Multi-omics analyses on the response mechanisms of 'Shine Muscat' grapevine to low degree of excess copper stress (Low-ECS)

How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications

MAIN CONCLUSION

Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.

Dynamic Regulation of Intracellular Labile Cu(I)/Cu(II) Cycle in Microalgae Chlamydomonas reinhardtii: Disrupting the Balance by Cu Stress

The labile metal pool involved in intracellular trafficking and homeostasis is the portion susceptible to environmental stress. Herein, we visualized the different intracellular distributions of labile Cu(I) and Cu(II) pools in the alga Chlamydomonas reinhardtii. We first demonstrated that labile Cu(I) predominantly accumulated in the granules within the cytoplasmic matrix, whereas the labile Cu(II) pool primarily localized in the pyrenoid and chloroplast. The cell cycle played an integral role in balancing the labile Cu(I)/Cu(II) pools. Specifically, the labile Cu(II) pool primarily accumulated during the SM phase following cell division, while the labile Cu(I) pool dynamically changed during the G phase as cell size increased. Notably, the labile Cu(II) pool in algae at the SM stage exhibited heightened sensitivity to environmental Cu stress. Exogenous Cu stress disrupted the intracellular labile Cu(I)/Cu(II) cycle and balance, causing a shift toward the labile Cu(II) pool. Our proteomic analysis further identified a putative cupric reductase, potentially capable of reducing Cu(II) to Cu(I), and four putative multicopper oxidases, potentially capable of oxidizing Cu(I) to Cu(II), which may be involved in the conversion between the labile Cu(I) pool and labile Cu(II) pool. Our study elucidated a dynamic cycle of the intracellular labile Cu(I)/Cu(II) pools, which were accessible and responsive to environmental changes.

Effects of Different Mulching Practices on Soil Environment and Fruit Quality in Peach Orchards

Mulching practices have been used to improve peach growth and production across the globe. However, the impact of mulching on the physiochemical properties and soil characteristics of orchards remains largely unknown. This study aimed to decipher the impacts of various mulching patterns on the soil environment and the quality of Prunus persica fruit in "Zijinhuangcui". Three treatments were set up, which included black ground fabric mulch (BF) and two living grass mulch treatments (HV: hairy vetch and RG: ryegrass). The results showed that different mulching treatments have different effects on soil, plant growth, and fruit quality. Living grass mulch treatments, especially the HV treatment, significantly improved soil nutrients by enhancing nitrogen-related indicators. Of note, the BF treatment had higher total phosphorus and available phosphorus contents than the HV and RG treatments. The HV treatment had the highest relative abundance of Proteobacteria (33.49%), which is associated with symbiotic nitrogen fixation, followed by RG (25.62%), and BF (22.38%) at the young fruit stage. Similarly, the abundance of Terrimonas, which has a unique nitrogen fixation system at the genus level, was significantly higher in the living grass mulch (HV, 1.30-3.13% and RG, 2.27-4.24%) than in the BF treatment. Living grass mulch also promoted tree growth, increased fruit sugar content, sugar-related components, and sugar-acid ratio, and reduced the acid content. Collectively, the findings of this study show that living grass mulch can promote tree growth and improve fruit quality by improving soil fertility, bacterial diversity, and richness.

VvATG6 contributes to copper stress tolerance by enhancing the antioxidant ability in transgenic grape calli

Autophagy, a conserved degradation and reuse process, plays a crucial role in plant cellular homeostasis during abiotic stress. Although numerous autophagy-related genes (ATGs) that regulate abiotic stress have been identified, few functional studies have shown how they confer tolerance to copper (Cu) stress. Here, we cloned a novel Vitis vinifera ATG6 gene (VvATG6) which was induced by 0.5 and 10 mM Cu stress based on transcriptomic data, and transgenic Arabidopsis thaliana, tobacco (Nicotiana tabacum), and grape calli were successfully obtained through Agrobacterium-mediated genetic transformation. The overexpression of VvATG6 enhanced the tolerance of transgenic lines to Cu. After Cu treatment, the lines that overexpressed VvATG6 grew better and increased their production of biomass compared with the wild-type. These changes were accompanied by higher activities of antioxidant enzymes and a lower accumulation of deleterious malondialdehyde and hydrogen peroxide in the transgenic plants. The activities of superoxide dismutase, peroxidase, and catalase were enhanced owing to the elevation of corresponding antioxidant gene expression in the VvATG6 overexpression plants under Cu stress, thereby promoting the clearance of reactive oxygen species (ROS). Simultaneously, there was a decrease in the levels of expression of RbohB and RbohC that are involved in ROS synthesis in transgenic plants under Cu stress. Thus, the accelerated removal of ROS and the inhibition of its synthesis led to a balanced ROS homeostasis environment, which alleviated the damage from Cu. This could benefit from the upregulation of other ATGs that are necessary for the production of autophagosomes under Cu stress. To our knowledge, this study is the first to demonstrate the protective role of VvATG6 in the Cu tolerance of plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01415-y.

Integrated transcriptomic, proteomic and metabolomic analysis provides new insights into tetracycline stress tolerance in pumpkin

The aim of this study was to conduct transcriptomic, proteomic, and metabolomic analysis to provide a comprehensive view of plant response to tetracycline stress. Pumpkin seeds were cultured for 7 days without or with tetracycline at 10 mg/L. Pumpkin roots showed excessive growth inhibition, but not yet strong growth restraining in cotyledons. Tetracycline affected the abundance of metabolites related to flavonoid biosynthesis and amino acid metabolism. Main changes of metabolites in flavonoid biosynthesis were consistent with mRNA changes. Amino acid changes are mainly mediated by proteins or mRNAs. To be specific, tetracycline treatment increased the levels of rutin, caffeate, cinnamaldehyde, 4-hydroxycinnamic acid, ferulic acid, naringenin, apigenin, luteolin, (-)-epigallocatechin, astragalin, L-serine, and glutathione and the transcript levels related to these compounds; and decreased the levels of indole pyruvate, indole acetaldehyde, L-arginine, S-adenosylhomocysteine, L-glutamine, and gamma-glutamylcysteine and the transcript levels related to these compounds. Tetracycline treatment also increased the levels of oxoglutaric acid, L-glutamic acid, gamma-aminobutyric acid, and gamma-glutamylalanine and enzymes involved in their production; and decreased the levels of L-isoleucine, L-valine, and L-leucine and enzymes involved in their production. We elucidated several biological processes (e.g. phenylpropanoid/flavonoid biosynthesis pathways, amino acid metabolic pathways) that were altered by tetracycline, and provided a multi-omic perspective on the mechanisms underlying the response to tetracycline stress in pumpkin roots. We provide a useful reference for the development of environmental quality management methods.

Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

Copper stress in grapevine: Consequences, responses, and a novel mitigation strategy using 5-aminolevulinic acid

Improper application of copper-based fungicides has made copper stress critical in viticulture, necessitating the need to identify substances that can mitigate it. In this study, leaves of 'Shine Muscat' ('SM') grapevine seedlings were treated with CuSO₄ solution (10 mM/L), CuSO₄ + 5-aminolevulinic acid (ALA) (50 mg/L), and distilled water to explore the mitigation effect of ALA. Physiological assays demonstrated that ALA effectively reduced malondialdehyde accumulation and increased peroxidase and superoxide dismutase activities in grapevine leaves under copper stress. Copper ion absorption, transport pathways, chlorophyll metabolism pathways, photosynthetic system, and antioxidant pathways play key roles in ALA alleviated-copper stress. Moreover, expression changes in genes, such as CHLH, ALAD, RCA, and DHAR, play vital roles in these processes. Furthermore, abscisic acid reduction caused by NCED down-regulation and decreased naringenin, leucopelargonidin, and betaine contents confirmed the alleviating effect of ALA. Taken together, these results reveal how grapevine responds to copper stress and the alleviating effects of ALA, thus providing a novel means of alleviating copper stress in viticulture.

Adaptive Responses of Citrus grandis Leaves to Copper Toxicity Revealed by RNA-Seq and Physiology

Copper (Cu)-toxic effects on Citrus grandis growth and Cu uptake, as well as gene expression and physiological parameters in leaves were investigated. Using RNA-Seq, 715 upregulated and 573 downregulated genes were identified in leaves of C. grandis seedlings exposed to Cu-toxicity (LCGSEC). Cu-toxicity altered the expression of 52 genes related to cell wall metabolism, thus impairing cell wall metabolism and lowering leaf growth. Cu-toxicity downregulated the expression of photosynthetic electron transport-related genes, thus reducing CO₂ assimilation. Some genes involved in thermal energy dissipation, photorespiration, reactive oxygen species scavenging and cell redox homeostasis and some antioxidants (reduced glutathione, phytochelatins, metallothioneins, l-tryptophan and total phenolics) were upregulated in LCGSEC, but they could not protect LCGSEC from oxidative damage. Several adaptive responses might occur in LCGSEC. LCGSEC displayed both enhanced capacities to maintain homeostasis of Cu via reducing Cu uptake by leaves and preventing release of vacuolar Cu into the cytoplasm, and to improve internal detoxification of Cu by accumulating Cu chelators (lignin, reduced glutathione, phytochelatins, metallothioneins, l-tryptophan and total phenolics). The capacities to maintain both energy homeostasis and Ca homeostasis might be upregulated in LCGSEC. Cu-toxicity increased abscisates (auxins) level, thus stimulating stomatal closure and lowering water loss (enhancing water use efficiency and photosynthesis).