In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis

In partially shaded plants, phytochrome A contributes to the adjustment of photosynthesis in shaded leaves but is not directly involved in the induction of leaf senescence

Related papers:

title: Chlorophyll Breakdown in Senescent Arabidopsis Leaves. Characterization of Chlorophyll Catabolites and of Chlorophyll Catabolic Enzymes Involved in the Degreening Reaction1
abstract: During senescence, chlorophyll (chl) is metabolized to colorless nonfluorescent chl catabolites (NCCs). A central reaction of the breakdown pathway is the ring cleavage of pheophorbide (pheide) a to a primary fluorescent chl catabolite. Two enzymes catalyze this reaction, pheide a oxygenase (PAO) and red chl catabolite reductase. Five NCCs and three fluorescent chl catabolites (FCCs) accumulated during dark-induced chl breakdown in Arabidopsis (Arabidopsis thaliana). Three of these NCCs and one FCC (primary fluorescent chl catabolite-1) were identical to known catabolites from canola (Brassica napus). The presence in Arabidopsis of two modified FCCs supports the hypothesis that modifications, as present in NCCs, occur at the level of FCC. Chl degradation in Arabidopsis correlated with the accumulation of FCCs and NCCs, as well as with an increase in PAO activity. This increase was due to an up-regulation of Pao gene expression. In contrast, red chl catabolite reductase is not regulated during leaf development and senescence. A pao1 knockout mutant was identified and analyzed. The mutant showed an age- and light-dependent cell death phenotype on leaves and in flowers caused by the accumulation of photoreactive pheide a. In the dark, pao1 exhibited a stay-green phenotype. The key role of PAO in chl breakdown is discussed.

title: Senescence-associated degradation of chloroplast proteins inside and outside the organelle.
abstract: Leaf proteins, and in particular the photosynthetic proteins of plastids, are extensively degraded during senescence. Although this involves massive amounts of protein, the mechanisms responsible for chloroplast protein degradation are largely unknown. Degradation within the plastid itself is supported by the observation that chloroplasts contain active proteases, and that chloroplasts isolated from senescing leaves can cleave Rubisco to release partially digested fragments. It is less clear whether chloroplasts can complete Rubisco degradation. Chloroplastic proteases are likely involved in the breakdown of the D1 and LHCII proteins of photosystem II. Small senescence-associated vacuoles (SAVs) with high-proteolytic activity develop in senescing leaf cells, and there is evidence that SAVs contain chloroplast proteins. Thus, an extra-plastidic pathway involving SAVs might participate in the degradation of some chloroplast proteins. Plastidic and extra-plastidic pathways might cooperate in the degradation of chloroplast proteins, or they might represent alternative, redundant pathways for photosynthetic protein degradation.

title: The molecular analysis of leaf senescence--a genomics approach.
abstract: Senescence in green plants is a complex and highly regulated process that occurs as part of plant development or can be prematurely induced by stress. In the last decade, the main focus of research has been on the identification of senescence mutants, as well as on genes that show enhanced expression during senescence. Analysis of these is beginning to expand our understanding of the processes by which senescence functions. Recent rapid advances in genomics resources, especially for the model plant species Arabidopsis, are providing scientists with a dazzling array of tools for the identification and functional analysis of the genes and pathways involved in senescence. In this review, we present the current understanding of the mechanisms by which plants control senescence and the processes that are involved.

title: Phosphorus Distribution and Remobilization in Bean Plants as Influenced by Phosphorus Nutrition
abstract: Remobilization of P from vegetative tissues can be an important source of grain P in common bean (Phaseolus vulgaris L.). Yet, data on the extent of remobilization of P from roots is scarce. We measured P remobilization from roots and leaves and examined the influence of P nutrition on remobilization patterns and tissue longevity. A split-root system was used to expose a portion of the root system (compartment roots) to low-P treatments independently from those imposed on the main root system. Phosphorus content of retained leaves, abscised leaves, stems, pods, seeds, and roots were observed over time. Leaf remobilization supplied over half of the pod plus seed P. Flux analysis suggested that leaf remobilization occurred earlier in low-P than it did in high-P plants. Root P content of compartment roots did not decrease with ontogeny. We compared remobilization patterns of root Pin low-P and high-P plants in a short-term experiment using 32 P applied to roots grown in either low-P or high-P compartments. Compartment roots retained over 80% of absorbed 32 P almost all cases. The exception was roots of high-P plants grown in a high-P compartment, which retained only 20% of absorbed 32 P. Together these results indicate common bean roots retain P when soil P levels are low. This behavior is in contrast to that of leaves and stems which remobilize P to the grain at both low and high levels of soil P fertility.

title: Leaf nitrogen remobilisation for plant development and grain filling.
abstract: A major challenge of modern agriculture is to reduce the excessive input of fertilisers and, at the same time, to improve grain quality without affecting yield. One way to achieve this goal is to improve plant nitrogen economy through manipulating nitrogen recycling, and especially nitrogen remobilisation, from senescing plant organs. In this review, the contribution of nitrogen remobilisation efficiency (NRE) to global nitrogen use efficiency (NUE), and tools dedicated to the determination of NRE are described. An overall examination of the physiological, metabolic and genetic aspects of nitrogen remobilisation is presented.

title: Gene expression during leaf senescence.
abstract: Leaf senescence is a hiphly-controlled sequence of events comprising the final stage of development. Cells remain viable during the process and new gene expression is required. There is some similarity between senescence in plants and programmed cell death in animals. In this review, different classes of senescence-related genes are defined and progress towards isolating such genes is reported. A range of internal and external factors which appear to cause leaf senescence is considered and various models for the mechanism of senescence- initiation are described. The current understanding of senescence at the wrganelle and molecular levels is presented. Finally, same ideas are mooted as to why senescence occurs and why it should be studied further.  Progress in the understanding of senescence at the molecular level 434 VII. The control of senescence in animals and plants 440 VIII. Why is senescence necessary? 441 IX. Why study senescence? 441 References 442.

title: Senescence is induced in individually darkened Arabidopsis leaves, but inhibited in whole darkened plants.
abstract: It has long been known that leaf senescence can be induced in many plant species by detaching leaves and placing them in the darkness. It recently has been shown that entire Arabidopsis plants placed in the darkness are not induced to senesce, as judged by visible yellowing and certain molecular markers. Here, we show that when individual Arabidopsis leaves are darkened, but not when entire plants are darkened, senescence is induced in the covered leaves. This induction of senescence is highly localized. The phenomenon is leaf age dependent in that it occurs more rapidly and strongly in older leaves than in younger ones, as is the case with many forms of induced senescence. Whole adult plants placed in darkness, in contrast, show delayed senescence, although seedlings lacking primary leaves do not. These observations imply that the light status of the entire plant affects the senescence of individual leaves. A model summarizing the results is presented.

title: The different fates of mitochondria and chloroplasts during dark-induced senescence in Arabidopsis leaves.
abstract: Senescence is an active process allowing the reallocation of valuable nutrients from the senescing organ towards storage and/or growing tissues. Using Arabidopsis thaliana leaves from both whole darkened plants (DPs) and individually darkened leaves (IDLs), we investigated the fate of mitochondria and chloroplasts during dark-induced leaf senescence. Combining in vivo visualization of fates of the two organelles by three-dimensional reconstructions of abaxial parts of leaves with functional measurements of photosynthesis and respiration, we showed that the two experimental systems displayed major differences during 6 d of dark treatment. In whole DPs, organelles were largely retained in both epidermal and mesophyll cells. However, while the photosynthetic capacity was maintained, the capacity of mitochondrial respiration decreased. In contrast, IDLs showed a rapid decline in photosynthetic capacity while maintaining a high capacity for mitochondrial respiration throughout the treatment. In addition, we noticed an unequal degradation of organelles in the different cell types of the senescing leaf. From these data, we suggest that metabolism in leaves of the whole DPs enters a 'stand-by mode' to preserve the photosynthetic machinery for as long as possible. However, in IDLs, mitochondria actively provide energy and carbon skeletons for the degradation of cell constituents, facilitating the retrieval of nutrients. Finally, the heterogeneity of the degradation processes involved during senescence is discussed with regard to the fate of mitochondria and chloroplasts in the different cell types.

title: The impact of light intensity on shade-induced leaf senescence.
abstract: Plants often have to cope with altered light conditions, which in leaves induce various physiological responses ranging from photosynthetic acclimation to leaf senescence. However, our knowledge of the regulatory pathways by which shade and darkness induce leaf senescence remains incomplete. To determine to what extent reduced light intensities regulate the induction of leaf senescence, we performed a functional comparison between Arabidopsis leaves subjected to a range of shading treatments. Individually covered leaves, which remained attached to the plant, were compared with respect to chlorophyll, protein, histology, expression of senescence-associated genes, capacity for photosynthesis and respiration, and light compensation point (LCP). Mild shading induced photosynthetic acclimation and resource partitioning, which, together with a decreased respiration, lowered the LCP. Leaf senescence was induced only under strong shade, coinciding with a negative carbon balance and independent of the red/far-red ratio. Interestingly, while senescence was significantly delayed at very low light compared with darkness, phytochrome A mutant plants showed enhanced chlorophyll degradation under all shading treatments except complete darkness. Taken together, our results suggest that the induction of leaf senescence during shading depends on the efficiency of carbon fixation, which in turn appears to be modulated via light receptors such as phytochrome A.

title: Phytochrome functions in Arabidopsis development.
abstract: Light signals are fundamental to the growth and development of plants. Red and far-red light are sensed using the phytochrome family of plant photoreceptors. Individual phytochromes display both unique and overlapping roles throughout the life cycle of plants, regulating a range of developmental processes from seed germination to the timing of reproductive development. The evolution of multiple phytochrome photoreceptors has enhanced plant sensitivity to fluctuating light environments, diversifying phytochrome function, and facilitating conditional cross-talk with other signalling systems. The isolation of null mutants, deficient in all individual phytochromes, has greatly advanced understanding of phytochrome functions in the model species, Arabidopsis thaliana. The creation of mutants null for multiple phytochrome combinations has enabled the dissection of redundant interactions between family members, revealing novel regulatory roles for this important photoreceptor family. In this review, current knowledge of phytochrome functions in the light-regulated development of Arabidopsis is summarised.

title: An Integrative Model for Phytochrome B Mediated Photomorphogenesis: From Protein Dynamics to Physiology
abstract: Plants have evolved various sophisticated mechanisms to respond and adapt to changes of abiotic factors in their natural environment. Light is one of the most important abiotic environmental factors and it regulates plant growth and development throughout their entire life cycle. To monitor the intensity and spectral composition of the ambient light environment, plants have evolved multiple photoreceptors, including the red/far-red light-sensing phytochromes.  We have developed an integrative mathematical model that describes how phytochrome B (phyB), an essential receptor in Arabidopsis thaliana, controls growth. Our model is based on a multiscale approach and connects the mesoscopic intracellular phyB protein dynamics to the macroscopic growth phenotype. To establish reliable and relevant parameters for the model phyB regulated growth we measured: accumulation and degradation, dark reversion kinetics and the dynamic behavior of different nuclear phyB pools using in vivo spectroscopy, western blotting and Fluorescence Recovery After Photobleaching (FRAP) technique, respectively.  The newly developed model predicts that the phyB-containing nuclear bodies (NBs) (i) serve as storage sites for phyB and (ii) control prolonged dark reversion kinetics as well as partial reversibility of phyB Pfr in extended darkness. The predictive power of this mathematical model is further validated by the fact that we are able to formalize a basic photobiological observation, namely that in light-grown seedlings hypocotyl length depends on the total amount of phyB. In addition, we demonstrate that our theoretical predictions are in excellent agreement with quantitative data concerning phyB levels and the corresponding hypocotyl lengths. Hence, we conclude that the integrative model suggested in this study captures the main features of phyB-mediated photomorphogenesis in Arabidopsis.

title: Decoding of light signals by plant phytochromes and their interacting proteins.
abstract: Phytochromes are red/far-red light photoreceptors that convert the information contained in external light into biological signals. The decoding process starts with the perception of red light, which occurs through photoisomerization of a chromophore located within the phytochrome, leading to structural changes that include the disruption of intramolecular interactions between the N- and C-terminal domains of the phytochrome. This disruption exposes surfaces required for interactions with other proteins. In contrast, the perception of far-red light reverses the photoisomerization, restores the intramolecular interaction, and closes the interacting surfaces. Light information represented by the concentration of opened interacting surfaces is converted into biological signals through the modulating activity of interacting proteins. This review summarizes plant phytochromes, phytochrome-interacting proteins, and signal transmission from phytochromes to their interacting proteins.

title: Plant hormone signaling lightens up: integrators of light and hormones.
abstract: Light is an important environmental signal that regulates diverse growth and developmental processes in plants. In these light-regulated processes, multiple hormonal pathways are often modulated by light to mediate the developmental changes. Conversely, hormone levels in plants also serve as endogenous cues in influencing light responsiveness. Although interactions between light and hormone signaling pathways have long been observed, recent studies have advanced our understanding by identifying signaling integrators that connect the pathways. These integrators, namely PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), PIF4, PIF3-LIKE 5 (PIL5)/PIF1 and LONG HYPOCOTYL 5 (HY5), are key light signaling components and they link light signals to the signaling of phytohormones, such as gibberellin (GA), abscisic acid (ABA), auxin and cytokinin, in regulating seedling photomorphogenesis and seed germination. This review focuses on these integrators in illustrating how light and hormone interact.

title: Control of senescence in marchantia by phytochrome.
abstract: Mature green tissue of Marchantia polymorpha L. bleaches markedly when placed in continuous darkness for 4 days but remains green when given daily 1-hour photoperiods of white light. The tissue, however, is induced to bleach when each daily 1-hour photoperiod is terminated with a brief irradiation with far red light. The bleaching does not occur when each irradiation with far red light is followed by a brief irradiation with red light. The bleaching is taken as an index of senescence since the loss of chlorophyll in the bleached tissue is accompanied by a breakdown of cell organelles and cytoplasm. Phytochrome is clearly implicated in the control of senescence by light. It was also found that 5 minutes of red light given once a day was as effective as the 1-hour photoperiods with white light in preventing the bleaching and that bleaching was induced when each daily 5-minute irradiation with red light was followed by a 10-minute irradiation with far red light.

title: PHOTOCONTROL OF LEAF SENESCENCE
abstract: Senescence is the last phase of leaf development. It is basically a process of degreening and produces changes at all levels of cellular and sub-cellular organizations of leaves. The precise mechanism of senescence induction is not known, although the process, in principle. is known to be under genetic control (Stoddart and Thomas, 1982). Once senescence is triggered, it is subject to environmental modulations and the reports on the effects of various environmental factors on leaf senescence are extensive (Biswal et al., 1983b). Light, one of the important environmental factors, plays a very crucial role in photosynthetic green plants. In addition to its role in photosynthesis, it also decisively controls plant development and morphogenesis (Mohr and Shropshire. 1983). Light absorption by various photoreceptors, transmission of the signal and the final photoresponses in the greening process are well investigated (Kasemir. 1983). However, nothing definite is known about the mechanism of light action in controlling leaf senescence, although light has been known either to stimulate or retard the process (Maunders and Brown. 1983; Biswal et al., 1983a,b,c; Panigrahi and Biswal, 1983; Satler and Thimann, 1983; Iordanov and M. G. Merakchilska-Nikolova, 1983; Rao, 1983; Schmutz et al . , 1983). It has been known that photostimulation of chlorophyll loss during leaf senescence is mostly non-metabolic. The major photoreceptors involved are chlorophylls which are photobleached at high intensity of light. This may cause a significant loss in photosynthetic efficiency of green leaves leading ultimately to their senescence. This type of senescence normally occurs in deciduous plants. Maunders and Brown (1983) have shown light to degrade chlorophyll faster than dark. On the other hand, the differences between the leaves incubated in dark and light with respect to soluble protein, cytoplasmic RNA and free aminonitrogen are much less marked. These results would suggest that light action on chlorophyll degradation is non-metabolic in nature since it does not show its effect on other senscence-associated changes. It is therefore important to differentiate between situations where light has got a direct photochemical role in the Photostimulation of leaf senescence. degradation of chlorophyll and light as a metabolic modulator of pigment degradation during leaf senescence. Whether light should act as a metabolic modulator or a photodecomposer depends on the intensity of light and the plant system. This is clearly demonstrated by Pjon (1981) in leaf senescence of maize and hydrangea. He has shown the differential ability of leaf tissue of maize and hydrangea to dissipate their absorbed light quanta. The loss of chlorophyll in maize leaves has been attributed to the process of photooxidation of pigments, because continuous white light results in loss of maize leaf chlorophyll. but retards the loss of protein. Photobleaching of chlorophyll in this system may be compared with the degradation of the pigments during aging of isolated chloroplasts (Raval et al., 1982; Panigrahi and Biswal, 1983). Recent reports of Lichtenthaler et a l . (1982) and Meier and Lichtenthaler (1983) provide new information on photostimulation of leaf senescence of seedlings grown in high and low light intensities. They have demonstrated that compared to low light, strong light (light quanta fluence rates) leads to the formation of sun type chloroplasts which exhibit high photosynthetic rates and simultaneously an acceleration of leaf development, which also results in an earlier leaf senescence. High light intensities not on ly accelerate chlorophyll breakdown, but also lead to ultrastructural modifications and loss in soluble carbohydrates. These changes, in addition to the breakdown of chlorophyll as shown by the authors, prevent a generalization that light stimulation of senescence is because of simple photooxidation of chlorophylls only. The action of light in controlling leaf senescence is normally attributed to its effect in delaying senescence. It is to the economy of leaves that these should remain in a functional state for as long as possible once the energy has been invested in their formation. Therefore, it is logical to imagine the retarding effect of light in senescence once the leaves are matured. The reports on the precise role of light in retarding the process are controversial with mainly two different views, whether the action is photosynthetic or photomorphogenic (Biswal et al., 1983b). This review is an attempt to report and rationalize the work from various laboratories engaged in this field. Since this is the first review in the field, some of the Photoretardation of leaf senescence.

title: Two Long-Term Effects of Light that Control the Stability of Proteins Related to Photosynthesis during Senescence of Rice Leaves
abstract: Rate of light-saturated photosynthesis (Pmal) decreased during senescence, with no or small changes in the initial slope of the light-response curve ($), an index of light-harvesting and light-utilization capacity. Senescence of rice leaves was associated with shading of the leaves by upper younger leaves and evidence indicated that a major modulator of the light-response curve during senescence is the light environment of leaves. Chi and proteins in leaves were largely degraded during several days in darkness, and proteins that are related to P max and fa were stabilized by light at different intensities. A decline in Pma, during senescence was related to degradation of Rubisco, Cyt/and the P subunit of ATPase that was completely suppressed only at about 300/anol quanta m~ 2 s -1 and, hence, proceeded in the darkened environments caused by shading. By contrast, 0, remained relatively constant during senescence because Chi and proteins related to the light-harvesting Chi proteins and the reaction center complexes were effectively stabilized by very weak light. Evidence was obtained indicating that phytochrome is involved in the stabilization of Chi, whereas the photoprotection of Rubisco is a complex reaction involving photosynthesis and a signal function^) of light. Physiological or ecophysiological significance of the two long-term effects of light that differentially stabilize the two groups of proteins are discussed.

title: Far-red enrichment and photosynthetically active radiation level influence leaf senescence in field-grown sunflower
abstract: Basal leaves frequently senesce before anthesis in high population density crops. This paper evaluates the hypothesis that quantitative and qualitative changes in the light environment associated with a high leaf area index (LAI) trigger leaf senescence in sunflower (Helianthus annuus L.) canopies. Mean leaf duration (LD, time from achievement of maximum leaf area) of leaf 8 was significantly (P < 0.05) reduced from 51 to 19 days as crop population density was increased from 0.47 to 4.76 plants m−2. High compared to low plant population density was associated with earlier reduction in the photosynthetically active radiation (PAR) and red/far-red ratio (R/FR) reaching the target leaf. However the changes in R/FR preceded those in PAR. When the light environment of individual leaves of isolated plants growing under field conditions was manipulated using filters and FR-reflecting mirrors, LD was positively and linearly related with the mean daily PAR (MDR) received in the FR- (no FR enrichment) treatments. FR enrichment of light reaching the abaxial surface of the leaf significantly (P < 0.05) reduced LD by 9 days at intermediate PAR levels with respect to FR-controls, but did not affect LD at the maximum PAR used in these experiments. However, when light reaching both leaf surfaces was enriched with FR, LD (for leaves receiving maximum PAR) was 13 days shorter than that of the FR- control. These results show that basal leaf senescence in sunflower is enhanced both by a decrease in PAR and by a decrease in R/FR.

title: Directed overexpression of PHYA locally suppresses stem elongation and leaf senescence responses to far‐red radiation
abstract: Ectopic overexpression of an oat PHYA cDNA in tobacco under the cauliflower mosaic virus 35S promoter results in plants with reduced morphological responses to far-red radiation (FR). We have tested the hypothesis that it is possible to molecularly ‘mask’ steins and leaves to FR-induced elongation and senescence responses by targeting the over-expression of PHYA with appropriate promoters. Oat PHYA was expressed in tobacco (Nicotiana tabacum L. cv Xanthi) under the 35S and two Arabidopsis promoters: UBQ1 and CAB. The internodes of wild type, UBQ:PHYA, and CAB:PHYA plants, which exhibited little or no oat PHYA overexpression, responded to localized FR treatments with a marked increase in elongation. In contrast, 35S:PHYA plants, which overexpressed PHYA to high levels in all parts of the shoot, did not respond to FR treatments directed to their stems. Leaf senescence responses to FR were remarkably localized, and sensitivity to FR was also inversely correlated with the local PHYA expression level. Thus, chlorophyll content, specific leaf weight, and nitrate reductase activity in leaf spots treated with FR were highly reduced in wild type and UBQ:PHYA plants, but not in the CAB:PHYA and 35S:PHYA counterparts. Our results suggest that it may be feasible to obtain transgenic crop plants in which certain organs or tissues are made ‘blind’ to phytochrome-perceived signals of canopy density, but whose general photomorphogenic competence is not greatly disturbed.

title: Species-specific variation in the importance of the spectral quality gradient in canopies as a signal for photosynthetic resource partitioning.
abstract: Plants adjust the distribution of photosynthetic capacity and chlorophyll to canopy density. The importance of the gradient in the red : far-red ratio (R : FR) relative to the irradiance gradient was studied for its perception with respect to this partitioning of photosynthetic resources. Whether the relative importance of these two signals varied between six species of different growth habit (Phaseolus vulgaris, Lysimachia vulgaris, Hedera helix, Ficus benjamina, Carex acutiformis and Brachypodium pinnatum) was investigated further.



Single leaves of plants were shaded in daylight by a spectrally neutral filter or a leaf. In another experiment, leaves were treated with supplemental FR. In most cases, treatment effects were evaluated after 2 weeks.



Nitrogen and photosynthetic capacity (Amax) per leaf area, parameters pertaining to between-leaf resource partitioning, were strongly reduced in neutral shade but not additionally by spectral leaf shade. Supplemental FR reduced these parameters also, except in Carex. Acceleration of induction of senescence was observed in spectral leaf shade in primary bean leaves. Amax per unit chlorophyll, a parameter pertaining to within-leaf resource partitioning, was reduced in neutral shade, but not in spectral leaf shade or supplemental FR.



Signalling mechanisms associated with perception of the R : FR gradient in canopies were less important than those associated with the irradiance gradient for between-leaf and within-leaf partitioning of photosynthetic resources. The relative importance of the signals differed between species because Carex was the only species for which no indications were found for an involvement of the spectral gradient in perception of canopy density.

title: Leaf senescence in maize hybrids: plant population, row spacing and kernel set effects
abstract: Maize crop management involves decision making on several cultural practices aimed to maximize grain yield, like plant population and row spacing. These practices affect the light environment perceived by plants and the post-flowering source–sink ratio, but there is scarce information on the way they influence plant leaf senescence. The objectives of our research were to: (i) characterize the development of leaf area senescence for contrasting canopy architectures (i.e. plant population×row spacing), and (ii) analyze the response of leaf senescence to changes in the light environment and the post-flowering source–sink ratio. Field experiments were conducted in Argentina between 1997/1998 and 2000/2001. Four hybrids were grown at a wide range of plant populations (3, 9, 10 and 12 plants m−2), row spacings (0.35, 0.7 and 1 m) and pollination treatments (natural and restricted pollination). Senescence development was well described (r2=0.61–0.99,P

title: Heterologous expression of Arabidopsis phytochrome B in transgenic potato influences photosynthetic performance and tuber development.
abstract: Transgenic potato (Solanum tuberosum) plants expressing Arabidopsis phytochrome B were characterized morphologically and physiologically under white light in a greenhouse to explore their potential for improved photosynthesis and higher tuber yields. As expected, overexpression of functional phytochrome B caused pleiotropic effects such as semidwarfism, decreased apical dominance, a higher number of smaller but thicker leaves, and increased pigmentation. Because of increased numbers of chloroplasts in elongated palisade cells, photosynthesis per leaf area and in each individual plant increased. In addition, photosynthesis was less sensitive to photoinactivation under prolonged light stress. The beginning of senescence was not delayed, but deceleration of chlorophyll degradation extended the lifetime of photosynthetically active plants. Both the higher photosynthetic performance and the longer lifespan of the transgenic plants allowed greater biomass production, resulting in extended underground organs with increased tuber yields.

title: A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing.
abstract: The PHYD gene of the Wassilewskija (Ws) ecotype of Arabidopsis contains a 14-bp deletion (the phyD-1 mutation) beginning at amino acid 29 of the reading frame, resulting in translation termination at a nonsense codon 138 nucleotides downstream of the deletion end point. Immunoblot analyses showed that Ws lacks phyD but contains normal levels of phyA, phyB, and phyC. By backcrossing into the Ws and Landsberg erecta genetic backgrounds, we constructed sibling pairs of PHYD+ and phyD-1 lines and of phyB- PHYD+ and phyB- phyD- lines. Hypocotyl lengths after growth under white or red light increased sequentially in strains that were B+D+, B+D-, B-D+, and B-D-. In the Ws genetic background, an increase in petiole length, a reduction in cotyledon area and in anthocyanin accumulation in seedling stems, a diminished effect of an end-of-day pulse of far-red light on hypocotyl elongation, and a decrease in the number of rosette leaves at the onset of flowering were also seen sequentially in these lines. Thus, phyD, which is approximately 80% identical in amino acid sequence to phyB, acts in conjunction with phyB in regulating many shade avoidance responses. The existence of the apparently naturally occurring phyD-1 mutation indicates that phyD is not essential in some natural environments.

title: Phytochrome A and Phytochrome B Have Overlapping but Distinct Functions in Arabidopsis Development
abstract: Plant responses to red and far-red light are mediated by a family of photoreceptors called phytochromes. In Arabidopsis thaliana, there are genes encoding at least five phytochromes, and it is of interest to learn if the different phytochromes have overlapping or distinct functions. To address this question for two of the phytochromes in Arabidopsis, we have compared light responses of the wild type with those of a phyA null mutant, a phyB null mutant, and a phyA phyB double mutant. We have found that both phyA and phyB mutants have a deficiency in germination, the phyA mutant in far-red light and the phyB mutant in the dark. Furthermore, the germination defect caused by the phyA mutation in far-red light could be suppressed by a phyB mutation, suggesting that phytochrome B (PHYB) can have an inhibitory as well as a stimulatory effect on germination. In red light, the phyA phyB double mutant, but neither single mutant, had poorly developed cotyledons, as well as reduced red-light induction of CAB gene expression and potentiation of chlorophyll induction. The phyA mutant was deficient in sensing a flowering response inductive photoperiod, suggesting that PHYA participates in sensing daylength. In contrast, the phyB mutant flowered earlier than the wild type (and the phyA mutant) under all photoperiods tested, but responded to an inductive photoperiod. Thus, PHYA and PHYB appear to have complementary functions in controlling germination, seedling development, and flowering. We discuss the implications of these results for possible mechanisms of PHYA and PHYB signal transduction.

title: Missense Mutation in the PAS2 Domain of Phytochrome A Impairs Subnuclear Localization and a Subset of Responses Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.000521.
abstract: Phytochrome A signaling shows two photobiologically discrete outputs: so-called very-low-fluence responses (VLFR) and high-irradiance responses (HIR). By modifying previous screening protocols, we isolated two Arabidopsis mutants retaining VLFR and lacking HIR. Phytochrome A negatively or positively regulates phytochrome B signaling, depending on light conditions. These mutants retained the negative but lacked the positive regulation. Both mutants carry the novel phyA-302 allele, in which Glu-777 (a residue conserved in angiosperm phytochromes) changed to Lys in the PAS2 motif of the C-terminal domain. The phyA-302 mutants showed a 50% reduction in phytochrome A levels in darkness, but this difference was compensated for by greater stability under continuous far-red light. phyA-302:green fluorescent protein fusion proteins showed normal translocation from the cytosol to the nucleus under continuous far-red light but failed to produce nuclear spots, suggesting that nuclear speckles could be involved in HIR signaling and phytochrome A degradation. We propose that the PAS2 domain of phytochrome A is necessary to initiate signaling in HIR but not in VLFR, likely via interaction with a specific partner.

title: Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: verification of the concentration of chlorophyll standards by atomic absorption spectroscopy
abstract: The extinction coefficients for chlorophylls a and b in diethylether (Smith, J.H.C. and Benitez, A. (1955) in Modern Methods of Plant Analysis (Paech, K. and Tracey, M.V., eds.), Vol. 4, pp. 143–196, Springer-Verlag, Berlin), used in this paper as primary standards, were verified, to within an error of less than 1%, by magnesium determination using atomic absorbance spectrophotometry. We also report the determination of accurate extinction coefficients for chlorophylls a and b in N,N′-dimethylformamide, methanol or buffered 80% aqueous acetone. Highly purified chlorophylls were used and methods were employed which not only minimize errors due to evaporation of the volatile solvents employed in their estimation but also eliminate variable micro-contamination by chlorophyll degradation products, a potential source of inconsistency between the extinction coefficients obtained in each of these three solvents. Using these new coefficients, expressed as both millimolar and specific coefficients, we have derived new simultaneous equations to obtain chlorophyll concentrations as nmol/ml and μg/ml, respectively. These equations were applied to data obtained with leaf discs from spinach and Flindersia brayleyana extracted with the three specified solvents and to a concentrated solution (in N,N′ -dimethylformamide) of a chlorophyll a + b mixture added to the threesolvent systems. The validity of these equations is proven by the consistency of the chlorophyll determinations and of the chlorophyll a/b ratios. New simultaneous equations, compatible with the equations derived for the threesolvents, are presented for the assay of chlorophylls a and b converted to their cyclic hydroxylactone derivatives by extraction with alkaline pyridine reagent (2.1 M pyridine in 0.35 M NaOH). Most chlorophyll analyses in higher plants, including the chlorophyll content and chlorophyll a/b ratios of plant thylakoids and chlorophyll-protein complexes, have been obtained in 80% aqueous acetone with the much used simultaneous equations of Arnon (Arnon, D.I. (1949) Plant Physiol. 24, 1–15). For this reason we include conversion factors whichcorrect these earlier data and make it compatible with data calculated with the simultaneous equations presented in this paper. The importance of these corrections to the formulation of meaningful models of the photosynthetic apparatus is demonstrated. Our results also indicate that grinding leaf discs with N,N′-dimethylformamide is a more reliable method for extracting all chlorophylls than shaking with this solvent for 24 h.

title: Leaf Senescence Is Accompanied by an Early Disruption of the Microtubule Network in Arabidopsis1[C][W]
abstract: The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.

title: Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light
abstract: Phytochrome A (phyA) is the only photoreceptor in plants, initiating responses in far-red light and, as such, essential for survival in canopy shade. Although the absorption and the ratio of active versus total phyA are maximal in red light, far-red light is the most efficient trigger of phyA-dependent responses. Using a joint experimental-theoretical approach, we unravel the mechanism underlying this shift of the phyA action peak from red to far-red light and show that it relies on specific molecular interactions rather than on intrinsic changes to phyA's spectral properties. According to our model, the dissociation rate of the phyA-FHY1/FHL nuclear import complex is a principle determinant of the phyA action peak. The findings suggest how higher plants acquired the ability to sense far-red light from an ancestral photoreceptor tuned to respond to red light.

title: Two Photobiological Pathways of Phytochrome A Activity, Only One of Which Shows Dominant Negative Suppression by Phytochrome B
abstract: The plant receptor phytochrome A (phyA) mediates responses like hypocotyl growth inhibition and cotyledon unfolding that require continuous far-red (FR) light for maximum expression (high-irradiance responses, HIR), and responses like seed germination that can be induced by a single pulse of FR (very-low-fluence responses, VLFR). It is not known whether this duality results from either phyA interaction with different end-point processes or from the intrinsic properties of phyA activity. Etiolated seedlings of Arabidopsis thaliana were exposed to pulses of FR (3 min) separated by dark intervals of different duration. Hypocotyl-growth inhibition and cotyledon unfolding showed two phases. The first phase (VLFR) between 0.17 and 0.5 pulses·h−1, a plateau between 0.5 and 2 pulses·h−1 and a second phase (HIR) at higher frequencies. Reciprocity between fluence rate and duration of FR was observed within phases, not between phases. The fluence rate for half the maximum effect was 0.1 and 3 μmol·m−2·s−1 for hourly pulses of FR (VLFR) and continuous FR (HIR), respectively. Overexpression of phytochrome B caused dominant negative suppression under continuous but not under hourly FR. We conclude that phyA is intrinsically able to initiate two discrete photoresponses even when a single end-point process is considered.

title: Phytochrome A is an irradiance-dependent red light sensor.
abstract: Plants perceive red (R) and far-red (FR) light signals using the phytochrome family of photoreceptors. In Arabidopsis thaliana, five phytochromes (phyA-phyE) have been identified and characterized. Unlike other family members, phyA is subject to rapid light-induced proteolytic degradation and so accumulates to relatively high levels in dark-grown seedlings. The insensitivity of phyA mutant seedlings to prolonged FR and wild-type appearance in R has led to suggestions that phyA functions predominantly as an FR sensor during the early stages of seedling establishment. The majority of published photomorphogenesis experiments have, however, used <50 micromol m(-2) sec(-1) of R when characterizing phytochrome functions. Here we reveal considerable phyA activity in R at higher (>160 micromol m(-2) sec(-1)) photon irradiances. Under these conditions, plant architecture was observed to be largely regulated by the redundant actions of phytochromes A, B and D. Moreover, quadruple phyBphyCphyDphyE mutants containing only functional phyA displayed R-mediated de-etiolation and survived to flowering. The enhanced activity of phyA in continuous R (Rc) of high photon irradiance correlates with retarded degradation of the endogenous protein in wild-type plants and prolonged epifluorescence of nuclear-localized phyA:YFP in transgenic lines. Such observations suggest irradiance-dependent 'photoprotection' of nuclear phyA in R, providing a possible explanation for the increased activity observed. The discovery that phyA can function as an effective irradiance sensor, even in light environments that establish a high Pfr concentration, raises the possibility that phyA may contribute significantly to the regulation of growth and development in daylight-grown plants.

title: Enzymes of chlorophyll biosynthesis
abstract: The enzymes responsible for chlorophyll biosynthesis in plants, algae and cyanobacteria are identified and described, with emphasis on their protein composition and structure, required cofactors, physical and catalytic properties, protein-protein interactions and allosteric modulation of activity. Properties and features of the pathway that enable it to operate in a coordinated way while using unstable and light-sensitive intermediates in potentially hostile biochemical environments are discussed. The evolutionary relationships and possible origins of the chlorophyll biosynthetic enzymes are also discussed.

title: Biosynthesis of chlorophyll b and the chlorophyll cycle
abstract: Recent progress in the knowledge of chlorophyll b biosynthesis from chlorophyllide a and reduction of chlorophyll b to chlorophyll a is described. The minireview includes a description of the enzymes involved in these reactions and, where appropriate, of the genes encoding these enzymes. The possible physiological role of the mutual transformation of chlorophylls a and b (chlorophyll cycle) and the evolution of chlorophyll b formation are discussed.

title: Tetrapyrrole biosynthesis in higher plants.
abstract: Tetrapyrroles play vital roles in various biological processes, including photosynthesis and respiration. Higher plants contain four classes of tetrapyrroles, namely, chlorophyll, heme, siroheme, and phytochromobilin. All of the tetrapyrroles are derived from a common biosynthetic pathway. Here we review recent progress in the research of tetrapyrrole biosynthesis from a cellular biological view. The progress consists of biochemical, structural, and genetic analyses, which contribute to our understanding of how the flow and the synthesis of tetrapyrrole molecules are regulated and how the potentially toxic intermediates of tetrapyrrole synthesis are maintained at low levels. We also describe interactions of tetrapyrrole biosynthesis and other cellular processes including the stay-green events, the cell-death program, and the plastid-to-nucleus signal transduction. Finally, we present several reports on attempts for agricultural and horticultural applications in which the tetrapyrrole biosynthesis pathway was genetically modified.

title: STAY-GREEN and Chlorophyll Catabolic Enzymes Interact at Light-Harvesting Complex II for Chlorophyll Detoxification during Leaf Senescence in Arabidopsis[C][W]
abstract: This work shows that the chloroplast-localized components of the chlorophyll catabolic pathway dynamically interact with each other, possibly forming a multiprotein complex specifically localizing to light-harvesting complex II. This interaction likely channels chlorophyll breakdown intermediates and thereby prevents potential chlorophyll-derived phototoxicity during leaf senescence. During leaf senescence, plants degrade chlorophyll to colorless linear tetrapyrroles that are stored in the vacuole of senescing cells. The early steps of chlorophyll breakdown occur in plastids. To date, five chlorophyll catabolic enzymes (CCEs), NONYELLOW COLORING1 (NYC1), NYC1-LIKE, pheophytinase, pheophorbide a oxygenase (PAO), and red chlorophyll catabolite reductase, have been identified; these enzymes catalyze the stepwise degradation of chlorophyll to a fluorescent intermediate, pFCC, which is then exported from the plastid. In addition, STAY-GREEN (SGR), Mendel’s green cotyledon gene encoding a chloroplast protein, is required for the initiation of chlorophyll breakdown in plastids. Senescence-induced SGR binds to light-harvesting complex II (LHCII), but its exact role remains elusive. Here, we show that all five CCEs also specifically interact with LHCII. In addition, SGR and CCEs interact directly or indirectly with each other at LHCII, and SGR is essential for recruiting CCEs in senescing chloroplasts. PAO, which had been attributed to the inner envelope, is found to localize in the thylakoid membrane. These data indicate a predominant role for the SGR-CCE-LHCII protein interaction in the breakdown of LHCII-located chlorophyll, likely to allow metabolic channeling of phototoxic chlorophyll breakdown intermediates upstream of nontoxic pFCC.

title: Developmental and age-related processes that influence the longevity and senescence of photosynthetic tissues in arabidopsis.
abstract: Factors that influence the longevity and senescence of photosynthetic tissues of Arabidopsis were investigated. To determine the influence of reproductive development on the timing of somatic tissue senescence, the longevity of rosette leaves of the Landsberg erecta strain and of isogenic mutant lines in which flowering is delayed (co-2) or sterile flowers are produced (ms1-1) were compared. No difference in the timing of senescence of individual leaves was observed between these lines, indicating that somatic tissue longevity is not governed by reproductive development in this species. To examine the role of differential gene expression in the process of leaf senescence, cDNA clones representing genes that are differentially expressed in senescing tissues were isolated. Sequence analysis of one such clone indicated homology to previously cloned cysteine proteinases, which is consistent with a role for the product of this gene in nitrogen salvage. RNA gel blot analysis revealed that increased expression of senescence-associated genes is preceded by declines in photosynthesis and in the expression of photosynthesis-associated genes. A model is presented in which it is postulated that leaf senescence is triggered by age-related declines in photosynthetic processes.

title: Molecular analysis of natural leaf senescence in Arabidopsis thaliana
abstract: We have analyzed macromolecular changes that are associated with natural leaf senescence in Arabidopsis thaliana. The loss of chlorophyll that is characteristic of leaf senescence is accompanied by a specific pattern of decline of total RNA and protein levels. We have constructed two cDNA libraries representing mRNAs from Arabidopsis leaves at different senescence stages. Six cDNA clones corresponding to mRNAs that substantially increase in abundance during senescence were isolated. The levels of these mRNAs remain elevated into the late stages of senescence when most of the chlorophyll and protein of the leaf has been degraded. Sis cDNA clones that correspond to mRNAs that exhibit contrasting behavior were also identified: the levels of these mRNAs decrease to undetectable levels during senescence. The changes in the levels of these specific mRNAs during the course of senescence are presented. The results indicate that major changes in gene expression occur in Arabidopsis leaves during the process of senescence.

title: Phytochrome regulation of leaf senescence in cucumber and tomato
abstract: A brief irradiation with red light was as effective as continuous white light and kinetin in arresting the losses of chlorophyll and protein in detached whole leaves and leaf discs of cucumber and tomato plants. The effect of red light was completely reversed by a consecutive brief irradiation with far-red light. These results suggesr the involvement of the phytochrome system.

title: The role of sugars in integrating environmental signals during the regulation of leaf senescence.
abstract: Although leaf senescence results in a loss of photosynthetic carbon fixation, the senescence-dependent release of nutrients, especially of nitrogen, is important for the growth of young leaves and for reproduction. Environmental regulation of senescence is therefore a vital factor in the carbon and nitrogen economy of plants. Leaf senescence is a highly plastic trait that is affected by a range of different environmental factors including light, nutrient supply, CO2 concentration, and abiotic and biotic stress. In this review, the focus is on the impact of environmental conditions on sugar accumulation and sugar signalling during senescence. By signalling a high availability of carbon relative to nitrogen in the old leaves, sugar accumulation can trigger leaf senescence. Sugar-induced senescence is therefore particularly important under low nitrogen availability and may also play a role in light signalling. Whether or not sugars are involved in regulating the senescence response of plants to elevated CO2 remains unresolved. Senescence can be delayed or accelerated in elevated CO2 and no clear relationship between sugar accumulation and senescence has been found. Plasticity in the response to environmental factors, such as daylength and sugar accumulation, varies between different Arabidopsis accessions. This natural variation can be exploited to analyse the genetic basis of the regulation of senescence and the consequences for growth and fecundity. Different evolutionary strategies, i.e. early senescence combined with a high reproductive effort or late senescence combined with a low reproductive effort, may be an important adaptation of Arabidopsis accessions to their natural habitat.

title: The control of chlorophyll catabolism and the status of yellowing as a biomarker of leaf senescence.
abstract: The pathway of chlorophyll catabolism during leaf senescence is known in a fair amount of biochemical and cell biological detail. In the last few years, genes encoding a number of the catabolic enzymes have been characterized, including the key ring-opening activities, phaeophorbide a oxygenase (PaO) and red chlorophyll catabolite reductase (RCCR). Recently, a gene that modulates disassembly of chlorophyll-protein complexes and activation of pigment ring-opening has been isolated by comparative mapping in monocot species, positional cloning exploiting rice genomics resources and functional testing in Arabidopsis. The corresponding gene in pea has been identified as Mendel's I locus (green/yellow cotyledons). Mutations in this and other chlorophyll catabolic genes have significant consequences, both for the course of leaf senescence and senescence-like stress responses, notably hypersensitivity to pathogen challenge. Loss of chlorophyll can occur via routes other than the PaO/RCCR pathway, resulting in changes that superficially resemble senescence. Such 'pseudosenescence' responses tend to be pathological rather than physiological and may differ from senescence in fundamental aspects of biochemistry and regulation.

title: Chlorophyll cycle regulates the construction and destruction of the light-harvesting complexes.
abstract: Chlorophyll a and chlorophyll b are the major constituents of the photosynthetic apparatus in land plants and green algae. Chlorophyll a is essential in photochemistry, while chlorophyll b is apparently dispensable for their photosynthesis. Instead, chlorophyll b is necessary for stabilizing the major light-harvesting chlorophyll-binding proteins. Chlorophyll b is synthesized from chlorophyll a and is catabolized after it is reconverted to chlorophyll a. This interconversion system between chlorophyll a and chlorophyll b refers to the chlorophyll cycle. The chlorophyll b levels are determined by the activity of the three enzymes participating in the chlorophyll cycle, namely, chlorophyllide a oxygenase, chlorophyll b reductase, and 7-hydroxymethyl-chlorophyll reductase. This article reviews the recent progress on the analysis of the chlorophyll cycle and its enzymes. In particular, we emphasize the impact of genetic modification of chlorophyll cycle enzymes on the construction and destruction of the photosynthetic machinery. These studies reveal that plants regulate the construction and destruction of a specific subset of light-harvesting complexes through the chlorophyll cycle. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.

title: Regulation and evolution of chlorophyll metabolism.
abstract: Chlorophylls are the most abundant tetrapyrrole molecules essential for photosynthesis in photosynthetic organisms. After many years of intensive research, most of the genes encoding the enzymes for the pathway have been identified, and recently the underlying molecular mechanisms have been elucidated. These studies revealed that the regulation of chlorophyll metabolism includes all levels of control to allow a balanced metabolic flow in response to external and endogenous factors and to ensure adaptation to varying needs of chlorophyll during plant development. Furthermore, identification of biosynthetic genes from various organisms and genetic analysis of functions of identified genes enables us to predict the evolutionary scenario of chlorophyll metabolism. In this review, based on recent findings, we discuss the regulation and evolution of chlorophyll metabolism.

title: Post-translational control of tetrapyrrole biosynthesis in plants, algae, and cyanobacteria.
abstract: The tetrapyrrole biosynthetic pathway provides the vital cofactors and pigments for photoautotrophic growth (chlorophyll), several essential redox reactions in electron transport chains (haem), N- and S-assimilation (sirohaem), and photomorphogenic processes (phytochromobilin). While the biochemistry of the pathway is well understood and almost all genes encoding enzymes of tetrapyrrole biosynthesis have been identified in plants, the post-translational control and organization of the pathway remains to be clarified. Post-translational mechanisms controlling metabolic activities are of particular interest since tetrapyrrole biosynthesis needs adaptation to environmental challenges. This review surveys post-translational mechanisms that have been reported to modulate metabolic activities and organization of the tetrapyrrole biosynthesis pathway.

title: Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors
abstract: PIF3 is a phytochrome-interacting basic helix–loop–helix transcription factor that negatively regulates light responses, including hypocotyl elongation, cotyledon opening, and hypocotyl negative gravitropism. However, the role of PIF3 in chlorophyll biosynthesis has not been clearly defined. Here, we show that PIF3 also negatively regulates chlorophyll biosynthesis by repressing biosynthetic genes in the dark. Consistent with the gene expression patterns, the etiolated pif3 mutant accumulated a higher amount of protochlorophyllide and was bleached severely when transferred into light. The photobleaching phenotype of pif3 could be suppressed by the gun5 mutation and mimicked by overexpression of GUN5. When 4 negative phytochrome-interacting protein genes (PIF1, PIF3, PIF4, and PIF5) were mutated, the resulting quadruple mutant seedlings displayed constitutive photomorphogenic phenotypes, including short hypocotyls, open cotyledons, and disrupted hypocotyl gravitropism in the dark. Microarray analysis further confirmed that the dark-grown quadruple mutant has a gene expression pattern similar to that of red light-grown WT. Together, our data indicate that 4 phytochrome-interacting proteins are required for skotomorphogenesis and phytochromes activate photomorphogenesis by inhibiting these factors.

title: Multiple transcription-factor genes are early targets of phytochrome A signaling
abstract: The phytochrome family of sensory photoreceptors directs adaptational changes in gene expression in response to environmental light signals. Using oligonucleotide microarrays to measure expression profiles in wild-type and phytochrome A (phyA) null-mutant Arabidopsis seedlings, we have shown that 10% of the genes represented on the array are regulated by phyA in response to a continuous far-red light signal. Strikingly, 44% of the genes responding to the signal within 1 h are predicted to encode multiple classes of transcriptional regulators. Together with previous data, this observation suggests that phyA may regulate seedling photomorphogenesis by direct targeting of light signals to the promoters of genes encoding a master set of diverse transcriptional regulators, responsible in turn for orchestrating the expression of multiple downstream target genes in various branches of a phyA-regulated transcriptional network.

title: Phytochrome regulates translation of mRNA in the cytosol
abstract: An array of photoreceptors including cryptochromes, phototropin, and phytochromes regulates various light responses in plants. Among these photoreceptors, phytochromes perceive red and far-red light by switching between two interconvertible spectral forms (Pr and Pfr). The Pfr form promotes light responses partly by destabilizing negatively acting, phytochrome-interacting basic helix-loop-helix transcription factors (PIFs), thus modulating transcription in the nucleus. The Pfr form is also present in the cytosol. However, the role of phytochromes in the cytosol is not well understood. Here we show that the Pfr form interacts with the cytosolic protein PENTA1 (PNT1) and inhibits the translation of protochlorophyllide reductase (PORA) mRNA. PNT1 possesses five C3H-type zinc finger domains and displays similarity to various RNA binding proteins including Tristetraprolin, which regulates stabilities of mRNAs such as TNF-α mRNA in humans. Consistent with its function as an RNA binding protein, PNT1 directly binds to mRNA of a key chlorophyll biosynthetic gene, protochlorophyllide reductase in vivo and inhibits the translation of PORA mRNA in the presence of phytochromes. The present results demonstrate that phytochromes transmit light signals to regulate not only transcription in the nucleus through PIFs, but also translation in the cytosol through PNT1.

title: Photoreceptor signaling networks in plant responses to shade.
abstract: The dynamic light environment of vegetation canopies is perceived by phytochromes, cryptochromes, phototropins, and UV RESISTANCE LOCUS 8 (UVR8). These receptors control avoidance responses to preclude exposure to limiting or excessive light and acclimation responses to cope with conditions that cannot be avoided. The low red/far-red ratios of shade light reduce phytochrome B activity, which allows PHYTOCHROME INTERACTING FACTORS (PIFs) to directly activate the transcription of auxin-synthesis genes, leading to shade-avoidance responses. Direct PIF interaction with DELLA proteins links gibberellin and brassinosteroid signaling to shade avoidance. Shade avoidance also requires CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), a target of cryptochromes, phytochromes, and UVR8. Multiple regulatory loops and the input of the circadian clock create a complex network able to respond even to subtle threats of competition with neighbors while still compensating for major environmental fluctuations such as the day-night cycles.

title: PIF3 is a repressor of chloroplast development
abstract: The phytochrome-interacting factor PIF3 has been proposed to act as a positive regulator of chloroplast development. Here, we show that the pif3 mutant has a phenotype that is similar to the pif1 mutant, lacking the repressor of chloroplast development PIF1, and that a pif1pif3 double mutant has an additive phenotype in all respects. The pif mutants showed elevated protochlorophyllide levels in the dark, and etioplasts of pif mutants contained smaller prolamellar bodies and more prothylakoid membranes than corresponding wild-type seedlings, similar to previous reports of constitutive photomorphogenic mutants. Consistent with this observation, pif1, pif3, and pif1pif3 showed reduced hypocotyl elongation and increased cotyledon opening in the dark. Transfer of 4-d-old dark-grown seedlings to white light resulted in more chlorophyll synthesis in pif mutants over the first 2 h, and analysis of gene expression in dark-grown pif mutants indicated that key tetrapyrrole regulatory genes such as HEMA1 encoding the rate-limiting step in tetrapyrrole synthesis were already elevated 2 d after germination. Circadian regulation of HEMA1 in the dark also showed reduced amplitude and a shorter, variable period in the pif mutants, whereas expression of the core clock components TOC1, CCA1, and LHY was largely unaffected. Expression of both PIF1 and PIF3 was circadian regulated in dark-grown seedlings. PIF1 and PIF3 are proposed to be negative regulators that function to integrate light and circadian control in the regulation of chloroplast development.

title: PIFs: pivotal components in a cellular signaling hub.
abstract: A small subset of basic helix-loop-helix transcription factors called PIFs (phytochrome-interacting factors) act to repress seed germination, promote seedling skotomorphogenesis and promote shade-avoidance through regulated expression of over a thousand genes. Light-activated phytochrome molecules directly reverse these activities by inducing rapid degradation of the PIF proteins. Here, we review recent advances in dissecting this signaling pathway and examine emerging evidence that indicates that other pathways also converge to regulate PIF activity, including the gibberellin pathway, the circadian clock and high temperature. Thus PIFs have broader roles than previously appreciated, functioning as a cellular signaling hub that integrates multiple signals to orchestrate regulation of the transcriptional network that drives multiple facets of downstream morphogenesis. The relative contributions of the individual PIFs to this spectrum of regulatory functions ranges from quantitatively redundant to qualitatively distinct.

title: PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis
abstract: Plants depend on light signals to modulate many aspects of their development and optimize their photosynthetic capacity. Phytochromes (phys), a family of photoreceptors, initiate a signal transduction pathway that alters expression of a large number of genes to induce these responses. Recently, phyA and phyB were shown to bind members of a basic helix–loop–helix family of transcription factors called phy-interacting factors (PIFs). PIF1 negatively regulates chlorophyll biosynthesis and seed germination in the dark, and light-induced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Here, we report that PIF1 regulates expression of a discrete set of genes in the dark, including protochlorophyllide oxidoreductase (POR), ferrochelatase (FeChII), and heme oxygenase (HO3), which are involved in controlling the chlorophyll biosynthetic pathway. Using ChIP and DNA gel-shift assays, we demonstrate that PIF1 directly binds to a G-box (CACGTG) DNA sequence element present in the PORC promoter. Moreover, in transient assays, PIF1 activates transcription of PORC in a G-box-dependent manner. These data strongly suggest that PIF1 directly and indirectly regulates key genes involved in chlorophyll biosynthesis to optimize the greening process in Arabidopsis.

title: Light and diurnal regulation of plant respiratory gene expression.
abstract: Light is both the energy source and the dominant signalling input for photosynthetic organisms. Accordingly, up to 30–50% of the genes expressed in plant leaves are directly or indirectly regulated by light, and virtually all aspects of plant metabolism support photosynthesis, depend upon the products of photosynthesis or are affected by photosynthesis-related changes in metabolite levels. Though not directly tied to photosynthesis per se, mitochondria support several light-associated processes, including photorespiration, nitrogen metabolism, reductant transport and the maintenance of redox balance. Recently, it has become increasingly apparent that diverse light signalling pathways intersect with the mitochondrion, and that cellular respiration and photosynthesis display tight functional and regulatory coordination. In addition, global transcript analyses performed on plants exposed to different light qualities and intensities have started to provide promising starting points for the next series of investigations of light/diurnal regulation of respiratory metabolism.

title: Phytochrome-mediated regulation of plant respiration and photorespiration.
abstract: The expression of genes encoding various enzymes participating in photosynthetic and respiratory metabolism is regulated by light via the phytochrome system. While many photosynthetic, photorespiratory and some respiratory enzymes, such as the rotenone-insensitive NADH and NADPH dehydrogenases and the alternative oxidase, are stimulated by light, succinate dehydrogenase, subunits of the pyruvate dehydrogenase complex, cytochrome oxidase and fumarase are inhibited via the phytochrome mechanism. The effect of light, therefore, imposes limitations on the tricarboxylic acid cycle and on the mitochondrial electron transport coupled to ATP synthesis, while the non-coupled pathways become activated. Phytochrome-mediated regulation of gene expression also creates characteristic distribution patterns of photosynthetic, photorespiratory and respiratory enzymes across the leaf generating different populations of mitochondria, either enriched by glycine decarboxylase (in the upper part) or by succinate dehydrogenase (in the bottom part of the leaf).

title: Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis.
abstract: An analysis of changes in global gene expression patterns during developmental leaf senescence in Arabidopsis has identified more than 800 genes that show a reproducible increase in transcript abundance. This extensive change illustrates the dramatic alterations in cell metabolism that underpin the developmental transition from a photosynthetically active leaf to a senescing organ which functions as a source of mobilizable nutrients. Comparison of changes in gene expression patterns during natural leaf senescence with those identified, when senescence is artificially induced in leaves induced to senesce by darkness or during sucrose starvation-induced senescence in cell suspension cultures, has shown not only similarities but also considerable differences. The data suggest that alternative pathways for essential metabolic processes such as nitrogen mobilization are used in different senescent systems. Gene expression patterns in the senescent cell suspension cultures are more similar to those for dark-induced senescence and this may be a consequence of sugar starvation in both tissues. Gene expression analysis in senescing leaves of plant lines defective in signalling pathways involving salicylic acid (SA), jasmonic acid (JA) and ethylene has shown that these three pathways are all required for expression of many genes during developmental senescence. The JA/ethylene pathways also appear to operate in regulating gene expression in dark-induced and cell suspension senescence whereas the SA pathway is not involved. The importance of the SA pathway in the senescence process is illustrated by the discovery that developmental leaf senescence, but not dark-induced senescence, is delayed in plants defective in the SA pathway.