Peroxisomes Extend Peroxules in a Fast Response to Stress via a Reactive Oxygen Species-Mediated Induction of the Peroxin PEX11a

Cadmium exposure induced light/dark- and time-dependent redox changes at subcellular level in Arabidopsis plants

Cadmium (Cd) is one of the most toxic heavy metals for plants and humans. Reactive oxygen species (ROS) are some of the primary signaling molecules produced after Cd treatment in plants but the contribution of different organelles and specific cell types, together with the impact of light is unknown. We used Arabidopsis lines expressing GRX1-roGFP2 (glutaredoxin1-roGFP) targeted to different cell compartments and analysed changes in redox state over 24 h light/dark cycle in Cd-treated leaf discs. We imaged redox state changes in peroxisomes and chloroplasts in leaf tissue. Chloroplasts and peroxisomes were the most affected organelles in the dark and blocking the photosynthetic electron transport chain (pETC) by DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) promotes higher Cd-dependent oxidation in all organelles. Peroxisomes underwent the most rapid changes in redox state in response to Cd and DCMU and silencing chloroplastic NTRC (NADPH thioredoxin reductase C) considerably increases peroxisome oxidation. Total NAD(P)H and cytosolic NADH decreased during exposure to Cd, while Ca+2 content in chloroplasts and cytosol increased in the dark period. Our results demonstrate a Cd-, time- and light-dependent increase of oxidation of all organelles analysed, that could be in part triggered by disturbances in pETC and photorespiration, the decrease of NAD(P)H availability, and differential antioxidants expression at subcellular level.

Redox regulation of gene expression: proteomics reveals multiple previously undescribed redox-sensitive cysteines in transcription complexes and chromatin modifiers

Redox signalling is crucial for regulating plant development and adaptation to environmental changes. Proteins with redox-sensitive cysteines can sense oxidative stress and modulate their functions. Recent proteomics efforts have comprehensively mapped the proteins targeted by oxidative modifications. The nucleus, the epicentre of transcriptional reprogramming, contains a large number of proteins that control gene expression. Specific redox-sensitive transcription factors have long been recognized as key players in decoding redox signals in the nucleus and thus in regulating transcriptional responses. Consequently, the redox regulation of the nuclear transcription machinery and its cofactors has received less attention. In this review, we screened proteomic datasets for redox-sensitive cysteines on proteins of the core transcription complexes and chromatin modifiers in Arabidopsis thaliana. Our analysis indicates that redox regulation affects every step of gene transcription, from initiation to elongation and termination. We report previously undescribed redox-sensitive subunits in transcription complexes and discuss the emerging challenges in unravelling the landscape of redox-regulated processes involved in nuclear gene transcription.

Talk to your neighbors in an emergency: Stromule-mediated chloroplast-nucleus communication in plant immunity

Hypersensitive response-programmed cell death (HR-PCD) is a response mounted by plants to defend themselves against pathogens. Communication between the chloroplast and the nucleus is critical for the progression of HR-PCD. Tubular protrusions of chloroplasts, known as stromules, are tightly associated with the HR-PCD progression. There is emerging evidence that signaling molecules originating from chloroplasts are transferred to the nucleus through stromules. The translocation of signaling molecules from the chloroplast to the nucleus might trigger defense responses, including transcriptional reprogramming. In this review, we discuss the possible functions of stromules in the rapid transfer of signaling molecules in the chloroplast-nucleus communication.

Diverse projected climate change scenarios affect the physiology of broccoli plants to different extents

Climate change caused by global warming involves crucial plant growth factors such as atmospheric CO2 concentration, ambient temperature or water availability. These stressors usually co-occur, causing intricate alterations in plant physiology and development. This work focuses on how elevated atmospheric CO2 levels, together with the concomitant high temperature, would affect the physiology of a relevant crop, such as broccoli. Particular attention has been paid to those defence mechanisms that contribute to plant fitness under abiotic stress. Results show that both photosynthesis and leaf transpiration were reduced in plants grown under climate change environments compared to those grown under current climate conditions. Furthermore, an induction of carbohydrate catabolism pointed to a redistribution from primary to secondary metabolism. This result could be related to a reinforcement of cell walls, as well as to an increase in the pool of antioxidants in the leaves. Broccoli plants, a C3 crop, grown under an intermediate condition showed activation of those adaptive mechanisms, which would contribute to coping with abiotic stress, as confirmed by reduced levels of lipid peroxidation relative to current climate conditions. On the contrary, the most severe climate change scenario exceeded the adaptive capacity of broccoli plants, as shown by the inhibition of growth and reduced vigour of plants. In conclusion, only a moderate increase in atmospheric CO2 concentration and temperature would not have a negative impact on broccoli crop yields.

Picky eaters: selective autophagy in plant cells

Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.

Visualizing the dynamics of plant energy organelles

Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly for short-range movement. The distribution and motility of organelles in the plant cell are fundamentally important to robust plant growth and defense. Chloroplasts, mitochondria, and peroxisomes are essential organelles in plants that function independently and coordinately during energy metabolism and other key metabolic processes. In response to developmental and environmental stimuli, these energy organelles modulate their metabolism, morphology, abundance, distribution and motility in the cell to meet the need of the plant. Consistent with their metabolic links in processes like photorespiration and fatty acid mobilization is the frequently observed inter-organellar physical interaction, sometimes through organelle membranous protrusions. The development of various organelle-specific fluorescent protein tags has allowed the simultaneous visualization of organelle movement in living plant cells by confocal microscopy. These energy organelles display an array of morphology and movement patterns and redistribute within the cell in response to changes such as varying light conditions, temperature fluctuations, ROS-inducible treatments, and during pollen tube development and immune response, independently or in association with one another. Although there are more reports on the mechanism of chloroplast movement than that of peroxisomes and mitochondria, our knowledge of how and why these three energy organelles move and distribute in the plant cell is still scarce at the functional and mechanistic level. It is critical to identify factors that control organelle motility coupled with plant growth, development, and stress response.

Systematic Proteomics Study on the Embryonic Development of Danio rerio

The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish's embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish's early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.

Organellomic gradients in the fourth dimension

Organelles function as hubs of cellular metabolism and elements of cellular architecture. In addition to 3 spatial dimensions that describe the morphology and localization of each organelle, the time dimension describes complexity of the organelle life cycle, comprising formation, maturation, functioning, decay, and degradation. Thus, structurally identical organelles could be biochemically different. All organelles present in a biological system at a given moment of time constitute the organellome. The homeostasis of the organellome is maintained by complex feedback and feedforward interactions between cellular chemical reactions and by the energy demands. Synchronized changes of organelle structure, activity, and abundance in response to environmental cues generate the fourth dimension of plant polarity. Temporal variability of the organellome highlights the importance of organellomic parameters for understanding plant phenotypic plasticity and environmental resiliency. Organellomics involves experimental approaches for characterizing structural diversity and quantifying the abundance of organelles in individual cells, tissues, or organs. Expanding the arsenal of appropriate organellomics tools and determining parameters of the organellome complexity would complement existing -omics approaches in comprehending the phenomenon of plant polarity. To highlight the importance of the fourth dimension, this review provides examples of organellome plasticity during different developmental or environmental situations.

Nitric Oxide and Globin Glb1 Regulate Fusarium oxysporum Infection of Arabidopsis thaliana

Plants continuously interact with fungi, some of which, such as Fusarium oxysporum, are lethal, leading to reduced crop yields. Recently, nitric oxide (NO) has been found to play a regulatory role in plant responses to F. oxysporum, although the underlying mechanisms involved are poorly understood. In this study, we show that Arabidopsis mutants with altered levels of phytoglobin 1 (Glb1) have a higher survival rate than wild type (WT) after infection with F. oxysporum, although all the genotypes analyzed exhibited a similar fungal burden. None of the defense responses that were analyzed in Glb1 lines, such as phenols, iron metabolism, peroxidase activity, or reactive oxygen species (ROS) production, appear to explain their higher survival rates. However, the early induction of the PR genes may be one of the reasons for the observed survival rate of Glb1 lines infected with F. oxysporum. Furthermore, while PR1 expression was induced in Glb1 lines very early on the response to F. oxysporum, this induction was not observed in WT plants.

Effects of Fogging System and Nitric Oxide on Growth and Yield of 'Naomi' Mango Trees Exposed to Frost Stress

In years with unfavorable weather, winter frost during the blossoming season can play a significant role in reducing fruit yield and impacting the profitability of cultivation. The mango Naomi cultivar Mangifera indica L. has a low canopy that is severely affected by the effects of frost stress. As a result of the canopy being exposed to physiological problems, vegetative development is significantly inhibited. The current investigation aimed to study the influence of spraying nitric oxide and fogging spray systems on Naomi mango trees grafted on 'Succary' rootstock under frost stress conditions. The treatments were as follows: nitric oxide (NO) 50 and 100 μM, fogging spray system, and control. In comparison to the control, the use of nitric oxide and a fogging system significantly improved the leaf area, photosynthesis pigments of the leaf, the membrane stability index, yield, and physical and chemical characteristics of the Naomi mango cultivar. For instance, the application of 50 μM NO, 100 μM NO, and the fogging spray system resulted in an increase in yield by 41.32, 106.12, and 121.43% during the 2020 season, and by 39.37, 101.30, and 124.68% during the 2021 season compared to the control, respectively. The fogging spray system and highest level of NO decreased electrolyte leakage, proline content, total phenolic content, catalase (CAT), peroxidases (POX), and polyphenol oxidase (PPO) enzyme activities in leaves. Furthermore, the number of damaged leaves per shoot was significantly reduced after the application of fogging spray systems and nitric oxide in comparison to the control. Regarding vegetative growth, our results indicated that the fogging spray system and spraying nitric oxide at 100 μM enhanced the leaf surface area compared to the control and other treatments. A similar trend was noticed regarding yield and fruit quality, whereas the best values were obtained when the fogging spray system using nitric oxide was sprayed at a concentration of 100 μM. The application of fogging spray systems and nitric oxide can improve the production and fruit quality of Naomi mango trees by reducing the effects of adverse frost stress conditions.

miRNA transcriptome reveals key miRNAs and their targets contributing to the difference in Cd tolerance of two contrasting maize genotypes

Soil cadmium (Cd) contamination is a global environmental and food safety production issue. microRNAs (miRNAs) are proven to be involved in plant growth and development, and abiotic/biotic stress response, but their role in Cd tolerance is largely unknown in maize. To understand the genetic basis of Cd tolerance, two maize genotypes differing in Cd tolerance (L42, a sensitive genotype and L63, a tolerant genotype) were selected, and miRNA sequencing was carried out at nine-day-old seedlings exposed to 24 h Cd stress (5 μM CdCl₂). A total of 151 differentially expressed miRNAs were identified, including 20 known miRNAs and 131 novel miRNAs. The results revealed that 90 and 22 miRNAs were up-regulated and down-regulated by Cd in Cd-tolerant genotype L63, and there were 23 and 43 miRNAs in Cd-sensitive genotype L42, respectively. Twenty-six miRNAs were up-regulated in L42 and unchanged or down-regulated in L63, or unchanged in L42 and down-regulated in L63. There were 108 miRNAs that were up-regulated in L63 and unchanged or down-regulated in L42, or unchanged in L63 and down-regulated in L42. Their target genes were enriched mainly in peroxisomes, glutathione (GSH) metabolism, ABC transporter, and ubiquitin-protease system. Among them, target genes involved in the peroxisome pathway and GSH metabolism might play key roles in Cd tolerance in L63. Besides, several ABC transporters which might involve in Cd uptake and transport were identified. The differentially expressed miRNAs or target genes could be used for breeding low grain Cd accumulation and high Cd tolerance cultivars in maize.

Organelle Membrane Extensions in Mammalian Cells

Organelles within eukaryotic cells are not isolated static compartments, instead being morphologically diverse and highly dynamic in order to respond to cellular needs and carry out their diverse and cooperative functions. One phenomenon exemplifying this plasticity, and increasingly gaining attention, is the extension and retraction of thin tubules from organelle membranes. While these protrusions have been observed in morphological studies for decades, their formation, properties and functions are only beginning to be understood. In this review, we provide an overview of what is known and still to be discovered about organelle membrane protrusions in mammalian cells, focusing on the best-characterised examples of these membrane extensions arising from peroxisomes (ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis) and mitochondria. We summarise the current knowledge on the diversity of peroxisomal/mitochondrial membrane extensions, as well as the molecular mechanisms by which they extend and retract, necessitating dynamic membrane remodelling, pulling forces and lipid flow. We also propose broad cellular functions for these membrane extensions in inter-organelle communication, organelle biogenesis, metabolism and protection, and finally present a mathematical model that suggests that extending protrusions is the most efficient way for an organelle to explore its surroundings.

Cadmium-induced oxidative stress responses and acclimation in plants require fine-tuning of redox biology at subcellular level

Cadmium (Cd) is one of the most toxic compounds released into our environment and is harmful to human health, urging the need to remediate Cd-polluted soils. To this end, it is important to increase our insight into the molecular mechanisms underlying Cd stress responses in plants, ultimately leading to acclimation, and to develop novel strategies for economic validation of these soils. Albeit its non-redox-active nature, Cd causes a cellular oxidative challenge, which is a crucial determinant in the onset of diverse signalling cascades required for long-term acclimation and survival of Cd-exposed plants. Although it is well known that Cd affects reactive oxygen species (ROS) production and scavenging, the contribution of individual organelles to Cd-induced oxidative stress responses is less well studied. Here, we provide an overview of the current information on Cd-induced organellar responses with special attention to redox biology. We propose that an integration of organellar ROS signals with other signalling pathways is essential to finetune plant acclimation to Cd stress.

Assessment of Black Rot in Oilseed Rape Grown under Climate Change Conditions Using Biochemical Methods and Computer Vision

Global warming is a challenge for plants and pathogens, involving profound changes in the physiology of both contenders to adapt to the new environmental conditions and to succeed in their interaction. Studies have been conducted on the behavior of oilseed rape plants and two races (1 and 4) of the bacterium Xanthomonas campestris pv. campestris (Xcc) and their interaction to anticipate our response in the possible future climate. Symptoms caused by both races of Xcc were very similar to each other under any climatic condition assayed, although the bacterial count from infected leaves differed for each race. Climate change caused an earlier onset of Xcc symptoms by at least 3 days, linked to oxidative stress and a change in pigment composition. Xcc infection aggravated the leaf senescence already induced by climate change. To identify Xcc-infected plants early under any climatic condition, four classifying algorithms were trained with parameters obtained from the images of green fluorescence, two vegetation indices and thermography recorded on Xcc-symptomless leaves. Classification accuracies were above 0.85 out of 1.0 in all cases, with k-nearest neighbor analysis and support vector machines performing best under the tested climatic conditions.

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.

Induced defense responses in cultivated and wild chickpea genotypes against Helicoverpa armigera infestation

Five desi (GL 12,021, GL 29,095, GL 29,078, H11 22 and CSJ 515) and three wild (GLW 22, GLW 58 and GLW 187) chickpea cultivars showed induced defense response against Helicoverpa armigera infestation as a result of enhanced activities of superoxide dismutase, catalase, peroxidase, ascorbate peroxidase, glutathione reductase, polyphenol oxidase, phenylalanine ammonia lyase, tyrosine ammonia lyase in leaves, pod walls and seeds. Catalase activity increased in leaves of GL 12,021, H11 22, GL 29,095, CSJ 515, GLW 22, and GL 29,078 after infestation compared to resistant check; catalase and peroxidase activities in GL 29,095 and GL 29,078; ascorbate peroxidase and glutathione reductase activities in leaves of GLW 58. The increased activity of superoxide dismutase in pod wall of H1122; catalase in pod wall of 29,078, GL 29,095 and GL 22; ascorbate peroxidase and glutathione reductase in pod wall of GLW 58; phenylalanine ammonia lyase and tyrosine ammonia lyase in pod wall of GLW 187, H11 22, GL 20,978, GLW 22 and GLW 58 after infestation as compared to resistant check might be responsible for mitigating infestation induced oxidative stress. MDA content decreased in leaves, pod wall and seeds of GLW 187 and GL 12,021 after infestation. Lower percent pod damage (9.58-12.44%) in GL 12,021, GLW 187, GL 29,095, H11 22, GL 29,078, GLW 22 and GLW 58 as compared to resistant (16.18%) and susceptible (21.50) checks might be attributed to differential induced defense mechanism in them. The identified desi and wild genotypes might be used in breeding program to develop cultivars with improved resistance to herbivore.

Heat and drought induced transcriptomic changes in barley varieties with contrasting stress response phenotypes

Drought and heat stress substantially impact plant growth and productivity. When subjected to drought or heat stress, plants exhibit reduction in growth resulting in yield losses. The occurrence of these two stresses together intensifies their negative effects. Unraveling the molecular changes in response to combined abiotic stress is essential to breed climate-resilient crops. In this study, transcriptome profiles were compared between stress-tolerant (Otis), and stress-sensitive (Golden Promise) barley genotypes subjected to drought, heat, and combined heat and drought stress for five days during heading stage. The major differences that emerged from the transcriptome analysis were the overall number of differentially expressed genes was relatively higher in Golden Promise (GP) compared to Otis. The differential expression of more than 900 transcription factors in GP and Otis may aid this transcriptional reprogramming in response to abiotic stress. Secondly, combined heat and water deficit stress results in a unique and massive transcriptomic response that cannot be predicted from individual stress responses. Enrichment analyses of gene ontology terms revealed unique and stress type-specific adjustments of gene expression. Weighted Gene Co-expression Network Analysis identified genes associated with RNA metabolism and Hsp70 chaperone components as hub genes that can be useful for engineering tolerance to multiple abiotic stresses. Comparison of the transcriptomes of unstressed Otis and GP plants identified several genes associated with biosynthesis of antioxidants and osmolytes were higher in the former that maybe providing innate tolerance capabilities to effectively combat hostile conditions. Lines with different repertoire of innate tolerance mechanisms can be effectively leveraged in breeding programs for developing climate-resilient barley varieties with superior end-use traits.

Review of the Mechanisms by Which Transcription Factors and Exogenous Substances Regulate ROS Metabolism under Abiotic Stress

Reactive oxygen species (ROS) are signaling molecules that regulate many biological processes in plants. However, excess ROS induced by biotic and abiotic stresses can destroy biological macromolecules and cause oxidative damage to plants. As the global environment continues to deteriorate, plants inevitably experience abiotic stress. Therefore, in-depth exploration of ROS metabolism and an improved understanding of its regulatory mechanisms are of great importance for regulating cultivated plant growth and developing cultivars that are resilient to abiotic stresses. This review presents current research on the generation and scavenging of ROS in plants and summarizes recent progress in elucidating transcription factor-mediated regulation of ROS metabolism. Most importantly, the effects of applying exogenous substances on ROS metabolism and the potential regulatory mechanisms at play under abiotic stress are summarized. Given the important role of ROS in plants and other organisms, our findings provide insights for optimizing cultivation patterns and for improving plant stress tolerance and growth regulation.

Gene network downstream plant stress response modulated by peroxisomal H2O2

Reactive oxygen species (ROS) act as secondary messengers that can be sensed by specific redox-sensitive proteins responsible for the activation of signal transduction culminating in altered gene expression. The subcellular site, in which modifications in the ROS/oxidation state occur, can also act as a specific cellular redox network signal. The chemical identity of ROS and their subcellular origin is actually a specific imprint on the transcriptome response. In recent years, a number of transcriptomic studies related to altered ROS metabolism in plant peroxisomes have been carried out. In this study, we conducted a meta-analysis of these transcriptomic findings to identify common transcriptional footprints for plant peroxisomal-dependent signaling at early and later time points. These footprints highlight the regulation of various metabolic pathways and gene families, which are also found in plant responses to several abiotic stresses. Major peroxisomal-dependent genes are associated with protein and endoplasmic reticulum (ER) protection at later stages of stress while, at earlier stages, these genes are related to hormone biosynthesis and signaling regulation. Furthermore, in silico analyses allowed us to assign human orthologs to some of the peroxisomal-dependent proteins, which are mainly associated with different cancer pathologies. Peroxisomal footprints provide a valuable resource for assessing and supporting key peroxisomal functions in cellular metabolism under control and stress conditions across species.

Plant peroxisome proteostasis-establishing, renovating, and dismantling the peroxisomal proteome

Plant peroxisomes host critical metabolic reactions and insulate the rest of the cell from reactive byproducts. The specialization of peroxisomal reactions is rooted in how the organelle modulates its proteome to be suitable for the tissue, environment, and developmental stage of the organism. The story of plant peroxisomal proteostasis begins with transcriptional regulation of peroxisomal protein genes and the synthesis, trafficking, import, and folding of peroxisomal proteins. The saga continues with assembly and disaggregation by chaperones and degradation via proteases or the proteasome. The story concludes with organelle recycling via autophagy. Some of these processes as well as the proteins that facilitate them are peroxisome-specific, while others are shared among organelles. Our understanding of translational regulation of plant peroxisomal protein transcripts and proteins necessary for pexophagy remain based in findings from other models. Recent strides to elucidate transcriptional control, membrane dynamics, protein trafficking, and conditions that induce peroxisome turnover have expanded our knowledge of plant peroxisomal proteostasis. Here we review our current understanding of the processes and proteins necessary for plant peroxisome proteostasis-the emergence, maintenance, and clearance of the peroxisomal proteome.

Reactive oxygen species signalling in plant stress responses

Reactive oxygen species (ROS) are key signalling molecules that enable cells to rapidly respond to different stimuli. In plants, ROS play a crucial role in abiotic and biotic stress sensing, integration of different environmental signals and activation of stress-response networks, thus contributing to the establishment of defence mechanisms and plant resilience. Recent advances in the study of ROS signalling in plants include the identification of ROS receptors and key regulatory hubs that connect ROS signalling with other important stress-response signal transduction pathways and hormones, as well as new roles for ROS in organelle-to-organelle and cell-to-cell signalling. Our understanding of how ROS are regulated in cells by balancing production, scavenging and transport has also increased. In this Review, we discuss these promising developments and how they might be used to increase plant resilience to environmental stress.

Association between DNA methylation variability and self-reported exposure to heavy metals

Individuals encounter varying environmental exposures throughout their lifetimes. Some exposures such as smoking are readily observed and have high personal recall; others are more indirect or sporadic and might only be inferred from long occupational histories or lifestyles. We evaluated the utility of using lifetime-long self-reported exposures for identifying differential methylation in an amyotrophic lateral sclerosis cases-control cohort of 855 individuals. Individuals submitted paper-based surveys on exposure and occupational histories as well as whole blood samples. Genome-wide DNA methylation levels were quantified using the Illumina Infinium Human Methylation450 array. We analyzed 15 environmental exposures using the OSCA software linear and MOA models, where we regressed exposures individually by methylation adjusted for batch effects and disease status as well as predicted scores for age, sex, cell count, and smoking status. We also regressed on the first principal components on clustered environmental exposures to detect DNA methylation changes associated with a more generalised definition of environmental exposure. Five DNA methylation probes across three environmental exposures (cadmium, mercury and metalwork) were significantly associated using the MOA models and seven through the linear models, with one additionally across a principal component representing chemical exposures. Methylome-wide significance for four of these markers was driven by extreme hyper/hypo-methylation in small numbers of individuals. The results indicate the potential for using self-reported exposure histories in detecting DNA methylation changes in response to the environment, but also highlight the confounded nature of environmental exposure in cohort studies.

Fission Impossible (?)-New Insights into Disorders of Peroxisome Dynamics

Peroxisomes are highly dynamic and responsive organelles, which can adjust their morphology, number, intracellular position, and metabolic functions according to cellular needs. Peroxisome multiplication in mammalian cells involves the concerted action of the membrane-shaping protein PEX11β and division proteins, such as the membrane adaptors FIS1 and MFF, which recruit the fission GTPase DRP1 to the peroxisomal membrane. The latter proteins are also involved in mitochondrial division. Patients with loss of DRP1, MFF or PEX11β function have been identified, showing abnormalities in peroxisomal (and, for the shared proteins, mitochondrial) dynamics as well as developmental and neurological defects, whereas the metabolic functions of the organelles are often unaffected. Here, we provide a timely update on peroxisomal membrane dynamics with a particular focus on peroxisome formation by membrane growth and division. We address the function of PEX11β in these processes, as well as the role of peroxisome–ER contacts in lipid transfer for peroxisomal membrane expansion. Furthermore, we summarize the clinical phenotypes and pathophysiology of patients with defects in the key division proteins DRP1, MFF, and PEX11β as well as in the peroxisome–ER tether ACBD5. Potential therapeutic strategies for these rare disorders with limited treatment options are discussed.

Drought Tolerance Strategies and Autophagy in Resilient Wheat Genotypes

Drought resiliency strategies combine developmental, physiological, cellular, and molecular mechanisms. Here, we compare drought responses in two resilient spring wheat (Triticum aestivum) genotypes: a well-studied drought-resilient Drysdale and a resilient genotype from the US Pacific North-West Hollis. While both genotypes utilize higher water use efficiency through the reduction of stomatal conductance, other mechanisms differ. First, Hollis deploys the drought escape mechanism to a greater extent than Drysdale by accelerating the flowering time and reducing root growth. Second, Drysdale uses physiological mechanisms such as non-photochemical quenching (NPQ) to dissipate the excess of harvested light energy and sustain higher Fv/Fm and ϕPSII, whereas Hollis maintains constant NPQ but lower Fv/Fm and ϕPSII values. Furthermore, more electron donors of the electron transport chain are in the oxidized state in Hollis than in Drysdale. Third, many ROS homeostasis parameters, including peroxisome abundance, transcription of peroxisome biogenesis genes PEX11 and CAT, catalase protein level, and enzymatic activity, are higher in Hollis than in Drysdale. Fourth, transcription of autophagy flux marker ATG8.4 is upregulated to a greater degree in Hollis than in Drysdale under drought, whereas relative ATG8 protein abundance under drought stress is lower in Hollis than in Drysdale. These data demonstrate the activation of autophagy in both genotypes and a greater autophagic flux in Hollis. In conclusion, wheat varieties utilize different drought tolerance mechanisms. Combining these mechanisms within one genotype offers a promising strategy to advance crop resiliency.

The role of NADPH oxidases in regulating leaf gas exchange and ion homeostasis in Arabidopsis plants under cadmium stress

NADPH oxidase, an enzyme associated with the plasma membrane, constitutes one of the main sources of reactive oxygen species (ROS) which regulate different developmental and adaptive responses in plants. In this work, the involvement of NADPH oxidases in the regulation of photosynthesis and cell ionic homeostasis in response to short cadmium exposure was compared between wild type (WT) and three RBOHs (Respiratory Burst Oxidase Homologues) Arabidopsis mutants (AtrbohC, AtrbohD, and AtrbohF). Plants were grown under hydroponic conditions and supplemented with 50 µM CdCl₂ for 24 h. Cadmium treatment differentially affected photosynthesis, stomatal conductance, transpiration, and antioxidative responses in WT and Atrbohs mutants. The loss of function of RBOH isoforms resulted in higher Cd²⁺ influx, mainly in the elongation zone of roots, which was more evident in AtrbohD and AtrbohF mutants. In the mature zone, the highest Cd²⁺ influx was observed in rbohC mutant. The lack of functional RBOH isoforms also resulted in altered patterns of net K⁺ transport across cellular membranes, both in the root epidermis and leaf mesophyll. The analysis of expression of metal transporters by qPCR demonstrated that a loss of functional RBOH isoforms has altered transcript levels for metal NRAMP3, NRAMP6 and IRT1 and the K⁺ transporters outward-rectifying K⁺ efflux GORK channel, while RBOHD specifically regulated transcripts for high-affinity K⁺ transporters KUP8 and HAK5, and IRT1 and RBOHD and F regulated the transcription factors TGA3 and TGA10. It is concluded that RBOH-dependent H₂O₂ regulation of ion homeostasis and Cd is a highly complex process involving multilevel regulation from transpirational water flow to transcriptional and posttranslational modifications of K/metals transporters.

HPR1 Is Required for High Light Intensity Induced Photorespiration in Arabidopsis thaliana

High light intensity as one of the stresses could lead to generation of large amounts of reactive oxygen species (ROS) in plants, resulting in severe plant growth retardation. The photorespiration metabolism plays an important role in producing and removing a variety of ROS, maintaining the dynamic balance of the redox reaction, and preventing photoinhibition. Arabidopsis hydroxypyruvate reductase 1 (HPR1) is a primary metabolic enzyme in the photorespiration cycle. However, the role of HPR1 in plants response to high light is not clear. Here, we found that the expression of HPR1 could be induced by high light intensity. The growth and photosynthetic capacity of hpr1 mutants are seriously affected under high light intensity. The absence of HPR1 suppresses the rates of photorepair of Photosystem II (PSII), aggravates the production of ROS, and accelerates photorespiration rates. Moreover, the activity of ROS scavenging enzymes in the hpr1 mutants is significantly higher. These results indicate that HPR1 is involved in plant response to high light intensity and is essential for maintaining the dynamic balance of ROS and photorespiration.

A glossary of plant cell structures: Current insights and future questions

In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

Peroxisomal PEX7 Receptor Affects Cadmium-Induced ROS and Auxin Homeostasis in Arabidopsis Root System

Peroxisomes are important in plant physiological functions and stress responses. Through the production of reactive oxygen and nitrogen species (ROS and RNS), and antioxidant defense enzymes, peroxisomes control cellular redox homeostasis. Peroxin (PEX) proteins, such as PEX7 and PEX5, recognize peroxisome targeting signals (PTS1/PTS2) important for transporting proteins from cytosol to peroxisomal matrix. pex7-1 mutant displays reduced PTS2 protein import and altered peroxisomal metabolism. In this research we analyzed the role of PEX7 in the Arabidopsis thaliana root system exposed to 30 or 60 μM CdSO₄. Cd uptake and translocation, indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) levels, and reactive oxygen species (ROS) and reactive nitrogen species (RNS) levels and catalase activity were analyzed in pex7-1 mutant primary and lateral roots in comparison with the wild type (wt). The peroxisomal defect due to PEX7 mutation did not reduce Cd-uptake but reduced its translocation to the shoot and the root cell peroxisomal signal detected by 8-(4-Nitrophenyl) Bodipy (N-BODIPY) probe. The trend of nitric oxide (NO) and peroxynitrite in pex7-1 roots, exposed/not exposed to Cd, was as in wt, with the higher Cd-concentration inducing higher levels of these RNS. By contrast, PEX7 mutation caused changes in Cd-induced hydrogen peroxide (H₂O₂) and superoxide anion (O₂^●-) levels in the roots, delaying ROS-scavenging. Results show that PEX7 is involved in counteracting Cd toxicity in Arabidopsis root system by controlling ROS metabolism and affecting auxin levels. These results add further information to the important role of peroxisomes in plant responses to Cd.

Characterization of the biochemical basis for copper homeostasis and tolerance in Biscutella auriculata L

Biscutella auriculata L. is a plant that belongs to the Brassicaceae family and it has been found growing in a metal-contaminated area of the San Quíntín mine (Ciudad Real, Spain). The purpose of this work was to evaluate the mechanisms that allow this plant to tolerate high concentrations of copper. Seedlings were grown in a semi-hydroponic system for 15 days under 125 μM of Cu (NO₃ )₂ . Exposure to copper resulted in growth inhibition and reduction in the photosynthetic parameters. Copper was mainly accumulated in vascular tissue and vacuoles of the roots and only a minor proportion was transferred to the shoot. Biothiol analysis showed a greater enhancement of reduced glutathione in leaves and increases of phytochelatins (PC2 and PC3) in both leaves and roots. Copper treatment induced oxidative stress, which triggered a response of the enzymatic and non-enzymatic antioxidant mechanisms. The results show that B. auriculata is able to tolerate high metal levels through the activation of specific mechanisms to neutralize the oxidative stress produced and also by metal sequestration through phytochelatins. The preferential accumulation of copper in roots provides clues for further studies on the use of this plant for phytostabilization and environmental recovery purposes in Cu-contaminated areas.

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.

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.

Organelle extensions in plant cells

The life strategy of plants includes their ability to respond quickly at the cellular level to changes in their environment. The use of targeted fluorescent protein probes and imaging of living cells has revealed several rapidly induced organelle responses that create the efficient sub-cellular machinery for maintaining homeostasis in the plant cell. Several organelles, including plastids, mitochondria, and peroxisomes, extend and retract thin tubules that have been named stromules, matrixules, and peroxules, respectively. Here, I combine all these thin tubular forms under the common head of organelle extensions. All extensions change shape continuously and in their elongated form considerably increase organelle outreach into the surrounding cytoplasm. Their pleomorphy reflects their interactions with the dynamic endoplasmic reticulum and cytoskeletal elements. Here, using foundational images and time-lapse movies, and providing salient information on some molecular and biochemically characterized mutants with increased organelle extensions, I draw attention to their common role in maintaining homeostasis in plant cells.

Review: Morphology, behaviour and interactions of organelles

High quality transmission electron micrographs have played a major role in shaping our views on organelles in plant cells. However, these snapshots of dead, fixed and sectioned tissue do not automatically convey an appreciation of the dynamic nature of organelles in living cells. Advances in the imaging of subcellular structures in living cells using multicoloured, targeted fluorescent proteins reveal considerable changes in organelle pleomorphy that might be limited to small regions of the cell. The fresh data and insights also challenge several existing ideas on organelle behaviour and interactivity. Here, using succinct examples from plastids, mitochondria, peroxisomes, and the endoplasmic reticulum I present an evolving view of subcellular dynamics in the plant cell.

Overexpression of a Novel Arabidopsis Gene SUPA Leads to Various Morphological and Abiotic Stress Tolerance Alternations in Arabidopsis and Poplar

With the development of sequencing technology, the availability of genome data is rapidly increasing, while functional annotation of genes largely lags behind. In Arabidopsis, the functions of nearly half of the proteins are unknown and this remains one of the main challenges in current biological research. In an attempt to identify novel and rapid abiotic stress responsive genes, a number of salt-up (SUP) regulated genes were isolated by analyzing the public transcriptomic data, and one of them, SUPA, was characterized in this study. The expression of SUPA transcripts was rapidly up-regulated by various abiotic stress factors (<15 min), and SUPA protein is mainly localized in the peroxisome. Overexpression of SUPA in Arabidopsis leads to the elevated accumulation of reactive oxygen species (ROS), strong morphological changes and alternations in abiotic stress tolerance. The transcriptome analysis showed changes in expression of genes involved in stress response and plant development. Interestingly, ectopic overexpression of SUPA in poplar leads to a dwarf phenotype with severely curved leaves and changes in the plant tolerance of abiotic stresses. Our study reinforces the potential roles of SUPA in normal plant growth and the abiotic stress response.

A Comprehensive Toolkit for Quick and Easy Visualization of Marker Proteins, Protein-Protein Interactions and Cell Morphology in Marchantia polymorpha

Even though stable genomic transformation of sporelings and thalli of Marchantia polymorpha is straightforward and efficient, numerous problems can arise during critical phases of the process such as efficient spore production, poor selection capacity of antibiotics or low transformation efficiency. It is therefore also desirable to establish quick methods not relying on stable transgenics to analyze the localization, interactions and functions of proteins of interest. The introduction of foreign DNA into living cells via biolistic mechanisms has been first reported roughly 30 years ago and has been commonly exploited in established plant model species such as Arabidopsis thaliana or Nicotiana benthamiana. Here, we report the fast and reliable transient biolistic transformation of Marchantia thallus epidermal cells using fluorescent protein fusions. We present a catalog of fluorescent markers which can be readily used for tagging of a variety of subcellular compartments. Moreover, we report the functionality of the bimolecular fluorescence complementation (BiFC) in M. polymorpha with the example of the p-body markers MpDCP1/2. Finally, we provide standard staining procedures for live cell imaging in M. polymorpha, applicable to visualize cell boundaries or cellular structures, to complement or support protein localizations and to understand how results gained by transient transformations can be embedded in cell architecture and dynamics. Taken together, we offer a set of easy and quick tools for experiments that aim at understanding subcellular localization, protein-protein interactions and thus functions of proteins of interest in the emerging early diverging land plant model M. polymorpha.

Getting around the cell: physical transport in the intracellular world

Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.

Nitric oxide is essential for cadmium-induced peroxule formation and peroxisome proliferation

Nitric oxide (NO) and nitrosylated derivatives are produced in peroxisomes, but the impact of NO metabolism on organelle functions remains largely uncharacterised. Double and triple NO-related mutants expressing cyan florescent protein (CFP)-SKL (nox1 × px-ck and nia1 nia2 × px-ck) were generated to determine whether NO regulates peroxisomal dynamics in response to cadmium (Cd) stress using confocal microscopy. Peroxule production was compromised in the nia1 nia2 mutants, which had lower NO levels than the wild-type plants. These findings show that NO is produced early in the response to Cd stress and was involved in peroxule production. Cd-induced peroxisomal proliferation was analysed using electron microscopy and by the accumulation of the peroxisomal marker PEX14. Peroxisomal proliferation was inhibited in the nia1 nia2 mutants. However, the phenotype was recovered by exogenous NO treatment. The number of peroxisomes and oxidative metabolism were changed in the NO-related mutant cells. Furthermore, the pattern of oxidative modification and S-nitrosylation of the catalase (CAT) protein was changed in the NO-related mutants in both the absence and presence of Cd stress. Peroxisome-dependent signalling was also affected in the NO-related mutants. Taken together, these results show that NO metabolism plays an important role in peroxisome functions and signalling.

Characterization of mechanisms involved in tolerance and accumulation of Cd in Biscutella auriculata L

Biscutella auriculata L. is one of the rare species that is able to grow in a very contaminated mining area in Villamayor de Calatrava (Ciudad Real, Spain). In an effort to understand the mechanisms involved in the tolerance of this plant to high metal concentrations, we grew B. auriculata in the presence of 125 μM Cd(NO₃)₂ for 15 days and analysed different parameters associated with plant growth, nitric oxide and reactive oxygen species metabolism, metal uptake and translocation, photosynthesis rate and biothiol (glutathione and phytochelatins) content. Treatment with Cd led to growth inhibition in both the leaves and the roots, as well as a reduction of photosynthetic parameters, transpiration and stomatal conductance. The metal was mainly accumulated in the roots and in the vascular tissue, although most Cd was detected in areas surrounding their epidermal cells, while in the leaves the metal accumulated mainly in spongy mesophyll, stomata and trichrome. Based on the Cd bioaccumulation (5.93) and translocation (0.15) factors, this species denoted enrichment of the metal in the roots and its low translocation to the upper tissues. Biothiol analysis showed a Cd-dependent increase of reduced glutathione (GSH) as well as the phytochelatins (PC2 and PC3) in both roots and leaves. Cd-promoted oxidative damage occurred mainly in the leaves due to disturbances in enzymatic and nonenzymatic antioxidants, while the roots did not show significant damage as a result of induction of antioxidant defences. It can be concluded that B. auriculata is a new Cd-tolerant plant with an ability to activate efficient metal-sequestering mechanisms in the root surface and leaves and to induce PCs, as well as antioxidative defences in roots.

Paclitaxel Promotes Tumor-Infiltrating Macrophages in Breast Cancer

OBJECTIVE

Breast cancer remains the most threatening triggers of cancer death in women. Drug resistance inevitably leads to the weakness of treatment for breast cancer. Macrophages, as one of the most abundant immune cells in tumor immune-infiltrating microenvironment, involves in cell survival, migration, and invasion of breast cancer.

METHODS

In this study, we compared the proportions of macrophages in patients with breast cancer with and without paclitaxel treatment, and investigated the targeted genes associated with macrophages for paclitaxel response. To explore the relationship between drug-related genes and breast cancer prognosis, survival analysis based on the drug-related genes were performed by website of Kaplan-Meier plotter with the threshold of significant P value < .05.

RESULTS

Compared to the normal samples, we revealed that paclitaxel significantly enhanced the ratio of macrophages in the tumor microenvironment. Furthermore, the expression of 3 drug-related genes (IFT46, PEX11A, and TMEM223) were significantly negatively associated with the proportions of macrophages. And it is worth to notice that PEX11A and TMEM223 were associated with better progression-free survival outcomes of patients with breast cancer. Moreover, PEX11A was associated with longer overall survival time of breast cancer.

CONCLUSION

Taken all together, all the findings support to gain a better understanding to the development of more effective therapies targeted with paclitaxel.

Cadmium and arsenic-induced-stress differentially modulates Arabidopsis root architecture, peroxisome distribution, enzymatic activities and their nitric oxide content

In plant cells, cadmium (Cd) and arsenic (As) exert toxicity mainly by inducing oxidative stress through an imbalance between the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS), and their detoxification. Nitric oxide (NO) is a RNS acting as signalling molecule coordinating plant development and stress responses, but also as oxidative stress inducer, depending on its cellular concentration. Peroxisomes are versatile organelles involved in plant metabolism and signalling, with a role in cellular redox balance thanks to their antioxidant enzymes, and their RNS (mainly NO) and ROS. This study analysed Cd or As effects on peroxisomes, and NO production and distribution in the root system, including primary root (PR) and lateral roots (LRs). Arabidopsis thaliana wild-type and transgenic plants enabling peroxisomes to be visualized in vivo, through the expression of the 35S-cyan fluorescent protein fused to the peroxisomal targeting signal1 (PTS1) were used. Peroxisomal enzymatic activities including the antioxidant catalase, the H₂O₂-generating glycolate oxidase, and the hydroxypyruvate reductase, and root system morphology were also evaluated under Cd/As exposure. Results showed that Cd and As differently modulate these activities, however, catalase activity was inhibited by both. Moreover, Arabidopsis root system was altered, with the pollutants differently affecting PR growth, but similarly enhancing LR formation. Only in the PR apex, and not in LR one, Cd more than As caused significant changes in peroxisome distribution, size, and in peroxisomal NO content. By contrast, neither pollutant caused significant changes in peroxisomes size and peroxisomal NO content in the LR apex.

Cuminal Inhibits Trichothecium roseum Growth by Triggering Cell Starvation: Transcriptome and Proteome Analysis

Trichothecium roseum is a harmful postharvest fungus causing serious damage, together with the secretion of insidious mycotoxins, on apples, melons, and other important fruits. Cuminal, a predominant component of Cuminum cyminum essential oil has proven to successfully inhibit the growth of T. roseum in vitro and in vivo. Electron microscopic observations revealed cuminal exposure impaired the fungal morphology and ultrastructure, particularly the plasmalemma. Transcriptome and proteome analysis was used to investigate the responses of T. roseum to exposure of cuminal. In total, 2825 differentially expressed transcripts (1516 up and 1309 down) and 225 differentially expressed proteins (90 up and 135 down) were determined. Overall, notable parts of these differentially expressed genes functionally belong to subcellular localities of the membrane system and cytosol, along with ribosomes, mitochondria and peroxisomes. According to the localization analysis and the biological annotation of these genes, carbohydrate and lipids metabolism, redox homeostasis, and asexual reproduction were among the most enriched gene ontology (GO) terms. Biological pathway enrichment analysis showed that lipids and amino acid degradation, ATP-binding cassette transporters, membrane reconstitution, mRNA surveillance pathway and peroxisome were elevated, whereas secondary metabolite biosynthesis, cell cycle, and glycolysis/gluconeogenesis were down regulated. Further integrated omics analysis showed that cuminal exposure first impaired the polarity of the cytoplasmic membrane and then triggered the reconstitution and dysfunction of fungal plasmalemma, resulting in handicapped nutrient procurement of the cells. Consequently, fungal cells showed starvation stress with limited carbohydrate metabolism, resulting a metabolic shift to catabolism of the cell's own components in response to the stress. Additionally, these predicaments brought about oxidative stress, which, in collaboration with the starvation, damaged certain critical organelles such as mitochondria. Such degeneration, accompanied by energy deficiency, suppressed the biosynthesis of essential proteins and inhibited fungal growth.

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.

On the move: redox-dependent protein relocation in plants

Compartmentation of proteins and processes is a defining feature of eukaryotic cells. The growth and development of organisms is critically dependent on the accurate sorting of proteins within cells. The mechanisms by which cytosol-synthesized proteins are delivered to the membranes and membrane compartments have been extensively characterized. However, the protein complement of any given compartment is not precisely fixed and some proteins can move between compartments in response to metabolic or environmental triggers. The mechanisms and processes that mediate such relocation events are largely uncharacterized. Many proteins can in addition perform multiple functions, catalysing alternative reactions or performing structural, non-enzymatic functions. These alternative functions can be equally important functions in each cellular compartment. Such proteins are generally not dual-targeted proteins in the classic sense of having targeting sequences that direct de novo synthesized proteins to specific cellular locations. We propose that redox post-translational modifications (PTMs) can control the compartmentation of many such proteins, including antioxidant and/or redox-associated enzymes.

Stripe rust induced defence mechanisms in the leaves of contrasting barley genotypes (Hordeum vulgare L.) at the seedling stage

Puccinia striiformis f. sp. hordei, the causal organism of stripe rust in barley poses serious threats to its production. The present study examined the seedling response and changes in antioxidant defence system along with NADPH oxidase, hydrogen peroxide, and lipid peroxidation marker-malondialdehyde (MDA) in the four barley genotypes namely Jyoti, RD2900, RD2901, and RD2552 in response to M and G-races of stripe rust pathogen. Disease reaction showed Jyoti as susceptible genotype, RD2901 and RD2552 as resistant, whereas RD2900 behaved differentially to both the races. M-race which is predominant was found to be more virulent than G-race of barley stripe rust pathogen. RD2901 showed an increase in activities of NADPH oxidase, catalase, peroxidase, and enzymes of ascorbate-glutathione pathway along with ascorbate and glutathione pool on inoculation with M-race, which was accompanied by the decrease in hydrogen peroxide and MDA contents. Jyoti, on the other hand, showed an increase in peroxidase and glutathione-S-transferase activities only which were unable to maintain redox homeostasis. The scrutiny of data indicated an increase in ASA/DHA ratio on infection in all the genotypes irrespective of their behaviour towards the races. However, GSH/GSSG ratio significantly declined in Jyoti and increased or remained unaffected in the resistant genotypes which suggested that GSH/GSSG might be playing a vital role in imparting tolerance against stripe rust. Further, correlation studies also revealed that leaf damage was positively correlated with H₂O₂ and MDA contents.

Assessment of Subcellular ROS and NO Metabolism in Higher Plants: Multifunctional Signaling Molecules

Reactive oxygen species (ROS) and nitric oxide (NO) are produced in all aerobic life forms under both physiological and adverse conditions. Unregulated ROS/NO generation causes nitro-oxidative damage, which has a detrimental impact on the function of essential macromolecules. ROS/NO production is also involved in signaling processes as secondary messengers in plant cells under physiological conditions. ROS/NO generation takes place in different subcellular compartments including chloroplasts, mitochondria, peroxisomes, vacuoles, and a diverse range of plant membranes. This compartmentalization has been identified as an additional cellular strategy for regulating these molecules. This assessment of subcellular ROS/NO metabolisms includes the following processes: ROS/NO generation in different plant cell sites; ROS interactions with other signaling molecules, such as mitogen-activated protein kinases (MAPKs), phosphatase, calcium (Ca²⁺), and activator proteins; redox-sensitive genes regulated by the iron-responsive element/iron regulatory protein (IRE-IRP) system and iron regulatory transporter 1(IRT1); and ROS/NO crosstalk during signal transduction. All these processes highlight the complex relationship between ROS and NO metabolism which needs to be evaluated from a broad perspective.

Co-regulation map of the human proteome enables identification of protein functions

Assigning functions to the vast array of proteins present in eukaryotic cells remains challenging. To identify relationships between proteins, and thereby enable functional annotation of proteins, we determined changes in abundance of 10,323 human proteins in response to 294 biological perturbations using isotope-labeling mass spectrometry. We applied the machine learning algorithm treeClust to reveal functional associations between co-regulated human proteins from ProteomeHD, a compilation of our own data and datasets from the Proteomics Identifications database. This produced a co-regulation map of the human proteome. Co-regulation was able to capture relationships between proteins that do not physically interact or colocalize. For example, co-regulation of the peroxisomal membrane protein PEX11β with mitochondrial respiration factors led us to discover an organelle interface between peroxisomes and mitochondria in mammalian cells. We also predicted the functions of microproteins that are difficult to study with traditional methods. The co-regulation map can be explored at www.proteomeHD.net .

Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications

Peroxisomes, which are ubiquitous organelles in all eukaryotes, are highly dynamic organelles that are essential for development and stress responses. Plant peroxisomes are involved in major metabolic pathways, such as fatty acid β-oxidation, photorespiration, ureide and polyamine metabolism, in the biosynthesis of jasmonic, indolacetic, and salicylic acid hormones, as well as in signaling molecules such as reactive oxygen and nitrogen species (ROS/RNS). Peroxisomes are involved in the perception of environmental changes, which is a complex process involving the regulation of gene expression and protein functionality by protein post-translational modifications (PTMs). Although there has been a growing interest in individual PTMs in peroxisomes over the last ten years, their role and cross-talk in the whole peroxisomal proteome remain unclear. This review provides up-to-date information on the function and crosstalk of the main peroxisomal PTMs. Analysis of whole peroxisomal proteomes shows that a very large number of peroxisomal proteins are targeted by multiple PTMs, which affect redox balance, photorespiration, the glyoxylate cycle, and lipid metabolism. This multilevel PTM regulation could boost the plasticity of peroxisomes and their capacity to regulate metabolism in response to environmental changes.