Right place, right time

Abstract

Recent advances in our understanding of the roles of photoreceptors in light-dependent regulation of plant growth and development have been rapid and significant. Developments have been reported for numerous plant photoreceptor signaling pathways, yet researchers have made the most progress in increasing our comprehension of the roles of phytochrome family members, as well as the intracellular roles of phytochromes and phytochrome-interacting proteins in light-dependent signaling. An understudied, but vitally important, area of phytochrome biology centers on the roles phytochromes play in intercellular and interorgan signaling at the molecular level that results in the coordination of growth responses between distinct tissues and organs. This frontier of research into the spatiotemporal roles of phytochromes, and more generally plant photoreceptors, which is only beginning to be investigated and understood at the molecular genetic level, has a rich history of physiological data.

Introduction

A number of recent perspective and review articles have discussed the understudied area of spatiotemporal light signaling.^1–3 The authors of these reviews have recognized some of the documented physiological analyses of tissue- and organ-specific light responses; nevertheless, they point to a dearth of studies on the molecular basis of these subsets of light responses. Here, I provide a broad review of past studies that sought to increase our understanding of tissue- and organ-specific photoregulation in plants and to resolve spatiotemporal light responses through the use of localized irradiation and light activation of dissected tissues. Furthermore, I assess recent studies that have begun to explore the molecular bases of some of these spatiotemporal light responses.

Light Sensing and Photomorphogenesis in Plants

The ability of higher plants to adapt their growth and development to changes in the ambient light environment has significant effects on plant productivity and survival. Many light-regulated growth and developmental responses have been observed in plants, including seed germination, acquisition of photosynthetic capacity, anthocyanin accumulation, leaf development, hypocotyl and internode elongation, flowering and senescence (reviewed in refs. ^4–6). Plants possess multiple photomorphogenic photoreceptors that enable them to monitor and exhibit developmental plasticity in response to ambient light conditions, including UV-B, blue/UV-A (B/UV-A) and red/far-red (R/FR) light (reviewed in ref. 7). The most widely studied of these photoreceptors are the phytochromes, a family of photoreversible biliproteins maximally absorbing in the R and FR regions of the visible spectrum (reviewed in refs. ⁶ and ⁸).

Phytochrome synthesis and function in planta.

Functional phytochromes (phy) consist of an apoprotein with a covalently attached light-absorbing, linear tetrapyrrole chromophore (bilin). All higher plant species investigated have numerous phytochrome species whose apoproteins are encoded by a nuclear gene family. Five phytochrome apoprotein genes have been isolated from Arabidopsis and designated PHYA-PHYE.^9–11 Each higher plant phytochrome utilizes a single chromophore, phytochromobilin, for light absorption and its photoregulatory function.¹² Results from recent studies demonstrated that multiple genes encode key enzymes of the plastid-localized chromophore biosynthetic pathway in Arabidopsis.^13–15 The production of photoactive holophytochrome thus depends upon the convergence of two physically separated biosynthetic pathways.

The biological functions of phytochromes have been investigated using plants that harbor mutations in genes encoding for phytochrome apoproteins or chromophore biosynthetic enzymes. Apoprotein mutants have been essential in investigations of the discrete photo-regulatory activities of individual phytochrome family members and their distinct, as well as redundant, regulatory roles in photomorphogenesis (reviewed in refs. ^16–18). Studies of chromophore-deficient mutants have yielded insight into the global photosensory roles of phytochromes in plant development. Chromophore-deficient plants exhibit defects in light-mediated growth and development both as seedlings and adults, corresponding to a universal deficiency in phytochrome regulatory activities (reviewed in ref. 19).

Phytochrome family members are subdivided into light-labile phytochrome phyA and light stable phytochromes phyB–phyE (reviewed in ref. 20). PhyA is primarily responsible for sensing FR light,^21–23 although recently it has been shown that phyA operates as a red light (RL) sensor under specific conditions.²⁴ Together, phyA and phyB control plant growth and developmental responses to RL, with the other phytochromes having some distinct, but largely redundant, functions in RL (reviewed in refs. ^25–27). Specifically, phyB is involved in de-etiolation in response to RL exposure and in delay of flowering.²⁸ PhyC is involved in RL-dependent regulation of leaf development and it modulates phyB-mediated inhibition of hypocotyl elongation in response to RL.^29,30 PhyC also has a role in daylength perception,³⁰ and a significant role in blue light (BL) sensing.²⁹ PhyD is involved in the shade avoidance response.^31,32 PhyE regulates FR-dependent seed germination,³³ as well as internode elongation and flowering responses characteristic of shade avoidance.³⁴

Molecular bases of phytochrome functions.

Past studies in several laboratories have contributed a great deal to our understanding of the global biological functions of phytochrome family members described above and more recently to elucidating the intracellular signaling mechanisms of phytochromes. At the intracellular level, phytochromes in both shoots and roots move from the cytosol into the nucleus, where they interact with transcription factors to regulate gene expression.^20,35–38 This nuclear translocation of phytochromes occurs in a light-dependent fashion, at least for phyA and phyB.^36,37,39 The remaining phytochrome family members—phyC, phyD and phyE—appear to be largely constitutively localized in the nucleus, though their localization in nuclear speckles is impacted by light.^37,39 The nuclear translocation of phyA has been shown to be regulated by two phytochrome-interacting proteins, FHY1 and FHL, whereas the translocation of phyB appears to result from light-dependent intramolecular structural changes (reviewed in ref. 27). Light-dependent nuclear translocation of phytochromes is important for intracellular phytochrome signaling and regulation of downstream responses.

Phytochromes influence the stability of some nuclear-localized, phytochrome-interacting factors (PIFs) in response to light.^40,41 Recent results demonstrated that PIF1, PIF3, PIF4 and PIF5 are phosphorylated and subsequently degraded via the ubiquitin/ proteasome-dependent pathway after interacting with photoactivated phytochromes.^41–44 As PIFs are transcriptional regulators (reviewed in ref. 3), control of their turnover likely results in light-dependent changes in gene expression and subsequently the promotion of photomorphogenesis. However, it has also been shown that some PIFs may act through regulating the abundance of phytochromes.^45,46 For example, PIF3, PIF4 and PIF7 appear to act redundantly to repress accumulation of phyB.⁴⁶ In addition, some phytochrome responses are modulated directly by the phosphorylation state of phytochromes, which is regulated by their intrinsic kinase activity, as well as the activity of kinases and phosphatases in trans.^47–51

Time and place in light-dependent regulation of plant growth and development.

In addition to being localized in different subcellular compartments under defined conditions, recent results demonstrated that flavoprotein cryptochromes and biliprotein phytochromes have different regulatory roles in distinct subcellular compartments.^52,53 Both phyA⁵² and cry1⁵³ exhibit distinct nuclear and cytoplasmic functions. Nuclear phyA regulates hypocotyl elongation, cotyledon opening and germination, whereas cytoplasmic phyA apparently mediates BL-dependent inhibition of hypocotyl elongation, BL-dependent negative gravitropism and the RL enhancement of phototropism.⁵² For cry1, nuclear localization of the photoreceptor is required for BL-dependent inhibition of hypocotyl and petiole elongation.⁵³ Cytoplasmic cry1 has opposing effects to nuclear cry1 in its impact on primary root growth and cotyledon expansion, with cytoplasmic cry1 promoting these responses and nuclear cry1 inhibiting them.⁵³

Phytochromes and cryptochromes also accumulate to different levels, in distinct tissues and in developmentally determined patterns for individual isoforms.^54–60 Although there is certainly overlap in the patterns of accumulation of the five phytochrome family members, the distinct patterns of accumulation may be related to defined responses of different tissues and organs to light. Notably, recent reports also demonstrated that light results in distinct patterns of gene expression changes in different plant tissue or organ types, and at different development stages,^61–63 likely resulting in tissue- and organ-specific light responses in plants. Despite the progress that has been made in understanding the phytochrome signaling network, we lack definitive molecular evidence about sub-organismal sites of phytochrome photoperception and intercellular and interorgan phytochrome signaling, which govern tissue- and organ-specific phytochrome responses in planta.^1–3

Spatiotemporal-specific Photoreceptor Responses

Physiological evidence for spatiotemporal phytochrome responses.

To investigate the cell- and tissue-specific roles of phytochromes, a number of early physiological studies utilized detached plant parts or microbeam irradiation to photoactivate phytochromes in discrete plant tissues.^64–75 Such experiments were designed to induce phytochrome activity in a localized region of a plant and to assay for particular phytochrome-mediated responses at local or discrete sites in the plant. These studies allowed researchers to test the hypothesis that tissue- and organ-specific pools of phytochromes control distinct aspects of light-dependent growth and development and mediate both cell-autonomous and cell non-autonomous responses in plants.

A number of tissue- or spatial-specific phytochrome responses were identified through light-dependent physiological experiments. For example, detection of FR by internode-localized phytochromes is responsible for inducing stem elongation in response to neighbor detection in some plants.^76,77 Also, phytochromes localized in the epicotyl regulate FR-dependent epicotyl elongation in cowpea.⁷⁸ Similarly, phytochrome activity is correlated with cell elongation and reorganization of microtubules in epidermal cells in the maize coleoptile.⁷⁹ In the distinct site of apical meristems, phytochromes are involved in the regulation of calcium and pH patterns during photoperiodic induction of flowering in Chenopodium species.⁸⁰

Results from experiments with detached tomato fruits demonstrated that fruit-localized phytochromes regulate the induction of carotenoid synthesis in response to light.^73,75,81,82 Some of these fruit-localized responses are also tissue-specific, as light induces accumulation of particular pigments in the cuticle.⁷³ This spatial-specific regulation of tomato fruit pigmentation occurs, at least partly, through regulation of phytoene synthase activity by phytochrome.⁸³

Phytochromes, apparently located in the roots themselves, regulate root elongation and gravitropism in A. thaliana in response to RL.⁸⁴ Notably, root-localized phytochromes appear to have a role in regulating root growth in response to light, as well as in darkness.⁸⁴ These results suggest a role for the red-light absorbing form of phytochrome Pr, which is generally thought of as biologically inactive, in root growth and development.⁸⁴ Phytochromes also regulate root hair formation in A. thaliana,⁸⁵ as well as light-dependent root phototropism.^86–88

Spatial-specific responses for other photoreceptors.

In addition to phytochromes, other photoreceptors have been shown to exhibit tissue-specific light responses. The blue-light receptor cryptochrome 2 (cry2) operates in vascular bundles to regulate flowering in response to BL.⁸⁹ This tissue-specific response results in a cell-autonomous increase in expression of downstream flowering regulator gene FT.⁸⁹

BL has been shown to have the greatest impact on phototropic curvature in coleoptile tips in monocots and below the hypocotyl hook in dicots (reviewed in ref. 90). Notably, recent immunochemical studies demonstrated that the BL receptor phototropin accumulates to higher levels in coleoptilar tissue in monocots and in tissue below the apical hook in dicots corresponding to tissues that are most sensitive to BL in phototropic curvature assays.⁹¹ Also, BL is perceived in the root cap resulting in phototropic curvature of the root in the elongation zone in maize seedlings.⁹²

Intercellular Phytochrome Signaling

Although tissue-specific responses have been noted for a number of photoreceptors, the occurrence of intercellular and interorgan photoreceptor-dependent signaling is best established for phytochromes. These noted non-cell-autonomous responses include photosynthetic gene expression and leaf development, hypocotyl elongation, and the photoperiodic induction of flowering—perhaps the most recognized of intercellular phytochrome-controlled responses—among others. Several of these intercellular, phytochrome-dependent responses, which have been detected both through physiological analyses (see Table 1) and more recently through molecular-based investigations (see Table 2), are discussed in detail.

Table 1.

Physiological evidence for phytochrome-dependent intercellular and interorgan signaling

Irradiation condition	Location of light perception by phytochrome(s)	Location of growth or gene expression response	Refs.
Ra	Cotyledon	Hypocotyl	64, 95
R	Cotyledon subregions	Distinct cotyledon cells or subregions	93, 94, 107
R	Cotyledon	Apical hook	65, 74
R	Leaf	Meristem	95
R	Leaf/stem	Leaf	67
R	Mesophyll	Vascular bundle	95
R	Shoot	Root	38
FRb	Leaf	Internode	72, 97
FR	Cotyledon/leaf	Hypocotyl	96; Warnasooriya and Montgomery, submitted
FR	Cotyledon or cotyledon/apex	Apical meristem	106
FR	Shoot vascular tissue	Root	99, 100
Bc + FR	Leaf	Internode	98
B	Cotyledon	Apical meristem	Warnasooriya and Montgomery, submitted
B	Leaf/sepal	Corolla	108

^aR, red light

^bFR, far red light

^cB, blue light.

Table 2.

Molecular evidence for photoreceptor-dependent intercellular and interorgan signaling

Photoreceptor	Location of photoactive photoreceptor(s)	Location of growth or gene expression response	Refs.
phyA	Cotyledon	Hypocotyl	96
phyA	Mesophyll cells	Hypocotyl	Warnasooriya and Montgomery, submitted
phyB	Mesophyll cells	Hypocotyl, apical meristem	95
phyB	Mesophyll cells	Vascular bundles	95
phyB	Mesophyll cells	Apical meristem	95
phyB	Shoot	Lateral roots	38
cry2	Vascular bundles	Apical meristem	89

Cotyledon and leaf development.

Phytochrome-dependent intercellular signals were shown to play a role in light-dependent induction of the chlorophyll a/b-binding protein (CAB) gene promoter.^93,94 Photoactivation of phytochromes in both leaves and plant stems, and interactions between these pools of phytochromes, i.e., inter-organ phytochrome cooperativity, are important for full control of leaf expansion⁶⁷ and development of plastid ultrastructure.⁶⁹ These results suggest that interactions between phytochrome-dependent signals in distinct tissues are important for this process.

Hypocotyl and internode elongation.

Absorption of RL by cotyledon-localized phytochromes results in inhibition of hypocotyl elongation in some plants.^64,95 FR perception by cotyledon-localized phytochromes also is essential for inhibition of hypocotyl elongation in Arabidopsis (Warnasooriya and Montgomery, submitted). Thus, a phytochrome-dependent signal is transmitted from cotyledons to hypocotyls in the photocontrol of hypocotyl elongation. At the molecular level, results from gene expression assays demonstrated that cotyledon-localized phytochromes have specific effects on reporter gene expression in the hypocotyl that are likely to be important for the impact of FR-enriched light on hypocotyl or stem elongation.⁹⁶ Some of these intercellular responses appear to be auxin dependent, others are not.⁹⁶

Phytochromes in cotyledons also regulate light-dependent apical hook opening.^65,74 This intercellular phytochrome response is rapid; neither defoliation nor FR reversal is effective greatly in reversing the impact of RL exposure of leaves on apical hook opening, suggesting phytochrome control of an intercellular biophysical signal.⁶⁵ Perception of light by leaves has also been shown to be important for interorgan phytochrome-dependent control of internode elongation.^72,97 This observation that leaf-localized phytochromes exert control over internode extension also is true with regard to the impact of FR-enriched illumination on the induction of stem elongation characteristic of shade avoidance or end-of-day FR treatments in mustard.⁹⁸

Root development.

Experiments with herbaceous plants indicate that light is conducted effectively through the internal axis from the shoots, which are directly exposed to external light, to the roots underground, which themselves exhibit effective axial light conduction.⁹⁹ This axial conduction of light appears to be most effective for FR light⁹⁹ and thus has implications for intercellular and interorgan phytochrome-mediated processes. The ability of plants to conduct light internally points to the possibility that light absorbed by above-ground tissues has long-range, intercellular effects on light-dependent processes in underground plant tissues. Prior studies demonstrated that spectral properties of light conducted by woody plants are similar to those reported for herbaceous plant species;¹⁰⁰ thus, plants generally may be exposed to FR-enriched internal light environments.

Additional recent work has demonstrated that in Arabidopsis, root-localized phytochromes are able to detect light directly.^38,87 However, in the absence of direct exposure to RL, phytochromes activated in the shoot still exert an impact on root development, suggesting intercellular phytochrome signaling.³⁸ Notably, these authors suggested that the intercellular regulation may be due to phytochrome-exerted control over auxin transport or distribution.³⁸ Other investigations have shown that the expression of a significant number of genes located in roots are affected by light.^62,101

Flowering.

One of the mostly widely recognized light-dependent interorgan responses is phytochrome-dependent regulation of the photoperiodic induction of flowering (reviewed in refs. ^102–105). Mesophyll-specific phyB was demonstrated to exhibit tissue-specific control over flowering regulator FLOWERING LOCUS T (FT).⁹⁵ This regulation involves phytochrome signaling between two distinct tissue types, as mesophyll-specific phyB was shown to regulate FT expression in vascular bundles.⁹⁵ Cotyledon-localized phyB also regulates WL-dependent inhibition of hypocotyl elongation.⁹⁵

In the short-day plant Pharbitis nil FR-light perception by leaves results in the inhibition of flowering.¹⁰⁶ Interorgan cooperativity between the shoot apex and cotyledons in this phytochrome-dependent regulation of flowering was established by simultaneous exposure of both of these organs to FR light, which resulted in a greater inhibition in flowering than cotyledon-localized exposure alone.¹⁰⁶ Notably, recent results with Arabidopsis suggest a similar coordination between the shoot apex and leaves in the BL-dependent regulation of flowering by phytochromes (Warnasooriya and Montgomery, submitted).

Anthocyanin production.

Although light-dependent anthocyanin synthesis occurs largely as a local, intracellular response, results from microbeam irradiation studies with mustard seedlings suggest that the response of inducing anthocyanin synthesis in local cells is integrated by an inhibitory intercellular phytochrome signal that is involved in the regulation of anthocyanin synthesis at the organismal level.¹⁰⁷ Light perceived in leaves and sepals also results in intercellular phytochrome regulation of anthocyanin accumulation in corollas of Petunia flowers.¹⁰⁸

Molecular Effectors Involved in Tissue-specific Light Signaling

To date, only a small number of factors downstream of the photoreceptors have been shown definitively to be involved in tissue-specific light signaling pathways (see Table 3). However, recent gene expression studies have shown that organ-specific, light-dependent regulation of gene expression exists in both rice and Arabidopsis.⁶¹ This organ-specific photoregulation of gene expression was shown to correlate with the overrepresentation of distinct flanking sequences identified around known light-responsive cis-elements (e.g., G-box elements) in light-responsive promoters.^2,61 These findings suggest that specific factors downstream of the photoreceptors are regulated by light in distinct tissues and organs. Reverse genetic studies of genes whose expression is rapidly and significantly changed in response to light exposure resulted in the identification of six genes that may be involved specifically in hypocotyl-localized phytochrome responses.¹⁰⁹ Earlier studies also demonstrated that the photomorphogenesis repressor COP1 is regulated by light in regard to its subcellular localization, specifically in hypocotyl tissues.¹¹⁰ In addition, DET1, which encodes a negative regulator of photomorphogenesis, also acts in the spatiotemporal photoregulation of gene expression.¹¹¹

Table 3.

Molecular effectors in tissue- and organ-specific light signaling

Molecular effector	Function	Tissue localization of response	Photoregulation	Refs.
14-3-3 μ	Interaction with COa	Leaf tissue	R	117
14-3-3 υ	Interaction with CO	Leaf tissue	R	117
ACT7	Actin	Upregulated in hypocotyl	Wb	112
COP1	Negative regulator	Hypocotyl	W	110
CUE1	Unknown	Mesophyll cells	R/B	118
DET1	Transcriptional repressor	Leaves, flowers	W	111
Dof1	Transcriptional activator	Leaves	W	114
OBP3	Transcriptional activator	Vascular tissue	W/R/B	115
PKS1	Positive regulator	Roots	R	88, 116
TUB1	Tubulin	Downregulated in hypocotyl	FR (phyA), R (phyB)	113

^aCO, CONSTANS

^bW, white light; all other abbreviations in this column are as in Table 1.

Light has defined effects on cell elongation during the photocontrol of hypocotyl and internode elongation in plants (see discussion above). Some of the molecular effectors that act downstream of photoreceptors in this photoregulation of cell elongation have been reported. For instance, the expression of ACT7, which encodes an actin protein in Arabidopsis, is regulated by light in vegetative tissues.¹¹² ACT7 is expressed at high levels in etiolated hypocotyls—tissue that contains cells undergoing rapid elongation.¹¹² Arabidopsis phyA and phyB regulate tissue-specific expression of tubulin genes in the hypocotyl.¹¹³ As tubulin-containing microtubules control the direction of cell elongation, phytochrome regulation of tubulin gene expression controls light-dependent cell elongation.¹¹³ Notably, Leu et al., report that phytochrome activity in response to light results in downregulation of tubulin gene expression,¹¹³ conditions under which cell elongation is inhibited in hypocotyls.

A number of other molecular effectors with undefined or incompletely defined molecular and/or biochemical roles also have been reported to exhibit tissue-specific roles in light-dependent processes. For example, two maize proteins, Dof1 and Dof2 (DNA binding with _one _finger), have been implicated as central molecular players in tissue-specific, light-regulated gene expression.¹¹⁴ These two proteins likely function as an activator and repressor of transcriptional activation, respectively.¹¹⁴ Dof1 appears to be a light-activated, or at least light-dependent, transcriptional activator.¹¹⁴ Dof1 and Dof2 display distinct tissue specificity as well,¹¹⁴ which suggests an interesting relationship between the two in tissue-specific, light-dependent regulation of gene expression. Notably, a related protein in Arabidopsis, OBP3, which is a putative Dof transcription factor, exhibits light-dependent, tissue-specific accumulation.¹¹⁵ The OBP3 protein appears to be involved in phyB-dependent inhibition of hypocotyl elongation in response to RL and cry2-dependent cotyledon expansion in response to BL.¹¹⁵

Phytochrome kinase substrate 1 (PKS1) was first identified as a cytosolic phytochrome-interacting factor that is phosphorylated by photoactivated phytochrome.¹¹⁶ PKS1 was recently shown to have a role in modulating the RL-dependent positive phototropism of Arabidopsis roots.⁸⁸ PKS1 is regulated by phyA and phyB and appears to control RL-dependent negative curvature in roots.⁸⁸

The 14-3-3 proteins have been implicated as signal transduction regulators or integrators in a wide range of organisms. Recently, Mayfield et al., reported that Arabidopsis 14-3-3 isoforms have a role in the photoperiodic flowering pathway, as well as the RL-dependent inhibition of hypocotyl elongation.¹¹⁷ These proteins interact with floral regulator CONSTANS in the photoregulation of flowering.¹¹⁷

CUE1 is an effector that functions in light-dependent, mesophyll-specific gene expression.¹¹⁸ Photobiological analyses indicate that CUE1 functions downstream of RL- and BL-dependent photoreceptors in the light-dependent regulation of chloroplast development.¹¹⁸ Thus, CUE1 was proposed to function as a cell-type-specific integrator of light-dependent and developmental growth responses.¹¹⁸

Phytochrome and hormone interactions in spatiotemporal regulation of development.

Both auxin and ABA have been implicated as mediators of phytochrome-dependent responses.⁹⁶ Auxin is known to move from cell to cell in plants, and it may be an important part of a phytochrome-dependent intercellular signal between cotyledons and hypocotyls.⁹⁶ As noted above, recent findings implicate auxin in some phytochrome-dependent intercellular responses.

Results from inhibitor studies demonstrate that phytochrome-dependent epicotyl elongation in response to FR illumination is mediated by gibberellins (GAs) in cowpea.⁷⁸ Light and GAs generally exhibit opposite effects on hypocotyl elongation, with light inhibiting hypocotyl elongation and GAs promoting elongation. Recent results show that the antagonistic impacts of light and GAs are mediated at the molecular level, at least in part, through the interaction of DELLA proteins with PIF3 and PIF4, which promote hypocotyl elongation and are inactivated by photoactivated phytochromes.^119,120 DELLAs, whose accumulation is induced by light-activated phytochromes, inhibit GA-regulated gene expression and promote the inhibition of hypocotyl elongation in light.¹²¹

Future Directions for Spatiotemporal Photoreceptor Studies

The results from many of the early studies described above were obscured by the ability of microbeam irradiation to be transmitted far from the site of application, and by the impact of light scattering in irradiated tissues.^122,123 Furthermore, recent results from studies with herbaceous plants demonstrated that light in the FR region of the spectrum is conducted efficiently in the vascular tissue of plant stems and roots.⁹⁹ These observations about light piping and scattering make it difficult to conclude definitively that a particular site(s) of light application is the sole source of light responsible for an observed phytochrome-dependent response. However, more recent advances in our understanding of spatiotemporal-specific light responses gained through the application of emergent molecular tools have confirmed many responses previously identified through physiological analyses, as well as resulting in the identification of novel spatiotemporal light responses.

These molecular-based studies largely have employed tissue-specific gene expression analyses or have incorporated the use of tissue-specific promoters and enhancer trapping to direct tissue-specific accumulation or ablation of photoreceptors. The gene expression studies are important for identifying putative genes, which may be involved in distinct aspects of spatiotemporal light responses, for further study.^61,62,109 Spatial-specific expression of photoreceptors using tissue-specific promoters for cry2,⁸⁹ or enhancer-trap studies for phyB⁹⁵ resulted in novel insights into both cell autonomous roles for cry2 and intercellular functions of phyB in distinct aspects of photomorphogenesis. The use of tissue-specific promoters for spatial-specific phytochrome disruption also yielded novel information about the role of phyA in the regulation of hypocotyl elongation (Warnasooriya and Montgomery, submitted).

Future investigations into spatial-specific photoreceptor responses will be facilitated by combining experimental approaches. For example, following tissue-specific expression of photoreceptors or downstream effectors or, alternatively, tissue-specific ablation of such components where applicable, with gene expression or proteomic analyses could be greatly beneficial. These types of combinatorial assays could aid in the identification of specific molecular components involved in spatial-specific photoregulation. Other avenues for exploring spatiotemporal aspects of photomorphogenesis include using laser capture microdissection together with genome- or proteome-wide analysis tools. Advancements in the applications of such innovative tools and additional pioneering methods undoubtedly will result in continuing breakthroughs in the understudied area of spatiotemporal light regulation during plant growth and development.

Abbreviations

B/UV-A

blue/UV-A

BL

blue light

CAB

chlorophyll a/b-binding protein

FR

far-red

PIF

phytochrome-interacting factor

PKS1

phytochrome kinase substrate 1

RL

red light

UV-A

ultraviolet A

UV-B

ultraviolet B