory, and J. N. Maloof
Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light
PNAS,
February 26, 2008;
105(8):
3157 - 3162.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
R.-C. Lin, H.-J. Park, and H.-Y. Wang
Role of Arabidopsis RAP2.4 in Regulating Light- and Ethylene-Mediated Developmental Processes and Drought Stress Tolerance
Mol Plant,
January 1, 2008;
1(1):
42 - 57.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
J. D. Mayfield, K. M. Folta, A.-L. Paul, and R. J. Ferl
The 14-3-3 Proteins {micro} and {upsilon} Influence Transition to Flowering and Early Phytochrome Response
Plant Physiology,
December 1, 2007;
145(4):
1692 - 1702.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
T. H. Kebrom and T. P. Brutnell
The molecular analysis of the shade avoidance syndrome in the grasses has begun
J. Exp. Bot.,
October 5, 2007;
(2007)
erm205v1.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
E. Kevei, E. Schafer, and F. Nagy
Light-regulated nucleo-cytoplasmic partitioning of phytochromes
J. Exp. Bot.,
September 27, 2007;
(2007)
erm145v1.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
E. Monte, B. Al-Sady, P. Leivar, and P. H. Quail
Out of the dark: how the PIFs are unmasking a dual temporal mechanism of phytochrome signalling
J. Exp. Bot.,
September 12, 2007;
(2007)
erm186v1.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
Y.-s. Su and J. C. Lagarias
Light-Independent Phytochrome Signaling Mediated by Dominant GAF Domain Tyrosine Mutants of Arabidopsis Phytochromes in Transgenic Plants
PLANT CELL,
July 1, 2007;
19(7):
2124 - 2139.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
A. Faigon-Soverna, F. G. Harmon, L. Storani, E. Karayekov, R. J. Staneloni, W. Gassmann, P. Mas, J. J. Casal, S. A. Kay, and M. J. Yanovsky
A Constitutive Shade-Avoidance Mutant Implicates TIR-NBS-LRR Proteins in Arabidopsis Photomorphogenic Development
PLANT CELL,
November 1, 2006;
18(11):
2919 - 2928.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
J. R. Bennett and S. Mathews
Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A
Am. J. Botany,
July 1, 2006;
93(7):
1039 - 1051.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
T. J. Emborg, J. M. Walker, B. Noh, and R. D. Vierstra
Multiple Heme Oxygenase Family Members Contribute to the Biosynthesis of the Phytochrome Chromophore in Arabidopsis
Plant Physiology,
March 1, 2006;
140(3):
856 - 868.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
G. Sessa, M. Carabelli, M. Sassi, A. Ciolfi, M. Possenti, F. Mittempergher, J. Becker, G. Morelli, and I. Ruberti
A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis
Genes & Dev.,
December 1, 2005;
19(23):
2811 - 2815.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
Y. Shen, S. Feng, L. Ma, R. Lin, L.-J. Qu, Z. Chen, H. Wang, and X. W. Deng
Arabidopsis FHY1 Protein Stability Is Regulated by Light via Phytochrome A and 26S Proteasome
Plant Physiology,
November 1, 2005;
139(3):
1234 - 1243.
[Abstract]
[Full Text]
[PDF]
|
 |
|

|
 |

|
 |
 
K. A. FRANKLIN and G. C. WHITELAM
Phytochromes and Shade-avoidance Responses in Plants
Ann. Bot.,
August 1, 2005;
96(2):
169 - 175.
[Abstract]
[Full Text]
[PDF]
|
 |
|
|