Rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments

Comparative analysis of synteny and functional divergence of APX genes in Fragaria vesca and Fragaria×ananassa

BACKGROUND

Ascorbate peroxidase (APX) is a key enzyme that removes reactive oxygen species (ROS) in the ascorbic acid-glutathione cycle. Although APX genes have been reported in many species, comparative analysis of genome-wide, promoters, and gene functions between F. vesca (Fragaria vesca L.) and F. × ananassa (Fragaria×ananassa Duch.) have not been comprehensively explored.

RESULTS

In this study, seven FvAPX and twenty FaAPX genes were divided into five subgroups. By comparative analysis of the 5 motifs between F. vesca and F. × ananassa, it was found that some fragments were gained/lost. These amino acid fragments might be closely related to the function of the APX genes. Synteny analysis of F. vesca and F. × ananassa showed that there were more collinearity genes with grapes. Compared with F. × ananassa, the FvAPX2, FvAPX3, FvAPX4, and FvAPX6 proteins were more likely to use Val and Leu in F. vesca. The RT‒qPCR results confirmed that FaAPX5 and FvAPX7 were obviously upregulated under the NaCl, PEG, and H2O2 treatments. The GUS assay showed that FvAPX7 had stronger promoter activity than FaAPX5. Additionally, the overexpression of FvAPX7 and FaAPX5 in 'Benihoppe' leaves and Arabidopsis (Arabidopsis thaliana) improved activities of POD, SOD, CAT, and APX, and decreased the relative electrical conductivity and H2O2 content under NaCl, H2O2, and drought stresses.

CONCLUSIONS

Collectively, our study provides comprehensive insight regarding the evolutionary relationship between F. vesca and F. × ananassa and offers substantial opportunities for further research on the functions of APX genes.

Decoding the role of durum wheat ascorbate peroxidase TdAPX7B-2 in abiotic stress response

APX proteins are H2O2-scavenging enzymes induced during oxidative stress. In the first part of this study, we provided an extensive knowledge on the APX family of Triticum durum, TdAPX and their related TdAPX-R, via the genome wide analysis. The outcomes showed that these proteins are clustered into four major subgroups. Furthermore, the exon-intron structure and the synteny analyses revealed that during evolution the genes TdAPX and TdAPX-R are relatively conserved. Besides, during their evolution, these genes underwent purifying selection pressure and were duplicated in segmental. In parallel, the analysis of the conserved motifs and the multiple sequence alignment demonstrated that the residues involved in the active sites, heme- and cations-binding are conserved only in TdAPX proteins. Following the RNA-seq data and the regulatory elements analyses, we focused in the second part of this study on the functional characterization of TdAPX7B-2. The qRT-PCR data showed the upregulation of TdAPX7B-2 essentially in leaves of durum wheat exposed to salt, cold, drought, metals and ABA treatments. The tolerance phenotype of the TdAPX7B-2-expressing Arabidopsis lines to salt, direct-induced oxidative stress and heavy metals was manifested by the development of root system, proline accumulation and induction of the antioxidant CAT, SOD and POD enzymes to maintain the non-toxic H2O2 levels. Likewise, the response to salt stress and direct-oxidative stress of the transgenic lines was accompanied mainly by the induction of AtNCED3, AtRD29A/B and AtERD1.

Identification of Host Factors Interacting with Movement Proteins of the 30K Family in Nicotiana tabacum

The interaction of viral proteins with host factors represents a crucial aspect of the infection process in plants. In this work, we developed a strategy to identify host factors in Nicotiana tabacum that interact with movement proteins (MPs) of the 30K family, a group of viral proteins around 30 kDa related to the MP of tobacco mosaic virus, which enables virus movement between plant cells. Using the alfalfa mosaic virus (AMV) MP as a model, we incorporated tags into its coding sequence, without affecting its functionality, enabling the identification of 121 potential interactors through in vivo immunoprecipitation of the tagged MP. Further analysis of five selected candidates (histone 2B (H2B), actin, 14-3-3A protein, eukaryotic initiation factor 4A (elF4A), and a peroxidase-POX-) were conducted using bimolecular fluorescence complementation (BiFC). The interactions between these factors were also studied, revealing that some form part of protein complexes associated with AMV MP. Moreover, H2B, actin, 14-3-3, and eIF4A interacted with other MPs of the 30K family. This observation suggests that, beyond functional and structural features, 30K family MPs may share common interactors. Our results demonstrate that tagging 30K family MPs is an effective strategy to identify host factors associated with these proteins during viral infection.

Systematic analysis and functional verification of citrus ascorbate peroxidases reveal that CsAPX01 and CsAPX02 negatively regulate citrus bacterial canker through the hydrogen peroxide regulation

Ascorbate peroxidases (APXs) are antioxidant enzymes that play vital roles in redox homeostasis in plants. Citrus is susceptible to infection by Xanthomonas citri subsp. citri (Xcc), resulting in citrus bacterial canker (CBC). The present study used bioinformatic and expression analyses to investigate the APX family in Citrus sinensis. Bioinformatic research revealed the chromosomal locations, phylogeny, gene structure, promoter elements, functional domains, conserved motifs, and most likely physicochemical properties of the sequences. Six APXs clustered in three groups were identified, with each protein containing a single peroxidase domain. The promoter regions contained a variety of transcription factor-binding and hormone-response components. Xcc infection induced different CsAPX01 and CsAPX02 expressions in the CBC-susceptible Wanjincheng and CBC-resistant Kumquat varieties. Subcellular localization and transient expression showed that CsAPX01 and CsAPX02 were expressed in the cytoplasm and nucleus and had hydrogen peroxide (H2O2)-scavenging activity. Virus-induced gene silencing (VIGS) of CsAPX01 and CsAPX02 resulted in strong resistance to CBC and H2O2 bursts without effects on the plant phenotype. The current study focused on investigating and characterizing the citrus APX family. It was found that CsAPX01 and CsAPX02 exacerbated CBC by altering the balance of H2O2. These findings emphasize the importance of APXs in enhancing plant resistance to pathogens.

Ascorbate peroxidase in fruits and modulation of its activity by reactive species

Ascorbate peroxidase (APX) is one of the enzymes of the ascorbate-glutathione cycle and is the key enzyme that breaks down H2O2 with the aid of ascorbate as an electron source. APX is present in all photosynthetic eukaryotes from algae to higher plants and, at the cellular level, it is localized in all subcellular compartments where H2O2 is generated, including the apoplast, cytosol, plastids, mitochondria, and peroxisomes, either in soluble form or attached to the organelle membranes. APX activity can be modulated by various post-translational modifications including tyrosine nitration, S-nitrosation, persulfidation, and S-sulfenylation. This allows the connection of H2O2 metabolism with other relevant signaling molecules such as NO and H2S, thus building a complex coordination system. In both climacteric and non-climacteric fruits, APX plays a key role during the ripening process and during post-harvest, since it participates in the regulation of both H2O2 and ascorbate levels affecting fruit quality. Currently, the exogenous application of molecules such as NO, H2S, H2O2, and, more recently, melatonin is seen as a new alternative to maintain and extend the shelf life and quality of fruits because they can modulate APX activity as well as other antioxidant systems. Therefore, these molecules are being considered as new biotechnological tools to improve crop quality in the horticultural industry.

QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued

Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.

Comprehensive characterization and expression analysis of enzymatic antioxidant gene families in passion fruit (Passiflora edulis)

Passion fruit, a valuable tropical fruit, faces climate-related growth challenges. Antioxidant enzymes are vital for both stress protection and growth regulation in plants. We first provided systemic analysis of enzymatic antioxidant gene families in passion fruit, identifying 90 members including 11 PeSODs, 45 PeAPXs, 8 PeCATs, 7 PeGPXs, 6 PeMDHARs, 8 PeDHARs, and 5 PeGRs. Gene members in each gene family with same subcellular localization showed closer phylogenetic relationship. Many antioxidant genes exhibited tissue- or developmental stage-specific expression patterns during floral and fruit development, with some widely expressed. Their co-expressed genes were linked to photosynthesis and energy metabolism, suggesting roles in protecting highly proliferating tissues from oxidative damage. Potential genes for enhancing temperature stress resistance were identified. The involvement of diverse regulatory factors including miRNAs, transcription factors, and CREs might contribute to the complex roles of antioxidant genes. This study informs future research on antioxidant genes and passion fruit breeding.

A synthetic light-inducible photorespiratory bypass enhances photosynthesis to improve rice growth and grain yield

Bioengineering of photorespiratory bypasses is an effective strategy for improving plant productivity by modulating photosynthesis. In previous work, two photorespiratory bypasses, the GOC and GCGT bypasses, increased photosynthetic rates but decreased seed-setting rate in rice (Oryza sativa), probably owing to excess photosynthate accumulation in the stem. To solve this bottleneck, we successfully developed a new synthetic photorespiratory bypass (called the GMA bypass) in rice chloroplasts by introducing Oryza sativa glycolate oxidase 1 (OsGLO1), Cucurbita maxima malate synthase (CmMS), and Oryza sativa ascorbate peroxidase7 (OsAPX7) into the rice genome using a high-efficiency transgene stacking system. Unlike the GOC and GCGT bypass genes driven by constitutive promoters, OsGLO1 in GMA plants was driven by a light-inducible Rubisco small subunit promoter (pRbcS); its expression dynamically changed in response to light, producing a more moderate increase in photosynthate. Photosynthetic rates were significantly increased in GMA plants, and grain yields were significantly improved under greenhouse and field conditions. Transgenic GMA rice showed no reduction in seed-setting rate under either test condition, unlike previous photorespiratory-bypass rice, probably reflecting proper modulation of the photorespiratory bypass. Together, these results imply that appropriate engineering of the GMA bypass can enhance rice growth and grain yield without affecting seed-setting rate.

Salinity stress and nanoparticles: Insights into antioxidative enzymatic resistance, signaling, and defense mechanisms

Salinized land is slowly spreading across the world. Reduced crop yields and quality due to salt stress threaten the ability to feed a growing population. We discussed the mechanisms behind nano-enabled antioxidant enzyme-mediated plant tolerance, such as maintaining reactive oxygen species (ROS) homeostasis, enhancing the capacity of plants to retain K+ and eliminate Na+, increasing the production of nitric oxide, involving signaling pathways, and lowering lipoxygenase activities to lessen oxidative damage to membranes. Frequently used techniques were highlighted like protecting cells from oxidative stress and keeping balance in ionic state. Salt tolerance in plants enabled by nanotechnology is also discussed, along with the potential role of physiobiochemical and molecular mechanisms. As a whole, the goal of this review is meant to aid researchers in fields as diverse as plant science and nanoscience in better-comprehending potential with novel solutions to addressing salinity issues for sustainable agriculture.

Halotolerant endophytic bacteria alleviate salinity stress in rice (oryza sativa L.) by modulating ion content, endogenous hormones, the antioxidant system and gene expression

Excessive salinity reduces crop production and negatively impacts agriculture worldwide. We previously isolated endophytic bacterial strains from two halophytic species: Artemisia princeps and Chenopodium ficifolium. We used three bacterial isolates: ART-1 (Lysinibacillus fusiformis), ART-10 (Lysinibacillus sphaericus), and CAL-8 (Brevibacterium pityocampae) to alleviate the impact of salinity stress on rice. The impact of 160 mM NaCl salinity on rice was significantly mitigated following inoculation with these bacterial strains, resulting in increased growth and chlorophyll content. Furthermore, OsNHX1, OsAPX1, OsPIN1 and OsCATA expression was increased, but OsSOS expression was decreased. Inductively coupled plasma mass spectrometry (ICP-MS) revealed reduced K+ and Na+ levels in shoots of bacteria-inoculated plants, whereas that of Mg2+ was increased. Bacterial inoculation reduced the content of total flavonoids in rice leaves. Salinized plants inoculated with bacteria showed reduced levels of endogenous salicylic acid (SA) and abscisic acid (ABA) but increased levels of jasmonic acid (JA). In conclusion, the bacterial isolates ART-1, ART-10, and CAL-8 alleviated the adverse effect of salinity on rice growth, which justifies their use as an eco-friendly agricultural practice.

Achieving abiotic stress tolerance in plants through antioxidative defense mechanisms

Climate change has increased the overall impact of abiotic stress conditions such as drought, salinity, and extreme temperatures on plants. Abiotic stress adversely affects the growth, development, crop yield, and productivity of plants. When plants are subjected to various environmental stress conditions, the balance between the production of reactive oxygen species and its detoxification through antioxidant mechanisms is disturbed. The extent of disturbance depends on the severity, intensity, and duration of abiotic stress. The equilibrium between the production and elimination of reactive oxygen species is maintained due to both enzymatic and non-enzymatic antioxidative defense mechanisms. Non-enzymatic antioxidants include both lipid-soluble (α-tocopherol and β-carotene) and water-soluble (glutathione, ascorbate, etc.) antioxidants. Ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR) are major enzymatic antioxidants that are essential for ROS homeostasis. In this review, we intend to discuss various antioxidative defense approaches used to improve abiotic stress tolerance in plants and the mechanism of action of the genes or enzymes involved.

Genome-wide characterization of ascorbate peroxidase gene family in pepper (Capsicum annuum L.) in response to multiple abiotic stresses

Pepper is widely grown all over the world, so it faces many abiotic stresses, such as drought, high temperature, low temperature, salt damage, and so on. Stresses causing the accumulation of reactive oxidative species (ROS) in plants are removed by antioxidant defense systems, and ascorbate peroxidase (APX) is an important antioxidant enzyme. Therefore, the present study performed genome-wide identification of the APX gene family in pepper. We identified nine members of the APX gene family in the pepper genome according to the APX proteins' conserved domain in Arabidopsis thaliana. The physicochemical property analysis showed that CaAPX3 had the longest protein sequence and the largest molecular weight of all genes, while CaAPX9 had the shortest protein sequence and the smallest MW. The gene structure analysis showed that CaAPXs were composed of seven to 10 introns. The CaAPX genes were divided into four groups. The APX genes of groups I and IV were localized in the peroxisomes and chloroplasts, respectively; the group II genes were localized in the chloroplasts and mitochondria; and the group III genes were located in the cytoplasm and extracell. The conservative motif analysis showed that all APX genes in the pepper had motif 2, motif 3, and motif 5. The APX gene family members were distributed on five chromosomes (Chr. 2, 4, 6, 8, and 9). The cis-acting element analysis showed that most CaAPX genes contain a variety of cis-elements related to plant hormones and abiotic stress. RNA-seq expression analysis showed that the expression patterns of nine APXs were different in vegetative and reproductive organs at different growth and development stages. In addition, the qRT-PCR analysis of the CaAPX genes revealed significant differential expression in response to high temperature, low temperature, and salinity stresses in leaf tissue. In conclusion, our study identified the APX gene family members in the pepper and predicted the functions of this gene family, which would provide resources for further functional characterization of CaAPX genes.

Identification of citrus APX gene family and their response to CYVCV infection

Ascorbate peroxidase (APX) is one of the most important antioxidant enzymes in the reactive oxygen metabolic pathway of plants. The role of APX under biotic and abiotic stress conditions has been explored, but the response pattern of APX under biotic stresses is relatively less known. In this study, seven CsAPXs gene family members were identified based on the sweet orange (Citrus sinensis) genome and subjected to evolutionary and structural analysis using bioinformatics software. The APX genes of lemon (ClAPXs) were cloned and showed a high conservation to CsAPXs by sequences alignment. In citrus yellow vein clearing virus (CYVCV)-infected Eureka lemons (C. limon) at 30th day post inoculation, APX activity and accumulation of hydrogen peroxide (H₂O₂) and malondialdehyde were measured to be 3.63, 2.29, and 1.73 times to that of the healthy control. The expression levels of 7 ClAPX genes in different periods of CYVCV-infected Eureka lemon were analyzed. Notably, ClAPX1, ClAPX5, and ClAPX7 showed higher expression levels compared to healthy plants, while ClAPX2, ClAPX3, and ClAPX4 showed lower expression levels. Functional identification of ClAPX1 in Nicotiana benthamiana showed that increasing the expression of ClAPX1 could significantly reduce the accumulation of H₂O₂, and it was verified that ClAPX1 is located in the plasma membrane of the cell. The present study provided information on the evolution and function of citrus APXs and revealed for the first time their response pattern to CYVCV infection.

Stromal Ascorbate Peroxidase (OsAPX7) Modulates Drought Stress Tolerance in Rice (Oryza sativa)

Chloroplast ascorbate peroxidases exert an important role in the maintenance of hydrogen peroxide levels in chloroplasts by using ascorbate as the specific electron donor. In this work, we performed a functional study of the stromal APX in rice (OsAPX7) and demonstrated that silencing of OsAPX7 did not impact plant growth, redox state, or photosynthesis parameters. Nevertheless, when subjected to drought stress, silenced plants (APX7i) show a higher capacity to maintain stomata aperture and photosynthesis performance, resulting in a higher tolerance when compared to non-transformed plants. RNA-seq analyses indicate that the silencing of OsAPX7 did not lead to changes in the global expression of genes related to reactive oxygen species metabolism. In addition, the drought-mediated induction of several genes related to the proteasome pathway and the down-regulation of genes related to nitrogen and carotenoid metabolism was impaired in APX7i plants. During drought stress, APX7i showed an up-regulation of genes encoding flavonoid and tyrosine metabolism enzymes and a down-regulation of genes related to phytohormones signal transduction and nicotinate and nicotinamide metabolism. Our results demonstrate that OsAPX7 might be involved in signaling transduction pathways related to drought stress response, contributing to the understanding of the physiological role of chloroplast APX isoforms in rice.

Ascorbate-Glutathione Cycle Genes Families in Euphorbiaceae: Characterization and Evolutionary Analysis

Ascorbate peroxidase (APX), Monodehydroascorbate Reductase (MDAR), Dehydroascorbate Reductase (DHAR) and Glutathione Reductase (GR) enzymes participate in the ascorbate-glutathione cycle, which exerts a central role in the antioxidant metabolism in plants. Despite the importance of this antioxidant system in different signal transduction networks related to development and response to environmental stresses, the pathway has not yet been comprehensively characterized in many crop plants. Among different eudicotyledons, the Euphorbiaceae family is particularly diverse with some species highly tolerant to drought. Here the APX, MDAR, DHAR, and GR genes in Ricinus communis, Jatropha curcas, Manihot esculenta, and Hevea brasiliensis were identified and characterized. The comprehensive phylogenetic and genomic analyses allowed the classification of the genes into different classes, equivalent to cytosolic, peroxisomal, chloroplastic, and mitochondrial enzymes, and revealed the duplication events that contribute to the expansion of these families within plant genomes. Due to the high drought stress tolerance of Ricinus communis, the expression patterns of ascorbate-glutathione cycle genes in response to drought were also analyzed in leaves and roots, indicating a differential expression during the stress. Altogether, these data contributed to the characterization of the expression pattern and evolutionary analysis of these genes, filling the gap in the proposed functions of core components of the antioxidant mechanism during stress response in an economically relevant group of plants.

Genome-wide, evolutionary, and functional analyses of ascorbate peroxidase (APX) family in Poaceae species

Ascorbate peroxidases (APXs) are heme peroxidases involved in the control of hydrogen peroxide levels and signal transduction pathways related to development and stress responses. Here, a total of 238 APX, 30 APX-related (APX-R), and 34 APX-like (APX-L) genes were identified from 24 species from the Poaceae family. Phylogenetic analysis of APX indicated five distinct clades, equivalent to cytosolic (cAPX), peroxisomal (pAPX), mitochondrial (mitAPX), stromal (sAPX), and thylakoidal (tAPX) isoforms. Duplication events contributed to the expansion of this family and the divergence times. Different from other APX isoforms, the emergence of Poaceae mitAPXs occurred independently after eudicot and monocot divergence. Our results showed that the constitutive silencing of mitAPX genes is not viable in rice plants, suggesting that these isoforms are essential for rice regeneration or development. We also obtained rice plants silenced individually to sAPX isoforms, demonstrating that, different to plants double silenced to both sAPX and tAPX or single silenced to tAPX previously obtained, these plants do not show changes in the total APX activity and hydrogen peroxide content in the shoot. Among rice plants silenced to different isoforms, plants silenced to cAPX showed a higher decrease in total APX activity and an increase in hydrogen peroxide levels. These results suggest that the cAPXs are the main isoforms responsible for regulating hydrogen peroxide levels in the cell, whereas in the chloroplast, this role is provided mainly by the tAPX isoform. In addition to broadening our understanding of the core components of the antioxidant defense in Poaceae species, the present study also provides a platform for their functional characterization.

Chloroplastic ascorbate peroxidases targeted to stroma or thylakoid membrane: The chicken or egg dilemma

Ascorbate peroxidases (APXs) are heme peroxidases that remove hydrogen peroxide in different subcellular compartments with concomitant ascorbate cycling. Here, we analysed and discussed phylogenetic and molecular features of the APX family. Ancient APX originated as a soluble stromal enzyme, and early during plant evolution, acquired both chloroplast-targeting and mitochondrion-targeting sequences and an alternative splicing mechanism whereby it could be expressed as a soluble or thylakoid membrane-bound enzyme. Later, independent duplication and neofunctionalization events in some angiosperm groups resulted in individual genes encoding stromal, thylakoidal and mitochondrial isoforms. These data reaffirm the complexity of plant antioxidant defenses that allow diverse plant species to acquire new means to adapt to changing environmental conditions.

Transcriptome Analyses in a Selected Gene Set Indicate Alternative Oxidase (AOX) and Early Enhanced Fermentation as Critical for Salinity Tolerance in Rice

Plants subjected to stress need to respond rapidly and efficiently to acclimatize and survive. In this paper, we investigated a selected gene set potentially involved in early cell reprogramming in two rice genotypes with contrasting salinity tolerance (Pokkali tolerant and IR29 susceptible) in order to advance knowledge of early molecular mechanisms of rice in dealing with salt stress. Selected genes were evaluated in available transcriptomic data over a short period of 24 h and involved enzymes that avoid ROS formation (AOX, UCP and PTOX), impact ATP production (PFK, ADH and COX) or relate to the antioxidant system. Higher transcript accumulation of AOX (ROS balancing), PFK and ADH (alcohol fermentation) was detected in the tolerant genotype, while the sensitive genotype revealed higher UCP and PTOX transcript levels, indicating a predominant role for early transcription of AOX and fermentation in conferring salt stress tolerance to rice. Antioxidant gene analyses supported higher oxidative stress in IR29, with transcript increases of cytosolic CAT and SOD from all cell compartments (cytoplasm, peroxisome, chloroplast and mitochondria). In contrast, Pokkali increased mRNA levels from the AsA-GSH cycle as cytosolic/mitochondrial DHAR was involved in ascorbate recovery. In addition, these responses occurred from 2 h in IR29 and 10 h in Pokkali, indicating early but ineffective antioxidant activity in the susceptible genotype. Overall, our data suggest that AOX and ADH can play a critical role during early cell reprogramming for improving salt stress tolerance by efficiently controlling ROS formation in mitochondria. We discuss our results in relation to gene engineering and editing approaches to develop salinity-tolerant crops.

A New Method for Rapid Subcellular Localization and Gene Function Analysis in Cotton Based on Barley Stripe Mosaic Virus

The difficulty of genetic transformation has restricted research on functional genomics in cotton. Thus, a rapid and efficient method for gene overexpression that does not rely on genetic transformation is needed. Virus-based vectors offer a reasonable alternative for protein expression, as viruses can infect the host systemically to achieve expression and replication without transgene integration. Previously, a novel four-component barley stripe mosaic virus (BSMV) was reported to overexpress large fragments of target genes in plants over a long period of time, which greatly simplified the study of gene overexpression. However, whether this system can infect cotton and stably overexpress target genes has not yet been studied. In this study, we verified that this new BSMV system can infect cotton through seed imbibition and systemically overexpress large fragments of genes (up to 2340 bp) in cotton. The target gene that was fused with GFP was expressed at a high level in the roots, stems, and cotyledons of cotton seedlings, and stable fluorescence signals were detected in the cotton roots and leaves even after 4 weeks. Based on the BSMV overexpression system, the subcellular localization marker line of endogenous proteins localized in the nucleus, endoplasmic reticulum, plasma membrane, Golgi body, mitochondria, peroxisomes, tonoplast, and plastids were quickly established. The overexpression of a cotton Bile Acid Sodium Symporter GhBASS5 using the BSMV system indicated that GhBASS5 negatively regulated salt tolerance in cotton by transporting Na⁺ from underground to the shoots. Furthermore, multiple proteins were co-delivered, enabling co-localization and the study of protein–protein interactions through co-transformation. We also confirmed that the BSMV system can be used to conduct DNA-free gene editing in cotton by delivering split-SpCas9/sgRNA. Ultimately, the present work demonstrated that this BSMV system could be used as an efficient overexpression system for future cotton gene function research.

OsQHB Improves Salt Tolerance by Scavenging Reactive Oxygen Species in Rice

Soil salinity is a major environmental stress that restricts the growth and yield of crops. Mining the key genes involved in the balance of rice salt tolerance and yield will be extremely important for us to cultivate salt-tolerance rice varieties. In this study, we report a WUSCHEL-related homeobox (WOX) gene, quiescent-center-specific homeobox (OsQHB), positively regulates yield-related traits and negatively regulates salt tolerance in rice. Mutation in OsQHB led to a decrease in plant height, tiller number, panicle length, grain length and grain width, and an increase in salt tolerance. Transcriptome and qPCR analysis showed that reactive oxygen species (ROS) scavenging-related genes were regulated by OsQHB. Moreover, the osqhb mutants have higher ROS-scavenging enzymes activities and lower accumulation of ROS and malondialdehyde (MDA) under salt stress. Thus, our findings provide new insights into the role of rice WOX gene family in rice development and salt tolerance, and suggest that OsQHB is a valuable target for improving rice production in environments characterized by salt stress.

Identification and charactering of APX genes provide new insights in abiotic stresses response in Brassica napus

Ascorbate peroxidase (APX) plays an important role in scavenging H₂O₂ and balancing ROS content in plant cells, which is of great significance for the growth and development of life and resistance to external stress. However, up to now, APXs in Brassica napus (B. napus) have not been systematically characterized. In this study, a total of 26 BnaAPX genes were identified, which were distributed on 13 chromosomes and divided into five phylogenetic branches. Gene structure analysis showed that they had a wide varied number of exons while BnaAPXs proteins contained more similar motifs in the same phylogenetic branches. qRT-PCR analysis of 26 BnaAPX gene expression patterns showed that three putative cytosol BnaAPX genes BnaAPX1, BnaAPX2, BnaAPX9, two putatice microsomal genes BnaAPX18 and BnaAPX25 were up-regulated rapidly and robustly under high salt, water shortage and high temperature stresses. In addition, the above three abiotic stresses led to a significant increase in APX activity. The results provide basic and comprehensive information for further functional characterization of APX gene family in B. napus.

Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress

Winter Brassica rapa (B. rapa) is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. Ascorbate peroxidase (APX) plays important roles in the response of this plant to abiotic stress and in scavenging free radicals. In this study, the roles of APX proteins in the cold response and superoxide metabolism pathways in rapeseed species were investigated, and a comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profiles in the APX gene family was conducted. Most BrAPX genes were specifically expressed under cold stress and behaved significantly differently in cold-tolerant and weakly cold-resistant varieties. Quantitative real-time-PCR (qRT-PCR) was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress. The expression of five BrAPX genes was significantly upregulated in growth cones at 3 h of cold stress, while their expression was significantly lower at 24 h than at 3 h. The expression of Bra015403 and Bra003918 was significantly higher in “Longyou-7” growth cones than in other treatments. Five BrAPXs (Bra035235, Bra003918, Bra033040, Bra017120, and Bra031934) were closely associated with abiotic stress responses in B. rapa. These candidate genes may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

Characterisation of the class III peroxidase gene family in carrot taproots and its role in anthocyanin and lignin accumulation

Plant class III peroxidases (CIII Prxs) are involved in numerous essential plant life processes, such as plant development and differentiation, lignification and seed germination, and defence against pathogens. However, there is limited information about the structure-function relationships of Prxs in carrots. This study identified 75 carrot peroxidases (DcPrxs) and classified them into seven subgroups based on phylogenetic analysis. Gene structure analysis revealed that these DcPrxs had between one and eight introns, while conserved motif analysis showed a typical motif composition and arrangement for CIII Prx. In addition, eighteen tandem duplication events, but only eight segmental duplications, were identified among these DcPrxs, indicating that tandem duplication was the main contributor to the expansion of this gene family. Histochemical analyses showed that lignin was mainly localised in the cell walls of xylem, and Prx activity was determined in the epidermal region of taproots. The xylem always showed higher lignin concentration and lower Prx activity compared to the phloem in the taproots of both carrot cultivars. Combining these observations with RNA sequencing, some Prx genes were identified as candidate genes related to lignification and pigmentation. Three peroxidases (DcPrx30, DcPrx32, DcPrx62) were upregulated in the phloem of both genotypes. Carrot taproots are an attractive resource for natural food colourants and this study elucidated genome-wide insights of Prx for the first time, developing hypotheses concerning their involvement with lignin and anthocyanin in purple carrots. The findings provide an essential foundation for further studies of Prx genes in carrot, especially on pigmentation and lignification mechanisms.

Heavy metal stress in rice: Uptake, transport, signaling, and tolerance mechanisms

Heavy metal contamination of agricultural fields has become a global concern as it causes a direct impact on human health. Rice is the major food crop for almost half of the world population and is grown under diverse environmental conditions, including heavy metal-contaminated soil. In recent years, the impact of heavy metal contamination on rice yield and grain quality has been shown through multiple approaches. In this review article, different aspects of heavy metal stress, that is uptake, transport, signaling and tolerance mechanisms, are comprehensively discussed with special emphasis on rice. For uptake, some of the transporters have specificity to one or two metal ions, whereas many other transporters are able to transport many different ions. After uptake, the intercellular signaling is mediated through different signaling pathways involving the regulation of various hormones, alteration of calcium levels, and the activation of mitogen-activated protein kinases. Heavy metal stress signals from various intermediate molecules activate various transcription factors, which triggers the expression of various antioxidant enzymes. Activated antioxidant enzymes then scavenge various reactive oxygen species, which eventually leads to stress tolerance in plants. Non-enzymatic antioxidants, such as ascorbate, metalloids, and even metal-binding peptides (metallothionein and phytochelatin) can also help to reduce metal toxicity in plants. Genetic engineering has been successfully used in rice and many other crops to increase metal tolerance and reduce heavy metals accumulation. A comprehensive understanding of uptake, transport, signaling, and tolerance mechanisms will help to grow rice plants in agricultural fields with less heavy metal accumulation in grains.

Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice.

Modulation of photosynthesis and other proteins during water-stress

Protein changes under drought or water stress conditions have been widely investigated. These investigations have given us enormous understanding of how drought is manifested in plants and how plants respond and adopt to such conditions. Chlorophyll fluoroescence, gas exchange, OMICS, biochemical and molecular analyses have shed light on regulation of physiology and photosynthesis of plants under drought. Use of proteomics has greatly increased the repertoire of drought-associated proteins which nevertheless, need to be investigated for their mechanistic and functional roles. Roles of such proteins have been succinctly discussed in various review articles, however more information on their functional role in countering drought is needed. In this review, recent developments in the field, alterations in the abundance of plant proteins in response to drought, monitored through numerous proteomic and immuno-blot analyses, and how these could affect plants growth and development, are discussed.

Ascorbate Peroxidase Neofunctionalization at the Origin of APX-R and APX-L: Evidence from Basal Archaeplastida

Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases named ascorbate peroxidase-related (APX-R) and ascorbate peroxidase-like (APX-L). As APX, APX-R harbor all catalytic residues required for peroxidatic activity. Nevertheless, proteins of this family do not contain residues known to be critical for ascorbate binding and therefore cannot use it as an electron donor. On the other hand, APX-L proteins not only lack ascorbate-binding residues, but also every other residue known to be essential for peroxidase activity. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, the present study discloses the existence of hybrid proteins, which combine features of these three families. The results here presented show that the prevalence of hybrid proteins varies among distinct groups of organisms, accounting for up to 33% of total APX homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APX-R and APX-L and suggests the occurrence of a process characterized by the progressive deterioration of ascorbate-binding and catalytic sites towards neofunctionalization.

Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa

Ascorbate peroxidase (APX) is a member of class I of the heme-containing peroxidase family. The enzyme plays important roles in scavenging reactive oxygen species for protection against oxidative damage and maintaining normal plant growth and development, as well as in biotic stress responses. In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and leaves. Real-time quantitative PCR (RT-qPCR) analysis indicated that PtrAPX transcription was induced in response to drought, salinity, high ammonium concentration, and exogenous abscisic acid treatment. These results provide important information on the phylogenetic relationships and functions of the APX gene family in P. trichocarpa.

Ascorbic acid modulation by ABI4 transcriptional repression of VTC2 in the salt tolerance of Arabidopsis

BACKGROUND

Abscisic acid (ABA) plays an important role in plant abiotic stress responses, and ABA INSENSITIVE 4 (ABI4) is a pivotal transcription factor in the ABA signaling pathway. In Arabidopsis, ABI4 negatively regulates salt tolerance; however, the mechanism through which ABI4 regulates plant salt tolerance is poorly understood. Our previous study showed that ABI4 directly binds to the promoter of the VITAMIN C DEFECTIVE 2 (VTC2) gene, inhibiting the transcription of VTC2 and ascorbic acid (AsA) biosynthesis.

RESULTS

In the present study, we found that treatment with exogenous AsA could alleviate salt stress sensitivity of ABI4-overexpressing transgenic plants. The decreased AsA content and increased reactive oxygen species (ROS) levels in ABI4-overexpressing seedlings under salt treatment indicated that AsA-promoted ROS scavenging was related to ABI4-mediated salt tolerance. Gene expression analysis showed that ABI4 was induced at the early stage of salt stress, giving rise to reduced VTC2 expression. Accordingly, the abundance of the VTC2 protein decreased under the same salt stress conditions, and was absent in the ABI4 loss-of-function mutants, suggesting that the transcriptional inhibition of ABI4 on VTC2 resulted in the attenuation of VTC2 function. In addition, other encoding genes in the AsA biosynthesis and recycling pathways showed different responses to salt stress, demonstrating that AsA homeostasis is complicated under salinity stress.

CONCLUSIONS

This study elucidates the negative modulation of ABI4 in salt stress tolerance through the regulation of AsA biosynthesis and ROS accumulation in plants.

Advances and Challenges in the Breeding of Salt-Tolerant Rice

Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.

Molecular characterization of ascorbate peroxidase (APX) and APX-related (APX-R) genes in Triticum aestivum L

Ascorbate peroxidases (APXs) are heme-dependent H2O2 scavenging enzymes involved in myriad biological processes. Herein, a total of 21 TaAPX and six TaAPX-R genes were identified from the A, B and D sub-genomes of Triticum aestivum L. The occurrence of three paralogous gene pairs with unequal evolutionary rate suggested functional divergence. The phylogenetic analysis formed four distinct clades having conserved gene and protein architecture, and sub-cellular localization. The tertiary structure analysis revealed the presence of helices and coils and residues involved in ligand binding. Transcriptional profiling of each TaAPX and TaAPX-R gene suggested their specific role during development and stress response. Modulated transcript expression and APX enzyme activity during various stress conditions indicated their role in stress response. Interaction analyses suggested their association with other genes, miRNAs and various legends. The present study reported numerous features of these genes, and may provide a platform for their detailed functional characterization in future studies.

Molecular Evolution of Maize Ascorbate Peroxidase Genes and Their Functional Divergence

Ascorbate peroxidase (APX) is an important antioxidant enzyme. APXs in maize are encoded by multiple genes and exist as isoenzymes. The evolutionary history and functional divergence of the maize APX gene family were analyzed through comparative genomic and experimental data on the Internet in this paper. APX genes in higher plants were divided into classes A, B, and C. Each type of APX gene in angiosperms only had one ancestral gene that was duplicated along with the genome duplication or local (or tandem) duplication of the angiosperm. A total of eight genes were retained in maize and named APXa1, APXa2, APXa3, APXb1, APXb2, APXc1.1, APXc1.2, and APXc2. The APX genes of class A were located in the chloroplasts or mitochondria, and the class B and C genes were localized in the peroxisomes and cytoplasm, respectively. The expression patterns of eight APXs were different in vegetative and reproductive organs at different growth and development stages. APXa1 and APXb1 of maize may participate in the antioxidant metabolism of vegetative organs under normal conditions. APXa2, APXb2, APXc1.1, and APXc1.2 may be involved in the stress response, and APXb2 and APXc2 may participate in the senescence response. These results provide a basis for cultivating high-yield and resistant maize varieties.

Identification and expression profiling analysis of ascorbate peroxidase gene family in Actinidia chinensis (Hongyang)

Ascorbate peroxidase (APX) is one of the important antioxidant enzymes in the active oxygen metabolism pathway of plants and animals, especially it is the key enzyme to clear H₂O₂ in chloroplast and the main enzyme of vitamin C metabolism. However, knowledge about APX gene family members and their evolutionary and functional characteristics in kiwifruit is limited. In this study, we identified 13 members of the APX gene family in the kiwifruit (cultivar: Hongyang) genome according the APX proteins conserved domain of Arabidopsis thaliana. Phylogenetic analysis by maximum likelihood split these 13 genes into four groups. The APX gene family members were distributed on nine chromosomes (Nos. 4, 5, 11, 13, 20, 21, 23, 25, 28). Most of the encoded hydrophilic and lipid-soluble enzymes were predicted to be located in the cytoplasm, nucleus and chloroplast. Among them, AcAPX4, AcAPX5, AcAPX8, AcAPX12 were transmembrane proteins, and AcAPX8 and AcAPX12 had the same transmembrane domain. The gene structure analysis showed that AcAPXs were composed of 4-22 introns, except that AcAPX10 was intron-free. Multiple expectation maximization for motif elicitation program (MEME) analyzed 13 APX protein sequences of Actinidia chinensis and identified 10 conserved motifs ranging in length from 15 to 50 amino acid residues. Additionally, the predicted secondary structures of the main motifs consisted of α-helix and random coils. The gene expression of fruits in different growth stages and bagging treatment were determined by qRT-PCR. The results showed that 8 AcAPXs had the highest expression levels during the color turning period and only the gene expression of AcAPX3 was consistent with the ascorbic acid content; five AcAPXs were consistent with the ascorbic acid content after bagging. Our data provided evolutionary and functional information of AcAPX gene family members and revealed the gene expression of different members in different growth stages and bagging treatments These results may be useful for future studies of the structures and functions of AcAPX family members.

Ascorbate peroxidase 4 plays a role in the tolerance of Chlamydomonas reinhardtii to photo-oxidative stress

Ascorbate peroxidase (APX; EC 1.11.1.11) activity and transcript levels of CrAPX1, CrAPX2, and CrAPX4 of Chlamydomonas reinhardtii increased under 1,400 μE·m⁻²·s⁻¹ condition (HL). CrAPX4 expression was the most significant. So, CrAPX4 was downregulated using amiRNA technology to examine the role of APX for HL acclimation. The CrAPX4 knockdown amiRNA lines showed low APX activity and CrAPX4 transcript level without a change in CrAPX1 and CrAPX2 transcript levels, and monodehydroascorbate reductase (MDAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) activities and transcript levels. Upon exposure to HL, CrAPX4 knockdown amiRNA lines appeared a modification in the expression of genes encoding the enzymes in the ascorbate–glutathione cycle, including an increase in transcript level of CrVTC2, a key enzyme for ascorbate (AsA) biosynthesis but a decrease in MDAR and DHAR transcription and activity after 1 h, followed by increases in reactive oxygen species production and lipid peroxidation after 6 h and exhibited cell death after 9 h. Besides, AsA content and AsA/DHA (dehydroascorbate) ratio decreased in CrAPX4 knockdown amiRNA lines after prolonged HL treatment. Thus, CrAPX4 induction together with its association with the modulation of MDAR and DHAR expression for AsA regeneration is critical for Chlamydomonas to cope with photo-oxidative stress.

ROS Homeostasis in Abiotic Stress Tolerance in Plants

Climate change-induced abiotic stress results in crop yield and production losses. These stresses result in changes at the physiological and molecular level that affect the development and growth of the plant. Reactive oxygen species (ROS) is formed at high levels due to abiotic stress within different organelles, leading to cellular damage. Plants have evolved mechanisms to control the production and scavenging of ROS through enzymatic and non-enzymatic antioxidative processes. However, ROS has a dual function in abiotic stresses where, at high levels, they are toxic to cells while the same molecule can function as a signal transducer that activates a local and systemic plant defense response against stress. The effects, perception, signaling, and activation of ROS and their antioxidative responses are elaborated in this review. This review aims to provide a purview of processes involved in ROS homeostasis in plants and to identify genes that are triggered in response to abiotic-induced oxidative stress. This review articulates the importance of these genes and pathways in understanding the mechanism of resistance in plants and the importance of this information in breeding and genetically developing crops for resistance against abiotic stress in plants.

Biochemical and molecular approach of oxidative damage triggered by water stress and rewatering in sunflower seedlings of two inbred lines with different ability to tolerate water stress

Water stress accelerates the generation of reactive oxygen species, which trigger a cascade of antioxidative defence mechanisms comprising enzymatic and nonenzymatic antioxidants. The aim of this study was to investigate the oxidative damage and the antioxidative defence systems in seedlings of the water stress-tolerant (B71) and the sensitive (B59) inbred lines of sunflower (Helianthus annuus L.) in response to water stress and rewatering. In addition, we characterised the transcriptomic profile associated with enzymatic antioxidative defence. An elevated electrolyte leakage in B59 indicated increased plasmatic membrane permeability, which correlated with greater sensitivity to water stress. In response to water stress, both lines showed an increase in malondialdehyde and H2O2 content but these increases were more noticeable in the sensitive line. In both lines, an increase in enzymatic activity (e.g. peroxidase and ascorbate peroxidase) was not sufficient to overcome the H2O2 accumulation triggered by water stress. Upon water stress, the overall expression level of genes associated with the enzymatic antioxidant system increased in B71 and decreased in B59, which showed downregulated levels of most genes in the shoots. The general profile of phenolic compounds was clearly different between organs and between inbred lines. The B59 line activated nonenzymatic antioxidant responses to counteract the oxidative stress caused by water stress. The tolerance of B71 to water stress could be associated with compensatory antioxidant mechanisms based on the expression of genes encoding enzyme components of the ascorbate-glutathione and redoxin cycles, which contributed to explaining, at least partly, the response of this line.

Melatonin Suppressed the Heat Stress-Induced Damage in Wheat Seedlings by Modulating the Antioxidant Machinery

Melatonin (N-acetyl-5-methoxytryptamine) is a pleiotropic signaling molecule that plays a crucial role in the regulation of various environmental stresses, including heat stress (HS). In this study, a 100 μM melatonin (MT) pretreatment followed by exposure to heat stress for different time periods was found to efficiently reduce oxidative stress by preventing the over-accumulation of hydrogen peroxide (H₂O₂), lowering the lipid peroxidation content (malondialdehyde (MDA) content), and increasing proline (Pro) biosynthesis. Moreover, the activities of antioxidant enzymes, such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), were increased substantially in MT-pretreated wheat seedlings. The presence of MT significantly improved the heat tolerance of wheat seedlings by modulating their antioxidant defense system, activating the ascorbate–glutathione (AsA–GSH) cycle comprising ascorbate peroxidase (APX), and increasing glutathione reductase (GR) activities. It also held the photosynthetic machinery stable by increasing the chlorophyll content. Enhancement in the endogenous MT contents was also observed in the MT+HS-treated plants. Furthermore, the expression of reactive oxygen species (ROS)-related genes TaSOD, TaPOD, and TaCAT, and anti-stress responsive genes, such as TaMYB80, TaWRKY26, and TaWRKY39, was also induced in MT-treated seedlings. Due to these notable changes, an improvement in stress resistance was observed in MT-treated seedlings compared with control. Taken together, our findings suggest that MT can play a key role in boosting the stress tolerance of plants by modulating the antioxidant defense system and regulating the transcription of stress-responsive genes.

Impact of drought and heat stress individually and in combination on physio-biochemical parameters, antioxidant responses, and gene expression in Solanum lycopersicum

The present study was carried out to investigate the effect of individual drought, heat, and combined drought and heat stress on tomato plants. Combined stress resulted in the higher accumulation of Proline (101.9%), MDA (38.55%), H2O2 (101.19%), and lower levels of RWC (53.84%). Individual drought and heat stress decreased photosynthetic pigments like total chlorophyll content by (45.45%) and (25.35%), respectively, higher rates of pigment reduction (79.42%) were observed under combined drought and heat stress. Combined stress decreased PSII efficiency (Fv/Fm), quantum yield (ΦPSII), and photochemical efficiency (qp) and increased non-photochemical quenching (NPQ) levels. Moreover, the gas exchange parameters E, A, and Pn decreased by 5.36%, 36.45%, and 51.00%, respectively, in comparison to control plants. Antioxidant enzymes, SOD, APX, CAT, and GR showed a two- to threefold increase under combined drought and heat stress; however, the non-enzymatic antioxidants AsA and GSH displayed one-twofold increase under combined stress. Moreover, 2- to 2.5-fold decrease was observed in MDHAR and DHAR enzyme transcripts under combined stress conditions. The transcripts corresponding to AsA-GSH pathway enzymes SOD, APX, GR, DHAR, and MDHAR were up-regulated by 8- to 12-fold under combined drought and heat. Furthermore, DREB and LEA transcripts were up-regulated under drought and combined stress and down-regulated under drought stress. In the same manner, HSP70 and HSP90 transcripts were up-regulated under heat and combined stress; however, the transcription levels got down-regulated under drought stress. Additionally, rbcL and RCA transcripts were down-regulated especially under combined stress in comparison to individual drought and heat conditions. PSIP680 relative expression levels were up-regulated under drought stress; however, the transcripts were down-regulated under heat and combined stress. Taken together, the results suggest that the combined stress has a predominant effect over individual stress.

Catalase and Ascorbate Peroxidase in Euglenozoan Protists

In this work, we studied the biochemical properties and evolutionary histories of catalase (CAT) and ascorbate peroxidase (APX), two central enzymes of reactive oxygen species detoxification, across the highly diverse clade Eugenozoa. This clade encompasses free-living phototrophic and heterotrophic flagellates, as well as obligate parasites of insects, vertebrates, and plants. We present evidence of several independent acquisitions of CAT by horizontal gene transfers and evolutionary novelties associated with the APX presence. We posit that Euglenozoa recruit these detoxifying enzymes for specific molecular tasks, such as photosynthesis in euglenids and membrane-bound peroxidase activity in kinetoplastids and some diplonemids.

Melatonin: Awakening the Defense Mechanisms during Plant Oxidative Stress

Melatonin is a multifunctional signaling molecule that is ubiquitously distributed in different parts of a plant and responsible for stimulating several physio-chemical responses to adverse environmental conditions. In this review, we show that, although plants are able to biosynthesize melatonin, the exogenous application of melatonin to various crops can improve plant growth and development in response to various abiotic and biotic stresses (e.g., drought, unfavorable temperatures, high salinity, heavy metal contamination, acid rain, and combined stresses) by regulating antioxidant machinery of plants. Current knowledge suggests that exogenously applied melatonin can enhance the stress tolerance of plants by regulating both the enzymatic and non-enzymatic antioxidant defense systems. Enzymic antioxidants upregulated by exogenous melatonin include superoxide dismutase, catalase, glutathione peroxidase, and enzymes involved in the ascorbate–glutathione cycle (ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, and glutathione reductase), whereas levels of non-enzymatic antioxidants such as ascorbate, reduced glutathione, carotenoids, tocopherols, and phenolics are also higher under stress conditions. The enhanced antioxidant system consequently exhibits lower lipid peroxidation and greater plasma membrane integrity when under stress. However, these responses vary greatly from crop to crop and depend on the intensity and type of stress, and most studies to date have been conducted under controlled conditions. This means that a wider range of crop field trials and detailed transcriptomic analysis are required to reveal the gene regulatory networks involved in the between melatonin, antioxidants, and abiotic stress.

Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean

Genes related to the response to drought stress in leaf and root tissue of drought-susceptible (DS) and tolerant (DT) genotypes were characterized by RNA-Seq. In total, 54,750 transcripts, representative of 28,590 genes, were identified; of these, 1,648 were of high-fidelity (merge of 12 libraries) and described for the first time in the Andean germplasm. From the 1,239 differentially expressed genes (DEGs), 458 were identified in DT, with a predominance of genes in categories of oxidative stress, response to stimulus and kinase activity. Most genes related to oxidation-reduction terms in roots were early triggered in DT (T75) compared to DS (T150) suggestive of a mechanism of tolerance by reducing the damage from ROS. Among the KEGG enriched by DEGs up-regulated in DT leaves, two related to the formation of Sulfur-containing compounds, which are known for their involvement in tolerance to abiotic stresses, were common to all treatments. Through qPCR, 88.64% of the DEGs were validated. A total of 151,283 variants were identified and functional effects estimated for 85,780. The raw data files were submitted to the NCBI database. A transcriptome map revealed new genes and isoforms under drought. These results supports a better understanding of the drought tolerance mechanisms in beans.

Redox homeostasis in the growth zone of the rice leaf plays a key role in cold tolerance

We analysed the cellular and molecular changes in the leaf growth zone of tolerant and sensitive rice varieties in response to suboptimal temperatures. Cold reduced the final leaf length by 35% and 51% in tolerant and sensitive varieties, respectively. Tolerant lines exhibited a smaller reduction of the leaf elongation rate and greater compensation by an increased duration of leaf growth. Kinematic analysis showed that cold reduced cell production in the meristem and the expansion rate in the elongation zone, but the latter was compensated for by a doubling of the duration of cell expansion. We performed iTRAQ proteome analysis on proliferating and expanding parts of the leaf growth zone. We identified 559 and 542 proteins, of which 163 and 210 were differentially expressed between zones, and 96 and 68 between treatments, in the tolerant and sensitive lines, respectively. The categories protein biosynthesis and redox homeostasis were significantly overrepresented in the up-regulated proteins. We therefore measured redox metabolites and enzyme activities in the leaf growth zone, demonstrating that tolerance of rice lines to suboptimal temperatures correlates with the ability to up-regulate enzymatic antioxidants in the meristem and non-enzymatic antioxidants in the elongation zone.

PtomtAPX, a mitochondrial ascorbate peroxidase, plays an important role in maintaining the redox balance of Populus tomentosa Carr

Plant mitochondria are important energy-producing structure and ROS are generated as byproducts. APX is one enzyme of the AsA-GSH cycle to reduces H₂O₂ to water. We identified both PtomtAPX and PtosAPX are located in mitochondria of Populus tomentosa Carr. PtomtAPX is specifically targeted to mitochondria, while PtosAPX is dual targeted to both chloroplast and mitochondria. The expression of PtomtAPX in mitochondria was 60-fold that of PtosAPX by ELISA and qPCR analysis. Under high light stress, the expression levels of PtosAPX increased, while that of PtomtAPX only slightly changed. Compared to the WT, the antisense transgenic PtomtAPX cell lines showed slowed growth, smaller cells impaired mitochondria in MS medium under normal growth. RNA-seq results showed 3121 genes significantly altered expression in the antisense cells, and most of them are important for mitochondrial function, particularly in oxidative phosphorylation. Our findings demonstrates a mitochondrial location for one APX isoform, and provide valuable insight into the mechanism which ROS balance is modulated by AsA-GSH cycle in mitochondria.

Comparative analysis of ascorbate peroxidases (APXs) from selected plants with a special focus on Oryza sativa employing public databases

Reactive oxygen species (ROS) are produced by plants. Hydrogen peroxide (H₂O₂) is one important component of ROS and able to modulate plant growth and development at low level and damage plant cells at high concentrations. Ascorbate peroxidase (APX) shows high affinity towards H₂O₂ and plays vital roles in H₂O₂-scavenging. In order to explore the differences of APXs from selected plant species, bioinformatics methods and public databases were used to evaluate the physicochemical properties, conserved motifs, potential modifications and cis-elements in all the APXs, and protein-protein network and expression profiles of rice APXs. The results suggested that APXs in the selected plant species showed high evolutionary conservation and were able to divide into seven groups, group I to VII. Members in the groups contained abundant phosphorylation sites. Interestingly, group I and VII had only PKC site. Additionally, promoters of the APXs contained abundant stress-related cis-elements. APXs in rice plant were able to interact with dehydroascorbate reductase 2. The eight APXs expressed differently in root, leaf, panicle, anther, pistil and seed. Drought, Pi-free, Cd and Xanthomonas oryzae pv. oryzicola B8-12 treatments were able to significantly alter the expression profiles of rice APXs. This study increases our knowledge to further explore functions and mechanisms of APXs and also guides their applications.

Fly-Ash Pollution Modulates Growth, Biochemical Attributes, Antioxidant Activity and Gene Expression in Pithecellobium Dulce (Roxb) Benth

This study investigates the effect of fly ash (FA) on the Pithecellobium dulce (Roxb) Benth. trees growing at three different locations. FA stress caused significant changes in different leaf attributes like sugar, protein contents, photosynthetic pigments, nitrate content and nitrate reductase activity in foliar tissues of plants growing at a highly contaminated site, as compared to a low-pollution site. Lower rates of stomatal conductance (SC) were observed in P. dulce leaves under fly ash stress conditions that drastically reduced net photosynthetic rate (P_N); however, intercellular carbon dioxide concentration and stomatal index (SI) showed an increase under the same stress conditions. On the other hand, significant increase was also observed in the proline, sulphur and nitrogen contents. A significant increase in oxidative stress and, consequently, in antioxidant enzymes such as ascorbate peroxidase (APX), catalase (CAT), peroxidase (POD), and superoxidase dismutase (SOD) and Air pollution tolerance index were discovered at three different sites. The transcriptional expression of antioxidant and stress responsive genes was higher at HPS as compared to two other two sites of the study. Taken together the results demonstrated that the P. dulce is best suited as a fly ash stress tolerant plant species with the potential to provide an alternative for the reclamation of fly ash affected soils.

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation

Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginellamoellendorffii. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.

Advances in understanding salt tolerance in rice

This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.

Oxidative damage and antioxidative indicators in 48 h germinated rice embryos during the vitrification-cryopreservation procedure

Cu/Zn SOD and other genes may be critical indicators of a stress response to reactive oxygen species (ROS) accumulation in 48 h germinated rice embryos subjected to vitrification cryopreservation. In the current study, reactive oxygen species (ROS) accumulation was investigated in 48 h germinated rice embryos during the vitrification-cryopreservation process. We found that vitrification-cryopreservation significantly affected ROS levels, especially superoxide anion levels, in 48 h germinated rice embryos. Malonaldehyde content in the apical meristems of germinated embryos was significantly positively correlated with the rate of superoxide anion generation and the highest levels of malonaldehyde content were reached after vitrification treatment. Cell viability in 48 h germinated embryos was significantly negatively correlated with the rate of superoxide anion generation, malonaldehyde content, and electrolyte leakage. Spatial and temporal patterns in ROS accumulation in these embryos existed during the vitrification procedure. Among the vitrification-cryopreservation treatments we assessed, the preculture treatment was found to stimulate superoxide anion generation and to activate the response system in the apical meristems of germinated embryos. Loading treatments motivated the catalase and ascorbate peroxidase activities. During the vitrification-dehydration treatment, oxidative stress reached the highest levels causing an antioxidative response. This response involved antioxidant enzymes promoting detoxification of ROS. Based on a comprehensive correlation analysis involving ROS accumulation, cell viability, the activities of antioxidant enzymes, and gene expression profiles, Cu/Zn SOD, CAT1, APX7, GR2, GR3, MDHAR1, and DHAR1 may be critical indicators of oxidative stress affected by the vitrification-cryopreservation treatments. The investigation of these antioxidative responses in 48 h germinated rice embryos may, therefore, provide useful information with respect to plant vitrification-cryopreservation.

Apigenin pretreatment enhances growth and salinity tolerance of rice seedlings

Soil salinity is a limiting factor in rice production. Since flavonoids present in most plant tissues play multiple roles in plant-environment interactions, in this study, we focused on the contribution of flavone aglycone (Apigenin) to the adaptation of salinity-sensitive rice cultivar 'Koshihikari,' to salinity stress, for the first time. Rice seeds were soaked in Apigenin solution (10 ppm) for 24 h, then air-dried and grown hydroponically under 50 mM NaCl for 14 days. Apigenin pretreatment improved the growth of rice seedlings by enhancing shoot elongation and dry mass accumulation under both unstressed and NaCl-stress conditions, compared with that in the non-pretreated seedlings. Apigenin pretreatment significantly reduced Na⁺ accumulation in the salinity-stressed seedlings, and helped to maintain a lower Na⁺/K⁺ ratio in all plant organs, compared with that in the non-pretreated seedlings, possibly by regulating the expression of some important Na⁺ transporter-encoding genes (OsHKT2;1, OsCNGC1, OsSOS1). Higher levels of lipid peroxidation and hydrogen peroxide (H₂O₂) concentrations were observed in the shoots of the salinity-stressed seedlings; however, lower levels of lipid peroxidation and H₂O₂ concentration were detected in the Apigenin-treated seedlings. Apigenin pretreatment was associated with the induction of the rice antioxidant defense system represented by the induced activities of the antioxidant enzymes Catalase (CAT) and Ascorbate peroxidase (APX) in the roots, as well as by increased accumulation of the non-enzymatic antioxidants carotenoids and flavonoids in the shoots, relative to that in the untreated seedlings, under salinity stress conditions. Together, these results suggest that Apigenin pretreatment can alleviate the damaging effects of salinity on rice seedlings, presumably by regulating selective ion uptake by the roots and translocation to the shoots, thereby maintaining higher K⁺/Na⁺ ratios critical for normal plant growth under salinity stress, and by triggering the induction of the antioxidant defense system.

Proteomic and physiological approaches reveal new insights for uncover the role of rice thylakoidal APX in response to drought stress

Chloroplast APX isoforms display controversial roles as H₂O₂ scavengers and signaling players in response to abiotic stress and conclusive results are lacking. We tested the hypothesis that thylakoidal APX displays an important role for drought tolerance, especially by regulating abundance of essential protein species. For this, OsApx8 RNAi-silenced rice (apx8) and non-transformed plants (NT) were exposed to mild water deficit. The drought-sensitivity in apx8 plants was revealed by decreases in shoot growth, relative water content and photosynthesis, which was accompanied by increased membrane damage, all compared to NT plants. This higher sensitivity of apx8 plants to mild drought stress was also related to a lower accumulation of important protein species involved in several metabolic processes, especially photosynthesis, photorespiration and redox metabolism. Despite apx8 plants have displayed an effective induction of compensatory antioxidant mechanisms in well-watered conditions, it was not enough to maintain H₂O₂ homeostasis and avoid oxidative and physiological disturbances under mild drought conditions. Thus, thylakoidal APX is involved in several phenotypic modifications at proteomic profile level, possibly via a H₂O₂-induced signaling mechanism. Consequently, this APX isoform is crucial for rice plants effectively cope with a mild drought condition. BIOLOGICAL SIGNIFICANCE: This work provides for the first time an integrative study involving proteomic, physiological and biochemical analyses directed to elucidation of thylakoidal APX roles for drought tolerance in rice plants. Our data reveal that this enzyme is crucial for maintaining of growth and photosynthesis under mild water deficit conditions. This essential role is related to maintaining of H₂O₂ homeostasis and accumulation of essential proteins involved in several important metabolic pathways. Remarkably, for drought resistance was essential the accumulation of proteins involved with metabolism of photosynthesis, signaling, carbohydrates, protein synthesis/degradation and stress. These results can contribute to understand the role of chloroplast ascorbate peroxidases in drought tolerance, highlighting the physiological importance of key proteins in this process.