review article
Phytochromes and light signal perception by
plants—an emerging synthesis
Harry Smith
Department of Biology, University of Leicester, Leicester LE1 7RH, UK
For plants, the sensing of light in the environment is as important as vision is for animals. Fluctuations in light can be crucial
to competition and survival. One way plants sense light is through the phytochromes, a small family of diverse photochromic
protein photoreceptors whose origins have been traced to the photosynthetic prokaryotes. During their evolution, the
phytochromes have acquired sophisticated mechanisms to monitor light. Recent advances in understanding the molecular
mechanisms of phytochromes and their significance to evolutionary biology make possible an interim synthesis of this
rapidly advancing branch of photobiology.
T
he phytochromes are signal-transducing photoreceptors
that convert between inactive and active forms in
response to different wavelengths of light. This
conversion is used to synchronize plant development to
the exigencies of the light environment. Light signals
provide information of crucial ecological value at many stages in
development. Seed germination, seedling establishment, the proper
development of photosynthetic machinery, the architecture of the
vegetative plant, the timing of flowering, tuberization and bud
dormancy, the responses to neighbour competition, and the
allocation of resources to root, stem, leaf, reproductive or storage
structures are all potentially controlled by the perception of
environmental light signals by the phytochromes. We can now
begin to trace the biological significance of photoperception from
the molecular mechanisms to the life of plants in their natural
environment. Current research stretches from the photophysics of
the light sensor molecules to the population biology of plants in
the field. This article attempts an undoubtedly premature synthesis
of a research area that is advancing at remarkable speed.
Phytochromes as sensors of space and time
Light signal perception may be thought of as the means by which the
plant determines where it is in space and time. Although this sounds
anthropomorphic, it nevertheless describes the significance of the
perception of light signals by the phytochromes and other signaltransducing photoreceptors. The three classes of plant signal-transducing photoreceptors—phytochromes1, cryptochromes2 and phototropin3—have well characterized molecular details and functions.
Each group of photoreceptors operates both independently and in
concert with the others to regulate plant development.The ecophysiological functions of the phytochromes are determined by their photosensory characteristics, which in turn depend on photochemistry
(see Box 1). The striking characteristic of the phytochromes is their
reversible photochromism—the property of changing colour on
photon absorption and of reverting to the original form on the
absorption of another photon. The absorption maximum of the phytochrome ‘Pr’ form is close to that of the chlorophylls (red light), but
the ‘Pfr’ form absorbs at a longer wavelength (far-red light). In effect,
this means the phytochromes can be used as sensitive estimators of
the spectral changes that happen within plant communities when
daylight interacts with photosynthetic structures4. Daylight contains
roughly equal proportions of red and far-red light (red:far-red ≈ 1.2),
but within vegetation that ratio is lowered by the absorption of red
light by photosynthetic pigments. Changes in the red:far-red ratio
are much more reliable indicators of the proximity of potentially
competing neighbours than the concomitant reductions in the total
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amount of light penetrating the canopy. Within dense canopies, the
far-red radiation scattered or reflected from leaves is a unique and
unambiguous signal of the proximity of neighbours5, and hence of
community density6. Plants use the phytochromes as proximity sensors and modify their growth and development, constituting the
‘shade-avoidance syndrome ‘7. Upon sensing a low red:far-red ratio,
a shade-avoiding plant will exhibit enhanced elongation growth and,
if the stratagem is successful, will project its leaves into regions of
unattenuated daylight. If elongation is unsuccessful, other aspects of
the shade-avoidance syndrome cause accelerated flowering and early
production of seeds, enhancing the probability of survival. Shade
avoidance is a strategy employed by the majority of angiosperms,
ranging from small herbs to large trees, and is of major ecological
advantage. Phytochrome-mediated proximity sensing, in effect, provides the plant with positional information with respect to potentially competing neighbours.
Phytochromes also provide plants with temporal signals that
entrain the phases of the biological clock, and others that ensure crucial developmental steps are initiated at appropriate points in the life
cycle. Endogenous circadian rhythms synchronize development to
the changing seasons, as exemplified in the photoperiodic control of
flowering and dormancy. Even when employed as simple light detectors—such as in the stimulation of seed germination or the conversion of the etiolated seedling to photosynthetic competence—the
phytochromes may be thought of as timing agents. Germination of
the seed and maturation of the developing seedling, both dependent
upon limited stored reserves, are probably the most vulnerable stages
of the life cycle, and getting the timing right must be vital to longterm survival. In these processes, the phytochromes do not work
alone; the cryptochromes are often responsible for initiating germination and they have important roles in de-etiolation. One implication of this may be that getting the timing right is so crucial to
survival that reliance on one set of environmental light signals alone
is insufficient to guarantee success under all conditions.
Evolution of phytochrome function
The phytochrome genes encode a small family of photoreceptors. In
the model plant Arabidopsis thaliana, there are five members—phytochrome A (phyA) to phytochrome E (phyE)8. (Nomenclature
usage differs in some species.) Sequence comparisons from a wide
range of angiosperms indicate that the maximum family size is likely
to be five, although monocotyledonous plants may not contain phyE
homologues9. Phylogenetic analyses of higher plant PHY sequences
point to four major gene duplication events in the evolution of the
PHY genes10. The first, occurring about the time of the origin of seed
plants, generated the PHYA/C and PHYB/D/E lines. Two later dupli-
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Box 1
Sensors of environmental light signals
Phytochromes are photochromic photoreceptors
The central hypothesis of phytochrome action, proposed almost 50
years ago from pioneering investigations by S. Hendricks, H.
Borthwick and colleagues, is that the photoreceptors exist in two,
photoconvertible forms, Pr and Pfr. Pr is biologically inactive and
upon absorption of red photons is converted to Pfr, the active form.
Pfr is converted back to Pr by far-red photons. Biological action
stems from Pfr.
The photoconversions involve a number of intermediate forms in
both directions, and the establishment of an equilibrium between Pr
and Pfr takes several minutes even at daylight irradiance levels. The
absorption spectra of the phytochromes peak at about 665 nm and
730 nm. The absorption bands overlap, so radiation below about
700 nm activates photoconversion of both Pr and Pfr. Thus, in
daylight for example, a photoequlibrium of about 60% Pfr/P (where
P = total phytochrome) is established—in canopy shade or crowded
communities, the photoequilibrium can be as low as Pfr/P = 0.1.
This is the basis of the shade-avoidance syndrome.
Phytochromobilin
H
N
H
N
O
S
N
H
N
O
COOH COOH
Cys
Apoprotein
Pr
Absorption Spectra
Pfr
400
500
600
700 nm
Daylight
Spectra
Open
cations, at about the time of the origin of the flowering plants, separated PHYA from PHYC and PHYB/D from PHYE. PHYB and PHYD
diverged much more recently. Evolution within the phytochrome
family appears to be faster than other plant nuclear genes11.
These evolutionary pathways created a family of proteins that
detect identical environmental signals but employ those signals in
different functions. PHY-like genes occur not only in all green plants,
including gymnosperms, ferns, mosses and algae, but also in
cyanobacteria12-14 and even in certain other bacteria15,16. The chromophore-bearing domain is conserved between plants and bacteria,
and in most cases the bacterial chromophore is a bilin, as it is in
plants. In the purple photosynthetic bacterium Rhodospirillum centenum, the bilin attachment site is unoccupied, but the domain is
linked to a photoactive yellow protein (PYP) domain carrying phydroxycinnamic acid as a chromophore15. In the non-photosynthetic bacteria Deinococcus radiodurans and Pseudomonas aeruginosa, the
chromophore is a bilin, but its attachment is through a Schiff’s base
to a histidine, rather than a thio-ether linkage to the cysteine attachment site present in plant phytochromes16. Thus, although the chromophore is not always a bilin or attached to the same amino-acid
residue, the conserved region seems to be involved in photoperception in all organisms investigated. This might provide a clue to the
evolutionary origin of the conserved chromophore-bearing domain
of the phytochromes.
In the mosses and ferns, the phytochromes seem to be particularly
involved in phototropism17, a function mediated exclusively by the
blue-light absorbing phototropin in the angiosperms3. Indeed, in the
fern Adiantum, a gene has been characterized that encodes both a
typical phytochrome and a protein with sequence similarity to NPH1
(the Arabidopsis phototropin)18. The evolution of a chimaeric photoreceptor bearing properties of both red/far-red and blue light
absorption poses the question whether such molecules exist and
function elsewhere. Another chimaeric phytochrome gene has been
identified in the moss Ceratodon19, encoding a protein kinase carboxy-terminal segment, but whether this is functional has not been
determined.
In the angiosperms, the phytochromes have acquired new functions and fine-tuned existing functions during evolution (Box 2).
The individual family members have both distinct and overlapping
physiological functions20, and even antagonistic interactions have
been reported21. It is important to realize that phytochromes operate
quantitatively to limit the rates of ongoing processes, rather than
qualitatively to select between potential developmental fates. In other
words, phytochromes are more like speed limits than signposts on
the highways of development.
Phytochrome mechanisms
Canopy
Phytochrome absorption spectra drawn from data supplied by
J. C. Lagarias.
Chromophore is a linear tetrapyrrole
The chromophore is an open-chain linear tetrapyrrole—known as
phytochromobilin—and is closely related to phycocyanobilin, the
chromophore of the abundant algal pigment C-phycocyanin. In
higher plant phytochromes, the chromophore is covalently attached
to the protein through a thio-ether link at a cysteine positioned at
amino-acid residue 374 (numbering for phyA). Assembly of
apoproteins and chromophore occurs spontaneously, presumably
involving inherent chromophore lyase activity in the phytochrome
apoproteins. This property has allowed the construction of
recombinant phytochrome adducts with either phytochromobilin or
phycocyanobilin—both are spectrally photoreversible and active
when transgenically expressed in planta.
586
Most investigators propose that the phytochromes act through the
selective regulation of gene expression. The expression of several
genes, largely those encoding enzymes and other components of the
photosynthetic machinery, is regulated by light, often by phytochrome22,23. On the other hand, some phytochrome-mediated
responses are best explained by assuming rapid alterations in interor intra-cellular ion balances24. Some growth responses also occur
quite rapidly (within minutes25,26), posing the question whether
transduction chains involving the regulation of nuclear gene expression would be sufficiently quick. In certain algae, mosses and ferns, at
least part of the cellular phytochrome is cytoplasmic and dichroically
organized with respect to either the cell membrane or the cytoskeleton27. These phenomena imply a cytoplasmic growth-homeostasis
mechanism in which the photoreceptor continuously monitors the
light environment and mediates rapid changes in ionic concentrations within cell compartments that modulate extension growth.
Therefore, individual phytochromes may have at least two, separate
mechanisms of action: one that results in selective expression of target genes and another that rapidly and reversibly operates to modulate cellular ionic balances.
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Box 2
Molecular, physiological and ecological functions
1
Amino acid sequence
C-374
Chromophore
1210
COOH
NH2
Structural domains
1
Amino terminal
673 674
Carboxy terminal
1210
Chromophore lyase
Spectral integrity
Pr–Pfr conformational
changes
Dimerization
Sequence homology with
Synechocystis PHY
Photosensory specificity
Regulatory activity
Redrawn and simplified with permission from ref. 69.
Physiological and ecological functions
It is convenient to think of the phytochromes as being ‘singleinput/multiple-output’ sensory systems, in which a common signal
evokes a range of biological responses. Phytochromes are capable of
regulating almost all phases of plant development, but the control is
conditional or facultative, rather than obligatory.
Germination. Many small seeds with low levels of stored reserves
require light signals for germination, whereas most larger seeds do
not. For some buried seeds, the sensitivity is spectacular, sometimes
requiring only milliseconds of light exposure for full response.
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phyB
Ge
phyA
rmination
E stablishment
F lowering
?
chitecture
Ar
The phytochromes are chromoproteins with a relative molecular mass
of about 120,000–126,000. They are encoded by five PHY genes
(named PHYA–PHYE) in the model crucifer Arabidopsis thaliana
(family size and nomenclature may vary in other species). Isolation of
mis-sense mutations and transgenic expression of mutant
phytochromes enabled certain molecular functions to be attributed to
‘domains’. Thus, the molecule possesses two structural domains: a
globular N-terminal half and a more linear C-terminal half.
Chromophore lyase and spectral integrity are associated with the
chromophore-bearing N-terminal domain. The phytochromes are
dimers in solution, with putative dimerization sites located within the
C-terminal segment. Evidence from photophysical analysis indicates
that conversion from Pr to Pfr causes an ‘opening’ of the protein
conformation in relation to the chromophore, perhaps facilitating the
interaction of Pfr with its primary reaction partners. Transgenic
expression of constructs with the N- and C-terminal domains
exchanged between phyA and phyB show the photosensory
specificity is in the N-terminal half, and the regulatory specificity is in
the C-terminal half. Alignment with gene sequences from
cyanobacteria reveals common ancestry and provokes interesting
questions on the original adaptive value of the phytochromes.
phyD
phyE
?
Seedling establishment. This is the set of processes through which
a germinated seedling becomes photoautotrophic. Phytochromes cooperate with cryptochromes to regulate de-etiolation, leaf expansion
and chloroplast maturation.
Architecture of the mature plant. The size and disposition of
internodes and leaves, the balance between main stem and lateral
branches, the angles of petioles and leaf laminae are acutely sensitive
to the radiation environment.
Induction of flowering and dormancy. The photoperiodic
perception of day length, involving interaction with the biological
clock, is necessary (in some plants) for the induction of flowering and
bud dormancy.
Towards a life-history of phytochrome functions
Mutant studies70 and the use of transgenic plants expressing
individual phytochrome genes71 mean that we can reliably allocate
physiological and ecological function to four of the five phytochromes,
at least for Arabidopsis thaliana. Mutants null for phytochromes A, B,
D and E have been isolated and their physiological responses
extensively characterized. The overall picture is that phyB has a role at
all stages of the life cycle, whereas phyA, phyD and phyE exert their
principal functions at selected stages.
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Phytochrome action requires two partial processes at the level of
the photoreceptor molecule: perception of the light signal and its
transduction to a biochemical signal. Domain-swapping experiments
in which the amino-terminal and the carboxy-terminal halves of
phyA and phyB were exchanged verify the molecular specificity of
these sensory and regulatory activities with the photosensory functions of phyA and phyB present in the respective N-terminal half of
the molecule, and a common regulatory site present in the C-terminal
portion28. Thus, phytochromes exhibit dual molecular functions: a
sensory function responsible for detecting relevant light signals, and a
regulatory function in which the perceived information is transferred
to downstream transduction pathways. Interestingly, the sensory and
regulatory domains appear to be evolving at different rates, with the
C-terminal domain evolving at least twice as fast as the N-terminal
domain11.
Current ideas on the primary mechanism of phytochrome regulation of gene expression centre on two contrasting, but not necessarily
incompatible, hypotheses (Fig. 1). In one, phytochromes are considered to be kinases that act on multiple substrates thereby regulating
the expression of genes differentially. The other is that phytochromes
have one or more specific reaction partners that direct signal transduction towards the selective control of gene expression.
Phytochromes as kinases. The possibility that plant phytochromes
are kinases has long been controversial29. In the prokaryotes, the PHY
genes encode the sensory halves of two-component response systems,
and significant sequence similarity exists between the C-terminal
domains of eukaryotic phytochromes and bacterial response elements30. The bacteriophytochrome (named DrBphP) in D. radiodurans functions as a light-regulated histidine kinase, controlling the
synthesis of the carotenoid pigment deinoxanthin, which apparently
serves to protect the organism from bright light16. Immediately downstream of BphP is a coding region for a response regulator protein
(BphR), which acts as the phosphate acceptor for the kinase activity
of DrBphP. The closest sequence relative of BphR is the corresponding response regulator component of the Synechocistis phytochrome
(Rcp1), the proposed phosphate acceptor for the cyanobacterial phytochrome, Cph1 (ref. 14). The kinase activity of plant phytochromes
was confirmed by the construction of recombinant phytochromes
using PHY genes from Arabidopsis and the green alga Mougeotia.
After assembly with chromophore, the holoproteins possessed serine/threonine kinase activity, rather than the expected histidine
kinase activity31. The recombinant phytochromes autophosphorylated and, in a clinching experiment, transferred phosphate to recombinant Rcp1.
Support for the phytochrome-as-kinase concept comes from the
detection, by yeast two-hybrid screening, of a phytochrome kinase
substrate (PKS1), a cytosolic protein that accepts a phosphate from
phyA32. Phosphorylation is on a serine, and to a lower extent on a
threonine residue and is regulated by light, being about twofold higher with Pfr than Pr. Phosphorylation also occurs in vivo in a phytochrome-dependent manner. Transgenic expression shows that
PKS1 is a negative regulator of photomorphogenesis specific to phyB.
Other possible substrates of phytochrome kinase activity are the cryptochrome photoreceptors33. The situation is even more complex as
phyA also interacts with a nucleoside diphosphate kinase (NDPK2),
found in both the cytoplasm and the nucleus34. The kinase activity of
NDPK2 is increased about twofold when bound to recombinant
phyA in the Pfr form, but an in vitro activation of NDPK1 by red or
far-red radiation has not been reported. The regulation of gene
expression could, in principle, emanate from the kinase activity of
phytochrome per se, and/or activation of NDPK1.
Primary interaction partners. Yeast two-hybrid screens have revealed
several potential primary reaction partners for phyA and phyB.
Whether all of these will have important roles is in the balance, but
the most conclusive evidence yet is for PIF3 (phytochrome interacting
factor 3; ref. 35). PIF3 was found in a two-hybrid assay using the Cterminal portion of phyA as the bait. It interacts equally with the C
588
terminus of phyA and phyB, but preferentially with the intact phyB
protein. Interaction with intact phyB is light dependent36. PIF3 is a
basic helix—loop—helix (bHLH) protein with a PAS motif and
locates to the nucleus in transfection experiments. PIF3 binds poorly
to mis-sense phyB molecules mutated in the putative C-terminal
regulatory region, and furthermore, transgenic expression of sense
and anti-sense constructs of PIF3 perturbs the response to light.
Serendipitously, PIF3 was simultaneously identified as a transduction chain component by a screen for gain-of-function mutants
under red radiation treatment37. These data strongly support the
hypothesis that PIF3 is a functional primary reaction partner for
phyB.
Recent data on the phyB/PIF3 interaction point to a remarkable
shortcut mechanism in which light signals are targeted directly
through phyB to PIF3 bound to promoter elements of some lightregulated genes38. Promoter analysis has identified a number of cisacting light-responsive elements (LREs) and some DNA-binding
Sequestration?
Cytoplasmic
action
Pr
Red
Pfr
Far-red
PKS1
PKS1
Kinase
cascade
PKS1
Kinase
substrate
NDPK1
Inactive
Pr
Red
Active
Pfr
Far-red
Cytoplasm
Nuclear translocation
Pr
Red
Far-red
Pfr
Nucleus
NDPK1
Kinase
cascade
PIF3
bHLH
transcription
factor
PIF3
Phytochrome-regulated genes
Figure 1 Diagram of phytochrome action. Phytochromes undergo photoconversion
from the biologically inactive form (Pr) to the active form (Pfr). Pr and Pfr are shown as
dimers in the cell. The Pr–Pfr conversions are initiated by photon absorption in the
chromophore leading to steric changes, causing the holoprotein to `open up' and
facilitating interaction with putative reaction partners. The diagram shows the three
major theories for the subsequent actions of the phytochromes, although Pfr may
regulate growth and development by other processes. Pink area: both Pr and Pfr
interact with PKS1, the phytochrome kinase substrate, in the cytosol. This may be the
first step in a kinase cascade (orange area) culminating in action within the
cytoplasm. Alternatively, interaction with PKS1 may result in sequestration of
phytochrome in the cytosol, preventing translocation to the nucleus. Yellow area: Pfr
interacts with NDPK1, a nucleoside diphosphate kinase, which is located both in the
cytoplasm and the nucleus. Again, this interaction may initiate a kinase cascade
(orange) leading to ultimate action within the cytoplasm and/or nucleus. Green area:
Pfr translocates to the nucleus and Pr is translocated back to the cytoplasm. The
weights of the arrow emphasize the differential rates of import and export. Within the
nucleus, Pfr binds with PIF3 (phytochrome interacting factor 3) which is located
exclusively within the nucleus. PIF3 is a basic helix–loop–helix transcription factor
that binds to the promoters of selected light-regulated genes in combination with Pfr
and initiates or enhances transcription.
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proteins that may interact with LREs and thus regulate transcription39. One of these promoter elements, a G-box motif, is the core
PIF3 target element38. So, PIF3 associates with elements characteristically found in the promoters of certain genes whose expression is regulated by phytochrome. Moreover, phyB in the Pfr form complexes
with PIF3 bound to its DNA target site. PIF3 anti-sense plants displayed reduced levels of phytochrome-regulated gene expression for
some, but not all, light-regulated genes. These data provide a picture
of the direct transfer of light signals to the promoters of a subset of
light-regulated genes.
Light-regulated nuclear translocation
The phytochrome apoproteins are synthesized within the cytosol and
assemble autocatalytically with the plastid-derived chromophore. For
years phytochromes were considered to be entirely cytosolic, but now
there is strong evidence for photoactivated nuclear translocation of
phytochromes40. Both phyA and phyB tagged with green fluorescent
protein (GFP) show light-activated import into the nuclei of tobacco41
and Arabidopsis42 cells. Import of phyB occurs only in the Pfr form and
is slow, requiring several hours for full mobilization. Phytochrome A,
either as PfrA, or as PrA that has been photoconverted through PfrA and
back again, moves more rapidly (about 15min). The photobiological
criteria are satisfied as phyB transport is activated by red radiation and
inhibited by far-red radiation, whereas the transport of phyA is maximal under continuous far-red radiation. These facts provide a framework for understanding the phytochrome regulation of gene expression through the translocation of Pfr into the nucleus, interaction
with primary reaction partners (such as PIF3) and direct regulation of
the promoters of light-regulated genes. Alternatively, nuclear localization places Pfr in the appropriate cellular compartment for its activity
as a protein kinase to operate on factors regulating transcription.
It is worth considering whether all the correct questions are being
asked. The data on nuclear transport and gene expression described
come from experiments on dark-grown seedlings given light treatments. Seedlings treated in this way are induced to undergo a one-off
transition, which will not be repeated, and which under natural conditions prepares the plant for life in a photic environment. The
dynamics of nuclear translocation may only be mechanistically significant during this initial transition. Thereafter, except for newly
synthesized molecules, the phytochrome may remain principally
within the nucleus during daylight hours, where interaction with
light-responsive genes can occur rapidly. Superimposed on this there
will be daily gross movements of phytochrome into and out of the
nucleus conditioned by light and dark periods, and indeed it has
already been reported that nuclear translocation of phyB is under circadian control43. Such control may position phyB in the nucleus,
where it can rapidly control development in response to signals from
neighbouring plants, and so provide the sensitivity to environmental
fluctuations that is characteristic of shade avoidance in plant communities.
Phenotypic plasticity and evolutionary significance
Phytochrome-mediated shade avoidance is a model for the functional significance of physiological adaptation to environmental signals,
giving ecologists and evolutionary biologists a handle on the evolution of phenotypic plasticity. Phenotypic plasticity—the expression
of variability in the phenotype of individuals of identical genotype—
and its fitness consequences are crucial concerns for evolutionary
biologists44-46. There is controversy regarding the genetic mechanisms for the evolution of plasticity47,48, and clear-cut experimental
approaches are necessary to examine whether plasticity is adaptive, to
what extent it is constrained by trade-offs and linkage restrictions,
and how plasticity evolves. Phytochrome-mediated shade avoidance
is a successful example of two-way exchange between the reductionism of physiological and molecular analysis and the holistic approach
of evolutionary biology49.
The unique and unambiguous environmental signal of far-red
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radiation scattered from neighbouring vegetation evokes a range of
plastic outputs—enhanced elongation, strengthened apical dominance, elevated leaf angle, altered resource allocation and accelerated
flowering—that are assumed to allow adaptation to competition
from those neighbours. Shade avoidance therefore represents a classic
single-input, multiple-output system. The range of plasticity is huge,
and the assumption that such plasticity is adaptive is understandable,
but it has rarely been explicitly tested. Indeed it is difficult to test
because the plasticity itself prevents the expression of inappropriate
phenotypes in any given environment50. Though crude, some
approaches are possible, such as using mutant51,52 or transgenic53
plants disabled in signal perception, and these have supported the
adaptive plasticity hypothesis. Plasticity observed as variation in
physiological output must result from the selective expression of
genetic variation within these transduction pathways54. To extend the
earlier metaphor, as an individual plant responds to fluctuating environmental light signals, the speed limits on the branched developmental highways must be variously imposed or relieved to provide
appropriate responses.
What is not so obvious is that micro-evolution may operate differentially on the pathways emanating from the same signal. In a study
of more than 100 Arabidopsis ecotypes (accessions) with wide variations in response to reflected far-red light, there was no correlation
between hypocotyl elongation and accelerated flowering. That is,
ecotypes that responded strongly in elongation did not necessarily
respond strongly in floral acceleration, and vice versa (J. Botto and
H.S., unpublished data). When searching for the molecular basis of
such adaptive diversity within a single species, several targets of interest emerge. First, molecular variation in the photoreceptor genes may
lead to differential transduction of reflection signals. Second, downstream components specific to photomorphogenesis may vary
between ecotypes. Third, regulatory genes located in the basic
ground plan of development, but whose activity comes under the
influence of the phytochromes, may have been under selection pressure that resulted in differential output from the common signal. In
this regard, regulatory genes (that is, loci that control the expression
of other genes) are increasingly interesting to evolutionary biologists.
Such genes are expected to be important in the genetic architecture of
development, and functional polymorphism among such genes within species is likely to contribute significantly to micro-evolution55,56.
Regulatory genes encode sequence-specific DNA-binding transcriptional activators or cell—cell signalling molecules57, and some evolve
more rapidly than structural genes58,59. To search for the basis of
rapidly evolving differences in phenotypic plasticity to the light environment, the best way may be to concentrate on potential regulatory
genes specific to phytochrome-mediated signal transduction.
The PHY genes are evolving rapidly11, but they do not fall into the
strict definition of regulatory genes, even though their gene products
do regulate the expression of other genes through transcription factors such as PIF3. Molecular polymorphism of phytochromes within
species probably exists, and may result in different responsivities to
light signals in different genotypes. However, this would not account
for situations where a single genotype has different responsivities to a
single signal. Downstream components fall more readily into the regulatory gene category than the sensor genes themselves, as some, at
least, operate through the regulation of expression of other genes.
Therefore important information may be gained by a search for functional sequence diversity in putative regulatory genes within the phytochrome transduction pathways or for regulatory genes whose
expression varies specifically in relation to phytochrome-mediated
signal transduction.
The level of quantitative complexity is daunting, with many large
gene families potentially displaying high within-species variation in
expression, temporally and spatially, as part of the developmental
changes elicited by the reflection signal. Genomic and proteomic
technology will allow the analysis of molecular variation, but to identify the crucial elements that provide adaptive advantage, genetic
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analysis combined with ecological assessment of fitness attributes will
be necessary. Recently, great improvements have been made in the
application of quantitative genetic analysis to problems of plant
developmental physiology60 and in the exploitation of natural genetic
variation61. Important quantitative trait loci (QTL) are being rapidly
identified for, inter alia, seed size62, flowering time63 and circadian
rhythms64, and, coupled with molecular marker technology, will in
principle allow the characterization of the genes themselves. Application of these approaches to phytochrome-mediated phenotypic plasticity may yield the most important information. Having located
QTL specific for phytochrome-mediated responses of ecological significance, studies of QTL nucleotide diversity and its relationship to
phenotype should provide a basis for a comprehensive understanding of the genetic architecture of photomorphogenesis.
Prospect and speculation
This field is moving so rapidly that this review will already be less than
current when published. We are likely to see imminent advances in the
understanding of the molecular and cellular mechanisms of the
photoregulation of gene expression, although the equally important
mechanisms that modulate cell growth rates have not generated a similar intensity of interest. The application of genetic analysis to the evolutionary and ecological questions raised here is likely to be productive in the medium term, although it will initially be restricted to
model plants such as Arabidopsis. There is no doubt that exploitation
of photomorphogenesis to improve crop plant growth will generate
many new approaches. Already, manipulation of the expression of
phyA has led to major changes in plant architecture in the field, with
predictions of substantial increases in harvestable yield per plant65.
There are dozens of laboratories world-wide working on the development of genetically modified crop plants using the phytochrome
genes. Other applications include those that modify plant responses
to photoperiod, which may be of great benefit for certain crops 66.
To end with a speculation, it seems particularly fortuitous that the
phyB/D/E branch of the phytochrome family evolved from the
phyC/A branch coincidentally with the evolution of the seed plants,
and that its further subdivision coincided with, or preceded, the evolution of the flowering plants10. Phytochromes B, D and E act singly,
collectively, and to some extent redundantly, to mediate proximity
perception and shade avoidance. Gene duplication and function
acquisition within this phytochrome subfamily has reached a stage
where the perception of the relative proportions of red and far-red
radiation within plant communities provides an exceptionally sensitive response to potential neighbour competition. This capacity is
most highly expressed, and most widespread, in the angiosperms.
Ferns and mosses generally react to density by shade tolerance
reactions, and of non-angiosperm plants, only the gymnosperms
seem capable of true shade avoidance, and that is limited in extent
and distribution. Perhaps the evolution of the ability to detect light
signals reflected from neighbours was crucial to the advance of the
angiosperms to their present dominant status within the plant
kingdom—without phytochrome B, would we still be surrounded by
a carboniferous flora? This notion is far-fetched and tongue-incheek, but it could be supported by studies using gene duplication
analysis within the phytochromes as an approach toward rooting the
angiosperms67,68. Phytochromes originated in prokaryotic progenitors of present-day plants, presumably acting as simple light
sensors. Their unique capacity for photochromic conversion between
two molecular forms may have been functionally insignificant
within the early prokaryotes, but this property has been selected
and refined through the evolution of the land plants into a multicomponent sensor system of equal global significance to that of
vision in animals.
■
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Acknowledgements
I thank the following for information and comment: J. Chory, M. Furuya, J. C. Lagarias, P. H. Quail,
J. Schmitt, P.-S. Song. The author’s research on shade avoidance was supported by the UK Natural
Environment Research Council, the UK Biotechnology and Biological Sciences Research Council and the
Council of the European Commission. The literature survey for this article was completed on 31 March 2000.
Correspondence should be addressed to H.S. (e-mail: has@le.ac.uk).
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