Analysis of the molecular evolutionary history of the ascorbate peroxidase gene family: inferences from the rice genome

Physiological function and regulation of ascorbate peroxidase isoforms

Ascorbate peroxidase (APX) reduces H2O2 to H2O by utilizing ascorbate as a specific electron donor and constitutes the ascorbate-glutathione cycle in organelles of plants including chloroplasts, cytosol, mitochondria, and peroxisomes. It has been almost 40 years since APX was discovered as an important plant-specific H2O2-scavenging enzyme, during which time many research groups have conducted molecular physiological analyses. It is now clear that APX isoforms function not only just as antioxidant enzymes but also as important factors in intracellular redox regulation through the metabolism of reactive oxygen species. The function of APX isoforms is regulated at multiple steps, from the transcriptional level to post-translational modifications of enzymes, thereby allowing them to respond flexibly to ever-changing environmental factors and physiological phenomena such as cell growth and signal transduction. In this review, we summarize the physiological functions and regulation mechanisms of expression of each APX isoform.

An effector SsCVNH promotes the virulence of Sclerotinia sclerotiorum through targeting class III peroxidase AtPRX71

Many plant pathogens secrete effector proteins into the host plant to suppress host immunity and facilitate pathogen colonization. The necrotrophic pathogen Sclerotinia sclerotiorum causes severe plant diseases and results in enormous economic losses, in which secreted proteins play a crucial role. SsCVNH was previously reported as a secreted protein, and its expression is significantly upregulated at 3 h after inoculation on the host plant. Here, we further demonstrated that deletion of SsCVNH leads to attenuated virulence. Heterologous expression of SsCVNH in Arabidopsis enhanced pathogen infection, inhibited the host PAMP-triggered immunity (PTI) response and increased plant susceptibility to S. sclerotiorum. SsCVNH interacted with class III peroxidase AtPRX71, a positive regulator of innate immunity against plant pathogens. SsCVNH could also interact with other class III peroxidases, thus reducing peroxidase activity and suppressing plant immunity. Our results reveal a new infection strategy employed by S. sclerotiorum in which the fungus suppresses the function of class III peroxidases, the major component of PTI to promote its own infection.

Enzymes Involved in Antioxidant and Detoxification Processes Present Changes in the Expression Levels of Their Coding Genes under the Stress Caused by the Presence of Antimony in Tomato

Currently, there is an increasing presence of heavy metals and metalloids in soils and water due to anthropogenic activities. However, the biggest problem caused by this increase is the difficulty in recycling these elements and their high permanence in soils. There are plants with great capacity to assimilate these elements or make them less accessible to other organisms. We analyzed the behavior of Solanum lycopersicum L., a crop with great agronomic interest, under the stress caused by antimony (Sb). We evaluated the antioxidant response throughout different exposure times to the metalloid. Our results showed that the enzymes involved in the AsA-GSH cycle show changes in their expression level under the stress caused by Sb but could not find a relationship between the NITROSOGLUTATHIONE REDUCTASE (GSNOR) expression data and nitric oxide (NO) content in tomato roots exposed to Sb. We hypothesize that a better understanding of how these enzymes work could be key to develop more tolerant varieties to this kind of abiotic stress and could explain a greater or lesser phytoremediation capacity. Moreover, we deepened our knowledge about Glutathione S-transferase (GST) and Glutathione Reductase (GR) due to their involvement in the elimination of the xenobiotic component.

Genome-Wide Identification, Evolutionary Analysis, and Functional Studies of APX Genes in Melon (Cucuis melo L.)

The antioxidative enzyme ascorbate peroxidase (APX) exerts a critically important function through scavenging reactive oxygen species (ROS), alleviating oxidative damage in plants, and enhancing their tolerance to salinity. Here, we identified 28 CmAPX genes that display an uneven distribution pattern throughout the 12 chromosomes of the melon genome by carrying out a bioinformatics analysis. Phylogenetic analyses revealed that the CmAPX gene family comprised seven different clades, with each clade of genes exhibiting comparable motifs and structures. We cloned 28 CmAPX genes to infer their encoded protein sequences; we then compared these sequences with proteins encoded by rice APX proteins (OsAPX2), Puccinellia tenuiflora APX proteins (PutAPX) and with pea APX proteins. We found that the CmAPX17, CmAPX24, and CmAPX27 genes in Clade I were closely related, and their structures were highly conserved. CmAPX27 (MELO3C020719.2.1) was found to promote resistance to 150 mM NaCl salt stress, according to quantitative real-time fluorescence PCR. Transcriptome data revealed that CmAPX27 was differentially expressed among tissues, and the observed differences in expression were significant. Virus-induced gene silencing of CmAPX27 significantly decreased salinity tolerance, and CmAPX27 exhibited differential expression in the leaf, stem, and root tissues of melon plants. This finding demonstrates that CmAPX27 exerts a key function in melon's tolerance to salt stress. Generally, CmAPX27 could be a target in molecular breeding efforts aimed at improving the salt tolerance of melon; further studies of CmAPX27 could unveil novel physiological mechanisms through which antioxidant enzymes mitigate the deleterious effects of ROS stress.

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.

Prioritizing strategies for wheat biofortification: Inspiration from underutilized species

The relationship between malnutrition and climate change is still poorly understood but a comprehensive knowledge of their interactions is needed to address the global public health agenda. Limited studies have been conducted to propose robust and economic-friendly strategies to augment the food basket with underutilized species and biofortify the staples for nutritional security. Sea-buckthorn is a known "superfood" rich in vitamin C and iron content. It is found naturally in northern hemispherical temperate Eurasia and can be utilized as a model species for genetic biofortification in cash crops like wheat. This review focuses on the impacts of climate change on inorganic (iron, zinc) and organic (vitamin C) micronutrient malnutrition employing wheat as highly domesticated crop and processed food commodity. As iron and zinc are particularly stored in the outer aleurone and endosperm layers, they are prone to processing losses. Moreover, only 5% Fe and 25% Zn are bioavailable once consumed calling to enhance the bioavailability of these micronutrients. Vitamin C converts non-available iron (Fe3+) to available form (Fe2+) and helps in the synthesis of ferritin while protecting it from degradation at the same time. Similarly, reduced phytic acid content also enhances its bioavailability. This relation urges scientists to look for a common mechanism and genes underlying biosynthesis of vitamin C and uptake of Fe/Zn to biofortify these micronutrients concurrently. The study proposes to scale up the biofortification breeding strategies by focusing on all dimensions i.e., increasing micronutrient content and boosters (vitamin C) and simultaneously reducing anti-nutritional compounds (phytic acid). Mutually, this review identified that genes from the Aldo-keto reductase family are involved both in Fe/Zn uptake and vitamin C biosynthesis and can potentially be targeted for genetic biofortification in crop plants.

Molecular Mechanism of Response and Adaptation of Antioxidant Enzyme System to Salt Stress in Leaves of Gymnocarpos przewalskii

The antioxidant enzyme system is the main defense system responsible for maintaining cellular reactive oxygen species (ROS) homeostasis and normal plant growth and development after saline stress. In this study, we identified and characterized the members of the SOD, APX and CAT gene families of the antioxidant enzyme system in Gymnocarpos przewalskii, using plant physiology and molecular biology methods, and analyzed the pattern of enzyme activity in response to NaCl stress. It was found that seven, six and two genes of SOD, APX and CAT gene families, respectively, were expressed in the leaf tissue of G. przewalskii, in which most of the genes were significantly upregulated under NaCl stress, and the enzymatic activities were in accordance with the gene expression. Three positive selection sites in the GpCAT1 gene can increase the hydrophilicity of the GpCAT1 protein, increase the volume of the active site and increase the affinity for H2O2, thus improving the catalytic efficiency of GpCAT1. The results of the present study provide new insights for further investigations of the evolution and function of the SOD, APX and CAT gene families in G. przewalskii and their essential roles under salt stress, and the findings will be useful for revealing the molecular mechanism of salt tolerance and breeding of salt-tolerant plants.

IRR1 contributes to de novo root regeneration from Arabidopsis thaliana leaf explants

Plants are capable of regenerating adventitious roots (ARs), which is important for plant response to stress and survival. Although great advances in understanding AR formation of leaf explants have been made, the regulatory mechanisms of AR formation still need to be investigated. In this study, irr1-1 (impaired root regeneration) was isolated with the inhibition of adventitious rooting from Arabidopsis leaf explants. The β-glucuronidase (GUS) signals of IRR1pro::GUS in detached leaves could be detected at 2-6 days after culture. IRR1 is annotated to encode a Class III peroxidase localized in the cell wall. The total peroxidase (POD) activity of irr1 mutants was significantly lower than that of the wild type. Detached leaves of irr1 mutants showed enhanced reactive oxygen species (ROS) accumulation 4 days after leaves were excised from seedlings. Moreover, thiourea, a ROS scavenger, was able to rescue the adventitious rooting rate in leaf explants of irr1 mutants. Addition of 0.1 μM indole-3-acetic acid (IAA) improved the adventitious rooting from leaf explants of irr1 mutants. Taken together, these results indicated that IRR1 was involved in AR formation of leaf explants, which was associated with ROS homeostasis to some extent.

Genome-Wide Analysis of Exocyst Complex Subunit Exo70 Gene Family in Cucumber

Cucumber (Cucumis sativus L.) is an important vegetable worldwide, but its yield is affected by a wide range of pathogens and pests. As the major subunit of the exocyst complex, the roles of Exo70 members have been shown in Arabidopsis and rice, but their function are unknown in cucumber. Here, we identified 18 CsExo70 members in cucumber, which were divided into three groups (Exo70.1-Exo70.3) and nine subgroups (Exo70A-Exo70I) based on the phylogenetic tree. Subsequently, systematical analyses were performed, including collinearity, gene structure, cis-acting elements, conserved motifs, expression patterns, and subcellular localization. Our results showed that CsExo70 genes were generally expressed in all tissues, and CsExo70C1 and CsExo70C2 were highly expressed in the stamen. Moreover, the expression levels of most CsExo70 genes were induced by Pseudomonas syringae pv. lachrymans (Psl) and Fusarium oxysporum f. sp. cucumerinum Owen (Foc), especially CsExo70E2 and CsExo70H3. In addition, these CsExo70s displayed similar location patterns with discrete and punctate signals in the cytoplasm. Together, our results indicate that CsExo70 members may be involved in plant development and resistance, and provide a reference for future in-depth studies of Exo70 genes in cucumber.

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.

A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids

In planta, H2O2 is produced as a by-product of enzymatic reactions and during defense responses. Ascorbate peroxidase (APX) is a key enzyme involved in scavenging cytotoxic H2O2. Here, we report the crystal structure of cytosolic APX from sorghum (Sorghum bicolor) (Sobic.001G410200). While the overall structure of SbAPX was similar to that of other APXs, SbAPX uniquely displayed four bound ascorbates rather than one. In addition to the ɣ-heme pocket identified in other APXs, ascorbates were bound at the δ-meso and two solvent-exposed pockets. Consistent with the presence of multiple binding sites, our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Bound ascorbate at two surface sites established an intricate proton network with ascorbate at the ɣ-heme edge and δ-meso sites. Based on crystal structures, steady-state kinetics, and site-directed mutagenesis results, both ascorbate molecules at the ɣ-heme edge and the one at the surface are expected to participate in the oxidation reaction. We provide evidence that the H2O2-dependent oxidation of ascorbate by APX produces a C2-hydrated bicyclic hemiketal form of dehydroascorbic acid at the ɣ-heme edge, indicating two successive electron transfers from a single-bound ascorbate. In addition, the δ-meso site was shared with several organic compounds, including p-coumaric acid and other phenylpropanoids, for the potential radicalization reaction. Site-directed mutagenesis of the critical residue at the ɣ-heme edge (R172A) only partially reduced polymerization activity. Thus, APX removes stress-generated H2O2 with ascorbates, and also uses this same H2O2 to potentially fortify cell walls via oxidative polymerization of phenylpropanoids in response to stress.

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.

Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut (Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance

Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.

Whole-Genome Identification of APX and CAT Gene Families in Cultivated and Wild Soybeans and Their Regulatory Function in Plant Development and Stress Response

Plants coevolved with their antioxidant defense systems, which detoxify and adjust levels of reactive oxygen species (ROS) under multiple plant stresses. We performed whole-genome identification of ascorbate peroxidase (APX) and catalase (CAT) families in cultivated and wild soybeans. In cultivated and wild soybean genomes, we identified 11 and 10 APX genes, respectively, whereas the numbers of identified CAT genes were four in each species. Comparative phylogenetic analysis revealed more homology among cultivated and wild soybeans relative to other legumes. Exon/intron structure, motif and synteny blocks are conserved in cultivated and wild species. According to the Ka/Ks value, purifying selection is a major force for evolution of these gene families in wild soybean; however, the APX gene family was evolved by both positive and purifying selection in cultivated soybean. Segmental duplication was a major factor involved in the expansion of APX and CAT genes. Expression patterns revealed that APX and CAT genes are differentially expressed across fourteen different soybean tissues under water deficit (WD), heat stress (HS) and combined drought plus heat stress (WD + HS). Altogether, the current study provides broad insights into these gene families in soybeans. Our results indicate that APX and CAT gene families modulate multiple stress response in soybeans.

Detection of Genomic Regions Controlling the Antioxidant Enzymes, Phenolic Content, and Antioxidant Activities in Rice Grain through Association Mapping

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice.

Characterization of APX and APX-R gene family in Brassica juncea and B. rapa for tolerance against abiotic stresses

APX and APX-R gene families were identified and characterized in two important oilseed species of Brassica. Gene expression under abiotic stress conditions, recombinant protein expression, and analysis further divulged their drought, heat, and salt-responsive behavior. Ascorbate peroxidases (APX) are heme-dependent enzymes that rid the cells of H₂O₂ and regulate diverse biological processes. In the present study, we performed APX gene family characterization in two Brassica sp. (B. juncea and B. rapa) as these are commercially important oilseed crops and affected severely by abiotic stresses. We identified 16 BjuAPX and 9 BraAPX genes and 2 APX-R genes each in B. juncea and B. rapa genomes, respectively. Phylogenetic analysis divided the APX genes into five distinct clades, which exhibited conservation in the gene structure, motif organization, and sub-cellular location within the clade. Structural analysis of APX and APX-R proteins revealed the amino acid substitutions in conserved domains of APX-R proteins. The expression profiling of BjuAPX and BraAPX genes showed that 3 BjuAPX, 7BraAPX, and 2 BraAPX-R genes were drought and heat responsive. Notably, BjuAAPX1a, BjuAPX1d, BjuAAPX6, BraAAPX1a, BraAAPX2, and BraAAPX3b showed high expression levels in RT-qPCR. Cis-regulatory elements in APX and APX-R gene promoters supported the differential behavior of these genes. Further, two stress-responsive genes BjuAPX1d and BraAAPX2 were cloned, characterized, and their roles were validated under heat, drought, salt, and cold stress in bacterial expression system. This study for the first time reports the presence of APX activity in dimeric and LMW form of purified BraAAPX2 protein. The study may help pave way for developing abiotic stress-tolerant Brassica crops.

Cyclic electron flow (CEF) and ascorbate pathway activity provide constitutive photoprotection for the photopsychrophile, Chlamydomonas sp. UWO 241 (renamed Chlamydomonas priscuii)

Under environmental stress, plants and algae employ a variety of strategies to protect the photosynthetic apparatus and maintain photostasis. To date, most studies on stress acclimation have focused on model organisms which possess limited to no tolerance to stressful extremes. We studied the ability of the Antarctic alga Chlamydomonas sp. UWO 241 (UWO 241) to acclimate to low temperature, high salinity or high light. UWO 241 maintained robust growth and photosynthetic activity at levels of temperature (2 °C) and salinity (700 mM NaCl) which were nonpermissive for a mesophilic sister species, Chlamydomonas raudensis SAG 49.72 (SAG 49.72). Acclimation in the mesophile involved classic mechanisms, including downregulation of light harvesting and shifts in excitation energy between photosystem I and II. In contrast, UWO 241 exhibited high rates of PSI-driven cyclic electron flow (CEF) and a larger capacity for nonphotochemical quenching (NPQ). Furthermore, UWO 241 exhibited constitutively high activity of two key ascorbate cycle enzymes, ascorbate peroxidase and glutathione reductase and maintained a large ascorbate pool. These results matched the ability of the psychrophile to maintain low ROS under short-term photoinhibition conditions. We conclude that tight control over photostasis and ROS levels are essential for photosynthetic life to flourish in a native habitat of permanent photooxidative stress. We propose to rename this organism Chlamydomonas priscuii.

CfAPX, a cytosolic ascorbate peroxidase gene from Cryptomeria fortunei, confers tolerance to abiotic stress in transgenic Arabidopsis

Plants subjected to biotic or abiotic stresses produce a large amount of reactive oxygen species (ROS). If ROS cannot be cleared in time, they cause a series of harmful reactions in plants. Ascorbate peroxidase (APX) is a key enzyme that removes ROS from plant cells and plays a vital role in plant stress resistance. However, to date, no studies on APX homologs in Cryptomeria fortunei have been reported. In this study, we isolated complementary DNA (cDNA) encoding APXfrom C. fortunei needles, which is referred to as CfAPX, by rapid amplification of cDNA ends (RACE). The full-length CfAPX sequence was 1226 bp in length and included a 750-bp open reading frame (ORF) encoding a protein of 249 amino acids. Phylogenetic analysis showed that APXs of different plant species have been highly evolutionarily conserved. CfAPX was shown to belong to the cytoplasmic subgroup and was more closely related to GbAPX of the gymnosperm Ginkgo biloba. CfAPX showed no transcriptional activity in yeast cells but was highly expressed in cones. To better handle abiotic stresses, compared with wild-type (WT) Arabidopsis thaliana, 35S::CfAPX transgenic Arabidopsis strongly expressed CfAPX, presented increased antioxidant enzyme activities, ascorbic acid (AsA) contents, chlorophyll levels and fluorescence parameter and reduced malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) contents. In addition, CfAPX expression in C. fortunei was mostly upregulated under stress. In summary, CfAPX confers abiotic stress responses to plants, which provides a scientific basis for subsequent breeding for increased stress resistance in C. fortunei.

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.

Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L)

EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H₂O₂) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.

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.

Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae

The use of plant growth-promoting bacteria as agricultural inoculants of plants should be encouraged because of their prominent role in biological nitrogen fixation, the increase of nutrient uptake by roots, abiotic stress mitigation, and disease control. The complex mechanisms underlying the association between plant and beneficial bacteria have been increasingly studied, and proteomic tools can expand our perception regarding the fundamental molecular processes modulated by the interaction. In this study, we investigated the changes in protein expression in maize roots in response to treatment with the endophytic diazotrophic Herbaspirillum seropedicae and the activities of enzymes related to nitrogen metabolism. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was employed. Using this approach, we identified 123 differentially expressed proteins, of which 34 were upregulated enzymes, in maize roots cultivated with H. seropedicae. The maize root colonization of H. seropedicae modulated the differential expression of enzymes involved in the stress response, such as peroxidases, phenylalanine ammonia-lyase, and glutathione transferase. The differential protein profile obtained in the inoculated roots reflects the effect of colonization on plant growth and development compared with control plants.

Functional analysis of four Class III peroxidases from Chinese pear fruit: a critical role in lignin polymerization

Pear fruit could be used as good medicine to relieve coughs, promote salivation, nourish lungs, and reduce the risk of many diseases for its phytochemical action. Lignin is a major secondary metabolite in Chinese pear fruit. Class III peroxidase (Class III PRX) is an important enzyme in the biosynthesis of lignin in plants. However, we poorly understand the role of PRXs in lignin biosynthesis in Chinese pear fruit. In our study, we cloned five PRXs from Chinese pear (Pyrus bretschneideri), namely PbPRX2, PbPRX22, PbPRX34, PbPRX64, and PbPRX75, which contained 978 bp encoded 326 amino acids (AA), 2607 bp encoded 869 AA, 972 bp encoded 324 AA, 687 bp encoded 229 AA, and 1020 bp encoded 340 AA, respectively. Enzyme activity analysis showed that four recombinant PbPRX proteins had catalytic activities for pyrogallol, guaiacol, ferulic acid, coniferyl alcohol, and sinapyl alcohol. Subcellular localization experiments showed that these genes were located in the cell wall or cell membrane. Enzyme activity and kinetics of PbPRX2 revealed its role in polymerization of lignin in Chinese pear fruit. The present study suggested that PbPRXs played critical roles in lignin biosynthesis in Chinese pear fruit.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00949-9.

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.

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice

Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

Arabidopsis APx-R Is a Plastidial Ascorbate-Independent Peroxidase Regulated by Photomorphogenesis

Peroxidases are enzymes that catalyze the reduction of hydrogen peroxide, thus minimizing cell injury and modulating signaling pathways as response to this reactive oxygen species. Using a phylogenetic approach, we previously identified a new peroxidase family composed of a small subset of ascorbate peroxidase (APx) homologs with distinguished features, which we named ascorbate peroxidase-related (APx-R). In this study, we showed that APx-R is an ascorbate-independent heme peroxidase. Despite being annotated as a cytosolic protein in public databases, transient expression of AtAPx-R-YFP in Arabidopsis thaliana protoplasts and stable overexpression in plants showed that the protein is targeted to plastids. To characterize APx-R participation in the antioxidant metabolism, we analyzed loss-of-function mutants and AtAPx-R overexpressing lines. Molecular analysis showed that glutathione peroxidase 7 (GPx07) is specifically induced to compensate the absence of APx-R. APx-R overexpressing lines display faster germination rates, further confirming the involvement of APx-R in seed germination. The constitutive overexpression of AtAPx-R-YFP unraveled the existence of a post-translational mechanism that eliminates APx-R from most tissues, in a process coordinated with photomorphogenesis. Our results show a direct role of APx-R during germinative and post-germinative development associated with etioplasts differentiation.

High levels of glucose alter Physcomitrella patens metabolism and trigger a differential proteomic response

Sugars act not only as substrates for plant metabolism, but also have a pivotal role in signaling pathways. Glucose signaling has been widely studied in the vascular plant Arabidopsis thaliana, but it has remained unexplored in non-vascular species such as Physcomitrella patens. To investigate P. patens response to high glucose treatment, we explored the dynamic changes in metabolism and protein population by applying a metabolomic fingerprint analysis (DIESI-MS), carbohydrate and chlorophyll quantification, Fv/Fm determination and label-free untargeted proteomics. Glucose feeding causes specific changes in P. patens metabolomic fingerprint, carbohydrate contents and protein accumulation, which is clearly different from those of osmotically induced responses. The maximal rate of PSII was not affected although chlorophyll decreased in both treatments. The biological process, cellular component, and molecular function gene ontology (GO) classifications of the differentially expressed proteins indicate the translation process is the most represented category in response to glucose, followed by photosynthesis, cellular response to oxidative stress and protein refolding. Importantly, although several proteins have high fold changes, these proteins have no predicted identity. The most significant discovery of our study at the proteome level is that high glucose increase abundance of proteins related to the translation process, which was not previously evidenced in non-vascular plants, indicating that regulation by glucose at the translational level is a partially conserved response in both plant lineages. To our knowledge, this is the first time that metabolome fingerprint and proteomic analyses are performed after a high sugar treatment in non-vascular plants. These findings unravel evolutionarily shared and differential responses between vascular and non-vascular plants.

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.

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.

Reactive Oxygen Species (ROS) Metabolism and Nitric Oxide (NO) Content in Roots and Shoots of Rice (Oryza sativa L.) Plants under Arsenic-Induced Stress

Arsenic (As) is a highly toxic metalloid for all forms of life including plants. Rice is the main food source for different countries worldwide, although it can take up high amounts of As in comparison with other crops, showing toxic profiles such as decreases in plant growth and yield. The induction of oxidative stress is the main process underlying arsenic toxicity in plants, including rice, due to an alteration of the reactive oxygen species (ROS) metabolism. The aim of this work was to gain better knowledge on how the ROS metabolism and its interaction with nitric oxide (NO) operate under As stress conditions in rice plants. Thus, physiological and ROS-related biochemical parameters in roots and shoots from rice (Oryza sativa L.) were studied under 50 μM arsenate (AsV) stress, and the involvement of the main antioxidative systems and NO in the response of plants to those conditions was investigated. A decrease of 51% in root length and 27% in plant biomass was observed with 50 μM AsV treatment, as compared to control plants. The results of the activity of superoxide dismutase (SOD) isozymes, catalase, peroxidase (POD: total and isoenzymatic), and the enzymes of the ascorbate–glutathione cycle, besides the ascorbate and glutathione contents, showed that As accumulation provoked an overall significant increase of most of them, but with different profiles depending on the plant organ, either root or shoot. Among the seven identified POD isozymes, the induction of the POD-3 in shoots under As stress could help to maintain the hydrogen peroxide (H2O2) redox homeostasis and compensate the loss of the ascorbate peroxidase (APX) activity in both roots and shoots. Lipid peroxidation was slightly increased in roots and shoots from As-treated plants. The H2O2 and NO contents were enhanced in roots and shoots against arsenic stress. In spite of the increase of most antioxidative systems, a mild oxidative stress situation appears to be consolidated overall, since the growth parameters and those from the oxidative damage could not be totally counteracted. In these conditions, the higher levels of H2O2 and NO suggest that signaling events are simultaneously occurring in the whole plant.

Exogenous Melatonin Enhances Rice Plant Resistance Against Xanthomonas oryzae pv. oryzae

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae, is one of the most serious diseases of rice. In this study we found that exogenous melatonin can increase rice resistance to BB. Treatment of rice plants with exogenous melatonin (20 µg/ml) increased nitrate reductase, nitric oxide synthase, and peroxidase activity, enabling high intracellular concentrations of melatonin, nitric oxide, and H₂O₂. The expression of NPR1, a key regulator in the salicylic acid signaling pathway, was upregulated more than 10-fold when the plants were challenged with melatonin. Similarly, the messenger RNA level of PDF1.2, a jasmonic acid-induced defense marker, was 15 times higher in the treated plants than in the control plants. Moreover, three pathogenesis-related proteins, PR1b, PR8a, and PR9, were upregulated 20-fold in the presence of melatonin. The application of melatonin (100 µg/ml) to soil-grown rice reduced the incidence of BB by 86.21%. Taken together, these results not only provide a better understanding of melatonin-mediated innate immunity to X. oryzae pv. oryzae in rice but also represent a promising cultivation strategy to protect rice against X. oryzae pv. oryzae infection.

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.

Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture

Cultivated grapevines, Vitis vinifera subsp. sativa, are thought to have been domesticated from wild populations of Vitis vinifera subsp. sylvestris in Central Asia. V. vinifera subsp. sativa is one of the most economically important fruit crops worldwide. Since cultivated grapevines are susceptible to multiple biotic and abiotic soil factors, they also need to be grafted on resistant rootstocks that are mostly developed though hybridization between American wild grapevine species (V. berlandieri, V. riparia, and V. rupestris). Therefore, wild grapevine species are essential genetic materials for viticulture to face biotic and abiotic stresses in both cultivar and rootstock parts. Actually, viticulture faces several environmental constraints that are further intensified by climate change. Recently, several reports on biotic and abiotic stresses-response in wild grapevines revealed accessions tolerant to different constraints. The emergence of advanced techniques such as omics technologies, marker-assisted selection (MAS), and functional analysis tools allowed a more detailed characterization of resistance mechanisms in these wild grapevines and suggest a number of species (V. rotundifolia, V. rupestris, V. riparia, V. berlandieri and V. amurensis) have untapped potential for new resistance traits including disease resistance loci and key tolerance genes. The present review reports on the importance of different biotechnological tools in exploring and examining wild grapevines tolerance mechanisms that can be employed to promote elite cultivated grapevines under climate change conditions.

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.

Transgenic crops for the agricultural improvement in Pakistan: a perspective of environmental stresses and the current status of genetically modified crops

Transgenic technologies have emerged as a powerful tool for crop improvement in terms of yield, quality, and quantity in many countries of the world. However, concerns also exist about the possible risks involved in transgenic crop cultivation. In this review, literature is analyzed to gauge the real intensity of the issues caused by environmental stresses in Pakistan. In addition, the research work on genetically modified organisms (GMOs) development and their performance is analyzed to serve as a guide for the scientists to help them select useful genes for crop transformation in Pakistan. The funding of GMOs research in Pakistan shows that it does not follow the global trend. We also present socio-economic impact of GM crops and political dimensions in the seed sector and the policies of the government. We envisage that this review provides guidelines for public and private sectors as well as the policy makers in Pakistan and in other countries that face similar environmental threats posed by the changing climate.

Vitamin C in Plants: From Functions to Biofortification

Vitamin C (l-ascorbic acid) is an excellent free radical scavenger, not only for its capability to donate reducing equivalents but also for the relative stability of the derived monodehydroascorbate radical. However, vitamin C is not only an antioxidant, since it is also a cofactor for numerous enzymes involved in plant and human metabolism. In humans, vitamin C takes part in various physiological processes, such as iron absorption, collagen synthesis, immune stimulation, and epigenetic regulation. Due to the functional loss of the gene coding for l-gulonolactone oxidase, humans cannot synthesize vitamin C; thus, they principally utilize plant-based foods for their needs. For this reason, increasing the vitamin C content of crops could have helpful effects on human health. To achieve this objective, exhaustive knowledge of the metabolism and functions of vitamin C in plants is needed. In this review, the multiple roles of vitamin C in plant physiology as well as the regulation of its content, through biosynthetic or recycling pathways, are analyzed. Finally, attention is paid to the strategies that have been used to increase the content of vitamin C in crops, emphasizing not only the improvement of nutritional value of the crops but also the acquisition of plant stress resistance.

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.

Cytosolic APX2 is a pleiotropic protein involved in H2O2 homeostasis, chloroplast protection, plant architecture and fertility maintenance

Rice cytoplasmic APX2 is a pleiotropic protein, densely distributed around chloroplasts. It plays key roles in H₂O₂ homeostasis and chloroplast protection, and is related to plant architecture and fertility regulation. Ascorbate peroxidases (APXs) catalyze the conversion of H₂O₂ into H₂O. In this report, we systematically investigated the function of cytosolic APX2 using a T-DNA knockout mutant. Loss of OsAPX2 altered rice architecture including shoot height and leaf inclination, resulting in shoot dwarfing, leaf dispersion and fertility decline. Sixty-five differentially expressed proteins were identified in flag leaves of the milk-ripe stage, mainly involved in photosynthesis, glycolysis and TCA cycle, redox homeostasis, and defense. The absence of APX2 severely impacted the stability of chloroplast proteins, and dramatically reduced their expression levels. Subcellular localization showed that APX2 was enriched around each chloroplast to form a high concentration sphere, highlighting chloroplasts as key targets protected by the protein. Accumulation of H₂O₂ was suppressed in the KO-APX2 mutant, which may benefit from increased CAT activity and functional complementation of APX family members. Unexpectedly, the accumulation of soluble sugar, especially sucrose increased significantly, suggesting that APX2 was involved in regulation of sugar metabolism. Obviously, roles of the cytosolic APX2 are very profound and complex in rice. It can be concluded that the cytosolic APX2 is a pleiotropic protein and an important regulator in ROS homeostasis, chloroplast protection, carbohydrate metabolism as well as plant architecture and fertility maintenance.

Revealing proteins associated with symbiotic germination of Gastrodia elata by proteomic analysis

BACKGROUND

Gastrodia elata, a mycoheterotrophic orchid, is a well-known medicinal herb. In nature, the seed germination of G. elata requires proper fungal association, because of the absence of endosperm. To germinate successfully, G. elata obtains nutrition from mycorrhizal fungi such as Mycena. However, Mycena is not able to supply nutrition for the further development and enlargement of protocorms into tubers, flowering and fruit setting of G. elata. To date, current genomic studies on this topic are limited. Here we used the proteomic approach to explore changes in G. elata at different stages of symbiotic germination.

RESULTS

Using mass spectrometry, 3787 unique proteins were identified, of which 599 were classified as differentially accumulated proteins. Most of these differentially accumulated proteins were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Among them, the defense genes (e.g., pathogenesis-/wound-related proteins, peroxidases, and serine/threonine-protein kinase) were highly expressed in late-stage protocorms, suggesting that fungal colonization triggered the significant defense responses of G. elata.

CONCLUSIONS

The present study indicated the metabolic change and defensive reaction could disrupt the balance between Mycena and G. elata during mycorrhizal symbiotic germination.

A Novel L-ascorbate Peroxidase 6 Gene, ScAPX6, Plays an Important Role in the Regulation of Response to Biotic and Abiotic Stresses in Sugarcane

The L-ascorbate peroxidase 6 gene (APX6) is one of the most important genes for scavenging H₂O₂ and plays a vital role in plant resistance to environmental stresses. In this study, a novel ScAPX6 gene (GenBank Accession No. KT907352) was obtained from a sugarcane variety (ROC22). Bioinformatics analysis showed that ScAPX6 has a cDNA length of 1,086 bp and encoded 333 amino acid residues. Subcellular localization confirmed that ScAPX6 was located in the chloroplast. Enhanced growth of Escherichia coli BL21 cells that expressed ScAPX6 showed high tolerance under copper (Cu) stress. Real-time quantitative PCR analysis revealed that ScAPX6 was constitutively expressed wherein with the highest expression levels in sugarcane pith and leaf and the lowest in the root. ScAPX6 was down-regulated by salicylic acid (SA), hydrogen peroxide (H₂O₂), polyethylene glycol (PEG) and sodium chloride (NaCl) stimuli. Interestingly, it was significantly up-regulated under the stresses of abscisic acid (ABA) and methyl jasmonate (MeJA) wherein with the highest inducible expression levels at 6 h at 6.0- and 70.0-times higher, respectively than that of control. Overexpression of ScAPX6 in Nicotiana benthamiana leaves enhanced the resistance to the infection of tobacco pathogens Pseudomonas solanacearum and Fusarium solani var. coeruleum. These results implied that ScAPX6 might positively respond to ABA, MeJA, and Cu, but might negatively respond to the stresses of SA, H₂O₂, PEG, and NaCl. Keeping in view the current investigation, ScAPX6 could be associated with the hypersensitive response (HR) or immunity of sugarcane, which will provide a baseline for the function identification of sugarcane ScAPX6.

Genome-wide investigation and expression profiling of APX gene family in Gossypium hirsutum provide new insights in redox homeostasis maintenance during different fiber development stages

Ascorbate peroxidase (APX) is a member of heme-containing peroxidases which catalyze the H₂O₂-dependent oxidation of a wide range of substrates in plants and animals. As is known, H₂O₂ acts as a signaling molecule in the regulation of fiber development. Our previous work reported that ascorbate peroxidase 1 (GhAPX1) was important for cotton fiber elongation. However, knowledge about APX gene family members and their evolutionary and functional characteristics in cotton is limited. Here, we report 26 GhAPX genes by genome-wide investigation of tetraploid cotton Gossypium hirsutum. Phylogenetic and gene structure analyses classified these APX members into five clades and syntenic analysis suggested two duplication events. Expression profiling of the 26 APXs revealed that ten members are expressed in cotton fibers. Notably, GhAPX10A, GhAPX10D, GhAPX12A, and GhAPX12D showed high expression levels in 30-day fiber, while GhAPX1A/D, GhAPX3A/D, and GhAPX6A/D showed very low expression levels. The enzyme activity and H₂O₂ content assays revealed that cotton fiber kept high enzyme activity and the lowest H₂O₂ level in 30-day fibers, indicating that other than GhAPX1, the newly reported APX members are responsible for the reactive oxygen species homeostasis in the cotton fiber maturation stages. Expression profiling of ten fiber-expressed APXs after phytohormone treatments revealed their regulation patterns by different stimuli, suggesting that GhAPX1, GhAPX12A, and GhAPX12D are responsible to most phytohormone treatments. Our data provided evolutionary and functional information of GhAPX gene family members and revealed that different members are responsible to redox homeostasis during different cotton fiber development stages.

Response to in vitro salt stress in sugarcane is conditioned by concentration and condition of exposure to NaCl

La salinidad es uno de los principales factores de estrés ambiental, además de interferir en el crecimiento de las plantas perjudica directamente la producción agrícola. En ese contexto, se destaca la importancia de investigaciones direccionadas a la respuesta de las plantas sometidas al estrés salino, con el fin de evaluar el comportamiento fisiológico y bioquímico con el objetivo de seleccionar genotipos tolerantes a dicha condición. Una de las técnicas más utilizadas para uniformizar la respuesta de las plantas a una condición en particular es el cultivo de tejidos in vitro. Por lo tanto, el objetivo de este estudio fue evaluar la respuesta de dos variedades comerciales de caña de azúcar (RB931011 e RB872552) expuestas a estrés salino con NaCl (56 mM e 112 mM) en diferentes condiciones, gradual y abrupta. Las respuestas del sistema antioxidante enzimático (catalasa, peroxidasa y ascorbato peroxidasa) y prolina libre, asi como las concentraciones de Na+ e K+ fueron evaluadas 30 días después del inicio de los tratamientos. Fueron observadas diferencias en la respuesta de las variedades en función del modo de inducción del estrés salino, graduado o abrupto, y no solo en función de las concentraciones de NaCl en el medio de cultivo. La respuesta al estrés es condicionada no solo por la concentración de sal sino también por la forma de exposición al medio salino.

PGPR strain Paenibacillus polymyxa SQR-21 potentially benefits watermelon growth by re-shaping root protein expression

Paenibacillus polymyxa (SQR-21) is not only a plant growth-promoting rhizobacteria, but also an effective biocontrol agent against Fusarium wilt disease of watermelon. For the better understanding and clarifying the potential mechanisms of SQR-21 to improve watermelon growth and disease resistance, a split-root methodology in hydroponic and LC-MS technology with the label free method was used to analyze the key root proteins involved in watermelon metabolism and disease resistance after the inoculation of SQR-21. Out of 623 identified proteins, 119 proteins were differentially expressed when treatment (SQR-21 inoculation) and control (no bacterial inoculation) were compared. Among those, 57 and 62 proteins were up-regulated and down-regulated, respectively. These differentially expressed proteins were identified to be involved in signal transduction (ADP-ribosylation factor, phospholipase D), transport (aspartate amino-transferase), carbohydratemetabolic (glucose-6-phosphate dehydrogenase, UDP-glucose pyrophosphorylase), defense and response to stress (glutathione S-transferase, Ubiquitin-activating enzyme E1), and oxidation-reduction process (thioredoxin peroxidase, ascorbate peroxidase). The results of this study indicated that SQR-21 inoculation on the watermelon roots benefits plant by inducing the expression of several proteins involved in growth, photosynthesis, and other metabolic and physiological activities.

Biochemistry and Physiology of Reactive Oxygen Species in Euglena

Reactive oxygen species (ROS) such as superoxide and hydrogen peroxide are by-products of various metabolic processes in aerobic organisms including Euglena. Chloroplasts and mitochondria are the main sites of ROS generation by photosynthesis and respiration, respectively, through the active electron transport chain. An efficient antioxidant network is required to maintain intracellular ROS pools at optimal conditions for redox homeostasis. A comparison with the networks of plants and animals revealed that Euglena has acquired some aspects of ROS metabolic process. Euglena lacks catalase and a typical selenocysteine containing animal-type glutathione peroxidase for hydrogen peroxide scavenging, but contains enzymes involved in ascorbate-glutathione cycle solely in the cytosol. Ascorbate peroxidase in Euglena, which plays a central role in the ascorbate-glutathione cycle, forms a unique intra-molecular dimer structure that is related to the recognition of peroxides. We recently identified peroxiredoxin and NADPH-dependent thioredoxin reductase isoforms in cellular compartments including chloroplasts and mitochondria, indicating the physiological significance of the thioredoxin system in metabolism of ROS. Besides glutathione, Euglena contains the unusual thiol compound trypanothione, an unusual form of glutathione involving two molecules of glutathione joined by a spermidine linker, which has been identified in pathogenic protists such as Trypanosomatida and Schizopyrenida. Furthermore, in contrast to plants, photosynthesis by Euglena is not susceptible to hydrogen peroxide because of resistance of the Calvin cycle enzymes fructose-1,6-bisphosphatse, NADP⁺-glyceraldehyde-3-phosphatase, sedoheptulose-1,7-bisphosphatase, and phosphoribulokinase to hydrogen peroxide. Consequently, these characteristics of Euglena appear to exemplify a strategy for survival and adaptation to various environmental conditions during the evolutionary process of euglenoids.

Rice peroxisomal ascorbate peroxidase knockdown affects ROS signaling and triggers early leaf senescence

H₂O₂, which is continually produced by aerobic metabolism, is a cytotoxic molecule when in high levels. However, low levels can act as a signaling molecule able to regulate the expression of stress responses, senescence, programmed cell death, plant growth, and development. Ascorbate peroxidase (APX) enzyme plays an essential role in the control of intracellular H₂O₂ levels. Here, the function of a gene encoding a peroxisomal APX (OsAPX4) from rice (Oryza sativa L.) was studied. OsAPX4 gene expression can be detected in roots and panicles, but the highest expression level occurs in leaves. Silencing of OsAPX4 and OsAPX3 expression in RNAiOsAPX4 did not affect the growth of plants under growth chamber conditions, but aging transgenic plants interestingly displayed an early senescence phenotype. Leaf fragments from silenced plants were also more sensitive to induced senescence conditions. RNAiOsAPX4 plants did not present detectable changes in intracellular H₂O₂ levels, but biochemical analyses showed that transgenic plants displayed some decreased APX activity in the chloroplastic fraction. Also, the peroxisomal enzyme glycolate oxidase exhibited lower activity, whereas catalase activity was similar to non-transformed rice. The results imply that OsAPX4 gene has an important role in leaf senescence pathway mediated by ROS signaling.

Gene expression and activity of antioxidant enzymes in rice plants, cv. BRS AG, under saline stress

The rice cultivar (Oryza sativa L.) BRS AG, developed by Embrapa Clima Temperado, is the first cultivar designed for purposes other than human consumption. It may be used in ethanol production and animal feed. Different abiotic stresses negatively affect plant growth. Soil salinity is responsible for a serious reduction in productivity. Therefore, the objective of this study was to evaluate the gene expression and the activity of antioxidant enzymes (SOD, CAT, APX and GR) and identify their functions in controlling ROS levels in rice plants, cultivar BRS AG, after a saline stress period. The plants were grown in vitro with two NaCl concentrations (0 and 136 mM), collected at 10, 15 and 20 days of cultivation. The results indicated that the activity of the enzymes evaluated promotes protection against oxidative stress. Although, there was an increase of reactive oxygen species, there was no increase in MDA levels. Regarding genes encoding isoforms of antioxidant enzymes, it was observed that OsSOD3-CU/Zn, OsSOD2-Cu/Zn, OsSOD-Cu/Zn, OsSOD4-Cu/Zn, OsSODCc1-Cu/Zn, OsSOD-Fe, OsAPX1, OsCATB and OsGR2 were the most responsive. The increase in the transcription of all genes among evaluated isoforms, except for OsAPX6, which remained stable, contributed to the increase or the maintenance of enzyme activity. Thus, it is possible to infer that the cv. BRS AG has defense mechanisms against salt stress.