The Superoxide Dismutase Gene Family in Nicotiana tabacum: Genome-Wide Identification, Characterization, Expression Profiling and Functional Analysis in Response to Heavy Metal Stress

In silico genome-wide analysis of the growth-regulating factor gene family and their expression profiling in Vitis vinifera under biotic stress

Growth regulatory factors (GRFs) are transcription factors that encode the proteins involved in plant growth and development. However, no comprehensive analysis of Vitis vinifera GRF genes has yet been conducted. In the current study, we performed a genome-wide analysis of the GRF gene family to explore the VvGRF gene's role in Vitis vinifera. We identified 30 VvGRF genes in the Vitis vinifera genome, localized over 20 chromosomes. Based on evolutionary analysis, 49 GRF genes (nine AtGRF, ten FvGRF, and 30 VvGRF) were clustered into six groups. Many cis-elements involved in light control, defense, and plant growth have been identified in the promoter region of VvGRF genes, and multiple miRNAs have been predicted to be involved in regulating VvGRF gene expression. Protein-protein interaction analysis showed that nine VvGRF proteins formed a complex protein interaction network. Furthermore, the gene expression analysis of VvGRF revealed that VvGRF-5 and VvGRF-6 were highly upregulated suggesting that these genes are involved in biotic responses. This study provides comprehensive insights into the functional characteristics and occurrence of the VvGRF gene family in Vitis vinifera, which may be applied in breeding programs to enhance the growth of Vitis vinifera varieties under stress and growth changes.

Identification and Analysis of the Superoxide Dismutase (SOD) Gene Family and Potential Roles in High-Temperature Stress Response of Herbaceous Peony (Paeonia lactiflora Pall.)

The herbaceous peony (Paeonia lactiflora Pall.) plant is world-renowned for its ornamental, medicinal, edible, and oil values. As global warming intensifies, its growth and development are often affected by high-temperature stress, especially in low-latitude regions. Superoxide dismutase (SOD) is an important enzyme in the plant antioxidant systems and plays vital roles in stress response by maintaining the dynamic balance of reactive oxygen species (ROS) concentrations. To reveal the members of then SOD gene family and their potential roles under high-temperature stress, we performed a comprehensive identification of the SOD gene family in the low-latitude cultivar 'Hang Baishao' and analyzed the expression patterns of SOD family genes (PlSODs) in response to high-temperature stress and exogenous hormones. The present study identified ten potential PlSOD genes, encoding 145-261 amino acids, and their molecular weights varied from 15.319 to 29.973 kDa. Phylogenetic analysis indicated that PlSOD genes were categorized into three sub-families, and members within each sub-family exhibited similar conserved motifs. Gene expression analysis suggested that SOD genes were highly expressed in leaves, stems, and dormancy buds. Moreover, RNA-seq data revealed that PlCSD1-1, PlCSD3, and PlFSD1 may be related to high-temperature stress response. Finally, based on the Quantitative Real-time PCR (qRT-PCR) results, seven SOD genes were significantly upregulated in response to high-temperature stress, and exogenous EBR and ABA treatments can enhance high-temperature tolerance in P. lactiflora. Overall, these discoveries lay the foundation for elucidating the function of PlSOD genes for the thermotolerance of herbaceous peony and facilitating the genetic breeding of herbaceous peony cultivars with strong high-temperature resistance.

Genome-wide association scan reveals the reinforcing effect of nano-potassium in improving the yield and quality of salt-stressed barley via enhancing the antioxidant defense system

Salinity is one of the major environmental factor that can greatly impact the growth, development, and productivity of barley. Our study aims to detect the natural phenotypic variation of morphological and physiological traits under both salinity and potassium nanoparticles (n-K) treatment. In addition to understanding the genetic basis of salt tolerance in barley is a critical aspect of plant breeding for stress resilience. Therefore, a foliar application of n-K was applied at the vegetative stage for 138 barley accessions to enhance salt stress resilience. Interestingly, barley accessions showed high significant increment under n-K treatment compared to saline soil. Based on genome-wide association studies (GWAS) analysis, causative alleles /reliable genomic regions were discovered underlying improved salt resilience through the application of potassium nanoparticles. On chromosome 2H, a highly significant QTN marker (A:C) was located at position 36,665,559 bp which is associated with APX, AsA, GSH, GS, WGS, and TKW under n-K treatment. Inside this region, our candidate gene is HORVU.MOREX.r3.2HG0111480 that annotated as NAC domain protein. Allelic variation detected that the accessions carrying C allele showed higher antioxidants (APX, AsA, and GSH) and barley yield traits (GS, WGS, and TKW) than the accessions carrying A allele, suggesting a positive selection of the accessions carrying C allele that could be used to develop barley varieties with improved salt stress resilience.

Superoxide Dismutase Premodulates Oxidative Stress in Plastids for Protection of Tobacco Plants from Cold Damage Ultrastructure Damage

ROS-dependent induction of oxidative damage can be used as a trigger initiating genetically determined non-specific protection in plant cells and tissues. Plants are potentially able to withstand various specific (toxic, osmotic) factors of abiotic effects, but do not have sufficient or specific sensitivity to form an adequate effective response. In this work, we demonstrate one of the possible approaches for successful cold acclimation through the formation of effective protection of photosynthetic structures due to the insertion of the heterologous FeSOD gene into the tobacco genome under the control of the constitutive promoter and equipped with a signal sequence targeting the protein to plastid. The increased enzymatic activity of superoxide dismutase in the plastid compartment of transgenic tobacco plants enables them to tolerate the oxidative factor of environmental stresses scavenging ROS. On the other hand, the cost of such resistance is quite high and, when grown under normal conditions, disturbs the arrangement of the intrachloroplastic subdomains leading to the modification of stromal thylakoids, probably significantly affecting the photosynthesis processes that regulate the efficiency of photosystem II. This is partially compensated for by the fact that, at the same time, under normal conditions, the production of peroxide induces the activation of ROS detoxification enzymes. However, a violation of a number of processes, such as the metabolism of accumulation, and utilization and transportation of sugars and starch, is significantly altered, which leads to a shift in metabolic chains. The expected step for further improvement of the applied technology could be both the use of inducible promoters in the expression cassette, and the addition of other genes encoding for hydrogen peroxide-scavenging enzymes in the genetic construct that are downstream in the metabolic chain.

Identification and characterization of the critical genes encoding Cd-induced enhancement of SOD isozymes activities in Zhe-Maidong (Ophiopogon japonicus)

Superoxide dismutase (SOD) protects plants from abiotic stress-induced reactive oxygen species (ROS) damage. Here, the effects of cadmium (Cd) exposure on ROS accumulation and SOD isozymes, as well as the identification of significant SOD isozyme genes, were investigated under different Cd stress treatments to Zhe-Maidong (Ophiopogon japonicus). The exposure to Cd stress resulted in a notable elevation in the SOD activity in roots. Cu/ZnSODa and Cu/ZnSODb were the most critical SOD isozymes in response to Cd stress, as indicated by the detection results for SOD isozymes. A total of 22 OjSOD genes were identified and classified into three subgroups, including 10 OjCu/ZnSODs, 6 OjMnSODs, and 6 OjFeSODs, based on the analysis of conserved motif and phylogenetic tree. Cu/ZnSOD-15, Cu/ZnSOD-18, Cu/ZnSOD-20, and Cu/ZnSOD-22 were the main genes that control the increase in SOD activity under Cd stress, as revealed via quantitative PCR and transcriptome analysis. Additionally, under various heavy metal stress (Cu2+, Fe2+, Zn2+, Mn2+), Cu/ZnSOD-15, Cu/ZnSOD-18, and Cu/ZnSOD-22 gene expression were significantly upregulated, indicating that these three genes play a critical part in resisting heavy metal stress. The molecular docking experiments performed on the interaction between oxygen ion (O2•-) and OjSOD protein have revealed that the critical amino acid residues involved in the binding of Cu/ZnSOD-22 to the substrate were Pro135, Ile136, Ile140, and Arg144. Our findings provide a solid foundation for additional functional investigations on the OjSOD genes, as well as suggestions for improving genetic breeding and agricultural management strategies to increase Cd resistance in O. japonicus.

Overexpression of NtGPX8a Improved Cadmium Accumulation and Tolerance in Tobacco (Nicotiana tabacum L.)

Cadmium (Cd)-induced oxidative stress detrimentally affects hyperaccumulator growth, thereby diminishing the efficacy of phytoremediation technology aimed at Cd pollution abatement. In the domain of plant antioxidant mechanisms, the role of glutathione peroxidase (GPX) in conferring Cd tolerance to tobacco (Nicotiana tabacum) remained unclear. Our investigation employed genome-wide analysis to identify 14 NtGPX genes in tobacco, revealing their organization into seven subgroups characterized by analogous conserved domain patterns. Notably, qPCR analysis highlighted NtGPX8a as markedly responsive to Cd2+ stress. Subsequent exploration through yeast two-hybridization unveiled NtGPX8a's utilization of thioredoxins AtTrxZ and AtTrxm2 as electron donors, and without interaction with AtTrx5. Introduction of NtGPX8a into Escherichia coli significantly ameliorated Cd-induced adverse effects on bacterial growth. Transgenic tobacco overexpressing NtGPX8a demonstrated significantly augmented activities of GPX, SOD, POD, and CAT under Cd2+ stress compared to the wild type (WT). Conversely, these transgenic plants exhibited markedly reduced levels of MDA, H2O2, and proline. Intriguingly, the expression of NtGPX8a in both E. coli and transgenic tobacco led to increased Cd accumulation, confirming its dual role in enhancing Cd tolerance and accumulation. Consequently, NtGPX8a emerges as a promising candidate gene for engineering transgenic hyperaccumulators endowed with robust tolerance for Cd-contaminated phytoremediation.

Chlorella pyrenoidosa as a potential bioremediator: Its tolerance and molecular responses to cadmium and lead

Heavy metal contamination negatively affects plants and animals in water as well as soils. Some microalgae can remove heavy metal contaminants from wastewater. The aim of this study was to screen green microalgae (GM) to identify those that tolerate high concentrations of toxic heavy metals in water as possible candidates for phytoremediation. Analyses of the tolerance, physiological parameters, ultrastructure, and transcriptomes of GM under Cd/Pb treatments were conducted. Compared with the other GM, Chlorella pyrenoidosa showed stronger tolerance to high concentrations of Cd/Pb. The reduced glutathione content and peroxidase activity were higher in C. pyrenoidosa than those in the other GM. Ultrastructural observations showed that, compared with other GM, C. pyrenoidosa had less damage to the cell surface and interior under Cd/Pb toxicity. Transcriptome analyses indicated that the "peroxisome" and "sulfur metabolism" pathways were enriched with differentially expressed genes under Cd/Pb treatments, and that CpSAT, CpSBP, CpKAT2, Cp2HPCL, CpACOX, CpACOX2, and CpACOX4, all of which encode antioxidant enzymes, were up-regulated under Cd/Pb treatments. These results show that C. pyrenoidosa has potential applications in the remediation of polluted water, and indicate that antioxidant enzymes contribute to Cd/Pb detoxification. These findings will be useful for producing algal strains for the purpose of bioremediation in water contamination.

Separation of anti-TMV active components and modes of action of Omphalia lapidescens

BACKGROUND

Omphalia lapidescens is a saprophytic and parasitic fungus belonging to the Polypora genus of Tricholomataceae. It has repellent, insecticidal, anti-inflammatory and immunomodulatory effects.

RESULT

This study found that the extract of O. lapidescens had significant anti-TMV activity, and the main active component was homopolysaccharide LW-1 by Bioassay-guided fractionation. LW-1 is a glucan with β-(1,3) glucoside bond as the main chain and β-(1,6) glucoside bond as the branch chain, with molecular weight in the range of 172,916-338,827 Da. The protective and inactive efficacies of LW-1(100 mg/L) against TMV were 78.10% and 48.20%, but had no direct effect on the morphology of TMV particles. The results of mechanism of action showed that LW-1 induced the increase of the activity of defense enzymes such as POD, SOD and PAL in Nicotiana glutinosa. The overexpression of resistance genes such as NPR1, PR1 and PR5, and the increase of SA content. Further transcriptome sequencing showed that LW-1 activated MAPK signaling pathway, plant-pathogen interaction pathway and glucosinolide metabolic pathway in Arabidopsis thaliana. Besides, LW-1 induced crops resistance against plant pathogenic fungi.

CONCLUSION

Taken together, the anti-TMV mechanism of LW-1 was to activate MAPK signaling pathway, inducing overexpression of resistance genes, activating plant immune system, and improving the synthesis and accumulation of plant defencins such as glucosinolide. LW-1-induced plant disease resistance has the advantages of broad spectrum and long duration, which has the potential to be developed as a new antiviral agent or plant immune resistance inducer.

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.

New seed coating containing Trichoderma viride with anti-pathogenic properties

Background

To ensure food security in the face of climate change and the growing world population, multi-pronged measures should be taken. One promising approach uses plant growth-promoting fungi (PGPF), such as Trichoderma, to reduce the usage of agrochemicals and increase plant yield, stress tolerance, and nutritional value. However, large-scale applications of PGPF have been hampered by several constraints, and, consequently, usage on a large scale is still limited. Seed coating, a process that consists of covering seeds with low quantities of exogenous materials, is gaining attention as an efficient and feasible delivery system for PGPF.

Methods

We have designed a new seed coating composed of chitin, methylcellulose, and Trichoderma viride spores and assessed its effect on canola (Brassica napus L.) growth and development. For this purpose, we analyzed the antifungal activity of T. viride against common canola pathogenic fungi (Botrytis cinerea, Fusarium culmorum, and Colletotrichum sp.). Moreover, the effect of seed coating on germination ratio and seedling growth was evaluated. To verify the effect of seed coating on plant metabolism, we determined superoxide dismutase (SOD) activity and expression of the stress-related RSH (RelA/SpoT homologs).

Results

Our results showed that the T. viride strains used for seed coating significantly restricted the growth of all three pathogens, especially F. culmorum, for which the growth was inhibited by over 40%. Additionally, the new seed coating did not negatively affect the ability of the seeds to complete germination, increased seedling growth, and did not induce the plant stress response. To summarize, we have successfully developed a cost-effective and environmentally responsible seed coating, which will also be easy to exploit on an industrial scale.

Comparative Transcriptome Analysis Reveals the Effect of miR156a Overexpression on Mineral Nutrient Homeostasis in Nicotiana tabacum

Mineral nutrition plays an important role in crop growth, yield and quality. MiR156 is a regulatory hub for growth and development. To date, the understanding of miR156-mediated mineral homeostasis is limited. In this study, we overexpressed Nta-miR156a in the tobacco cultivar TN90 and analyzed the effects of miR156 on mineral element homeostasis in tobacco by comparative transcriptome analysis. The results showed that the overexpression of miR156a caused significant morphological changes in transgenic tobacco. Chlorophyll and three anti-resistance markers, proline, total phenolics, and total flavonoids, were altered due to increased miR156 expression levels. Interestingly, the distribution of Cu, Mn, Zn, and Fe in different tissues of transgenic tobacco was disordered compared with that of the wild type. Comparative transcriptome analysis showed that the overexpression of miR156 resulted in 2656 significantly differentially expressed genes. The expression levels of several metal-transport-related genes, such as NtABC, NtZIP, NtHMA, and NtCAX, were significantly increased or decreased in transgenic tobacco. These results suggest that miR156 plays an essential role in regulating mineral homeostasis. Our study provides a new perspective for the further study of mineral nutrient homeostasis in plants.

The NtSPL Gene Family in Nicotiana tabacum: Genome-Wide Investigation and Expression Analysis in Response to Cadmium Stress

The SQUAMOSA promoter binding protein-like (SPL)SPL family genes play an important role in regulating plant growth and development, synthesis of secondary metabolites, and resistance to stress. Understanding of the role of the SPL family in tobacco is still limited. In this study, 42 NtSPL genes were identified from the genome of the tobacco variety TN90. According to the results of the conserved motif and phylogenetic tree, the NtSPL genes were divided into eight subgroups, and the genes in the same subgroup showed similar gene structures and conserved domains. The cis-acting element analysis of the NtSPL promoters showed that the NtSPL genes were regulated by plant hormones and stresses. Twenty-eight of the 42 NtSPL genes can be targeted by miR156. Transcriptome data and qPCR results indicated that the expression pattern of miR156-targeted NtSPL genes was usually tissue specific. The expression level of miR156 in tobacco was induced by Cd stress, and the expression pattern of NtSPL4a showed a significant negative correlation with that of miR156. These results suggest that miR156-NtSPL4a may mediate the tobacco response to Cd stress. This study lays a foundation for further research on the function of the NtSPL gene and provides new insights into the involvement of NtSPL genes in the plant response to heavy metal stress.

Crosstalk of nitro-oxidative stress and iron in plant immunity

Accumulation of oxygen and nitrogen radicals and their derivatives, known as reactive oxygen species (ROS) and reactive nitrogen species (RNS), occurs throughout various phases of plant growth in association with biotic and abiotic stresses. One of the consequences of environmental stresses is disruption of homeostasis between production and scavenging of ROS and RNS, which leads to nitro-oxidative burst and affects other defense-related mechanisms, such as polyamines levels, phenolics, lignin and callose as defense components related to plant cell wall reinforcement. Although this subject has attracted huge interest, the cross-talk between these signaling molecules and iron, as a main metal element involved in the activity of various enzymes and numerous vital processes in the living cells, remains largely unexplored. Therefore, it seems necessary to pay more in depth attention to the mechanisms of plant resistance against various environmental stimuli for designing novel and effective plant protection strategies. This review is focused on advances in recent knowledge related to the role of ROS, RNS, and association of these signaling molecules with iron in plant immunity. Furthermore, the role of cell wall fortification as a main physical barrier involved in plant defense have been discussed in association with reactive species and iron ions.