Cryptochrome 2 extensively regulates transcription of the chloroplast genome in tomato

Light-Dependent Regulatory Interactions between the Redox System and miRNAs and Their Biochemical and Physiological Effects in Plants

Light intensity and spectrum play a major role in the regulation of the growth, development, and stress response of plants. Changes in the light conditions affect the formation of reactive oxygen species, the activity of the antioxidants, and, consequently, the redox environment in the plant tissues. Many metabolic processes, thus the biogenesis and function of miRNAs, are redox-responsive. The miRNAs, in turn, can modulate various components of the redox system, and this process is also associated with the alteration in the intensity and spectrum of the light. In this review, we would like to summarise the possible regulatory mechanisms by which the alterations in the light conditions can influence miRNAs in a redox-dependent manner. Daily and seasonal fluctuations in the intensity and spectral composition of the light can affect the expression of miRNAs, which can fine-tune the various physiological and biochemical processes due to their effect on their target genes. The interactions between the redox system and miRNAs may be modulated by light conditions, and the proposed function of this regulatory network and its effect on the various biochemical and physiological processes will be introduced in plants.

Plant photoreceptors and their signalling components in chloroplastic anterograde and retrograde communication

The red phytochrome and blue cryptochrome plant photoreceptors play essential roles in promoting genome-wide changes in nuclear and chloroplastic gene expression for photomorphogenesis, plastid development, and greening. While their importance in anterograde signalling has been long recognized, the molecular mechanisms involved remain under active investigation. More recently, the intertwining of the light signalling cascades with the retrograde signals for the optimization of chloroplast functions has been acknowledged. Advances in the field support the participation of phytochromes, cryptochromes, and key light-modulated transcription factors, including HY5 and the PIFs, in the regulation of chloroplastic biochemical pathways that produce retrograde signals, including the tetrapyrroles and the chloroplastic MEP-isoprenoids. Interestingly, in a feedback loop, the photoreceptors and their signalling components are targets themselves of these retrograde signals, aimed at optimizing photomorphogenesis to the status of the chloroplasts, with GUN proteins functioning at the convergence points. High light and shade are also conditions where the photoreceptors tune growth responses to chloroplast functions. Interestingly, photoreceptors and retrograde signals also converge in the modulation of dual-localized proteins (chloroplastic/nuclear) including WHIRLY and HEMERA/pTAC12, whose functions are required for the optimization of photosynthetic activities in changing environments and are proposed to act themselves as retrograde signals.

Cryptochromes and the Circadian Clock: The Story of a Very Complex Relationship in a Spinning World

Cryptochromes are flavin-containing blue light photoreceptors, present in most kingdoms, including archaea, bacteria, plants, animals and fungi. They are structurally similar to photolyases, a class of flavoproteins involved in light-dependent repair of UV-damaged DNA. Cryptochromes were first discovered in Arabidopsis thaliana in which they control many light-regulated physiological processes like seed germination, de-etiolation, photoperiodic control of the flowering time, cotyledon opening and expansion, anthocyanin accumulation, chloroplast development and root growth. They also regulate the entrainment of plant circadian clock to the phase of light-dark daily cycles. Here, we review the molecular mechanisms by which plant cryptochromes control the synchronisation of the clock with the environmental light. Furthermore, we summarise the circadian clock-mediated changes in cell cycle regulation and chromatin organisation and, finally, we discuss a putative role for plant cryptochromes in the epigenetic regulation of genes.

Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions

Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.

Coordinating light responses between the nucleus and the chloroplast, a role for plant cryptochromes and phytochromes

To promote photomorphogenesis, including plastid development and metabolism, the phytochrome (phy) and the cryptochrome (cry) photoreceptors orchestrate genome-wide changes in gene expression in response to Red (R)- and Blue (B)-light cues. While phys and crys have a clear role in modulating photosynthesis, their role in the coordination of the nuclear genome and the plastome, essential for functional chloroplasts, remains underexplored. Using publicly available genome datasets for WT and phyABCDE or cry1cry2 Arabidopsis seedlings, grown, respectively, under R- or B-light, we bioinformatically analyzed the influence of light inputs and photoreceptors in the control of nuclear genes with a function in the chloroplast, and evaluated the role of phyB in the modulation of plastome-encoded genes. We show gene co-induction by R-phys and B-crys for genes with a chloroplastic function, and also apparent photoreceptor-driven preferential responses. Evidence from phyB in Arabidopsis together with published evidence from CRY2 in tomato also supports the participation of both photoreceptor families in the global modulation of the plastome genes. To begin addressing how these light-sensors orchestrate changes in an organellar genome, we evaluated their effect over genes with potential functions in plastid gene-expression regulation based on their TAIR annotation. Results indicate that both crys and phys modulate 'plastome-regulatory genes' with enrichment in the contribution of crys to all processes and of phys to post-transcription and transcription. Furthermore, we identified a new role for HY5 as a relevant light-signaling component in photoreceptor-based anterograde signaling leading to plastome gene regulation.

Pivotal Roles of Cryptochromes 1a and 2 in Tomato Development and Physiology

Cryptochromes are flavin-containing blue/UVA light photoreceptors that regulate various plant light-induced physiological processes. In Arabidopsis (Arabidopsis thaliana), cryptochromes mediate de-etiolation, photoperiodic control of flowering, entrainment of the circadian clock, cotyledon opening and expansion, anthocyanin accumulation, and root growth. In tomato (Solanum lycopersicum), cryptochromes are encoded by a multigene family, comprising CRY1a, CRY1b, CRY2, and CRY3 We have previously reported the phenotypes of tomato cry1a mutants and CRY2 overexpressing plants. Here, we report the isolation by targeting induced local lesions in genomes, of a tomato cry2 knock-out mutant, its introgression in the indeterminate Moneymaker background, and the phenotypes of cry1a/cry2 single and double mutants. The cry1a/cry2 mutant showed phenotypes similar to its Arabidopsis counterpart (long hypocotyls in white and blue light), but also several additional features such as increased seed weight and internode length, enhanced hypocotyl length in red light, inhibited primary root growth under different light conditions, anticipation of flowering under long-day conditions, and alteration of the phase of circadian leaf movements. Both cry1a and cry2 control the levels of photosynthetic pigments in leaves, but cry2 has a predominant role in fruit pigmentation. Metabolites of the sterol, tocopherol, quinone, and sugar classes are differentially accumulated in cry1a and cry2 leaves and fruits. These results demonstrate a pivotal role of cryptochromes in controlling tomato development and physiology. The manipulation of these photoreceptors represents a powerful tool to influence important agronomic traits such as flowering time and fruit quality.

Influence of light intensity on chloroplast development and pigment accumulation in the wild-type and etiolated mutant plants of Anthurium andraeanum 'Sonate'

Seedlings of wild-type and etiolate mutant plants of Anthurium andraeanum cultivar 'Sonate' were treated for 15 d with different light intensities (20, 100, and 400 µmol·m^-2·s^-1) to analyze leaf plastid development and pigment content. Significant changes appeared in treated seedlings, including in leaf color, plastid ultrastructure, chloroplast development gene AaGLK expression, chlorophyll and anthocyanin contents, and protoplast shape. Wild-type and etiolated plants exhibited different plastid structures under the same light condition. The results suggest that light intensity is a crucial environmental factor influencing plastid development and leaf color formation in the A. andraeanum cultivar 'Sonate'.

Tomato plants use non-enzymatic antioxidant pathways to cope with moderate UV-A/B irradiation: A contribution to the use of UV-A/B in horticulture

Plants developed receptors for solar UV-A/B radiation, which regulate a complex network of functions through the plant's life cycle. However, greenhouse grown crops, like tomato, are exposed to strongly reduced UV radiation, contrarily to their open-field counterparts. A new paradigm of modern horticulture is to supplement adequate levels of UV to greenhouse cultures, inducing a positive mild stress necessary to stimulate oxidative stress pathways and antioxidant mechanisms. Protected cultures of Solanum (cv MicroTom) were supplemented with moderate UV-A (1h and 4h) and UV-B (1min and 5min) doses during the flowering/fruiting period. After 30days, flowering/fruit ripening synchronization were enhanced, paralleled by the upregulation of blue/UV-A and UV-B receptors' genes cry1a and uvr8. UV-B caused moreover an increase in the expression of hy5, of HY5 repressor cop1 and of a repressor of COP1, uvr8. While all UV-A/B conditions increased SOD activity, increases of the generated H₂O₂, as well as lipid peroxidation and cell mebrane disruption, were minimal. However, the activity of antioxidant enzymes downstream from SOD (CAT, APX, GPX) was not significant. These results suggest that the major antioxidant pathways involve phenylpropanoid compounds, which also have an important role in UV screening. This hypothesis was confirmed by the increase of phenolic compounds and by the upregulation of chs and fls, coding for CHS and FLS enzymes involved in the phenylpropanoid synthesis. Overall, all doses of UV-A or UV-B were beneficial to flowering/fruiting but lower UV-A/B doses induced lower redox disorders and were more effective in the fruiting process/synchronization. Considering the benefits observed on flowering/fruiting, with minimal impacts in the vegetative part, we demonstrate that both UV-A/B could be used in protected tomato horticulture systems.

Photoreceptor Mediated Plant Growth Responses: Implications for Photoreceptor Engineering toward Improved Performance in Crops

Rising temperatures during growing seasons coupled with altered precipitation rates presents a challenging task of improving crop productivity for overcoming such altered weather patterns and cater to a growing population. Light is a critical environmental factor that exerts a powerful influence on plant growth and development ranging from seed germination to flowering and fruiting. Higher plants utilize a suite of complex photoreceptor proteins to perceive surrounding red/far-red (phytochromes), blue/UV-A (cryptochromes, phototropins, ZTL/FKF1/LKP2), and UV-B light (UVR8). While genomic studies have also shown that light induces extensive reprogramming of gene expression patterns in plants, molecular genetic studies have shown that manipulation of one or more photoreceptors can result in modification of agronomically beneficial traits. Such information can assist researchers to engineer photoreceptors via genome editing technologies to alter expression or even sensitivity thresholds of native photoreceptors for targeting aspects of plant growth that can confer superior agronomic value to the engineered crops. Here we summarize the agronomically important plant growth processes influenced by photoreceptors in crop species, alongwith the functional interactions between different photoreceptors and phytohormones in regulating these responses. We also discuss the potential utility of synthetic biology approaches in photobiology for improving agronomically beneficial traits of crop plants by engineering designer photoreceptors.

Deficiency in phytochrome A alters photosynthetic activity, leaf starch metabolism and shoot biomass production in tomato

Photosynthesis is a key process that promotes plant growth and development. Light provides photosynthetic organisms with a major source of energy to fix carbon dioxide into organic matter. Of the entire visible light spectrum, red/blue light are known to maximise photosynthetic performance and are thus essential for proper growth and development of plants. Red and blue light stimulate synthesis of chlorophyll and orchestrate the positioning of leaves and chloroplasts for optimal utilisation of light, both of which are critical for photosynthesis. The response of plants to external light cues is accomplished via finely tuned complex photoreceptors and signaling mechanisms which enable them to continually monitor light availability and quality for optimal utilisation of light energy towards enhancing their growth. Higher plants contain a suite of photoreceptor proteins that allow them to perceive red, blue/UV-A and UV-B light. Analyses of the phyA mutant of tomato deficient in the red-light photoreceptor phytochrome A (phyA), showed reduced photosynthetic activity of isolated chloroplasts along with decreased shoot biomass in adult plants. The regulation of leaf transitory starch in the mutant was also altered as compared to the wild type (cv Moneymaker). Our results suggest a possible role for phyA in these processes in tomato.