Piecing the Puzzle Together: The Central Role of Reactive Oxygen Species and Redox Hubs in Chloroplast Retrograde Signaling

Reactive oxygen species: Multidimensional regulators of plant adaptation to abiotic stress and development

Reactive oxygen species (ROS) are produced as undesirable by-products of metabolism in various cellular compartments, especially in response to unfavorable environmental conditions, throughout the life cycle of plants. Stress-induced ROS production disrupts normal cellular function and leads to oxidative damage. To cope with excessive ROS, plants are equipped with a sophisticated antioxidative defense system consisting of enzymatic and non-enzymatic components that scavenge ROS or inhibit their harmful effects on biomolecules. Nonetheless, when maintained at relatively low levels, ROS act as signaling molecules that regulate plant growth, development, and adaptation to adverse conditions. Here, we provide an overview of current approaches for detecting ROS. We also discuss recent advances in understanding ROS signaling, ROS metabolism, and the roles of ROS in plant growth and responses to various abiotic stresses.

Singlet Oxygen and Superoxide Anion Radical Detection by EPR Spin Trapping in Thylakoid Preparations

Reactive oxygen species (ROS) are produced by energy transfer and electron transport in plant chloroplast thylakoids at non-toxic levels under normal growth conditions, but at threatening levels under adverse or fluctuating environmental conditions. Among chloroplast ROS, singlet oxygen and superoxide anion radical, respectively, produced by photosystem II (PSII) and PSI, are known to be the major ROS under several stress conditions. Both are very unlikely to diffuse out of chloroplasts, but they are instead capable of triggering ROS-mediated chloroplast operational retrograde signalling to activate defence gene expression in concert with hormones and other molecular compounds. Therefore, their detection, identification and localization in vivo or in biological preparations is a priority for a deeper understanding of their role in (concurrent) regulation of plant growth and defence responses. Here, we present two EPR spin traps, abbreviated as TEMPD-HCl and DEPMPO, to detect and identify ROS in complex systems, such as isolated thylakoids, together with some hints and cautions to perform reliable spin trapping experiments.

Quantifying the impact of dynamic plant-environment interactions on metabolic regulation

A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.

Salicylate and jasmonate intertwine in ROS-triggered chloroplast-to-nucleus retrograde signaling

Plants, being sessile, are frequently exposed to environmental perturbations, affecting their sustenance and survival. In response, distinct inherent mechanisms emerged during plant evolution to deal with environmental stresses. Among various organelles, chloroplast plays an indispensable role in plant cells. Besides providing the site for photosynthesis and biosynthesis of many important primary and secondary metabolites, including hormones, chloroplasts also act as environmental sensors. Any environmental perturbation directly influences the photosynthetic electron transport chain, leading to excess accumulation of reactive oxygen species (ROS), causing oxidative damages to biomolecules in the vicinity. To prevent excess ROS accumulation and the consequent oxidative damages, the chloroplast activates retrograde signaling (RS) pathways to reprogramme nuclear gene expression, defining plant's response to stress. Based on levels and site of ROS accumulation, distinct biomolecules are oxidized, generating specific derivatives that act as genuine signaling molecules, triggering specific RS pathways to instigate distinctive responses, including growth inhibition, acclimation, and programmed cell death. Though various RS pathways independently modulate nuclear gene expression, they also implicate the defense hormone salicylic acid (SA) and oxylipins, including 12-oxo-phytodienoic acid (OPDA) and jasmonic acid (JA), by promoting their biosynthesis and utilizing them for intra- and intercellular communications. Several studies reported the involvement of both hormones in individual RS pathways, but the precise dissection of their activation and participation in a given RS pathway remains an enigma. The present review describes the current understanding of how SA and JA intertwine in ROS-triggered RS pathways. We have also emphasized the future perspectives for elucidating stress specificity and spatiotemporal accumulation of respective hormones in a given RS pathway.

Genome-Wide Analysis and Expression Profiling of the Glutathione Peroxidase-like Enzyme Gene Family in Solanum tuberosum

Glutathione peroxidase-like enzyme is an important enzymatic antioxidant in plants. It is involved in scavenging reactive oxygen species, which can effectively prevent oxidative damage and improve resistance. GPXL has been studied in many plants but has not been reported in potatoes, the world's fourth-largest food crop. This study identified eight StGPXL genes in potatoes for the first time through genome-wide bioinformatics analysis and further studied the expression patterns of these genes using qRT-PCR. The results showed that the expression of StGPXL1 was significantly upregulated under high-temperature stress, indicating its involvement in potato defense against high-temperature stress, while the expression levels of StGPXL4 and StGPXL5 were significantly downregulated. The expression of StGPXL1, StGPXL2, StGPXL3, and StGPXL6 was significantly upregulated under drought stress, indicating their involvement in potato defense against drought stress. After MeJA hormone treatment, the expression level of StGPXL6 was significantly upregulated, indicating its involvement in the chemical defense mechanism of potatoes. The expression of all StGPXL genes is inhibited under biotic stress, which indicates that GPXL is a multifunctional gene family, which may endow plants with resistance to various stresses. This study will help deepen the understanding of the function of the potato GPXL gene family, provide comprehensive information for the further analysis of the molecular function of the potato GPXL gene family as well as a theoretical basis for potato molecular breeding.

Salt stress-induced chloroplastic hydrogen peroxide stimulates pdTPI sulfenylation and methylglyoxal accumulation

High salinity, an adverse environmental factor affecting about 20% of irrigated arable land worldwide, inhibits plant growth and development by causing oxidative stress, damaging cellular components, and disturbing global metabolism. However, whether and how reactive oxygen species disturb the metabolism of salt-stressed plants remain elusive. Here, we report that salt-induced hydrogen peroxide (H2O2) inhibits the activity of plastid triose phosphate isomerase (pdTPI) to promote methylglyoxal (MG) accumulation and stimulates the sulfenylation of pdTPI at cysteine 74. We also show that MG is a key factor limiting the plant growth, as a decrease in MG levels completely rescued the stunted growth and repressed salt stress tolerance of the pdtpi mutant. Furthermore, targeting CATALASE 2 into chloroplasts to prevent salt-induced overaccumulation of H2O2 conferred salt stress tolerance, revealing a role for chloroplastic H2O2 in salt-caused plant damage. In addition, we demonstrate that the H2O2-mediated accumulation of MG in turn induces H2O2 production, thus forming a regulatory loop that further inhibits the pdTPI activity in salt-stressed plants. Our findings, therefore, illustrate how salt stress induces MG production to inhibit the plant growth.

Photosynthetic acclimation to changing environments

Plants are exposed to environments that fluctuate of timescales varying from seconds to months. Leaves that develop in one set of conditions optimise their metabolism to the conditions experienced, in a process called developmental acclimation. However, when plants experience a sustained change in conditions, existing leaves will also acclimate dynamically to the new conditions. Typically this process takes several days. In this review, we discuss this dynamic acclimation process, focussing on the responses of the photosynthetic apparatus to light and temperature. We briefly discuss the principal changes occurring in the chloroplast, before examining what is known, and not known, about the sensing and signalling processes that underlie acclimation, identifying likely regulators of acclimation.

Co-regulation of mitochondrial and chloroplast function: Molecular components and mechanisms

The metabolic interdependence, interactions, and coordination of functions between chloroplasts and mitochondria are established and intensively studied. However, less is known about the regulatory components that control these interactions and their responses to external stimuli. Here, we outline how chloroplastic and mitochondrial activities are coordinated via common components involved in signal transduction pathways, gene regulatory events, and post-transcriptional processes. The endoplasmic reticulum emerges as a point of convergence for both transcriptional and post-transcriptional pathways that coordinate chloroplast and mitochondrial functions. Although the identification of molecular components and mechanisms of chloroplast and mitochondrial signaling increasingly suggests common players, this raises the question of how these allow for distinct organelle-specific downstream pathways. Outstanding questions with respect to the regulation of post-transcriptional pathways and the cell and/or tissue specificity of organelle signaling are crucial for understanding how these pathways are integrated at a whole-plant level to optimize plant growth and its response to changing environmental conditions.

Plant hormones and neurotransmitter interactions mediate antioxidant defenses under induced oxidative stress in plants

Due to global climate change, abiotic stresses are affecting plant growth, productivity, and the quality of cultivated crops. Stressful conditions disrupt physiological activities and suppress defensive mechanisms, resulting in stress-sensitive plants. Consequently, plants implement various endogenous strategies, including plant hormone biosynthesis (e.g., abscisic acid, jasmonic acid, salicylic acid, brassinosteroids, indole-3-acetic acid, cytokinins, ethylene, gibberellic acid, and strigolactones) to withstand stress conditions. Combined or single abiotic stress disrupts the normal transportation of solutes, causes electron leakage, and triggers reactive oxygen species (ROS) production, creating oxidative stress in plants. Several enzymatic and non-enzymatic defense systems marshal a plant's antioxidant defenses. While stress responses and the protective role of the antioxidant defense system have been well-documented in recent investigations, the interrelationships among plant hormones, plant neurotransmitters (NTs, such as serotonin, melatonin, dopamine, acetylcholine, and γ-aminobutyric acid), and antioxidant defenses are not well explained. Thus, this review discusses recent advances in plant hormones, transgenic and metabolic developments, and the potential interaction of plant hormones with NTs in plant stress response and tolerance mechanisms. Furthermore, we discuss current challenges and future directions (transgenic breeding and genome editing) for metabolic improvement in plants using modern molecular tools. The interaction of plant hormones and NTs involved in regulating antioxidant defense systems, molecular hormone networks, and abiotic-induced oxidative stress tolerance in plants are also discussed.

ROS production and signalling in chloroplasts: cornerstones and evolving concepts

Reactive oxygen species (ROS) such as singlet oxygen, superoxide (O₂^●- ) and hydrogen peroxide (H₂ O₂ ) are the markers of living cells. Oxygenic photosynthesis produces ROS in abundance, which act as a readout of a functional electron transport system and metabolism. The concept that photosynthetic ROS production is a major driving force in chloroplast to nucleus retrograde signalling is embedded in the literature, as is the role of chloroplasts as environmental sensors. The different complexes and components of the photosynthetic electron transport chain (PETC) regulate O₂^●- production in relation to light energy availability and the redox state of the stromal Cys-based redox systems. All of the ROS generated in chloroplasts have the potential to act as signals and there are many sulphhydryl-containing proteins and peptides in chloroplasts that have the potential to act as H₂ O₂ sensors and function in signal transduction. While ROS may directly move out of the chloroplasts to other cellular compartments, ROS signalling pathways can only be triggered if appropriate ROS-sensing proteins are present at or near the site of ROS production. Chloroplast antioxidant systems serve either to propagate these signals or to remove excess ROS that cannot effectively be harnessed in signalling. The key challenge is to understand how regulated ROS delivery from the PETC to the Cys-based redox machinery is organised to transmit redox signals from the environment to the nucleus. Redox changes associated with stromal carbohydrate metabolism also play a key role in chloroplast signalling pathways.

Receptor for Activated C Kinase1B (OsRACK1B) Impairs Fertility in Rice through NADPH-Dependent H2O2 Signaling Pathway

The scaffold protein receptor for Activated C Kinase1 (RACK1) regulates multiple aspects of plants, including seed germination, growth, environmental stress responses, and flowering. Recent studies have revealed that RACK1 is associated with NADPH-dependent reactive oxygen species (ROS) signaling in plants. ROS, as a double-edged sword, can modulate several developmental pathways in plants. Thus, the resulting physiological consequences of perturbing the RACK1 expression-induced ROS balance remain to be explored. Herein, we combined molecular, pharmacological, and ultrastructure analysis approaches to investigate the hypothesized connection using T-DNA-mediated activation-tagged RACK1B overexpressed (OX) transgenic rice plants. In this study, we find that OsRACK1B-OX plants display reduced pollen viability, defective anther dehiscence, and abnormal spikelet morphology, leading to partial spikelet sterility. Microscopic observation of the mature pollen grains from the OX plants revealed abnormalities in the exine and intine structures and decreased starch granules in the pollen, resulting in a reduced number of grains per locule from the OX rice plants as compared to that of the wild-type (WT). Histochemical staining revealed a global increase in hydrogen peroxide (H₂O₂) in the leaves and roots of the transgenic lines overexpressing OsRACK1B compared to that of the WT. However, the elevated H₂O₂ in tissues from the OX plants can be reversed by pre-treatment with diphenylidonium (DPI), an NADPH oxidase inhibitor, indicating that the source of H₂O₂ could be, in part, NADPH oxidase. Expression analysis showed a differential expression of the NADPH/respiratory burst oxidase homolog D (RbohD) and antioxidant enzyme-related genes, suggesting a homeostatic mechanism of H₂O₂ production and antioxidant enzyme activity. BiFC analysis demonstrated that OsRACK1B interacts with the N-terminal region of RbohD in vivo. Taken together, these data indicate that elevated OsRACK1B accumulates a threshold level of ROS, in this case H₂O₂, which negatively regulates pollen development and fertility. In conclusion, we hypothesized that an optimal expression of RACK1 is critical for fertility in rice plants.

Simultaneous Ozone and High Light Treatments Reveal an Important Role for the Chloroplast in Co-ordination of Defense Signaling

Plants live in a world of changing environments, where they are continuously challenged by alternating biotic and abiotic stresses. To transfer information from the environment to appropriate protective responses, plants use many different signaling molecules and pathways. Reactive oxygen species (ROS) are critical signaling molecules in the regulation of plant stress responses, both inside and between cells. In natural environments, plants can experience multiple stresses simultaneously. Laboratory studies on stress interaction and crosstalk at regulation of gene expression, imply that plant responses to multiple stresses are distinctly different from single treatments. We analyzed the expression of selected marker genes and reassessed publicly available datasets to find signaling pathways regulated by ozone, which produces apoplastic ROS, and high light treatment, which produces chloroplastic ROS. Genes related to cell death regulation were differentially regulated by ozone versus high light. In a combined ozone + high light treatment, the light treatment enhanced ozone-induced cell death in leaves. The distinct responses from ozone versus high light treatments show that plants can activate stress signaling pathways in a highly precise manner.

GUN1 involvement in the redox changes occurring during biogenic retrograde signaling

Chloroplast biogenesis requires a tight communication between nucleus and plastids. By retrograde signals, plastids transmit information about their functional and developmental state to adjust nuclear gene expression, accordingly. GENOMES UNCOUPLED 1 (GUN1), a chloroplast-localized protein integrating several developmental and stress-related signals, is one of the main players of retrograde signaling. Here, we focused on the interplay between GUN1 and redox regulation during biogenic retrograde signaling, by investigating redox parameters in Arabidopsis wild type and gun1 seedlings. Our data highlight that during biogenic retrograde signaling superoxide anion (O₂^-) and hydrogen peroxide (H₂O₂) play a different role in response to GUN1. Under physiological conditions, even in the absence of a visible phenotype, gun1 mutants show low activity of superoxide dismutase (SOD) and ascorbate peroxidase (APX), with an increase in O₂^- accumulation and lipid peroxidation, suggesting that GUN1 indirectly protects chloroplasts from oxidative damage. In wild type seedlings, perturbation of chloroplast development with lincomycin causes H₂O₂ accumulation, in parallel with the decrease of ROS-removal metabolites and enzymes. These redox changes do not take place in gun1 mutants which, in contrast, enhance SOD, APX and catalase activities. Our results indicate that in response to lincomycin, GUN1 is necessary for the H₂O₂-dependent oxidation of cellular environment, which might contribute to the redox-dependent plastid-to nucleus communication.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

A New Approach to the Study of Plastidial Stress Granules: The Integrated Use of Arabidopsis thaliana and Chlamydomonas reinhardtii as Model Organisms

The field of stress granules (SGs) has recently emerged in the study of the plant stress response, yet these structures, their dynamics and importance remain poorly characterized. There is currently a gap in our understanding of the physiological function of SGs during stress. Since there are only a few studies addressing SGs in planta, which are primarily focused on cytoplasmic SGs. The recent observation of SG-like foci in the chloroplast (cpSGs) of Arabidopsis thaliana opened even more questions regarding the role of these subcellular features. In this opinion article, we review the current knowledge of cpSGs and propose a workflow for the joint use of the long-established model organisms Chlamydomonas reinhardtii and A. thaliana to accelerate the evaluation of individual plant cpSGs components and their impact on stress responses. Finally, we present a short outlook and what we believe are the significant gaps that need to be addressed in the following years.

Impacts of phosphatidylglycerol on plastid gene expression and light induction of nuclear photosynthetic genes

Phosphatidylglycerol (PG) is the only major phospholipid in the thylakoid membrane of chloroplasts. PG is essential for photosynthesis, and loss of PG in Arabidopsis thaliana results in severe defects of growth and chloroplast development, with decreased chlorophyll accumulation, impaired thylakoid formation, and down-regulation of photosynthesis-associated genes encoded in nuclear and plastid genomes. However, how the absence of PG affects gene expression and plant growth remains unclear. To elucidate this mechanism, we investigated transcriptional profiles of a PG-deficient Arabidopsis mutant pgp1-2 under various light conditions. Microarray analysis demonstrated that reactive oxygen species (ROS)-responsive genes were up-regulated in pgp1-2. However, ROS production was not enhanced in the mutant even under strong light, indicating limited impacts of photooxidative stress on the defects of pgp1-2. Illumination to dark-adapted pgp1-2 triggered down-regulation of photosynthesis-associated nuclear-encoded genes (PhANGs), while plastid-encoded genes were constantly suppressed. Overexpression of GOLDEN2-LIKE1 (GLK1), a transcription factor gene regulating chloroplast development, in pgp1-2 up-regulated PhANGs but not plastid-encoded genes along with chlorophyll accumulation. Our data suggest a broad impact of PG biosynthesis on nuclear-encoded genes partially via GLK1 and a specific involvement of this lipid in plastid gene expression and plant development.

Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment

BACKGROUND

For translational genomics, a roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species. This knowledge is invaluable for the selection of target genes and pathways to alter downstream in response to the same stimuli. Here, the transcriptomic responses to six treatments including hormones (abscisic acid - ABA and salicylic acid - SA); treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - MV); inhibit respiration (antimycin A - AA) or induce genetic damage (ultraviolet radiation -UV) were analysed and compared between Arabidopsis (Arabidopsis thaliana), barley (Hordeum vulgare) and rice (Oryza sativa).

RESULTS

Common and opposite responses were identified between species, with the number of differentially expressed genes (DEGs) varying greatly between treatments and species. At least 70% of DEGs overlapped with at least one other treatment within a species, indicating overlapping response networks. Remarkably, 15 to 34% of orthologous DEGs showed opposite responses between species, indicating diversity in responses, despite orthology. Orthologous DEGs with common responses to multiple treatments across the three species were correlated with experimental data showing the functional importance of these genes in biotic/abiotic stress responses. The mitochondrial dysfunction response was revealed to be highly conserved in all three species in terms of responsive genes and regulation via the mitochondrial dysfunction element.

CONCLUSIONS

The orthologous DEGs that showed a common response between species indicate conserved transcriptomic responses of these pathways between species. However, many genes, including prominent salt-stress responsive genes, were oppositely responsive in multiple-stresses, highlighting fundamental differences in the responses and regulation of these genes between species. This work provides a resource for translation of knowledge or functions between species.

Foliar sieve elements: Nexus of the leaf

In this review, a central position of foliar sieve elements in linking leaf structure and function is explored. Results from studies involving plants grown under, and acclimated to, different growth regimes are used to identify significant, linear relationships between features of minor vein sieve elements and those of 1) leaf photosynthetic capacity that drives sugar synthesis, 2) overall leaf structure that serves as the platform for sugar production, 3) phloem components that facilitate the loading of sugars (companion & phloem parenchyma cells), and 4) the tracheary elements that import water to support photosynthesis (and stomatal opening) as well as mass flow of sugars out of the leaf. Despite comprising only a small fraction of physical space within the leaf, sieve elements represent a hub through which multiple functions of the leaf intersect. As the conduits for export of energy-rich carbohydrates, essential mineral nutrients, and information carriers, sieve elements play a central role in fueling and orchestrating development and function of the plant as well as, by extension, of natural and human communities that depend on plants as producers and partners in the global carbon cycle.

Reactive oxygen species and organellar signaling

The evolution of photosynthesis and its associated metabolic pathways has been crucial to the successful establishment of plants, but has also challenged plant cells in the form of production of reactive oxygen species (ROS). Intriguingly, multiple forms of ROS are generated in virtually every plant cell compartment through diverse pathways. As a result, a sophisticated network of ROS detoxification and signaling that is simultaneously tailored to individual organelles and safeguards the entire cell is necessary. Here we take an organelle-centric view on the principal sources and sinks of ROS across the plant cell and provide insights into the ROS-induced organelle to nucleus retrograde signaling pathways needed for operational readjustments during environmental stresses.

FERONIA Confers Resistance to Photooxidative Stress in Arabidopsis

Plants absorb light energy required for photosynthesis, but excess light can damage plant cells. To protect themselves, plants have developed diverse signaling pathways which are activated under high-intensity light. Plant photoprotection mechanisms have been mainly investigated under conditions of extremely high amount of light; thus, it is largely unknown how plants manage photooxidative damage under moderate light intensities. In the present study, we found that FERONIA (FER) is a key protein that confers resistance to photooxidative stress in plants under moderate light intensity. FER-deficient mutants were highly susceptible to increasing light intensity and exhibited photobleaching even under moderately elevated light intensity (ML). Light-induced expression of stress genes was largely diminished by the fer-4 mutation. In addition, excitation pressure on Photosystem II was significantly increased in fer-4 mutants under ML. Consistently, reactive oxygen species, particularly singlet oxygen, accumulated in fer-4 mutants grown under ML. FER protein abundance was found to be elevated after exposure to ML, which is indirectly affected by the ubiquitin-proteasome pathway. Altogether, our findings showed that plants require FER-mediated photoprotection to maintain their photosystems even under moderate light intensity.

A Holistic Approach to Study Photosynthetic Acclimation Responses of Plants to Fluctuating Light

Plants in natural environments receive light through sunflecks, the duration and distribution of these being highly variable across the day. Consequently, plants need to adjust their photosynthetic processes to avoid photoinhibition and maximize yield. Changes in the composition of the photosynthetic apparatus in response to sustained changes in the environment are referred to as photosynthetic acclimation, a process that involves changes in protein content and composition. Considering this definition, acclimation differs from regulation, which involves processes that alter the activity of individual proteins over short-time periods, without changing the abundance of those proteins. The interconnection and overlapping of the short- and long-term photosynthetic responses, which can occur simultaneously or/and sequentially over time, make the study of long-term acclimation to fluctuating light in plants challenging. In this review we identify short-term responses of plants to fluctuating light that could act as sensors and signals for acclimation responses, with the aim of understanding how plants integrate environmental fluctuations over time and tailor their responses accordingly. Mathematical modeling has the potential to integrate physiological processes over different timescales and to help disentangle short-term regulatory responses from long-term acclimation responses. We review existing mathematical modeling techniques for studying photosynthetic responses to fluctuating light and propose new methods for addressing the topic from a holistic point of view.

Papain-like cysteine proteases are required for the regulation of photosynthetic gene expression and acclimation to high light stress

Chloroplasts are considered to be devoid of cysteine proteases. Using transgenic Arabidopsis lines expressing the rice cystatin, oryzacystatin I (OC-I), in the chloroplasts (PC lines) or cytosol (CYS lines), we explored the hypothesis that cysteine proteases regulate photosynthesis. The CYS and PC lines flowered later than the wild type (WT) and accumulated more biomass after flowering. In contrast to the PC rosettes, which accumulated more leaf chlorophyll and carotenoid pigments than the WT, the CYS lines had lower amounts of leaf pigments. High-light-dependent decreases in photosynthetic carbon assimilation and the abundance of the Rubisco large subunit protein, the D1 protein, and the phosphorylated form of D1 proteins were attenuated in the CYS lines and reversed in the PC lines relative to the WT. However, the transgenic lines had higher amounts of LHC, rbcs, pasbA, and pasbD transcripts than the WT, and also showed modified chloroplast to nucleus signalling. We conclude that cysteine proteases accelerate the reconfiguration of the chloroplast proteome after flowering and in response to high-light stress. Inhibition of cysteine proteases, such as AtCEP1, slows chloroplast protein degradation and stimulates photosynthetic gene expression and chloroplast to nucleus signalling, enhancing stress tolerance traits.

Acclimation in plants - the Green Hub consortium

Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.

N4-methylcytidine ribosomal RNA methylation in chloroplasts is crucial for chloroplast function, development, and abscisic acid response in Arabidopsis

Although the essential role of messenger RNA methylation in the nucleus is increasingly understood, the nature of ribosomal RNA (rRNA) methyltransferases and the role of rRNA methylation in chloroplasts remain largely unknown. A recent study revealed that CMAL (for Chloroplast mr aW- Like) is a chloroplast-localized rRNA methyltransferase that is responsible for N4-methylcytidine (m⁴ C) in 16S chloroplast rRNA in Arabidopsis thaliana. In this study, we further examined the role of CMAL in chloroplast biogenesis and function, development, and hormone response. The cmal mutant showed reduced chlorophyll biosynthesis, photosynthetic activity, and growth-defect phenotypes, including severely stunted stems, fewer siliques, and lower seed yield. The cmal mutant was hypersensitive to chloroplast translation inhibitors, such as lincomycin and erythromycin, indicating that the m⁴ C-methylation defect in the 16S rRNA leads to a reduced translational activity in chloroplasts. Importantly, the stunted stem of the cmal mutant was partially rescued by exogenous gibberellic acid or auxin. The cmal mutant grew poorer than wild type, whereas the CMAL-overexpressing transgenic Arabidopsis plants grew better than wild type in the presence of abscisic acid. Altogether, these results indicate that CMAL is an indispensable rRNA methyltransferase in chloroplasts and is crucial for chloroplast biogenesis and function, photosynthesis, and hormone response during plant growth and development.

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves

The stimulation of plant innate immunity by elicitors is an emerging technique in agriculture that contributes more and more to residue-free crop protection. Here, we used RNA-sequencing to study gene transcription in tomato leaves treated three times with the chitooligosaccharides-oligogalacturonides (COS-OGA) elicitor FytoSave® that induces plants to fend off against biotrophic pathogens. Results showed a clear upregulation of sequences that code for chloroplast proteins of the electron transport chain, especially Photosystem I (PSI) and ferredoxin. Concomitantly, stomatal conductance decreased by half, reduced nicotinamide adenine dinucleotide phosphate [NAD(P)H] content and reactive oxygen species production doubled, but fresh and dry weights were unaffected. Chlorophyll, β-carotene, violaxanthin, and neoxanthin contents decreased consistently upon repeated elicitations. Fluorescence measurements indicated a transient decrease of the effective PSII quantum yield and a non-photochemical quenching increase but only after the first spraying. Taken together, this suggests that plant defense induction by COS-OGA induces a long-term acclimation mechanism and increases the role of the electron transport chain of the chloroplast to supply electrons needed to mount defenses targeted to the apoplast without compromising biomass accumulation.

Chloroplast Transition Metal Regulation for Efficient Photosynthesis

Plants require sunlight, water, CO₂, and essential nutrients to drive photosynthesis and fulfill their life cycle. The photosynthetic apparatus resides in chloroplasts and fundamentally relies on transition metals as catalysts and cofactors. Accordingly, chloroplasts are particularly rich in iron (Fe), manganese (Mn), and copper (Cu). Owing to their redox properties, those metals need to be carefully balanced within the cell. However, the regulation of transition metal homeostasis in chloroplasts is poorly understood. With the availability of the arabidopsis genome information and membrane protein databases, a wider catalogue for searching chloroplast metal transporters has considerably advanced the study of transition metal regulation. This review provides an updated overview of the chloroplast transition metal requirements and the transporters involved for efficient photosynthesis in higher plants.

Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells

Endosymbiotic organelles of eukaryotic cells, the plastids, including chloroplasts and mitochondria, are highly integrated into cellular signalling networks. In both heterotrophic and autotrophic organisms, plastids and/or mitochondria require extensive organelle-to-nucleus communication in order to establish a coordinated expression of their own genomes with the nuclear genome, which encodes the majority of the components of these organelles. This goal is achieved by the use of a variety of signals that inform the cell nucleus about the number and developmental status of the organelles and their reaction to changing external environments. Such signals have been identified in both photosynthetic and non-photosynthetic eukaryotes (known as retrograde signalling and retrograde response, respectively) and, therefore, appear to be universal mechanisms acting in eukaryotes of all kingdoms. In particular, chloroplasts and mitochondria both harbour crucial redox reactions that are the basis of eukaryotic life and are, therefore, especially susceptible to stress from the environment, which they signal to the rest of the cell. These signals are crucial for cell survival, lifespan and environmental adjustment, and regulate quality control and targeted degradation of dysfunctional organelles, metabolic adjustments, and developmental signalling, as well as induction of apoptosis. The functional similarities between retrograde signalling pathways in autotrophic and non-autotrophic organisms are striking, suggesting the existence of common principles in signalling mechanisms or similarities in their evolution. Here, we provide a survey for the newcomers to this field of research and discuss the importance of retrograde signalling in the context of eukaryotic evolution. Furthermore, we discuss commonalities and differences in retrograde signalling mechanisms and propose retrograde signalling as a general signalling mechanism in eukaryotic cells that will be also of interest for the specialist. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Reactive oxygen species or reactive sulfur species: why we should consider the latter

The biological effects of oxidants, especially reactive oxygen species (ROS), include signaling functions (oxidative eustress), initiation of measures to reduce elevated ROS (oxidative stress), and a cascade of pathophysiological events that accompany excessive ROS (oxidative distress). Although these effects have long been studied in animal models with perturbed ROS, their actions under physiological conditions are less clear. I propose that some of the apparent uncertainty may be due to confusion of ROS with endogenously generated reactive sulfur species (RSS). ROS and RSS are chemically similar, but RSS are more reactive and versatile, and can be stored and reused. Both ROS and RSS signal via oxidation reactions with protein cysteine sulfur and they produce identical effector responses, but RSS appear to be more effective. RSS in the form of persulfidated cysteines (Cys-S-S) are produced endogenously and co-translationally introduced into proteins, and there is increasing evidence that many cellular proteins are persulfidated. A number of practical factors have contributed to confusion between ROS and RSS, and these are discussed herein. Furthermore, essentially all endogenous antioxidant enzymes appeared shortly after life began, some 3.8 billion years ago, when RSS metabolism dominated evolution. This was long before the rise in ROS, 600 million years ago, and I propose that these same enzymes, with only minor modifications, still effectively metabolize RSS in extant organisms. I am not suggesting that all ROS are RSS; however, I believe that the relative importance of ROS and RSS in biological systems needs further consideration.

Beyond the darkness: recent lessons from etiolation and de-etiolation studies

The state of etiolation is generally defined by the presence of non-green plastids (etioplasts) in plant tissues that would normally contain chloroplasts. In the commonly used dark-grown seedling system, etiolation is coupled with a type of growth called skotomorphogenesis. Upon illumination, de-etiolation occurs, marked by the transition from etioplast to chloroplast, and, at the seedling level, a switch to photomorphogenic growth. Etiolation and de-etiolation systems are therefore important for understanding both the acquisition of photosynthetic capacity during chloroplast biogenesis and plant responses to light-the most relevant signal in the life and growth of the organism. In this review, we discuss recent discoveries (within the past 2-3 years) in the field of etiolation and de-etiolation, with a particular focus on post-transcriptional processes and ultrastructural changes. We further discuss ambiguities in definitions of the term 'etiolation', and benefits and biases of common etiolation/de-etiolation systems. Finally, we raise several open questions and future research possibilities.

Unraveling the Linkage between Retrograde Signaling and RNA Metabolism in Plants

Retrograde signals are signals that originate in organelles to regulate nuclear gene expression. In plant cells, retrograde signaling from both chloroplasts and mitochondria is essential for plant development and growth. Over the past few years, substantial progress has been made in unraveling the linkages between chloroplast retrograde signaling and nuclear RNA metabolism processes or plastidial RNA editing. These findings add to the complexity of the regulation of organelle-to-nucleus communication. Chloroplast development and function rely on the coordinated regulation of chloroplast and nuclear gene expression, especially under stress conditions. A better understanding of retrograde signaling and RNA metabolism, as well as their connection, is essential for breeding stress-tolerant plants to cope with the dynamic and rapidly changing environment.

You Want it Sweeter: How Glycosylation Affects Plant Response to Oxidative Stress

Oxidative stress is a cellular threat which puts at risk the productivity of most of crops valorized by humankind in terms of food, feed, biomaterial, or bioenergy. It is therefore of crucial importance to understand the mechanisms by which plants mitigate the deleterious effects of oxidizing agents. Glycosylation of antioxidant molecules and phytohormones modifies their chemical properties as well as their cellular and histological repartition. This review emphasizes the mechanisms and the outcomes of this conjugation reaction on plant ability to face growing conditions favoring oxidative stress, in mirror with the activity of deglycosylating enzymes. Pioneer evidence bridging flavonoid, glycosylation, and redox homeostasis paved the way for numerous functional analyses of UDP-glycosyltransferases (UGTs), such as the identification of their substrates and their role to circumvent oxidative stress resulting from various environmental challenges. (De)glycosylation appears as a simple chemical reaction regulating the biosynthesis and/or the activity of a myriad of specialized metabolites partaking in response to pathogen and abiotic stresses. This outcome underlies the possibility to valorize UGTs potential to upgrade plant adaptation and fitness in a rising context of sub-optimal growing conditions subsequent to climate change.

Relationship of GUN1 to FUG1 in chloroplast protein homeostasis

GUN1 integrates retrograde signals in chloroplasts but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcriptional level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and system-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transiently more pronounced phenotypes regarding photosynthesis, leaf colouration, growth and cold acclimation. The gun1-103 mutation also enhances variegation in the var2 mutant, increasing the fraction of white sectors, while fug1-3 suppresses the var2 phenotype. The transcriptomes of fug1-3 and gun1-103 plants are very similar, but absence of GUN1 alone has almost no effect on protein levels, whereas steady-state levels of chloroplast proteins are markedly decreased in fug1-3. In fug1 gun1 double mutants, effects on transcriptomes and particularly on proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased rates of synthesis (fug1) or degradation (var2) of chloroplast proteins, or by low temperatures. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 helps to maintain chloroplast protein homeostasis (proteostasis).

Essential and Detrimental - an Update on Intracellular Iron Trafficking and Homeostasis

Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes.

Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors

Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles.

Most plant cells contain two types of compartments, the mitochondria and the chloroplasts, which work together to supply the chemical energy required by life processes. Genes located in another part of the cell, the nucleus, encode for the majority of the proteins found in these compartments.

At any given time, the mitochondria and the chloroplasts send specific, ‘retrograde’ signals to the nucleus to turn on or off the genes they need. For example, mitochondria produce molecules known as reactive oxygen species (ROS) if they are having problems generating energy. These molecules activate several regulatory proteins that move into the nucleus and switch on MDS genes, a set of genes which helps to repair the mitochondria. Chloroplasts also produce ROS that can act as retrograde signals. It is still unclear how the nucleus integrates signals from both chloroplasts and mitochondria to ‘decide’ which genes to switch on, but a protein called RCD1 may play a role in this process. Indeed, previous studies have found that Arabidopsis plants that lack RCD1 have defects in both their mitochondria and chloroplasts. In these mutant plants, the MDS genes are constantly active and the chloroplasts have problems making ROS.

To investigate this further, Shapiguzov, Vainonen et al. use biochemical and genetic approaches to study RCD1 in Arabidopsis. The experiments confirm that this protein allows a dialog to take place between the retrograde signals of both mitochondria and chloroplasts. On one hand, RCD1 binds to and inhibits the regulatory proteins that usually activate the MDS genes under the control of mitochondria. This explains why, in the absence of RCD1, the MDS genes are always active, which is ultimately disturbing how these compartments work.

On the other hand, RCD1 is also found to be sensitive to the ROS that chloroplasts produce. This means that chloroplasts may be able to affect when mitochondria generate energy by regulating the protein. Finally, further experiments show that MDS genes can affect both mitochondria and chloroplasts: by influencing how these genes are regulated, RCD1 therefore acts on the two types of compartments.

Overall, the work by Shapiguzov, Vainonen et al. describes a new way Arabidopsis coordinates its mitochondria and chloroplasts. Further studies will improve our understanding of how plants regulate these compartments in different environments to produce the energy they need. In practice, this may also help plant breeders create new varieties of crops that produce energy more efficiently and which better resist to stress.

In vivo detection of protein cysteine sulfenylation in plastids

Protein cysteine thiols are post-translationally modified under oxidative stress conditions. Illuminated chloroplasts are one of the important sources of hydrogen peroxide (H₂ O₂ ) and are highly sensitive to environmental stimuli, yet a comprehensive view of the oxidation-sensitive chloroplast proteome is still missing. By targeting the sulfenic acid YAP1C-trapping technology to the plastids of light-grown Arabidopsis cells, we identified 132 putatively sulfenylated plastid proteins upon H₂ O₂ pulse treatment. Almost half of the sulfenylated proteins are enzymes of the amino acid metabolism. Using metabolomics, we observed a reversible decrease in the levels of the amino acids Ala, Asn, Cys, Gln, Glu, His, Ile, Leu, Lys, Phe, Ser, Thr and Val after H₂ O₂ treatment, which is in line with an anticipated decrease in the levels of the glycolysis and tricarboxylic acid metabolites. Through the identification of an organelle-tailored proteome, we demonstrated that the subcellular targeting of the YAP1C probe enables us to study in vivo cysteine sulfenylation at the organellar level. All in all, the identification of these oxidation events in plastids revealed that several enzymes of the amino acid metabolism rapidly undergo cysteine oxidation upon oxidative stress.

Reactive Oxygen Species in Plant Signaling

As fixed organisms, plants are especially affected by changes in their environment and have consequently evolved extensive mechanisms for acclimation and adaptation. Initially considered by-products from aerobic metabolism, reactive oxygen species (ROS) have emerged as major regulatory molecules in plants and their roles in early signaling events initiated by cellular metabolic perturbation and environmental stimuli are now established. Here, we review recent advances in ROS signaling. Compartment-specific and cross-compartmental signaling pathways initiated by the presence of ROS are discussed. Special attention is dedicated to established and hypothetical ROS-sensing events. The roles of ROS in long-distance signaling, immune responses, and plant development are evaluated. Finally, we outline the most challenging contemporary questions in the field of plant ROS biology and the need to further elucidate mechanisms allowing sensing, signaling specificity, and coordination of multiple signals.