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

Genome-wide analysis of ascorbate peroxidase and functional characterization of SpAPX249b and SpAPX285c for salt tolerance in Sesuvium portulacastrum L

KEY MESSAGE

We have identified 33 SpAPXs from S. portulacastrum genome and found SpAPX249b and SpAPX285c are important for halophyte salt tolerance. Ascorbate peroxidase (APX) is a vital antioxidant enzyme, involved in plant development and stress response by scavenging excessive reactive oxygen species (ROS). APX genes have been characterized in many plant species. However, their role in Sesuvium portulacastrum L. has not yet to be fully investigated. Here, we identified 33 SpAPXs from its genome and divided them into five subgroups across the 16 chromosomes. Cis-element analysis of their promoters indicated that all the detected SpAPXs showed potential roles in response to biotic and abiotic stresses as well as phytohormone effects on the plant growth and development. Transcriptomic data of the different tissues revealed that 9 SpAPX genes were specifically expressed in root and 13 ones were specifically expressed in leaves, with SpAPX249b prominently expressed in root and SpAPX285c in leaves. Moreover, quantitative real-time PCR analysis revealed that both SpAPX249b and SpAPX285c genes expressed only after NaCl application and were sharply induced in the high concentration of NaCl treatments. Our findings suggested that SpAPX249b and SpAPX285c may associate with plant salt tolerance and can serve as valuable genes for enhancing salt tolerance in other plants. By introducing these genes into other plants, it is possible to develop new varieties of salt-tolerant crops, thereby expanding the utilization of saline-alkali land and increasing agricultural productivity. In coastal saline-alkali wetlands, this halophyte can thrive in large numbers due to its inherent salt-tolerant genes, contributing to the restoration of polluted or ecologically degraded coastal saline-alkali wetlands.

Positive influence of selenium on the modulation of ascorbate-glutathione cycle in salt stressed Setaria italica L

Soil salinity is a significant abiotic factor affecting crop yield and global distribution, hence selecting salt-tolerant crop species is crucial for food security. Foxtail millet is a resilient crop suitable for hilly, salinity, and drought-prone areas due to its ability to withstand environmental stressors. In this study, foxtail millet was subjected to high NaCl concentrations (150 mM and 200 mM) and selenium (1 μM, 5 μM, and 10 μM) as a stress mitigator. Increased salinity in foxtail plants hampered the growth with decreased pigment levels, increased H₂O₂ levels (153.6%), lipid peroxidation (32.1%), and electrolyte leakage (155.5%). The application of 1 μM Se positively influenced the root-to-shoot ratio (R) (59.2%), photosynthetic pigments, phenolic content (25.1%), flavonoid content (7%) and hence the antioxidant potential of the salt stressed plants there by decreasing the H₂O₂ levels (26.8%) and suggesting a greater ability to scavenge radicals. Both NaCl and Se induced the AsA-GSH pathway. Se supplementation significantly improved AsA-GSH pathway components such as AsA/DHA (40.8%) and GSH/GSSG ratios (39.6%) in salt-stressed foxtail millet, reducing oxidative stress and efficiently neutralizing H₂O₂. Gene expression validation confirmed that SiAPX, SiDHAR, SiMDHAR, and SiGR showed significant upregulation with 1 μM Se application in salt-stressed foxtail millet plants. However, higher Se concentrations (5 μM and 10 μM) led to a reduced fresh weight along with R, increased the MDA and H₂O₂ levels, and did not positively contribute to osmolyte accumulation or improve the AsA/DHA and GSH/GSSG ratios. Elevated Se levels also led to a decreased antioxidant potential. Among the enzymes of the AsA-GSH cycle, higher Se concentrations negatively affected APX, DHAR, MDHAR, and GR activities, indicating stress aggravation rather than mitigation at elevated doses.

RsWRKY75 promotes ROS scavenging and cadmium efflux via activating the transcription of RsAPX1 and RsPDR8 in radish (Raphanus sativus L.)

KEY MESSAGE

Acting as a nucleus-localized transcriptional activator, RsWRKY75 promotes ROS scavenging and Cd efflux by activating the transcription of RsAPX1 and RsPDR8 in radish. Radish (Raphanus sativus L.) is an important economical root vegetable crop worldwide. As a toxic heavy metal, cadmium (Cd) can dramatically hamper radish taproot quality as well as threaten human health. Although the WRKY transcription factors (TFs) play crucial roles in plant response to Cd stress, how WRKY TFs mediate Cd uptake and efflux remains elusive in radish. Herein, the RsWRKY75, belonging to the WRKY-IIc sub-group, displayed high expression in vascular cambium at the expanding stage, whose promoter activity and expression were obviously induced by Cd exposure at 24 h in radish root. RsWRKY75 was localized primarily to the nucleus and had transactivation activity in yeast and tobacco leaf cells. Transient transformation indicated that RsWRKY75 promoted Cd-induced ROS scavenging in radish cotyledons. Overexpression of RsWRKY75 led to increased root elongation but decreased Cd accumulation in Arabidopsis plants. Both in vitro and in vivo assays revealed that RsWRKY75 bound to the RsAPX1 promoter and activated its expression to eliminate excessive ROS accumulation. Moreover, RsWRKY75 activated RsPDR8 transcription by directly binding to its promoter, thereby promoting Cd efflux in the radish root. Collectively, we revealed a novel module of RsWRKY75-mediated ROS scavenging and Cd efflux in radish. These results would facilitate to establish genetic strategies to achieve RsWRKY75-dependent Cd extrusion and detoxification in radish.

Genome-Wide Identification and Analysis of BrTCP Transcription Factor Family Genes Involved in Cold Stress Tolerance in Winter Rapeseed (Brassica rapa L.)

TCP transcription factors are important during plant growth and stress responses. However, their role in the cold stress response of Brassica rapa L. remains poorly understood. In this research, we identified the TCPs gene family in B. rapa to learn the features of the BrTCP gene family, functionally annotating the interacting proteins of TCP4 and analyzing their expression levels. Our results illustrated the presence of 19 members of the BrTCPs family in B. rapa, exhibiting molecular weights ranging from 27,367.45 to 59,433.64 Da. All identified proteins were classified as unstable, with isoelectric points ranging from 5.5 to 9.48. Subcellular localization forecasted that TCP proteins were all positioned in the nucleus. The BrTCP gene structure is relatively simple, with only seven members possessing introns, and none of the members contain UTR regions. BrTCPs comprise hormone-, light-, and stress-responsive elements. We found that the frequency of photoresponsive elements was greatest in the promoter region, suggesting that BrTCP genes are regulated by light signals and function synergistically with plant growth and development. In addition, five candidate interaction proteins of BrTCP4 were identified using yeast two-hybrid screening. RNA-Seq and q-PCR analyses of the interacting genes revealed differential expression of BrTCP family genes across various tissues following cold stress. Significant responses were observed under low-temperature stress, drought stress, and rehydration treatment, suggesting that these genes play crucial roles as regulators of the molecular network mechanisms responding to stress. This study enhances our understanding of the BrTCP family and provides significant insights into the stress tolerance mechanisms of B. rapa.

Glucosinolates Mediated Regulation of Enzymatic Activity in Response to Oxidative Stress in Brassica spp

Brassica crops are vital as they supply essential minerals, antioxidants, and bioactive substances like anthocyanins, glucosinolates, and carotenoids. However, biotic and abiotic elements that cause oxidative stress through heavy metals and other eco-toxicants pose a risk to Brassica plants. Increased generation of Reactive Oxygen Species (ROS) causes oxidative stress, which damages biomolecules and interferes with plant growth, productivity, and cellular equilibrium. Plants producing Brassica need an intricate enzyme defence mechanism to fend off oxidative stress. All the enzymes that have been addressed are found in mitochondria, peroxisomes, chloroplasts, and other cell components. They are in charge of removing ROS and preserving the cell's redox balance. Additionally, Brassica plants use secondary metabolites called Glucosinolates (GLs), which have the capacity to regulate enzymatic activity and act as antioxidants. By breaking down compounds like sulforaphane, GLs boost antioxidant enzymes and provide protection against oxidative stress. To develop methods for improving agricultural crop stress tolerance and productivity in Brassica, it is necessary to comprehend the dynamic interaction between GL metabolism and enzymatic antioxidant systems. This highlights the possibility of maximizing antioxidant defences and raising the nutritional and commercial value of Brassica across the globe by utilizing genetic diversity and environmental interactions.

Genome-Wide Identification of APX Gene Family in Citrus maxima and Expression Analysis at Different Postharvest Preservation Times

Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism.

Genome-wide identification and analysis of ascorbate peroxidase (APX) gene family in hemp (Cannabis sativa L.) under various abiotic stresses

Ascorbate peroxidase (APX) plays a critical role in molecular mechanisms such as plant development and defense against abiotic stresses. As an important economic crop, hemp (Cannabis sativa L.) is vulnerable to adverse environmental conditions, such as drought, cold, salt, and oxidative stress, which lead to a decline in yield and quality. Although APX genes have been characterized in a variety of plants, members of the APX gene family in hemp have not been completely identified. In this study, we (1) identified eight members of the CsAPX gene family in hemp and mapped their locations on the chromosomes using bioinformatics analysis; (2) examined the physicochemical characteristics of the proteins encoded by these CsAPX gene family members; (3) investigated their intraspecific collinearity, gene structure, conserved domains, conserved motifs, and cis-acting elements; (4) constructed a phylogenetic tree and analyzed interspecific collinearity; and (5) ascertained expression differences in leaf tissue subjected to cold, drought, salt, and oxidative stresses using quantitative real-time-PCR (qRT-PCR). Under all four stresses, CsAPX6, CsAPX7, and CsAPX8 consistently exhibited significant upregulation, whereas CsAPX2 displayed notably higher expression levels under drought stress than under the other stresses. Taken together, the results of this study provide basic genomic information on the expression of the APX gene family and pave the way for studying the role of APX genes in abiotic stress.

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

Brassica crops are well known for the accumulation of glucosinolates-secondary metabolites crucial for plants' adaptation to various stresses. Glucosinolates also functioning as defence compounds pose challenges to food quality due to their goitrogenic properties. Their disruption leaves plants susceptible to insect pests and diseases. Hence, a targeted reduction in seed glucosinolate content is of paramount importance to increase food acceptance. GLUCOSINOLATE TRANSPORTERS (GTRs) present a promising avenue for selectively reducing glucosinolate concentrations in seeds while preserving biosynthesis elsewhere. In this study, 54 putative GTR protein sequences found in Brassica were retrieved, employing Arabidopsis GTR1 and GTR2 templates. Comprehensive bioinformatics analyses, encompassing gene structure organization, domain analysis, motif assessments, promoter analysis, and cis-regulatory elements, affirmed the existence of transporter domains and stress-related regulatory elements. Phylogenetic analysis revealed patterns of conservation and divergence across species. Glucosinolates have been shown to increase under stress conditions, indicating a potential role in stress response. To elucidate the role of GTRs in glucosinolate transportation under NaCl stress in two distinct Brassica species, B. juncea and B. napus, plants were subjected to 0, 100, or 200 mM NaCl. Based on the literature, key GTR genes were chosen and their expression across various plant parts was assessed. Both species displayed divergent trends in their biochemical profiles as well as glucosinolate contents under elevated salt stress conditions. Statistical modelling identified significant contributors to glucosinolate variations, guiding the development of targeted breeding strategies for low-glucosinolate varieties. Notably, GTR2A2 exhibited pronounced expressions in stems, contributing approximately 52% to glucosinolate content variance, while GTR2B1/C2 displayed significant expression in flowers. Additionally, GTR2A1 and GTR1A2/B1 demonstrated noteworthy expression in roots. This study enhances our understanding of glucosinolate regulation under stress conditions, offering avenues to improve Brassica crop quality and resilience.

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.

Genome-Wide Identification of GSTs Gene Family and Functional Analysis of BraGSTF2 of Winter Rapeseed (Brassica rapa L.) under Cold Stress

The largest gene families in plants were found to be Glutathione transferases (GSTs), which played significant roles in regulating plant growth, development, and stress response. Within the GSTs gene family, members were found to play a crucial role in the low-temperature response process of plants. A comprehensive study identified a total of 70 BraGSTs genes. Cluster analysis results demonstrated that the BraGSTs in Brassica rapa (B. rapa) could be categorized into eight sub-families and were unevenly distributed across ten chromosomes. The 39 BraGSTs genes were found to be organized into 15 tandem gene clusters, with the promoters containing multiple cis-elements associated with low-temperature response. Cold stress was observed to stimulate the expression of 15 genes, with the BraGSTF2 gene exhibiting the highest level of expression, suggesting its significant involvement in winter B. rapa's response to low-temperature stress. Subcellular localization analysis of the BraGSTF2 protein indicated its potential expression in both the cell membrane and nucleus. The analysis of stress resistance in BraGSTF2 transgenic Arabidopsis thaliana lines demonstrated that the over-expression of this gene resulted in significantly elevated levels of SOD, POD activity, and SP content compared to the wild type following exposure to low temperatures. These levels reached their peak after 24 h of treatment. Conversely, the MDA content was lower in the transgenic plants compared to the wild-type (WT) Arabidopsis (Arabidopsis thaliana L.). Additionally, the survival rate of BraGSTF2 transgenic Arabidopsis was higher than that of the WT Arabidopsis thaliana, suggesting that the BraGSTF2 gene may play a crucial role in enhancing the cold stress tolerance of winter B. rapa. This study lays a foundation for further research on the role of the BraGSTs gene in the molecular regulation of cold resistance in winter B. rapa.

Gaining Insight into Large Gene Families with the Aid of Bioinformatic Tools

Proteins participating in plant cell morphogenesis are often encoded by large gene families, in some cases comprising paralogs with variable (modular) domain organization, as in the case of the formin (FH2 protein) family of actin nucleators that can have also additional functions. Unravelling the phylogeny of such a complex gene family brings a number of specific challenges but may be crucial for predictions of protein function and for experimental design. Here we present an overview of our "cottage industry" semi-manual bioinformatic approach, based mostly, though not exclusively, on freely available software tools, which we used to obtain insight into the evolutionary history of plant FH2 proteins and some other components of the plant cell morphogenesis apparatus.

Genome-Wide Identification of C2H2 ZFPs and Functional Analysis of BRZAT12 under Low-Temperature Stress in Winter Rapeseed (Brassica rapa)

Zinc-finger protein (ZFP) transcription factors are among the largest families of transcription factors in plants. They participate in various biological processes such as apoptosis, autophagy, and stemness maintenance and play important roles in regulating plant growth and development and the response to stress. To elucidate the functions of ZFP genes in the low-temperature response of winter (Brassica rapa L.) B. rapa, this study identified 141 members of the C2H2 ZFP gene family from B. rapa, which are heterogeneously distributed on 10 chromosomes and have multiple cis-acting elements related to hormone regulation and abiotic stress of adversity. Most of the genes in this family contain only one CDS, and genes distributed in the same evolutionary branch share mostly the same motifs and are highly conserved in the evolution of cruciferous species. The genes were significantly upregulated in the roots and growth cones of ‘Longyou-7’, indicating that they play a role in the stress-response process of winter B. rapa. The expression level of the Bra002528 gene was higher in the strongly cold-resistant varieties than in the weakly cold-resistant varieties after low-temperature stress. The survival rate and BrZAT12 gene expression of trans-BrZAT12 Arabidopsis thaliana (Arabidopsis) were significantly higher than those of the wild-type plants at low temperature, and the enzyme activities in vivo were higher than those of the wild-type plants, indicating that the BrZAT12 gene could improve the cold resistance of winter B. rapa. BrZAT12 expression and superoxide dismutase and ascorbate peroxidase enzyme activities were upregulated in winter B. rapa after exogenous ABA treatment. BrZAT12 expression and enzyme activities decreased after the PD98059 treatment, and BrZAT12 expression and enzyme activities were higher than in the PD98059 treatment but lower than in the control after both treatments together. It is speculated that BrZAT12 plays a role in the ABA signaling process in which MAPKK is involved. This study provides a theoretical basis for the resolution of cold-resistance mechanisms in strong winter B. rapa.

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.