Unravelling calcium-alleviated aluminium toxicity in Arabidopsis thaliana: Insights into regulatory mechanisms using proteomics

Physiological and proteomic characterization revealed the response mechanisms underlying aluminium tolerance in lentil (Lens culinaris Medikus)

Aluminium (Al) toxicity causes major plant distress, affecting root growth, nutrient uptake and, ultimately, agricultural productivity. Lentil, which is a cheap source of vegetarian protein, is recognized to be sensitive to Al toxicity. Therefore, it is important to dissect the physiological and molecular mechanisms of Al tolerance in lentil. To understand the physiological system and proteome composition underlying Al tolerance, two genotypes [L-4602 (Al-tolerant) and BM-4 (Al-sensitive)] were studied at the seedling stage. L-4602 maintained a significantly higher root tolerance index and malate secretion with reduced Al accumulation than BM-4. Also, label-free proteomic analysis using ultra-performance liquid chromatography-tandem mass spectrometer exhibited significant regulation of Al-responsive proteins associated with antioxidants, signal transduction, calcium homeostasis, and regulation of glycolysis in L-4602 as compared to BM-4. Functional annotation suggested that transporter proteins (transmembrane protein, adenosine triphosphate-binding cassette transport-related protein and multi drug resistance protein), antioxidants associated proteins (nicotinamide adenine dinucleotide dependent oxidoreductase, oxidoreductase molybdopterin binding protein & peroxidases), kinases (calmodulin-domain kinase & protein kinase), and carbohydrate metabolism associated proteins (dihydrolipoamide acetyltransferase) were found to be abundant in tolerant genotype providing protection against Al toxicity. Overall, the root proteome uncovered in this study at seedling stage, along with the physiological parameters measured, allow a greater understanding of Al tolerance mechanism in lentil, thereby assisting in future crop improvement programmes.

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.

Seed Nano-Priming with Calcium Oxide Maintains the Redox State by Boosting the Antioxidant Defense System in Water-Stressed Carom (Trachyspermum ammi L.) Plants to Confer Drought Tolerance

This paper explores the potential of nano seed priming with calcium oxide nanoparticles in maintaining the redox status in carom (Trachyspermum ammi L.) plants by modulating non-enzymatic antioxidants and enzymatic antioxidants. Calcium oxide nanoparticles were prepared in four testing regimes comprising 25, 50, 75, and 100 ppm along with the control treatment of 0 ppm (distilled water). Priming was performed by soaking the carom seeds in the aerated water, and plants were grown under split plots corresponding to drought and water. Seed priming with 75 ppm CaONPs reduced hydrogen peroxide, malondialdehyde contents and electrolyte leakage by 23.3%, 35.9% and 31.6%, respectively, in the water-stressed carom plants. The glutathione s-transferase, superoxide dismutase and peroxidase functions improved under water stress by 42.3%, 24.1% and 44.8%, respectively, in the carom plants raised through 100 ppm primed seeds with CaO_NPs. Priming induced better Ca²⁺ signaling, which affected the enzymes of the ascorbate glutathione cycle, enabling them to maintain redox status in the carom plants exposed to drought stress. The morpho-agronomic traits of carom plants in terms of number of umbels, hundred seeds weights, shoot and root length and biomass improved significantly upon seed priming treatments. Seed priming with CaO_NPs is a viable strategy to combat reactive oxygen species-mediated damages in the carom plants.

Unearthing the alleviatory mechanisms of hydrogen sulfide in aluminum toxicity in rice

Hydrogen sulfide (H₂S) improves aluminum (Al) resistance in rice, however, the underlying mechanism remains unclear. In the present study, treatment with 30-μM Al significantly inhibited rice root growth and increased the total Al content, apoplastic and cytoplasm Al concentration in the rice roots. However, pretreatment with NaHS (H₂S donor) reversed these negative effects. Pretreatment with NaHS significantly increased energy production under Al toxicity conditions, such as by increasing the content of ATP and nonstructural carbohydrates. In addition, NaHS stimulated the AsA-GSH cycle to decrease the peroxidation damage induced by Al toxicity. Pretreatment with NaHS significantly inhibited ethylene emissions in the rice and then inhibited pectin synthesis and increased the pectin methylation degree to reduce cell wall Al deposition. The phytohormones indole-3-acetic and brassinolide were also involved in the alleviation of Al toxicity by H₂S. The transcriptome results further confirmed that H₂S alleviates Al toxicity by increasing the pathways relating to material and energy metabolism, redox reactions, cell wall components, and signal transduction. These findings improve our understanding of how H₂S affects rice responses to Al toxicity, which will facilitate further studies on crop safety.

Physiological, Proteomic Analysis, and Calcium-Related Gene Expression Reveal Taxus wallichiana var. mairei Adaptability to Acid Rain Stress Under Various Calcium Levels

As one of the serious environmental problems worldwide, acid rain (AR) has always caused continuous damage to the forestry ecosystem. Studies have shown that AR can leach calcium ions from plants and soil. Calcium (Ca) is also a crucial regulator of the plant stress response, whereas there are few reports on how Ca regulates the response of AR-resistant woody plants to AR stress. In this study, by setting different exogenous Ca levels, we study the physiological and molecular mechanism of Ca in regulating the Taxus wallichiana var. mairei response to AR stress. Our results showed that low Ca level leads to photosynthesis, and antioxidant defense system decreases in T. wallichiana var. mairei leaves; however, these negative effects could be reversed at high Ca level. In addition, proteomic analyses identified 44 differentially expressed proteins in different Ca level treatments of T. wallichiana var. mairei under AR stress. These proteins were classified into seven groups, which include metabolic process, photosynthesis and energy pathway, cell rescue and defense, transcription and translation, protein modification and degradation, signal transduction, etc. Furthermore, the study found that low Ca level leads to an obvious increase of Ca-related gene expression under AR stress in T. wallichiana var. mairei using qRT-PCR analyses and however can be reversed at high Ca level. These findings would enrich and extend the Ca signaling pathways of AR stress in AR-resistant woody plants and are expected to have important theoretical and practical significance in revealing the mechanism of woody plants tolerating AR stress and protecting forestry ecosystem in soil environment under different Ca levels.

Alleviating aluminum toxicity in plants: Implications of reactive oxygen species signaling and crosstalk with other signaling pathways

Aluminum (Al) toxicity is a major limiting factor for plant growth and productivity in acidic soil. At pH lower than 5.0 (pH < 5.0), the soluble and toxic form of Al (Al³⁺ ions) enters root cells and inhibits root growth and uptake of water and nutrients. The organic acids malate, citrate, and oxalate are secreted by the roots and chelate Al³⁺ to form a non-toxic Al-OA complex, which decreases the entry of Al³⁺ into the root cells. When Al³⁺ enters, it leads to the production of reactive oxygen species (ROS) in cells, which are toxic and cause damage to biomolecules like lipids, carbohydrates, proteins, and nucleic acids. When ROS levels rise beyond the threshold, plants activate an antioxidant defense system that comprises of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione S-transferase (GST), ascorbic acid (ASA), phenolics and alkaloids etc., which protect plant cells from oxidative damage by scavenging and neutralizing ROS. Besides, ROS also play an important role in signal transduction and influence many molecular and cellular process like hormone signaling, gene expression, cell wall modification, cell cycle, programed cell death (PCD), and development. In the present review, the mechanisms of Al-induced ROS generation, ROS signaling, and crosstalk with other signaling pathways helping to combat Al toxicity have been summarized, which will help researchers to understand the intricacies of Al-induced plant response at cellular level and plan research for developing Al-toxicity tolerant crops for sustainable agriculture in acid soil-affected regions of the world.

Basic physiology and biochemistry in environmental/experimental plant studies: How to quantify and interpret metabolites correctly

As a reviewer of ca. 50 manuscripts per year submitted to various journals, I often come across questionable metabolic data (both over- or under-estimated) mainly in the journals from the section of Environmental Sciences of Web of Science. Though the trends of visibly incorrect metabolite values may be informative (changes in response to applied treatments or environmental factors), absolute values must be precise enough to allow inter-specific comparison and eventual subsequent calculations. Technical correctness of quantification and calculation of such data is therefore often questionable. One problem arises when calculating metabolites concentration (often nmol or μmol/g of biomass) and another problem is the impact of altered water content on metabolite level (then trend per gram of fresh or dry biomass will differ). Recent discrepancies I found when searching for the literature prompted me to write this technical note aimed at focusing attention of researchers on these problems. I exclude any conflict of interest when discussing the quoted published studies. I strongly urge interested researchers to verify the correctness of metabolite quantification (extraction, dilution/calculation and alternative methods) and also to study similar literature for comparison in order to prevent the spread of incorrect data in the scientific literature.

The Differential Metabolic Profiles Between Deltamethrin-Resistant and -Susceptible Strains of Aedes albopictus (Diptera: Culicidae) by 1H-NMR

Metabolomics can indicate the physiological and biochemical responses of mosquitoes to different stimulants, including insecticides, which allow them to adapt to different inhospitable environments. Though metabolic differences between insecticide-resistant and -susceptible strains have been established for other mosquito species, such as Anopheles and Culex, it is yet to be done for Aedes albopictus (Skuse). In this study, nuclear magnetic resonance (NMR) spectroscopy-based metabolomic analysis performed on Ae. albopictus deltamethrin-resistant and -susceptible strains showed significant differences in amino acid, organic acid, and sugar metabolism. Concentrations of neutral amino acids and sugars tended to be lower in the deltamethrin-resistant strain than in the deltamethrin-suceptible strain, but the concentration of basic and acidic amino acids and organic acids increased. All these changes might accommodate biochemical and physiological needs in deltamethrin-resistant mosquitoes, such as enzyme synthesis and detoxification. This was further confirmed by the predictable draft metabolic map. This is the first report using NMR spectroscopy to investigate the metabolic differences between deltamethrin-resistant and -susceptible strains of Ae. albopictus. To a certain degree, this demonstrates how Ae. albopictus develop insecticide resistance by metabolic reprograming to survive under the insecticide pressure.

Proteomics and plant biology: contributions to date and a look towards the next decade

INTRODUCTION

This review presents the view of the author, that is opinionable and even speculative, on the field of proteomics, its application to plant biology knowledge, and translation to biotechnology. Written in a more academic than scientific style, it is based on past original and review articles by the author´s group, and those published by leading scientists in the last two years.

AREAS COVERED

Starting with a general definition and references to historical milestones, it covers sections devoted to the different platforms employed, the plant biology discourse in the protein language, challenges and future prospects, ending with the author opinion.

EXPERT OPINION

In 25 years, five proteomics platform generations have appeared. We are now moving from proteomics to Systems Biology. While feasible with model organisms, proteomics of orphan species remains challenging. Proteomics, even in its simplest approach, sheds light on plant biological processes, central dogma, and molecular bases of phenotypes of interest, and it can be translated to areas such as food traceability and allergen detection. Proteomics should be validated and optimized to each experimental system, objectives, and hypothesis. It has limitations, artifacts, and biases. We should not blindly accept proteomics data and just create a list of proteins, networks, and avoid speculative biological interpretations. From the hundred to thousand proteins identified and quantified, it is important to obtain a focus and validate some of them, otherwise it is merely. We are starting to have the protein pieces, so let, from now, build the proteomics and biological puzzle.

Transcriptome analysis reveals significant difference in gene expression and pathways between two peanut cultivars under Al stress

Aluminum (Al) toxicity is an important factor in limiting peanut growth on acidic soil. The molecular mechanisms underlying peanut responses to Al stress are largely unknown. In this study, we performed transcriptome analysis of the root tips (0-1 cm) of peanut cultivar ZH2 (Al-sensitive) and 99-1507 (Al-tolerant) respectively. Root tips of peanuts that treated with 100 μM Al for 8 h and 24 h were analyzed by RNA-Seq, and a total of 8,587 differentially expressed genes (DEGs) were identified. GO and KEGG pathway analysis excavated a group of important Al-responsive genes related to organic acid transport, metal cation transport, transcription regulation and programmed cell death (PCD). These homologs were promising targets to modulate Al tolerance in peanuts. It was found that the rapid transcriptomic response to Al stress in 99-1507 helped to activate effective Al tolerance mechanisms. Protein and protein interaction analysis indicated that MAPK signal transduction played important roles in the early response to Al stress in peanuts. Moreover, weighted correlation network analysis (WGCNA) identified a predicted EIL (EIN3-like) gene with greatly increased expression as an Al-associated gene, and revealed a link between ethylene signaling transduction and Al resistance related genes in peanut, which suggested the enhanced signal transduction mediated the rapid transcriptomic responses. Our results revealed key pathways and genes associated with Al stress, and improved the understanding of Al response in peanut.

Quantitative proteomic analysis reveals complex regulatory and metabolic response of Iris lactea Pall. var. chinensis to cadmium toxicity

Cadmium pollution has become a serious environmental problem. Iris lactea var. chinensis showed strong Cd tolerance and accumulation ability, which has significant potential to be applied for the phytoremediation of Cd-contaminated soil. However, the lack of molecular information on the mechanism of I. lactea response to Cd limited the improvement of phytoremediation efficiency. In this study, label-free proteomics analysis of Cd response in I. lactea showed that there were 163 and 196 differentially expressed proteins (DEPs) in the shoots and roots, respectively. Bioinformatics analysis indicated the DEPs responding to Cd stress mainly involved in signal transduction, ion transport, redox etc., and participate in the pathway of amino acid biosynthesis, lignin biosynthesis, glycerolipid metabolism and glutathione metabolism. Besides, differential expression of seven DEPs was validated via gene expression analysis. Finally, we found that a Cd-induced mannose-specific lectin (IlMSL) from I. lactea enhanced the Cd sensitivity and increased Cd accumulation in yeast. The results of this study will enhance our understanding of the molecular mechanism of Cd tolerance and accumulation in I. lactea and ultimately provide valuable resources for using Cd tolerant genes for developing efficient strategies for phytoremediation of Cd-contaminated soils or limiting Cd accumulation in food crops.

Oxidative stress response mechanism of Scenedesmus obliquus to ionic liquids with different number of methyl-substituents

Ionic liquids (ILs) have become persistent contaminants in water because of their good solubility and low biodegradability. The oxidative stress responses of Scenedesmus obliquus to three imidazole ILs with different number of methyl-substituents, i.e., 1-decyl-imidazolium chloride ([C₁₀IM]Cl), 1-decyl-3-methylimidazolium chloride ([C₁₀MIM]Cl), and 1-decyl-2,3-dimethylimidazolium chloride ([C₁₀DMIM]Cl), were studied. There was a positive correlation between ROS level and IL concentration. The activities of antioxidant enzymes, i.e., superoxide dismutase, catalase, peroxidase, ascorbate peroxidase, and glutathione peroxidase, and the content of antioxidants, i.e., ascorbic acid and glutathione, changed in IL treatment with a concentration-dependent effect. Proline accumulation increased with increasing IL concentration. Integrated biomarker response (IBR) index analysis, based on the eight oxidative stress response indicators, revealed that the toxicity order was: [C₁₀IM]Cl < [C₁₀DMIM]Cl < [C₁₀MIM]Cl. Proteomic analysis showed that IL affect the type and distribution of proteins in S. obliquus. Chloroplast and photosystem II were affected as cellular component, and the proteins related to oxidative stress are annotated in GO categories. IBR index and proteomic analysis indicate that oxidative stress response is one of the main biomarkers of IL stress.

Molecular biological methods in environmental engineering

Microbes are sensitive to environmental changes and can respond in a short time. Genomics, proteomics, transcriptomics, metabolomics, and multigroup association are used to characterize the composition, function, and metabolism of microorganisms, and to evaluate the environment according to the changes in microorganisms, which has important reference and guiding significance of environmental monitoring, management, and repair. In this paper, the application of molecular biological methods to study environmental microorganisms in the fields of wastewater treatment, pollution control, soil improvement, and environmental monitoring in 2019 is reviewed.

Transcriptome analysis of two soybean cultivars identifies an aluminum respon-sive antioxidant enzyme GmCAT1

This study investigated the antioxidant defense system involved in the tolerance of soybean (Glycine max) to aluminum (Al) stress. Physiological assays showed that the amount of superoxide free radicals (O2 -), hydrogen peroxide (H2O2), and malondialdehyde (MDA) were significantly lower in an Al-resistant soybean cultivar (cv. PI416937) than in an Al-sensitive soybean cultivar (cv. Huachun18). Comparative analysis of microarray data from both genotypes following Al-stress treatment revealed that the expression of a series of antioxidant enzymes genes was induced in the Al-resistant cultivar. The quantitative real time-PCR (qRT-PCR) assay showed that the transcript levels of genes encoding antioxidant enzymes, including GmCAT1, GmPOD1, GmGST1, GmAPX, GmGSH1, and GmSOD, were higher in the Al-resistant cultivar than in the Al-sensitive cultivar in Al-stress conditions. Furthermore, GmCAT1-overexpressing Arabidopsis plants had improved tolerance to Al-stress and lower O2 -, H2O2, and MDA contents than wild-type plants. Therefore, providing evidence that the antioxidant defense system is essential for Al tolerance in soybean.

ABBREVIATIONS

Al: aluminum; O2 -: superoxide free radicals; ROS: reactive oxygen species; H2O2: hydrogen peroxide; MDA: malondialdehyde; qRT-PCR: quantitative reverse transcription polymerase chain reaction; GO: gene ontology; WT: wild type; MS medium: Murashige and Skoog medium.

Enhanced exudation of malate in the rhizosphere due to AtALMT1 overexpression in blackgram (Vigna mungo L.) confers increased aluminium tolerance

Worldwide, 50% of soil is acidic, which induces aluminium (Al) toxicity in plants, as the phyto-availability of Al³⁺ increases in acidic soil. Plants responds to Al³⁺ toxicity by exuding organic acids into the rhizosphere. The organic acid responsible for Al³⁺ stress response varies from species to species, which in the case of blackgram (Vigna mungo L.) is citrate. In blackgram, an Arabidopsis malate transporter, AtALMT1, was overexpressed with the motive of inducing enhanced exudation of malate. Transgenics were generated using cotyledon node explants through Agrobacterium tumefaciens-mediated transformation. The putative transgenics were initially screened by AtALMT1-specific genomic DNA PCR, followed by quantitative PCR. Two independent transgenic events were identified and functionally characterized in the T₃ generation. The transgenic lines, Line 1 and 2, showed better root growth, relative water content and chlorophyll content under Al³⁺ stress. Both lines also accounted for less oxidative damage, due to reduced accumulation of ROS molecules. Photosynthetic efficiency, as measured in terms of F_v /F_m , NPQ and Y(II), increased when compared to the wild type (WT). Relative expression of genes (VmSTOP1, VmALS3, VmMATE) responsible for Al³⁺ stress response in blackgram showed that overexpression of a malate transporter did not have any effect on their expression. Malate exudation increased whereas citrate exudation did not show any divergence from the WT. A pot stress assay found that the transgenics showed better adaptation to acidic soil. This report demonstrates that the overexpression of a malate transporter in a non-malate exuding species improves adaptation to Al³⁺ toxicity in acidic soil without effecting its stress response mechanism.

Increased bound putrescine accumulation contributes to the maintenance of antioxidant enzymes and higher aluminum tolerance in wheat

The accumulation of bound and conjugated polyamines (PAs) is an important protective trait in plants under adverse environmental conditions. However, their role in plant responses to aluminum (Al) stress remains largely unknown. In this study, we showed that Al treatment increased bound putrescine (Put) levels in the wheat root tips of Al-tolerant Xi Aimai-1, with little effect on its bound spermidine and conjugated PAs or that of Al-sensitive Yangmai-5. Terminating bound Put increments with a synthesis inhibitor (Phenanthroline, o-phen) exacerbated Al-induced root inhibition and callose production. However, it had no significant effect on Al uptake or distribution under Al stress. Instead, Al-induced reactive oxygen species (ROS) production and thus, oxidative damage, was greatly exacerbated by o-phen in the roots of Xi Aimai-1. Application of o-phen barely affected the two ROS generating enzymes (plasma membrane NADPH oxidase and cell wall-bound polyamine oxidase) in wheat roots. However, exogenous o-phen significantly reduced antioxidant enzyme (superoxide dismutase, ascorbate peroxidase, and catalase) activity, which positively correlated with the level of bound Put in Xi Aimai-1. These results clearly suggest that bound Put accumulation works to protect against Al-induced oxidative damage, possibly by maintaining antioxidant capacity in wheat.