Fluence-response curves and action spectra for promotion and inhibition of seed germination in wildtype and long-hypocotyl mutants of Arabidopsis thaliana L

Application of Multi-Omics Technologies to the Study of Phytochromes in Plants

Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.

Phytochrome B links the environment to transcription

Phytochrome B (phyB) senses the difference between darkness and light, the level of irradiance, the red/far-red ratio, and temperature. Thanks to these sensory capacities, phyB perceives whether plant organs are buried in the soil, exposed to full sunlight, in the presence of nearby vegetation, and/or under risk of heat stress. In some species, phyB perceives seasonal daylength cues. phyB affects the activity of several transcriptional regulators either by direct physical interaction or indirectly by physical interaction with proteins involved in the turnover of transcriptional regulators. Typically, interaction of a protein with phyB has either negative or positive effects on the interaction of the latter with a third party, this being another protein or DNA. Thus, phyB mediates the context-dependent modulation of the transcriptome underlying changes in plant morphology, physiology, and susceptibility to biotic and abiotic stress. phyB operates as a dynamic switch that improves carbon balance, prioritizing light interception and photosynthetic capacity in open places and the projection of the shoot towards light in the soil, under shade and in warm conditions.

Seed dormancy and germination

Seed dormancy allows seeds to overcome periods that are unfavourable for seedling established and is therefore important for plant ecology and agriculture. Several processes are known to be involved in the induction of dormancy and in the switch from the dormant to the germinating state. The role of plant hormones, the different tissues and genes involved, including newly identified genes in dormancy and germination are described in this chapter, as well as the use transcriptome, proteome and metabolome analyses to study these mechanistically not well understood processes.

Tomato seed germination: regulation of different response modes by phytochrome B2 and phytochrome A

Lycopersicon esculentum seeds germinate after rehydration in complete darkness. This response was inhibited by a far-red light (FR) pulse, and the inhibition was reversed by a red light (R) pulse. Comparison of germination in phytochrome-deficient mutants (phyA, phyB1, phyB2, phyAB1, phyB1B2 and phyAB1B2) showed that phytochrome B2 (PhyB2) mediates both responses. The germination was inhibited by strong continuous R (38 micromol m(-2) s(-1)), whereas weak R (28 nmol m(-2) s(-1)) stimulated seed germination. Hourly applied R pulses of the same photon fluence partially replaced the effect of strong continuous R. This response was called 'antagonistic' because it counteracts the low fluence response (LFR) induced by a single R pulse. This antagonistic response might be an adaptation to a situation where the seeds sit on the soil surface in full sunlight (adverse for germination), while weak R might reflect that situation under a layer of soil. Unexpectedly, the effects of continuous R or repeated R pulses were mediated by phytochrome A (PhyA). We therefore suggest that low levels of PhyA in its FR-absorbing form (Pfr) cause inhibition of seed germination produced either by extended R irradiation (by degradation of PhyA-Pfr) or by extended FR irradiation [keeping a low Pfr/R-absorbing form (Pr) ratio].

Changes in the light sensitivity of buried Polygonum aviculare seeds in relation to cold-induced dormancy loss: development of a predictive model

The effect of cold (stratification) temperature on changes in the sensitivity of Polygonum aviculare seeds to light was investigated. Seeds buried in pots were stored under stratification temperatures (1.6, 7 and 12 degrees C) for 137 d. Seeds exhumed at regular intervals during storage were exposed to different light treatments. Germination responses obtained for seeds exposed to different light treatments and stratification temperatures were used to develop a model to predict the sensitivity of buried seeds to light. Seed sensitivity to light increased as dormancy loss progressed, showing the successive acquisition of low-fluence responses (LFR), very low-fluence responses (VLFR), and the loss of the light requirement for germination for a fraction of the seed population. These changes were inversely correlated to stratification temperature, allowing the use of a thermal time index to relate observed changes in seed light sensitivity to stratification temperature. The rate of increase in sensitivity of P. aviculare seeds to light during stratification is inversely correlated to soil temperature, and these changes in light sensitivity could be predicted in relation to temperature using thermal-time models.

Phenotypic characterization of a photomorphogenic mutant

Light is arguably the most important abiotic factor controlling plant growth and development throughout their life cycle. Plants have evolved sophisticated light-sensing mechanisms to monitor fluctuations in light quality, intensity, direction and periodicity (day length). In Arabidopsis, three families of photoreceptors have been identified by molecular genetic studies. The UV-A/blue light receptors cryptochromes and the red/far-red receptors phytochromes control an overlapping set of responses including photoperiodic flowering induction and de-etiolation. Phototropins are the primary photoreceptors for a set of specific responses to UV-A/blue light such as phototropism, chloroplast movement and stomatal opening. Mutants affecting a photoreceptor have a characteristic phenotype. It is therefore possible to determine the specific developmental responses and the photoreceptor pathway(s) affected in a mutant by performing an appropriate set of photobiological and genetic experiments. In this paper, we outline the principal and easiest experiments that can be performed to obtain a first indication about the nature of the photobiological defect in a given mutant.

Phytochrome regulation of seed germination

Seed germination of many plant species is influenced by light. Of the various photoreceptor systems, phytochrome plays an especially important role in seed germination. The existence of at least five phytochrome genes has led to the proposal that different members of the family have different roles in the photoregulation of seed germination. Physiological analysis of seed germination ofArabidopsis thaliana (L.) Heynh. with phytochrome-deficient mutants showed for the first time that phytochrome A and phytochrome B modulate the timing of seed germination in distinct actions. Phytochrome A photo-irreversibly triggers the photoinduction of seed germination after irradiation with extremely low fluence light in a wide range of wavelengths, from UV-A, to visible, to far-red. In contrast, phytochrome B mediates the well-characterized photoreversible reaction, responding to red and far-red light of fluences four orders of magnitude higher than those to which PhyA responds. Wild plants, such asA. thaliana, survive under ground as dormant seeds for long periods, and the timing of seed germination is crucial for optimizing growth and reproduction. It therefore seems reasonable for plants to possess at least two different physiological systems for sensing the light environment over a wide spectral range with exquisite sensitivity of different phytochromes. This redundancy seems to enhance plant survival in a fluctuating environment.

Flowers into shoots: photo and hormonal control of a meristem identity switch in Arabidopsis

Little is known about the signals that govern the network of meristem and organ identity genes that control flower development. In Arabidopsis, we can induce a heterochronic switch from flower to shoot development, a process known as floral meristem reversion, by manipulating photo-period in the floral homeotic mutant agamous and in plants heterozygous for the meristem identity gene leafy. The transformation from flower to shoot meristem is suppressed by hy1, a mutation blocking phytochrome activity, by spindly, a mutation that activates basal gibberellin signal transduction in a hormone independent manner, or by the exogenous application of gibberellins. We propose that LFY and AG play an important role in the maintenance of flower meristem identity and that floral meristem reversion in heterozygous lfy and in ag flowers is regulated by a phytochrome and gibberellin signal transduction cascade.

LIGHT CONTROL OF SEEDLING DEVELOPMENT

Light control of plant development is most dramatically illustrated by seedling development. Seedling development patterns under light (photomorphogenesis) are distinct from those in darkness (skotomorphogenesis or etiolation) with respect to gene expression, cellular and subcellular differentiation, and organ morphology. A complex network of molecular interactions couples the regulatory photoreceptors to developmental decisions. Rapid progress in defining the roles of individual photoreceptors and the downstream regulators mediating light control of seedling development has been achieved in recent years, predominantly because of molecular genetic studies in Arabidopsis thaliana and other species. This review summarizes those important recent advances and highlights the working models underlying the light control of cellular development. We focus mainly on seedling morphogenesis in Arabidopsis but include complementary findings from other species.

Impaired splicing of phytochrome B pre-mRNA in a novel phyB mutant of Arabidopsis

Phytochrome is the red/far-red absorbing photoreceptor active in photomorphogenesis, the apoprotein of which is encoded by a small gene family (PHYA, PHYB, PHYC, PHYD and PHYE). A novel phytochrome B-deficient mutant, phyB-103, was isolated from a screen of EMS-mutagenised Arabidopsis M2 seed. phyB-103 carries a G-to-A base substitution at the 5' splice site +1 G nucleotide of intron 1 of PHYB. The phyB-103 PHYB transcript is larger than the wild-type PHYB transcript and DNA sequence analysis showed that the entire intron is retained in the mature PHYB transcript of phyB-103. Thus the phyB-103 G-to-A substitution prevents intron splicing. The retained intron contains within it an in-frame stop codon, and the predicted PHYB-003 apoprotein thus terminates prematurely. phyB-103 is therefore likely to be a null allele of PHYB, consistent with the observation that the phenotype conferred by phyB-103 is as severe as that conferred by previously described phyB null alleles.

In vitro formation of a photoreversible adduct of phycocyanobilin and tobacco apophytochrome B

The light-stable tobacco phytochrome apoprotein (PHYB) expressed in yeast can be assembled with phycocyanobilin to give a photoreversible adduct. The spectral properties of the reconstituted PHYB-phycocyanobilin species were determined by absorbacen and difference absorbance spectroscopies. The holoprotein exhibits absorbance maxima at 408 nm and 712 nm for the far-red-light-absorbing (Pfr) form and 356 nm and 658 nm for the red-light-absorbing (Pr) form. The ligation of the chromophores to the dimeric PHYB apoprotein resulted in a PHYB-phycocyanobilin adduct with the spectral properties of the Pr form. Kinetic analyses of the in vitro reconstitution for PHYB apoprotein under saturating concentrations of phycocyanobilin revealed a pseudo first-order rate constant of 2.8 x 10(-2)s.-1. The similarity with the reported rate constant for the reconstitution of light-labile phytochrome (PHYA) from oat [Li, L. & Lagarias, J.C. (1992) Phytochrome assembly, J. Biol. Chem. 267, 19,204-19,210] suggests that the mechanisms of chromophore attachment are probably very similar for PHYA and PHYB.

Phytochrome-regulated expression of genes encoding light-harvesting chlorophyll a/b-protein in two long hypocotyl mutants and wild type plants of Arabidopsis thaliana

The cab genes which encode the light-harvesting chlorophyll a/b-protein (LHCP) are expressed normally with respect to phytochrome regulation in the hy-3 and hy-5 long hypocotyl mutants of Arabidopsis thaliana. In etiolated seedlings of these mutants as well as of the wild type, 1 min of red light elevates cab mRNA levels substantially within 2 h; this increase is reversed if far-red light is given immediately after the red light treatment. We conclude that the genetic defects in these mutants do not affect steps in the signal transduction pathway leading to the regulated expression of cab genes. Additionally, the mRNA from one of the three known A. thaliana cab genes, AB140, is similar in quantity to the mRNAs from the other two, AB165 and AB180, in dark-grown seedlings of hy-3 and hy-5 as well as the parent A. thaliana (Landsberg) after a brief red light treatment. This aspect of cab gene expression differs from the strain Columbia of A. thaliana in which AB140 mRNA is the predominant message. In mature white light-grown plants of the strain Columbia, AB140 as well as a combination of AB165 and AB180 mRNAs are expressed at high levels, suggesting that AB165 and/or AB180 may be developmentally regulated.

Phytochrome regulation of greening in wild type and long-hypocotyl mutants ofArabidopsis thaliana

A brief pulse of red light (R) given to darkgrown seedlings ofArabidopsis thaliana (L.) Heyn. potentiates rapid synthesis of chlorophyll upon transfer to continuous white light. The time course for potentiation of rapid greening shows that a R pulse in the LF (low fluence) range has maximal effect within a few hours, and that there is a small VLF (very low fluence) component as well. Partial reversal of the effect of R by far-red light (FR) indicates that the pulse acts through phytochrome. As it does in the wild-type (WT), a pulse of R accelerates greening of long-hypocotyl (hy) mutants. The extent of induction by the R pulse was about the same in the WT and in allhy mutants studied. Reversibility by FR was greatly decreased in thehy-1 andhy-2 strains. It is possible that these mutants contain a species of phytochrome with defective phototransformation kinetics. If there is such a defective phytochrome species, it nevertheless appears to be active in the potentiation of rapid greening.