The levels of peroxisomal catalase protein and activity modulate the onset of cell death in tobacco BY-2 cells via reactive oxygen species levels and autophagy

Transcriptome analysis to identify genes related to programmed cell death resulted from manipulating of BnaFAH ortholog by CRISPR/Cas9 in Brassica napus

Fumarylacetoacetate hydrolase (FAH) catalyzes the final step of the tyrosine degradation pathway. In this study, we isolated and characterized two homologous BnaFAH genes in Brassica napus L. variant Westar, and then used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with single or double-null bnafah alleles. Among these mutant lines, the aacc (bnafah) double-null mutant line, rather than the aaCC (bnaa06fah) mutant line, exhibited programmed cell death (PCD) under short days (SD). Histochemical staining and content measurement confirmed that the accumulation of reactive oxygen species (ROS) in bnafah was significantly higher than that in bnaa06fah. To further elucidate the mechanism of PCD, we performed transcriptomic analyses of bnaa06fah and bnafah at different SD stages. A heatmap cluster of differentially expressed genes (DEGs) revealed that PCD may be related to various redox regulatory genes involved in antioxidant activity, ROS-responsive regulation and calcium signaling. Combined with the results of previous studies, our work revealed that the expression levels of BnaC04CAT2, BnaA09/C09SAL1, BnaA08/C08ACO2, BnaA07/C06ERO1, BnaA08ACA1, BnaC04BIK1, BnaA09CRK36 and BnaA03CPK4 were significantly different and that these genes might be candidate hub genes for PCD. Together, our results underscore the ability of different PCD phenotypes to alter BnaFAH orthologs through gene editing and further elucidated the molecular mechanisms of oxidative stress-induced PCD in plants.

What can reactive oxygen species (ROS) tell us about the action mechanism of herbicides and other phytotoxins?

Reactive oxygen species (ROS) are formed in plant cells continuously. When ROS production exceeds the antioxidant capacity of the cells, oxidative stress develops which causes damage of cell components and may even lead to the induction of programmed cell death (PCD). The levels of ROS production increase upon abiotic stress, but also during pathogen attack in response to elicitors, and upon application of toxic compounds such as synthetic herbicides or natural phytotoxins. The commercial value of many synthetic herbicides is based on weed death as result of oxidative stress, and for a number of them, the site and the mechanism of ROS production have been characterized. This review summarizes the current knowledge on ROS production in plants subjected to different groups of synthetic herbicides and natural phytotoxins. We suggest that the use of ROS-specific fluorescent probes and of ROS-specific marker genes can provide important information on the mechanism of action of these toxins. Furthermore, we propose that, apart from oxidative damage, elicitation of ROS-induced PCD is emerging as one of the important processes underlying the action of herbicides and phytotoxins.

Plant Heterotrophic Cultures: No Food, No Growth

Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.

Product safety aspects of plant molecular farming

Plant molecular farming (PMF) has been promoted since the 1990s as a rapid, cost-effective and (most of all) safe alternative to the cultivation of bacteria or animal cells for the production of biopharmaceutical proteins. Numerous plant species have been investigated for the production of a broad range of protein-based drug candidates. The inherent safety of these products is frequently highlighted as an advantage of PMF because plant viruses do not replicate in humans and vice versa. However, a more nuanced analysis of this principle is required when considering other pathogens because toxic compounds pose a risk even in the absence of replication. Similarly, it is necessary to assess the risks associated with the host system (e.g., the presence of toxic secondary metabolites) and the production approach (e.g., transient expression based on bacterial infiltration substantially increases the endotoxin load). This review considers the most relevant host systems in terms of their toxicity profile, including the presence of secondary metabolites, and the risks arising from the persistence of these substances after downstream processing and product purification. Similarly, we discuss a range of plant pathogens and disease vectors that can influence product safety, for example, due to the release of toxins. The ability of downstream unit operations to remove contaminants and process-related toxic impurities such as endotoxins is also addressed. This overview of plant-based production, focusing on product safety aspects, provides recommendations that will allow stakeholders to choose the most appropriate strategies for process development.

Deciphering peroxisomal reactive species interactome and redox signalling networks

Plant peroxisomes are highly dynamic organelles with regard to metabolic pathways, number and morphology and participate in different metabolic processes and cell responses to their environment. Peroxisomes from animal and plant cells house a complex system of reactive oxygen species (ROS) production associated to different metabolic pathways which are under control of an important set of enzymatic and non enzymatic antioxidative defenses. Nitric oxide (NO) and its derivate reactive nitrogen species (RNS) are also produced in these organelles. Peroxisomes can regulate ROS and NO/RNS levels to allow their role as signalling molecules. The metabolism of other reactive species such as carbonyl reactive species (CRS) and sulfur reactive species (SRS) in peroxisomes and their relationship with ROS and NO have not been explored in depth. In this review, we define a peroxisomal reactive species interactome (PRSI), including all reactive species ROS, RNS, CRS and SRS, their interaction and effect on target molecules contributing to the dynamic redox/ROS homeostasis and plasticity of peroxisomes, enabling fine-tuned regulation of signalling networks associated with peroxisome-dependent H₂O₂. Particular attention will be paid to update the information available on H₂O₂-dependent peroxisomal retrograde signalling and to discuss a specific peroxisomal footprint.

Peroxisome-Mediated Reactive Oxygen Species Signals Modulate Programmed Cell Death in Plants

Peroxisomes are a class of simple organelles that play an important role in plant reactive oxygen species (ROS) metabolism. Experimental evidence reveals the involvement of ROS in programmed cell death (PCD) in plants. Plant PCD is crucial for the regulation of plant growth, development and environmental stress resistance. However, it is unclear whether the ROS originated from peroxisomes participated in cellular PCD. Enzymes involved in the peroxisomal ROS metabolic pathways are key mediators to figure out the relationship between peroxisome-derived ROS and PCD. Here, we summarize the peroxisomal ROS generation and scavenging pathways and explain how peroxisome-derived ROS participate in PCD based on recent progress in the functional study of enzymes related to peroxisomal ROS generation or scavenging. We aimed to elucidate the role of the peroxisomal ROS regulatory system in cellular PCD to show its potential in terms of accurate PCD regulation, which contribute to environmental stress resistance.

Autophagy and the Energy Status of Plant Cells

Abstract

In plant cells the homeostatic control of energy balance involves the production and recycling of adenylates with macroergic bonds, ATP and ADP. The maintenance of anabolic processes requires the relative saturation of the adenylate pool with high energy phosphoanhydride bonds. The bulk of ATP synthesis is carried out both in mitochondria and in chloroplasts while optimal ATP levels within other cell compartments are maintained by adenylate kinases (AK). AK activity was recently found in cytosol, mitochondria, plastids and the nucleus. ATP synthesis in energy-producing organelles, as well as redistribution of nutrients among cellular compartments, requires fine-tuned regulation of ion homeostasis. A special role in energy metabolism is played by autophagy, a process of active degradation of unwanted and/or damaged cell components and macromolecules within the central lytic vacuole. So-called constitutive autophagy controls the quality of cellular contents under favorable conditions, i.e., when the cellular energy status is high. Energy depletion can lead to the activation of the pro-survival process of autophagic removal and utilization of damaged structures; the breakdown products are then used for ATP regeneration and de novo synthesis of macromolecules. Mitophagy and chlorophagy maintain the populations of healthy and functional energy-producing “stations”, preventing accumulation of defective mitochondria and chloroplasts as potential sources of dangerous reactive oxygen species. However, the increase of autophagic flux above a threshold level can lead to the execution of the vacuolar type of programmed cell death (PCD). In this case autophagy also contributes to preservation of energy through support of the outflow of nutrients from dying cells to healthy neighboring tissues. In plants, two central protein kinases, SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin), are responsible for the regulation of the metabolic switch between anabolic and catabolic pathways. TOR promotes the energy-demanding metabolic reactions in response to nutrient availability and simultaneously suppresses catabolism including autophagy. SnRK1, the antagonist of TOR, senses a decline in cellular energy supply and reacts by inducing autophagy through several independent pathways. Here, we provide an overview of the recent knowledge about the interplay between SnRK1 and TOR, autophagy and PCD in course of the regulation of energy balance in plants.

Peroxisomes as redox-signaling nodes in intracellular communication and stress responses

Peroxisomes are redox nodes playing a diverse range of roles in cell functionality and in the perception of and responses to changes in their environment.

Programmed cell death (PCD) control in plants: New insights from the Arabidopsis thaliana deathosome

Programmed cell death (PCD) is a genetically controlled process that leads to cell suicide in both eukaryotic and prokaryotic organisms. In plants PCD occurs during development, defence response and when exposed to adverse conditions. PCD acts controlling the number of cells by eliminating damaged, old, or unnecessary cells to maintain cellular homeostasis. Unlike in animals, the knowledge about PCD in plants is limited. The molecular network that controls plant PCD is poorly understood. Here we present a review of the current mechanisms involved with the genetic control of PCD in plants. We also present an updated version of the AtLSD1 deathosome, which was previously proposed as a network controlling HR-mediated cell death in Arabidopsis thaliana. Finally, we discuss the unclear points and open questions related to the AtLSD1 deathosome.

Peroxisomes: versatile organelles with diverse roles in plants

Peroxisomes are small, ubiquitous organelles that are delimited by a single membrane and lack genetic material. However, these simple-structured organelles are highly versatile in morphology, abundance and protein content in response to various developmental and environmental cues. In plants, peroxisomes are essential for growth and development and perform diverse metabolic functions, many of which are carried out coordinately by peroxisomes and other organelles physically interacting with peroxisomes. Recent studies have added greatly to our knowledge of peroxisomes, addressing areas such as the diverse proteome, regulation of division and protein import, pexophagy, matrix protein degradation, solute transport, signaling, redox homeostasis and various metabolic and physiological functions. This review summarizes our current understanding of plant peroxisomes, focusing on recent discoveries. Current problems and future efforts required to better understand these organelles are also discussed. An improved understanding of peroxisomes will be important not only to the understanding of eukaryotic cell biology and metabolism, but also to agricultural efforts aimed at improving crop performance and defense.

Autophagic Machinery of Plant Peroxisomes

Peroxisomes are cell organelles that play an important role in plants in many physiological and developmental processes. The plant peroxisomes harbor enzymes of the β-oxidation of fatty acids and the glyoxylate cycle; photorespiration; detoxification of reactive oxygen and nitrogen species; as well as biosynthesis of hormones and signal molecules. The function of peroxisomes in plant cells changes during plant growth and development. They are transformed from organelles involved in storage lipid breakdown during seed germination and seedling growth into leaf peroxisomes involved in photorespiration in green parts of the plant. Additionally, intensive oxidative metabolism of peroxisomes causes damage to their components. Therefore, unnecessary or damaged peroxisomes are degraded by selective autophagy, called pexophagy. This is an important element of the quality control system of peroxisomes in plant cells. Despite the fact that the mechanism of pexophagy has already been described for yeasts and mammals, the molecular mechanisms by which plant cells recognize peroxisomes that will be degraded via pexophagy still remain unclear. It seems that a plant-specific mechanism exists for the selective degradation of peroxisomes. In this review, we describe the physiological role of pexophagy in plant cells and the current hypotheses concerning the mechanism of plant pexophagy.

Selective Autophagy of Peroxisomes in Plants: From Housekeeping to Development and Stress Responses

Peroxisomes are dynamic organelles involved in multiple functions, including oxygen and nitrogen reactive species metabolism. In plants, these organelles have a close relationship with chloroplasts and mitochondria, characterized by intense metabolic activity and signal transduction. Peroxisomes undergo rapid changes in size, morphology, and abundance depending on the plant development stage and environmental conditions. As peroxisomes are essential not only for redox homeostasis but also for sensing stress, signaling transduction, and cell survival, their formation and degradation need to be rigorously regulated. In this review, new insights into the regulation of plant peroxisomes are briefly described, with a particular emphasis on pexophagy components and their regulation.

24-Epibrassinolide-alleviated drought stress damage influences antioxidant enzymes and autophagy changes in peach (Prunus persicae L.) leaves

Drought stress is a serious threat to agriculture and the environment. Brassinosteroids (BRs) increase tolerance to drought stress of plant. Autophagy plays important roles in plant responses to drought stress; however, there are few reports on autophagy in peach (Prunus persica). In total, 23 putative autophagy-related genes (ATGs) in peach were identified using ATGs from the Arabidopsis thaliana genome as query in BLASTx algorithm-based searches. Under drought stress, the photosynthetic abilities of peach leaves decreased, while antioxidant enzyme activities, autophagy and ATG expression increased. A correlation analysis showed that antioxidant enzyme activities are inversely correlated to the expression levels of the PpATGs. During drought, the PpATG8s and some PpATG18s had the strongest responses. To investigate enhanced drought-stress tolerance, peach was treated with water, 100 nM 24-epibrassinolide (EBR), 1 μM EBR, 10 μM EBR and 1 μM voriconazole. Exogenous EBR at 1 μM decreased the malondialdehyde (MDA) content under drought stress when compared with water-, 1 μM voriconazole-, 100 nM EBR- and 10 μM EBR-treated peach leaf. The 1-μM EBR application increased superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX) and glutathione peroxidase (GR) activities during drought stress. In addition, the expression levels of PpATGs were inhibited by EBR. Thus, the 1-μM EBR treatment alleviated drought-stress damage to peach leaves, decreased PpATG expression levels and reduced the number of autophagosomes.